[pism/pism] 3af1c5: Use pism-parameters in more places plus formatting...

0 views

Skip to first unread message

Constantine Khrulev

unread,

Dec 3, 2021, 7:01:03 PM12/3/21

to pism....@gmail.com

Branch: refs/heads/main
Home: https://github.com/pism/pism
Commit: 3af1c5fa4c945d81bccd09f58514b0b6b565a050
https://github.com/pism/pism/commit/3af1c5fa4c945d81bccd09f58514b0b6b565a050
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-12 (Fri, 12 Jun 2020)

Changed paths:
M doc/sphinx/manual/modeling-choices/subglacier/bed-deformation.rst
M src/pism_config.cdl

Log Message:
-----------
Use pism-parameters in more places plus formatting fixes

Commit: f253a3f5999962a07340f5abe27fd006b02683df
https://github.com/pism/pism/commit/f253a3f5999962a07340f5abe27fd006b02683df
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-12 (Fri, 12 Jun 2020)

Changed paths:
M doc/sphinx/climate_forcing/atmosphere.rst
M doc/sphinx/manual/modeling-choices/subglacier/bed-deformation.rst
M doc/sphinx/pism_config.py
M src/pism_config.cdl

Log Message:
-----------
More formatting fixes

Commit: 8bd55f8946ba271ee6eb9bd5c7642227cd62e9e8
https://github.com/pism/pism/commit/8bd55f8946ba271ee6eb9bd5c7642227cd62e9e8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-12 (Fri, 12 Jun 2020)

Changed paths:
M doc/sphinx/pism_config.py

Log Message:
-----------
Remove parameter name prefixes in compact lists

Commit: 36b222649b142a525e532dfdfe5c5a5a1aeba135
https://github.com/pism/pism/commit/36b222649b142a525e532dfdfe5c5a5a1aeba135
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-12 (Fri, 12 Jun 2020)

Changed paths:
M doc/sphinx/climate_forcing/atmosphere.rst
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst
M doc/sphinx/manual/modeling-choices/subglacier/bed-deformation.rst
M src/pism_config.cdl

Log Message:
-----------
Documentation tweaks

Commit: 47a5eb1dca3852b7c5ba6fa0bff6386a6cba423c
https://github.com/pism/pism/commit/47a5eb1dca3852b7c5ba6fa0bff6386a6cba423c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-12 (Fri, 12 Jun 2020)

Changed paths:
M doc/sphinx/pism_config.py

Log Message:
-----------
Make the compact list even more compact

Commit: cc07848bf13218ae4a75c33c4c3b042a04f116fd
https://github.com/pism/pism/commit/cc07848bf13218ae4a75c33c4c3b042a04f116fd
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-12 (Fri, 12 Jun 2020)

Changed paths:
M doc/sphinx/climate_forcing/ocean.rst
M src/pism_config.cdl

Log Message:
-----------
Improve PICO documentation

Commit: eaadf14d64d6290125d1817d4a7254c4fd1f9213
https://github.com/pism/pism/commit/eaadf14d64d6290125d1817d4a7254c4fd1f9213
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-12 (Fri, 12 Jun 2020)

Changed paths:
M doc/sphinx/authorship.rst

Log Message:
-----------
Fix the copyright year in the manual

Commit: c96c78def91293c862bc7cd5117f27da785cbd18
https://github.com/pism/pism/commit/c96c78def91293c862bc7cd5117f27da785cbd18
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-12 (Fri, 12 Jun 2020)

Changed paths:
M src/pism_config.cdl

Log Message:
-----------
Formatting fixes

Commit: 74ef4a89a443728ef0f2eeb29d2d4d15cca29088
https://github.com/pism/pism/commit/74ef4a89a443728ef0f2eeb29d2d4d15cca29088
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-12 (Fri, 12 Jun 2020)

Changed paths:
M doc/sphinx/CMakeLists.txt
M doc/sphinx/Makefile
M doc/sphinx/authorship.rst
M doc/sphinx/climate_forcing/atmosphere.rst
M doc/sphinx/climate_forcing/ocean.rst
M doc/sphinx/conf.py
M doc/sphinx/global.txt
R doc/sphinx/list_parameters.py
M doc/sphinx/manual/modeling-choices/marine/calving.rst
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst
M doc/sphinx/manual/modeling-choices/subglacier/bed-deformation.rst
M doc/sphinx/manual/parameters/index.rst
R doc/sphinx/manual/parameters/parameter-list.txt
A doc/sphinx/pism_config.py
M src/pism_config.cdl
A src/pism_config.py

Log Message:
-----------
Merge branch 'ckhroulev/manual' into dev

Commit: 0e538f0d6a260b330cc86cb3568779c7b0d12914
https://github.com/pism/pism/commit/0e538f0d6a260b330cc86cb3568779c7b0d12914
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-12 (Fri, 12 Jun 2020)

Changed paths:
M test/CMakeLists.txt
A test/regression/sorted_parameters.sh

Log Message:
-----------
Add a regression test checking if parameters are sorted

This will make it easier to maintain the list of parameters later on.

Commit: 2526b60d011c012fb430de5b29ed377edf2ae821
https://github.com/pism/pism/commit/2526b60d011c012fb430de5b29ed377edf2ae821
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-12 (Fri, 12 Jun 2020)

Changed paths:
M src/pism_config.cdl

Log Message:
-----------
Sort configuration parameters

Hopefully this will be the last major re-ordering.

Commit: c722536c36458461e1dac19f956d7baba0d84a6c
https://github.com/pism/pism/commit/c722536c36458461e1dac19f956d7baba0d84a6c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-15 (Mon, 15 Jun 2020)

Changed paths:
M doc/sphinx/CMakeLists.txt

Log Message:
-----------
Look for ncgen in doc/sphinx/CMakeLists.txt

We need pism_config.nc to build the manual. We use ncgen to generate pism_config.nc.

NCGEN_PROGRAM is set by a different CMake script when the manual is built as a part of
PISM. This change restores the ability to build the manual without PISM's prerequisites.

Commit: 7d62afd89a9f1d99d60f3b7c304266033c98f4ca
https://github.com/pism/pism/commit/7d62afd89a9f1d99d60f3b7c304266033c98f4ca
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-15 (Mon, 15 Jun 2020)

Changed paths:
M doc/sphinx/installation/documentation.rst

Log Message:
-----------
Mention that ncgen and netcdf4-python are used to build the manual

Commit: be441085ad8c90a1ccc875874d7abb394c89995d
https://github.com/pism/pism/commit/be441085ad8c90a1ccc875874d7abb394c89995d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-15 (Mon, 15 Jun 2020)

Changed paths:
M .circleci/config.yml
M doc/sphinx/conf.py
M doc/sphinx/installation/documentation.rst
M docker/ubuntu/CMakeLists.txt
M docker/ubuntu/Dockerfile.in

Log Message:
-----------
Fixes related to building the Sphinx manual

- we need Sphinx 3.0 or newer
- we need to modify sys.path so that Sphinx can find PISM's extension
- Ubuntu 20.04 provides an old Sphinx version, so we need to install it using PIP in the
Docker image
- CircleCI setup needs to use the new Docker image

Commit: 76f2aa1c42d9222ac99d81555abdef49bf1e7c59
https://github.com/pism/pism/commit/76f2aa1c42d9222ac99d81555abdef49bf1e7c59
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-15 (Mon, 15 Jun 2020)

Changed paths:
M .circleci/config.yml

Log Message:
-----------
Save the cache before running regression tests

This way we don't have to re-build it all if regression tests fail.

Commit: f076a761f1c40302f7990b3ec8d3f10b12fb84e1
https://github.com/pism/pism/commit/f076a761f1c40302f7990b3ec8d3f10b12fb84e1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-15 (Mon, 15 Jun 2020)

Changed paths:
M .circleci/config.yml

Log Message:
-----------
Don't run regression tests in parallel

This seems to cause trouble and does not provide much benefit.

Commit: cc0c016abc42f8ef13e9bb6d92ddd9285b1298fa
https://github.com/pism/pism/commit/cc0c016abc42f8ef13e9bb6d92ddd9285b1298fa
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-15 (Mon, 15 Jun 2020)

Changed paths:
M src/pismv.cc

Log Message:
-----------
Restore the "-no_report" option in pismv

Commit: c359b70e528798366bf0089e16bbd8d6c6cb3412
https://github.com/pism/pism/commit/c359b70e528798366bf0089e16bbd8d6c6cb3412
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-15 (Mon, 15 Jun 2020)

Changed paths:
M test/regression/temp_continuity.py

Log Message:
-----------
Fix up an old regression test

This regression test is supposed to check that the difference between the basal
temperature in the ice and the temperature at the top of the bedrock decreases as you
refine in time.

At some point in time the test broke: after some change PISM computes higher
diffusivities, making the -max_dt option in the test ineffective (with adaptive time
steppint choosing time steps of ~50 years -max_dt 100 does nothing).

This change was not caught because the test incorrectly used ">" instead of ">=" to decide
if it failed.

This commit cleans up the script, removing its dependence on NCO and fixes the bug
described above.

Commit: a59a3ce0c621ffb1710a489614be5cc7afff4532
https://github.com/pism/pism/commit/a59a3ce0c621ffb1710a489614be5cc7afff4532
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-06-15 (Mon, 15 Jun 2020)

Changed paths:
M test/regression/test_29.py

Log Message:
-----------
No need to use mpiexec to run PISM in serial

Commit: 5ab4aea6a10d26e15a1f1c832439eef22c2caa6d
https://github.com/pism/pism/commit/5ab4aea6a10d26e15a1f1c832439eef22c2caa6d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-07-14 (Tue, 14 Jul 2020)

Changed paths:
M test/mass_transport.py

Log Message:
-----------
Fix wording in a regression test

Commit: 8188f1db80f10340435ec16ae32dea277702b376
https://github.com/pism/pism/commit/8188f1db80f10340435ec16ae32dea277702b376
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-07-14 (Tue, 14 Jul 2020)

Changed paths:
M src/geometry/GeometryEvolution.cc
M src/geometry/GeometryEvolution.hh
M src/icemodel/IceModel.cc
M test/mass_transport.py

Log Message:
-----------
Compute interface fluxes and *then* limit them

This commit removes a premature optimization: now we compute interface fluxes in two steps

1) Compute fluxes
2) Limit them

Also, it should not be necessary to use the velocity BC mask. Before this commit we used
the velocity BC mask in a way that allowed one to think about BC locations as locations
where ice *flux* is prescribed, but this was not used. Now it is a little harder to
predict the flux resulting from prescribing ice velocity and thickness, but the code is
simpler and more extensible.

Commit: eee97359884b94c903d6fd13138baaed759ff0e3
https://github.com/pism/pism/commit/eee97359884b94c903d6fd13138baaed759ff0e3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-07-14 (Tue, 14 Jul 2020)

Changed paths:
M src/geometry/GeometryEvolution.cc

Log Message:
-----------
Simplify staggered velocity computation in GeometryEvolution

Commit: abefd4183458076cf80a833b9b2895ce0b92abce
https://github.com/pism/pism/commit/abefd4183458076cf80a833b9b2895ce0b92abce
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-07-22 (Wed, 22 Jul 2020)

Changed paths:
M src/geometry/Geometry.cc
M src/geometry/Geometry.hh

Log Message:
-----------
Add Geometry::dump() to simplify debugging

Commit: ab8b8dab99047886e1c935a237df5efa4373a072
https://github.com/pism/pism/commit/ab8b8dab99047886e1c935a237df5efa4373a072
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-07-22 (Wed, 22 Jul 2020)

Changed paths:
M test/grounded_cell_fraction/grounded_cell_fraction.py

Log Message:
-----------
Turn grounded_cell_fraction.py into a proper test

Commit: 6a7b1e8d4902ec99852db00a943b34980902c354
https://github.com/pism/pism/commit/6a7b1e8d4902ec99852db00a943b34980902c354
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-07-22 (Wed, 22 Jul 2020)

Changed paths:
M src/geometry/grounded_cell_fraction.cc

Log Message:
-----------
Fix #462 (Asymmetry in subgl code)

An one-character typo resulted in asymmetric results given symmetric inputs.

Commit: 583c1390ff93f18edd1bd64967916b73394969a7
https://github.com/pism/pism/commit/583c1390ff93f18edd1bd64967916b73394969a7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-07-22 (Wed, 22 Jul 2020)

Changed paths:
M src/geometry/grounded_cell_fraction.cc

Log Message:
-----------
Cosmetic changes

This little bit of cleanup helped with debugging #462: it makes it easy to inspect *all*
the values of the floatation function in the vicinity of a particular grid cell.

Commit: 3b2b9cfdb365890949edcbfb010dd5f943ee01e9
https://github.com/pism/pism/commit/3b2b9cfdb365890949edcbfb010dd5f943ee01e9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-07-22 (Wed, 22 Jul 2020)

Changed paths:
M test/CMakeLists.txt
A test/grounded_cell_fraction.py
R test/grounded_cell_fraction/grounded_cell_fraction.mac
R test/grounded_cell_fraction/grounded_cell_fraction.py

Log Message:
-----------
Use grounded_cell_fraction.py as a regression test

Commit: 0d66e3ea0c43013ab788d311af2840dd0d2da352
https://github.com/pism/pism/commit/0d66e3ea0c43013ab788d311af2840dd0d2da352
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-07-22 (Wed, 22 Jul 2020)

Changed paths:
M src/geometry/Geometry.cc
M src/geometry/Geometry.hh
M src/geometry/grounded_cell_fraction.cc
M test/CMakeLists.txt
A test/grounded_cell_fraction.py
R test/grounded_cell_fraction/grounded_cell_fraction.mac
R test/grounded_cell_fraction/grounded_cell_fraction.py

Log Message:
-----------
Merge branch 'ckhroulev/cell_grounded_fraction' into dev

Commit: 04a692b499aca57f486369b37de4730bed50991a
https://github.com/pism/pism/commit/04a692b499aca57f486369b37de4730bed50991a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-07-23 (Thu, 23 Jul 2020)

Changed paths:
M src/pythonbindings/pism_calving.i

Log Message:
-----------
Add the iceberg remover to Python bindings

Commit: e94f4c734ae0d49701b3c5d4fffff683ee153d41
https://github.com/pism/pism/commit/e94f4c734ae0d49701b3c5d4fffff683ee153d41
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-08-19 (Wed, 19 Aug 2020)

Changed paths:
M src/icemodel/frontretreat.cc
M src/icemodel/initialization.cc

Log Message:
-----------
Fix a bug that made it impossible to use Hayhurst calving

We need to remember to allocate the front retreat mechanism.

Reported by Sebastian Hinck.

Commit: 8e3b020ab9a777d18f270e756a40922ef2ea9095
https://github.com/pism/pism/commit/8e3b020ab9a777d18f270e756a40922ef2ea9095
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-08-19 (Wed, 19 Aug 2020)

Changed paths:
M src/util/io/File.cc

Log Message:
-----------
Clean up I/O back-end allocation

Commit: a557fdf9b42cdc0ba80c62f6dc2f2afac3425f10
https://github.com/pism/pism/commit/a557fdf9b42cdc0ba80c62f6dc2f2afac3425f10
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-08-19 (Wed, 19 Aug 2020)

Changed paths:
M src/util/io/NC3File.cc
M src/util/io/NC3File.hh
M src/util/io/NC4File.hh
M src/util/io/NC4_Par.cc
M src/util/io/NC4_Par.hh
M src/util/io/NCFile.cc
M src/util/io/NCFile.hh
M src/util/io/PNCFile.cc
M src/util/io/PNCFile.hh
M src/util/io/ParallelIO.cc
M src/util/io/ParallelIO.hh

Log Message:
-----------
Add set_compression_level(int level) to the NCFile API

Commit: db75ed4ef204794b3fe5d890f14fc851f1147767
https://github.com/pism/pism/commit/db75ed4ef204794b3fe5d890f14fc851f1147767
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-08-19 (Wed, 19 Aug 2020)

Changed paths:
M src/util/CMakeLists.txt
M src/util/io/File.cc
R src/util/io/NC3File.cc
R src/util/io/NC3File.hh
A src/util/io/NC_Serial.cc
A src/util/io/NC_Serial.hh

Log Message:
-----------
Rename NC3File to NC_Serial

I am working on a way to write NetCDF-4 files using PISM's old code that uses rank 0 to
write data. It would not make sense to create a class writing NetCDF-4 files that is
derived from NC3File, which is named after NetCDF-3.

This will make it possible to write *compressed* NetCDF-4 files using serial HDF5 and
NetCDF libraries.

Commit: 32b0f9973a374c9f12ad2a8c5b09934950f71594
https://github.com/pism/pism/commit/32b0f9973a374c9f12ad2a8c5b09934950f71594
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-08-19 (Wed, 19 Aug 2020)

Changed paths:
M src/util/CMakeLists.txt
M src/util/io/NC4_Serial.cc
M src/util/io/NC4_Serial.hh
M src/util/io/NC_Serial.hh

Log Message:
-----------
Implement NC4_Serial

This class uses rank 0 to write NetCDF-4 files.

Commit: 7e4468a6cfc45413563e9dfdbb5fa05e8811b580
https://github.com/pism/pism/commit/7e4468a6cfc45413563e9dfdbb5fa05e8811b580
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-08-19 (Wed, 19 Aug 2020)

Changed paths:
M src/icemodel/output.cc
M src/pism_config.cdl
M src/util/io/File.cc
M src/util/io/File.hh
M src/util/io/IO_Flags.hh

Log Message:
-----------
Add File::set_compression_level() and add PISM_NETCDF4_SERIAL

Also, add netcdf4_serial to output.format. This format corresponds to writing HDF5-based
NetCDF-4 files using serial code that copies data to rank 0.

This makes it possible to use compression. Use output.compression_level to tell
PISM (currently: pismr, pisms, and pismv) to compress 2D and 3D variables in output files.

Use File::set_compression_level() to set compression level in the code.

Valid levels go from 0 (disabled) to 9 (maximum).

Commit: b71192212897db1e6dee99355242c11494553940
https://github.com/pism/pism/commit/b71192212897db1e6dee99355242c11494553940
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-08-31 (Mon, 31 Aug 2020)

Changed paths:
M src/regional/SSAFD_Regional.cc
M src/regional/SSAFD_Regional.hh
M src/stressbalance/factory.cc
M src/stressbalance/ssa/SSAFEM.cc

Log Message:
-----------
Re-enable stress_balance.ssa.method

IceModel (i.e. pismr) no longer ignores stress_balance.ssa.method.

Commit: a19a853acf41efb7eb0e3cbe18a1a6b0793075ce
https://github.com/pism/pism/commit/a19a853acf41efb7eb0e3cbe18a1a6b0793075ce
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-08-31 (Mon, 31 Aug 2020)

Changed paths:
M CHANGES.rst
M doc/sphinx/climate_forcing/atmosphere.rst
M src/coupler/atmosphere/Frac_P.cc
M src/coupler/atmosphere/Frac_P.hh
M test/regression/atmosphere_models.py

Log Message:
-----------
Support 2D scaling factors in -atmosphere ...,frac_P

Checks the number of dimensions of the variable `frac_P` in the input
file (atmosphere.frac_P.file). Reads it as a scalar time series if it has 1 dimension,
otherwise tries to read it as a time-and-space-dependent field.

Commit: a8a94e3ae096627f48acff791b2a52aa1b685ad1
https://github.com/pism/pism/commit/a8a94e3ae096627f48acff791b2a52aa1b685ad1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-02 (Wed, 02 Sep 2020)

Changed paths:
M src/hydrology/Routing.cc
M src/util/pism_utilities.hh

Log Message:
-----------
Make pism::clip() a template function

Commit: f164875ee604e7d07a7846f195e177d9df833788
https://github.com/pism/pism/commit/f164875ee604e7d07a7846f195e177d9df833788
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-02 (Wed, 02 Sep 2020)

Changed paths:
M src/util/io/NC4_Serial.cc

Log Message:
-----------
Ensure that the compression level is within the range

Commit: 248f662426ef77e6d416307ecee2b5adc5725c05
https://github.com/pism/pism/commit/248f662426ef77e6d416307ecee2b5adc5725c05
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-02 (Wed, 02 Sep 2020)

Changed paths:
M src/util/io/NC4File.cc
M src/util/io/NC4_Serial.cc

Log Message:
-----------
Ignore nc_def_var_deflate() failures

PISM may be built with NetCDF that does not support compression. Before this commit runs
using

-output.format netcdf4_serial -output.compression_level N

and

-output.format netcdf4_parallel -output.compression_level N

failed or succeeded depending on HDF5 and NetCDF versions in use.

Commit: 2569f50d02573fe13c26bd01d365e1d646165af2
https://github.com/pism/pism/commit/2569f50d02573fe13c26bd01d365e1d646165af2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-02 (Wed, 02 Sep 2020)

Changed paths:
M CHANGES.rst

Log Message:
-----------
Update the change log

Commit: 523b6ae5b4222add2f840422cc4ad55e8a13a48e
https://github.com/pism/pism/commit/523b6ae5b4222add2f840422cc4ad55e8a13a48e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-02 (Wed, 02 Sep 2020)

Changed paths:
M doc/sphinx/installation/code/hdf5.sh
M doc/sphinx/installation/code/netcdf.sh
M doc/sphinx/installation/code/parallelio.sh

Log Message:
-----------
Update HDF5, NetCDF, and ParallelIO versions used in build scripts

Commit: 629da07372220cd7da4bafb98581c970430bb928
https://github.com/pism/pism/commit/629da07372220cd7da4bafb98581c970430bb928
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-02 (Wed, 02 Sep 2020)

Changed paths:
M src/pism_config.cdl

Log Message:
-----------
Clean up formatting in pism_config.cdl

Commit: f3cef3200924a5fab2d504d10add8dbcd78777ba
https://github.com/pism/pism/commit/f3cef3200924a5fab2d504d10add8dbcd78777ba
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-02 (Wed, 02 Sep 2020)

Changed paths:
M test/regression/file.py

Log Message:
-----------
Improve a regression test

Commit: 5ed98cee17337437a80c9101e63fe1a99541f859
https://github.com/pism/pism/commit/5ed98cee17337437a80c9101e63fe1a99541f859
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-09 (Wed, 09 Sep 2020)

Changed paths:
M test/regression/temp_continuity.py
M test/regression/test_29.py

Log Message:
-----------
Remove f-strings

Now I can run tests using Python 3.5.

Commit: 7d1c83713b4ab7bd9a986e0202b87a72c53584ff
https://github.com/pism/pism/commit/7d1c83713b4ab7bd9a986e0202b87a72c53584ff
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-09 (Wed, 09 Sep 2020)

Changed paths:
M site-packages/PISM/testing.py

Log Message:
-----------
Don't use PISM.Timeseries() in create_scalar_forcing()

Commit: 7a77a123278037ae6c0c2d8180e262ef9f1dd78a
https://github.com/pism/pism/commit/7a77a123278037ae6c0c2d8180e262ef9f1dd78a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-09 (Wed, 09 Sep 2020)

Changed paths:
M src/coupler/atmosphere/WeatherStation.cc
M src/coupler/surface/TemperatureIndex.cc
M src/coupler/util/ScalarForcing.cc
M src/energy/EnergyModel.cc
M src/icemodel/diagnostics.cc
M src/icemodel/output.cc
M src/stressbalance/ssa/SSATestCase.cc
M src/util/Diagnostic.cc
M src/util/Diagnostic.hh
M src/util/Timeseries.cc
M src/util/Timeseries.hh
M src/util/VariableMetadata.cc
M src/util/io/io_helpers.cc
M src/util/io/io_helpers.hh
M src/verification/iceCompModel.cc
M test/miscellaneous.py

Log Message:
-----------
Clean up time series code

- remove Timeseries::{times,time_bounds,values}()
- fix Timeseries::read() (no longer uses the hard-wired dimension name)
- remove the extra write_timeseries() function and use initializer lists instead
- update interpolation tests

Commit: 6f0c3303e185aa3eb34ef7d78e39abb40603ca1d
https://github.com/pism/pism/commit/6f0c3303e185aa3eb34ef7d78e39abb40603ca1d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-09 (Wed, 09 Sep 2020)

Changed paths:
M src/icemodel/output.cc
M src/icemodel/output_extra.cc
M src/stressbalance/ssa/SSATestCase.cc
M src/util/Diagnostic.cc
M src/util/Diagnostic.hh
M src/util/io/io_helpers.cc
M src/util/io/io_helpers.hh
M src/verification/iceCompModel.cc
M test/icemodelvec2t.py
M test/regression/surface_models.py

Log Message:
-----------
write_timeseries() and write_time_bounds() no longer define variables

Commit: b2bf47e0b93114a63dc34aa2831d904837010e4c
https://github.com/pism/pism/commit/b2bf47e0b93114a63dc34aa2831d904837010e4c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-09 (Wed, 09 Sep 2020)

Changed paths:
M src/coupler/atmosphere/WeatherStation.cc
M src/coupler/util/ScalarForcing.cc
M src/hydrology/SteadyState.cc
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/pythonbindings/pism_Timeseries.i
M src/pythonbindings/pism_VariableMetadata.i
M src/stressbalance/ssa/SSATestCase.cc
M src/util/Diagnostic.cc
M src/util/Diagnostic.hh
M src/util/Time_Calendar.cc
M src/util/Timeseries.cc
M src/util/Timeseries.hh
M src/util/VariableMetadata.cc
M src/util/VariableMetadata.hh
M src/util/iceModelVec2T.cc
M src/verification/iceCompModel.cc
M test/icemodelvec2t.py
M test/miscellaneous.py
M test/regression/surface_models.py

Log Message:
-----------
Remove TimeseriesMetadata and TimeBoundsMetadata

Commit: b1e14d1c3ae49952348dd21694d671dd6957187c
https://github.com/pism/pism/commit/b1e14d1c3ae49952348dd21694d671dd6957187c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-09 (Wed, 09 Sep 2020)

Changed paths:
M src/util/iceModelVec.hh
M src/util/io/io_helpers.cc

Log Message:
-----------
Cleanup in io_helpers.cc

Commit: 92b2731297e162db4df0d1e47ebff414b03898db
https://github.com/pism/pism/commit/92b2731297e162db4df0d1e47ebff414b03898db
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-09 (Wed, 09 Sep 2020)

Changed paths:
M src/verification/iceCompModel.cc

Log Message:
-----------
Fix "pismv -report_file file.nc"

This rewrite was needed because of the changes in the time series code.

Commit: cefa76c79ec7d8a070b6d8e5eb0102ce8b32a1d1
https://github.com/pism/pism/commit/cefa76c79ec7d8a070b6d8e5eb0102ce8b32a1d1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-09 (Wed, 09 Sep 2020)

Changed paths:
M site-packages/PISM/testing.py

Log Message:
-----------
PISM.testing.create_scalar_forcing(): support custom time dimension names

Commit: 61bf047aeb9160d2eb4be279fa992ef2760ce8ad
https://github.com/pism/pism/commit/61bf047aeb9160d2eb4be279fa992ef2760ce8ad
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-09 (Wed, 09 Sep 2020)

Changed paths:
M site-packages/PISM/testing.py

Log Message:
-----------
PISM.testing.create_scalar_forcing(): don't overwrite the output file

This way we can store more than one time-series on the same file.

Commit: f14f3ec270f052661087e1ef1ea172e39934bab3
https://github.com/pism/pism/commit/f14f3ec270f052661087e1ef1ea172e39934bab3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-09 (Wed, 09 Sep 2020)

Changed paths:
M test/miscellaneous.py

Log Message:
-----------
Improve the Timeseries regression test

- use uuid4() to generate file names (I should do this in all test to avoid file name
clashes)
- store both time-series in the same file, using a custom time dimension name for one of
them

Commit: 01c8ba727503c1bee1b63c94d0d0f03a4bc0c9a8
https://github.com/pism/pism/commit/01c8ba727503c1bee1b63c94d0d0f03a4bc0c9a8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-09 (Wed, 09 Sep 2020)

Changed paths:
M site-packages/PISM/testing.py
M src/coupler/atmosphere/WeatherStation.cc
M src/coupler/surface/TemperatureIndex.cc
M src/coupler/util/ScalarForcing.cc
M src/energy/EnergyModel.cc
M src/hydrology/SteadyState.cc
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/diagnostics.cc
M src/icemodel/output.cc
M src/icemodel/output_extra.cc
M src/pythonbindings/pism_Timeseries.i
M src/pythonbindings/pism_VariableMetadata.i
M src/stressbalance/ssa/SSATestCase.cc
M src/util/Diagnostic.cc
M src/util/Diagnostic.hh
M src/util/Time_Calendar.cc
M src/util/Timeseries.cc
M src/util/Timeseries.hh
M src/util/VariableMetadata.cc
M src/util/VariableMetadata.hh
M src/util/iceModelVec.hh
M src/util/iceModelVec2T.cc
M src/util/io/io_helpers.cc
M src/util/io/io_helpers.hh
M src/verification/iceCompModel.cc
M test/icemodelvec2t.py
M test/miscellaneous.py
M test/regression/surface_models.py

Log Message:
-----------
Merge branch 'ckhroulev/fix-scalar-forcing' into dev

Commit: 7fe1683624d67727953c0b746b831d3cdf814450
https://github.com/pism/pism/commit/7fe1683624d67727953c0b746b831d3cdf814450
Author: Andy Aschwanden <andy.as...@gmail.com>
Date: 2020-09-16 (Wed, 16 Sep 2020)

Changed paths:
M src/coupler/ocean/GivenTH.cc
M src/pism_config.cdl

Log Message:
-----------
Exchange coefficients in ocean model should not be hard-wired.

Moved hard-wired coefficients in GivenTH to the config file.

Commit: 59e633189e21066477d7d6e75050be7f44c3ef54
https://github.com/pism/pism/commit/59e633189e21066477d7d6e75050be7f44c3ef54
Author: Andy Aschwanden <andy.as...@gmail.com>
Date: 2020-09-16 (Wed, 16 Sep 2020)

Changed paths:
M src/pism_config.cdl

Log Message:
-----------
Added missing "type" in config file

Commit: fd5a5c1fcc88fecfc0151484c1f56ca0fa66559c
https://github.com/pism/pism/commit/fd5a5c1fcc88fecfc0151484c1f56ca0fa66559c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-16 (Wed, 16 Sep 2020)

Changed paths:
M src/pism_config.cdl

Log Message:
-----------
Make sure that configuration parameters are sorted

Maintaining alphabetical order makes it easier to merge branches and track changes over
time. (Note: one of the tests performed by "make test" checks if parameters are sorted.)

Commit: c67de8cd0f41dafb5adb3e5d978d76678e057bde
https://github.com/pism/pism/commit/c67de8cd0f41dafb5adb3e5d978d76678e057bde
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-16 (Wed, 16 Sep 2020)

Changed paths:
M src/util/Time.cc
M src/util/Time_Calendar.cc
M src/util/Time_Calendar.hh

Log Message:
-----------
Remove date(), start_date(), and end_date() from Time_Calendar()

Commit: 7ef497ad3c2e3da3119e7e5289ee6dcf2712049f
https://github.com/pism/pism/commit/7ef497ad3c2e3da3119e7e5289ee6dcf2712049f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-16 (Wed, 16 Sep 2020)

Changed paths:
M doc/sphinx/climate_forcing/ocean.rst
M src/coupler/ocean/GivenTH.cc
M src/pism_config.cdl

Log Message:
-----------
Fix the name of a configuration parameter (ocean.th.clip_salinity)

This parameter used to be called ocean.three_equation_model_clip_salinity. A recent commit
renamed it to ocean.th.three_equation_model_clip_salinity, but that is
redundant ("ocean.th" is the "three equation model").

Also: update the reference to this parameter in the manual (note: this inconsistency was
caught by PISM's CI setup).

Commit: fd832a2d66b8c1d53a6a122a30037dc5eeaa5c0d
https://github.com/pism/pism/commit/fd832a2d66b8c1d53a6a122a30037dc5eeaa5c0d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-17 (Thu, 17 Sep 2020)

Changed paths:
M src/pism_config.cdl

Log Message:
-----------
Fix the order of configuration parameters (again!)

Commit: 6821bb56608f80a4b798f7e9fc7f98baf2c11917
https://github.com/pism/pism/commit/6821bb56608f80a4b798f7e9fc7f98baf2c11917
Author: Andy Aschwanden <andy.as...@gmail.com>
Date: 2020-09-21 (Mon, 21 Sep 2020)

Changed paths:
M util/adjust_timeline.py
M util/create_timeline.py

Log Message:
-----------
Replaced deprecated netcdftime with cftime

Commit: 7bdd61e35dd0e543626e395cea362b89a6c20843
https://github.com/pism/pism/commit/7bdd61e35dd0e543626e395cea362b89a6c20843
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-23 (Wed, 23 Sep 2020)

Changed paths:
M doc/sphinx/global.txt

Log Message:
-----------
Update Elizabeth's e-mail address in the installation manual

Commit: 4d454c28318dcb7433a94c75ddd6aa9d2dd9be0e
https://github.com/pism/pism/commit/4d454c28318dcb7433a94c75ddd6aa9d2dd9be0e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-23 (Wed, 23 Sep 2020)

Changed paths:
M src/coupler/frontalmelt/Given.cc

Log Message:
-----------
Replace nullptr with std::shared_ptr<FrontalMelt>()

This should help us support Intel compilers.

Commit: e488ff35e6823caa963a3c39bfe27a7299d7659f
https://github.com/pism/pism/commit/e488ff35e6823caa963a3c39bfe27a7299d7659f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-28 (Mon, 28 Sep 2020)

Changed paths:
M src/util/ColumnSystem.cc
M src/util/io/PNCFile.cc
M src/util/io/ParallelIO.cc
M src/util/options.cc

Log Message:
-----------
Include <cstring> in source files using memset()

Commit: 7de76fa35a7c9a004a52cc7bf4f89122500fb8c1
https://github.com/pism/pism/commit/7de76fa35a7c9a004a52cc7bf4f89122500fb8c1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-09-28 (Mon, 28 Sep 2020)

Changed paths:
M src/util/io/NC4File.cc
M src/util/io/NC_Serial.cc

Log Message:
-----------
Remove unnecessary #includes

Commit: 9964da54254723a8f5197c101b364b194dd5ee5f
https://github.com/pism/pism/commit/9964da54254723a8f5197c101b364b194dd5ee5f
Author: Andy Aschwanden <andy.as...@gmail.com>
Date: 2020-09-30 (Wed, 30 Sep 2020)

Changed paths:
M examples/jako/preprocess.sh

Log Message:
-----------
Fix preprocess script by adding `--no-check-certificate`

Commit: 6ed7ee9892473787543d11922854f86048276d00
https://github.com/pism/pism/commit/6ed7ee9892473787543d11922854f86048276d00
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-12 (Mon, 12 Oct 2020)

Changed paths:
M doc/sphinx/CMakeLists.txt

Log Message:
-----------
Add the manual_autobuild make target

This will make it easier to edit the manual.

Commit: 684f5bc41fd7fa21a4bfaa3df9a8180887002b8b
https://github.com/pism/pism/commit/684f5bc41fd7fa21a4bfaa3df9a8180887002b8b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-12 (Mon, 12 Oct 2020)

Changed paths:
M doc/sphinx/contributing/development-workflow.rst

Log Message:
-----------
Update the manual section explaining how to edit the manual

Commit: 45d3cdd71ef77ab4f66a4dd2011c9fbb403e8cac
https://github.com/pism/pism/commit/45d3cdd71ef77ab4f66a4dd2011c9fbb403e8cac
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-12 (Mon, 12 Oct 2020)

Changed paths:
M doc/sphinx/climate_forcing/time.rst

Log Message:
-----------
Document PISM's interpretation of forcing inputs

- 2D fluxes: piecewise-constant in time
- 2D (other): piecewise-linear in time
- scalar (with time bounds): piecewise-constant
- scalar (without time bounds): piecewise-linear

Commit: 68a3e8dfe6ba3719a49d51e256e2ccfdcf62a902
https://github.com/pism/pism/commit/68a3e8dfe6ba3719a49d51e256e2ccfdcf62a902
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-12 (Mon, 12 Oct 2020)

Changed paths:
M examples/labgum/preprocess.py

Log Message:
-----------
Fix the pre-processing script in examples/labgum

Commit: 60739ae417da1c4b106d9a4d9ab22a165194bdb6
https://github.com/pism/pism/commit/60739ae417da1c4b106d9a4d9ab22a165194bdb6
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M CHANGES.rst
M src/util/io/io_helpers.cc

Log Message:
-----------
Stop PISM if a variable in an input file has missing values

We check if some values of a variable match the _FillValue attribute.

Commit: bb2d15a4e6914f50930c5dc2150faba05d16d9aa
https://github.com/pism/pism/commit/bb2d15a4e6914f50930c5dc2150faba05d16d9aa
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/coupler/surface/localMassBalance.hh
M src/earth/BedDef.hh
M src/energy/enthSystem.hh
M src/inverse/IPDesignVariableParameterization.hh
M src/inverse/IP_SSAHardavForwardProblem.hh
M src/inverse/IP_SSATaucForwardProblem.hh
M src/inverse/functional/IPFunctional.hh
M src/inverse/functional/IPMeanSquareFunctional.hh
M src/inverse/functional/IP_H1NormFunctional.hh
M src/rheology/FlowLaw.hh
M src/stressbalance/sia/BedSmoother.hh
M src/util/Component.hh
M src/util/Field.hh
M src/util/IceGrid.hh
M src/util/Time.hh
M src/util/io/IO_Flags.hh

Log Message:
-----------
Clean up Doxygen comments

Commit: 9352b7d92e547f2154de91e27d34f0413ea3b688
https://github.com/pism/pism/commit/9352b7d92e547f2154de91e27d34f0413ea3b688
Author: Constantine Khroulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/ssa/SSAFEM.cc

Log Message:
-----------
Work on switching quadratures at the boundary in SSAFEM

Commit: 041a87e4e93f945d87b5c2c3890385fd7c4faeda
https://github.com/pism/pism/commit/041a87e4e93f945d87b5c2c3890385fd7c4faeda
Author: Constantine Khroulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/FETools.cc
M src/util/FETools.hh

Log Message:
-----------
Work on supporting more general boundary quadratures and outward normals

Commit: 046e571525de033780a055e2f501252c05663f55
https://github.com/pism/pism/commit/046e571525de033780a055e2f501252c05663f55
Author: Constantine Khroulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/FETools.cc

Log Message:
-----------
FETools: Move static functions to the top of the file

Commit: 46cb45cd751d281d29b2a1f0f6de55b91c8c7ddc
https://github.com/pism/pism/commit/46cb45cd751d281d29b2a1f0f6de55b91c8c7ddc
Author: Constantine Khroulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/ssa/SSAFEM.cc

Log Message:
-----------
SSAFEM: Use fem::q1::outward_normals()

Commit: f79a9e1e03279a28a28ccc7bbd2408833aa1f28d
https://github.com/pism/pism/commit/f79a9e1e03279a28a28ccc7bbd2408833aa1f28d
Author: Constantine Khroulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/ssa/SSAFEM.cc

Log Message:
-----------
Some more work on generalizing SSAFEM

I need to make common interfaces for Q1 and P1 boundary quadratures and
maps of incident nodes.

Commit: d788e993b999b49f636d7d5617823155dbe54c50
https://github.com/pism/pism/commit/d788e993b999b49f636d7d5617823155dbe54c50
Author: Constantine Khroulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/ssa/SSAFEM.cc
M src/util/FETools.cc
M src/util/FETools.hh

Log Message:
-----------
Add a class isolating element geometry info

Now we can easily switch between Q1 and P1 elements.

Next: add a similar class for boundary quadratures.

Commit: 005f5140aaa3090d6520ba176864247aecbd98a8
https://github.com/pism/pism/commit/005f5140aaa3090d6520ba176864247aecbd98a8
Author: Constantine Khroulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/ssa/doc/fem_p1.mac
A src/stressbalance/ssa/doc/fem_p1_boundary.mac
A src/stressbalance/ssa/doc/fem_q1.mac
A src/stressbalance/ssa/doc/fem_q1_boundary.mac

Log Message:
-----------
Add Maxima scripts documenting boundary treatment

Commit: 0dd84134473f6f505f1a7b0b4fb00c57b050f72b
https://github.com/pism/pism/commit/0dd84134473f6f505f1a7b0b4fb00c57b050f72b
Author: Constantine Khroulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/ssa/SSAFEM.cc
M src/util/FETools.cc

Log Message:
-----------
More cleanup in SSAFEM

Commit: e4513241419d09d868018130076d875fc66a31ad
https://github.com/pism/pism/commit/e4513241419d09d868018130076d875fc66a31ad
Author: Constantine Khroulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/ssa/SSAFEM.cc
M src/util/FETools.cc
M src/util/FETools.hh

Log Message:
-----------
SSAFEM CFBC test passes with the new fem::BoundaryQuadrature

Next: implement fem::p1::BoundaryQuadrature2 (2-point Gaussian
quadrature on sides of P1 elements).

Commit: a348932bc3caf28d2d21534baffeaafdec1efebd
https://github.com/pism/pism/commit/a348932bc3caf28d2d21534baffeaafdec1efebd
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/FETools.cc

Log Message:
-----------
Clean up FETools.cc

Commit: efa5aecbd3e0fdc934391cfc82022c70c206ded6
https://github.com/pism/pism/commit/efa5aecbd3e0fdc934391cfc82022c70c206ded6
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/inverse/IP_SSAHardavForwardProblem.cc
M src/inverse/IP_SSATaucForwardProblem.cc
M src/stressbalance/ssa/SSAFEM.cc
M src/stressbalance/ssa/SSAFEM.hh

Log Message:
-----------
Make copies of bc_mask and bc_values instead of copying pointers

... to avoid the possibility of having dangling pointers.

Commit: 9d2cafb85c9bdc7bb0c55ced78d555c68ddbdcce
https://github.com/pism/pism/commit/9d2cafb85c9bdc7bb0c55ced78d555c68ddbdcce
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/node_types.cc

Log Message:
-----------
Use BoxStencil in node_types.cc

Commit: deda53aabdc2841d97ef4875c093b899d37e721c
https://github.com/pism/pism/commit/deda53aabdc2841d97ef4875c093b899d37e721c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/node_types.cc

Log Message:
-----------
Fix the code computing node types

Commit: 1f1b9fd54ca0495634274fe85ead773cb1bfd4d9
https://github.com/pism/pism/commit/1f1b9fd54ca0495634274fe85ead773cb1bfd4d9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/FETools.cc

Log Message:
-----------
Improve boundary quadrature code (I hope so, anyway)

Commit: c82f63fa5a32fe49f40ccf87810b2300d35ba230
https://github.com/pism/pism/commit/c82f63fa5a32fe49f40ccf87810b2300d35ba230
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/miscellaneous.py

Log Message:
-----------
Add a regression test for Q1 boundary quadrature code

This is not enough but is better than no tests at all.

Commit: 1983bc1c73c152ddc7de9d33501ca2a3ff3890ab
https://github.com/pism/pism/commit/1983bc1c73c152ddc7de9d33501ca2a3ff3890ab
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
A test/regression/ssa/ssafem.py

Log Message:
-----------
Add a simple script running the SSAFEM solver

Right now I use this to debug boundary quadrature code.

Commit: 8f167e842c8a89c0bfea1cfd3647fd4cd3f9173f
https://github.com/pism/pism/commit/8f167e842c8a89c0bfea1cfd3647fd4cd3f9173f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/regression/ssa/ssafem.py

Log Message:
-----------
Simplify ssafem.py for now

Commit: f2bd36a5fd5ecff8152b453e851b2cb32650230a
https://github.com/pism/pism/commit/f2bd36a5fd5ecff8152b453e851b2cb32650230a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/ssa/SSAFEM.cc

Log Message:
-----------
Fix SSAFEM code using boundary quadratures

Commit: 830c7fa68a3f6bb6d9619f5551849137e000e403
https://github.com/pism/pism/commit/830c7fa68a3f6bb6d9619f5551849137e000e403
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/ssa/SSAFEM.cc

Log Message:
-----------
Use consistent conditions to find element types

Commit: e1d9148208383d50da751be64a5152603bc36b4d
https://github.com/pism/pism/commit/e1d9148208383d50da751be64a5152603bc36b4d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/regression/ssa/ssafem.py

Log Message:
-----------
Improve the test script

Bigger grid, variable "peninsula" lengths, save velocity magnitude

Commit: cf9082c7029682e67bd78cc76083f6dcc0377f16
https://github.com/pism/pism/commit/cf9082c7029682e67bd78cc76083f6dcc0377f16
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/FETools.hh

Log Message:
-----------
Clean up a comment

Commit: a9a11fdaa6095e17cc0ec9ad0ef42a69f10bbabb
https://github.com/pism/pism/commit/a9a11fdaa6095e17cc0ec9ad0ef42a69f10bbabb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/ssa/SSAFEM.cc

Log Message:
-----------
Work on P1 element stuff

Commit: cacebf8959d839d181da91e4e8de7685f7f1e704
https://github.com/pism/pism/commit/cacebf8959d839d181da91e4e8de7685f7f1e704
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/FETools.cc
M src/util/FETools.hh

Log Message:
-----------
Clean up fem::q1::BoundaryQuadrature2

Commit: cdd1a01a8ff48486792792da390182bdc2e7f91c
https://github.com/pism/pism/commit/cdd1a01a8ff48486792792da390182bdc2e7f91c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/FETools.hh

Log Message:
-----------
Add p1::BoundaryQuadrature2

Commit: 715c9f0bfb63959982581358a8f934960352448f
https://github.com/pism/pism/commit/715c9f0bfb63959982581358a8f934960352448f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pythonbindings/PISM.i
M src/stressbalance/ssa/SSAFEM.cc
M src/util/FETools.cc
M src/util/FETools.hh

Log Message:
-----------
Work on P1 elements

Commit: 495de1ef6d5d179d4d902a90e7c94e322cd06b44
https://github.com/pism/pism/commit/495de1ef6d5d179d4d902a90e7c94e322cd06b44
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/inverse/IP_SSAHardavForwardProblem.cc
M src/inverse/IP_SSATaucForwardProblem.cc
M src/inverse/functional/IPGroundedIceH1NormFunctional.cc
M src/inverse/functional/IPTotalVariationFunctional.cc
M src/inverse/functional/IP_H1NormFunctional.cc
M src/inverse/functional/IP_L2NormFunctional.cc
M src/stressbalance/ssa/SSAFEM.cc
M src/util/FETools.hh

Log Message:
-----------
Move the "Germs" typedef into Quadrature

Commit: 754dad692139e5e23f5fc1502494eca2263d8972
https://github.com/pism/pism/commit/754dad692139e5e23f5fc1502494eca2263d8972
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/inverse/IP_SSAHardavForwardProblem.hh
M src/inverse/IP_SSATaucForwardProblem.hh
M src/inverse/functional/IPFunctional.hh
M src/stressbalance/ssa/SSAFEM.hh
M src/util/FETools.cc
M src/util/FETools.hh

Log Message:
-----------
Rename ElementMap to Element

Commit: bc50d75214690fab12ac342ef55b3b0c44435a2e
https://github.com/pism/pism/commit/bc50d75214690fab12ac342ef55b3b0c44435a2e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/inverse/IP_SSAHardavForwardProblem.cc
M src/inverse/IP_SSATaucForwardProblem.cc
M src/inverse/functional/IPGroundedIceH1NormFunctional.cc
M src/inverse/functional/IPTotalVariationFunctional.cc
M src/inverse/functional/IP_H1NormFunctional.cc
M src/inverse/functional/IP_L2NormFunctional.cc
M src/stressbalance/ssa/SSAFEM.cc
M src/util/FETools.cc
M src/util/FETools.hh
M test/miscellaneous.py

Log Message:
-----------
Work on de-optimizing the code in FETools.{cc,hh}

... to make it easier to switch element types.

Commit: 3bf519f9b51c4993e9ea5cb99a632ba0f3065f64
https://github.com/pism/pism/commit/3bf519f9b51c4993e9ea5cb99a632ba0f3065f64
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/inverse/IP_SSAHardavForwardProblem.cc
M src/inverse/IP_SSAHardavForwardProblem.hh
M src/inverse/IP_SSATaucForwardProblem.cc
M src/inverse/IP_SSATaucForwardProblem.hh
M src/inverse/functional/IPFunctional.hh
M src/inverse/functional/IPGroundedIceH1NormFunctional.cc
M src/inverse/functional/IPTotalVariationFunctional.cc
M src/inverse/functional/IP_H1NormFunctional.cc
M src/inverse/functional/IP_L2NormFunctional.cc
M src/pythonbindings/PISM.i
M src/stressbalance/ssa/SSAFEM.cc
M src/stressbalance/ssa/SSAFEM.hh
M src/stressbalance/ssa/doc/fem_p1.mac
M src/util/CMakeLists.txt
R src/util/FETools.cc
R src/util/FETools.hh
A src/util/fem/DirichletData.cc
A src/util/fem/DirichletData.hh
A src/util/fem/Element.cc
A src/util/fem/Element.hh
A src/util/fem/ElementIterator.cc
A src/util/fem/ElementIterator.hh
A src/util/fem/FEM.cc
A src/util/fem/FEM.hh
A src/util/fem/Quadrature.cc
A src/util/fem/Quadrature.hh

Log Message:
-----------
Commit work on re-organizing 2D FEM code (compiles but does not work)

This should make it easier to maintain the code and switch between Q1 and P1 elements as
necessary.

Commit: 039e73db6fbe108af1f1ff906dee1e5ef507d7a7
https://github.com/pism/pism/commit/039e73db6fbe108af1f1ff906dee1e5ef507d7a7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.cc
M src/util/fem/Element.hh

Log Message:
-----------
Implement P1 element stuff

Commit: d8617930ff9356810e93dd1b344495dee0a654d1
https://github.com/pism/pism/commit/d8617930ff9356810e93dd1b344495dee0a654d1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pythonbindings/PISM.i
M src/util/fem/FEM.cc
M src/util/fem/FEM.hh
M src/util/fem/Quadrature.cc
M src/util/fem/Quadrature.hh

Log Message:
-----------
Add a 1D 2-point Gaussian quadrature

Commit: 88d21dd3d756d7407e74e7a38b494927273e5799
https://github.com/pism/pism/commit/88d21dd3d756d7407e74e7a38b494927273e5799
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/ssa/SSAFEM.cc
M test/regression/ssa/ssafem.py

Log Message:
-----------
Trying to use new code in SSAFEM

Commit: 7840d1fe2ccd856cb57cfdb4b7214c8e3511e1b7
https://github.com/pism/pism/commit/7840d1fe2ccd856cb57cfdb4b7214c8e3511e1b7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/ssa/SSAFEM.cc
M src/stressbalance/ssa/SSAFEM.hh

Log Message:
-----------
More work on switching between Q1 and P1

Commit: 729803ed286bacb89d63e8ca8bc43f779321d2a4
https://github.com/pism/pism/commit/729803ed286bacb89d63e8ca8bc43f779321d2a4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Quadrature.hh

Log Message:
-----------
Clean up 2-pt Gaussian quadrature code

Commit: 0e0c73888c56bed52798e9679ccae8685d46372e
https://github.com/pism/pism/commit/0e0c73888c56bed52798e9679ccae8685d46372e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/FEM.cc
M src/util/fem/FEM.hh

Log Message:
-----------
Add fem::element_type()

Commit: b92221e118710416ddc61e5842f485e00dbd8a8e
https://github.com/pism/pism/commit/b92221e118710416ddc61e5842f485e00dbd8a8e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/ssa/SSAFEM.cc

Log Message:
-----------
Use fem::element_type() in SSAFEM

Commit: 5b67230e9ab18e7b591b9a1d4cb9e397ad1d8553
https://github.com/pism/pism/commit/5b67230e9ab18e7b591b9a1d4cb9e397ad1d8553
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.cc

Log Message:
-----------
Fix Element::add_contribution() and related P1 element code

Commit: 0f975c00da52cb8ba3c801402e21c8164be7f521
https://github.com/pism/pism/commit/0f975c00da52cb8ba3c801402e21c8164be7f521
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/regression/ssa/ssafem.py

Log Message:
-----------
Update the test script (runs but produces asymmetric results)

Commit: 53c4764ed57ca0ed921c499332c84882c9723cc4
https://github.com/pism/pism/commit/53c4764ed57ca0ed921c499332c84882c9723cc4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.cc

Log Message:
-----------
Fix normal vectors of P1 elements

Commit: 33f1c00ac8470eaa7654fcd04fa5932bb5801c16
https://github.com/pism/pism/commit/33f1c00ac8470eaa7654fcd04fa5932bb5801c16
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/node_types.cc

Log Message:
-----------
Fix node type computations

Commit: 6a9c78861b0e47e86d1629e2291550bc6a7b1865
https://github.com/pism/pism/commit/6a9c78861b0e47e86d1629e2291550bc6a7b1865
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.cc

Log Message:
-----------
Initialize m_row[k].c and m_col[k].c

This should not change anything (but good to do anyway).

Commit: 46347270882728066436fe5a72169b433a92a171
https://github.com/pism/pism/commit/46347270882728066436fe5a72169b433a92a171
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/regression/ssa/ssafem.py

Log Message:
-----------
Reduce grid size down to 3x3

Commit: 3fdc627208382e546a3fff75c7a817d5d5addbb7
https://github.com/pism/pism/commit/3fdc627208382e546a3fff75c7a817d5d5addbb7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/regression/ssa/ssafem.py

Log Message:
-----------
Add code for saving and plotting

Commit: c8ef9e7abf462e1d08e820bab64b6a6f45bf8955
https://github.com/pism/pism/commit/c8ef9e7abf462e1d08e820bab64b6a6f45bf8955
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.cc

Log Message:
-----------
Zero out m_row, m_col, and m_germs

Commit: 0d388c9a7c2c10344d154c10626c2fb26f0c93d9
https://github.com/pism/pism/commit/0d388c9a7c2c10344d154c10626c2fb26f0c93d9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.cc

Log Message:
-----------
Fix node coordinates in P1Element

Commit: 9e29f844b6458b584ef7e6d38380ad3c28647ed7
https://github.com/pism/pism/commit/9e29f844b6458b584ef7e6d38380ad3c28647ed7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/regression/ssa/ssafem.py

Log Message:
-----------
Improve the test script

Commit: a4f1327be5d6ebccca188241311468c5c72efc32
https://github.com/pism/pism/commit/a4f1327be5d6ebccca188241311468c5c72efc32
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/DirichletData.cc

Log Message:
-----------
Fix DirichletData

Commit: 9e3e28e41e2ef4385f27906b1ccf4e417d3e4ee7
https://github.com/pism/pism/commit/9e3e28e41e2ef4385f27906b1ccf4e417d3e4ee7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M examples/marine/circular/circular_dirichlet.py

Log Message:
-----------
Update a variable name in circular_dirichlet.py

Commit: c68ad659c43a47bc48b3ee830217064bd4df20de
https://github.com/pism/pism/commit/c68ad659c43a47bc48b3ee830217064bd4df20de
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/frontretreat/util/remove_narrow_tongues.cc

Log Message:
-----------
Clean up remove_narrow_tongues()

Commit: e29a3234f5f21aa12a65e2677f1469313bef8993
https://github.com/pism/pism/commit/e29a3234f5f21aa12a65e2677f1469313bef8993
Author: Constantine Khroulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/CMakeLists.txt
M src/pism_config.cdl
M src/pythonbindings/CMakeLists.txt
M src/pythonbindings/PISM.i
A src/pythonbindings/pism_blatter.i
M src/stressbalance/CMakeLists.txt
A src/stressbalance/blatter/BlatterStressBalance.cc
A src/stressbalance/blatter/BlatterStressBalance.hh
A src/stressbalance/blatter/Blatter_implementation.c
A src/stressbalance/blatter/Blatter_implementation.h
A src/stressbalance/blatter/CMakeLists.txt
A src/stressbalance/blatter/FE3DTools.h
A src/stressbalance/blatter/README.org
A src/stressbalance/blatter/doc/Makefile
A src/stressbalance/blatter/doc/notes.tex
A test/blatter.py

Log Message:
-----------
Restore the Blatter stress balance code

This reverts commit 8e3d7390c622fb3e44040fc3b603f73d896e71d1.

Also:
- remove blatter_test.cc and add test/blatter.py instead
- fix compilation issues
- support current PETSc
- clean up

Commit: 390a8a90e4e3ab6c10491bd15ca6772483e0387b
https://github.com/pism/pism/commit/390a8a90e4e3ab6c10491bd15ca6772483e0387b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/BlatterStressBalance.cc

Log Message:
-----------
Clean up Blatter stress balance code

Commit: 4b7a2ac9dad303ccfe9e162474ef2ecfe7068691
https://github.com/pism/pism/commit/4b7a2ac9dad303ccfe9e162474ef2ecfe7068691
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter_implementation.c

Log Message:
-----------
Add a comment

Commit: 362b5ec6616855d96ab56151019f5489b80ac001
https://github.com/pism/pism/commit/362b5ec6616855d96ab56151019f5489b80ac001
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter_implementation.c

Log Message:
-----------
Cleanup: rename variables, tweak comments, etc

Commit: 3e329c72d8ec1305b56d942b376a054bdb06322b
https://github.com/pism/pism/commit/3e329c72d8ec1305b56d942b376a054bdb06322b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter_implementation.c

Log Message:
-----------
Rename jw -> W

Commit: bb59dd429c7d2145ff0eb7e1cd77283635bd47cd
https://github.com/pism/pism/commit/bb59dd429c7d2145ff0eb7e1cd77283635bd47cd
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/BlatterStressBalance.cc
M src/stressbalance/blatter/BlatterStressBalance.hh

Log Message:
-----------
Add a field storing bottom elevation of the ice

Commit: 154f8e9255e6fe120b3c1a20c59ac0dbbc34bf7f
https://github.com/pism/pism/commit/154f8e9255e6fe120b3c1a20c59ac0dbbc34bf7f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/BlatterStressBalance.cc

Log Message:
-----------
Use ice_bottom_surface() in BlatterStressBalance::setup()

Commit: 179cc31b6b3fde97020fe67a958477c9ae2b77ea
https://github.com/pism/pism/commit/179cc31b6b3fde97020fe67a958477c9ae2b77ea
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/BlatterStressBalance.cc
M src/stressbalance/blatter/BlatterStressBalance.hh
M src/stressbalance/blatter/Blatter_implementation.h

Log Message:
-----------
Add node type to 2D parameters

Commit: 2ecc5926e57ab44bc9cd989a7914f00d089703cb
https://github.com/pism/pism/commit/2ecc5926e57ab44bc9cd989a7914f00d089703cb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/BlatterStressBalance.cc
M src/stressbalance/blatter/Blatter_implementation.c

Log Message:
-----------
Use spatially-variable ice hardness (needs testing)

Commit: 2466d14199038694efb2d39ff25ef4e5827cd3e2
https://github.com/pism/pism/commit/2466d14199038694efb2d39ff25ef4e5827cd3e2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pythonbindings/pism_energy.i

Log Message:
-----------
Add energy/utilities.hh to Python bindings

Commit: 9242cc8a5c222a53f8dfe004c92f6779fe05cecb
https://github.com/pism/pism/commit/9242cc8a5c222a53f8dfe004c92f6779fe05cecb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/blatter.py

Log Message:
-----------
Modify blatter.py so that it does not need an input file

Commit: 85a0e50e2ff1a4462f2b7c5e56629dba3fc27512
https://github.com/pism/pism/commit/85a0e50e2ff1a4462f2b7c5e56629dba3fc27512
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/CMakeLists.txt
A src/stressbalance/blatter/Poisson.cc

Log Message:
-----------
Add Poisson.cc based on src/snes/examples/tutorials/ex14.c

Commit: 938e67f373b8f5aeaf4bda2088a6bea09d7eb50d
https://github.com/pism/pism/commit/938e67f373b8f5aeaf4bda2088a6bea09d7eb50d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/CMakeLists.txt
R src/stressbalance/blatter/Poisson.cc
A src/stressbalance/blatter/Poisson3.cc
A src/stressbalance/blatter/Poisson3.hh

Log Message:
-----------
More fiddles

Commit: c6ec6d123846a5c65a746dc6e3a10cb98b7affe0
https://github.com/pism/pism/commit/c6ec6d123846a5c65a746dc6e3a10cb98b7affe0
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pythonbindings/pism_blatter.i

Log Message:
-----------
Add a Python wrapper

Commit: 6ba003a67b188e9946028ad7af588426830e1719
https://github.com/pism/pism/commit/6ba003a67b188e9946028ad7af588426830e1719
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Use a more interesting initial guess

Commit: 20c0d4268802cf754908bbce3df453f89cb21741
https://github.com/pism/pism/commit/20c0d4268802cf754908bbce3df453f89cb21741
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Remove the broken pointer wrapper

Commit: 533af460ee402a14e506c8801dcabca9ddbb6dbb
https://github.com/pism/pism/commit/533af460ee402a14e506c8801dcabca9ddbb6dbb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
More work on the 3D Poisson solver

Commit: 7050b55523cc62fe6f1ff359b274c196076cea88
https://github.com/pism/pism/commit/7050b55523cc62fe6f1ff359b274c196076cea88
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/inverse/IP_SSAHardavForwardProblem.cc
M src/inverse/IP_SSATaucForwardProblem.cc
M src/inverse/functional/IPGroundedIceH1NormFunctional.cc
M src/inverse/functional/IPTotalVariationFunctional.cc
M src/inverse/functional/IP_H1NormFunctional.cc
M src/inverse/functional/IP_L2NormFunctional.cc
M src/stressbalance/blatter/BlatterStressBalance.cc
M src/stressbalance/ssa/SSAFEM.cc
M src/util/fem/DirichletData.cc
M src/util/fem/Element.hh
M src/util/iceModelVec.hh
M src/util/iceModelVec2.cc

Log Message:
-----------
Remove extra Element::nodal_values()

Also:

- Rename get_array() to array() (there is no set_array(), so "get_" is implied).
- IceModelVec::array() does not call begin_access() any more.

Commit: 859054c54e09cb7cc2dbbe605b28515b394455fe
https://github.com/pism/pism/commit/859054c54e09cb7cc2dbbe605b28515b394455fe
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/FEM.cc
M src/util/fem/FEM.hh
M src/util/fem/Quadrature.cc

Log Message:
-----------
Add the third dimension to QuadPoint and Germ

Commit: bf3cc6807093a0adf930844fe40628647d23e1a9
https://github.com/pism/pism/commit/bf3cc6807093a0adf930844fe40628647d23e1a9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/inverse/functional/IPGroundedIceH1NormFunctional.cc
M src/inverse/functional/IPTotalVariationFunctional.cc
M src/inverse/functional/IP_H1NormFunctional.cc
M src/inverse/functional/IP_L2NormFunctional.cc
M src/stressbalance/ssa/SSAFEM.cc
M src/util/fem/DirichletData.cc
M src/util/fem/DirichletData.hh
M src/util/fem/Element.cc
M src/util/fem/Element.hh
M src/util/fem/FEM.cc
M src/util/fem/FEM.hh

Log Message:
-----------
More work on FEM code

Now I'm ready to write the 3D Q1 element code.

Commit: 414dedb51793dcd32ffe3b420b9a2a041f50e8ac
https://github.com/pism/pism/commit/414dedb51793dcd32ffe3b420b9a2a041f50e8ac
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.cc
M src/util/fem/Element.hh

Log Message:
-----------
Start implementing 3D elements

Commit: f81a918318348f4b5b1f82152a7bc53c347fb00e
https://github.com/pism/pism/commit/f81a918318348f4b5b1f82152a7bc53c347fb00e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/inverse/IP_SSAHardavForwardProblem.hh
M src/inverse/IP_SSATaucForwardProblem.hh
M src/inverse/functional/IPFunctional.hh
M src/stressbalance/ssa/SSAFEM.cc
M src/stressbalance/ssa/SSAFEM.hh
M src/util/fem/Element.cc
M src/util/fem/Element.hh

Log Message:
-----------
Rename {P,Q}1Element to {P,Q}1Element2

Now all element names have a suffix corresponding to the number of dimensions.

Commit: 41c72cf2a6860337c3fde74618605dbf5952d7be
https://github.com/pism/pism/commit/41c72cf2a6860337c3fde74618605dbf5952d7be
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.cc
M src/util/fem/Element.hh

Log Message:
-----------
Finish implementing 3D Q1 elements

Commit: b774254e6a4f60822d025c773ca1a04131f5c37e
https://github.com/pism/pism/commit/b774254e6a4f60822d025c773ca1a04131f5c37e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.cc

Log Message:
-----------
Clean up

Commit: 7e3c014db5a8fab34b950ea3a81a70e60e3c576c
https://github.com/pism/pism/commit/7e3c014db5a8fab34b950ea3a81a70e60e3c576c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Quadrature.cc
M src/util/fem/Quadrature.hh

Log Message:
-----------
Implement the 8-point quadrature on [-1,1]*[-1,1]*[-1,1]

Commit: 377504a652eca456644254d0120de12663ec5fa3
https://github.com/pism/pism/commit/377504a652eca456644254d0120de12663ec5fa3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh

Log Message:
-----------
Rename Poisson3::compute_local_function() to compute_residual()

Commit: 02a285982101797e6ebc1b3f05771436cbf9e9db
https://github.com/pism/pism/commit/02a285982101797e6ebc1b3f05771436cbf9e9db
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Try to create a 3D Q1 element

Commit: c6ba2b5e24b4499ee4e0c4ae8d1452e671d233fc
https://github.com/pism/pism/commit/c6ba2b5e24b4499ee4e0c4ae8d1452e671d233fc
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.hh

Log Message:
-----------
Fix a typo

Commit: 9d53d1387bea8077a659fca4b7faf58fca94c790
https://github.com/pism/pism/commit/9d53d1387bea8077a659fca4b7faf58fca94c790
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Implement something resembling a Poisson equation solver

Commit: 0fc3ec7253b22481e3df67026ab6c264f045c196
https://github.com/pism/pism/commit/0fc3ec7253b22481e3df67026ab6c264f045c196
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pythonbindings/PISM.i
M src/util/fem/Element.cc
M src/util/fem/Element.hh

Log Message:
-----------
Numerous fixes in the 3D FEM code

Commit: f3ba885e6d5e1fb5d6e34952badad79f5e06589d
https://github.com/pism/pism/commit/f3ba885e6d5e1fb5d6e34952badad79f5e06589d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh

Log Message:
-----------
Rename x() to solution() and m_xx to m_solution

Commit: 15ca19e2eb4ee2fb8e5a826885354c31589c19f2
https://github.com/pism/pism/commit/15ca19e2eb4ee2fb8e5a826885354c31589c19f2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.hh

Log Message:
-----------
fem::Element3: Return global indexes in a struct

Commit: ea17f186c7df18032c25a32487017bc95f617e3c
https://github.com/pism/pism/commit/ea17f186c7df18032c25a32487017bc95f617e3c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
More work on the Poisson solver

Commit: a839a3e93fe30ae84912f903f1ea617d31239aa2
https://github.com/pism/pism/commit/a839a3e93fe30ae84912f903f1ea617d31239aa2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh

Log Message:
-----------
Remove Poisson3::m_r

Commit: 139debe21a7f77259ec2eac4e9ec63d5e8044598
https://github.com/pism/pism/commit/139debe21a7f77259ec2eac4e9ec63d5e8044598
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.hh

Log Message:
-----------
Add local_to_global() that does not use m_{i,j,k}

The node ordering is the same for all elements and should be available before
Element3::reset() is called.

Commit: 7faa0fe457517941d2f1a1d65c6f49a78b3bbbee
https://github.com/pism/pism/commit/7faa0fe457517941d2f1a1d65c6f49a78b3bbbee
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Making the code more general in preparation for testing

... using an exact solution and a more sophisticated Dirichlet BC.

Commit: 7a80ed005b22951b438d6715f28f6985878c8e2d
https://github.com/pism/pism/commit/7a80ed005b22951b438d6715f28f6985878c8e2d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Use more interesting BC

Commit: 9591ef73a717e0f71fd90bcb9d36ec085889af82
https://github.com/pism/pism/commit/9591ef73a717e0f71fd90bcb9d36ec085889af82
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Implement spatially-variable F

Commit: c84e271e8b314c4509d8369057c7ea5935e85d45
https://github.com/pism/pism/commit/c84e271e8b314c4509d8369057c7ea5935e85d45
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Combine loops over owned nodes

We can set the residual at Dirichlet nodes as we zero out the rest of the residual in
preparation for the loop over elements.

Commit: 7df68e26f45d57d9650be742b52222aa12eb216b
https://github.com/pism/pism/commit/7df68e26f45d57d9650be742b52222aa12eb216b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh

Log Message:
-----------
Compute exact solutions

Commit: 590067586d41403e3e4db11755a54b0711c7d4b9
https://github.com/pism/pism/commit/590067586d41403e3e4db11755a54b0711c7d4b9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh

Log Message:
-----------
Add Poisson3::error()

Commit: f5d7580718cf8a8c28c6903734e8332b4c51b765
https://github.com/pism/pism/commit/f5d7580718cf8a8c28c6903734e8332b4c51b765
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pythonbindings/pism_blatter.i

Log Message:
-----------
Clean up

Commit: f56034a9cae774683924507686c2e6503fd16495
https://github.com/pism/pism/commit/f56034a9cae774683924507686c2e6503fd16495
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh

Log Message:
-----------
Move b and H to m_b, m_H

Commit: ee471bd7a99b8be5bfcaf9cba1779202cc962428
https://github.com/pism/pism/commit/ee471bd7a99b8be5bfcaf9cba1779202cc962428
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.cc
M src/util/fem/Element.hh

Log Message:
-----------
Add the DMDALocalInfo-based constructor to Q1Element2

Commit: 46b58312f05cd9cbca1bcc1d31b52cf856bc2b25
https://github.com/pism/pism/commit/46b58312f05cd9cbca1bcc1d31b52cf856bc2b25
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Quadrature.cc
M src/util/fem/Quadrature.hh

Log Message:
-----------
Add the 1-point 3D Q1 quadrature (for testing)

Commit: a1f7a0753ebf8bc318e0be904340e285475f81c0
https://github.com/pism/pism/commit/a1f7a0753ebf8bc318e0be904340e285475f81c0
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pythonbindings/pism_blatter.i
M src/stressbalance/blatter/CMakeLists.txt
A src/stressbalance/blatter/Poisson2.cc
A src/stressbalance/blatter/Poisson2.hh

Log Message:
-----------
Add Poisson2 (for testing)

Commit: e38cae01a9904b907ff2ce7d99516d32d517cb72
https://github.com/pism/pism/commit/e38cae01a9904b907ff2ce7d99516d32d517cb72
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh

Log Message:
-----------
More work on the Poisson3 solver

Seems to show quadratic convergence for u_bc() not dependent on z.

Commit: d12badda8d2048f34ae0ab7dc584079a9ee0283e
https://github.com/pism/pism/commit/d12badda8d2048f34ae0ab7dc584079a9ee0283e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh

Log Message:
-----------
Add b(x,y) and H(x,y)

Commit: 9e802d3f956e69934cb84897a8f52a2f9d5274b4
https://github.com/pism/pism/commit/9e802d3f956e69934cb84897a8f52a2f9d5274b4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Quadrature.cc
M src/util/fem/Quadrature.hh

Log Message:
-----------
Add a 1-point 2D quadrature on [-1,1]*[-1,1]

Commit: c1a186292065729c183207535849a42e91c87e35
https://github.com/pism/pism/commit/c1a186292065729c183207535849a42e91c87e35
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
A src/util/fem/q1_3d_boundary.mac

Log Message:
-----------
Add a Maxima script deriving quadrature weights on element sides

Commit: 2f393a0159a6a0b79aa63268786f0364882e9cf0
https://github.com/pism/pism/commit/2f393a0159a6a0b79aa63268786f0364882e9cf0
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Quadrature.cc

Log Message:
-----------
Clean up Quadrature.cc

Commit: e74abd09762fc081d9c0a0260a7940cc782c5651
https://github.com/pism/pism/commit/e74abd09762fc081d9c0a0260a7940cc782c5651
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.hh

Log Message:
-----------
Clean up in Element.hh

This commit makes Element::add_contribution(), mark_row_invalid(), and mark_col_invalid()
protected.

Commit: 026c45ac3272c964eceda114ba4efde92cd671c3
https://github.com/pism/pism/commit/026c45ac3272c964eceda114ba4efde92cd671c3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.cc
M src/util/fem/Element.hh
M src/util/fem/FEM.hh

Log Message:
-----------
More work on integrating over element faces

Commit: 95ba380e9097f6927d7cadb0c0997d19350b2bba
https://github.com/pism/pism/commit/95ba380e9097f6927d7cadb0c0997d19350b2bba
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
A test/poisson3_test.py

Log Message:
-----------
Add poisson3_test.py (for now)

This script runs a verification test for the Poisson3 solver.

Commit: 0f7274f6a96921e72f6ace0d353e3cbd7ca12478
https://github.com/pism/pism/commit/0f7274f6a96921e72f6ace0d353e3cbd7ca12478
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Implement Neumann BC and test the code

... by using Neumann BC on the bottom (z = 0) side of the domain.

So far it works as expected for flat bottoms. I need to come up with a test case using
b(x,y) that is not a constant.

Commit: 33938c79c0008660eddd019c3a6fca242bdaf3d1
https://github.com/pism/pism/commit/33938c79c0008660eddd019c3a6fca242bdaf3d1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/util/fem/Element.cc
M src/util/fem/Element.hh

Log Message:
-----------
Q1Element3Side: don't return partial derivatives

... because they are wrong. (I would have needed to compute inverse(J) at each quadrature
point.)

Commit: 1d9eeba49ffed2c8e0c0ebfc53bd5f45cf76b85e
https://github.com/pism/pism/commit/1d9eeba49ffed2c8e0c0ebfc53bd5f45cf76b85e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/util/fem/Element.cc
M src/util/fem/Element.hh
M src/util/fem/FEM.hh

Log Message:
-----------
Rename "side" to "face" in the 3D case

Commit: f681b2dce97abd1c42733e90ca84ed8a5e40b2e3
https://github.com/pism/pism/commit/f681b2dce97abd1c42733e90ca84ed8a5e40b2e3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/util/fem/Element.cc
M src/util/fem/Element.hh

Log Message:
-----------
Clean up generic FEM and Poisson3 implementations

Commit: 626d7a4422b68375e6d0d0977aed1ca1ccb36a13
https://github.com/pism/pism/commit/626d7a4422b68375e6d0d0977aed1ca1ccb36a13
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Use (x,y)-dependent Neumann BC

Commit: 1dd7d586f1898116d5e807435690e13083b58b37
https://github.com/pism/pism/commit/1dd7d586f1898116d5e807435690e13083b58b37
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Start work on Neumann BC on a vertical face

Commit: c82417a5e8ac36a5d11586d0f72c62ea0b29ed2d
https://github.com/pism/pism/commit/c82417a5e8ac36a5d11586d0f72c62ea0b29ed2d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Implement Neumann BC at two vertical sides of the domain

Commit: b09fe317568dcdcbb931fd0a236631647808e677
https://github.com/pism/pism/commit/b09fe317568dcdcbb931fd0a236631647808e677
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/poisson3_test.py

Log Message:
-----------
poisson3_test.py: plot only if rank == 0

Commit: 1570ff504c32d6096e20103c52778698a0dfdb48
https://github.com/pism/pism/commit/1570ff504c32d6096e20103c52778698a0dfdb48
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
More cleanup

Commit: 1ce426312bdfa2a350631bb526bc3534f247e6c5
https://github.com/pism/pism/commit/1ce426312bdfa2a350631bb526bc3534f247e6c5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh

Log Message:
-----------
Allocate storage for 2D parameters

So far this is just bed elevation and thickness. The Blatter solver will add tauc to this
list.

Commit: 592bcc741285855bc4698be8d009d8cc631e3649
https://github.com/pism/pism/commit/592bcc741285855bc4698be8d009d8cc631e3649
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh

Log Message:
-----------
Initialize 2D parameters

Commit: d3ace1c210a6e5d3d2b0944bbb91407d97cee8c9
https://github.com/pism/pism/commit/d3ace1c210a6e5d3d2b0944bbb91407d97cee8c9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Use 2D parameters (bed and thickness)

Commit: 7c931b9f80c0dc39981ce24b25d3e2e63c9bf228
https://github.com/pism/pism/commit/7c931b9f80c0dc39981ce24b25d3e2e63c9bf228
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M test/poisson3_test.py

Log Message:
-----------
Clean up

Commit: 400a279aca7700684d31aef1dfd23897e56063cb
https://github.com/pism/pism/commit/400a279aca7700684d31aef1dfd23897e56063cb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Add storage for 3D data inputs

Commit: ca87c139ab62d183152ca31e7762174eaa5085d2
https://github.com/pism/pism/commit/ca87c139ab62d183152ca31e7762174eaa5085d2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh

Log Message:
-----------
Initialize 3D inputs

Commit: 5e8fa245de7f0f41a3724bb24cd95645503a4dd2
https://github.com/pism/pism/commit/5e8fa245de7f0f41a3724bb24cd95645503a4dd2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Get the right hand side (F) from the 3D Vec

Commit: c68aee11e767cd70264d857be6549bc5c610f532
https://github.com/pism/pism/commit/c68aee11e767cd70264d857be6549bc5c610f532
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/util/fem/Element.cc

Log Message:
-----------
Clean up

Commit: 4d21f3db41a5fbf95bafeda2ecbe40fb23c1e423
https://github.com/pism/pism/commit/4d21f3db41a5fbf95bafeda2ecbe40fb23c1e423
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh

Log Message:
-----------
Add coarsening and restriction hooks

Now I can run the test script with "-pc_type mg -pc_mg_levels N" to get N coarsening
levels.

Commit: fdce5f7a79ea3257eb66befa9a9d36fc7bf4d1d7
https://github.com/pism/pism/commit/fdce5f7a79ea3257eb66befa9a9d36fc7bf4d1d7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh
M test/poisson3_test.py

Log Message:
-----------
cleanup

Commit: 6fd760737e4399d7c138261786656131a59c39e4
https://github.com/pism/pism/commit/6fd760737e4399d7c138261786656131a59c39e4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
A src/stressbalance/blatter/DataInput.hh
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Put DataInput in a separate header

Commit: 02d90ae5b26294ff1a008a178ef906ef2eb35c2e
https://github.com/pism/pism/commit/02d90ae5b26294ff1a008a178ef906ef2eb35c2e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/CMakeLists.txt
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh
A src/stressbalance/blatter/grid_hierarchy.cc
A src/stressbalance/blatter/grid_hierarchy.hh

Log Message:
-----------
Move grid hierarchy code into a separate file

Commit: 40c968e11f510641a4e98cb8f32e0f8d617b1cd8
https://github.com/pism/pism/commit/40c968e11f510641a4e98cb8f32e0f8d617b1cd8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Add a function that computes padding amount

... needed to be able to use a given number of levels in a grid hierarchy.

Commit: d7fc59594cbd04070ad15584f54aad38159690ab
https://github.com/pism/pism/commit/d7fc59594cbd04070ad15584f54aad38159690ab
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Start work on node types

Commit: f1fa671f8d30bea60a3af318c8cdb85bddaf259d
https://github.com/pism/pism/commit/f1fa671f8d30bea60a3af318c8cdb85bddaf259d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/grid_hierarchy.hh

Log Message:
-----------
Add min_thickness to GridInfo

We use it to compute node types.

Commit: 53237e0bd6ea1f08837d3be38cf0665a95a76b0d
https://github.com/pism/pism/commit/53237e0bd6ea1f08837d3be38cf0665a95a76b0d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Quadrature.hh

Log Message:
-----------
Fix a typo (this is a one-point quadrature)

Commit: d96fd80265b6297f1257059714f20132c614b125
https://github.com/pism/pism/commit/d96fd80265b6297f1257059714f20132c614b125
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Add a restriction hook that re-computes node type

Commit: 804ef4bcae082e0116688806d3340019caddea88
https://github.com/pism/pism/commit/804ef4bcae082e0116688806d3340019caddea88
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/q1_3d_boundary.mac

Log Message:
-----------
Fiddling with parameterizations

Commit: 9602fd0321381f6ba97d4e6b9121200db908a21d
https://github.com/pism/pism/commit/9602fd0321381f6ba97d4e6b9121200db908a21d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Switch to a simpler problem

This problem uses Dirichlet BC at z = 0 and z = 1 and Neumann BC at vertical faces
(x = -1, x = 1, y = -1, y = 1).

Commit: 99e4d09f75ddfdc500baf87a188ef7b027c15e0d
https://github.com/pism/pism/commit/99e4d09f75ddfdc500baf87a188ef7b027c15e0d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.cc
M src/util/fem/Element.hh
M src/util/fem/FEM.hh

Log Message:
-----------
Q1Element3Face provides outward-pointing unit normal vectors

Commit: 3fc766442e847ec54c34599aa34f8a44d30f0d7d
https://github.com/pism/pism/commit/3fc766442e847ec54c34599aa34f8a44d30f0d7d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Use normal vectors to set Neumann BC

Also: fix the sign in the integral over the Neumann boundary.

Commit: 696bce594afb38197266964459b6a99b3311831b
https://github.com/pism/pism/commit/696bce594afb38197266964459b6a99b3311831b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Use p3_coarsening_hook() in Poisson3

We need a custom coarsening hook because it sets the restriction hook for the next level.

Commit: 31f4b43236117534f6fba328a4282ece1ed8cb35
https://github.com/pism/pism/commit/31f4b43236117534f6fba328a4282ece1ed8cb35
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Use node_type to identify the Neumann boundary

Commit: bbbd058b985e0dce970549dc5f1491027b835a1f
https://github.com/pism/pism/commit/bbbd058b985e0dce970549dc5f1491027b835a1f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/grid_hierarchy.cc

Log Message:
-----------
Trying to use node_type to exclude a part of the domain

Commit: caddda87d8c52663dec8d5f54b58ff0413cf09a3
https://github.com/pism/pism/commit/caddda87d8c52663dec8d5f54b58ff0413cf09a3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/grid_hierarchy.cc

Log Message:
-----------
Fix reporting of grid info

Commit: 66b0c065378e15d3c43a9f40f4df71878ae7c32c
https://github.com/pism/pism/commit/66b0c065378e15d3c43a9f40f4df71878ae7c32c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Use the right MPI communicator

Commit: 3ef667e82bd3f233786e071c822ef670ba8a8f19
https://github.com/pism/pism/commit/3ef667e82bd3f233786e071c822ef670ba8a8f19
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Add a silly residual monitor

Commit: 4af09b19907356a3973dc16c93a6d8c86e54b93e
https://github.com/pism/pism/commit/4af09b19907356a3973dc16c93a6d8c86e54b93e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/poisson3_test.py

Log Message:
-----------
Fix the regression test

We need to make sure that the domain does not change as we refine the grid, otherwise
different refinement steps correspond to different BVPs.

Commit: 073edc635c4585d731b3752aec77ffbbc2a17b26
https://github.com/pism/pism/commit/073edc635c4585d731b3752aec77ffbbc2a17b26
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Remove the residual monitor and add more printing code

Commit: 1a358c56b93dcb6fb9ff4d63587ff1e90fe61d33
https://github.com/pism/pism/commit/1a358c56b93dcb6fb9ff4d63587ff1e90fe61d33
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/DataInput.hh
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/grid_hierarchy.cc
M src/stressbalance/blatter/grid_hierarchy.hh

Log Message:
-----------
Fix restrictions to coarser grids and remove printing code

Commit: 98094c1ad4f018adf4e94d7a1d8c3025bf88e72f
https://github.com/pism/pism/commit/98094c1ad4f018adf4e94d7a1d8c3025bf88e72f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh
M src/stressbalance/blatter/grid_hierarchy.cc
M src/stressbalance/blatter/grid_hierarchy.hh
M test/poisson3_test.py

Log Message:
-----------
Pad x and y to allow for a given number of coarsenings

Commit: 46a63f685a0f3125d007a0c853953cd39919f97c
https://github.com/pism/pism/commit/46a63f685a0f3125d007a0c853953cd39919f97c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh

Log Message:
-----------
Start work on the Jacobian callback

Commit: 22a1d1b0ca7107e37595f892f97e89bbdc40f6f5
https://github.com/pism/pism/commit/22a1d1b0ca7107e37595f892f97e89bbdc40f6f5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Fix the sign of the residual at Dirichlet nodes

Commit: f2dea0f1744f2f75ae6a552b7818dbd8df113a9f
https://github.com/pism/pism/commit/f2dea0f1744f2f75ae6a552b7818dbd8df113a9f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh

Log Message:
-----------
Scale residual and Jacobian entries at Dirichlet nodes

Commit: 9f3bca549c7f93bf3ead0637e639dce072e0925f
https://github.com/pism/pism/commit/9f3bca549c7f93bf3ead0637e639dce072e0925f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
A test/poisson3.py

Log Message:
-----------
Add a test script that runs Poisson3 once

Commit: c44eb50b0a1deea5579a5acfd5cb3bf26e911628
https://github.com/pism/pism/commit/c44eb50b0a1deea5579a5acfd5cb3bf26e911628
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
A src/stressbalance/blatter/DataAccess.hh
R src/stressbalance/blatter/DataInput.hh
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Rename DataInput to DataAccess (this is more appropriate)

Commit: c6b06202b0fb60ea7150ee1d40b0e0a27941e881
https://github.com/pism/pism/commit/c6b06202b0fb60ea7150ee1d40b0e0a27941e881
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Cosmetic changes

Commit: 0ddbff5aa83d99bb1fff57a2f23fb11af8d12a63
https://github.com/pism/pism/commit/0ddbff5aa83d99bb1fff57a2f23fb11af8d12a63
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Speed up Jacobian assembly by using symmetry

Commit: 32fe050e9791b9e9bd9aeb4aa5478d8facc5016d
https://github.com/pism/pism/commit/32fe050e9791b9e9bd9aeb4aa5478d8facc5016d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.cc

Log Message:
-----------
Use local_to_global() to mark invalid rows

Commit: 29c6e66b052ae4c551fc20a944d79ede13a15252
https://github.com/pism/pism/commit/29c6e66b052ae4c551fc20a944d79ede13a15252
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Cosmetic changes

Commit: 4e6694639fece2a80c7b6c9fbf6ab46fb9905488
https://github.com/pism/pism/commit/4e6694639fece2a80c7b6c9fbf6ab46fb9905488
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/grid_hierarchy.cc

Log Message:
-----------
Report *non-negative* coarsening levels

Commit: 29d138eaf908f1916f96e69ec6cbb91ec753357c
https://github.com/pism/pism/commit/29d138eaf908f1916f96e69ec6cbb91ec753357c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Use memset() to zero out element residual and Jacobian

Commit: d61f52271dce2aa9721be4f00a2062110e504972
https://github.com/pism/pism/commit/d61f52271dce2aa9721be4f00a2062110e504972
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/grid_hierarchy.cc
M src/util/fem/Element.cc
M src/util/fem/Element.hh

Log Message:
-----------
Transpose the storage order

... to ensure that vertical columns are stored contiguously and are not distributed across
multiple MPI processes.

Commit: 6cb17ee101ae3d50e53de5a7476f93b2a597f7e3
https://github.com/pism/pism/commit/6cb17ee101ae3d50e53de5a7476f93b2a597f7e3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc

Log Message:
-----------
Improve comments

Commit: 74f0f19e8d02869d58d502ab2c267569ceab50f3
https://github.com/pism/pism/commit/74f0f19e8d02869d58d502ab2c267569ceab50f3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/grid_hierarchy.cc
M src/stressbalance/blatter/grid_hierarchy.hh

Log Message:
-----------
Move generic code from Poisson3.cc to grid_hierarchy.cc

Commit: 075af03cb7c5f9c569342a23c22a33c530cc2024
https://github.com/pism/pism/commit/075af03cb7c5f9c569342a23c22a33c530cc2024
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pythonbindings/pism_blatter.i
M src/stressbalance/blatter/CMakeLists.txt
R src/stressbalance/blatter/Poisson2.cc
R src/stressbalance/blatter/Poisson2.hh

Log Message:
-----------
Remove Poisson2

Commit: b17bfe4bf2ced66e2ab5d1e0f314a485f9fd42f7
https://github.com/pism/pism/commit/b17bfe4bf2ced66e2ab5d1e0f314a485f9fd42f7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
A src/stressbalance/blatter/Blatter.cc
A src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/CMakeLists.txt
A src/stressbalance/blatter/doc/blatter.mac

Log Message:
-----------
Copy Poisson into Blatter.cc to use as a starting point

Commit: a5b372f5c280d075a0fe7f74200c02d590de017e
https://github.com/pism/pism/commit/a5b372f5c280d075a0fe7f74200c02d590de017e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Work on switching discretizations

Commit: 70f30e23a81856a96a3ade18653b32946da41d7e
https://github.com/pism/pism/commit/70f30e23a81856a96a3ade18653b32946da41d7e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Allocate the flow law

Commit: 2d97abaf7f7c46dba0ad609b0947e69ed625b18e
https://github.com/pism/pism/commit/2d97abaf7f7c46dba0ad609b0947e69ed625b18e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Get geometry and hardness from inputs

Commit: eec1a734c8c6e6fd243bc70e880926753f6cb79f
https://github.com/pism/pism/commit/eec1a734c8c6e6fd243bc70e880926753f6cb79f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
I cannot re-use compute_node_type()

Commit: 4416d00bd6568533a4db31b67d8879444918f4a1
https://github.com/pism/pism/commit/4416d00bd6568533a4db31b67d8879444918f4a1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pythonbindings/pism_blatter.i

Log Message:
-----------
Update the Python wrapper

Commit: 578acaf7c040aa41892cca049309b243f3276a28
https://github.com/pism/pism/commit/578acaf7c040aa41892cca049309b243f3276a28
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/blatter.py

Log Message:
-----------
Update the test script

Commit: 7df3854cc185e5fdaee94efa17a45bb676b21fe3
https://github.com/pism/pism/commit/7df3854cc185e5fdaee94efa17a45bb676b21fe3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Scale by rho*g

Commit: cf10636e791fa52a31a9f1c849e90bc03fa19123
https://github.com/pism/pism/commit/cf10636e791fa52a31a9f1c849e90bc03fa19123
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M examples/storglaciaren/create_warming_climate.py

Log Message:
-----------
Fix a Storglaciaren script

Commit: f5645248b417f0e33f2e937127ea81467da8efe4
https://github.com/pism/pism/commit/f5645248b417f0e33f2e937127ea81467da8efe4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/blatter.py

Log Message:
-----------
Run the Blatter solver with data from a file

Commit: df11953e8094cf511292addbb639b41e0b4fce02
https://github.com/pism/pism/commit/df11953e8094cf511292addbb639b41e0b4fce02
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Run update(inputs, false) to solve without re-setting the initial guess

Commit: 295a4ff1c322a4b46738b42906218160d71fb067
https://github.com/pism/pism/commit/295a4ff1c322a4b46738b42906218160d71fb067
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M test/blatter.py

Log Message:
-----------
Clean up; compute vertically-averaged velocity

Commit: 91d08be55d2d7928f1ac658c6ce9ffa74c218afa
https://github.com/pism/pism/commit/91d08be55d2d7928f1ac658c6ce9ffa74c218afa
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Isolate the code copying the solution and setting the initial guess

Commit: 4365794abcea4cc1e3f3873ffdbe638b771d6e70
https://github.com/pism/pism/commit/4365794abcea4cc1e3f3873ffdbe638b771d6e70
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Compute basal frictional heating

Commit: e8272c5faec45b946316913723c69a9ddee6f42c
https://github.com/pism/pism/commit/e8272c5faec45b946316913723c69a9ddee6f42c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Rename fields storing u,v on the sigma grid

Commit: 20884f3ce7e9305f8b5b9380d444b087e7b2bc64
https://github.com/pism/pism/commit/20884f3ce7e9305f8b5b9380d444b087e7b2bc64
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Compute ice velocity on the PISM vertical grid

Commit: ceef7a6c633036af7b713c5343cdae7a135dcb1a
https://github.com/pism/pism/commit/ceef7a6c633036af7b713c5343cdae7a135dcb1a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Get minimum thickness from a configuration file

Commit: 49d5ec231ba2ffbd6e185c1f087fee617a08a66a
https://github.com/pism/pism/commit/49d5ec231ba2ffbd6e185c1f087fee617a08a66a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/blatter.py

Log Message:
-----------
Use finer vertical grids in blatter.py

Commit: 6087823bf9697989c02aa79c1e57fb1945df8ed5
https://github.com/pism/pism/commit/6087823bf9697989c02aa79c1e57fb1945df8ed5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Improve initialization

Commit: d91dd319557b9f5096cf73880762c950b169f537
https://github.com/pism/pism/commit/d91dd319557b9f5096cf73880762c950b169f537
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Cleanup

- Using SIA velocities as an initial guess seems like a bad idea.
- Remove strain heating stuff

Commit: 53057efde1b2df796b23275bc830f14e7f99f5b5
https://github.com/pism/pism/commit/53057efde1b2df796b23275bc830f14e7f99f5b5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/StressBalance.cc

Log Message:
-----------
Cleanup in StressBalance

Commit: b7344dc1d52236a673707379497aa4028b1405cc
https://github.com/pism/pism/commit/b7344dc1d52236a673707379497aa4028b1405cc
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/blatter.py

Log Message:
-----------
Save velocity magnitude

Commit: c4e18314fac2c7949d705d8a672b9a4b74e9c003
https://github.com/pism/pism/commit/c4e18314fac2c7949d705d8a672b9a4b74e9c003
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Add basal drag

Commit: 55f80a4dbf5da31104badd26eb78c7fd98cb1896
https://github.com/pism/pism/commit/55f80a4dbf5da31104badd26eb78c7fd98cb1896
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/blatter.py

Log Message:
-----------
Increase the yield stress

Commit: 90ede34f3ae7fd868979585d7c439705427ecdb0
https://github.com/pism/pism/commit/90ede34f3ae7fd868979585d7c439705427ecdb0
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Use semi-coarsening

Commit: 59429a177498e7c18e5d5bc0691b785c5071d51b
https://github.com/pism/pism/commit/59429a177498e7c18e5d5bc0691b785c5071d51b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pism_config.cdl
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Add coarsening factor

Commit: 26a50f8fd26daf728b2e5d823d938a5ccfec450a
https://github.com/pism/pism/commit/26a50f8fd26daf728b2e5d823d938a5ccfec450a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/blatter.py

Log Message:
-----------
Don't pad

Commit: 45c1d0eb948f19ae1bb7f0b570018143ce137163
https://github.com/pism/pism/commit/45c1d0eb948f19ae1bb7f0b570018143ce137163
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
A src/stressbalance/blatter/BlatterMod.cc
A src/stressbalance/blatter/BlatterMod.hh
M src/stressbalance/blatter/CMakeLists.txt

Log Message:
-----------
Implement BlatterMod

This class (together with Blatter) will be used by pism::stressbalance::StressBalance.

Commit: c71bcdbcbcf89e31f137cd9da8a0a4533483e28c
https://github.com/pism/pism/commit/c71bcdbcbcf89e31f137cd9da8a0a4533483e28c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/SSB_Modifier.cc
M src/stressbalance/SSB_Modifier.hh

Log Message:
-----------
Cleanup in SSB_Modifier

- SSB_Modifier::diffusive_flux() and max_diffusivity() should not be virtual
- remove m_strain_heating (it is not used)

Commit: 301f9b160b766dbaea1aaae771e3d450d632bff3
https://github.com/pism/pism/commit/301f9b160b766dbaea1aaae771e3d450d632bff3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/StressBalance.cc
M src/stressbalance/StressBalance.hh
M src/stressbalance/factory.cc
M src/stressbalance/sia/siafd_test.cc
M src/util/fem/Element.cc

Log Message:
-----------
Use shared_ptr to pass sub-models to StressBalance

Commit: fd9a5c215615bdb1c947313ffe157c6db5eec729
https://github.com/pism/pism/commit/fd9a5c215615bdb1c947313ffe157c6db5eec729
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pythonbindings/PISM.i
M src/pythonbindings/pism_SIA.i
M src/pythonbindings/pism_SSA.i
M src/pythonbindings/pism_blatter.i
M test/blatter.py

Log Message:
-----------
Test Blatter and BlatterMod in a StressBalance instance

Commit: 7b691a4bfde0eb9dcdb26bde2b9dd5c0bb60ea77
https://github.com/pism/pism/commit/7b691a4bfde0eb9dcdb26bde2b9dd5c0bb60ea77
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pism_config.cdl
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/grid_hierarchy.cc
M src/stressbalance/blatter/grid_hierarchy.hh
M src/stressbalance/factory.cc

Log Message:
-----------
Add the Blatter stress balance to the stress balance factory

Now we can choose it in pismr and such by using "-stress_balance blatter".

Commit: a19b96580efd124193e9b9cf6bf5a0a6de89c56a
https://github.com/pism/pism/commit/a19b96580efd124193e9b9cf6bf5a0a6de89c56a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/icemodel/initialization.cc

Log Message:
-----------
Use the yield stress model with the Blatter solver

Commit: 8ce264064905fce01d689ef9fc8d728a27b225ea
https://github.com/pism/pism/commit/8ce264064905fce01d689ef9fc8d728a27b225ea
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/blatter.py

Log Message:
-----------
Update the test script

Commit: 633d8f2e48c9fca4aa1f79edc9f594e4bf9627bd
https://github.com/pism/pism/commit/633d8f2e48c9fca4aa1f79edc9f594e4bf9627bd
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/BlatterMod.cc

Log Message:
-----------
Update ghosts of stress balance outputs

Commit: 4b2abf34eaa1293daee5511fc38f740d07704e80
https://github.com/pism/pism/commit/4b2abf34eaa1293daee5511fc38f740d07704e80
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Trying to implement stress BC

Commit: 9dd01ded58008c37808569bedee8349489883298
https://github.com/pism/pism/commit/9dd01ded58008c37808569bedee8349489883298
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/DirichletData.cc

Log Message:
-----------
Include Context.hh now that IceGrid.hh does not do that

Commit: b3816e9331835f92bbbfe102a7fdb9483fa04d6b
https://github.com/pism/pism/commit/b3816e9331835f92bbbfe102a7fdb9483fa04d6b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
R src/stressbalance/blatter/BlatterStressBalance.cc
R src/stressbalance/blatter/BlatterStressBalance.hh
R src/stressbalance/blatter/Blatter_implementation.c
R src/stressbalance/blatter/Blatter_implementation.h
M src/stressbalance/blatter/CMakeLists.txt
R src/stressbalance/blatter/FE3DTools.h

Log Message:
-----------
Remove the old BP solver implementation

Commit: 7a42b86d181cedd0e87f5edd7e5c20f3a4609274
https://github.com/pism/pism/commit/7a42b86d181cedd0e87f5edd7e5c20f3a4609274
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M examples/inverse/pismi.py
M site-packages/PISM/invert/sipletools.py
M site-packages/PISM/invert/ssa_siple.py
M site-packages/PISM/model.py
M site-packages/PISM/sia.py
M site-packages/PISM/ssa.py
M src/age/AgeModel.cc
M src/coupler/frontalmelt/FrontalMelt.cc
M src/coupler/surface/ForceThickness.cc
M src/coupler/surface/Initialization.cc
M src/coupler/surface/TemperatureIndex.cc
M src/coupler/surface/localMassBalance.cc
M src/earth/BedDef.cc
M src/earth/BedDef.hh
M src/earth/LingleClark.cc
M src/earth/LingleClark.hh
M src/earth/PointwiseIsostasy.cc
M src/energy/BTU_Full.cc
M src/energy/BTU_Full.hh
M src/energy/BedThermalUnit.cc
M src/energy/BedThermalUnit.hh
M src/energy/EnergyModel.cc
M src/energy/TemperatureModel.cc
M src/energy/btutest.cc
M src/frontretreat/FrontRetreat.cc
M src/frontretreat/calving/StressCalving.cc
M src/frontretreat/calving/vonMisesCalving.cc
M src/geometry/GeometryEvolution.cc
M src/hydrology/EmptyingProblem.hh
M src/hydrology/Hydrology.hh
M src/hydrology/NullTransport.cc
M src/icebin/IBIceModel.cc
M src/icebin/IBSurfaceModel.cc
M src/icebin/MassEnergyBudget.cc
M src/icebin/MassEnergyBudget.hh
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/diagnostics.cc
M src/icemodel/energy.cc
M src/icemodel/fracture_density.cc
M src/icemodel/frontretreat.cc
M src/icemodel/initialization.cc
M src/icemodel/timestepping.cc
M src/inverse/IPTaoTikhonovProblem.hh
M src/inverse/IP_SSAHardavForwardProblem.cc
M src/inverse/IP_SSAHardavForwardProblem.hh
M src/inverse/IP_SSATaucForwardProblem.cc
M src/inverse/IP_SSATaucTaoTikhonovProblemLCL.cc
M src/inverse/IP_SSATaucTikhonovGNSolver.hh
M src/inverse/functional/IPFunctional.cc
M src/inverse/functional/IPLogRatioFunctional.cc
M src/inverse/functional/IPLogRelativeFunctional.cc
M src/inverse/functional/IPMeanSquareFunctional.cc
M src/inverse/functional/IP_L2NormFunctional.cc
M src/pythonbindings/pism_IceModelVec.i
M src/regional/EnthalpyModel_Regional.cc
M src/regional/IceRegionalModel.cc
M src/stressbalance/SSB_Modifier.cc
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/ShallowStressBalance.hh
M src/stressbalance/StressBalance.cc
M src/stressbalance/StressBalance_diagnostics.cc
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/BlatterMod.cc
M src/stressbalance/blatter/Poisson3.cc
M src/stressbalance/blatter/Poisson3.hh
M src/stressbalance/sia/BedSmoother.cc
M src/stressbalance/sia/BedSmoother.hh
M src/stressbalance/sia/SIAFD.cc
M src/stressbalance/sia/SIAFD_diagnostics.cc
M src/stressbalance/sia/siafd_test.cc
M src/stressbalance/ssa/SSA.cc
M src/stressbalance/ssa/SSAFD.cc
M src/stressbalance/ssa/SSAFEM.cc
M src/stressbalance/ssa/SSAFEM.hh
M src/stressbalance/ssa/SSATestCase.cc
M src/stressbalance/ssa/SSATestCase.hh
M src/stressbalance/timestepping.cc
M src/util/CMakeLists.txt
M src/util/Diagnostic.hh
M src/util/IceModelVec2CellType.hh
A src/util/IceModelVec2Struct.hh
A src/util/IceModelVec2V.hh
M src/util/IceModelVec_impl.hh
M src/util/IceModelVec_inline.hh
M src/util/Vars.cc
M src/util/fem/DirichletData.cc
M src/util/iceModelVec.cc
M src/util/iceModelVec.hh
M src/util/iceModelVec2.cc
M src/util/iceModelVec2V.cc
M src/util/iceModelVec3.cc
R src/util/iceModelVec3Custom.cc
R src/util/iceModelVec3Custom.hh
M src/util/projection.cc
M src/util/projection.hh
M src/verification/iCMthermo.cc
M src/verification/iceCompModel.cc
M test/bed_smoother.py
M test/miscellaneous.py

Log Message:
-----------
Improve IceModelVec and derived classes

... and update the rest of the code to match these changes.

- remove default constructors of IceModelVec2{Int,CellType,S,Stag,V}, IceModelVec3
- rename IceModelVec2Fat to IceModelVec2Struct to improve code re-use
- derive IceModelVec2V from IceModelVec2Struct
- clean up IceModelVec3

- rename getValZ(i, j, z) to interpolate(i, j, z)
- rename getHorSlice() to extract_surface()
- rename getSurfaceValues() to extract_surface()
- rename isLegalLevel() to legal_level()
- change the order of arguments of extract_surface(): the output argument should go
last.
- clean up IceModelVec3::sum_columns()

- remove IceModelVec3D and IceModelVec3Custom and move all the functionality into
IceModelVec3
- add IceModelVec2Struct::box(i, j) and star(i, j)
(this takes care of IceModelVec2V as well)
- add IceModelVec2Struct::array() const
- remove IceModelVec2Stag::staggered_to_regular()
- make IceModelVec constructor protected instead of public
- remove IceModelVec::reset_attrs()
- add a sanity check to the checksum implementation

Commit: cf76fdc195df3adaa020a2d34e864c37c855fdce
https://github.com/pism/pism/commit/cf76fdc195df3adaa020a2d34e864c37c855fdce
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pism_config.cdl

Log Message:
-----------
Sort Blatter-Pattyn parameters

Commit: ccb0b1659efd802bd584fe42c508a6bf979346bb
https://github.com/pism/pism/commit/ccb0b1659efd802bd584fe42c508a6bf979346bb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pism_config.cdl
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Add a surface slope limiter

This limiter reduces (and in some cases eliminates) unreasonable velocity spikes near
steep margins.

The idea comes from CISM's Blatter solver, but the implementation is different: we use
maximum cliff height dh (configuration parameter stress_balance.blatter.max_cliff_height,
default of 200 meters) instead of the unitless maximum slope. This way the limit is
automatically adjusted with the grid resolution. (The maximum slope is set to
dh / max(dx, dy).)

The default value chosen appears to be effective *and* is close to the one suggested in
"Upper and lower limits on the stability of calving glaciers from the yield strength
envelope of ice" by Bassis and Walker (2011) (doi:10.1098/rspa.2011.0422).

PS: CISM has the same issue but uses an "upstream" finite difference approximation
instead of limiting the slope. It is worth noting that due to the shape of the margin
this approach *also* has the effect of reducing the slope.

Commit: 70a8e7f1292baff36160cad6bde55ef6f28b9179
https://github.com/pism/pism/commit/70a8e7f1292baff36160cad6bde55ef6f28b9179
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Report iteration counts

Commit: 6555e5f2c394722051c2be5d9f15f1f9b1faafac
https://github.com/pism/pism/commit/6555e5f2c394722051c2be5d9f15f1f9b1faafac
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pythonbindings/pism_blatter.i
M src/stressbalance/blatter/CMakeLists.txt
R src/stressbalance/blatter/Poisson3.cc
R src/stressbalance/blatter/Poisson3.hh
M src/stressbalance/blatter/grid_hierarchy.cc
M src/stressbalance/blatter/grid_hierarchy.hh
R test/poisson3.py
R test/poisson3_test.py

Log Message:
-----------
Remove Poisson3

This code served its purpose and is not worth maintaining.

Commit: 5154480e61248785d18d4e59886d16c8bce73e95
https://github.com/pism/pism/commit/5154480e61248785d18d4e59886d16c8bce73e95
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Use the same number (1) to scale all trivial equations

I have no evidence that varying Dirichlet scaling is helpful.

Commit: dff625e2090f90cdd6103929104a66b177aed75a
https://github.com/pism/pism/commit/dff625e2090f90cdd6103929104a66b177aed75a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/FEM.hh

Log Message:
-----------
Fix a comment (there is no FETools.hh any more)

Commit: 98941d01119f6d009827913dfc6a7a4f2af37a68
https://github.com/pism/pism/commit/98941d01119f6d009827913dfc6a7a4f2af37a68
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Create exterior_element()

Commit: 51bf1fdbabb949fb0ffa901ee4063ca7cc284522
https://github.com/pism/pism/commit/51bf1fdbabb949fb0ffa901ee4063ca7cc284522
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Create neumann_bc_face()

Commit: 4378a76ed1b83a77b968c84b7413705f0b2080cc
https://github.com/pism/pism/commit/4378a76ed1b83a77b968c84b7413705f0b2080cc
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Use pointers to access face elements

This will make it easier to switch to a quadrature with more points at cells containing
the grounding line and partially-submerged vertical faces.

Commit: 6c0a430d75f832af84400af222c7696c8e48484e
https://github.com/pism/pism/commit/6c0a430d75f832af84400af222c7696c8e48484e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Rename a variable (for clarity)

Commit: 306fb2a6fd80eb6f8a17c2abb1cf619fec1c86d4
https://github.com/pism/pism/commit/306fb2a6fd80eb6f8a17c2abb1cf619fec1c86d4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Clean up declarations of local variables

Commit: 549e559bef32b8d15cf183b0aafd220bb63bfa19
https://github.com/pism/pism/commit/549e559bef32b8d15cf183b0aafd220bb63bfa19
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Use the floatation criterion at quad. points to compute basal drag

Commit: 78e635cea4eb8a5269e20026fc120203a1adb649
https://github.com/pism/pism/commit/78e635cea4eb8a5269e20026fc120203a1adb649
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Use lots of quadrature points near grounding lines and sea surface

Note: we take advantage of the fact that the floatation function is a linear function of
ice thickness, bed elevation, and sea level elevation. This allows us to compute it at
element nodes and use the FE basis expansion to compute values at quadrature points.

Commit: 3a3066e3aedca97a0257d43fe39ee413c25dd619
https://github.com/pism/pism/commit/3a3066e3aedca97a0257d43fe39ee413c25dd619
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Remove scaling of quadrature weights by rho * g

Commit: a62a92a2e4e006ece6bbcfbbbc75f4f240b27eb8
https://github.com/pism/pism/commit/a62a92a2e4e006ece6bbcfbbbc75f4f240b27eb8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/grid_hierarchy.cc

Log Message:
-----------
Remove grid padding in the x and y directions

Coarsening in x and y directions makes sense in periodic setups only, so we can sacrifice
multigrid efficiency in this very specific case to reduce code complexity a bit.

Commit: 01b3b59128bad0138808e9e4a60597ae3a36de4f
https://github.com/pism/pism/commit/01b3b59128bad0138808e9e4a60597ae3a36de4f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Improve comments

Commit: dc53356f64f70a27259882d5c166acb6613c4711
https://github.com/pism/pism/commit/dc53356f64f70a27259882d5c166acb6613c4711
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Create residual_dirichlet()

This function isolates the code computing the residual at Dirichlet nodes.

Commit: f513714a9548f5431cc03aae70fd8a3975f2f4db
https://github.com/pism/pism/commit/f513714a9548f5431cc03aae70fd8a3975f2f4db
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Create jacobian_dirichlet()

This function isolates the code computing the Jacobian at Dirichlet nodes.

Commit: 0c4fe2cd3dcf507a85acfa144d83f866871e911a
https://github.com/pism/pism/commit/0c4fe2cd3dcf507a85acfa144d83f866871e911a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/grid_hierarchy.cc
M src/stressbalance/blatter/grid_hierarchy.hh

Log Message:
-----------
Reduce code duplication by removing grid_xy()

... and replacing it my GridInfo methods.

Commit: 8dc689b41885c3ff9f79b47469749572c62dfcae
https://github.com/pism/pism/commit/8dc689b41885c3ff9f79b47469749572c62dfcae
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Get 2D parameters once per map-plane cell

This avoids redundant work of filling nodal values in each element in a vertical column.

Commit: f9e6248af1d7ad6145b6510cf163fbf8d5471067
https://github.com/pism/pism/commit/f9e6248af1d7ad6145b6510cf163fbf8d5471067
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Split off the surface gradient contribution

This will make it easier to replace the surface gradient by a "source term" needed to
verify this code using a manufactured solution.

Commit: 063f170dd46f5f2330791e870660e64f57adb500
https://github.com/pism/pism/commit/063f170dd46f5f2330791e870660e64f57adb500
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pism_config.cdl
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Remove the surface slope limiter

The surface slope limiter may produce "better looking" velocity fields in diagnostic
computations but it is a disaster when coupled to mass transport.

The problem is that limiting the surface slope in the stress balance solver allows the
model to develop very steep cliffs since the stress balance model cannot respond to these
changes in ice geometry. We avoid oscillations in ice velocity but the ice geometry is
wrong...

Commit: 35985bebd259ff21db232d2664f4e58988f0406d
https://github.com/pism/pism/commit/35985bebd259ff21db232d2664f4e58988f0406d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.hh

Log Message:
-----------
Element3::evaluate() should be "const"

Commit: 663b2ed8ad81d724e7fb8a7f4861e8f5ab51ca9b
https://github.com/pism/pism/commit/663b2ed8ad81d724e7fb8a7f4861e8f5ab51ca9b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
"Modularize" residual and Jacobian computations to simplify verification

- Add Blatter::residual_source_term()
- Add Blatter::residual_f() (the "main" part of the residual)
- Add Blatter::residual_basal()
- Add Blatter::residual_lateral()
- Add Blatter::jacobian_basal()
- Add Blatter::jacobian_f() (the "main" part of the Jacobian)

This way I can override parts of the residual and Jacobian assembly to replace the "source
term" in a MMS-based verification test, or replace the BC, or substitute a different
problem to test boundary conditions.

Commit: 323b4a817d8f8da5a0203e57a28229008a5f1fc8
https://github.com/pism/pism/commit/323b4a817d8f8da5a0203e57a28229008a5f1fc8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Fetch 2D parameters once per column in Blatter::compute_jacobian()

Commit: 6e32b56908fddee84a2298858530c541da989f02
https://github.com/pism/pism/commit/6e32b56908fddee84a2298858530c541da989f02
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/grid_hierarchy.cc
M src/stressbalance/blatter/grid_hierarchy.hh

Log Message:
-----------
Add a new class DMInfo

This class wraps outputs of PETSc's DMDAGetInfo and DMDAGetOwnershipRanges(), making them
easier to use.

Commit: a704a3be40e8f528e77c570c452db52ee2197eb7
https://github.com/pism/pism/commit/a704a3be40e8f528e77c570c452db52ee2197eb7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/util/fem/Element.cc
M src/util/fem/Element.hh

Log Message:
-----------
Use "const double *z" in Q1Element3{Face}::reset()

... instead of std::vector. This makes the API a bit more uniform. (It does make it harder
to test FE code from Python, but that's OK at this point).

Commit: 2e036e810f27f446a9918c47ed78fe13057af776
https://github.com/pism/pism/commit/2e036e810f27f446a9918c47ed78fe13057af776
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/grid_hierarchy.cc

Log Message:
-----------
Do not restrict 2D parameters to coarser multigrid levels

We use semi-coarsening in the vertical direction and so all multigrid levels use the same
2D grid. This means that we can initialize 2D parameters on the finest grid and use them
on all levels.

Commit: 1278a8441ef361ce449322bdc465830b066f7f26
https://github.com/pism/pism/commit/1278a8441ef361ce449322bdc465830b066f7f26
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/grid_hierarchy.hh

Log Message:
-----------
Remove unused members of GridInfo

Commit: 189f69ea19b849fbe8598fff17a64178f5857bf1
https://github.com/pism/pism/commit/189f69ea19b849fbe8598fff17a64178f5857bf1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/grid_hierarchy.cc

Log Message:
-----------
Cosmetic changes (mostly comments)

Commit: 137b8cf5e75aa681321d69903bec3688ff1a7909
https://github.com/pism/pism/commit/137b8cf5e75aa681321d69903bec3688ff1a7909
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Clean up

- rename a few variables
- add more comments

Commit: edce964c8c8ed7e25b2bf7ff8327c1673445535a
https://github.com/pism/pism/commit/edce964c8c8ed7e25b2bf7ff8327c1673445535a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Use DMInfo in Blatter::setup()

Commit: ec9cacdc85771e4e32d89f69f28ff5ffa6955502
https://github.com/pism/pism/commit/ec9cacdc85771e4e32d89f69f28ff5ffa6955502
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/CMakeLists.txt
A src/stressbalance/blatter/jacobian.cc
A src/stressbalance/blatter/residual.cc

Log Message:
-----------
Move residual and Jacobian evaluation code

This separates details of the discretization from the code allocating storage, iterating
over elements, assembling the Jacobian, restricting to a coarser grid, etc.

It should make it easier to create derived classes implementing verification tests.

Commit: 3aa3437750be1661b5fc873012d27e351c032429
https://github.com/pism/pism/commit/3aa3437750be1661b5fc873012d27e351c032429
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Add Blatter::m_face{4,100}

"Face" elements don't use the information about domain distribution (only nodal values for
the current element), so they can be created once and kept as data members.

(This was not true in the code that supported coarsening in horizontal directions: dx and
dy were different on different multigrid levels.)

Commit: 28020d92a2144664b47b4737a353d3b0d33cc4d4
https://github.com/pism/pism/commit/28020d92a2144664b47b4737a353d3b0d33cc4d4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/grid_hierarchy.cc
M src/stressbalance/blatter/grid_hierarchy.hh

Log Message:
-----------
Don't use GridInfo in the coarsening hook

It is not needed now that the horizontal grid is fixed. Previously, GridInfo was used to
allocate 2D storage on coarser levels (the coarsening hook needed to know the number of
DOF to allocate storage for).

Commit: dd936411d359bdd0565b3fe7d383cdbf2e357f20
https://github.com/pism/pism/commit/dd936411d359bdd0565b3fe7d383cdbf2e357f20
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Cosmetic changes

This commits unifies the order of methods in jacobian.cc and residual.cc

Commit: 8709042b1fb8686836f5b98339ac035f4eded879
https://github.com/pism/pism/commit/8709042b1fb8686836f5b98339ac035f4eded879
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/grid_hierarchy.hh
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Remove struct GridInfo

Commit: 5829ca50f0aaa93951b6dbd82bb96eaf03791627
https://github.com/pism/pism/commit/5829ca50f0aaa93951b6dbd82bb96eaf03791627
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc
M src/util/fem/Element.cc
M src/util/fem/Element.hh

Log Message:
-----------
Modify Q1Element3 so that elements know about physical coordinates

Commit: 117235c756fbc3b856386ad307f1afbe585af3b2
https://github.com/pism/pism/commit/117235c756fbc3b856386ad307f1afbe585af3b2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Use Q1Element3::{x,y,z}()

Commit: 8d21cbcb4bcdc01f36bde25002f907dc74121aed
https://github.com/pism/pism/commit/8d21cbcb4bcdc01f36bde25002f907dc74121aed
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/CMakeLists.txt
A src/stressbalance/blatter/verification/Makefile
A src/stressbalance/blatter/verification/blatter.py
A src/stressbalance/blatter/verification/blatter_mms.cc
A src/stressbalance/blatter/verification/manufactured_solutions.py
A src/stressbalance/blatter/verification/wiggles.py

Log Message:
-----------
Add SymPy code generating source terms for verification tests

This script will be used to generate source terms needed by verification tests using
manufactured solutions inspired by the Albany/FELIX description
paper (doi:10.5194/gmd-8-1197-2015).

Commit: ff40362d1c7e24fddd146f903d2392cf239aa7ec
https://github.com/pism/pism/commit/ff40362d1c7e24fddd146f903d2392cf239aa7ec
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Trying to make it easier to impose Dirichlet BCs

Commit: 776dd3029a37e67911451727145de468b23a23c5
https://github.com/pism/pism/commit/776dd3029a37e67911451727145de468b23a23c5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/blatter.py

Log Message:
-----------
Update the test script

Commit: 69413022414ff5f0b9570e669275be19bbd57b64
https://github.com/pism/pism/commit/69413022414ff5f0b9570e669275be19bbd57b64
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/blatter.py

Log Message:
-----------
Add the test B dome to test/blatter.py

Commit: 99fd14452f324c36a381ef6e9644c87ac9f12427
https://github.com/pism/pism/commit/99fd14452f324c36a381ef6e9644c87ac9f12427
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Quadrature.cc
M src/util/fem/Quadrature.hh

Log Message:
-----------
Add the 64-point Gaussian quadrature for 3D Q1 elements

... in case I need it later.

Commit: 3a133d30247d18bfd76fe3f200aa3e2fa3ab5ceb
https://github.com/pism/pism/commit/3a133d30247d18bfd76fe3f200aa3e2fa3ab5ceb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/verification/Makefile
M src/stressbalance/blatter/verification/blatter_mms.cc
A src/stressbalance/blatter/verification/blatter_mms.hh
M src/stressbalance/blatter/verification/manufactured_solutions.py

Log Message:
-----------
Generate function declarations (blatter_mms.hh)

Commit: 0ea5e409675393265efba3c003a06f7d1a056d6f
https://github.com/pism/pism/commit/0ea5e409675393265efba3c003a06f7d1a056d6f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Make some Blatter methods "virtual"

These methods will be overridden by derived classes that implement modifications needed by
verification tests.

Commit: dbd90eee69ba31d92cb75a5d9ee5e0591fced973
https://github.com/pism/pism/commit/dbd90eee69ba31d92cb75a5d9ee5e0591fced973
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/Element.hh

Log Message:
-----------
fem::Q1Element3::{x,y,z}() should be "const"

Commit: 19f1d14fa26e3b0b2a15d775e91ade8be6c0bcb5
https://github.com/pism/pism/commit/19f1d14fa26e3b0b2a15d775e91ade8be6c0bcb5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Use fem::Q1Element3 instead of fem::Element3

... because we need to use Q1Element3::{x,y,z}().

Commit: afa567063a1a4f77ed9ec094d4109d39234e4b64
https://github.com/pism/pism/commit/afa567063a1a4f77ed9ec094d4109d39234e4b64
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pythonbindings/pism_blatter.i
M src/stressbalance/blatter/CMakeLists.txt
A src/stressbalance/blatter/verification/BlatterTest1.cc
A src/stressbalance/blatter/verification/BlatterTest1.hh
A src/stressbalance/blatter/verification/test_template.cc
A test/blatter_verification.py

Log Message:
-----------
Add a verification test

Commit: a9d838b05fe943085937bbc9d5c31dfbdd33d38c
https://github.com/pism/pism/commit/a9d838b05fe943085937bbc9d5c31dfbdd33d38c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/CMakeLists.txt
M src/stressbalance/blatter/verification/BlatterTest1.cc
M src/stressbalance/blatter/verification/Makefile
R src/stressbalance/blatter/verification/blatter_mms.cc
R src/stressbalance/blatter/verification/blatter_mms.hh
A src/stressbalance/blatter/verification/manufactured_solutions.cc
A src/stressbalance/blatter/verification/manufactured_solutions.hh
M src/stressbalance/blatter/verification/manufactured_solutions.py

Log Message:
-----------
Cleanup

Commit: 386d279f2635af03e33debb1f73aa7858dff26e5
https://github.com/pism/pism/commit/386d279f2635af03e33debb1f73aa7858dff26e5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/verification/manufactured_solutions.py
A src/stressbalance/blatter/verification/xz_albany.py

Log Message:
-----------
Add source_xz_albany()

Commit: fd9d6d509f9b6e9d2d4ff4c29d422790ab9b113f
https://github.com/pism/pism/commit/fd9d6d509f9b6e9d2d4ff4c29d422790ab9b113f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Support x and y grid periodicity in Blatter:setup()

Commit: 0306ea62d7da795858d1563ec8e25d028e852a97
https://github.com/pism/pism/commit/0306ea62d7da795858d1563ec8e25d028e852a97
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Add Blatter::nodal_parameter_values()

This method isolates the code setting nodal values of 2D parameters. It can be
re-implemented in a derived class to add verification tests that use periodic boundary
conditions.

Commit: a823c9d992c786b0eccf4bea14a513bd807857ca
https://github.com/pism/pism/commit/a823c9d992c786b0eccf4bea14a513bd807857ca
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/CMakeLists.txt
R src/stressbalance/blatter/DataAccess.hh
R src/stressbalance/blatter/grid_hierarchy.cc
R src/stressbalance/blatter/grid_hierarchy.hh
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc
A src/stressbalance/blatter/util/DataAccess.hh
A src/stressbalance/blatter/util/grid_hierarchy.cc
A src/stressbalance/blatter/util/grid_hierarchy.hh

Log Message:
-----------
Move some boring code into a subdirectory

Commit: 13aa4b23c71afdc110a3cffc47f60269335ebc21
https://github.com/pism/pism/commit/13aa4b23c71afdc110a3cffc47f60269335ebc21
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/BlatterMod.cc

Log Message:
-----------
Add a couple of documenting comments

Commit: 02eb28f70337d74869e3f1c7d261dc7083d80a61
https://github.com/pism/pism/commit/02eb28f70337d74869e3f1c7d261dc7083d80a61
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pythonbindings/pism_blatter.i
M src/stressbalance/blatter/CMakeLists.txt
A src/stressbalance/blatter/ismip-hom/BlatterISMIPHOM.cc
A src/stressbalance/blatter/ismip-hom/BlatterISMIPHOM.hh
A test/ismip-hom/Makefile
A test/ismip-hom/README.rst
A test/ismip-hom/convert-ismiphom.py
A test/ismip-hom/plot-ismiphom.py
A test/ismip-hom/run-ismiphom.py

Log Message:
-----------
Implement ISMIP-HOM experiments

Commit: 67f3c9857df55e0014f8eaf93744133d6df0582e
https://github.com/pism/pism/commit/67f3c9857df55e0014f8eaf93744133d6df0582e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/ssa/tests/ssa_testi.cc

Log Message:
-----------
Clean up ssa_testi.cc

Commit: 474f951add5a021b9b29618fc94a1e6463007a8c
https://github.com/pism/pism/commit/474f951add5a021b9b29618fc94a1e6463007a8c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTest1.hh

Log Message:
-----------
Add an include guard I forgot earlier

Commit: 8b64a0436440e772ea4b86a69547f7471e2fe1c8
https://github.com/pism/pism/commit/8b64a0436440e772ea4b86a69547f7471e2fe1c8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/CMakeLists.txt
A src/stressbalance/blatter/verification/BlatterTest2.cc
A src/stressbalance/blatter/verification/BlatterTest2.hh

Log Message:
-----------
Commit work on the second verification test

Commit: b2d3a85d0057246d9bea4060b3f93f6b1278ce1e
https://github.com/pism/pism/commit/b2d3a85d0057246d9bea4060b3f93f6b1278ce1e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/ssa/tests/ssa_test_cfbc.cc

Log Message:
-----------
Clean up the SSA CFBC test

Commit: f82abf12061a691b20fedaa1fa49df12aff1ed5d
https://github.com/pism/pism/commit/f82abf12061a691b20fedaa1fa49df12aff1ed5d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/verification/blatter.py
M src/stressbalance/blatter/verification/manufactured_solutions.py

Log Message:
-----------
Allow changing the Glen exponent in the SymPy code

Commit: 6c44c7ded2329018341827995c6ea1be97b21ee4
https://github.com/pism/pism/commit/6c44c7ded2329018341827995c6ea1be97b21ee4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Throw an exception on failure

Commit: 83e90e43bc26c4d78ba70d488ed3bd6fe17b77b3
https://github.com/pism/pism/commit/83e90e43bc26c4d78ba70d488ed3bd6fe17b77b3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/util/fem/FEM.hh

Log Message:
-----------
Fix a typo

Commit: f01ecf94f3653a335895472ef98de12556bdfd4e
https://github.com/pism/pism/commit/f01ecf94f3653a335895472ef98de12556bdfd4e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Add Blatter::residual_surface()

This method is needed to implement the top-surface residual contributions in MMS-based
verification tests.

Commit: f4d9553e78a21f1b9a8160c82f11d2d169fa12a9
https://github.com/pism/pism/commit/f4d9553e78a21f1b9a8160c82f11d2d169fa12a9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pythonbindings/pism_blatter.i
M src/stressbalance/blatter/CMakeLists.txt
M src/stressbalance/blatter/util/grid_hierarchy.cc
R src/stressbalance/blatter/verification/BlatterTest1.cc
R src/stressbalance/blatter/verification/BlatterTest1.hh
R src/stressbalance/blatter/verification/BlatterTest2.cc
R src/stressbalance/blatter/verification/BlatterTest2.hh
A src/stressbalance/blatter/verification/BlatterTestXY.cc
A src/stressbalance/blatter/verification/BlatterTestXY.hh
A src/stressbalance/blatter/verification/BlatterTestXZ.cc
A src/stressbalance/blatter/verification/BlatterTestXZ.hh
M src/stressbalance/blatter/verification/Makefile
M src/stressbalance/blatter/verification/blatter.py
M src/stressbalance/blatter/verification/manufactured_solutions.cc
M src/stressbalance/blatter/verification/manufactured_solutions.hh
M src/stressbalance/blatter/verification/manufactured_solutions.py
A src/stressbalance/blatter/verification/test_xy.py
A src/stressbalance/blatter/verification/test_xz.py
R src/stressbalance/blatter/verification/xz_albany.py
M test/blatter_verification.py

Log Message:
-----------
More work on verification tests

Commit: 0315da8bcaeaeca06fd883b31e9be525fd9d578c
https://github.com/pism/pism/commit/0315da8bcaeaeca06fd883b31e9be525fd9d578c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/CMakeLists.txt
M test/blatter_verification.py

Log Message:
-----------
Add Blatter-Pattyn verification tests to regression tests

... and shorten refinement paths to make it faster.

Commit: 37fff64171929a93616328b5597802a4bfce0918
https://github.com/pism/pism/commit/37fff64171929a93616328b5597802a4bfce0918
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/residual.cc
M test/ismip-hom/run-ismiphom.py

Log Message:
-----------
Fix typos

Commit: e549bd9f0e09cddf94f1b0101ead5eeaaaaa2796
https://github.com/pism/pism/commit/e549bd9f0e09cddf94f1b0101ead5eeaaaaa2796
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/ismip-hom/README.rst
A test/ismip-hom/ismip-hom-a-5km.png

Log Message:
-----------
Improve the ISMIP-HOM README file and add a figure

Commit: e97cc4e8bd458053745e34d67c43aa6383eb8e17
https://github.com/pism/pism/commit/e97cc4e8bd458053745e34d67c43aa6383eb8e17
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Add a proper implementation of lateral BCs

Commit: 287a0b1914a16bcd63d05ad1cceaa750c5a3eecf
https://github.com/pism/pism/commit/287a0b1914a16bcd63d05ad1cceaa750c5a3eecf
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/pythonbindings/pism_blatter.i
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/CMakeLists.txt
M src/stressbalance/blatter/residual.cc
A src/stressbalance/blatter/verification/BlatterTestCFBC.cc
A src/stressbalance/blatter/verification/BlatterTestCFBC.hh
M test/blatter_verification.py

Log Message:
-----------
Start work on the verification test for the lateral BCs

Commit: 19d396f8a43f049717a4744782cc1b66f35f5809
https://github.com/pism/pism/commit/19d396f8a43f049717a4744782cc1b66f35f5809
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestCFBC.cc
M src/stressbalance/blatter/verification/BlatterTestCFBC.hh
M test/blatter_verification.py

Log Message:
-----------
More work on CFBC verification

Commit: eda95674def3aba53b6825428c3dd8b2bc11fb50
https://github.com/pism/pism/commit/eda95674def3aba53b6825428c3dd8b2bc11fb50
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/verification/manufactured_solutions.cc
M src/stressbalance/blatter/verification/manufactured_solutions.hh
M src/stressbalance/blatter/verification/manufactured_solutions.py
A src/stressbalance/blatter/verification/test_xz_cfbc.py

Log Message:
-----------
Add more generated code

Commit: 98759e4526420927d14903430e1f59dbb7c0e121
https://github.com/pism/pism/commit/98759e4526420927d14903430e1f59dbb7c0e121
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M src/stressbalance/blatter/residual.cc
M src/stressbalance/blatter/verification/BlatterTestCFBC.cc
M src/stressbalance/blatter/verification/BlatterTestCFBC.hh
M src/stressbalance/blatter/verification/manufactured_solutions.cc
M src/stressbalance/blatter/verification/manufactured_solutions.hh
M src/stressbalance/blatter/verification/test_xz_cfbc.py
M test/blatter_verification.py

Log Message:
-----------
More work on CFBC verification

Commit: 452f15e05f383479f03edc5068f6cb3ece09928c
https://github.com/pism/pism/commit/452f15e05f383479f03edc5068f6cb3ece09928c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-14 (Wed, 14 Oct 2020)

Changed paths:
M test/blatter_verification.py

Log Message:
-----------
Remove debugging calls

Commit: a9b4995cb62c2c35b38974d547565044b26acc13
https://github.com/pism/pism/commit/a9b4995cb62c2c35b38974d547565044b26acc13
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-27 (Tue, 27 Oct 2020)

Changed paths:
M src/stressbalance/blatter/jacobian.cc

Log Message:
-----------
Improve the Jacobian evaluation code

Now it should be a bit easier to understand.

Commit: 8cd023f8fdada26305832e60317bc53e99e2ea16
https://github.com/pism/pism/commit/8cd023f8fdada26305832e60317bc53e99e2ea16
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-27 (Tue, 27 Oct 2020)

Changed paths:
M doc/ice-bib.bib
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst
A doc/sphinx/technical/blatter-pattyn.rst
M doc/sphinx/technical/index.rst
M src/stressbalance/blatter/README.org
R src/stressbalance/blatter/doc/Makefile
R src/stressbalance/blatter/doc/blatter.mac
R src/stressbalance/blatter/doc/notes.tex
M test/blatter_verification.py

Log Message:
-----------
Document the BP solver

Commit: 0aa0aed825779ef478aeec2d3ac8912a77196a51
https://github.com/pism/pism/commit/0aa0aed825779ef478aeec2d3ac8912a77196a51
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-28 (Wed, 28 Oct 2020)

Changed paths:
M doc/sphinx/technical/blatter-pattyn.rst

Log Message:
-----------
Improve documentation of verification tests

Commit: cee4149f7b65240c84df9d066d464ac2099d05fc
https://github.com/pism/pism/commit/cee4149f7b65240c84df9d066d464ac2099d05fc
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-30 (Fri, 30 Oct 2020)

Changed paths:
M test/ismip-hom/Makefile
M test/ismip-hom/README.rst

Log Message:
-----------
Add more targets to make it easier to create ISMIP-HOM plots

Commit: 154bf214d95e00068d6b9e2476c09c9e90a54294
https://github.com/pism/pism/commit/154bf214d95e00068d6b9e2476c09c9e90a54294
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-30 (Fri, 30 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/residual.cc
M src/stressbalance/blatter/verification/BlatterTestXY.cc
M src/stressbalance/blatter/verification/BlatterTestXY.hh
M src/stressbalance/blatter/verification/BlatterTestXZ.cc
M src/stressbalance/blatter/verification/BlatterTestXZ.hh
M src/stressbalance/blatter/verification/test_template.cc

Log Message:
-----------
Rename Blatter::neumann_bc_face() to vertical_cliff_face()

The old name dates back the time when this code supported more generic Neumann BC.

Commit: 3c8ada13d09d16f57d1f8121232ca32077a85908
https://github.com/pism/pism/commit/3c8ada13d09d16f57d1f8121232ca32077a85908
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-30 (Fri, 30 Oct 2020)

Changed paths:
M doc/sphinx/technical/blatter-pattyn.rst

Log Message:
-----------
More edits

Commit: b4aea49ca71e3726a10d206134426d9be9e1bfee
https://github.com/pism/pism/commit/b4aea49ca71e3726a10d206134426d9be9e1bfee
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-30 (Fri, 30 Oct 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M test/blatter_verification.py
M test/ismip-hom/Makefile

Log Message:
-----------
Use the "-bp_" prefix for PETSc options controlling the BP solver

... and update some scripts to use this prefix.

Commit: 02af55dbb9b96f38015f36b1000f86e6d1e99900
https://github.com/pism/pism/commit/02af55dbb9b96f38015f36b1000f86e6d1e99900
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-30 (Fri, 30 Oct 2020)

Changed paths:
M src/stressbalance/blatter/util/grid_hierarchy.cc

Log Message:
-----------
Use the simpler vertical grid padding as described in the notes

Commit: 3f7767992a7de559e1fb33add4ec1bda0a43dde3
https://github.com/pism/pism/commit/3f7767992a7de559e1fb33add4ec1bda0a43dde3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-10-30 (Fri, 30 Oct 2020)

Changed paths:
M doc/sphinx/technical/blatter-pattyn.rst

Log Message:
-----------
More edits

Commit: 1e311595e51228302a4a3e8e6346cd015024ddc2
https://github.com/pism/pism/commit/1e311595e51228302a4a3e8e6346cd015024ddc2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M src/stressbalance/blatter/util/grid_hierarchy.cc

Log Message:
-----------
Edit vertical grid padding to match what's in the text

Commit: 30ac7b22e81e14625b0e0a8a5e16a2f5d59e4efa
https://github.com/pism/pism/commit/30ac7b22e81e14625b0e0a8a5e16a2f5d59e4efa
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M test/blatter.py

Log Message:
-----------
Edit test/blatter.py to make it easier to investigate wiggles

Commit: 7ac5deb12d4426dace81624b3b6f8bdfe5bbea28
https://github.com/pism/pism/commit/7ac5deb12d4426dace81624b3b6f8bdfe5bbea28
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M test/blatter.py

Log Message:
-----------
Add comments outlining things one could try

Commit: 25bcdf7355fc8cfb918126dce52bb13322aebe31
https://github.com/pism/pism/commit/25bcdf7355fc8cfb918126dce52bb13322aebe31
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M test/blatter.py

Log Message:
-----------
Experimenting with different thickness profiles

Commit: a609485fa0808f59b7bb97d8529bd1e1c5f14dc5
https://github.com/pism/pism/commit/a609485fa0808f59b7bb97d8529bd1e1c5f14dc5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Disable lateral BC for now

Commit: 60468600314ac53be41ab3ed8dc2c6976123f8a2
https://github.com/pism/pism/commit/60468600314ac53be41ab3ed8dc2c6976123f8a2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M src/pythonbindings/pism_blatter.i
M src/stressbalance/blatter/CMakeLists.txt
M src/stressbalance/blatter/verification/manufactured_solutions.cc
M src/stressbalance/blatter/verification/manufactured_solutions.hh
M src/stressbalance/blatter/verification/manufactured_solutions.py
A src/stressbalance/blatter/verification/test_xz_halfar.py

Log Message:
-----------
Add SymPy-generated code for the Halfar dome case

Commit: 04c8423caf5c60202990d3e20f1e55a524221d03
https://github.com/pism/pism/commit/04c8423caf5c60202990d3e20f1e55a524221d03
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
A src/stressbalance/blatter/verification/BlatterTestHalfar.cc
A src/stressbalance/blatter/verification/BlatterTestHalfar.hh

Log Message:
-----------
Add the C++ code for the Halfar dome test

Commit: 00d89547647efff7c580e3f09f4d4270cd8cb447
https://github.com/pism/pism/commit/00d89547647efff7c580e3f09f4d4270cd8cb447
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M src/stressbalance/blatter/verification/manufactured_solutions.cc
M src/stressbalance/blatter/verification/manufactured_solutions.hh
M src/stressbalance/blatter/verification/test_xz_halfar.py

Log Message:
-----------
Add lateral BC for the Halfar test case

Commit: 7b30cd250f159a24cb648b95b5fb4ce952bb061a
https://github.com/pism/pism/commit/7b30cd250f159a24cb648b95b5fb4ce952bb061a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M site-packages/PISM/testing.py

Log Message:
-----------
Update PISM.testing.create_forcing()

Commit: ac8f07b7ee738911d79163adec8b2ca28a7a8b2d
https://github.com/pism/pism/commit/ac8f07b7ee738911d79163adec8b2ca28a7a8b2d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M test/blatter.py

Log Message:
-----------
Update notes in test/blatter.py

Commit: b837a043a19c361b83d2319522db498fee2889e8
https://github.com/pism/pism/commit/b837a043a19c361b83d2319522db498fee2889e8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestHalfar.cc
M src/stressbalance/blatter/verification/BlatterTestHalfar.hh

Log Message:
-----------
Add lateral (margin) BC to the Halfar dome setup

Commit: a0c12f3463927eac2b0c365e313e4f5d03360d73
https://github.com/pism/pism/commit/a0c12f3463927eac2b0c365e313e4f5d03360d73
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M doc/ice-bib.bib

Log Message:
-----------
Fix the title of a paper

Commit: f2f0baa7442ec644045919982d5c2639db199bbe
https://github.com/pism/pism/commit/f2f0baa7442ec644045919982d5c2639db199bbe
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestXY.cc

Log Message:
-----------
A bit of cleanup

Commit: 5d26f7cf19780d460cb606126f8b7ffd27179c9b
https://github.com/pism/pism/commit/5d26f7cf19780d460cb606126f8b7ffd27179c9b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M src/pism_config.cdl
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/residual.cc
M src/stressbalance/blatter/verification/BlatterTestCFBC.cc
M src/stressbalance/blatter/verification/BlatterTestCFBC.hh
M src/stressbalance/blatter/verification/BlatterTestHalfar.cc
M src/stressbalance/blatter/verification/BlatterTestHalfar.hh
M src/stressbalance/blatter/verification/BlatterTestXY.cc
M src/stressbalance/blatter/verification/BlatterTestXY.hh
M src/stressbalance/blatter/verification/BlatterTestXZ.cc
M src/stressbalance/blatter/verification/BlatterTestXZ.hh
M src/stressbalance/blatter/verification/test_template.cc

Log Message:
-----------
Implement the eta transformation in the approximation of the surface gradient

Commit: 1300136f713f2ee9a32b99d7e7830c4f1511a1b3
https://github.com/pism/pism/commit/1300136f713f2ee9a32b99d7e7830c4f1511a1b3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
R test/blatter.py
A test/blatter_flowline.py

Log Message:
-----------
Improve the Python code for flow line Blatter-Pattyn runs

Commit: 31b25af90dbe1ad0cc0adaf732772ba68c4578cc
https://github.com/pism/pism/commit/31b25af90dbe1ad0cc0adaf732772ba68c4578cc
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M src/pythonbindings/pism_blatter.i
M src/stressbalance/blatter/CMakeLists.txt
A src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc
A src/stressbalance/blatter/verification/BlatterTestvanderVeen.hh

Log Message:
-----------
Implement a test based on the van der Veen profile

Needs more work (the Python part) and testing.

Commit: f982af5da4853fdf2ae7122c15bb7539c791ad87
https://github.com/pism/pism/commit/f982af5da4853fdf2ae7122c15bb7539c791ad87
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/verification/BlatterTestCFBC.cc
M src/stressbalance/blatter/verification/BlatterTestCFBC.hh
M src/stressbalance/blatter/verification/BlatterTestHalfar.cc
M src/stressbalance/blatter/verification/BlatterTestHalfar.hh
M src/stressbalance/blatter/verification/BlatterTestXY.cc
M src/stressbalance/blatter/verification/BlatterTestXY.hh
M src/stressbalance/blatter/verification/BlatterTestXZ.cc
M src/stressbalance/blatter/verification/BlatterTestXZ.hh
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.hh

Log Message:
-----------
Make Blatter::u_bc() "const"

Commit: 73e7368cbc30c0a20fb37f0ec02d1c8ff65e886f
https://github.com/pism/pism/commit/73e7368cbc30c0a20fb37f0ec02d1c8ff65e886f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.hh

Log Message:
-----------
Make BlatterTestvanderVeen::*_exact() "const"

Commit: de8d74e5a2d288b94688d128feb13ccaebdc4a01
https://github.com/pism/pism/commit/de8d74e5a2d288b94688d128feb13ccaebdc4a01
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestHalfar.cc
M src/stressbalance/blatter/verification/BlatterTestHalfar.hh

Log Message:
-----------
Improve BlatterTestHalfar

Commit: f9b8e877a63fc0279ef3f8e4452bdbfa3822d10e
https://github.com/pism/pism/commit/f9b8e877a63fc0279ef3f8e4452bdbfa3822d10e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc

Log Message:
-----------
Increase inflow thickness and velocity

Commit: f450f73f15832e0ba896793c1d2c1a93dbff77b8
https://github.com/pism/pism/commit/f450f73f15832e0ba896793c1d2c1a93dbff77b8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.hh

Log Message:
-----------
More tweaks...

Commit: a4e174fbe49f605181dd61a28e8763ee10957885
https://github.com/pism/pism/commit/a4e174fbe49f605181dd61a28e8763ee10957885
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Cleanup

Commit: 6b3a232672f1d27bbda87a5dc1b86a21f0bac383
https://github.com/pism/pism/commit/6b3a232672f1d27bbda87a5dc1b86a21f0bac383
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.hh

Log Message:
-----------
One more fiddle (needs more thinking)

Commit: 7752677c0c8ec4253d1c167c510d26f3d76760f2
https://github.com/pism/pism/commit/7752677c0c8ec4253d1c167c510d26f3d76760f2
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M examples/ross/plot.py
M examples/ross/preprocess.py

Log Message:
-----------
Updated data link in examples/ross

Commit: 7eb621303bbac739f2ad86be95170f4bfbb7c5c3
https://github.com/pism/pism/commit/7eb621303bbac739f2ad86be95170f4bfbb7c5c3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M doc/sphinx/installation/code/io_libraries.sh
M doc/sphinx/installation/code/parallelio.sh

Log Message:
-----------
Fix scripts installing I/O libraries

NCAR ParallelIO 2.5.1 does not compile using GCC 10, so we use the master branch for now.

Commit: 96e34b020ad47f48c9e5c1177c201aa9124e9aab
https://github.com/pism/pism/commit/96e34b020ad47f48c9e5c1177c201aa9124e9aab
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M doc/sphinx/installation/code/install_docu_libraries.sh

Log Message:
-----------
Fix the script installing software needed to edit the manual

Commit: fe82fe95fae8bbf67cf835553255a9c1d7b54c24
https://github.com/pism/pism/commit/fe82fe95fae8bbf67cf835553255a9c1d7b54c24
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-16 (Wed, 16 Dec 2020)

Changed paths:
M doc/sphinx/CMakeLists.txt
M doc/sphinx/conf.py

Log Message:
-----------
Use recent sphinxcontrib-bibtex and sphinx-autobuild versions

Commit: bbf1ee3cc6cd176362776daccae073d6fbe43e36
https://github.com/pism/pism/commit/bbf1ee3cc6cd176362776daccae073d6fbe43e36
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-17 (Thu, 17 Dec 2020)

Changed paths:
M test/regression/sorted_parameters.sh

Log Message:
-----------
Fix a regression test

"sort" uses different sorting order depending on locale settings.

Commit: bb760875a6d0b54cb2a09f66bcec72f5bb6d0131
https://github.com/pism/pism/commit/bb760875a6d0b54cb2a09f66bcec72f5bb6d0131
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2020-12-18 (Fri, 18 Dec 2020)

Changed paths:
M examples/ross/preprocess.py

Log Message:
-----------
Fix a typo

Commit: 7127427a26c7d85726a1b7b5ffa509d47414afd3
https://github.com/pism/pism/commit/7127427a26c7d85726a1b7b5ffa509d47414afd3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-05 (Tue, 05 Jan 2021)

Changed paths:
M src/stressbalance/ssa/SSAFD.cc

Log Message:
-----------
Remove IceModelVecX::create() calls in SSAFD

Commit: 90de77f1aea348f3da2660ccfcbaba52b0800940
https://github.com/pism/pism/commit/90de77f1aea348f3da2660ccfcbaba52b0800940
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-05 (Tue, 05 Jan 2021)

Changed paths:
M src/util/Vector2.hh

Log Message:
-----------
Add operator== and operator!= for Vector2 (for debugging)

Commit: 7fd54a16da319126024cf9b9b0a857da36ad0c03
https://github.com/pism/pism/commit/7fd54a16da319126024cf9b9b0a857da36ad0c03
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-05 (Tue, 05 Jan 2021)

Changed paths:
M src/stressbalance/sia/SIAFD.cc

Log Message:
-----------
Better handling of SIA diffusivity at domain boundaries

We need to check grid periodicity to support flow line runs.

Commit: 1cd1719189f1155bf56b4488338f1d6e53c29659
https://github.com/pism/pism/commit/1cd1719189f1155bf56b4488338f1d6e53c29659
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-13 (Wed, 13 Jan 2021)

Changed paths:
M CHANGES.rst
M site-packages/PISM/util.py

Log Message:
-----------
Add arguments "time_units" and "calendar" to PISM.util.prepare_output()

Commit: ba1825902f6df4c666b013469a90ed6ec51a4d37
https://github.com/pism/pism/commit/ba1825902f6df4c666b013469a90ed6ec51a4d37
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-13 (Wed, 13 Jan 2021)

Changed paths:
M src/pism_config.cdl

Log Message:
-----------
Fix a copy-paste error in the configuration file (and the manual)

Commit: a8255c5b2466c557b49e1ee23139983aed1b0603
https://github.com/pism/pism/commit/a8255c5b2466c557b49e1ee23139983aed1b0603
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-15 (Fri, 15 Jan 2021)

Changed paths:
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Fix a compiler warning

Commit: 2d16ac1c032e3a8471d3100438619af040921e8a
https://github.com/pism/pism/commit/2d16ac1c032e3a8471d3100438619af040921e8a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-15 (Fri, 15 Jan 2021)

Changed paths:
M test/regression/sorted_parameters.sh

Log Message:
-----------
Fix a regression test

"sort" uses different sorting order depending on locale settings.

Commit: 11031c3c0a690c454f0e290e0f31bbf67523cdb7
https://github.com/pism/pism/commit/11031c3c0a690c454f0e290e0f31bbf67523cdb7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-15 (Fri, 15 Jan 2021)

Changed paths:
M doc/sphinx/technical/blatter-pattyn.rst

Log Message:
-----------
Fix a typo

Commit: 7f2267515eedccb135a4542d1bdafb2715f61c45
https://github.com/pism/pism/commit/7f2267515eedccb135a4542d1bdafb2715f61c45
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-20 (Wed, 20 Jan 2021)

Changed paths:
M doc/sphinx/CMakeLists.txt
M doc/sphinx/conf.py

Log Message:
-----------
Use recent sphinxcontrib-bibtex and sphinx-autobuild versions

Commit: 758637092cfa20273a5162581708cfc48488d921
https://github.com/pism/pism/commit/758637092cfa20273a5162581708cfc48488d921
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-20 (Wed, 20 Jan 2021)

Changed paths:
M examples/python/ssa_tests/ssa_test_cfbc.py
M src/pism_config.cdl
M src/stressbalance/ssa/SSAFD.cc
M src/stressbalance/ssa/tests/ssa_test_cfbc.cc

Log Message:
-----------
Implement stress_balance.ssa.fd.flow_line_mode

With this flag SSAFD assembles the system in which v = 0 is prescribed at each location.

Commit: 45194cdef9bd72ebc702a5a876d86fc376ca8481
https://github.com/pism/pism/commit/45194cdef9bd72ebc702a5a876d86fc376ca8481
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-20 (Wed, 20 Jan 2021)

Changed paths:
M src/stressbalance/ssa/SSAFD.cc

Log Message:
-----------
Fix grid edge treatment in SSAFD::assemble_rhs()

Commit: 2bff2615c59dbc957c39cee880811bfa8fbe8eb7
https://github.com/pism/pism/commit/2bff2615c59dbc957c39cee880811bfa8fbe8eb7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-20 (Wed, 20 Jan 2021)

Changed paths:
M test/regression/btu_regression.sh
M test/regression/ssa/ssa_test_cfbc_fd.sh
M test/regression/ssa/ssa_test_cfbc_fem.sh
M test/regression/ssa/ssa_testi_fd.sh
M test/regression/ssa/ssa_testi_fem.sh
M test/regression/ssa/ssa_testj_fd.sh
M test/regression/ssa/ssa_testj_fem.sh
M test/regression/ssa/ssafem_test_linear.sh
M test/regression/ssa/ssafem_test_plug.sh
M test/regression/test_15.sh
M test/regression/test_16.sh
M test/regression/test_17.sh
M test/regression/test_18.sh

Log Message:
-----------
Improve regression tests

Some regression tests use temporary files. Now we use mktemp to create files with unique
file names. This avoids race conditions when tests are executed in parallel.

Commit: bb8552832d6f9d4b3fd676919905b2ba1ebc4860
https://github.com/pism/pism/commit/bb8552832d6f9d4b3fd676919905b2ba1ebc4860
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-20 (Wed, 20 Jan 2021)

Changed paths:
M .circleci/config.yml

Log Message:
-----------
Try to run tests in parallel (on CircleCI)

Commit: a17fcd1bdcbe9f980baf82076f7a54fcb4bbeb86
https://github.com/pism/pism/commit/a17fcd1bdcbe9f980baf82076f7a54fcb4bbeb86
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-20 (Wed, 20 Jan 2021)

Changed paths:
M .circleci/config.yml

Log Message:
-----------
Print ccache stats (mostly out of curiosity)

Commit: 4d9932e01f00b36257ebbdce6b283adabea6953e
https://github.com/pism/pism/commit/4d9932e01f00b36257ebbdce6b283adabea6953e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-20 (Wed, 20 Jan 2021)

Changed paths:
M .circleci/config.yml

Log Message:
-----------
Nope. Looks like parallel tests are a no-go.

Commit: 6f1b47324e32736176f845daf38afa0edc26e884
https://github.com/pism/pism/commit/6f1b47324e32736176f845daf38afa0edc26e884
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-20 (Wed, 20 Jan 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/climate_forcing/atmosphere.rst
M src/coupler/atmosphere/OrographicPrecipitationSerial.cc
M src/coupler/atmosphere/OrographicPrecipitationSerial.hh
M src/pism_config.cdl

Log Message:
-----------
Add surface elevation smoothing to the LTOP model

Commit: 3a8c565908092c7bdaea84f7bd8adcafa88fa911
https://github.com/pism/pism/commit/3a8c565908092c7bdaea84f7bd8adcafa88fa911
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-20 (Wed, 20 Jan 2021)

Changed paths:
M src/coupler/atmosphere/OrographicPrecipitation.cc

Log Message:
-----------
Support "flow-line" (3 grid points wide) runs with the LTOP model

I'm trying to do this by extending the grid in the X direction only if the grid is not
periodic in this direction, and same for Y. (Flow line setups are periodic in the
cross-flow direction.)

Commit: dfd86c619f57f9f3be22463115aff674a4cccd80
https://github.com/pism/pism/commit/dfd86c619f57f9f3be22463115aff674a4cccd80
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-20 (Wed, 20 Jan 2021)

Changed paths:
M test/regression/orographic_precipitation.py

Log Message:
-----------
Extend the LTOP regression test to cover flow-line runs

Commit: 4a1d7cbeb6d3326cab2095ff369bd189d972ccec
https://github.com/pism/pism/commit/4a1d7cbeb6d3326cab2095ff369bd189d972ccec
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-20 (Wed, 20 Jan 2021)

Changed paths:
M src/coupler/atmosphere/OrographicPrecipitationSerial.cc

Log Message:
-----------
Fix two typos in comments

Commit: d50358b17160bd00c2f00a61b86d096c87110589
https://github.com/pism/pism/commit/d50358b17160bd00c2f00a61b86d096c87110589
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-20 (Wed, 20 Jan 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/climate_forcing/atmosphere.rst
M src/coupler/atmosphere/OrographicPrecipitation.cc
M src/coupler/atmosphere/OrographicPrecipitationSerial.cc
M src/coupler/atmosphere/OrographicPrecipitationSerial.hh
M src/pism_config.cdl
M test/regression/orographic_precipitation.py

Log Message:
-----------
Merge branch 'ckhroulev/ltop' into dev

Commit: 81d74cd7de8545edf3d6a2a4c8498ab133a99203
https://github.com/pism/pism/commit/81d74cd7de8545edf3d6a2a4c8498ab133a99203
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-21 (Thu, 21 Jan 2021)

Changed paths:
M site-packages/PISM/ssa.py
M src/stressbalance/ssa/tests/ssa_test_cfbc.cc
M src/stressbalance/ssa/tests/ssa_test_const.cc
M src/stressbalance/ssa/tests/ssa_test_linear.cc
M src/stressbalance/ssa/tests/ssa_test_plug.cc
M src/stressbalance/ssa/tests/ssa_testi.cc
M src/stressbalance/ssa/tests/ssa_testj.cc

Log Message:
-----------
Make SSA tests respect "-o_size none"

This should help with race conditions when running tests in parallel.

Commit: 74930c277b961e0d5f983fc5583479ca98daa1c7
https://github.com/pism/pism/commit/74930c277b961e0d5f983fc5583479ca98daa1c7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-28 (Thu, 28 Jan 2021)

Changed paths:
A doc/sphinx/installation/code/petsc.sh

Log Message:
-----------
Add a PETSc build script

This script is used to install PETSc in the Docker image used for regression testing.

Commit: be4dcf09c221a3d1092f85cd7c3bb55ae0a3ca47
https://github.com/pism/pism/commit/be4dcf09c221a3d1092f85cd7c3bb55ae0a3ca47
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-28 (Thu, 28 Jan 2021)

Changed paths:
M test/regression/inverse/build_tiny.py
M test/regression/inverse/tiny_nlcg.sh
M test/regression/inverse/tiny_tikhonov_lmvm.sh

Log Message:
-----------
Regression tests should use different file names

... to avoid race conditions.

Commit: d1f88d2cbed2f296931aa4674048dac610f4d303
https://github.com/pism/pism/commit/d1f88d2cbed2f296931aa4674048dac610f4d303
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-28 (Thu, 28 Jan 2021)

Changed paths:
M docker/CMakeLists.txt
M docker/ubuntu/CMakeLists.txt
M docker/ubuntu/Dockerfile.in

Log Message:
-----------
Update the Docker image used for regression testing

- Install PETSc from sources because Ubuntu's package uses HDF5 and this causes library
conflicts
- Use MPICH instead of OpenMPI (no compiler warnings from MPI headers, no messing with
environment variables to make it work in a container). A separate Docker image will test
PISM with OpenMPI.
- Use LLD to speed up linking
- Run regression tests in parallel
- Use petsc4py shipped with PETSc: this way it is always up to date

Commit: 0da7adcacb6085a023a0894aa43eed993172fff1
https://github.com/pism/pism/commit/0da7adcacb6085a023a0894aa43eed993172fff1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-28 (Thu, 28 Jan 2021)

Changed paths:
M .circleci/config.yml

Log Message:
-----------
Update the CircleCI config

- Use ckhrulev/pism-ubuntu:0.1.2
- Run tests in parallel
- Use LLD

Commit: 635c60d1cdf368ed805c3bc1eb15aa09d6565415
https://github.com/pism/pism/commit/635c60d1cdf368ed805c3bc1eb15aa09d6565415
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M .circleci/config.yml

Log Message:
-----------
Make it easier to use more cores to run "circleci local"

CircleCI allows us to use 2 CPUs per job and 4 jobs appears to be appropriate there, we
can do better when running tests in a Docker container locally. For example, use

circleci local execute --env N=8 --job=build-clang

To build and test using 8 parallel jobs.

Commit: 0f90167ad34ac4ec7caeacd08cd0d24e23f33871
https://github.com/pism/pism/commit/0f90167ad34ac4ec7caeacd08cd0d24e23f33871
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M test/regression/ssa/ssa_testj_fem.sh

Log Message:
-----------
Output problematic results in a regression test

Commit: 7d97b453920da320e754e5dc0f491e3909969d08
https://github.com/pism/pism/commit/7d97b453920da320e754e5dc0f491e3909969d08
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M src/coupler/OceanModel.hh
M src/coupler/ocean/Cache.cc
M src/coupler/ocean/Cache.hh
M src/coupler/ocean/Constant.cc
M src/coupler/ocean/ConstantPIK.cc
M src/coupler/ocean/Frac_MBP.cc
M src/coupler/ocean/Frac_MBP.hh
M src/coupler/ocean/GivenClimate.cc
M src/coupler/ocean/GivenTH.cc
M src/coupler/ocean/Initialization.cc
M src/coupler/ocean/Initialization.hh
M src/coupler/ocean/OceanModel.cc
M src/coupler/ocean/Pico.cc
M src/icemodel/IceModel.cc
M src/inverse/IP_SSAHardavForwardProblem.cc
M src/inverse/IP_SSATaucForwardProblem.cc
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/ShallowStressBalance.hh
M src/stressbalance/StressBalance.cc
M src/stressbalance/StressBalance.hh
M src/stressbalance/sia/siafd_test.cc
M src/stressbalance/ssa/SSAFD.cc
M src/stressbalance/ssa/SSATestCase.cc
M src/stressbalance/ssa/SSATestCase.hh
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh
M test/regression/ocean_models.py

Log Message:
-----------
Add OceanModel::integrated_water_column_pressure()

... to replace melange back pressure fraction.

Commit: 176ad577d892805f53e21d09fb5249c9bdbc89bc
https://github.com/pism/pism/commit/176ad577d892805f53e21d09fb5249c9bdbc89bc
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M test/regression/ocean_models.py

Log Message:
-----------
Improve test coverage a little bit

Commit: dc79efcfae12b0901b9746c04c678a039edea561
https://github.com/pism/pism/commit/dc79efcfae12b0901b9746c04c678a039edea561
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M doc/sphinx/climate_forcing/ocean.rst
M doc/sphinx/manual/modeling-choices/marine/melange.rst
M doc/sphinx/math-definitions.txt
M doc/sphinx/technical/ssafd-cfbc.rst
M src/util/pism_utilities.cc

Log Message:
-----------
Start updating the manual

Commit: 97b9cb99738b11fae77018aee46b8eab0487a017
https://github.com/pism/pism/commit/97b9cb99738b11fae77018aee46b8eab0487a017
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M src/coupler/OceanModel.hh
M src/coupler/ocean/Cache.cc
M src/coupler/ocean/Cache.hh
M src/coupler/ocean/Constant.cc
M src/coupler/ocean/ConstantPIK.cc
M src/coupler/ocean/Frac_MBP.cc
M src/coupler/ocean/Frac_MBP.hh
M src/coupler/ocean/GivenClimate.cc
M src/coupler/ocean/GivenTH.cc
M src/coupler/ocean/Initialization.cc
M src/coupler/ocean/Initialization.hh
M src/coupler/ocean/OceanModel.cc
M src/coupler/ocean/Pico.cc
M src/icemodel/IceModel.cc
M src/icemodel/diagnostics.cc
M src/inverse/IP_SSAHardavForwardProblem.cc
M src/inverse/IP_SSATaucForwardProblem.cc
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/ShallowStressBalance.hh
M src/stressbalance/StressBalance.cc
M src/stressbalance/StressBalance.hh
M src/stressbalance/sia/siafd_test.cc
M src/stressbalance/ssa/SSAFD.cc
M src/stressbalance/ssa/SSAFEM.cc
M src/stressbalance/ssa/SSATestCase.cc
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh
M test/regression/ocean_models.py

Log Message:
-----------
Rename from "integrated" to average_water_column_pressure()

Commit: 239de678476038a275f2c2f4e645e17188818987
https://github.com/pism/pism/commit/239de678476038a275f2c2f4e645e17188818987
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M src/stressbalance/ssa/SSAFEM.cc

Log Message:
-----------
Update the CFBC implementation in SSAFEM

Commit: 71e2597a0379e973fe3548ad1769fef3d83665a1
https://github.com/pism/pism/commit/71e2597a0379e973fe3548ad1769fef3d83665a1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M src/icemodel/diagnostics.cc
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/ShallowStressBalance.hh

Log Message:
-----------
Remove margin_pressure_difference and update the diagnostic

Now ice_margin_pressure_difference reports the vertically-averaged pressure difference in
Pa instead of the integral in "Pa m".

Commit: 6a2cec1ce73c7a35ebfa255063becee5296f78bb
https://github.com/pism/pism/commit/6a2cec1ce73c7a35ebfa255063becee5296f78bb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M doc/sphinx/climate_forcing/ocean.rst

Log Message:
-----------
Improve the documentation of the frac_MBP ocean modifier

Commit: ef4bdf26cf424eda3d4d7823d6a02ab79477faea
https://github.com/pism/pism/commit/ef4bdf26cf424eda3d4d7823d6a02ab79477faea
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M CHANGES.rst
M src/pism_config.cdl

Log Message:
-----------
Remove ocean.melange_back_pressure_fraction

The current implementation no longer uses this parameter

Commit: b7a14e9cb7910eaca57f3066284f81c2fac32538
https://github.com/pism/pism/commit/b7a14e9cb7910eaca57f3066284f81c2fac32538
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/climate_forcing/ocean.rst
M src/coupler/CMakeLists.txt
A src/coupler/ocean/Delta_MBP.cc
A src/coupler/ocean/Delta_MBP.hh
M src/coupler/ocean/Factory.cc
M src/coupler/ocean/OceanModel.cc
M src/pism_config.cdl
M src/pythonbindings/pism_ocean.i
M test/regression/ocean_models.py

Log Message:
-----------
Implement, document, and add a test for -ocean ...,delta_MBP

Commit: 393f2b661b5dbfb64c511e97b509f111f6385459
https://github.com/pism/pism/commit/393f2b661b5dbfb64c511e97b509f111f6385459
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M CHANGES.rst
M src/coupler/ocean/sea_level/SeaLevel.cc
M src/pism_config.cdl

Log Message:
-----------
Add sea_level.constant.value

Commit: 2d9ae7ab812c91e798bc9c91d531c514aa662507
https://github.com/pism/pism/commit/2d9ae7ab812c91e798bc9c91d531c514aa662507
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M src/coupler/ocean/Constant.cc
M src/coupler/ocean/ConstantPIK.cc
M src/coupler/ocean/Pico.cc

Log Message:
-----------
Compute water pressure in init_impl() of ocean models

Commit: 7b712624184edb9071754f2ae8e668e58aa0bb99
https://github.com/pism/pism/commit/7b712624184edb9071754f2ae8e668e58aa0bb99
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M CHANGES.rst
M examples/marine/flowline/createSetup_flowline.py
M examples/mismip/mismip2d/run.py
M examples/mismip/mismip3d/preprocess.py
M src/coupler/ocean/Constant.cc
M src/icemodel/IceEISModel.cc
M src/icemodel/diagnostics.cc
M src/pism_config.cdl
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/ShallowStressBalance.hh
M src/stressbalance/ssa/SSAFD.cc
M src/stressbalance/ssa/SSAFEM.cc
M src/util/Mask.hh
M src/verification/iceCompModel.cc

Log Message:
-----------
Remove ocean.always_grounded

Now that we have sea_level.constant.value, we can set it to some large negative value to
ensure that all ice is grounded.

Commit: 1d625ab9ea1d5d979a91feee8b7f68d1e4580feb
https://github.com/pism/pism/commit/1d625ab9ea1d5d979a91feee8b7f68d1e4580feb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/climate_forcing/ocean.rst
M doc/sphinx/manual/modeling-choices/marine/melange.rst
M doc/sphinx/math-definitions.txt
M doc/sphinx/technical/ssafd-cfbc.rst
M src/coupler/CMakeLists.txt
M src/coupler/OceanModel.hh
M src/coupler/ocean/Cache.cc
M src/coupler/ocean/Cache.hh
M src/coupler/ocean/Constant.cc
M src/coupler/ocean/ConstantPIK.cc
A src/coupler/ocean/Delta_MBP.cc
A src/coupler/ocean/Delta_MBP.hh
M src/coupler/ocean/Factory.cc
M src/coupler/ocean/Frac_MBP.cc
M src/coupler/ocean/Frac_MBP.hh
M src/coupler/ocean/GivenClimate.cc
M src/coupler/ocean/GivenTH.cc
M src/coupler/ocean/Initialization.cc
M src/coupler/ocean/Initialization.hh
M src/coupler/ocean/OceanModel.cc
M src/coupler/ocean/Pico.cc
M src/icemodel/IceModel.cc
M src/icemodel/diagnostics.cc
M src/inverse/IP_SSAHardavForwardProblem.cc
M src/inverse/IP_SSATaucForwardProblem.cc
M src/pism_config.cdl
M src/pythonbindings/pism_ocean.i
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/ShallowStressBalance.hh
M src/stressbalance/StressBalance.cc
M src/stressbalance/StressBalance.hh
M src/stressbalance/sia/siafd_test.cc
M src/stressbalance/ssa/SSAFD.cc
M src/stressbalance/ssa/SSAFEM.cc
M src/stressbalance/ssa/SSATestCase.cc
M src/stressbalance/ssa/SSATestCase.hh
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh
M test/regression/ocean_models.py

Log Message:
-----------
Merge branch 'ckhroulev/melange' into dev

Commit: 21d95426c16db5309a9b6130e9e2a20fe1e31bf3
https://github.com/pism/pism/commit/21d95426c16db5309a9b6130e9e2a20fe1e31bf3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M src/earth/CMakeLists.txt
A src/earth/Given.cc
A src/earth/Given.hh
M src/icemodel/initialization.cc
M src/pism_config.cdl
M src/pythonbindings/pism_BedDef.i
M test/CMakeLists.txt
A test/regression/beddef_given.py

Log Message:
-----------
Implement "-bed_def given"

This new class reads in a prescribed bed deformation history from a file.

It uses two input files:

1. Reference topography (variable "topg", in meters).
2. Time-dependent history of bed elevation changes relative to the reference topography
(variable "topg_delta", in meters).

The first is specified using the configuration parameter
"bed_deformation.given.reference_file", the second one using "bed_deformation.given.file".

This split makes it possible to combine high-resolution reference bed topography with
low-spatial-frequency bed elevation changes that can be stored on a coarser grid covering
the same domain.

Commit: 5e6f1f72436b03c6f469069a9bfa389251660afd
https://github.com/pism/pism/commit/5e6f1f72436b03c6f469069a9bfa389251660afd
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/manual/modeling-choices/subglacier/bed-deformation.rst

Log Message:
-----------
Added documentation for "-bed_def given" class.

Commit: 9c612af4a6c358f7cead3592e1930e89ac2dbd6a
https://github.com/pism/pism/commit/9c612af4a6c358f7cead3592e1930e89ac2dbd6a
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/subglacier/bed-deformation.rst

Log Message:
-----------
Added title underline in doc

Commit: d23bfde6d870d13121e68809009e9beee2600f14
https://github.com/pism/pism/commit/d23bfde6d870d13121e68809009e9beee2600f14
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-01-29 (Fri, 29 Jan 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/subglacier/bed-deformation.rst

Log Message:
-----------
Clean up wording in the section documenting -bed_def given

Commit: 60bd56ee287dedafbfaaa41018c3b2b88c02d2dc
https://github.com/pism/pism/commit/60bd56ee287dedafbfaaa41018c3b2b88c02d2dc
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-01 (Mon, 01 Feb 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/manual/modeling-choices/subglacier/bed-deformation.rst
M src/earth/CMakeLists.txt
A src/earth/Given.cc
A src/earth/Given.hh
M src/icemodel/initialization.cc
M src/pism_config.cdl
M src/pythonbindings/pism_BedDef.i
M test/CMakeLists.txt
A test/regression/beddef_given.py

Log Message:
-----------
Merge branch 'ckhroulev/beddef-given' into dev

Commit: e9bdb3aceb01dae49f820717c5e6c8b1d6926411
https://github.com/pism/pism/commit/e9bdb3aceb01dae49f820717c5e6c8b1d6926411
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-01 (Mon, 01 Feb 2021)

Changed paths:
M doc/ice-bib.bib
M doc/sphinx/climate_forcing/ocean.rst
M src/coupler/ocean/Delta_MBP.cc
M src/pism_config.cdl
M test/regression/ocean_models.py

Log Message:
-----------
Add ocean.delta_MBP.melange_thickness

Now we interpret delta_MBP (the scalar forcing read from a file) as melange back pressure
applied over the thickness of melange specified using this parameter.

Commit: f74004252b809578d5a35c7f1576f2927aaec3f5
https://github.com/pism/pism/commit/f74004252b809578d5a35c7f1576f2927aaec3f5
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-02-01 (Mon, 01 Feb 2021)

Changed paths:
M src/basalstrength/basal_resistance.cc
M src/basalstrength/basal_resistance.hh
M src/pism_config.cdl
M src/stressbalance/ShallowStressBalance.cc

Log Message:
-----------
Implemented regularized Coulomb sliding as in Zoet & Iverson, 2020, A slip law for glaciers on deformable beds, Eq. 3

Commit: d06ac5c81a466860e7d9aed243ff3ba01cb005de
https://github.com/pism/pism/commit/d06ac5c81a466860e7d9aed243ff3ba01cb005de
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-02-01 (Mon, 01 Feb 2021)

Changed paths:
M doc/ice-bib.bib
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst
M src/basalstrength/basal_resistance.cc
M src/pism_config.cdl

Log Message:
-----------
Added short doc about regularized Coulomb sliding

Commit: 6de30ae94ec96a15c4b9e3ec359aa5c68eb6d509
https://github.com/pism/pism/commit/6de30ae94ec96a15c4b9e3ec359aa5c68eb6d509
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-01 (Mon, 01 Feb 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst
M src/basalstrength/basal_resistance.cc

Log Message:
-----------
Clean up the code and the manual; add a change log entry

Commit: 6e2b3b71245ba2baba643e1e42b3c4ac5d3c59ca
https://github.com/pism/pism/commit/6e2b3b71245ba2baba643e1e42b3c4ac5d3c59ca
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-01 (Mon, 01 Feb 2021)

Changed paths:
M CHANGES.rst
M doc/ice-bib.bib
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst
M src/basalstrength/basal_resistance.cc
M src/basalstrength/basal_resistance.hh
M src/pism_config.cdl
M src/stressbalance/ShallowStressBalance.cc

Log Message:
-----------
Merge branch 'pik/reg_coulomb_sliding' into dev

Commit: 4c737d31d210d5006e2e9604ff4b968d075456e3
https://github.com/pism/pism/commit/4c737d31d210d5006e2e9604ff4b968d075456e3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-01 (Mon, 01 Feb 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/residual.cc
M src/stressbalance/blatter/verification/BlatterTestXY.cc
M src/stressbalance/blatter/verification/BlatterTestXY.hh
M src/stressbalance/blatter/verification/BlatterTestXZ.cc
M src/stressbalance/blatter/verification/BlatterTestXZ.hh
M src/stressbalance/blatter/verification/test_template.cc

Log Message:
-----------
Rename Blatter::vertical_cliff_face() to marine_boundary()

... in preparation for a change in lateral BC.

Commit: 2030075261f14ac388f7fff4c60bdddebe158c78
https://github.com/pism/pism/commit/2030075261f14ac388f7fff4c60bdddebe158c78
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-11 (Thu, 11 Feb 2021)

Changed paths:
M src/frontretreat/util/IcebergRemover.cc
M src/frontretreat/util/IcebergRemover.hh
M src/icemodel/initialization.cc

Log Message:
-----------
Remove IcebergRemover::init()

... because it does nothing.

Commit: 4242dac0a451d398f0e21f6b90d67a1f3937b6e0
https://github.com/pism/pism/commit/4242dac0a451d398f0e21f6b90d67a1f3937b6e0
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-11 (Thu, 11 Feb 2021)

Changed paths:
M src/frontretreat/util/IcebergRemover.cc
M src/frontretreat/util/IcebergRemover.hh

Log Message:
-----------
Make IcebergRemover::update_impl() virtual

in preparation for the work on the FEM version.

Commit: e13e9f6539cbdc5fbef2b50a19a4047a000edf9f
https://github.com/pism/pism/commit/e13e9f6539cbdc5fbef2b50a19a4047a000edf9f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-12 (Fri, 12 Feb 2021)

Changed paths:
M src/frontretreat/util/IcebergRemover.cc

Log Message:
-----------
Remove "== true" in condition checks

Commit: 638e7f3ae509d1c2592344ba1131d8aed3b4f727
https://github.com/pism/pism/commit/638e7f3ae509d1c2592344ba1131d8aed3b4f727
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-12 (Fri, 12 Feb 2021)

Changed paths:
M src/frontretreat/CMakeLists.txt
A src/frontretreat/util/IcebergRemoverFEM.cc
A src/frontretreat/util/IcebergRemoverFEM.hh
M src/pythonbindings/pism_calving.i

Log Message:
-----------
Implement the FEM version of the iceberg remover

Commit: 2eec496bee5b8f153c171f077c30a9bf12599798
https://github.com/pism/pism/commit/2eec496bee5b8f153c171f077c30a9bf12599798
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-12 (Fri, 12 Feb 2021)

Changed paths:
M test/CMakeLists.txt
A test/regression/iceberg_remover.py

Log Message:
-----------
Add regression tests for iceberg removers

Commit: 49f4d835136195fe0940275723f0aa335e0d4ca8
https://github.com/pism/pism/commit/49f4d835136195fe0940275723f0aa335e0d4ca8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-12 (Fri, 12 Feb 2021)

Changed paths:
M src/stressbalance/blatter/jacobian.cc

Log Message:
-----------
White space changes

Commit: 286200f6c2b67e97b9070de71c79553e841b27da
https://github.com/pism/pism/commit/286200f6c2b67e97b9070de71c79553e841b27da
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-12 (Fri, 12 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/Makefile

Log Message:
-----------
Switch from python to python3

Commit: d7ddf368d5ebe797b2664908780f291f47db4abf
https://github.com/pism/pism/commit/d7ddf368d5ebe797b2664908780f291f47db4abf
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-15 (Mon, 15 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/blatter.py
M src/stressbalance/blatter/verification/manufactured_solutions.cc

Log Message:
-----------
Use a more conventional definition of the BP stress "tensor"

Commit: d9fd09933f6d90c63bf98353c36c214f077f3a25
https://github.com/pism/pism/commit/d9fd09933f6d90c63bf98353c36c214f077f3a25
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-15 (Mon, 15 Feb 2021)

Changed paths:
R src/stressbalance/blatter/verification/test_template.cc

Log Message:
-----------
Remove test_template.cc

Commit: acb3c5afab94fb67c6497c5b807c18309c8ca408
https://github.com/pism/pism/commit/acb3c5afab94fb67c6497c5b807c18309c8ca408
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-16 (Tue, 16 Feb 2021)

Changed paths:
M src/stressbalance/blatter/residual.cc
M src/stressbalance/blatter/verification/BlatterTestHalfar.cc
M src/stressbalance/blatter/verification/BlatterTestXZ.cc
M src/stressbalance/blatter/verification/blatter.py

Log Message:
-----------
Cosmetic changes

Commit: ac4aea26489a1acc906be81908706dea6c0dfca7
https://github.com/pism/pism/commit/ac4aea26489a1acc906be81908706dea6c0dfca7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-16 (Tue, 16 Feb 2021)

Changed paths:
A src/stressbalance/blatter/verification/blatter_codegen.py
M src/stressbalance/blatter/verification/manufactured_solutions.py
M src/stressbalance/blatter/verification/test_xy.py
M src/stressbalance/blatter/verification/test_xz.py
M src/stressbalance/blatter/verification/test_xz_cfbc.py
M src/stressbalance/blatter/verification/test_xz_halfar.py

Log Message:
-----------
Clean up code generation

Commit: 4318f8fa5eb24f253fc8fedb91d045288948c39f
https://github.com/pism/pism/commit/4318f8fa5eb24f253fc8fedb91d045288948c39f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-16 (Tue, 16 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestHalfar.cc
M src/stressbalance/blatter/verification/manufactured_solutions.cc
M src/stressbalance/blatter/verification/test_xz_halfar.py

Log Message:
-----------
Fiddling with the Halfar test case

Commit: 113f29512b666dd488c1dab08ac5c4eae7430aa4
https://github.com/pism/pism/commit/113f29512b666dd488c1dab08ac5c4eae7430aa4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-16 (Tue, 16 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestHalfar.cc
M src/stressbalance/blatter/verification/manufactured_solutions.cc
M src/stressbalance/blatter/verification/manufactured_solutions.hh
M src/stressbalance/blatter/verification/test_xz_halfar.py

Log Message:
-----------
Working on the Halfar dome MMS setup

Commit: 5bacd947a3258f0c429112e6e1ae600fff89dd23
https://github.com/pism/pism/commit/5bacd947a3258f0c429112e6e1ae600fff89dd23
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-16 (Tue, 16 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/manufactured_solutions.cc
M src/stressbalance/blatter/verification/test_xz_cfbc.py

Log Message:
-----------
Fiddling with the CFBC test

Commit: d31a0f23710f1d031629218b87b452271f6806d0
https://github.com/pism/pism/commit/d31a0f23710f1d031629218b87b452271f6806d0
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-16 (Tue, 16 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestXZ.cc

Log Message:
-----------
Cosmetic changes

Commit: 395011e50d723ba687ba191c524eae24dccd49fb
https://github.com/pism/pism/commit/395011e50d723ba687ba191c524eae24dccd49fb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-16 (Tue, 16 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestHalfar.cc
M src/stressbalance/blatter/verification/BlatterTestHalfar.hh
M src/stressbalance/blatter/verification/manufactured_solutions.cc
M src/stressbalance/blatter/verification/test_xz_halfar.py

Log Message:
-----------
Add the top surface contribution to the residual

Commit: f6a80c97d12f1144a7f0b15024a970414c13f2da
https://github.com/pism/pism/commit/f6a80c97d12f1144a7f0b15024a970414c13f2da
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-18 (Thu, 18 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/blatter_codegen.py

Log Message:
-----------
Improve the code generation script

Commit: 5697f41ba6fe29f794003ec1dc498fc6b8cb98c3
https://github.com/pism/pism/commit/5697f41ba6fe29f794003ec1dc498fc6b8cb98c3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-18 (Thu, 18 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/blatter_codegen.py
M src/stressbalance/blatter/verification/manufactured_solutions.cc
M src/stressbalance/blatter/verification/manufactured_solutions.hh
M src/stressbalance/blatter/verification/manufactured_solutions.py
A src/stressbalance/blatter/verification/test_xz_vanderveen.py

Log Message:
-----------
Add a verification test based on the van der Veen profile

Commit: 13723217d99bbb0fadba6176e8cb6009a8f356dc
https://github.com/pism/pism/commit/13723217d99bbb0fadba6176e8cb6009a8f356dc
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-18 (Thu, 18 Feb 2021)

Changed paths:
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
We don't need this now that we have Blatter::marine_boundary()

Commit: dd147fed6e7b4f6261ae3642ef32acc9769dde02
https://github.com/pism/pism/commit/dd147fed6e7b4f6261ae3642ef32acc9769dde02
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-19 (Fri, 19 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.hh

Log Message:
-----------
Switch to generated code in the van der Veen test case

Commit: 2003cced293fee023561b5c4761dabe28642f887
https://github.com/pism/pism/commit/2003cced293fee023561b5c4761dabe28642f887
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-19 (Fri, 19 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/blatter_codegen.py
M src/stressbalance/blatter/verification/manufactured_solutions.cc
M src/stressbalance/blatter/verification/test_xz_halfar.py
M src/stressbalance/blatter/verification/test_xz_vanderveen.py

Log Message:
-----------
Clean up code generation scripts

Commit: ad8d07f5dc7b88428385fb28e7ba2bf80ef1fe2a
https://github.com/pism/pism/commit/ad8d07f5dc7b88428385fb28e7ba2bf80ef1fe2a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-19 (Fri, 19 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.hh

Log Message:
-----------
Add the surface BC term to the van der Veen test

Commit: a1313ac826cde256d677c5533d75eac331d3232c
https://github.com/pism/pism/commit/a1313ac826cde256d677c5533d75eac331d3232c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-19 (Fri, 19 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestHalfar.cc

Log Message:
-----------
Clean up the Halfar test a bit

Commit: ff93fff52fb98035194674053639d73b18157ac9
https://github.com/pism/pism/commit/ff93fff52fb98035194674053639d73b18157ac9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-20 (Sat, 20 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.hh

Log Message:
-----------
The van der Veen verification test works

Finally!

Commit: b4cf595ec1949056c89ba006ca0dd207d535b286
https://github.com/pism/pism/commit/b4cf595ec1949056c89ba006ca0dd207d535b286
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-20 (Sat, 20 Feb 2021)

Changed paths:
M test/blatter_verification.py

Log Message:
-----------
Add the new verification test to the test harness

... and fix the code restoring configuration parameters after a test.

Commit: df338ce537833647db755c46977b3ad73325745d
https://github.com/pism/pism/commit/df338ce537833647db755c46977b3ad73325745d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-20 (Sat, 20 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/manufactured_solutions.cc
M src/stressbalance/blatter/verification/test_xz_halfar.py

Log Message:
-----------
A bit more work on the Halfar dome MMS test

Commit: 6223a5d110574f19a546bd7f7ec0c018fad23359
https://github.com/pism/pism/commit/6223a5d110574f19a546bd7f7ec0c018fad23359
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-20 (Sat, 20 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestCFBC.cc
M src/stressbalance/blatter/verification/BlatterTestCFBC.hh
M src/stressbalance/blatter/verification/BlatterTestHalfar.hh
M src/stressbalance/blatter/verification/blatter.py
M src/stressbalance/blatter/verification/wiggles.py
M test/blatter_verification.py

Log Message:
-----------
Cosmetic changes

Commit: 2fcde805cda97f8497d7900699d878ddb2be5d8b
https://github.com/pism/pism/commit/2fcde805cda97f8497d7900699d878ddb2be5d8b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-22 (Mon, 22 Feb 2021)

Changed paths:
M doc/sphinx/global.txt
M doc/sphinx/technical/blatter-pattyn.rst

Log Message:
-----------
Update technical docs

Commit: 01e58e11f3e85a7df60ac0b71bb5ce2d6472a3b9
https://github.com/pism/pism/commit/01e58e11f3e85a7df60ac0b71bb5ce2d6472a3b9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-22 (Mon, 22 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc
M test/blatter_verification.py

Log Message:
-----------
Use non-trivial beta in the van der Veen profile test

Commit: f8133ab3c3e43ed6ce0ef678adb1a3fd27797f07
https://github.com/pism/pism/commit/f8133ab3c3e43ed6ce0ef678adb1a3fd27797f07
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-22 (Mon, 22 Feb 2021)

Changed paths:
M doc/sphinx/technical/blatter-pattyn.rst
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Add a FIXME comment

Commit: ab244fe0e226976efd48899146cd21d557efa110
https://github.com/pism/pism/commit/ab244fe0e226976efd48899146cd21d557efa110
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-22 (Mon, 22 Feb 2021)

Changed paths:
M doc/sphinx/manual/highlevelview/model-hierarchy.rst
M doc/sphinx/manual/highlevelview/stress-balance-models.rst
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst

Log Message:
-----------
Add FIXMEs to the manual

... to help me remember to document the Blatter-Pattyn stress balance solver.

Commit: ded405b8011bdf412eaa5bf54f04681f0ca37eec
https://github.com/pism/pism/commit/ded405b8011bdf412eaa5bf54f04681f0ca37eec
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-25 (Thu, 25 Feb 2021)

Changed paths:
M src/stressbalance/blatter/verification/BlatterTestHalfar.cc
M src/stressbalance/blatter/verification/BlatterTestHalfar.hh
M src/stressbalance/blatter/verification/manufactured_solutions.cc
M src/stressbalance/blatter/verification/manufactured_solutions.hh
M src/stressbalance/blatter/verification/test_xz_halfar.py
M test/blatter_verification.py

Log Message:
-----------
Finish one more verification test

This flow-line (X-Z) test uses the SIA velocity profile for the Halfar dome as a
manufactured solution. It uses a compensatory term, Dirichlet BC at [x_min, x_max], and
stress BC at both top and bottom boundaries.

It *may* be useful because the domain shape is more interesting than in other cases I
implemented: here we have a strongly varying ice thickness and element aspect ratios.

Commit: afc86401700817b28f8a9cfb49ecc5fdc972a25c
https://github.com/pism/pism/commit/afc86401700817b28f8a9cfb49ecc5fdc972a25c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-25 (Thu, 25 Feb 2021)

Changed paths:
A doc/sphinx/manual/modeling-choices/computational/figures/grid-vertical-pism.png
A doc/sphinx/manual/modeling-choices/computational/figures/grid-vertical-sigma.png
A doc/sphinx/manual/modeling-choices/computational/figures/grid-vertical.svg

Log Message:
-----------
Add figures showing the difference between PISM's and sigma grids

Commit: 8ef552f736dab0b1bfd7b135307fc5753b88db76
https://github.com/pism/pism/commit/8ef552f736dab0b1bfd7b135307fc5753b88db76
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-25 (Thu, 25 Feb 2021)

Changed paths:
M doc/sphinx/manual/highlevelview/figures/stressbalance.dot
M doc/sphinx/manual/highlevelview/figures/stressbalance.png

Log Message:
-----------
Update the figure documenting stress balance components

Commit: a5f215689db813c572dd3735024d5c3a1e5cd3ad
https://github.com/pism/pism/commit/a5f215689db813c572dd3735024d5c3a1e5cd3ad
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-25 (Thu, 25 Feb 2021)

Changed paths:
M doc/sphinx/conf.py

Log Message:
-----------
Update the copyright year in the manual

Commit: c37765962ee3fdf92d2bf8935ae22c2d60d67b1a
https://github.com/pism/pism/commit/c37765962ee3fdf92d2bf8935ae22c2d60d67b1a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-25 (Thu, 25 Feb 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/computational/grid.rst

Log Message:
-----------
Fiddles with the documentation of the computational grid

I need to mention the "sigma" vertical grid.

Commit: e99f25c325ed8efa88fed26d407cefbe6bbc88b8
https://github.com/pism/pism/commit/e99f25c325ed8efa88fed26d407cefbe6bbc88b8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-25 (Thu, 25 Feb 2021)

Changed paths:
M doc/sphinx/manual/highlevelview/model-hierarchy.rst
M doc/sphinx/manual/highlevelview/stress-balance-models.rst

Log Message:
-----------
Mention Blatter's stress balance model in the "high level view"

Commit: 77add3472a43f04f89cd024dec815884f9f51913
https://github.com/pism/pism/commit/77add3472a43f04f89cd024dec815884f9f51913
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-25 (Thu, 25 Feb 2021)

Changed paths:
M doc/ice-bib.bib
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst
M doc/sphinx/technical/blatter-pattyn.rst

Log Message:
-----------
Document the Blatter solver

Almost done.

Next steps:

- Document the eta transformation used here.
- Make PISM use the new iceberg elimination code when a FEM-based stress balance solver is
selected.

Commit: 47a495cc03f2724bec4729bf432e3fcc7bb6567d
https://github.com/pism/pism/commit/47a495cc03f2724bec4729bf432e3fcc7bb6567d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-25 (Thu, 25 Feb 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst

Log Message:
-----------
Minor wording changes

Commit: c04d3337fdf7853682f4aa97dcf48021fc19538f
https://github.com/pism/pism/commit/c04d3337fdf7853682f4aa97dcf48021fc19538f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-26 (Fri, 26 Feb 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/dynamics/rheology.rst

Log Message:
-----------
Edit the section about rheology

Commit: c55bc97a56cef1cfdccff24a74ed8fa509720243
https://github.com/pism/pism/commit/c55bc97a56cef1cfdccff24a74ed8fa509720243
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-26 (Fri, 26 Feb 2021)

Changed paths:
M src/pism_config.cdl

Log Message:
-----------
Add some shorter command-line options and clean up doc strings

Commit: 894aef981f44f7ab1b7d173a58e3b272cd01aca8
https://github.com/pism/pism/commit/894aef981f44f7ab1b7d173a58e3b272cd01aca8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-26 (Fri, 26 Feb 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst

Log Message:
-----------
Document remaining parameters controlling the Blatter solver

Commit: 10dfb1fe23f638af1b013cedbf650c6bff07fb95
https://github.com/pism/pism/commit/10dfb1fe23f638af1b013cedbf650c6bff07fb95
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-26 (Fri, 26 Feb 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst

Log Message:
-----------
Final cleanup

Commit: c258ece56a5b1f60fe3ab86382c2c39e173c46b6
https://github.com/pism/pism/commit/c258ece56a5b1f60fe3ab86382c2c39e173c46b6
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-26 (Fri, 26 Feb 2021)

Changed paths:
M src/icemodel/initialization.cc

Log Message:
-----------
Allocate the FEM version of the iceberg remover

... when SSAFEM or the Blatter solver is in use.

Commit: 80cdcad62f750891250ac6d6cba6386469132f52
https://github.com/pism/pism/commit/80cdcad62f750891250ac6d6cba6386469132f52
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-26 (Fri, 26 Feb 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst

Log Message:
-----------
A few edits based on Ed's feedback

I'm getting closer, but it still needs work.

Commit: 1b93be09b41b393ab2486e2645df452b05f8aff7
https://github.com/pism/pism/commit/1b93be09b41b393ab2486e2645df452b05f8aff7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-26 (Fri, 26 Feb 2021)

Changed paths:
M doc/ice-bib.bib
M doc/sphinx/conf.py
M doc/sphinx/global.txt
M doc/sphinx/manual/highlevelview/figures/stressbalance.dot
M doc/sphinx/manual/highlevelview/figures/stressbalance.png
M doc/sphinx/manual/highlevelview/model-hierarchy.rst
M doc/sphinx/manual/highlevelview/stress-balance-models.rst
A doc/sphinx/manual/modeling-choices/computational/figures/grid-vertical-pism.png
A doc/sphinx/manual/modeling-choices/computational/figures/grid-vertical-sigma.png
A doc/sphinx/manual/modeling-choices/computational/figures/grid-vertical.svg
M doc/sphinx/manual/modeling-choices/computational/grid.rst
M doc/sphinx/manual/modeling-choices/dynamics/rheology.rst
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst
A doc/sphinx/technical/blatter-pattyn.rst
M doc/sphinx/technical/index.rst
M examples/inverse/pismi.py
M examples/marine/circular/circular_dirichlet.py
M examples/storglaciaren/create_warming_climate.py
M site-packages/PISM/invert/sipletools.py
M site-packages/PISM/invert/ssa_siple.py
M site-packages/PISM/model.py
M site-packages/PISM/sia.py
M site-packages/PISM/ssa.py
M site-packages/PISM/testing.py
M src/CMakeLists.txt
M src/age/AgeModel.cc
M src/coupler/frontalmelt/FrontalMelt.cc
M src/coupler/surface/ForceThickness.cc
M src/coupler/surface/Initialization.cc
M src/coupler/surface/TemperatureIndex.cc
M src/coupler/surface/localMassBalance.cc
M src/coupler/surface/localMassBalance.hh
M src/earth/BedDef.cc
M src/earth/BedDef.hh
M src/earth/LingleClark.cc
M src/earth/LingleClark.hh
M src/earth/PointwiseIsostasy.cc
M src/energy/BTU_Full.cc
M src/energy/BTU_Full.hh
M src/energy/BedThermalUnit.cc
M src/energy/BedThermalUnit.hh
M src/energy/EnergyModel.cc
M src/energy/TemperatureModel.cc
M src/energy/btutest.cc
M src/energy/enthSystem.hh
M src/frontretreat/CMakeLists.txt
M src/frontretreat/FrontRetreat.cc
M src/frontretreat/calving/StressCalving.cc
M src/frontretreat/calving/vonMisesCalving.cc
M src/frontretreat/util/IcebergRemover.cc
M src/frontretreat/util/IcebergRemover.hh
A src/frontretreat/util/IcebergRemoverFEM.cc
A src/frontretreat/util/IcebergRemoverFEM.hh
M src/frontretreat/util/remove_narrow_tongues.cc
M src/geometry/GeometryEvolution.cc
M src/hydrology/EmptyingProblem.hh
M src/hydrology/Hydrology.hh
M src/hydrology/NullTransport.cc
M src/icebin/IBIceModel.cc
M src/icebin/IBSurfaceModel.cc
M src/icebin/MassEnergyBudget.cc
M src/icebin/MassEnergyBudget.hh
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/diagnostics.cc
M src/icemodel/energy.cc
M src/icemodel/fracture_density.cc
M src/icemodel/frontretreat.cc
M src/icemodel/initialization.cc
M src/icemodel/timestepping.cc
M src/inverse/IPDesignVariableParameterization.hh
M src/inverse/IPTaoTikhonovProblem.hh
M src/inverse/IP_SSAHardavForwardProblem.cc
M src/inverse/IP_SSAHardavForwardProblem.hh
M src/inverse/IP_SSATaucForwardProblem.cc
M src/inverse/IP_SSATaucForwardProblem.hh
M src/inverse/IP_SSATaucTaoTikhonovProblemLCL.cc
M src/inverse/IP_SSATaucTikhonovGNSolver.hh
M src/inverse/functional/IPFunctional.cc
M src/inverse/functional/IPFunctional.hh
M src/inverse/functional/IPGroundedIceH1NormFunctional.cc
M src/inverse/functional/IPLogRatioFunctional.cc
M src/inverse/functional/IPLogRelativeFunctional.cc
M src/inverse/functional/IPMeanSquareFunctional.cc
M src/inverse/functional/IPMeanSquareFunctional.hh
M src/inverse/functional/IPTotalVariationFunctional.cc
M src/inverse/functional/IP_H1NormFunctional.cc
M src/inverse/functional/IP_H1NormFunctional.hh
M src/inverse/functional/IP_L2NormFunctional.cc
M src/pism_config.cdl
M src/pythonbindings/CMakeLists.txt
M src/pythonbindings/PISM.i
M src/pythonbindings/pism_IceModelVec.i
M src/pythonbindings/pism_SIA.i
M src/pythonbindings/pism_SSA.i
A src/pythonbindings/pism_blatter.i
M src/pythonbindings/pism_calving.i
M src/pythonbindings/pism_energy.i
M src/regional/EnthalpyModel_Regional.cc
M src/regional/IceRegionalModel.cc
M src/rheology/FlowLaw.hh
M src/stressbalance/CMakeLists.txt
M src/stressbalance/SSB_Modifier.cc
M src/stressbalance/SSB_Modifier.hh
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/ShallowStressBalance.hh
M src/stressbalance/StressBalance.cc
M src/stressbalance/StressBalance.hh
M src/stressbalance/StressBalance_diagnostics.cc
A src/stressbalance/blatter/Blatter.cc
A src/stressbalance/blatter/Blatter.hh
A src/stressbalance/blatter/BlatterMod.cc
A src/stressbalance/blatter/BlatterMod.hh
A src/stressbalance/blatter/CMakeLists.txt
A src/stressbalance/blatter/README.org
A src/stressbalance/blatter/ismip-hom/BlatterISMIPHOM.cc
A src/stressbalance/blatter/ismip-hom/BlatterISMIPHOM.hh
A src/stressbalance/blatter/jacobian.cc
A src/stressbalance/blatter/residual.cc
A src/stressbalance/blatter/util/DataAccess.hh
A src/stressbalance/blatter/util/grid_hierarchy.cc
A src/stressbalance/blatter/util/grid_hierarchy.hh
A src/stressbalance/blatter/verification/BlatterTestCFBC.cc
A src/stressbalance/blatter/verification/BlatterTestCFBC.hh
A src/stressbalance/blatter/verification/BlatterTestHalfar.cc
A src/stressbalance/blatter/verification/BlatterTestHalfar.hh
A src/stressbalance/blatter/verification/BlatterTestXY.cc
A src/stressbalance/blatter/verification/BlatterTestXY.hh
A src/stressbalance/blatter/verification/BlatterTestXZ.cc
A src/stressbalance/blatter/verification/BlatterTestXZ.hh
A src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc
A src/stressbalance/blatter/verification/BlatterTestvanderVeen.hh
A src/stressbalance/blatter/verification/Makefile
A src/stressbalance/blatter/verification/blatter.py
A src/stressbalance/blatter/verification/blatter_codegen.py
A src/stressbalance/blatter/verification/manufactured_solutions.cc
A src/stressbalance/blatter/verification/manufactured_solutions.hh
A src/stressbalance/blatter/verification/manufactured_solutions.py
A src/stressbalance/blatter/verification/test_xy.py
A src/stressbalance/blatter/verification/test_xz.py
A src/stressbalance/blatter/verification/test_xz_cfbc.py
A src/stressbalance/blatter/verification/test_xz_halfar.py
A src/stressbalance/blatter/verification/test_xz_vanderveen.py
A src/stressbalance/blatter/verification/wiggles.py
M src/stressbalance/factory.cc
M src/stressbalance/sia/BedSmoother.cc
M src/stressbalance/sia/BedSmoother.hh
M src/stressbalance/sia/SIAFD.cc
M src/stressbalance/sia/SIAFD_diagnostics.cc
M src/stressbalance/sia/siafd_test.cc
M src/stressbalance/ssa/SSA.cc
M src/stressbalance/ssa/SSAFD.cc
M src/stressbalance/ssa/SSAFEM.cc
M src/stressbalance/ssa/SSAFEM.hh
M src/stressbalance/ssa/SSATestCase.cc
M src/stressbalance/ssa/SSATestCase.hh
M src/stressbalance/ssa/doc/fem_p1.mac
A src/stressbalance/ssa/doc/fem_p1_boundary.mac
A src/stressbalance/ssa/doc/fem_q1.mac
A src/stressbalance/ssa/doc/fem_q1_boundary.mac
M src/stressbalance/ssa/tests/ssa_test_cfbc.cc
M src/stressbalance/ssa/tests/ssa_testi.cc
M src/stressbalance/timestepping.cc
M src/util/CMakeLists.txt
M src/util/Component.hh
M src/util/Diagnostic.hh
R src/util/FETools.cc
R src/util/FETools.hh
M src/util/Field.hh
M src/util/IceGrid.hh
M src/util/IceModelVec2CellType.hh
A src/util/IceModelVec2Struct.hh
A src/util/IceModelVec2V.hh
M src/util/IceModelVec_impl.hh
M src/util/IceModelVec_inline.hh
M src/util/Time.hh
M src/util/Vars.cc
A src/util/fem/DirichletData.cc
A src/util/fem/DirichletData.hh
A src/util/fem/Element.cc
A src/util/fem/Element.hh
A src/util/fem/ElementIterator.cc
A src/util/fem/ElementIterator.hh
A src/util/fem/FEM.cc
A src/util/fem/FEM.hh
A src/util/fem/Quadrature.cc
A src/util/fem/Quadrature.hh
A src/util/fem/q1_3d_boundary.mac
M src/util/iceModelVec.cc
M src/util/iceModelVec.hh
M src/util/iceModelVec2.cc
M src/util/iceModelVec2V.cc
M src/util/iceModelVec3.cc
R src/util/iceModelVec3Custom.cc
R src/util/iceModelVec3Custom.hh
M src/util/io/IO_Flags.hh
M src/util/node_types.cc
M src/util/projection.cc
M src/util/projection.hh
M src/verification/iCMthermo.cc
M src/verification/iceCompModel.cc
M test/CMakeLists.txt
M test/bed_smoother.py
A test/blatter_flowline.py
A test/blatter_verification.py
A test/ismip-hom/Makefile
A test/ismip-hom/README.rst
A test/ismip-hom/convert-ismiphom.py
A test/ismip-hom/ismip-hom-a-5km.png
A test/ismip-hom/plot-ismiphom.py
A test/ismip-hom/run-ismiphom.py
M test/miscellaneous.py
A test/regression/iceberg_remover.py
A test/regression/ssa/ssafem.py

Log Message:
-----------
Merge branch 'ckhroulev/blatter' into dev

Commit: 513a4344aec693365134e89301aec831072c0f07
https://github.com/pism/pism/commit/513a4344aec693365134e89301aec831072c0f07
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-02-26 (Fri, 26 Feb 2021)

Changed paths:
M CHANGES.rst

Log Message:
-----------
Update CHANGES.rst

Commit: f097244ef59376654b932965add129a8a768ba5a
https://github.com/pism/pism/commit/f097244ef59376654b932965add129a8a768ba5a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-03-01 (Mon, 01 Mar 2021)

Changed paths:
M test/blatter_flowline.py

Log Message:
-----------
Remove my notes from a comment

Commit: 571dacb908f3842e96b61cb1dc31ebbef5197e61
https://github.com/pism/pism/commit/571dacb908f3842e96b61cb1dc31ebbef5197e61
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-03-01 (Mon, 01 Mar 2021)

Changed paths:
M src/util/options.cc

Log Message:
-----------
Cleanup: Use pism::printf() in pism::options::Real::Real()

... instead of a string stream.

Commit: 96836860b17347391d1929336e6cfe52912c0fc3
https://github.com/pism/pism/commit/96836860b17347391d1929336e6cfe52912c0fc3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-03-01 (Mon, 01 Mar 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/ismip-hom/BlatterISMIPHOM.cc
M src/stressbalance/blatter/ismip-hom/BlatterISMIPHOM.hh
M src/stressbalance/blatter/util/grid_hierarchy.cc
M src/stressbalance/blatter/util/grid_hierarchy.hh
M src/stressbalance/blatter/verification/BlatterTestCFBC.cc
M src/stressbalance/blatter/verification/BlatterTestCFBC.hh
M src/stressbalance/blatter/verification/BlatterTestHalfar.cc
M src/stressbalance/blatter/verification/BlatterTestHalfar.hh
M src/stressbalance/blatter/verification/BlatterTestXY.cc
M src/stressbalance/blatter/verification/BlatterTestXY.hh
M src/stressbalance/blatter/verification/BlatterTestXZ.cc
M src/stressbalance/blatter/verification/BlatterTestXZ.hh
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.hh
M src/stressbalance/factory.cc
M test/blatter_verification.py
M test/ismip-hom/run-ismiphom.py

Log Message:
-----------
Check if the Blatter vertical grid is compatible with MG settings

Now PISM stops with an error message like this one

PISM ERROR: Blatter stress balance solver: settings
stress_balance.blatter.Mz = 17,
stress_balance.blatter.coarsening_factor = 4,
and '-bp_pc_mg_levels 5' are not compatible.
To use N = 5 multigrid levels with the coarsening factor C = 4
stress_balance.blatter.Mz has to be equal to A * C^(N - 1) + 1
for some positive integer A, e.g. 257, 513, 769, ...

if selected parameters values are not compatible. We no longer try to increase the number
of vertical levels used by the Blatter solver.

Commit: bdb05bc710a999c3225cf1f54d08c66c940ac422
https://github.com/pism/pism/commit/bdb05bc710a999c3225cf1f54d08c66c940ac422
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-03-01 (Mon, 01 Mar 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst
M doc/sphinx/technical/blatter-pattyn.rst
M src/pism_config.cdl

Log Message:
-----------
Improve the "Blatter solver" section of the manual

Commit: 711dd320b7ad2c097ac5caef12b6fd9015b8af95
https://github.com/pism/pism/commit/711dd320b7ad2c097ac5caef12b6fd9015b8af95
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-03-01 (Mon, 01 Mar 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst

Log Message:
-----------
Add a FIXME comment

Commit: 52b4b26d856b4aea621128162854bad3d07ff37a
https://github.com/pism/pism/commit/52b4b26d856b4aea621128162854bad3d07ff37a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-03-03 (Wed, 03 Mar 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/util/grid_hierarchy.cc
M src/stressbalance/blatter/util/grid_hierarchy.hh

Log Message:
-----------
Number MG levels the way PETSc does it

0 is the coarsest level, (M-1) is the finest assuming that we are using M multigrid
levels.

Commit: 69fd08b98dd0368ad2818b592ce3baa9bcf5e8a5
https://github.com/pism/pism/commit/69fd08b98dd0368ad2818b592ce3baa9bcf5e8a5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-03-04 (Thu, 04 Mar 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
BP solver: report the reason of a KSP solver failure

Commit: 76f8bf7c09789fdd932934b51a74c0eb23b468b1
https://github.com/pism/pism/commit/76f8bf7c09789fdd932934b51a74c0eb23b468b1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-03-04 (Thu, 04 Mar 2021)

Changed paths:
M src/stressbalance/blatter/util/grid_hierarchy.cc

Log Message:
-----------
Improve wording in a stdout report

Commit: 09e33f1de0b44e6da176f70e7e67334c5dad8d10
https://github.com/pism/pism/commit/09e33f1de0b44e6da176f70e7e67334c5dad8d10
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-03-05 (Fri, 05 Mar 2021)

Changed paths:
M src/rheology/FlowLaw.cc
M src/rheology/FlowLaw.hh

Log Message:
-----------
Remove m_schoofLen and m_schoofVel from FlowLaw

Both variables are used exactly once: to set m_schoofReg.

Commit: 4e03d5e27c99b20ca7b127ca7e8d905bf09542c1
https://github.com/pism/pism/commit/4e03d5e27c99b20ca7b127ca7e8d905bf09542c1
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-03-06 (Sat, 06 Mar 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh

Log Message:
-----------
PICO: When an ice shelf is distributed over multiple basins, use weighted average of ocean inputs only over those basins, in which an ice shelf actually has a calving front

Commit: 08a1d44e5a3823a0186749e68ba1bcf7ec9f28c2
https://github.com/pism/pism/commit/08a1d44e5a3823a0186749e68ba1bcf7ec9f28c2
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-03-08 (Mon, 08 Mar 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh

Log Message:
-----------
PICO: Added function to find the two neighbor drainage basins

Commit: e06427712a5bf2874f741ca54067379c9a1b0c40
https://github.com/pism/pism/commit/e06427712a5bf2874f741ca54067379c9a1b0c40
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-03-08 (Mon, 08 Mar 2021)

Changed paths:
M test/miscellaneous.py

Log Message:
-----------
Improve some regression tests

Commit: 145df8041ee07227f80307322af76db1dbbb0cc4
https://github.com/pism/pism/commit/145df8041ee07227f80307322af76db1dbbb0cc4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-03-08 (Mon, 08 Mar 2021)

Changed paths:
M doc/sphinx/installation/code/petsc.sh

Log Message:
-----------
Update the PETSc build script: add hypre and MUMPS

Commit: d9cbd37161e05166e6d37b4d7863cbe434f14a27
https://github.com/pism/pism/commit/d9cbd37161e05166e6d37b4d7863cbe434f14a27
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-03-08 (Mon, 08 Mar 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Set option prefixes for other PETSc objects used by the Blatter solver

Commit: 0967760b52c58ead5ee64c597403c159b7c316c7
https://github.com/pism/pism/commit/0967760b52c58ead5ee64c597403c159b7c316c7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-03-08 (Mon, 08 Mar 2021)

Changed paths:
M doc/ice-bib.bib
M doc/sphinx/global.txt
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst

Log Message:
-----------
Document preconditioner options that seem to work in parallel

Commit: bf86537bb373f1d81b31db3e01a83d1ffe374c13
https://github.com/pism/pism/commit/bf86537bb373f1d81b31db3e01a83d1ffe374c13
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-03-10 (Wed, 10 Mar 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh

Log Message:
-----------
PICO: Added function to split shelf_mask for ice shelves spread over non-neighboring basins with calving fronts in those basins. Needs modularization, clean up and documentation!

Commit: 6bd7a67e9d99bd6381892fe56daa2b23f71bf2cd
https://github.com/pism/pism/commit/6bd7a67e9d99bd6381892fe56daa2b23f71bf2cd
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-03-10 (Wed, 10 Mar 2021)

Changed paths:
M doc/ice-bib.bib
M doc/sphinx/global.txt
M doc/sphinx/installation/code/petsc.sh
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst
M src/rheology/FlowLaw.cc
M src/rheology/FlowLaw.hh
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/util/grid_hierarchy.cc
M src/stressbalance/blatter/util/grid_hierarchy.hh
M test/miscellaneous.py

Log Message:
-----------
Merge branch 'dev' of ssh://github.com/pism/pism into pik/pico_merge

Commit: 1712ae809798c09c5c381153cd51031f90cb1efd
https://github.com/pism/pism/commit/1712ae809798c09c5c381153cd51031f90cb1efd
Author: Andy Aschwanden <andy.as...@gmail.com>
Date: 2021-03-18 (Thu, 18 Mar 2021)

Changed paths:
M util/nc2cdo.py

Log Message:
-----------
Avoid deprecation warning for newer proj version

Changed order of commands. "+init=epsg:3413" is deprecated and should
be replaced with "epsg"3413".

Commit: 66f186ce668c2bfb4bd6eb6b7755407d5e58b26b
https://github.com/pism/pism/commit/66f186ce668c2bfb4bd6eb6b7755407d5e58b26b
Author: Andy Aschwanden <andy.as...@gmail.com>
Date: 2021-03-18 (Thu, 18 Mar 2021)

Changed paths:
M doc/ice-bib.bib
M doc/sphinx/global.txt
M doc/sphinx/installation/code/petsc.sh
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst
M src/rheology/FlowLaw.cc
M src/rheology/FlowLaw.hh
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/util/grid_hierarchy.cc
M src/stressbalance/blatter/util/grid_hierarchy.hh
M test/miscellaneous.py

Log Message:
-----------
Merge branch 'dev' of https://github.com/pism/pism into dev

Commit: 24f15f68fc02864701175f259215716a0b96333d
https://github.com/pism/pism/commit/24f15f68fc02864701175f259215716a0b96333d
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-03-18 (Thu, 18 Mar 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
PICO: Moved basin_mask and split_ice_shelves() to PicoGeometry.cc

Commit: a3c0f566189a1b846f9239f1d4db29b94116bd44
https://github.com/pism/pism/commit/a3c0f566189a1b846f9239f1d4db29b94116bd44
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-03-19 (Fri, 19 Mar 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
PICO: Modularized get_basin_neighbors() and pass vector m_n_basin_neighbors

Commit: 8c840e0b29adc64091508ea2ab5850c29fda7673
https://github.com/pism/pism/commit/8c840e0b29adc64091508ea2ab5850c29fda7673
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-03-19 (Fri, 19 Mar 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
PICO: Modularized identify_calving_front_connection() and split shelf_mask in split_ice_shelves()

Commit: 93b6b7d6bb61833b9b9920e259225ab2996c8255
https://github.com/pism/pism/commit/93b6b7d6bb61833b9b9920e259225ab2996c8255
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-03-30 (Tue, 30 Mar 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
Fix compilation warnings

Note: only data members of classes should use the "m_" variable name prefix.

See http://pism.github.io/pism/contributing/coding_guidelines.html

Commit: dc5f8f960655db3e053184363f4c0d347436d5c3
https://github.com/pism/pism/commit/dc5f8f960655db3e053184363f4c0d347436d5c3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-03-30 (Tue, 30 Mar 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
A fix for my previous fix

- move the get_basin_neighbors() call to init()
- rename init_impl() to init()
- add placeholders for documenting comments
- remove edge_p() and use grid_edge() instead

Commit: 9c32530d7d4707afc3103a628c85950220d9ce10
https://github.com/pism/pism/commit/9c32530d7d4707afc3103a628c85950220d9ce10
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-04-01 (Thu, 01 Apr 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc
A test/test_pico_split/run_test.sh

Log Message:
-----------
PICO: Added some in-line description of the functions and a test case

Commit: 4916a2c727ec3a6e60bbb98ee8e4e44a7d2ab902
https://github.com/pism/pism/commit/4916a2c727ec3a6e60bbb98ee8e4e44a7d2ab902
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-04-09 (Fri, 09 Apr 2021)

Changed paths:
A test/test_pico_split/bedmap2_schmidtko14_50km.nc
M test/test_pico_split/run_test.sh

Log Message:
-----------
PICO: Added simple bash test for new PICO functionality

Commit: 9ac516a955cf51b3deeef43a9c10aa92ce1261c0
https://github.com/pism/pism/commit/9ac516a955cf51b3deeef43a9c10aa92ce1261c0
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-04-12 (Mon, 12 Apr 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/climate_forcing/ocean.rst

Log Message:
-----------
PICO: Add two lines to manual and CHANGES

Commit: 0dea06ff4309fbbf9a05ced3cf4cdba4ad281af4
https://github.com/pism/pism/commit/0dea06ff4309fbbf9a05ced3cf4cdba4ad281af4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-04-14 (Wed, 14 Apr 2021)

Changed paths:
M src/util/io/File.cc

Log Message:
-----------
Improve error messages about unsupported I/O backends

Commit: 1a9270461cfc08ea8b2421ab5ff290cd6d932f13
https://github.com/pism/pism/commit/1a9270461cfc08ea8b2421ab5ff290cd6d932f13
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-04-16 (Fri, 16 Apr 2021)

Changed paths:
M src/rheology/FlowLaw.cc
M src/rheology/FlowLaw.hh
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/ShallowStressBalance.hh
M src/stressbalance/StressBalance.cc
M src/stressbalance/sia/SIAFD.cc
M src/stressbalance/sia/SIAFD.hh
M src/stressbalance/ssa/SSA.cc
M src/stressbalance/ssa/SSAFD.cc

Log Message:
-----------
Remove FlowLaw::enhancement_factor() and enhancement_factor_interglacial()

The code using flow enhancement factors can get their values directly from the
configuration database instead of a FlowLaw instance.

Commit: abb1dd693722b5d707f9edb2b0734081512fce69
https://github.com/pism/pism/commit/abb1dd693722b5d707f9edb2b0734081512fce69
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-04-16 (Fri, 16 Apr 2021)

Changed paths:
M src/pism_config.cdl

Log Message:
-----------
Only SIA supports E-age coupling

Commit: a6e926b56b1e891406286c440e20860efd493cea
https://github.com/pism/pism/commit/a6e926b56b1e891406286c440e20860efd493cea
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-04-16 (Fri, 16 Apr 2021)

Changed paths:
M src/pism_config.cdl
M src/rheology/FlowLaw.cc
M src/rheology/FlowLaw.hh
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/ShallowStressBalance.hh
M src/stressbalance/StressBalance.cc
M src/stressbalance/sia/SIAFD.cc
M src/stressbalance/sia/SIAFD.hh
M src/stressbalance/ssa/SSA.cc
M src/stressbalance/ssa/SSAFD.cc

Log Message:
-----------
Merge branch 'ckhrulev/flow-enhancement' into dev

Commit: ddd406d5cdf1fd79a51a67a7f4c8f00b43ddfe50
https://github.com/pism/pism/commit/ddd406d5cdf1fd79a51a67a7f4c8f00b43ddfe50
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-04-16 (Fri, 16 Apr 2021)

Changed paths:
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/frontretreat.cc
M src/icemodel/initialization.cc
M src/pism_config.cdl

Log Message:
-----------
Implement calving.rate_scaling.file

... which reads in the time-dependent scalar variable "frac_calving_rate" from a file and
scales calving rates from eigen calving, von Mises, and Hayhurst's calving mechanisms.

Needs testing and documentation.

Commit: 015419e7fc060cddd69d026a0e3113c783019e1e
https://github.com/pism/pism/commit/015419e7fc060cddd69d026a0e3113c783019e1e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-04-16 (Fri, 16 Apr 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/marine/calving.rst
M doc/sphinx/manual/modeling-choices/marine/pik.rst
M src/pism_config.cdl

Log Message:
-----------
Improve the calving section in the manual

Commit: 6aec60d5fe173691fa7f423fb62f3489003b78b5
https://github.com/pism/pism/commit/6aec60d5fe173691fa7f423fb62f3489003b78b5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-04-16 (Fri, 16 Apr 2021)

Changed paths:
M CHANGES.rst

Log Message:
-----------
Update the change log

Commit: be5fe6c05155a50a636d9ebb2177726779ea6a75
https://github.com/pism/pism/commit/be5fe6c05155a50a636d9ebb2177726779ea6a75
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-04-16 (Fri, 16 Apr 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/manual/modeling-choices/marine/calving.rst
M doc/sphinx/manual/modeling-choices/marine/pik.rst
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/frontretreat.cc
M src/icemodel/initialization.cc
M src/pism_config.cdl

Log Message:
-----------
Merge branch 'ckhrulev/calving-rate-scaling' into dev

Commit: 9b43b58841619a8d9628b593e9a1a7befff12304
https://github.com/pism/pism/commit/9b43b58841619a8d9628b593e9a1a7befff12304
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-04-19 (Mon, 19 Apr 2021)

Changed paths:
M src/coupler/ocean/PicoPhysics.cc

Log Message:
-----------
Update PicoPhysics.cc

See #454

Commit: a5bf7f09d5dc8347c6961cd98b47c7c3a0c304f6
https://github.com/pism/pism/commit/a5bf7f09d5dc8347c6961cd98b47c7c3a0c304f6
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-04-30 (Fri, 30 Apr 2021)

Changed paths:
M src/rheology/GPBLD.cc
M src/rheology/GPBLD.hh

Log Message:
-----------
GPBLD flow law: a small optimization of the n=3 case

Commit: dbb302941ba7879d6651c20bcaa7ff987bbeeaff
https://github.com/pism/pism/commit/dbb302941ba7879d6651c20bcaa7ff987bbeeaff
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-04-30 (Fri, 30 Apr 2021)

Changed paths:
M src/rheology/GoldsbyKohlstedt.cc
M src/rheology/GoldsbyKohlstedt.hh

Log Message:
-----------
Remove some unused code

Commit: a0c3cf5db08e1e1dff7e60ac4886dbac6f8881ce
https://github.com/pism/pism/commit/a0c3cf5db08e1e1dff7e60ac4886dbac6f8881ce
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Remove the unnecessary context struct

Commit: fa167885b5e6f4756863966e083e4f80e0ebb99a
https://github.com/pism/pism/commit/fa167885b5e6f4756863966e083e4f80e0ebb99a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Cleaning up solver initialization

Commit: 9b818bd3724a22a490699e6f4fd720e41f69badf
https://github.com/pism/pism/commit/9b818bd3724a22a490699e6f4fd720e41f69badf
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc
M src/stressbalance/blatter/util/grid_hierarchy.cc
M src/stressbalance/blatter/verification/BlatterTestCFBC.cc

Log Message:
-----------
Use pism::IceModelVec2Struct to store 2D inputs

Commit: c7a84e455227737461bd35fad2b22c9c4a5ab348
https://github.com/pism/pism/commit/c7a84e455227737461bd35fad2b22c9c4a5ab348
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Some more cleanup

Commit: 18c8be979bea2dae60a18fc3225b9ef625bbc99c
https://github.com/pism/pism/commit/18c8be979bea2dae60a18fc3225b9ef625bbc99c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Use the coarse (2-node) vertical grid to get an initial guess

Commit: b48baff324b97ee351049d4c741993d3f954edbd
https://github.com/pism/pism/commit/b48baff324b97ee351049d4c741993d3f954edbd
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Revert "Use the coarse (2-node) vertical grid to get an initial guess"

This reverts commit a1d45abf566b95730a524944c7fad259df580cf7.

Using the coarse (2-node) vertical grid as a crude version of grid sequencing does not
seem to be effective. I'm saving this code in case I decide to try implementing proper
grid sequencing later.

Commit: b2ecf7181d5fc69c7457581e04d3cb4897e6f46c
https://github.com/pism/pism/commit/b2ecf7181d5fc69c7457581e04d3cb4897e6f46c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/rheology/FlowLaw.cc
M src/rheology/FlowLaw.hh

Log Message:
-----------
FlowLaw: eps (ice viscosity regularization) is a function argument

This should make it easier to implement parameter continuation

Commit: 03a617fbe020a478c44df0b91528664507987054
https://github.com/pism/pism/commit/03a617fbe020a478c44df0b91528664507987054
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Cosmetic change

Commit: 844161044afdef92ebe7839f435f48baf950db11
https://github.com/pism/pism/commit/844161044afdef92ebe7839f435f48baf950db11
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Initial implementation of the parameter continuation

... using the viscosity regularization as the parameter.

Commit: dc271b3c7f9cbe0a105bfff5781f80add9c32488
https://github.com/pism/pism/commit/dc271b3c7f9cbe0a105bfff5781f80add9c32488
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Add a Vec storing the previous initial guess

... during parameter continuation.

Commit: 7fc83a4b27832e09a9d7e8d6e3b870e9feefdc61
https://github.com/pism/pism/commit/7fc83a4b27832e09a9d7e8d6e3b870e9feefdc61
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Implement natural parameter continuation

... following LOCA (i.e. Trilinos).

Commit: 329d388d8d0567ef213becdaaa7456db0b38d3e6
https://github.com/pism/pism/commit/329d388d8d0567ef213becdaaa7456db0b38d3e6
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Use zero initial guess for the parameter continuation

The initial guess for the problem with the desired value of the regularization parameter
usually is not a good initial guess for the over-regularized problem at the beginning of
the parameter continuation process.

Commit: 10addb8fe3b871455fc16cc442cf346ad4af2e87
https://github.com/pism/pism/commit/10addb8fe3b871455fc16cc442cf346ad4af2e87
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Start with a smaller lambda and reduce the aggressiveness factor

Commit: e975c4fab3b5ec9be2e24722a9ab23ce8da28044
https://github.com/pism/pism/commit/e975c4fab3b5ec9be2e24722a9ab23ce8da28044
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Improve stdout reporting

Commit: 18de20581e13d90df52b35bbf9cf897478aa6847
https://github.com/pism/pism/commit/18de20581e13d90df52b35bbf9cf897478aa6847
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M doc/ice-bib.bib
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst

Log Message:
-----------
Add the stub of the parameter continuation section

Commit: 396d42c2a9aaa1f52c39a7b9f5559d76c2d3f8b1
https://github.com/pism/pism/commit/396d42c2a9aaa1f52c39a7b9f5559d76c2d3f8b1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
A bit of cleanup

Commit: 5dd9a2a7b5411adea00dbe0beb6ebde032e50fb6
https://github.com/pism/pism/commit/5dd9a2a7b5411adea00dbe0beb6ebde032e50fb6
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/util/grid_hierarchy.cc
M src/stressbalance/blatter/util/grid_hierarchy.hh

Log Message:
-----------
Remove pism::DMInfo (it is no longer needed)

Commit: b8451dcf9971888a74cf10f9738c471182e3e4f0
https://github.com/pism/pism/commit/b8451dcf9971888a74cf10f9738c471182e3e4f0
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Add FIXME comments

Commit: 2ea9d6694290224d5b601d1813b69e4dc4acb90c
https://github.com/pism/pism/commit/2ea9d6694290224d5b601d1813b69e4dc4acb90c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Improve stdout reporting

Commit: b66016c56af0bc7a8ab76c74156e38fe0576ee73
https://github.com/pism/pism/commit/b66016c56af0bc7a8ab76c74156e38fe0576ee73
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M test/blatter_verification.py

Log Message:
-----------
Improve verification tests a bit (mostly cosmetic changes)

Commit: e6ae01ce247948dd3b94a32b349c169a13a49d1c
https://github.com/pism/pism/commit/e6ae01ce247948dd3b94a32b349c169a13a49d1c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc
M src/stressbalance/blatter/verification/BlatterTestCFBC.cc
M src/stressbalance/blatter/verification/BlatterTestHalfar.cc
M src/stressbalance/blatter/verification/BlatterTestXY.cc
M src/stressbalance/blatter/verification/BlatterTestXZ.cc
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc

Log Message:
-----------
Scale quadrature weights

Commit: b08edc9108da568798751c7e9525ad997a440d12
https://github.com/pism/pism/commit/b08edc9108da568798751c7e9525ad997a440d12
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/jacobian.cc

Log Message:
-----------
Set the object name for the Jacobian matrix

Commit: 7db0e8d0be0917ec343bbc0610d04b545eff919b
https://github.com/pism/pism/commit/7db0e8d0be0917ec343bbc0610d04b545eff919b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
A cosmetic change in the residual code

Commit: ee9ad4adf89016f7084003810648ec5eead55e50
https://github.com/pism/pism/commit/ee9ad4adf89016f7084003810648ec5eead55e50
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Fix a bug in the initialization of 2D inputs

Commit: 91241bbd641b289d53925716ecf9affd6c6ab5f9
https://github.com/pism/pism/commit/91241bbd641b289d53925716ecf9affd6c6ab5f9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Improve reporting of mesh statistics

Commit: ad45f52edb473b2cdf9cc9ef163c8ea91e865851
https://github.com/pism/pism/commit/ad45f52edb473b2cdf9cc9ef163c8ea91e865851
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Report the number of KSP iterations on the coarse MG level

We would need to add extra code to sum up the number of iterations for the whole
SNESSolve() call, so it reports the number of KSP iterations on the coarse level needed by
the last KSP iteration in the last SNES iteration instead (for simplicity).

Commit: e18fc1897ed9eeb212452b9c8eee4ac4b9529c9f
https://github.com/pism/pism/commit/e18fc1897ed9eeb212452b9c8eee4ac4b9529c9f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/jacobian.cc

Log Message:
-----------
Set MAT_SUBSET_OFF_PROC_ENTRIES

Commit: 6379a7c26edab77b1d16f083d3006b32c8447691
https://github.com/pism/pism/commit/6379a7c26edab77b1d16f083d3006b32c8447691
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/jacobian.cc

Log Message:
-----------
Move MatSetOption() calls

Commit: f3c86c0c78a37b8de76322ccc32c96bc16ffc760
https://github.com/pism/pism/commit/f3c86c0c78a37b8de76322ccc32c96bc16ffc760
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Increase the maximum number of continuation steps

The parameter continuation code seems to work but does not provide any benefit, i.e. does
not decrease the number of SNES iterations needed for convergence.

Commit: 877d4e7af679f516a54b1ade5fe0ffa6a8eefc33
https://github.com/pism/pism/commit/877d4e7af679f516a54b1ade5fe0ffa6a8eefc33
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Report vertical grid resolution

Commit: 5d3b42f80c8f5e37ff391179bfab8f2b8eadaa6d
https://github.com/pism/pism/commit/5d3b42f80c8f5e37ff391179bfab8f2b8eadaa6d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Improve stdout reporting

Commit: d79ac3b47e963b567468f6bb8542473aa1eedccf
https://github.com/pism/pism/commit/d79ac3b47e963b567468f6bb8542473aa1eedccf
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M doc/sphinx/installation/code/petsc.sh

Log Message:
-----------
Update the PETSc build script

Commit: 38121c7c9321a4ae4aeaa0eb2a014607d69130b1
https://github.com/pism/pism/commit/38121c7c9321a4ae4aeaa0eb2a014607d69130b1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
A examples/arolla/Makefile
A examples/arolla/README.md
A examples/arolla/convert.py
A examples/arolla/plot.py
A examples/arolla/run.sh

Log Message:
-----------
Add examples/arolla, i.e. ISMIP-HOM Experiment E

Commit: 7811683572d5c54abc0d6a77b799ac6a06b2fe74
https://github.com/pism/pism/commit/7811683572d5c54abc0d6a77b799ac6a06b2fe74
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M src/stressbalance/ShallowStressBalance.cc

Log Message:
-----------
Cosmetic changes

Commit: b335c3150ebcbfd4194f457ed3f02b18ca7f9283
https://github.com/pism/pism/commit/b335c3150ebcbfd4194f457ed3f02b18ca7f9283
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M test/ismip-hom/Makefile
M test/ismip-hom/plot-ismiphom.py

Log Message:
-----------
Cleaning up ISMIP-HOM experiments A-D

Commit: fc3e05b67093087dcdfc4fec759dfffe0113b0da
https://github.com/pism/pism/commit/fc3e05b67093087dcdfc4fec759dfffe0113b0da
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
M test/ismip-hom/convert-ismiphom.py
M test/ismip-hom/plot-ismiphom.py

Log Message:
-----------
Switch from Bokeh to Matplotlib

Commit: 15fa579499df2ba52548ff0b9e82ff9ef5a9fdfb
https://github.com/pism/pism/commit/15fa579499df2ba52548ff0b9e82ff9ef5a9fdfb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-04 (Tue, 04 May 2021)

Changed paths:
R examples/arolla/Makefile
R examples/arolla/README.md
R examples/arolla/convert.py
R examples/arolla/plot.py
R examples/arolla/run.sh
A examples/ismip-hom/README.rst
A examples/ismip-hom/abcd/Makefile
A examples/ismip-hom/abcd/README.rst
A examples/ismip-hom/abcd/convert-ismiphom.py
A examples/ismip-hom/abcd/plot-ismiphom.py
A examples/ismip-hom/abcd/run-ismiphom.py
A examples/ismip-hom/e-arolla/Makefile
A examples/ismip-hom/e-arolla/README.md
A examples/ismip-hom/e-arolla/convert.py
A examples/ismip-hom/e-arolla/plot.py
A examples/ismip-hom/e-arolla/run.sh
R test/ismip-hom/Makefile
R test/ismip-hom/README.rst
R test/ismip-hom/convert-ismiphom.py
R test/ismip-hom/ismip-hom-a-5km.png
R test/ismip-hom/plot-ismiphom.py
R test/ismip-hom/run-ismiphom.py

Log Message:
-----------
Re-organize ISMIP-HOM scripts

Commit: 55f03f69620a935ffef6357e08969268a9478058
https://github.com/pism/pism/commit/55f03f69620a935ffef6357e08969268a9478058
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-05 (Wed, 05 May 2021)

Changed paths:
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-a.png
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-b.png
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-c.png
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-d.png
A doc/sphinx/manual/simplified-geometry/figures/uvel_no_slip.png
A doc/sphinx/manual/simplified-geometry/figures/uvel_sliding.png
A doc/sphinx/manual/simplified-geometry/figures/uvelsurf.png
M doc/sphinx/manual/simplified-geometry/index.rst
A doc/sphinx/manual/simplified-geometry/ismip-hom.rst
M examples/ismip-hom/abcd/plot-ismiphom.py
M examples/ismip-hom/e-arolla/plot.py

Log Message:
-----------
Add the ISMIP-HOM section to the manual

Commit: 9769bfe14ba468e2dc66e3c85b57b22487dda528
https://github.com/pism/pism/commit/9769bfe14ba468e2dc66e3c85b57b22487dda528
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-05 (Wed, 05 May 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst

Log Message:
-----------
Remove the parameter continuation section (the code is not ready)

Commit: dec8cebdbb569d545ed33598ff7a66056f576ddf
https://github.com/pism/pism/commit/dec8cebdbb569d545ed33598ff7a66056f576ddf
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-05 (Wed, 05 May 2021)

Changed paths:
M doc/ice-bib.bib
M doc/sphinx/installation/code/petsc.sh
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-a.png
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-b.png
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-c.png
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-d.png
A doc/sphinx/manual/simplified-geometry/figures/uvel_no_slip.png
A doc/sphinx/manual/simplified-geometry/figures/uvel_sliding.png
A doc/sphinx/manual/simplified-geometry/figures/uvelsurf.png
M doc/sphinx/manual/simplified-geometry/index.rst
A doc/sphinx/manual/simplified-geometry/ismip-hom.rst
A examples/ismip-hom/README.rst
A examples/ismip-hom/abcd/Makefile
A examples/ismip-hom/abcd/README.rst
A examples/ismip-hom/abcd/convert-ismiphom.py
A examples/ismip-hom/abcd/plot-ismiphom.py
A examples/ismip-hom/abcd/run-ismiphom.py
A examples/ismip-hom/e-arolla/Makefile
A examples/ismip-hom/e-arolla/README.md
A examples/ismip-hom/e-arolla/convert.py
A examples/ismip-hom/e-arolla/plot.py
A examples/ismip-hom/e-arolla/run.sh
M src/rheology/FlowLaw.cc
M src/rheology/FlowLaw.hh
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc
M src/stressbalance/blatter/util/grid_hierarchy.cc
M src/stressbalance/blatter/util/grid_hierarchy.hh
M src/stressbalance/blatter/verification/BlatterTestCFBC.cc
M src/stressbalance/blatter/verification/BlatterTestHalfar.cc
M src/stressbalance/blatter/verification/BlatterTestXY.cc
M src/stressbalance/blatter/verification/BlatterTestXZ.cc
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc
M test/blatter_verification.py
R test/ismip-hom/Makefile
R test/ismip-hom/README.rst
R test/ismip-hom/convert-ismiphom.py
R test/ismip-hom/ismip-hom-a-5km.png
R test/ismip-hom/plot-ismiphom.py
R test/ismip-hom/run-ismiphom.py

Log Message:
-----------
Merge branch 'ckhrulev/bp-improvements' into dev

Commit: b90fe34307f500ad38566f82b9ad9f1d8f9094b9
https://github.com/pism/pism/commit/b90fe34307f500ad38566f82b9ad9f1d8f9094b9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-07 (Fri, 07 May 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh

Log Message:
-----------
Temporarily disable -bp_snes_ksp_ew to increase robustness

- disable it when starting from a zero initial guess, and
- disable it if the solver failed with -bp_snes_ksp_ew.

Sometimes Newton iterations started from a bad initial guess fail if the linear system is
not solved accurately enough. One could avoid -bp_snes_ksp_ew altogether, but then we
would over-solve the linear system when we have a good initial guess an a lower accuracy
is sufficient.

Commit: 1e5ab2742a1745a75db94fa6be6685965de796ae
https://github.com/pism/pism/commit/1e5ab2742a1745a75db94fa6be6685965de796ae
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-07 (Fri, 07 May 2021)

Changed paths:
A doc/sphinx/installation/code/petsc-mkl-mumps-hypre.sh
A doc/sphinx/installation/code/petsc-mumps-hypre.sh
M doc/sphinx/installation/code/petsc.sh

Log Message:
-----------
Update PETSc build scripts

Commit: f2ed7fbab5f26598f99a976ada865b4a116d596f
https://github.com/pism/pism/commit/f2ed7fbab5f26598f99a976ada865b4a116d596f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-07 (Fri, 07 May 2021)

Changed paths:
M site-packages/PISM/testing.py
M test/regression/atmosphere_models.py
M test/regression/ocean_models.py

Log Message:
-----------
Use unique file names in atmosphere and ocean model tests

Commit: f9442d0428c15bda03664a66280e16538ce24fb8
https://github.com/pism/pism/commit/f9442d0428c15bda03664a66280e16538ce24fb8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-10 (Mon, 10 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Fix stdout reporting when starting parameter continuation

Commit: 6b28ebd85a9b9dc5f9eb79caacc98da3dd9bb720
https://github.com/pism/pism/commit/6b28ebd85a9b9dc5f9eb79caacc98da3dd9bb720
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-11 (Tue, 11 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc

Log Message:
-----------
Implement the flow enhancement factor in the Blatter solver

Now stress_balance.blatter.enhancement_factor actually does something.

Commit: e1a1783896a544169065945322abbb36891963dc
https://github.com/pism/pism/commit/e1a1783896a544169065945322abbb36891963dc
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-11 (Tue, 11 May 2021)

Changed paths:
M doc/sphinx/installation/code/petsc-mumps-hypre.sh

Log Message:
-----------
Add more external packages when building PETSc with MUMPS and hypre

Commit: 2494fd7399f1112958f9f3ba47c778d8094855f3
https://github.com/pism/pism/commit/2494fd7399f1112958f9f3ba47c778d8094855f3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-14 (Fri, 14 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Improve the recovery code

We don't need to reset the initial guess if the solver failed because it took too many
iterations.

Commit: bb6e0106f6ad6e5244f76620e4bfeff03abdad44
https://github.com/pism/pism/commit/bb6e0106f6ad6e5244f76620e4bfeff03abdad44
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-14 (Fri, 14 May 2021)

Changed paths:
M doc/pismpython/inverse/design.rst
M doc/pismpython/inverse/index.rst
M doc/pismpython/inverse/pism_ssa.rst
M doc/pismpython/inverse/pismi.rst
M doc/pismpython/inverse/refresher.rst
M doc/pismpython/inverse/ssa_forward.rst
M doc/pismpython/inverse/ssa_inverse.rst
M doc/sphinx/CMakeLists.txt
M doc/sphinx/climate_forcing/surface.rst
M doc/sphinx/conf.py
M doc/sphinx/manual/modeling-choices/dynamics/rheology.rst
M doc/sphinx/manual/modeling-choices/marine/melange.rst
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst
M doc/sphinx/manual/modeling-choices/subglacier/hydrology.rst
A doc/sphinx/math-definitions.tex
R doc/sphinx/math-definitions.txt
M doc/sphinx/pism_config.py
M doc/sphinx/technical/blatter-pattyn.rst
M doc/sphinx/technical/bombproof.rst
M doc/sphinx/technical/ssafd-cfbc.rst
M doc/sphinx/technical/steady-hydrology.rst
M doc/sphinx/technical/vertchange.rst

Log Message:
-----------
Fix the PDF version of the manual

- Fix pism_config.py ("make manual_pdf" was broken).
- Put all \newcommands into math-definitions.tex and use it for *both* HTML and LaTeX
versions.

Commit: 55c172e7677ca1cbd62800f82b87357bb034e00c
https://github.com/pism/pism/commit/55c172e7677ca1cbd62800f82b87357bb034e00c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-14 (Fri, 14 May 2021)

Changed paths:
M examples/ismip-hom/e-arolla/run.sh

Log Message:
-----------
Make it easier to adjust the number of vertical levels

Commit: 226ed09fc8f84b73c8837f0ef768b95489f711f8
https://github.com/pism/pism/commit/226ed09fc8f84b73c8837f0ef768b95489f711f8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-17 (Mon, 17 May 2021)

Changed paths:
M examples/ismip-hom/e-arolla/run.sh

Log Message:
-----------
Use more vertical levels and save more diagnostics

This makes it easier to look at the *vertical* velocity within the ice.

Commit: 02ee5087ce238cfc615050a145d1bbb9c234493c
https://github.com/pism/pism/commit/02ee5087ce238cfc615050a145d1bbb9c234493c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-17 (Mon, 17 May 2021)

Changed paths:
M src/energy/utilities.cc

Log Message:
-----------
Improve an error message (see #483)

Now PISM stops with a message like

PISM ERROR: Negative upward heat flux (-0.000144 W m-2) through the bottom of the ice column
is not allowed by PISM's ice temperature bootstrapping method.
Please check the temperature of the bedrock thermal layer at i=25, j=77.

Commit: 2c44c4cac7e17ffc8d3cec9a2d26165b36534dc6
https://github.com/pism/pism/commit/2c44c4cac7e17ffc8d3cec9a2d26165b36534dc6
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-20 (Thu, 20 May 2021)

Changed paths:
M examples/ismip-hom/e-arolla/Makefile
M examples/ismip-hom/e-arolla/convert.py
M examples/ismip-hom/e-arolla/plot.py
M examples/ismip-hom/e-arolla/run.sh

Log Message:
-----------
Extend the ISMIP-HOM Exp E setup

- support grid refinement in x and z
- run in parallel (now it depends on a parallel direct solver)
- extract flow line data using NCO

Commit: 4293172b4146b79bde30a0249957717782ed0b81
https://github.com/pism/pism/commit/4293172b4146b79bde30a0249957717782ed0b81
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-20 (Thu, 20 May 2021)

Changed paths:
M doc/ice-bib.bib

Log Message:
-----------
Add "institution" to Salinger2002

pybtex is picky and thinks that it is required.

Commit: ced3f09721450bd29ceb6a6de2194db705deaa98
https://github.com/pism/pism/commit/ced3f09721450bd29ceb6a6de2194db705deaa98
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-20 (Thu, 20 May 2021)

Changed paths:
M doc/Makefile
M doc/acknowledge.py

Log Message:
-----------
Remind users to specify the *version* of PISM in publications

Commit: e10faf7ffdfdf6fcf9b4a4ee71c9b03f893929be
https://github.com/pism/pism/commit/e10faf7ffdfdf6fcf9b4a4ee71c9b03f893929be
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-21 (Fri, 21 May 2021)

Changed paths:
M src/stressbalance/WeertmanSliding.cc

Log Message:
-----------
Fix a sign error (and units) in the Weertman sliding law

Equation 5 in Tomkin2007 is wrong.

Commit: 55917dac454355a601d4bc49712710d3d64a4bec
https://github.com/pism/pism/commit/55917dac454355a601d4bc49712710d3d64a4bec
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-21 (Fri, 21 May 2021)

Changed paths:
M doc/sphinx/pism_config.py

Log Message:
-----------
Fix pism_config.py

(Configuration parameters *in the text* did not show properly.

Commit: 3ce7691fe1cc43f4b2c43354ad48c2f8e4f5a489
https://github.com/pism/pism/commit/3ce7691fe1cc43f4b2c43354ad48c2f8e4f5a489
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-21 (Fri, 21 May 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst
M src/pism_config.cdl

Log Message:
-----------
Re-organize the stress balance section of the manual

Commit: 866bf6723376cc0259ff8da9d533901956571fea
https://github.com/pism/pism/commit/866bf6723376cc0259ff8da9d533901956571fea
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-21 (Fri, 21 May 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst
M doc/sphinx/technical/blatter-pattyn.rst

Log Message:
-----------
Document the use of time_stepping.adaptive_ratio with the BP solver

Commit: 99af666099dbea544d586d3804f2fa4453e79ca4
https://github.com/pism/pism/commit/99af666099dbea544d586d3804f2fa4453e79ca4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-21 (Fri, 21 May 2021)

Changed paths:
M doc/ice-bib.bib
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst

Log Message:
-----------
Mention optimized BLAS and LAPACK

Commit: db24010810b5b3e36727c087c0a86858d3cd69af
https://github.com/pism/pism/commit/db24010810b5b3e36727c087c0a86858d3cd69af
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-21 (Fri, 21 May 2021)

Changed paths:
M src/stressbalance/blatter/Blatter.cc

Log Message:
-----------
Improve wording in a message printer by the solver

Commit: 7afd6f16e9a1b9dc24a2c120def7805ad483648e
https://github.com/pism/pism/commit/7afd6f16e9a1b9dc24a2c120def7805ad483648e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-24 (Mon, 24 May 2021)

Changed paths:
M doc/sphinx/pism_config.py

Log Message:
-----------
Fix pism_config.py again

Now both "make manual_html" and "make manual_pdf" work as expected.

Commit: e66212029f7fd1ace5b2c6d18a26512fe909dc0b
https://github.com/pism/pism/commit/e66212029f7fd1ace5b2c6d18a26512fe909dc0b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-24 (Mon, 24 May 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/dynamics/age.rst
A doc/sphinx/manual/modeling-choices/dynamics/blatter.rst
M doc/sphinx/manual/modeling-choices/dynamics/index.rst
M doc/sphinx/manual/modeling-choices/dynamics/rheology.rst
A doc/sphinx/manual/modeling-choices/dynamics/sia.rst
A doc/sphinx/manual/modeling-choices/dynamics/ssa.rst
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst
R doc/sphinx/manual/modeling-choices/dynamics/surface-gradient.rst
A doc/sphinx/manual/modeling-choices/dynamics/weertman.rst
R doc/sphinx/manual/modeling-choices/subglacier/bed-roughness.rst
M doc/sphinx/manual/modeling-choices/subglacier/index.rst
M src/pism_config.cdl

Log Message:
-----------
Re-organize stress balance sections of the manual

Commit: 6a835a9ea18d06f880603e88fa16307b8cae5bb9
https://github.com/pism/pism/commit/6a835a9ea18d06f880603e88fa16307b8cae5bb9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-24 (Mon, 24 May 2021)

Changed paths:
M src/stressbalance/ssa/SSA.cc

Log Message:
-----------
Update a doxygen comment

Commit: bbe39c2f1faa4a22965d1763bb4e778f52408a57
https://github.com/pism/pism/commit/bbe39c2f1faa4a22965d1763bb4e778f52408a57
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-24 (Mon, 24 May 2021)

Changed paths:
M doc/sphinx/climate_forcing/atmosphere.rst
M doc/sphinx/climate_forcing/surface.rst
M doc/sphinx/climate_forcing/testing.rst
M doc/sphinx/technical/blatter-pattyn.rst

Log Message:
-----------
More edits in the manual

Commit: 743e8d5735513cf903f66f7b5ba801d72bb257d8
https://github.com/pism/pism/commit/743e8d5735513cf903f66f7b5ba801d72bb257d8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-24 (Mon, 24 May 2021)

Changed paths:
M docker/CMakeLists.txt
A docker/ubuntu-ci/CMakeLists.txt
A docker/ubuntu-ci/Dockerfile.in
A docker/ubuntu-ci/README.rst
R docker/ubuntu/CMakeLists.txt
R docker/ubuntu/Dockerfile.in
R docker/ubuntu/README.rst

Log Message:
-----------
Move the Docker setup for CI to docker/ubuntu-ci

Commit: 2a53f770315990d4b778cc851c9c5e153f88abdd
https://github.com/pism/pism/commit/2a53f770315990d4b778cc851c9c5e153f88abdd
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-24 (Mon, 24 May 2021)

Changed paths:
M doc/sphinx/installation/code/install_libraries.sh
M docker/CMakeLists.txt
A docker/ubuntu-minimal/CMakeLists.txt
A docker/ubuntu-minimal/Dockerfile.in
A docker/ubuntu-minimal/README.rst

Log Message:
-----------
Start work on a new Docker setup

... that will ensure that installation instructions in the manual are up to date.

Commit: 6f4ea1cd6ead1da43426c18d27715af66581e723
https://github.com/pism/pism/commit/6f4ea1cd6ead1da43426c18d27715af66581e723
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-24 (Mon, 24 May 2021)

Changed paths:
A doc/sphinx/installation/code/pism.sh

Log Message:
-----------
Add a forgotten script

Commit: 35dc8456434dcf2ff36da3d8bfa56b0bbec117cf
https://github.com/pism/pism/commit/35dc8456434dcf2ff36da3d8bfa56b0bbec117cf
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-24 (Mon, 24 May 2021)

Changed paths:
M doc/sphinx/installation/code/pism.sh
M docker/ubuntu-minimal/Dockerfile.in

Log Message:
-----------
Installs just fine, but one regression test fails

Commit: 8a6c6b065f25dd1630bc46057c6e54fac9ef4684
https://github.com/pism/pism/commit/8a6c6b065f25dd1630bc46057c6e54fac9ef4684
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-25 (Tue, 25 May 2021)

Changed paths:
M doc/sphinx/climate_forcing/atmosphere.rst
M doc/sphinx/installation/code/pism.sh
M doc/sphinx/manual/initialization/bootstrapping.rst
M doc/sphinx/manual/initialization/index.rst
M doc/sphinx/manual/initialization/restarting.rst
M doc/sphinx/manual/modeling-choices/computational/grid.rst
M doc/sphinx/manual/modeling-choices/dynamics/blatter.rst
M doc/sphinx/manual/modeling-choices/dynamics/sia.rst
M doc/sphinx/manual/modeling-choices/dynamics/ssa.rst
M doc/sphinx/manual/practical-usage/diagnostic-viewers.rst
M doc/sphinx/manual/practical-usage/flowline.rst
M doc/sphinx/manual/practical-usage/saving-diagnostics.rst
M doc/sphinx/manual/practical-usage/saving-snapshots.rst
M doc/sphinx/manual/practical-usage/saving-time-series.rst
M doc/sphinx/manual/practical-usage/time-stepping.rst
M doc/sphinx/manual/simplified-geometry/mismip3d.rst
M doc/sphinx/manual/std-greenland/grid-sequencing.rst
M doc/sphinx/manual/std-greenland/index.rst
M doc/sphinx/manual/verification/index.rst
M doc/sphinx/math-definitions.tex
M doc/sphinx/technical/blatter-pattyn.rst
M doc/sphinx/technical/bombproof.rst
M doc/sphinx/technical/steady-hydrology.rst
M src/pism_config.cdl

Log Message:
-----------
Numerous edits in the manual

Commit: 9aaf3924a0119934d6ccd421bb461f2e40a129b9
https://github.com/pism/pism/commit/9aaf3924a0119934d6ccd421bb461f2e40a129b9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-25 (Tue, 25 May 2021)

Changed paths:
M docker/ubuntu-minimal/CMakeLists.txt

Log Message:
-----------
Change the name of the Docker image

Commit: 3140763e717b7e70b7afa31eaf766d7a7db13156
https://github.com/pism/pism/commit/3140763e717b7e70b7afa31eaf766d7a7db13156
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-26 (Wed, 26 May 2021)

Changed paths:
M src/icemodel/IceModel.cc

Log Message:
-----------
Use "-o_size medium" when the stress balance update fails

This way the user has more control, e.g. can set output.sizes.medium to save particular
fields.

Commit: a13c83e90d613c29d03cef7d52ce8091df8e7d2b
https://github.com/pism/pism/commit/a13c83e90d613c29d03cef7d52ce8091df8e7d2b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-26 (Wed, 26 May 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/dynamics/blatter.rst

Log Message:
-----------
Mention that "-stress_balance blatter -skip" does not make sense

... because it would not save us much CPU time.

Commit: 136ad081eebc45ab7cf65fb888ff7829850e9538
https://github.com/pism/pism/commit/136ad081eebc45ab7cf65fb888ff7829850e9538
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-26 (Wed, 26 May 2021)

Changed paths:
R doc/sphinx/manual/modeling-choices/dynamics/figures/.DS_Store

Log Message:
-----------
Delete a file added by macOS

Commit: e0df9ea9f8d97e99853725ea45b58248a88e5af3
https://github.com/pism/pism/commit/e0df9ea9f8d97e99853725ea45b58248a88e5af3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-26 (Wed, 26 May 2021)

Changed paths:
M doc/sphinx/Makefile
M doc/sphinx/manual/diagnostics/diagnostics-list.txt
M src/icemodel/diagnostics.cc
M src/icemodel/printout.cc

Log Message:
-----------
Address the max_hor_vel confusion

Commit: df485e676edc951ffd4fcee2c3b7f073f35f3739
https://github.com/pism/pism/commit/df485e676edc951ffd4fcee2c3b7f073f35f3739
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-26 (Wed, 26 May 2021)

Changed paths:
M doc/sphinx/Makefile
M doc/sphinx/installation/debian.rst

Log Message:
-----------
Tweak Ubuntu/Debian installation instructions

Commit: d353ed5a5e2c0a755433f74c3a8f8d1b0b529f14
https://github.com/pism/pism/commit/d353ed5a5e2c0a755433f74c3a8f8d1b0b529f14
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-26 (Wed, 26 May 2021)

Changed paths:
M src/icemodel/timestepping.cc

Log Message:
-----------
Add a FIXME comment

Commit: 71e585d3ce6fecc9fb41cdc268df8c340d6053c8
https://github.com/pism/pism/commit/71e585d3ce6fecc9fb41cdc268df8c340d6053c8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-26 (Wed, 26 May 2021)

Changed paths:
M doc/sphinx/manual/practical-usage/index.rst

Log Message:
-----------
Move the time stepping section up a bit

Commit: 1faf9798bac8d08e3ea9a568be01423c07928b30
https://github.com/pism/pism/commit/1faf9798bac8d08e3ea9a568be01423c07928b30
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-26 (Wed, 26 May 2021)

Changed paths:
M doc/sphinx/manual/practical-usage/time-stepping.rst

Log Message:
-----------
Improve the manual section about adaptive time stepping

Commit: 694e513a6fecc8c4a4806a6bc69dcaed52c2c720
https://github.com/pism/pism/commit/694e513a6fecc8c4a4806a6bc69dcaed52c2c720
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-26 (Wed, 26 May 2021)

Changed paths:
M doc/sphinx/manual/simplified-geometry/eismint-2.rst
M src/pisms.cc

Log Message:
-----------
State that EISMINT II experiments G and H are not supported

Commit: c86c9da98ca557bf6ac365029ae096bac9489a93
https://github.com/pism/pism/commit/c86c9da98ca557bf6ac365029ae096bac9489a93
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-26 (Wed, 26 May 2021)

Changed paths:
M src/coupler/ocean/PicoPhysics.cc

Log Message:
-----------
Merge pull request #482 from pism/pik/pico_rm_assert_pos_Ts

Replace "std::min(T_s, 0.0)" with "T_s".

Commit: cd07d151a4c4a9430aa5d3d18e8bf302b1b8a7be
https://github.com/pism/pism/commit/cd07d151a4c4a9430aa5d3d18e8bf302b1b8a7be
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-27 (Thu, 27 May 2021)

Changed paths:
M test/regression/inverse/tiny_nlcg.sh
M test/regression/inverse/tiny_tikhonov_lmvm.sh

Log Message:
-----------
Use unique file names in more regression tests

... to avoid race conditions when tests are executed in parallel.

Commit: 78e56e7df93e927608d2ef669370b8aadbe62d5c
https://github.com/pism/pism/commit/78e56e7df93e927608d2ef669370b8aadbe62d5c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-27 (Thu, 27 May 2021)

Changed paths:
M examples/inverse/pismi.py
M site-packages/PISM/ssa.py

Log Message:
-----------
A small fix needed to make pismi.py behave

Before this it always created both foo.nc and foo.nc~ and failed to write *all* of its
outputs to foo.nc (some ended up in foo.nc~).

Commit: 8a15f410f30f73a5924fe96f6e0faee40239c887
https://github.com/pism/pism/commit/8a15f410f30f73a5924fe96f6e0faee40239c887
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-27 (Thu, 27 May 2021)

Changed paths:
M doc/sphinx/installation/code/petsc-mumps-hypre.sh

Log Message:
-----------
Use a different prefix to install PETSc with MUMPS and hypre

This will make it easier to re-build PISM with one or the other.

Commit: e68c89bed375aa39950288848f31cd33e6764a0d
https://github.com/pism/pism/commit/e68c89bed375aa39950288848f31cd33e6764a0d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-05-27 (Thu, 27 May 2021)

Changed paths:
M doc/sphinx/contributing/development-workflow.rst
M doc/sphinx/global.txt

Log Message:
-----------
Improve contributing guidelines

- Mention LLD and CTEST_PARALLEL_LEVEL.
- Document that we need to avoid file name clashes to run tests in parallel.

Commit: 4b2c1a6389a2265357ddeb476d9d506ecded1148
https://github.com/pism/pism/commit/4b2c1a6389a2265357ddeb476d9d506ecded1148
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M CMakeLists.txt

Log Message:
-----------
Add a Clang compiler flag to simiplify debugging with lldb

Commit: 76e172716ac28f03bc5d994638bf48d5c41c587b
https://github.com/pism/pism/commit/76e172716ac28f03bc5d994638bf48d5c41c587b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M examples/ismip-hom/README.rst
M examples/ismip-hom/e-arolla/run.sh

Log Message:
-----------
Final adjustments of ISMIP-HOM scripts

- Fix the README.

- Switch to CG+GAMG for the coarse MG level for experiment E.
Now this experiment does not use any external PETSc packages.

Commit: 48eed75573704b702b1156679a87a1bfa1e46350
https://github.com/pism/pism/commit/48eed75573704b702b1156679a87a1bfa1e46350
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M src/energy/EnergyModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/output.cc
M src/icemodel/output_extra.cc
M src/icemodel/output_save.cc
M src/icemodel/printout.cc
M src/icemodel/utilities.cc
M src/stressbalance/ssa/SSAFD.cc
M src/stressbalance/ssa/SSAFEM.cc
M src/util/Time.cc
M src/util/Time_Calendar.cc
M src/util/pism_utilities.cc

Log Message:
-----------
Replace snprintf() calls with pism::printf()

Commit: 49c8cd20517dcb5ac95f18d23f0fb2654c855cc8
https://github.com/pism/pism/commit/49c8cd20517dcb5ac95f18d23f0fb2654c855cc8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M src/regional/IceGrid_Regional.cc

Log Message:
-----------
Add "-refinement_factor N" to "pismr -regional"

Now

pismr -regional -bootstrap -i input.nc -x_range x_min,x_max -y_range y_min,y_max -refinement_factor N

will
* choose the smallest subset of the grid in input.nc that contains the rectangle [x_min, x_max]*[y_min, y_max] and
* create the grid that is N times finer than the one in input.nc.

Commit: a3a49eeacd3d1adeb0d3801682e1cd3e821178fb
https://github.com/pism/pism/commit/a3a49eeacd3d1adeb0d3801682e1cd3e821178fb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/manual/modeling-choices/regional/index.rst

Log Message:
-----------
Document -refinement_factor and update CHANGES.rst

Commit: cc75fed5a6defc7dadd667191bd6f1bec8c08650
https://github.com/pism/pism/commit/cc75fed5a6defc7dadd667191bd6f1bec8c08650
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M doc/sphinx/manual/initialization/bootstrapping.rst
M doc/sphinx/manual/modeling-choices/computational/box.rst

Log Message:
-----------
Mention that -x_range, -y_range work in regional mode only

Commit: 04e56973f4e9fd0df5b7654697fa1890645c3eda
https://github.com/pism/pism/commit/04e56973f4e9fd0df5b7654697fa1890645c3eda
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/timestepping.cc
M src/pism_config.cdl

Log Message:
-----------
Clean up and fix time stepping code

- IceModel::max_timestep() used input-output arguments, making it harder to maintain this.
Now it returns a struct containing all the outputs.

- the "skipping counter" was not computed properly at the end of the run or when the time
step is limited by time_stepping.maximum_time_step

- The configuration parameter time_stepping.hit_multiples should be an integer, not a
generic "number".

Commit: 20a3317cb2a33bce2ab7f70fa3e4d4b3ff4ef4eb
https://github.com/pism/pism/commit/20a3317cb2a33bce2ab7f70fa3e4d4b3ff4ef4eb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M src/icemodel/timestepping.cc

Log Message:
-----------
Fix a typo and re-order a couple of lines

Commit: c47b6e4e14c988394a6e86767a889fd155ac1894
https://github.com/pism/pism/commit/c47b6e4e14c988394a6e86767a889fd155ac1894
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M src/icemodel/timestepping.cc

Log Message:
-----------
Report which restriction was overridden by time_stepping.hit_multiples

Commit: b68d274edddfb87685a1297ca1730722b13f5437
https://github.com/pism/pism/commit/b68d274edddfb87685a1297ca1730722b13f5437
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M CHANGES.rst

Log Message:
-----------
Update the change log

Commit: 1bc19817e162fe596fbccf06892d470d5747c0c4
https://github.com/pism/pism/commit/1bc19817e162fe596fbccf06892d470d5747c0c4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M CHANGES.rst
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/timestepping.cc
M src/pism_config.cdl

Log Message:
-----------
Merge branch 'ckhroulev/time-stepping-cleanup' into dev

Commit: 4059310bee67c3cdb46bd519934a4d8dca6d4256
https://github.com/pism/pism/commit/4059310bee67c3cdb46bd519934a4d8dca6d4256
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh

Log Message:
-----------
PICO: When an ice shelf is distributed over multiple basins, use weighted average of ocean inputs only over those basins, in which an ice shelf actually has a calving front

Commit: edd7759c6f0006a030e37000adf2c17b35503ac6
https://github.com/pism/pism/commit/edd7759c6f0006a030e37000adf2c17b35503ac6
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh

Log Message:
-----------
PICO: Added function to find the two neighbor drainage basins

Commit: 3cc9052410884f6a09b1f09aef957019494bd5c7
https://github.com/pism/pism/commit/3cc9052410884f6a09b1f09aef957019494bd5c7
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh

Log Message:
-----------
PICO: Added function to split shelf_mask for ice shelves spread over non-neighboring basins with calving fronts in those basins. Needs modularization, clean up and documentation!

Commit: 48bb89c957882eb98ec0a0f33ab18e84d271aa94
https://github.com/pism/pism/commit/48bb89c957882eb98ec0a0f33ab18e84d271aa94
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
PICO: Moved basin_mask and split_ice_shelves() to PicoGeometry.cc

Commit: 975303a41951d64342945f6c3fe4123d7880e5e6
https://github.com/pism/pism/commit/975303a41951d64342945f6c3fe4123d7880e5e6
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
PICO: Modularized get_basin_neighbors() and pass vector m_n_basin_neighbors

Commit: c3f91f3fcc5d1f80ac1927f4e8f5aa1846584642
https://github.com/pism/pism/commit/c3f91f3fcc5d1f80ac1927f4e8f5aa1846584642
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
PICO: Modularized identify_calving_front_connection() and split shelf_mask in split_ice_shelves()

Commit: fb86762425eb2a20669862690f31ba6efa57ec99
https://github.com/pism/pism/commit/fb86762425eb2a20669862690f31ba6efa57ec99
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
Fix compilation warnings

Note: only data members of classes should use the "m_" variable name prefix.

See http://pism.github.io/pism/contributing/coding_guidelines.html

Commit: 0eb93e5498128107ac465c82c94d0948b1555d56
https://github.com/pism/pism/commit/0eb93e5498128107ac465c82c94d0948b1555d56
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
A fix for my previous fix

- move the get_basin_neighbors() call to init()
- rename init_impl() to init()
- add placeholders for documenting comments
- remove edge_p() and use grid_edge() instead

Commit: ab69e0b9dd29e7f69244e3d589a73526d54aa9dc
https://github.com/pism/pism/commit/ab69e0b9dd29e7f69244e3d589a73526d54aa9dc
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc
A test/test_pico_split/run_test.sh

Log Message:
-----------
PICO: Added some in-line description of the functions and a test case

Commit: ee820defafadea2a9f9dc7252b540f96716c401f
https://github.com/pism/pism/commit/ee820defafadea2a9f9dc7252b540f96716c401f
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
A test/test_pico_split/bedmap2_schmidtko14_50km.nc
M test/test_pico_split/run_test.sh

Log Message:
-----------
PICO: Added simple bash test for new PICO functionality

Commit: 1a48aa9066a7ee041a35354ce6890722bf589995
https://github.com/pism/pism/commit/1a48aa9066a7ee041a35354ce6890722bf589995
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/climate_forcing/ocean.rst

Log Message:
-----------
PICO: Add two lines to manual and CHANGES

Commit: 7228cf18d04e8078fffc701941b55b5bf3fcbbbc
https://github.com/pism/pism/commit/7228cf18d04e8078fffc701941b55b5bf3fcbbbc
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-01 (Tue, 01 Jun 2021)

Changed paths:
M CHANGES.rst

Log Message:
-----------
Mention ISMIP-HOM experiment E in CHANGES.rst

Commit: 3073fba613adea0006f7a8cd49ada80e75b13c78
https://github.com/pism/pism/commit/3073fba613adea0006f7a8cd49ada80e75b13c78
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-03 (Thu, 03 Jun 2021)

Changed paths:
M src/util/options.cc

Log Message:
-----------
Use PetscOptionsGetString() to avoid polluting "-help" output

Commit: 41c08c3ab075972d66f9564cf5dbf8c8bc7575f3
https://github.com/pism/pism/commit/41c08c3ab075972d66f9564cf5dbf8c8bc7575f3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-04 (Fri, 04 Jun 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/dynamics/blatter.rst

Log Message:
-----------
Fix a typo in the manual

Commit: 6d55a95d20753764a567d5039a3ace4215bc3823
https://github.com/pism/pism/commit/6d55a95d20753764a567d5039a3ace4215bc3823
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-07 (Mon, 07 Jun 2021)

Changed paths:
M test/regression/file.py

Log Message:
-----------
Improve a regression test

Commit: e67ba1307cfef64135c4c6fa1586dc17b1b01917
https://github.com/pism/pism/commit/e67ba1307cfef64135c4c6fa1586dc17b1b01917
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-09 (Wed, 09 Jun 2021)

Changed paths:
M .mailmap

Log Message:
-----------
Update .mailmap

Commit: 5718be7395a17e0d31cd24548ec795b29a0070e9
https://github.com/pism/pism/commit/5718be7395a17e0d31cd24548ec795b29a0070e9
Author: k202136 <k20...@mlogin102.hpc.dkrz.de>
Date: 2021-06-09 (Wed, 09 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh

Log Message:
-----------
PICO optimized communication

Commit: a016e86587fceb520e1f0cc51fd59975bdfc82c4
https://github.com/pism/pism/commit/a016e86587fceb520e1f0cc51fd59975bdfc82c4
Author: k202136 <k20...@mlogin102.hpc.dkrz.de>
Date: 2021-06-09 (Wed, 09 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc

Log Message:
-----------
clean up ocean - auxiliary vectors still needed for IntelMPI

Commit: 0f3886c40e6a8b484d6a8a55fa2a0fb912ae30a8
https://github.com/pism/pism/commit/0f3886c40e6a8b484d6a8a55fa2a0fb912ae30a8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-09 (Wed, 09 Jun 2021)

Changed paths:
M src/util/pism_utilities.cc

Log Message:
-----------
Ensure that input and output arguments of MPI_Allreduce are different

Commit: 87dfe901d91ea53bb7ee826b2a5c86a516252bf3
https://github.com/pism/pism/commit/87dfe901d91ea53bb7ee826b2a5c86a516252bf3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-09 (Wed, 09 Jun 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc

Log Message:
-----------
Remove unused variables in PicoGeometry.cc

Commit: d37a1871c1885c72f92cfbaf6c6ff45b51833f31
https://github.com/pism/pism/commit/d37a1871c1885c72f92cfbaf6c6ff45b51833f31
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-09 (Wed, 09 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc

Log Message:
-----------
No need to call std::vector<...>::clear() in PICO

This call does not free storage: according to cppreference.com std::vector<...>::clear()
does not change std::vector<...>::capacity(), i.e. "the number of elements that the
container has currently allocated space for."

Storage will be freed at the end of scope.

Commit: a114a36ce5dac3ae8235c1a5c1df5143102d7170
https://github.com/pism/pism/commit/a114a36ce5dac3ae8235c1a5c1df5143102d7170
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-09 (Wed, 09 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc

Log Message:
-----------
Remove double* arithmetic in Pico::compute_box_area()

For a std::vector container vector.data() is equivalent to &vector[0], so there is no need
to use vector.data() and increment the pointer to get the address of the second element:
&vector[1] will do the job.

Commit: 7b505c51b7710019b76c801ed1d1cdd6251d8998
https://github.com/pism/pism/commit/7b505c51b7710019b76c801ed1d1cdd6251d8998
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-09 (Wed, 09 Jun 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc

Log Message:
-----------
Remove an unnecessary #include

Commit: 58dfa19204c317974dcc72f92763a64c761f20f1
https://github.com/pism/pism/commit/58dfa19204c317974dcc72f92763a64c761f20f1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-09 (Wed, 09 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh

Log Message:
-----------
Merge Enrico Degregori's PICO improvements into dev

Commit: f1e8fe28406895a8760afafa043aaeb2d0bc6198
https://github.com/pism/pism/commit/f1e8fe28406895a8760afafa043aaeb2d0bc6198
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-10 (Thu, 10 Jun 2021)

Changed paths:
M src/util/connected_components.cc
M src/util/connected_components.hh

Log Message:
-----------
Re-implement the connected component labeling algorithm

This should be faster than the old implementation.

Commit: 496d939f271674469fc31535afedc26c45f027a0
https://github.com/pism/pism/commit/496d939f271674469fc31535afedc26c45f027a0
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-14 (Mon, 14 Jun 2021)

Changed paths:
M src/util/MaxTimestep.cc

Log Message:
-----------
Minor cleanup in MaxTimestep.cc

Commit: be35137bb935d7bc236197c989175cd1cd875745
https://github.com/pism/pism/commit/be35137bb935d7bc236197c989175cd1cd875745
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-17 (Thu, 17 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc

Log Message:
-----------
PICO: When an ice shelf is distributed over multiple basins, use weighted average of ocean inputs only over those basins, in which an ice shelf actually has a calving front

Commit: 458766cc755fe2d3a67d1431e94c5e225a770b2b
https://github.com/pism/pism/commit/458766cc755fe2d3a67d1431e94c5e225a770b2b
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-17 (Thu, 17 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh

Log Message:
-----------
PICO: Added function to find the two neighbor drainage basins

Commit: 4b63a37cfd1db969c684b1cf67aa79883bc69201
https://github.com/pism/pism/commit/4b63a37cfd1db969c684b1cf67aa79883bc69201
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-17 (Thu, 17 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh

Log Message:
-----------
PICO: Added function to split shelf_mask for ice shelves spread over non-neighboring basins with calving fronts in those basins. Needs modularization, clean up and documentation!

Commit: c2dfd5c49f613411146ae3604176583e5b22ae46
https://github.com/pism/pism/commit/c2dfd5c49f613411146ae3604176583e5b22ae46
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-18 (Fri, 18 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh

Log Message:
-----------
PICO: When an ice shelf is distributed over multiple basins, use weighted average of ocean inputs only over those basins, in which an ice shelf actually has a calving front

Commit: ab2e1bb4f993e1a03d82802376985c1905efced7
https://github.com/pism/pism/commit/ab2e1bb4f993e1a03d82802376985c1905efced7
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-18 (Fri, 18 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh

Log Message:
-----------
PICO: Added function to find the two neighbor drainage basins

Commit: 9cdb3a7806d491cee3cbb0fb29da6cf1465c5acd
https://github.com/pism/pism/commit/9cdb3a7806d491cee3cbb0fb29da6cf1465c5acd
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-18 (Fri, 18 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh

Log Message:
-----------
PICO: Added function to split shelf_mask for ice shelves spread over non-neighboring basins with calving fronts in those basins. Needs modularization, clean up and documentation!

Commit: a92aba48feaa03f08fd6732799cb6ff6784e6759
https://github.com/pism/pism/commit/a92aba48feaa03f08fd6732799cb6ff6784e6759
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-18 (Fri, 18 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
PICO: Moved basin_mask and split_ice_shelves() to PicoGeometry.cc

Commit: d32ae94adf4e9ff728f000a5a1873a14c695334e
https://github.com/pism/pism/commit/d32ae94adf4e9ff728f000a5a1873a14c695334e
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-18 (Fri, 18 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
PICO: Modularized get_basin_neighbors() and pass vector m_n_basin_neighbors

Commit: 8ee2f0f7167785b062a70d60d5d41db0c87658e4
https://github.com/pism/pism/commit/8ee2f0f7167785b062a70d60d5d41db0c87658e4
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-18 (Fri, 18 Jun 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
PICO: Modularized identify_calving_front_connection() and split shelf_mask in split_ice_shelves()

Commit: 4d2266198a796c0a1852a0054dbaa0268edce445
https://github.com/pism/pism/commit/4d2266198a796c0a1852a0054dbaa0268edce445
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-18 (Fri, 18 Jun 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
Fix compilation warnings

Note: only data members of classes should use the "m_" variable name prefix.

See http://pism.github.io/pism/contributing/coding_guidelines.html

Commit: d9a5d6fa40a0bdd0da703afb083ed288e664eda7
https://github.com/pism/pism/commit/d9a5d6fa40a0bdd0da703afb083ed288e664eda7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-18 (Fri, 18 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
A fix for my previous fix

- move the get_basin_neighbors() call to init()
- rename init_impl() to init()
- add placeholders for documenting comments
- remove edge_p() and use grid_edge() instead

Commit: 4decebd5310ffe9e19f0657aec5176349bcfea18
https://github.com/pism/pism/commit/4decebd5310ffe9e19f0657aec5176349bcfea18
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-18 (Fri, 18 Jun 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc
A test/test_pico_split/run_test.sh

Log Message:
-----------
PICO: Added some in-line description of the functions and a test case

Commit: 59bbd40fd7ce09df510928646ab0513947b31a11
https://github.com/pism/pism/commit/59bbd40fd7ce09df510928646ab0513947b31a11
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-18 (Fri, 18 Jun 2021)

Changed paths:
A test/test_pico_split/bedmap2_schmidtko14_50km.nc
M test/test_pico_split/run_test.sh

Log Message:
-----------
PICO: Added simple bash test for new PICO functionality

Commit: 3e9438e79e763a36d830dd4e21ac33624f12047a
https://github.com/pism/pism/commit/3e9438e79e763a36d830dd4e21ac33624f12047a
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-18 (Fri, 18 Jun 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/climate_forcing/ocean.rst

Log Message:
-----------
PICO: Add two lines to manual and CHANGES

Commit: 400eec7d7312aa530078bf78cc343cd8e67e8a4a
https://github.com/pism/pism/commit/400eec7d7312aa530078bf78cc343cd8e67e8a4a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-18 (Fri, 18 Jun 2021)

Changed paths:
M src/util/connected_components.cc
M src/util/connected_components.hh

Log Message:
-----------
Re-implement the connected component labeling algorithm

This should be faster than the old implementation.

Commit: 49004e481c7a10ed7b2a507fe3dc0062998902c7
https://github.com/pism/pism/commit/49004e481c7a10ed7b2a507fe3dc0062998902c7
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-18 (Fri, 18 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc
M test/test_pico_split/run_test.sh

Log Message:
-----------
More clean up in PICO code

Commit: 180fcfce2c351905cdde75a723e7c0bef5a5bca2
https://github.com/pism/pism/commit/180fcfce2c351905cdde75a723e7c0bef5a5bca2
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-18 (Fri, 18 Jun 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc

Log Message:
-----------
Reduce number of GlobalSum MPI communications in PcioGeometry split method

Commit: 8866968f07ea1c073f59a5a2d4a135e7105efb0a
https://github.com/pism/pism/commit/8866968f07ea1c073f59a5a2d4a135e7105efb0a
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-18 (Fri, 18 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc
M test/test_pico_split/run_test.sh

Log Message:
-----------
Merged into dev

Commit: 860bac8525094f28645ad7d5041e6d8d1d00a8e0
https://github.com/pism/pism/commit/860bac8525094f28645ad7d5041e6d8d1d00a8e0
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-19 (Sat, 19 Jun 2021)

Changed paths:
M .mailmap
M CHANGES.rst
M CMakeLists.txt
M doc/Makefile
M doc/acknowledge.py
M doc/ice-bib.bib
M doc/pismpython/inverse/design.rst
M doc/pismpython/inverse/index.rst
M doc/pismpython/inverse/pism_ssa.rst
M doc/pismpython/inverse/pismi.rst
M doc/pismpython/inverse/refresher.rst
M doc/pismpython/inverse/ssa_forward.rst
M doc/pismpython/inverse/ssa_inverse.rst
M doc/sphinx/CMakeLists.txt
M doc/sphinx/Makefile
M doc/sphinx/climate_forcing/atmosphere.rst
M doc/sphinx/climate_forcing/surface.rst
M doc/sphinx/climate_forcing/testing.rst
M doc/sphinx/conf.py
M doc/sphinx/contributing/development-workflow.rst
M doc/sphinx/global.txt
M doc/sphinx/installation/code/install_libraries.sh
A doc/sphinx/installation/code/petsc-mkl-mumps-hypre.sh
A doc/sphinx/installation/code/petsc-mumps-hypre.sh
M doc/sphinx/installation/code/petsc.sh
A doc/sphinx/installation/code/pism.sh
M doc/sphinx/installation/debian.rst
M doc/sphinx/manual/diagnostics/diagnostics-list.txt
M doc/sphinx/manual/initialization/bootstrapping.rst
M doc/sphinx/manual/initialization/index.rst
M doc/sphinx/manual/initialization/restarting.rst
M doc/sphinx/manual/modeling-choices/computational/box.rst
M doc/sphinx/manual/modeling-choices/computational/grid.rst
M doc/sphinx/manual/modeling-choices/dynamics/age.rst
A doc/sphinx/manual/modeling-choices/dynamics/blatter.rst
R doc/sphinx/manual/modeling-choices/dynamics/figures/.DS_Store
M doc/sphinx/manual/modeling-choices/dynamics/index.rst
M doc/sphinx/manual/modeling-choices/dynamics/rheology.rst
A doc/sphinx/manual/modeling-choices/dynamics/sia.rst
A doc/sphinx/manual/modeling-choices/dynamics/ssa.rst
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst
R doc/sphinx/manual/modeling-choices/dynamics/surface-gradient.rst
A doc/sphinx/manual/modeling-choices/dynamics/weertman.rst
M doc/sphinx/manual/modeling-choices/marine/calving.rst
M doc/sphinx/manual/modeling-choices/marine/melange.rst
M doc/sphinx/manual/modeling-choices/marine/pik.rst
M doc/sphinx/manual/modeling-choices/regional/index.rst
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst
R doc/sphinx/manual/modeling-choices/subglacier/bed-roughness.rst
M doc/sphinx/manual/modeling-choices/subglacier/hydrology.rst
M doc/sphinx/manual/modeling-choices/subglacier/index.rst
M doc/sphinx/manual/practical-usage/diagnostic-viewers.rst
M doc/sphinx/manual/practical-usage/flowline.rst
M doc/sphinx/manual/practical-usage/index.rst
M doc/sphinx/manual/practical-usage/saving-diagnostics.rst
M doc/sphinx/manual/practical-usage/saving-snapshots.rst
M doc/sphinx/manual/practical-usage/saving-time-series.rst
M doc/sphinx/manual/practical-usage/time-stepping.rst
M doc/sphinx/manual/simplified-geometry/eismint-2.rst
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-a.png
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-b.png
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-c.png
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-d.png
A doc/sphinx/manual/simplified-geometry/figures/uvel_no_slip.png
A doc/sphinx/manual/simplified-geometry/figures/uvel_sliding.png
A doc/sphinx/manual/simplified-geometry/figures/uvelsurf.png
M doc/sphinx/manual/simplified-geometry/index.rst
A doc/sphinx/manual/simplified-geometry/ismip-hom.rst
M doc/sphinx/manual/simplified-geometry/mismip3d.rst
M doc/sphinx/manual/std-greenland/grid-sequencing.rst
M doc/sphinx/manual/std-greenland/index.rst
M doc/sphinx/manual/verification/index.rst
A doc/sphinx/math-definitions.tex
R doc/sphinx/math-definitions.txt
M doc/sphinx/pism_config.py
M doc/sphinx/technical/blatter-pattyn.rst
M doc/sphinx/technical/bombproof.rst
M doc/sphinx/technical/ssafd-cfbc.rst
M doc/sphinx/technical/steady-hydrology.rst
M doc/sphinx/technical/vertchange.rst
M docker/CMakeLists.txt
A docker/ubuntu-ci/CMakeLists.txt
A docker/ubuntu-ci/Dockerfile.in
A docker/ubuntu-ci/README.rst
A docker/ubuntu-minimal/CMakeLists.txt
A docker/ubuntu-minimal/Dockerfile.in
A docker/ubuntu-minimal/README.rst
R docker/ubuntu/CMakeLists.txt
R docker/ubuntu/Dockerfile.in
R docker/ubuntu/README.rst
M examples/inverse/pismi.py
A examples/ismip-hom/README.rst
A examples/ismip-hom/abcd/Makefile
A examples/ismip-hom/abcd/README.rst
A examples/ismip-hom/abcd/convert-ismiphom.py
A examples/ismip-hom/abcd/plot-ismiphom.py
A examples/ismip-hom/abcd/run-ismiphom.py
A examples/ismip-hom/e-arolla/Makefile
A examples/ismip-hom/e-arolla/README.md
A examples/ismip-hom/e-arolla/convert.py
A examples/ismip-hom/e-arolla/plot.py
A examples/ismip-hom/e-arolla/run.sh
M site-packages/PISM/ssa.py
M site-packages/PISM/testing.py
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoPhysics.cc
M src/energy/EnergyModel.cc
M src/energy/utilities.cc
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/diagnostics.cc
M src/icemodel/frontretreat.cc
M src/icemodel/initialization.cc
M src/icemodel/output.cc
M src/icemodel/output_extra.cc
M src/icemodel/output_save.cc
M src/icemodel/printout.cc
M src/icemodel/timestepping.cc
M src/icemodel/utilities.cc
M src/pism_config.cdl
M src/pisms.cc
M src/regional/IceGrid_Regional.cc
M src/rheology/FlowLaw.cc
M src/rheology/FlowLaw.hh
M src/rheology/GPBLD.cc
M src/rheology/GPBLD.hh
M src/rheology/GoldsbyKohlstedt.cc
M src/rheology/GoldsbyKohlstedt.hh
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/ShallowStressBalance.hh
M src/stressbalance/StressBalance.cc
M src/stressbalance/WeertmanSliding.cc
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc
M src/stressbalance/blatter/util/grid_hierarchy.cc
M src/stressbalance/blatter/util/grid_hierarchy.hh
M src/stressbalance/blatter/verification/BlatterTestCFBC.cc
M src/stressbalance/blatter/verification/BlatterTestHalfar.cc
M src/stressbalance/blatter/verification/BlatterTestXY.cc
M src/stressbalance/blatter/verification/BlatterTestXZ.cc
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc
M src/stressbalance/sia/SIAFD.cc
M src/stressbalance/sia/SIAFD.hh
M src/stressbalance/ssa/SSA.cc
M src/stressbalance/ssa/SSAFD.cc
M src/stressbalance/ssa/SSAFEM.cc
M src/util/Time.cc
M src/util/Time_Calendar.cc
M src/util/connected_components.cc
M src/util/connected_components.hh
M src/util/io/File.cc
M src/util/options.cc
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh
M test/blatter_verification.py
R test/ismip-hom/Makefile
R test/ismip-hom/README.rst
R test/ismip-hom/convert-ismiphom.py
R test/ismip-hom/ismip-hom-a-5km.png
R test/ismip-hom/plot-ismiphom.py
R test/ismip-hom/run-ismiphom.py
M test/regression/atmosphere_models.py
M test/regression/file.py
M test/regression/inverse/tiny_nlcg.sh
M test/regression/inverse/tiny_tikhonov_lmvm.sh
M test/regression/ocean_models.py
M test/test_pico_split/run_test.sh
M util/nc2cdo.py

Log Message:
-----------
Merged PICO split into dev

Commit: bdd223f7c04793bf803669fa173e021456f9a0c5
https://github.com/pism/pism/commit/bdd223f7c04793bf803669fa173e021456f9a0c5
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-19 (Sat, 19 Jun 2021)

Changed paths:
M CHANGES.rst
M CMakeLists.txt
M doc/Makefile
M doc/acknowledge.py
M doc/ice-bib.bib
M doc/pismpython/inverse/design.rst
M doc/pismpython/inverse/index.rst
M doc/pismpython/inverse/pism_ssa.rst
M doc/pismpython/inverse/pismi.rst
M doc/pismpython/inverse/refresher.rst
M doc/pismpython/inverse/ssa_forward.rst
M doc/pismpython/inverse/ssa_inverse.rst
M doc/sphinx/CMakeLists.txt
M doc/sphinx/Makefile
M doc/sphinx/climate_forcing/atmosphere.rst
M doc/sphinx/climate_forcing/surface.rst
M doc/sphinx/climate_forcing/testing.rst
M doc/sphinx/conf.py
M doc/sphinx/contributing/development-workflow.rst
M doc/sphinx/global.txt
M doc/sphinx/installation/code/install_libraries.sh
A doc/sphinx/installation/code/petsc-mkl-mumps-hypre.sh
A doc/sphinx/installation/code/petsc-mumps-hypre.sh
M doc/sphinx/installation/code/petsc.sh
A doc/sphinx/installation/code/pism.sh
M doc/sphinx/installation/debian.rst
M doc/sphinx/manual/diagnostics/diagnostics-list.txt
M doc/sphinx/manual/initialization/bootstrapping.rst
M doc/sphinx/manual/initialization/index.rst
M doc/sphinx/manual/initialization/restarting.rst
M doc/sphinx/manual/modeling-choices/computational/box.rst
M doc/sphinx/manual/modeling-choices/computational/grid.rst
M doc/sphinx/manual/modeling-choices/dynamics/age.rst
A doc/sphinx/manual/modeling-choices/dynamics/blatter.rst
R doc/sphinx/manual/modeling-choices/dynamics/figures/.DS_Store
M doc/sphinx/manual/modeling-choices/dynamics/index.rst
M doc/sphinx/manual/modeling-choices/dynamics/rheology.rst
A doc/sphinx/manual/modeling-choices/dynamics/sia.rst
A doc/sphinx/manual/modeling-choices/dynamics/ssa.rst
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst
R doc/sphinx/manual/modeling-choices/dynamics/surface-gradient.rst
A doc/sphinx/manual/modeling-choices/dynamics/weertman.rst
M doc/sphinx/manual/modeling-choices/marine/calving.rst
M doc/sphinx/manual/modeling-choices/marine/melange.rst
M doc/sphinx/manual/modeling-choices/marine/pik.rst
M doc/sphinx/manual/modeling-choices/regional/index.rst
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst
R doc/sphinx/manual/modeling-choices/subglacier/bed-roughness.rst
M doc/sphinx/manual/modeling-choices/subglacier/hydrology.rst
M doc/sphinx/manual/modeling-choices/subglacier/index.rst
M doc/sphinx/manual/practical-usage/diagnostic-viewers.rst
M doc/sphinx/manual/practical-usage/flowline.rst
M doc/sphinx/manual/practical-usage/index.rst
M doc/sphinx/manual/practical-usage/saving-diagnostics.rst
M doc/sphinx/manual/practical-usage/saving-snapshots.rst
M doc/sphinx/manual/practical-usage/saving-time-series.rst
M doc/sphinx/manual/practical-usage/time-stepping.rst
M doc/sphinx/manual/simplified-geometry/eismint-2.rst
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-a.png
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-b.png
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-c.png
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-d.png
A doc/sphinx/manual/simplified-geometry/figures/uvel_no_slip.png
A doc/sphinx/manual/simplified-geometry/figures/uvel_sliding.png
A doc/sphinx/manual/simplified-geometry/figures/uvelsurf.png
M doc/sphinx/manual/simplified-geometry/index.rst
A doc/sphinx/manual/simplified-geometry/ismip-hom.rst
M doc/sphinx/manual/simplified-geometry/mismip3d.rst
M doc/sphinx/manual/std-greenland/grid-sequencing.rst
M doc/sphinx/manual/std-greenland/index.rst
M doc/sphinx/manual/verification/index.rst
A doc/sphinx/math-definitions.tex
R doc/sphinx/math-definitions.txt
M doc/sphinx/pism_config.py
M doc/sphinx/technical/blatter-pattyn.rst
M doc/sphinx/technical/bombproof.rst
M doc/sphinx/technical/ssafd-cfbc.rst
M doc/sphinx/technical/steady-hydrology.rst
M doc/sphinx/technical/vertchange.rst
M docker/CMakeLists.txt
A docker/ubuntu-ci/CMakeLists.txt
A docker/ubuntu-ci/Dockerfile.in
A docker/ubuntu-ci/README.rst
A docker/ubuntu-minimal/CMakeLists.txt
A docker/ubuntu-minimal/Dockerfile.in
A docker/ubuntu-minimal/README.rst
R docker/ubuntu/CMakeLists.txt
R docker/ubuntu/Dockerfile.in
R docker/ubuntu/README.rst
M examples/inverse/pismi.py
A examples/ismip-hom/README.rst
A examples/ismip-hom/abcd/Makefile
A examples/ismip-hom/abcd/README.rst
A examples/ismip-hom/abcd/convert-ismiphom.py
A examples/ismip-hom/abcd/plot-ismiphom.py
A examples/ismip-hom/abcd/run-ismiphom.py
A examples/ismip-hom/e-arolla/Makefile
A examples/ismip-hom/e-arolla/README.md
A examples/ismip-hom/e-arolla/convert.py
A examples/ismip-hom/e-arolla/plot.py
A examples/ismip-hom/e-arolla/run.sh
M site-packages/PISM/ssa.py
M site-packages/PISM/testing.py
M src/coupler/ocean/PicoPhysics.cc
M src/energy/EnergyModel.cc
M src/energy/utilities.cc
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/diagnostics.cc
M src/icemodel/frontretreat.cc
M src/icemodel/initialization.cc
M src/icemodel/output.cc
M src/icemodel/output_extra.cc
M src/icemodel/output_save.cc
M src/icemodel/printout.cc
M src/icemodel/timestepping.cc
M src/icemodel/utilities.cc
M src/pism_config.cdl
M src/pisms.cc
M src/regional/IceGrid_Regional.cc
M src/rheology/FlowLaw.cc
M src/rheology/FlowLaw.hh
M src/rheology/GPBLD.cc
M src/rheology/GPBLD.hh
M src/rheology/GoldsbyKohlstedt.cc
M src/rheology/GoldsbyKohlstedt.hh
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/ShallowStressBalance.hh
M src/stressbalance/StressBalance.cc
M src/stressbalance/WeertmanSliding.cc
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc
M src/stressbalance/blatter/util/grid_hierarchy.cc
M src/stressbalance/blatter/util/grid_hierarchy.hh
M src/stressbalance/blatter/verification/BlatterTestCFBC.cc
M src/stressbalance/blatter/verification/BlatterTestHalfar.cc
M src/stressbalance/blatter/verification/BlatterTestXY.cc
M src/stressbalance/blatter/verification/BlatterTestXZ.cc
M src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc
M src/stressbalance/sia/SIAFD.cc
M src/stressbalance/sia/SIAFD.hh
M src/stressbalance/ssa/SSA.cc
M src/stressbalance/ssa/SSAFD.cc
M src/stressbalance/ssa/SSAFEM.cc
M src/util/Time.cc
M src/util/Time_Calendar.cc
M src/util/connected_components.cc
M src/util/connected_components.hh
M src/util/io/File.cc
M src/util/pism_utilities.cc
M test/blatter_verification.py
R test/ismip-hom/Makefile
R test/ismip-hom/README.rst
R test/ismip-hom/convert-ismiphom.py
R test/ismip-hom/ismip-hom-a-5km.png
R test/ismip-hom/plot-ismiphom.py
R test/ismip-hom/run-ismiphom.py
M test/regression/atmosphere_models.py
M test/regression/inverse/tiny_nlcg.sh
M test/regression/inverse/tiny_tikhonov_lmvm.sh
M test/regression/ocean_models.py
M util/nc2cdo.py

Log Message:
-----------
Merged CHANGES

Commit: d1a5d26718a921eca1839c8d170a2a3aa69de451
https://github.com/pism/pism/commit/d1a5d26718a921eca1839c8d170a2a3aa69de451
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-19 (Sat, 19 Jun 2021)

Changed paths:
M .mailmap
M CHANGES.rst
M doc/sphinx/manual/modeling-choices/dynamics/blatter.rst
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc
M src/util/options.cc
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh
M test/regression/file.py
M test/test_pico_split/run_test.sh

Log Message:
-----------
Remerged CHANGES

Commit: aab111ec2871b56a20731e81a800c9e4cdfb1382
https://github.com/pism/pism/commit/aab111ec2871b56a20731e81a800c9e4cdfb1382
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-19 (Sat, 19 Jun 2021)

Changed paths:
M CHANGES.rst

Log Message:
-----------
Fix CHANGES.rst

Commit: bd2125871a04f5580eadfa87b84bb2535fc3af88
https://github.com/pism/pism/commit/bd2125871a04f5580eadfa87b84bb2535fc3af88
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-19 (Sat, 19 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc

Log Message:
-----------
Remove an unnecessary variable

Commit: dffd5694d7fbb4c960e4033ce3e57bf0f732603e
https://github.com/pism/pism/commit/dffd5694d7fbb4c960e4033ce3e57bf0f732603e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-19 (Sat, 19 Jun 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc

Log Message:
-----------
Remove code that has no effect

Commit: e96d372c43658ed214a270c8422810d788e6f2b2
https://github.com/pism/pism/commit/e96d372c43658ed214a270c8422810d788e6f2b2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-19 (Sat, 19 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc

Log Message:
-----------
Formatting changes

Commit: 2c812c1abcba51df316e9864192b7c3b5b77d20b
https://github.com/pism/pism/commit/2c812c1abcba51df316e9864192b7c3b5b77d20b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-19 (Sat, 19 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc

Log Message:
-----------
Fix a copy-and-paste error in Pico::write_model_state_impl()

Commit: 721b424d1f1e56edc8c3f26dc64e306e04d9debe
https://github.com/pism/pism/commit/721b424d1f1e56edc8c3f26dc64e306e04d9debe
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-21 (Mon, 21 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc

Log Message:
-----------
Formatting changes

Commit: 01e267df9c03b5a5528fb4ffd00972c6db924934
https://github.com/pism/pism/commit/01e267df9c03b5a5528fb4ffd00972c6db924934
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-21 (Mon, 21 Jun 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
Cleanup inspired by running clang-tidy

Commit: dc1886de73a956d4ea582c7f6a92923b159a64b5
https://github.com/pism/pism/commit/dc1886de73a956d4ea582c7f6a92923b159a64b5
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-06-22 (Tue, 22 Jun 2021)

Changed paths:
M test/test_pico_split/run_test.sh

Log Message:
-----------
Added exit status to pico split test

Commit: 97cd07a9ca042860284a503550176337ddd94e99
https://github.com/pism/pism/commit/97cd07a9ca042860284a503550176337ddd94e99
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-22 (Tue, 22 Jun 2021)

Changed paths:
M test/regression/CMakeLists.txt
A test/regression/pico_split/bedmap2_schmidtko14_50km.nc
A test/regression/pico_split/run_test.sh
R test/test_pico_split/bedmap2_schmidtko14_50km.nc
R test/test_pico_split/run_test.sh

Log Message:
-----------
Clean up the PICO regression test

Commit: d1ee2292ecbba5f258b9e0708c5d7c39b99054a9
https://github.com/pism/pism/commit/d1ee2292ecbba5f258b9e0708c5d7c39b99054a9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-22 (Tue, 22 Jun 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/climate_forcing/ocean.rst
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh
M src/util/connected_components.cc
M src/util/connected_components.hh
M test/regression/CMakeLists.txt
A test/regression/pico_split/bedmap2_schmidtko14_50km.nc
A test/regression/pico_split/run_test.sh

Log Message:
-----------
Merge pull request #481 from pism/pik/pico_merge

PICO split and merge

Commit: f5891b91aaced60dfea5056fbd4d6e1d46291c6b
https://github.com/pism/pism/commit/f5891b91aaced60dfea5056fbd4d6e1d46291c6b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-23 (Wed, 23 Jun 2021)

Changed paths:
M examples/inverse/make_synth_ssa.py
M examples/inverse/pismi.py
M site-packages/PISM/invert/ssa.py
M site-packages/PISM/invert/ssa_siple.py
M site-packages/PISM/model.py
M src/coupler/surface/EISMINTII.cc
M src/energy/btutest.cc
M src/fracturedensity/FractureDensity.cc
M src/icemodel/initialization.cc
M src/pisms.cc
M src/pismv.cc
M src/stressbalance/sia/siafd_test.cc
M src/stressbalance/ssa/SSAFEM.cc
M src/util/ConfigInterface.cc
M src/util/ConfigInterface.hh
M src/util/IceGrid.cc
M src/util/IceGrid.hh
M src/util/Time.cc
M src/util/options.cc
M src/util/pism_options.hh
M test/bed_smoother.py

Log Message:
-----------
Implement unit conversion for command-line options

Commit: 7bcaff29761aa67fcf55e6c980673ebd547fde92
https://github.com/pism/pism/commit/7bcaff29761aa67fcf55e6c980673ebd547fde92
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-23 (Wed, 23 Jun 2021)

Changed paths:
M src/pism_config.cdl

Log Message:
-----------
Switch time units from "years" to "365days"

This way "-y X" has a clear meaning, for example.

Commit: a51f40dad3ff57be49dfed777bcc236077d4a12e
https://github.com/pism/pism/commit/a51f40dad3ff57be49dfed777bcc236077d4a12e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-23 (Wed, 23 Jun 2021)

Changed paths:
M src/util/Time.cc

Log Message:
-----------
Minor cleanup

Commit: 42effefecb2e5544a0ccfb600cc3dc462316e261
https://github.com/pism/pism/commit/42effefecb2e5544a0ccfb600cc3dc462316e261
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-23 (Wed, 23 Jun 2021)

Changed paths:
M test/regression/test_01.sh

Log Message:
-----------
The pismr restartability test should actually use pismr

Commit: 3353e7d45db689b583bc23df3781193718caf60c
https://github.com/pism/pism/commit/3353e7d45db689b583bc23df3781193718caf60c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-23 (Wed, 23 Jun 2021)

Changed paths:
M src/pisms.cc
M src/pismv.cc
M test/regression/test_15.sh
M test/regression/test_16.sh
M test/regression/test_17.sh
M test/regression/test_18.sh

Log Message:
-----------
pisms and pismv no longer use the non-standard calendar "none"

Commit: 7da6867f61350f101564bfb19b5ba148a4263388
https://github.com/pism/pism/commit/7da6867f61350f101564bfb19b5ba148a4263388
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-23 (Wed, 23 Jun 2021)

Changed paths:
M CHANGES.rst

Log Message:
-----------
Update CHANGES.rst

Commit: a67f35e9b4532f3445f56766853fce0c2d9f2e35
https://github.com/pism/pism/commit/a67f35e9b4532f3445f56766853fce0c2d9f2e35
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-23 (Wed, 23 Jun 2021)

Changed paths:
M src/icemodel/timestepping.cc
M src/pism_config.cdl

Log Message:
-----------
Add time_stepping.resolution

This parameter (defaults to 1 second) makes PISM round the chosen time step length down to
a multiple of time_stepping.resolution.

This is needed to increase the likelihood of being able to *exactly* represent the model
time in a 64-bit floating point number (C++ type double).

Commit: 3d4f3569049a88d6610e44b5f1347573f297e950
https://github.com/pism/pism/commit/3d4f3569049a88d6610e44b5f1347573f297e950
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-23 (Wed, 23 Jun 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/manual/practical-usage/time-stepping.rst

Log Message:
-----------
Document time_stepping.resolution and update CHANGES.rst

Commit: 0dac23e9b3cd3fb29a6329a51b80414e8881c626
https://github.com/pism/pism/commit/0dac23e9b3cd3fb29a6329a51b80414e8881c626
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-23 (Wed, 23 Jun 2021)

Changed paths:
M test/regression/test_15.sh
M test/regression/test_17.sh
M test/regression/test_18.sh

Log Message:
-----------
Update regression tests

Commit: 8099c60f513024fb1eb460710453c98a9f636464
https://github.com/pism/pism/commit/8099c60f513024fb1eb460710453c98a9f636464
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-24 (Thu, 24 Jun 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/manual/practical-usage/time-stepping.rst
M src/icemodel/timestepping.cc
M src/pism_config.cdl
M test/regression/test_15.sh
M test/regression/test_17.sh
M test/regression/test_18.sh

Log Message:
-----------
Merge branch 'ckhroulev/max-timestep' into dev

Commit: 692f78b928480daa36cd7b0b514302dc1ed4d805
https://github.com/pism/pism/commit/692f78b928480daa36cd7b0b514302dc1ed4d805
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-24 (Thu, 24 Jun 2021)

Changed paths:
M src/util/pism_utilities.cc

Log Message:
-----------
Minor improvement in pism::split()

Commit: 648d821c8c4b0e8eaecb72714f957a2d75aa77f3
https://github.com/pism/pism/commit/648d821c8c4b0e8eaecb72714f957a2d75aa77f3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-24 (Thu, 24 Jun 2021)

Changed paths:
M src/util/Time.cc
M src/util/Time.hh
M src/util/Time_Calendar.cc
M src/util/Time_Calendar.hh

Log Message:
-----------
Minor cleanup in the time management code

Commit: b0a8f187d5244328a8613dadc114a9989b063017
https://github.com/pism/pism/commit/b0a8f187d5244328a8613dadc114a9989b063017
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-24 (Thu, 24 Jun 2021)

Changed paths:
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/output.cc
M src/icemodel/output_extra.cc
M src/icemodel/output_save.cc
M src/icemodel/output_ts.cc

Log Message:
-----------
Use time_stepping.resolution in more places

These modifications are needed to make examples/labgum work as designed.

Commit: 84e2698a0c0fc278e554744ce241163befc91b00
https://github.com/pism/pism/commit/84e2698a0c0fc278e554744ce241163befc91b00
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-24 (Thu, 24 Jun 2021)

Changed paths:
M examples/labgum/rungum.sh

Log Message:
-----------
Clean up examples/labgum

- specify a more appropriate time resolution
- use more convenient units in command-line options

Commit: b6870e466e90dc31dd9373e4fc6415e608917544
https://github.com/pism/pism/commit/b6870e466e90dc31dd9373e4fc6415e608917544
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-24 (Thu, 24 Jun 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst

Log Message:
-----------
Shorten some a couple of lines in the manual

Commit: 1278a5ef05b81f945ec1ac61d49289ad46ab7855
https://github.com/pism/pism/commit/1278a5ef05b81f945ec1ac61d49289ad46ab7855
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-24 (Thu, 24 Jun 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst

Log Message:
-----------
Specify 1m/s as 1m/s instead of 3.1556926e7 m/year

Commit: 7888f363016d3d0136d1ca8a48717861073a1926
https://github.com/pism/pism/commit/7888f363016d3d0136d1ca8a48717861073a1926
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-24 (Thu, 24 Jun 2021)

Changed paths:
M examples/std-greenland/spinup.sh

Log Message:
-----------
Fix #474

Commit: c11e459c2176f9e599ccf2336a91c0d34601eec9
https://github.com/pism/pism/commit/c11e459c2176f9e599ccf2336a91c0d34601eec9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-25 (Fri, 25 Jun 2021)

Changed paths:
M src/pismv.cc

Log Message:
-----------
Fix a typo in pismv.cc

Commit: 040b08a885ecac948f65cd089be70e1233b2d8f0
https://github.com/pism/pism/commit/040b08a885ecac948f65cd089be70e1233b2d8f0
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-25 (Fri, 25 Jun 2021)

Changed paths:
M src/icemodel/IceEISModel.cc
M src/icemodel/IceEISModel.hh
M src/pisms.cc
M src/util/IceGrid.cc

Log Message:
-----------
IceGrid::FromOptions can create grids using config. defaults

Commit: e97a76d546e1b7737ec59a7752d52a9e43f33a02
https://github.com/pism/pism/commit/e97a76d546e1b7737ec59a7752d52a9e43f33a02
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-25 (Fri, 25 Jun 2021)

Changed paths:
M src/pisms.cc

Log Message:
-----------
Use context_from_options() in pisms.cc

Commit: 71e1cbb902054035796b5658151b4da840c41df8
https://github.com/pism/pism/commit/71e1cbb902054035796b5658151b4da840c41df8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-25 (Fri, 25 Jun 2021)

Changed paths:
M src/util/Context.cc
M src/util/Context.hh

Log Message:
-----------
Make printing of configuration parameters optional

Commit: 997be29e9cc327c7ad3562ba7da832c0a863fa35
https://github.com/pism/pism/commit/997be29e9cc327c7ad3562ba7da832c0a863fa35
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-25 (Fri, 25 Jun 2021)

Changed paths:
M src/CMakeLists.txt
M src/pismr.cc
R src/pisms.cc

Log Message:
-----------
Remove pisms and replace it with "pismr -eisII X"

Commit: 435a18416f7383ddb7c28eb8c8413ef0d8e17f1e
https://github.com/pism/pism/commit/435a18416f7383ddb7c28eb8c8413ef0d8e17f1e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-25 (Fri, 25 Jun 2021)

Changed paths:
M doc/browser/petsc.md
M doc/sphinx/Makefile
M doc/sphinx/climate_forcing/testing.rst
M doc/sphinx/installation/arch.rst
M doc/sphinx/installation/quick-tests.rst
M doc/sphinx/manual/initialization/index.rst
M doc/sphinx/manual/initialization/restarting.rst
M doc/sphinx/manual/modeling-choices/computational/grid.rst
M doc/sphinx/manual/modeling-choices/computational/time.rst
M doc/sphinx/manual/modeling-choices/dynamics/sia.rst
M doc/sphinx/manual/modeling-choices/subglacier/bed-deformation.rst
M doc/sphinx/manual/practical-usage/input-output.rst
M doc/sphinx/manual/practical-usage/regridding.rst
M doc/sphinx/manual/simplified-geometry/eismint-2.rst
M examples/eismintII/runexp.sh
M src/coupler/surface/EISMINTII.hh
M src/icemodel/IceEISModel.cc
M test/regression/beddef_lc_restart.sh
M test/regression/temp_continuity.py
M test/regression/test_01.sh
M test/regression/test_03.sh
M test/regression/test_05.sh
M test/regression/test_08.sh
M test/regression/test_09.sh
M test/regression/test_10.sh
M test/regression/test_13.sh
M test/regression/test_23.sh
M test/regression/test_27.sh
M test/regression/test_28.sh
M test/regression/test_31.sh
M test/regression/test_32.sh
M test/regression/test_33.sh
M test/regression/test_epsg_processing.py
M test/regression/vertical_grid_expansion.sh

Log Message:
-----------
Update regression scripts and the manual

Commit: 124e6d84d405fd774dce1839befce6d65e657cf5
https://github.com/pism/pism/commit/124e6d84d405fd774dce1839befce6d65e657cf5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-28 (Mon, 28 Jun 2021)

Changed paths:
M src/pismr.cc
M test/regression/beddef_lc_restart.sh

Log Message:
-----------
Remove two last occurrences of "pisms"

Commit: 0a1cc8f365081a1c15107c71701fb43f0b55f6e5
https://github.com/pism/pism/commit/0a1cc8f365081a1c15107c71701fb43f0b55f6e5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-06-28 (Mon, 28 Jun 2021)

Changed paths:
M src/icemodel/IceEISModel.cc
M src/icemodel/IceEISModel.hh
M src/pismr.cc

Log Message:
-----------
Clean up iceEISModel

Commit: f9325fe9bdfac57eac627532be998b3e62bcd7aa
https://github.com/pism/pism/commit/f9325fe9bdfac57eac627532be998b3e62bcd7aa
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-07-06 (Tue, 06 Jul 2021)

Changed paths:
M src/basalstrength/MohrCoulombYieldStress.hh
M src/coupler/atmosphere/Anomaly.hh
M src/coupler/atmosphere/ElevationChange.hh
M src/coupler/atmosphere/Frac_P.hh
M src/coupler/atmosphere/GivenClimate.hh
M src/coupler/frontalmelt/DischargeGiven.hh
M src/coupler/frontalmelt/DischargeRouting.hh
M src/coupler/frontalmelt/Given.hh
M src/coupler/ocean/Anomaly.hh
M src/coupler/ocean/GivenClimate.hh
M src/coupler/ocean/GivenTH.hh
M src/coupler/ocean/Pico.hh
M src/coupler/ocean/sea_level/Delta_SL_2D.hh
M src/coupler/surface/Anomaly.hh
M src/coupler/surface/ElevationChange.hh
M src/coupler/surface/GivenClimate.hh
M src/coupler/surface/ISMIP6Climate.hh
M src/coupler/surface/TemperatureIndex.hh
M src/earth/Given.hh
M src/frontretreat/PrescribedRetreat.hh
M src/util/iceModelVec2T.cc
M src/util/iceModelVec2T.hh

Log Message:
-----------
Remove typedef std::shared_ptr<IceModelVec2T> Ptr

Commit: 08e536a257630c03d48f6faf25875b2cc058eea5
https://github.com/pism/pism/commit/08e536a257630c03d48f6faf25875b2cc058eea5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-07-06 (Tue, 06 Jul 2021)

Changed paths:
M src/frontretreat/calving/CalvingAtThickness.cc
M src/frontretreat/calving/CalvingAtThickness.hh
M src/icemodel/frontretreat.cc
M src/pism_config.cdl

Log Message:
-----------
Implement the time-dependent calving thickness threshold

Renamed calving.thickness_calving.threshold_file to calving.thickness_calving.file for
consistency with other components using time-dependent forcing inputs.

Commit: 4f9a8adbd3ff9b7a9efac5292e5f7b5e5a15475a
https://github.com/pism/pism/commit/4f9a8adbd3ff9b7a9efac5292e5f7b5e5a15475a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-07-06 (Tue, 06 Jul 2021)

Changed paths:
M test/miscellaneous.py

Log Message:
-----------
Add a regression test

Commit: 06cb9d1200926c41b1a6f8e1fdf859b07f564c81
https://github.com/pism/pism/commit/06cb9d1200926c41b1a6f8e1fdf859b07f564c81
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-07-06 (Tue, 06 Jul 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/marine/calving.rst

Log Message:
-----------
Update the configuration parameter name in the manual

Commit: edb3692c3b3edb5bf18e24495a46d31d168b185e
https://github.com/pism/pism/commit/edb3692c3b3edb5bf18e24495a46d31d168b185e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-07-06 (Tue, 06 Jul 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/marine/calving.rst

Log Message:
-----------
Fix a variable name in the manual

It should be thickness_calving_threshold instead of calving_threshold.

Commit: 12a66699a193832cc8d2d67df38884d7ac61cfd9
https://github.com/pism/pism/commit/12a66699a193832cc8d2d67df38884d7ac61cfd9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-07-11 (Sun, 11 Jul 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/marine/calving.rst
M src/frontretreat/calving/CalvingAtThickness.cc
M src/frontretreat/calving/CalvingAtThickness.hh
M src/icemodel/frontretreat.cc
M src/pism_config.cdl
M test/miscellaneous.py

Log Message:
-----------
Merge branch 'ckhroulev/calving-thickness-threshold' into dev

Commit: dc87a59cce9002f7580b7509f541d35bd5239517
https://github.com/pism/pism/commit/dc87a59cce9002f7580b7509f541d35bd5239517
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-07-11 (Sun, 11 Jul 2021)

Changed paths:
M CHANGES.rst

Log Message:
-----------
Update the change log

Commit: 0c4c79141e1a57399fbf81e820632b7324ab3327
https://github.com/pism/pism/commit/0c4c79141e1a57399fbf81e820632b7324ab3327
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-02 (Mon, 02 Aug 2021)

Changed paths:
M .circleci/config.yml

Log Message:
-----------
Trying to deploy the manual to a different repository

Commit: a66794fbc07e50caa044835892c6e9d7d83f75ec
https://github.com/pism/pism/commit/a66794fbc07e50caa044835892c6e9d7d83f75ec
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-03 (Tue, 03 Aug 2021)

Changed paths:
M doc/browser/doxyfile

Log Message:
-----------
Update the doxyfile

- use SVG figures (more appropriate if we're going to commit doxygen output to GitHub)
- use MathJax to avoid the LaTeX dependency and lots of figures it would generate
- remove graphs illustrating include dependencies (to save space)

Commit: 5013d641a5615bf389709ad4d26d52f4ccadd56b
https://github.com/pism/pism/commit/5013d641a5615bf389709ad4d26d52f4ccadd56b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-03 (Tue, 03 Aug 2021)

Changed paths:
M doc/sphinx/installation/code/install_libraries.sh
M doc/sphinx/installation/debian-packages.csv

Log Message:
-----------
Remove python3-petsc4py because it is installed with PETSc

Commit: 5b8126691d31bbd0d133bfc7ac855a09d41519f6
https://github.com/pism/pism/commit/5b8126691d31bbd0d133bfc7ac855a09d41519f6
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-03 (Tue, 03 Aug 2021)

Changed paths:
M doc/sphinx/installation/code/petsc-mkl-mumps-hypre.sh
M doc/sphinx/installation/code/petsc-mumps-hypre.sh
M doc/sphinx/installation/code/petsc.sh

Log Message:
-----------
Make installation scripts executable

Commit: b7b1f511a592194e11b812a31e89fedf320b4c93
https://github.com/pism/pism/commit/b7b1f511a592194e11b812a31e89fedf320b4c93
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-03 (Tue, 03 Aug 2021)

Changed paths:
M docker/ubuntu-ci/CMakeLists.txt
M docker/ubuntu-ci/Dockerfile.in

Log Message:
-----------
Update the Docker image used to test PISM

- use Ubuntu 21.04
- don't install python3-petsc4py (installed with PETSc)
- don't install PIP
- install python3-sphinx and python3-sphinxcontrib.bibtex

Commit: cd7491c2ce0dedb91551b3ee23c742f764e0c833
https://github.com/pism/pism/commit/cd7491c2ce0dedb91551b3ee23c742f764e0c833
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-03 (Tue, 03 Aug 2021)

Changed paths:
M docker/ubuntu-ci/Dockerfile.in

Log Message:
-----------
Add doxygen and graphviz so that we can re-build the source code browser

Commit: dcc3c1c6edfdd4b913d708fab34888b0c9029ecd
https://github.com/pism/pism/commit/dcc3c1c6edfdd4b913d708fab34888b0c9029ecd
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-03 (Tue, 03 Aug 2021)

Changed paths:
M doc/CMakeLists.txt
M doc/browser/CMakeLists.txt
R doc/browser/doxybib.bst
R doc/browser/doxybib.dbj
R doc/browser/doxybib.py
M doc/browser/doxyfile
R doc/browser/figures/ssastencil.png
A doc/browser/list_references.py
R doc/browser/petsc.md
R doc/browser/pism.sty

Log Message:
-----------
Remove outdated parts of the source code browser

... and use pybtex to generate the list of references.

Commit: 94bfeb331015aa3dacdb6011b35f616d782d0b3c
https://github.com/pism/pism/commit/94bfeb331015aa3dacdb6011b35f616d782d0b3c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-03 (Tue, 03 Aug 2021)

Changed paths:
M .circleci/config.yml
M doc/CMakeLists.txt
M doc/browser/CMakeLists.txt
M docker/ubuntu-ci/Dockerfile.in

Log Message:
-----------
Add the build-source-browser job to the CircleCI config

Commit: da0fc27f23a09e793331fecca3deff535524de6a
https://github.com/pism/pism/commit/da0fc27f23a09e793331fecca3deff535524de6a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-03 (Tue, 03 Aug 2021)

Changed paths:
M doc/sphinx/installation/code/parallelio.sh
M docker/ubuntu-ci/Dockerfile.in

Log Message:
-----------
Make sure we use a specific ParallelIO version (2.5.4)

This way re-building this image will always produce the same software stack.

Commit: 36199d38205466ee09a0bb28709ea0749efb74c6
https://github.com/pism/pism/commit/36199d38205466ee09a0bb28709ea0749efb74c6
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-03 (Tue, 03 Aug 2021)

Changed paths:
M .circleci/config.yml

Log Message:
-----------
More work on the CircleCI setup

- save the PDF file so that we can easily download it
- fix copy-paste errors
- start work on deploying the PDF version of the manual and the source code browser

Commit: df385ba966dcb436017eeb635af1b706f7588495
https://github.com/pism/pism/commit/df385ba966dcb436017eeb635af1b706f7588495
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-03 (Tue, 03 Aug 2021)

Changed paths:
M .circleci/config.yml

Log Message:
-----------
Trying to fix the CircleCI config

Commit: 40dcf0c4cf2bb302d17cfdaff49641f2a266705a
https://github.com/pism/pism/commit/40dcf0c4cf2bb302d17cfdaff49641f2a266705a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-04 (Wed, 04 Aug 2021)

Changed paths:
M .circleci/config.yml

Log Message:
-----------
Try to deploy the PDF version of the manual to GitHub

Commit: 1c8c94d251ea714cec301ee1b7f7f92dd075358c
https://github.com/pism/pism/commit/1c8c94d251ea714cec301ee1b7f7f92dd075358c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-04 (Wed, 04 Aug 2021)

Changed paths:
M .circleci/config.yml

Log Message:
-----------
Don't deploy PDFs corresponding to broken code

Commit: 6b2e108eb45de55a83c01a3d4a065eb113f2410c
https://github.com/pism/pism/commit/6b2e108eb45de55a83c01a3d4a065eb113f2410c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-04 (Wed, 04 Aug 2021)

Changed paths:
M .circleci/config.yml

Log Message:
-----------
Try to deploy the source code browser

Commit: 7ccbe78892ba1017f2dd3638c2ba67797e5cc221
https://github.com/pism/pism/commit/7ccbe78892ba1017f2dd3638c2ba67797e5cc221
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-04 (Wed, 04 Aug 2021)

Changed paths:
M .circleci/config.yml

Log Message:
-----------
Fix the path to the source code browser

Commit: ff7830fb5b2f9656f744bd17e18deffd1299865e
https://github.com/pism/pism/commit/ff7830fb5b2f9656f744bd17e18deffd1299865e
Author: Kyle Blum <kbl...@alaska.edu>
Date: 2021-08-04 (Wed, 04 Aug 2021)

Changed paths:
M examples/searise-antarctica/antspin-coarse.sh

Log Message:
-----------
Fix antspin-coarse.sh

Added missing option bootstrap and Lz 5000 to the course simulation.

Commit: 71ef366f2c3cd369a9ef267c241674f41ad61abb
https://github.com/pism/pism/commit/71ef366f2c3cd369a9ef267c241674f41ad61abb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-04 (Wed, 04 Aug 2021)

Changed paths:
M doc/browser/mainpage.md
M doc/citing-pism.bib
M doc/ice-bib.bib
M doc/sphinx/global.txt
M doc/sphinx/installation/arch.rst
M doc/sphinx/manual/index.rst
M doc/sphinx/manual/jakobshavn/index.rst
M doc/sphinx/manual/practical-usage/modifying-pism.rst
M doc/sphinx/technical/release_checklist.rst

Log Message:
-----------
Update a few links

- CalCalcs home page is still broken, and there's no replacement
- use https where appropriate
- remove all mentions of pism-docs.org and replace with pism.github.io

Commit: 4ea1ccf9056341cdb2a3e8138f4db2d9dca86a20
https://github.com/pism/pism/commit/4ea1ccf9056341cdb2a3e8138f4db2d9dca86a20
Author: Simon Schöll <18572439...@users.noreply.github.com>
Date: 2021-08-11 (Wed, 11 Aug 2021)

Changed paths:
M src/frontretreat/calving/CalvingAtThickness.cc

Log Message:
-----------
Fix: thickness calving did not work with constant threshold

The previous condition to check for the file didn't work, because the filename defaults to the input file.

Commit: ea9c4343d2e3c0ed2937d18c2d6b0d293db455a0
https://github.com/pism/pism/commit/ea9c4343d2e3c0ed2937d18c2d6b0d293db455a0
Author: Andy Aschwanden <andy.as...@gmail.com>
Date: 2021-08-16 (Mon, 16 Aug 2021)

Changed paths:
M src/frontretreat/calving/CalvingAtThickness.cc

Log Message:
-----------
Merge pull request #489 from sschoell/sschoell/fix_thickness_calving

Fix: thickness calving does not work with constant threshold in dev branch

Commit: d3b0120d2472b8fe4afaa27da3c927b5f6c6e4ff
https://github.com/pism/pism/commit/d3b0120d2472b8fe4afaa27da3c927b5f6c6e4ff
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-16 (Mon, 16 Aug 2021)

Changed paths:
R examples/bedmap2/README.md
R examples/bedmap2/readgeom.py

Log Message:
-----------
Remove examples/bedmap2

Commit: 158ac5488e8c898159ba0ba69814491de68d7edf
https://github.com/pism/pism/commit/158ac5488e8c898159ba0ba69814491de68d7edf
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-16 (Mon, 16 Aug 2021)

Changed paths:
M examples/marine/flood/Makefile
M examples/marine/flood/README.md

Log Message:
-----------
Clean up examples/marine/flood

Commit: c462dc9ca675947b03a6d665b49c490769bef3f0
https://github.com/pism/pism/commit/c462dc9ca675947b03a6d665b49c490769bef3f0
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-16 (Mon, 16 Aug 2021)

Changed paths:
M examples/ismip-hom/abcd/Makefile
M examples/ismip-hom/abcd/README.rst

Log Message:
-----------
Improve examples/ismip-hom/abcd

Commit: d15cb349dc8b89d68ec018080b88526c01dcbf43
https://github.com/pism/pism/commit/d15cb349dc8b89d68ec018080b88526c01dcbf43
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-17 (Tue, 17 Aug 2021)

Changed paths:
M src/util/IceModelVec2V.hh
M src/util/iceModelVec.hh
M src/util/iceModelVec2.cc
M src/util/iceModelVec2V.cc
M src/util/iceModelVec_helpers.hh

Log Message:
-----------
IceModelVec methods add() and copy_from() don't need to be virtual

Now we can change argument types and have them (i.e. types) checked by the compiler.

Commit: 53533b4bd0f9d48272edfdfc580eadad2245d03f
https://github.com/pism/pism/commit/53533b4bd0f9d48272edfdfc580eadad2245d03f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-17 (Tue, 17 Aug 2021)

Changed paths:
M src/util/iceModelVec.hh
M src/util/iceModelVec3.cc

Log Message:
-----------
Add IceModelVec3::copy_from()

Commit: de4748da81cdb1ac8acdcad6d9ae76e4574e853b
https://github.com/pism/pism/commit/de4748da81cdb1ac8acdcad6d9ae76e4574e853b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-17 (Tue, 17 Aug 2021)

Changed paths:
M src/util/IceModelVec2V.hh
M src/util/iceModelVec.hh
M src/util/iceModelVec2.cc
M src/util/iceModelVec2V.cc

Log Message:
-----------
Add IceModelVec2{S,V}::allocate_copy()

... that allocates copies without ghosts that are used for diagnostic quantities.

Commit: 3d8b387d4b0b983f4edffee54bf2cc4796c4bcc3
https://github.com/pism/pism/commit/3d8b387d4b0b983f4edffee54bf2cc4796c4bcc3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-17 (Tue, 17 Aug 2021)

Changed paths:
M src/util/Diagnostic.hh

Log Message:
-----------
Use allocate_copy() in DiagWithDedicatedStorage::compute_impl()

Commit: 262a4280cb3ff9d1aaa3c2765a65320120e1a223
https://github.com/pism/pism/commit/262a4280cb3ff9d1aaa3c2765a65320120e1a223
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-17 (Tue, 17 Aug 2021)

Changed paths:
M src/util/Diagnostic.cc
M src/util/Diagnostic.hh

Log Message:
-----------
Use a template to implement Diagnostic::wrap()

Commit: 4eb70275f21fc1b886701397306a3ffb5d30ce7a
https://github.com/pism/pism/commit/4eb70275f21fc1b886701397306a3ffb5d30ce7a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-17 (Tue, 17 Aug 2021)

Changed paths:
M src/util/Diagnostic.hh

Log Message:
-----------
Use std::vector<>::emplace_back() in Diagnostic

Commit: 031c5a5ff1844f531e3f01f373dd8afc8785aeeb
https://github.com/pism/pism/commit/031c5a5ff1844f531e3f01f373dd8afc8785aeeb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-17 (Tue, 17 Aug 2021)

Changed paths:
M src/util/iceModelVec.hh
M src/util/iceModelVec3.cc

Log Message:
-----------
Implement IceModelVec3::allocate_copy()

Commit: 54f864e27ccd15d7bf13488f817212c29e67f19d
https://github.com/pism/pism/commit/54f864e27ccd15d7bf13488f817212c29e67f19d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-17 (Tue, 17 Aug 2021)

Changed paths:
M src/energy/CHSystem.cc
M src/energy/CHSystem.hh

Log Message:
-----------
CHSystem reports the ch_enthalpy diagnostic

Commit: b788549bd9d9ee1c0a0c13457309682901fecfa6
https://github.com/pism/pism/commit/b788549bd9d9ee1c0a0c13457309682901fecfa6
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-17 (Tue, 17 Aug 2021)

Changed paths:
M src/energy/EnergyModel.cc

Log Message:
-----------
Clean up EnergyModel

Now we can use Diagnostic::wrap() to report ice enthalpy (diagnostic "enthalpy").

Commit: aa56a7e1b6c64ccec4cc8a7732d5e3c956fe39e0
https://github.com/pism/pism/commit/aa56a7e1b6c64ccec4cc8a7732d5e3c956fe39e0
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-17 (Tue, 17 Aug 2021)

Changed paths:
M src/util/Diagnostic.cc
M src/util/Diagnostic.hh

Log Message:
-----------
A couple more fixes in Diagnostic.{cc,hh}

Commit: 2ce9940dccdba42a70f89531f749e9992376d8d2
https://github.com/pism/pism/commit/2ce9940dccdba42a70f89531f749e9992376d8d2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-23 (Mon, 23 Aug 2021)

Changed paths:
M doc/sphinx/global.txt

Log Message:
-----------
Update CalCalcs URLs

Commit: 16b7ec9f9934d2fd6172b14c9ff6e1afcd7e6cae
https://github.com/pism/pism/commit/16b7ec9f9934d2fd6172b14c9ff6e1afcd7e6cae
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-23 (Mon, 23 Aug 2021)

Changed paths:
M doc/sphinx/climate_forcing/surface.rst
M doc/sphinx/math-definitions.tex

Log Message:
-----------
Fix documentation of the "-surface elevation" model

Commit: a35bd9dd8a1029ef5a1f9013d657641fa2920162
https://github.com/pism/pism/commit/a35bd9dd8a1029ef5a1f9013d657641fa2920162
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-24 (Tue, 24 Aug 2021)

Changed paths:
M src/util/VariableMetadata.cc
M src/util/iceModelVec.hh

Log Message:
-----------
Minor cleanup

Commit: aef768acb5f94ffa2050e0e78f702353e9c49152
https://github.com/pism/pism/commit/aef768acb5f94ffa2050e0e78f702353e9c49152
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-24 (Tue, 24 Aug 2021)

Changed paths:
M examples/inverse/pismi.py
M src/util/iceModelVec.cc
M src/util/iceModelVec.hh

Log Message:
-----------
Remove IceModelVec::read_attributes()

Commit: 2be32305f05f5729f84b3fe4bef0a161ce1d3003
https://github.com/pism/pism/commit/2be32305f05f5729f84b3fe4bef0a161ce1d3003
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-24 (Tue, 24 Aug 2021)

Changed paths:
M src/util/StarStencil.hh

Log Message:
-----------
Minor cleanup

Commit: 00a2841892172cd4ebfb47995ad641576b1a90f2
https://github.com/pism/pism/commit/00a2841892172cd4ebfb47995ad641576b1a90f2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-25 (Wed, 25 Aug 2021)

Changed paths:
M src/earth/LingleClark.cc
M src/icemodel/diagnostics.cc
M src/util/Config.cc
M src/util/VariableMetadata.cc
M src/util/VariableMetadata.hh
M src/util/iceModelVec3.cc
M src/util/io/io_helpers.cc
M src/util/projection.cc

Log Message:
-----------
Clean up VariableMetadata

Remove "get_" from a few VariableMetadata and SpatialVariableMetadata methods (these do
not have corresponding "set_" methods).

Commit: ab5bffa8097b4e36101c784fc7c9ca162d229d70
https://github.com/pism/pism/commit/ab5bffa8097b4e36101c784fc7c9ca162d229d70
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-25 (Wed, 25 Aug 2021)

Changed paths:
M src/util/iceModelVec.cc

Log Message:
-----------
Use static_assert to check type compatibility

Commit: ded9000acf0ea5773267f96b94ea3ff24f38c8fa
https://github.com/pism/pism/commit/ded9000acf0ea5773267f96b94ea3ff24f38c8fa
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-26 (Thu, 26 Aug 2021)

Changed paths:
M src/util/options.cc
M src/util/pism_options.hh

Log Message:
-----------
Remove options::StringList and StringSet

Commit: 1d3068a2d9648c32524876472dc5b5df108ee59f
https://github.com/pism/pism/commit/1d3068a2d9648c32524876472dc5b5df108ee59f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/MaxTimestep.cc

Log Message:
-----------
Ensure that time steps are positive

Commit: 00c29ae8345562b27f23b439e34a05b64888ef8d
https://github.com/pism/pism/commit/00c29ae8345562b27f23b439e34a05b64888ef8d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/Time_Calendar.cc

Log Message:
-----------
Time_Calendar::date(double t) prints time as well (in hours)

Commit: 873f72561a99143a358466c902aa6b3139048cee
https://github.com/pism/pism/commit/873f72561a99143a358466c902aa6b3139048cee
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/Time_Calendar.cc
M src/util/Time_Calendar.hh

Log Message:
-----------
Time_Calendar::mod() works for simple calendars

... i.e. ones with constant year lengths.

Commit: 8e5c601e55f248e6721ae2450a0c2b80f432fa19
https://github.com/pism/pism/commit/8e5c601e55f248e6721ae2450a0c2b80f432fa19
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/Time.cc
M src/util/Time.hh
M src/util/Time_Calendar.cc
M src/util/Time_Calendar.hh

Log Message:
-----------
Move m_simple_calendar to Time

Commit: 1b485445492c5107543cedf1b719f917afc7a7fd
https://github.com/pism/pism/commit/1b485445492c5107543cedf1b719f917afc7a7fd
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/energy/btutest.cc
M src/pism_config.cdl
M src/util/Time.cc
M src/util/Time_Calendar.cc
M test/regression/beddef_lc_restart.sh
M test/regression/btu_regression.sh

Log Message:
-----------
Remove no_leap and none calendars

Commit: 5d4f69c8528f4aa457f88afd8041181cbceeb2dc
https://github.com/pism/pism/commit/5d4f69c8528f4aa457f88afd8041181cbceeb2dc
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/Time.cc
M src/util/Time.hh

Log Message:
-----------
Some cleanup

Commit: 040fa98f1f3317c991781e594fffa1dc9eadb806
https://github.com/pism/pism/commit/040fa98f1f3317c991781e594fffa1dc9eadb806
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/Time_Calendar.cc
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh

Log Message:
-----------
Move string_strip() to utilities

Commit: 6eb669d85e195e72a0f7ee4e85746fc597b5fae3
https://github.com/pism/pism/commit/6eb669d85e195e72a0f7ee4e85746fc597b5fae3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/Time.cc
M src/util/Time.hh

Log Message:
-----------
Tell C++ to generate a default destructor

Commit: fe4f48611ce1594c4ad292004eea9d572dc1c01a
https://github.com/pism/pism/commit/fe4f48611ce1594c4ad292004eea9d572dc1c01a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/pism_config.cdl

Log Message:
-----------
Rename time.start_year to time.start and add time.end

Commit: c14e5549f392546cae5312bd37b09898c7d111f3
https://github.com/pism/pism/commit/c14e5549f392546cae5312bd37b09898c7d111f3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/Time.cc

Log Message:
-----------
Always use Time_Calendar

Commit: 30233f17dece2c8ff86c0f754d2482cef0fe17a9
https://github.com/pism/pism/commit/30233f17dece2c8ff86c0f754d2482cef0fe17a9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/Time.cc
M src/util/Time.hh
M src/util/Time_Calendar.cc
M src/util/Time_Calendar.hh

Log Message:
-----------
Time_Calendar::increment_date() supports fractional years

Commit: dba044317b03dbd2a258ea04b46ffc1d2486b0dc
https://github.com/pism/pism/commit/dba044317b03dbd2a258ea04b46ffc1d2486b0dc
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/Time.cc
M src/util/Time_Calendar.cc

Log Message:
-----------
Some progress related to cleaning up the Time class

Commit: 555da9d40b222d75ed43090b89ba499c0d97b93f
https://github.com/pism/pism/commit/555da9d40b222d75ed43090b89ba499c0d97b93f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/energy/btutest.cc
M src/pism_config.cdl
M src/pismv.cc
M src/util/Context.cc
M src/util/Time.cc
M src/util/Time.hh
M src/util/Time_Calendar.cc
M src/util/Time_Calendar.hh
M src/util/Timeseries.cc
M src/util/iceModelVec2T.cc
M src/util/io/io_helpers.cc
M src/util/io/io_helpers.hh
M test/miscellaneous.py
M test/regression/beddef_lc_restart.sh

Log Message:
-----------
Work in progress

Regression tests pass

Commit: f4260001a78b96c60a3df3ee738f5cccf74b7dd7
https://github.com/pism/pism/commit/f4260001a78b96c60a3df3ee738f5cccf74b7dd7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/earth/LingleClark.cc
M src/hydrology/SteadyState.cc
M src/icebin/IBIceModel.cc
M src/icebin/VecBundleWriter.cc
M src/icemodel/initialization.cc
M src/util/Diagnostic.cc
M src/util/Time.cc
M src/util/Time.hh
M src/util/Time_Calendar.cc
M src/util/Time_Calendar.hh
M src/util/Timeseries.cc
M src/util/iceModelVec2T.cc
M src/util/io/io_helpers.cc
M src/util/io/io_helpers.hh

Log Message:
-----------
More cleaning up of time-related things

Commit: df58729b205f3c0aa740b2ec36f87d28a8d48265
https://github.com/pism/pism/commit/df58729b205f3c0aa740b2ec36f87d28a8d48265
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/energy/btutest.cc
M src/pism_config.cdl
M src/util/Time.cc
M src/util/Time.hh
M src/util/Time_Calendar.cc
M src/util/Time_Calendar.hh

Log Message:
-----------
Add time.file and time.file.continue

These parameters replace old options -time_file and -time_file_continue_run.

Commit: dc46752e611b33ffae80d8ce60804ea0a8da6163
https://github.com/pism/pism/commit/dc46752e611b33ffae80d8ce60804ea0a8da6163
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/Time.cc
M src/util/Time.hh
M src/util/Time_Calendar.cc
M src/util/Time_Calendar.hh

Log Message:
-----------
Even more cleaning up of time-related things

Commit: b19e5a798ed4683752d1c337cf337ddd02add9cc
https://github.com/pism/pism/commit/b19e5a798ed4683752d1c337cf337ddd02add9cc
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/energy/btutest.cc
M src/pismv.cc
M src/pythonbindings/PISM.i
M src/util/CMakeLists.txt
M src/util/Context.cc
M src/util/IceGrid.cc
M src/util/Time.cc
M src/util/Time.hh
R src/util/Time_Calendar.cc
R src/util/Time_Calendar.hh
M test/miscellaneous.py

Log Message:
-----------
Remove Time_Calendar

Commit: 7fa45ccae220c1e7b1e2763b42c1102cfebaf7a2
https://github.com/pism/pism/commit/7fa45ccae220c1e7b1e2763b42c1102cfebaf7a2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/Time.cc

Log Message:
-----------
Fix parse_date()

Commit: a099555bccf7933d448c6a976ee7be60c9bd658f
https://github.com/pism/pism/commit/a099555bccf7933d448c6a976ee7be60c9bd658f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/Time.cc

Log Message:
-----------
Cleanup

Commit: 13a26b6f3d2f2eeac83445783f56c67eaa7a0d90
https://github.com/pism/pism/commit/13a26b6f3d2f2eeac83445783f56c67eaa7a0d90
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/util/ScalarForcing.cc
M src/util/Time.cc
M src/util/Time.hh
M src/util/iceModelVec2T.cc

Log Message:
-----------
Rename Time::mod() to modulo() to make it easier to find all the uses

Commit: 40a7accc605acc4fd087bbe53147337b086840b1
https://github.com/pism/pism/commit/40a7accc605acc4fd087bbe53147337b086840b1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/atmosphere/WeatherStation.cc
M src/coupler/util/ScalarForcing.cc
M src/util/Timeseries.cc
M src/util/Timeseries.hh

Log Message:
-----------
Timeseries::read() takes time units instead of the time manager object

Commit: 26c1205bfb6dba4f4ff63ffb6e510838b361987a
https://github.com/pism/pism/commit/26c1205bfb6dba4f4ff63ffb6e510838b361987a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/atmosphere/WeatherStation.cc
M src/coupler/util/ScalarForcing.cc
M src/util/Timeseries.cc
M src/util/Timeseries.hh
M test/miscellaneous.py

Log Message:
-----------
A bit of cleanup in Timeseries

Commit: faa667713a8fde19bdae15ffa05f9deacd779945
https://github.com/pism/pism/commit/faa667713a8fde19bdae15ffa05f9deacd779945
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc
M src/icemodel/initialization.cc
M src/pythonbindings/PISM.i
M src/util/iceModelVec.cc
M src/util/iceModelVec.hh
M test/bed_smoother.py

Log Message:
-----------
Use std::array<double, 2> in IceModelVec::range()

Commit: c8d5d2fc88e49fe0755681db064c306158db8897
https://github.com/pism/pism/commit/c8d5d2fc88e49fe0755681db064c306158db8897
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/Timeseries.cc
M src/util/Timeseries.hh

Log Message:
-----------
Add Timeseries::time_interval()

Commit: d997f7804cad5c110271e02cc007bf374176c23a
https://github.com/pism/pism/commit/d997f7804cad5c110271e02cc007bf374176c23a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/util/ScalarForcing.cc
M src/coupler/util/ScalarForcing.hh

Log Message:
-----------
Re-write the periodic case in ScalarForcing

... using Timeseries::time_interval().

Commit: 91496a9e9a6680c6122ab96190b856d5e01a52e7
https://github.com/pism/pism/commit/91496a9e9a6680c6122ab96190b856d5e01a52e7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec.cc

Log Message:
-----------
Improve int_to_normtype()

We don't need a separate sanity check: the default case will do the job.

Commit: a1e92dd3a096b0c73077a4e3af2f56cd8b7a56d0
https://github.com/pism/pism/commit/a1e92dd3a096b0c73077a4e3af2f56cd8b7a56d0
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc

Log Message:
-----------
Use time_stepping.resolution in IceModelVec2T::max_timestep()

Commit: c43288df9fdb57d81ff5fea6552a372c552bbe03
https://github.com/pism/pism/commit/c43288df9fdb57d81ff5fea6552a372c552bbe03
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/atmosphere/CosineYearlyCycle.cc
M src/coupler/atmosphere/Delta_P.cc
M src/coupler/atmosphere/Delta_T.cc
M src/coupler/atmosphere/Frac_P.cc
M src/coupler/atmosphere/PrecipitationScaling.cc
M src/coupler/ocean/Delta_MBP.cc
M src/coupler/ocean/Delta_SMB.cc
M src/coupler/ocean/Delta_T.cc
M src/coupler/ocean/Frac_MBP.cc
M src/coupler/ocean/Frac_SMB.cc
M src/coupler/ocean/Runoff_SMB.cc
M src/coupler/ocean/sea_level/Delta_SL.cc
M src/coupler/surface/Delta_T.cc
M src/coupler/util/ScalarForcing.cc
M src/coupler/util/ScalarForcing.hh
M src/icemodel/initialization.cc
M test/regression/atmosphere_models.py
M test/regression/ocean_models.py
M test/regression/surface_models.py

Log Message:
-----------
Remove ScalarForcing::init() and do all of its work in the constructor

Commit: 92e79e9ca8d2d0ebd690c946020d322c97e2be22
https://github.com/pism/pism/commit/92e79e9ca8d2d0ebd690c946020d322c97e2be22
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/basalstrength/MohrCoulombYieldStress.cc
M src/coupler/atmosphere/Anomaly.cc
M src/coupler/atmosphere/ElevationChange.cc
M src/coupler/atmosphere/Frac_P.cc
M src/coupler/atmosphere/GivenClimate.cc
M src/coupler/frontalmelt/DischargeGiven.cc
M src/coupler/frontalmelt/DischargeRouting.cc
M src/coupler/frontalmelt/Given.cc
M src/coupler/ocean/Anomaly.cc
M src/coupler/ocean/GivenClimate.cc
M src/coupler/ocean/GivenTH.cc
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/sea_level/Delta_SL_2D.cc
M src/coupler/surface/Anomaly.cc
M src/coupler/surface/ElevationChange.cc
M src/coupler/surface/GivenClimate.cc
M src/coupler/surface/ISMIP6Climate.cc
M src/coupler/surface/TemperatureIndex.cc
M src/coupler/surface/TemperatureIndex.hh
M src/coupler/util/options.cc
M src/coupler/util/options.hh
M src/earth/Given.cc
M src/frontretreat/PrescribedRetreat.cc
M src/icemodel/IceModel.cc
M src/icemodel/initialization.cc
M src/pism_config.cdl
M src/util/iceModelVec2T.cc
M src/util/iceModelVec2T.hh
M test/icemodelvec2t.py
M test/miscellaneous.py
M test/regression/surface_models.py

Log Message:
-----------
IceModelVec2T::init() will deduce period length

Commit: 9854ed687df02c64151e75beb8d3fbaf5a1d806a
https://github.com/pism/pism/commit/9854ed687df02c64151e75beb8d3fbaf5a1d806a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/util/ScalarForcing.cc

Log Message:
-----------
Fix the use of "prefix + .periodic" in ScalarForcing

Commit: 7abe6fe343e1ac82ba16bc69833f2bc422df45bf
https://github.com/pism/pism/commit/7abe6fe343e1ac82ba16bc69833f2bc422df45bf
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/util/ScalarForcing.cc
M src/util/iceModelVec2T.cc
M test/icemodelvec2t.py

Log Message:
-----------
Fix periodic data handling in IceModelVec2T and ScalarForcing

Commit: b1a32c55b7fb933e51d7f3863b5c9d1141eb1851
https://github.com/pism/pism/commit/b1a32c55b7fb933e51d7f3863b5c9d1141eb1851
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/Time.cc
M src/util/Time.hh

Log Message:
-----------
Remove Time::modulo()

Commit: fd1c9a25f09ac4e139e1989a85a69c627c252f4d
https://github.com/pism/pism/commit/fd1c9a25f09ac4e139e1989a85a69c627c252f4d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/stressbalance/blatter/util/grid_hierarchy.cc

Log Message:
-----------
Exclude a few lines from coverage reports

Commit: 53dc57fc21ea26c5ac06967acefa10438566e83c
https://github.com/pism/pism/commit/53dc57fc21ea26c5ac06967acefa10438566e83c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/util/ScalarForcing.cc
M src/coupler/util/ScalarForcing.hh

Log Message:
-----------
Clean up ScalarForcing

Commit: f67414c614e27cb448cd5e7024668720185c4db2
https://github.com/pism/pism/commit/f67414c614e27cb448cd5e7024668720185c4db2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/atmosphere/CosineYearlyCycle.cc
M src/coupler/atmosphere/Delta_P.cc
M src/coupler/atmosphere/Delta_T.cc
M src/coupler/atmosphere/Frac_P.cc
M src/coupler/atmosphere/PrecipitationScaling.cc
M src/coupler/ocean/Delta_MBP.cc
M src/coupler/ocean/Delta_SMB.cc
M src/coupler/ocean/Delta_T.cc
M src/coupler/ocean/Frac_MBP.cc
M src/coupler/ocean/Frac_SMB.cc
M src/coupler/ocean/Runoff_SMB.cc
M src/coupler/ocean/sea_level/Delta_SL.cc
M src/coupler/surface/Delta_T.cc
M src/coupler/util/ScalarForcing.cc
M src/coupler/util/ScalarForcing.hh
M src/icemodel/initialization.cc

Log Message:
-----------
Use a const reference to Context in ScalarForcing

Commit: e9bee6a642dc35af6aefdb055eefe9a47a42bd32
https://github.com/pism/pism/commit/e9bee6a642dc35af6aefdb055eefe9a47a42bd32
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/util/ScalarForcing.hh

Log Message:
-----------
Fix an include guard

No need to use identifiers starting with an underscore

Commit: 87525ed690160dd654316796bc9922ac719062c1
https://github.com/pism/pism/commit/87525ed690160dd654316796bc9922ac719062c1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc

Log Message:
-----------
A few fixes inspired by clang-tidy

Commit: dddf7c802643a8d7507f5fd189abade90776eb4d
https://github.com/pism/pism/commit/dddf7c802643a8d7507f5fd189abade90776eb4d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/pythonbindings/PISM.i
M test/miscellaneous.py

Log Message:
-----------
Add a regression test to improve code coverage a bit

Commit: 1f0f9a93054061b48ae7387074291868cade60ca
https://github.com/pism/pism/commit/1f0f9a93054061b48ae7387074291868cade60ca
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/frontretreat/calving/CalvingAtThickness.cc
M src/pism_config.cdl

Log Message:
-----------
Update calving at a threshold thickness

Commit: d48fa90d894082ee1f90abc1dcceb2e7be80c88b
https://github.com/pism/pism/commit/d48fa90d894082ee1f90abc1dcceb2e7be80c88b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/util/ScalarForcing.cc

Log Message:
-----------
Better error message printed if reading a scalar forcing failed

Commit: 73a3d6253b713875dee681245731c5666d33e558
https://github.com/pism/pism/commit/73a3d6253b713875dee681245731c5666d33e558
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M site-packages/PISM/testing.py
M src/coupler/atmosphere/CosineYearlyCycle.cc
M src/coupler/atmosphere/Delta_P.cc
M src/coupler/atmosphere/Delta_T.cc
M src/coupler/atmosphere/Frac_P.cc
M src/coupler/atmosphere/PrecipitationScaling.cc
M src/coupler/atmosphere/SeariseGreenland.hh
M src/coupler/ocean/Cache.cc
M src/coupler/ocean/Cache.hh
M src/coupler/ocean/Delta_MBP.cc
M src/coupler/ocean/Delta_SMB.cc
M src/coupler/ocean/Delta_T.cc
M src/coupler/ocean/Frac_MBP.cc
M src/coupler/ocean/Frac_SMB.cc
M src/coupler/ocean/Runoff_SMB.cc
M src/coupler/ocean/sea_level/Delta_SL.cc
M src/coupler/surface/Cache.cc
M src/coupler/surface/Cache.hh
M src/coupler/surface/Delta_T.cc
M src/coupler/util/ScalarForcing.cc
M src/coupler/util/ScalarForcing.hh
M src/icemodel/frontretreat.cc
M src/pism_config.cdl
M src/util/Diagnostic.hh
M test/regression/surface_models.py

Log Message:
-----------
More work on ScalarForcing

Commit: e8f9dc5115f6810e7387fd3308300117b33aa302
https://github.com/pism/pism/commit/e8f9dc5115f6810e7387fd3308300117b33aa302
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/CMakeLists.txt
M src/coupler/atmosphere/CosineYearlyCycle.cc
M src/coupler/atmosphere/Delta_P.cc
M src/coupler/atmosphere/Delta_T.cc
M src/coupler/atmosphere/Frac_P.cc
M src/coupler/atmosphere/PrecipitationScaling.cc
M src/coupler/atmosphere/PrecipitationScaling.hh
M src/coupler/ocean/Delta_MBP.cc
M src/coupler/ocean/Delta_SMB.cc
M src/coupler/ocean/Delta_T.cc
M src/coupler/ocean/Frac_MBP.cc
M src/coupler/ocean/Frac_SMB.cc
M src/coupler/ocean/Runoff_SMB.cc
M src/coupler/ocean/sea_level/Delta_SL.cc
M src/coupler/surface/Delta_T.cc
R src/coupler/util/ScalarForcing.cc
R src/coupler/util/ScalarForcing.hh
M src/icemodel/IceModel.cc
M src/icemodel/frontretreat.cc
M src/icemodel/initialization.cc
M src/pythonbindings/PISM.i
M src/util/CMakeLists.txt
A src/util/ScalarForcing.cc
A src/util/ScalarForcing.hh

Log Message:
-----------
Move ScalarForcing from coupler/util/ to util/

Commit: e7f6a6c5ab91c93eb232487487286e2496f5322c
https://github.com/pism/pism/commit/e7f6a6c5ab91c93eb232487487286e2496f5322c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/ScalarForcing.cc

Log Message:
-----------
A bit of cleanup in ScalarForcing

Commit: 2a902a2e59230122542dc981f01341a08ffe6301
https://github.com/pism/pism/commit/2a902a2e59230122542dc981f01341a08ffe6301
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M test/miscellaneous.py

Log Message:
-----------
Add a test of interpolation of periodic forcing

Commit: 7ed5c948a88710271c64625fa29a729f23dcb9b8
https://github.com/pism/pism/commit/7ed5c948a88710271c64625fa29a729f23dcb9b8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/io/io_helpers.cc

Log Message:
-----------
Improve an error message

Commit: 45f8ff0733aa8f9d83cb90e560a30c8ae9c17bd5
https://github.com/pism/pism/commit/45f8ff0733aa8f9d83cb90e560a30c8ae9c17bd5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/ScalarForcing.cc

Log Message:
-----------
Remove an unnecessary sanity check

Commit: bfe98ad6264ba900a04f629ec88858eede21928c
https://github.com/pism/pism/commit/bfe98ad6264ba900a04f629ec88858eede21928c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M test/miscellaneous.py

Log Message:
-----------
Improve test coverage

Commit: 789812666b58c7d6f197e4a5b25ecf1da313e3f6
https://github.com/pism/pism/commit/789812666b58c7d6f197e4a5b25ecf1da313e3f6
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/ScalarForcing.cc
M src/util/ScalarForcing.hh

Log Message:
-----------
Work on ScalarForcing::average(t, dt)

Commit: 5a48cd36fad652990465c121da991010841d78ac
https://github.com/pism/pism/commit/5a48cd36fad652990465c121da991010841d78ac
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/atmosphere/CosineYearlyCycle.cc

Log Message:
-----------
Silence compiler warnings

Commit: c01fb360c41fc5ac91ce8929c224669cf423e31d
https://github.com/pism/pism/commit/c01fb360c41fc5ac91ce8929c224669cf423e31d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M test/miscellaneous.py

Log Message:
-----------
Add more regression tests

Commit: b588094a9e0f1d380ec815183e1ae1c57f12c6ce
https://github.com/pism/pism/commit/b588094a9e0f1d380ec815183e1ae1c57f12c6ce
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/frontalmelt/DischargeGiven.cc
M src/coupler/frontalmelt/DischargeRouting.cc
M src/coupler/frontalmelt/Given.cc
M src/coupler/ocean/GivenTH.cc
M src/coupler/surface/TemperatureIndex.cc
M src/frontretreat/calving/CalvingAtThickness.cc
M src/util/iceModelVec2T.cc
M src/util/iceModelVec2T.hh
M test/icemodelvec2t.py

Log Message:
-----------
Add IceModelVec2T::Constant() and remove init_constant()

Commit: 60df2f5ec57b3bf272d2a6650cf524d7bd01a06c
https://github.com/pism/pism/commit/60df2f5ec57b3bf272d2a6650cf524d7bd01a06c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/ScalarForcing.cc
M src/util/ScalarForcing.hh

Log Message:
-----------
Add a ScalarForcing constructor that does not use Config

Commit: dcd8c42d12e6576f0729a2029cc8cb33102fe6d9
https://github.com/pism/pism/commit/dcd8c42d12e6576f0729a2029cc8cb33102fe6d9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/atmosphere/WeatherStation.cc
M src/coupler/atmosphere/WeatherStation.hh

Log Message:
-----------
Use ScalarForcing in atmosphere::WeatherStation

Commit: bdd81870272a819806bfec7562b188b667ad0f88
https://github.com/pism/pism/commit/bdd81870272a819806bfec7562b188b667ad0f88
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M doc/browser/mainpage.md
M src/pythonbindings/CMakeLists.txt
M src/pythonbindings/PISM.i
R src/pythonbindings/pism_Timeseries.i
M src/util/CMakeLists.txt
R src/util/Timeseries.cc
R src/util/Timeseries.hh
M test/miscellaneous.py

Log Message:
-----------
Remove Timeseries (it is replaced by ScalarForcing)

Commit: e35ce45fbe69b15ce4bf74a2ee1dc5abd4595b27
https://github.com/pism/pism/commit/e35ce45fbe69b15ce4bf74a2ee1dc5abd4595b27
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc

Log Message:
-----------
Fix a comparison now that IceModelVec2T::Data::period is a double

Commit: 3eba046601510f196e266f8f52b8fe8f2b8aebb5
https://github.com/pism/pism/commit/3eba046601510f196e266f8f52b8fe8f2b8aebb5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc

Log Message:
-----------
Add a couple of comments

Commit: eb0772072db9b2ca38d106979af69c4426158b11
https://github.com/pism/pism/commit/eb0772072db9b2ca38d106979af69c4426158b11
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/pism_config.cdl
M src/util/ScalarForcing.cc

Log Message:
-----------
Start work on input.forcing.time_extrapolation

Commit: 07f0bfc70a5cb408ef3740af414554778efe845b
https://github.com/pism/pism/commit/07f0bfc70a5cb408ef3740af414554778efe845b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/energy/btutest.cc
M src/icebin/IBIceModel.cc
M src/icemodel/initialization.cc
M src/icemodel/output_extra.cc
M src/icemodel/output_save.cc
M src/icemodel/printout.cc
M src/icemodel/utilities.cc
M src/util/Time.cc
M src/util/Time.hh

Log Message:
-----------
Clean up: remove Time::date(), start_date(), and end_date()

Also: methods of Time don't need to be virtual any more

Commit: 50738416e8823cc10238bad0b56e9221cd309e54
https://github.com/pism/pism/commit/50738416e8823cc10238bad0b56e9221cd309e54
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/Time.cc

Log Message:
-----------
Print times with more precision

Commit: 273760b882badbbf2d4be72f1eaa20c491d0cb55
https://github.com/pism/pism/commit/273760b882badbbf2d4be72f1eaa20c491d0cb55
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/ScalarForcing.cc
M test/miscellaneous.py

Log Message:
-----------
Always use time bounds in ScalarForcing

- times are deduced from time bounds using mid-points of intervals in time bounds

- in the non-periodic case we extrapolate past mid-points of the first and last intervals
using *constant* extrapolation. This ensures that values returned by
ScalarForcing::value() are always within [min(data), max(data)]

- Stop the model if forcing data do not span the modeled time interval. This should
prevent some user mistakes. Disable this behavior by setting
input.forcing.time_extrapolation to "true".

- update tests to maintain 100% test (line) coverage of ScalarForcing

Commit: e8b0869c82a06260950fff9e7d4aebdd7fdfb767
https://github.com/pism/pism/commit/e8b0869c82a06260950fff9e7d4aebdd7fdfb767
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M CHANGES.rst

Log Message:
-----------
Update the change log

Commit: bb37918ff225097b36a5c4c2f00a42d9acf3addc
https://github.com/pism/pism/commit/bb37918ff225097b36a5c4c2f00a42d9acf3addc
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M doc/sphinx/climate_forcing/ocean.rst
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst

Log Message:
-----------
Remove last mentions of "xxx.period" and "xxx.reference_year" from the manual

Commit: ebf6d2acabcdf3c4f23d80a71a9d8af82d0a9100
https://github.com/pism/pism/commit/ebf6d2acabcdf3c4f23d80a71a9d8af82d0a9100
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M doc/sphinx/climate_forcing/atmosphere.rst
M doc/sphinx/climate_forcing/index.rst
M doc/sphinx/climate_forcing/ocean.rst
M doc/sphinx/climate_forcing/surface.rst
A doc/sphinx/climate_forcing/time-dependent.rst
R doc/sphinx/climate_forcing/time.rst
A doc/sphinx/climate_forcing/time.txt
M doc/sphinx/manual/highlevelview/climate-inputs.rst
M src/coupler/surface/TemperatureIndex.cc
M src/pism_config.cdl
M test/regression/surface_models.py

Log Message:
-----------
Update the climate forcing manual

- Use .. pism-parameters:: to generate lists of parameters

- Rename parameters with the prefix surface.pdd.std_dev so that all of them have a
consistent prefix. Most importantly, rename surface.pdd.std_dev to
surface.pdd.std_dev.value.

- Remove more mentions of ..._reference_year and ..._period.

Commit: 1775086c70acd92535331b08f17ba1b344dffdfc
https://github.com/pism/pism/commit/1775086c70acd92535331b08f17ba1b344dffdfc
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M examples/nbreen/README.md
M examples/nbreen/fake-inputtobed.py
M examples/nbreen/run.sh

Log Message:
-----------
Update examples/nbreen

Commit: bf20c2b7ea7fe20c9f2ba4bd79b2709c587c2b5c
https://github.com/pism/pism/commit/bf20c2b7ea7fe20c9f2ba4bd79b2709c587c2b5c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
A doc/sphinx/climate_forcing/delta_T.cdl
M doc/sphinx/climate_forcing/time-dependent.rst

Log Message:
-----------
More work on documenting how to use time-dependent forcing

Commit: 57e332dd992773714e4c41911392590ffce7b855
https://github.com/pism/pism/commit/57e332dd992773714e4c41911392590ffce7b855
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/ScalarForcing.cc
M test/miscellaneous.py
M test/regression/atmosphere_models.py
M test/regression/ocean_models.py
M test/regression/surface_models.py

Log Message:
-----------
Fix up ScalarForcing::initialize()

- Now we use times stored in the file instead of overriding them and validate both times
and time bounds.

- Always require time bounds

Commit: fdd38d200d2aa76cd53e18f66429c38d98358e82
https://github.com/pism/pism/commit/fdd38d200d2aa76cd53e18f66429c38d98358e82
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M doc/sphinx/climate_forcing/time-dependent.rst

Log Message:
-----------
Add notes about units and calendars

Commit: 71249438f81140fe44a7305e450219dc91edc97c
https://github.com/pism/pism/commit/71249438f81140fe44a7305e450219dc91edc97c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/Time.cc

Log Message:
-----------
Fix calendar initialization

Commit: 79d5a981425e67bd662a48bf6617dcb11cf26814
https://github.com/pism/pism/commit/79d5a981425e67bd662a48bf6617dcb11cf26814
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/ScalarForcing.cc
M src/util/io/io_helpers.cc
M src/util/io/io_helpers.hh

Log Message:
-----------
Create read_time_info() in io_helpers.cc

We can re-use this code in IceModelVec2T.

Commit: 6bcf880a186426223e3d1c2f2b20be00afe36399
https://github.com/pism/pism/commit/6bcf880a186426223e3d1c2f2b20be00afe36399
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc

Log Message:
-----------
Start work on IceModelVec2T::init()

Commit: fef0fb1950da504c7039b7743e3b2cba5a34ff74
https://github.com/pism/pism/commit/fef0fb1950da504c7039b7743e3b2cba5a34ff74
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/io/File.cc

Log Message:
-----------
A bit of cleanup in File::nrecords()

Commit: 62e8e404818b496a161b8d4b58004be0224cd14b
https://github.com/pism/pism/commit/62e8e404818b496a161b8d4b58004be0224cd14b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc

Log Message:
-----------
Improve the code checking if a variable has one record only

Commit: 9ec1b792472eca0c61a75858d50de7b8da2488c1
https://github.com/pism/pism/commit/9ec1b792472eca0c61a75858d50de7b8da2488c1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M test/icemodelvec2t.py

Log Message:
-----------
Update IceModelVec2T regression tests

Commit: ed4aa09a9cdcd08d1b89d02f48bb58044fe8d6e3
https://github.com/pism/pism/commit/ed4aa09a9cdcd08d1b89d02f48bb58044fe8d6e3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc

Log Message:
-----------
Fix the initialization of interpolation in IceModelVec2T

Commit: 27027a2843bc90b4f9a3bf0a44f7cba6f5caf0ae
https://github.com/pism/pism/commit/27027a2843bc90b4f9a3bf0a44f7cba6f5caf0ae
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M test/regression/beddef_given.py

Log Message:
-----------
Add time bounds to the -bed_def given regression test

Commit: b4af37dedca50a2c60726219f14279c2f402a053
https://github.com/pism/pism/commit/b4af37dedca50a2c60726219f14279c2f402a053
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M test/icemodelvec2t.py

Log Message:
-----------
Add one more IceModelVec2T test

Commit: e86af05b596497c0a7bda2a3160f0c06849b213f
https://github.com/pism/pism/commit/e86af05b596497c0a7bda2a3160f0c06849b213f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M site-packages/PISM/testing.py

Log Message:
-----------
Fix PISM.testing.create_forcing()

Now it respects "times" if both "times" and "time_bounds" are provided.

Commit: 23be39558dc971342a9c8a5dcb2ef9c4c80b47fc
https://github.com/pism/pism/commit/23be39558dc971342a9c8a5dcb2ef9c4c80b47fc
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M test/miscellaneous.py

Log Message:
-----------
Add time bounds to a regression test

Commit: 211ae204875e9c2860cf3c280f318d82bbb38560
https://github.com/pism/pism/commit/211ae204875e9c2860cf3c280f318d82bbb38560
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M test/regression/ocean_models.py

Log Message:
-----------
Add time bounds to one more regression test

Commit: fce5d5369b56b6f99b2ecc5ad9fe857667be0b83
https://github.com/pism/pism/commit/fce5d5369b56b6f99b2ecc5ad9fe857667be0b83
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc
M test/icemodelvec2t.py

Log Message:
-----------
Improve testing of IceModelVec2T

Also: IceModelVec2T::interp() respects the chosen interpolation type.

Commit: 60c841ff2c841f35d0ff697ce2ca1a9c9f40307a
https://github.com/pism/pism/commit/60c841ff2c841f35d0ff697ce2ca1a9c9f40307a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc

Log Message:
-----------
Avoid an unnecessary cast

Commit: 70aa823710e8d0356f2525a6944a25312f4edc7d
https://github.com/pism/pism/commit/70aa823710e8d0356f2525a6944a25312f4edc7d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc

Log Message:
-----------
Minor cleanup in IceModelVec2T

Commit: 09717fd14ace6a7b2695f522af84726778949530
https://github.com/pism/pism/commit/09717fd14ace6a7b2695f522af84726778949530
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc

Log Message:
-----------
Add a FIXME comment

Commit: 9913927077a85c54817380cbe9acaac01b567bc5
https://github.com/pism/pism/commit/9913927077a85c54817380cbe9acaac01b567bc5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/coupler/atmosphere/GivenClimate.cc
M src/coupler/ocean/GivenClimate.cc
M src/coupler/ocean/GivenTH.cc
M src/coupler/ocean/Pico.cc
M src/coupler/surface/GivenClimate.cc
M src/util/iceModelVec2T.cc
M src/util/iceModelVec2T.hh

Log Message:
-----------
Rename IceModelVec2T::n_records() to buffer_size()

Commit: e46fc5b29175ac0a69ef479134d0a8aed4495406
https://github.com/pism/pism/commit/e46fc5b29175ac0a69ef479134d0a8aed4495406
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc

Log Message:
-----------
Rename IceModelVec2T::Data::N to n_records

Commit: c9c1d40ecf38a66d502a861854f8664fdf6df6e4
https://github.com/pism/pism/commit/c9c1d40ecf38a66d502a861854f8664fdf6df6e4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc

Log Message:
-----------
Time bounds are never empty

Commit: 64d5521b16e5db17dd4d6b1f95f560936ba8605b
https://github.com/pism/pism/commit/64d5521b16e5db17dd4d6b1f95f560936ba8605b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/ScalarForcing.cc
M src/util/Time.cc
M src/util/Time.hh

Log Message:
-----------
Add check_forcing_duration()

This function checks if the modeled time interval is a subset of the interval in a forcing
file and stops PISM if it is not.

Commit: c8074d08cb6b78e9e6d6372ce32af96e3d58bdcb
https://github.com/pism/pism/commit/c8074d08cb6b78e9e6d6372ce32af96e3d58bdcb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc
M test/icemodelvec2t.py
M test/regression/beddef_given.py
M test/regression/surface_models.py

Log Message:
-----------
IceModelVec2T checks the forcing duration

Commit: 4adee1a4db60d9027e627b3b5ecf7a38ada5256b
https://github.com/pism/pism/commit/4adee1a4db60d9027e627b3b5ecf7a38ada5256b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M test/miscellaneous.py

Log Message:
-----------
Clean up some regression tests

Commit: edebcfc18e59a01e4919e05e009c5f41d1380bee
https://github.com/pism/pism/commit/edebcfc18e59a01e4919e05e009c5f41d1380bee
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/interpolation.cc
M src/util/interpolation.hh

Log Message:
-----------
Compute integration weights in the piece-wise constant case

Commit: 6e2cb621cdf92a0912e0da62521ac0f6caa94979
https://github.com/pism/pism/commit/6e2cb621cdf92a0912e0da62521ac0f6caa94979
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/interpolation.cc
M test/miscellaneous.py

Log Message:
-----------
Clean up interpolation code

... and add more regression tests

Commit: d521dfe027e6bd98cd23775b25a66e424420ae22
https://github.com/pism/pism/commit/d521dfe027e6bd98cd23775b25a66e424420ae22
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc
M src/util/iceModelVec2T.hh

Log Message:
-----------
Use the Interpolation class in IceModelVec2T::average()

Commit: deee07356255d804fc468d081b42d90b9598ccab
https://github.com/pism/pism/commit/deee07356255d804fc468d081b42d90b9598ccab
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M test/regression/beddef_given.py
M test/regression/ocean_models.py

Log Message:
-----------
Update some regression tests

Commit: 0bcf4592e1fb6ef31cb3ff823568bf69601eb2cd
https://github.com/pism/pism/commit/0bcf4592e1fb6ef31cb3ff823568bf69601eb2cd
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/ScalarForcing.cc
M src/util/interpolation.cc

Log Message:
-----------
Add comments explaining gsl_interp_bsearch() calls

Commit: 2de7769841efef675a6334246ad88d850baa41df
https://github.com/pism/pism/commit/2de7769841efef675a6334246ad88d850baa41df
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc
M src/util/interpolation.cc
M src/util/interpolation.hh
M test/miscellaneous.py

Log Message:
-----------
Rename Interpolation::integral() to integrate()

Commit: 97ad0b0b293538fa5416e4c72eefba2930eff5d4
https://github.com/pism/pism/commit/97ad0b0b293538fa5416e4c72eefba2930eff5d4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/pythonbindings/PISM.i
M src/util/iceModelVec2T.cc
M src/util/interpolation.cc
M src/util/interpolation.hh
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh
M test/miscellaneous.py

Log Message:
-----------
Isolate the code computing integration weights

Commit: c6b29cafef3290ba4a714503ffcf6535c94496d5
https://github.com/pism/pism/commit/c6b29cafef3290ba4a714503ffcf6535c94496d5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M test/miscellaneous.py

Log Message:
-----------
Improve regression tests

Commit: 956bf1a2d05fb05ea8ada7844578594752fc3a74
https://github.com/pism/pism/commit/956bf1a2d05fb05ea8ada7844578594752fc3a74
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc
M src/util/iceModelVec2T.hh

Log Message:
-----------
Remove an unused IceModelVec2T method

Commit: 581d226689e54205fc22c7a68a8d127af5eaedc3
https://github.com/pism/pism/commit/581d226689e54205fc22c7a68a8d127af5eaedc3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc
M src/util/iceModelVec2T.hh
M test/icemodelvec2t.py

Log Message:
-----------
More work on IceModelVec2T

- Work on averaging periodic data

- Better max_timestep() implementation. Instead of allowing steps up to the next record
only now we allow time steps to the last record that would fit in the buffer.

- Isolate the code initializing periodic data. Now we add two records (at the beginning
and the end of the period) to simplify interpolation.

- Remove time bounds from the implementation. In the piece-wise constant case time bounds
override times (this simplifies the search for the appropriate record to use at a given
time). In the linear case time bounds are not used (except to set the start and the
length of the period and check the duration of the forcing). In either case we do not
need to store time bounds explicitly.

Commit: a5556dff7362ab13047211ebfa78691b51fa228d
https://github.com/pism/pism/commit/a5556dff7362ab13047211ebfa78691b51fa228d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-08-30 (Mon, 30 Aug 2021)

Changed paths:
M src/util/iceModelVec2T.cc
M src/util/interpolation.cc
M src/util/interpolation.hh
M test/miscellaneous.py

Log Message:
-----------
Remove old code for piece-wise linear periodic interpolation

The new approach is better.

Commit: 8bf62674dbd10059e51b8198107f4dff86a28a9e
https://github.com/pism/pism/commit/8bf62674dbd10059e51b8198107f4dff86a28a9e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-09 (Thu, 09 Sep 2021)

Changed paths:
M CHANGES.rst
M src/basalstrength/MohrCoulombYieldStress.cc
M src/coupler/atmosphere/Anomaly.cc
M src/coupler/atmosphere/ElevationChange.cc
M src/coupler/atmosphere/Frac_P.cc
M src/coupler/atmosphere/GivenClimate.cc
M src/coupler/frontalmelt/DischargeGiven.cc
M src/coupler/frontalmelt/DischargeRouting.cc
M src/coupler/frontalmelt/Given.cc
M src/coupler/ocean/Anomaly.cc
M src/coupler/ocean/GivenClimate.cc
M src/coupler/ocean/GivenTH.cc
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/sea_level/Delta_SL_2D.cc
M src/coupler/surface/Anomaly.cc
M src/coupler/surface/ElevationChange.cc
M src/coupler/surface/GivenClimate.cc
M src/coupler/surface/ISMIP6Climate.cc
M src/coupler/surface/TemperatureIndex.cc
M src/earth/Given.cc
M src/frontretreat/PrescribedRetreat.cc
M src/frontretreat/calving/CalvingAtThickness.cc
M src/icemodel/IceModel.cc
M src/pism_config.cdl
M src/util/iceModelVec2T.cc
M src/util/iceModelVec2T.hh
M test/icemodelvec2t.py
M test/miscellaneous.py

Log Message:
-----------
Remove input.forcing.evaluations_per_year

Commit: f1b7821fe0cfc63d63551cca15a2167e1cd72824
https://github.com/pism/pism/commit/f1b7821fe0cfc63d63551cca15a2167e1cd72824
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-09 (Thu, 09 Sep 2021)

Changed paths:
R doc/sphinx/climate_forcing/time.txt

Log Message:
-----------
Remove the old manual section about managing time

Commit: 4e5da605f22a5f15d40079f379edcf14dca311ca
https://github.com/pism/pism/commit/4e5da605f22a5f15d40079f379edcf14dca311ca
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-09 (Thu, 09 Sep 2021)

Changed paths:
M CHANGES.rst

Log Message:
-----------
Update the change log

Commit: 5678c496dcbb41580dd55d7b312f8d50831a5e32
https://github.com/pism/pism/commit/5678c496dcbb41580dd55d7b312f8d50831a5e32
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-09 (Thu, 09 Sep 2021)

Changed paths:
M CHANGES.rst
M doc/browser/mainpage.md
M doc/sphinx/climate_forcing/atmosphere.rst
A doc/sphinx/climate_forcing/delta_T.cdl
M doc/sphinx/climate_forcing/index.rst
M doc/sphinx/climate_forcing/ocean.rst
M doc/sphinx/climate_forcing/surface.rst
A doc/sphinx/climate_forcing/time-dependent.rst
R doc/sphinx/climate_forcing/time.rst
M doc/sphinx/manual/highlevelview/climate-inputs.rst
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst
M examples/nbreen/README.md
M examples/nbreen/fake-inputtobed.py
M examples/nbreen/run.sh
M site-packages/PISM/testing.py
M src/basalstrength/MohrCoulombYieldStress.cc
M src/coupler/CMakeLists.txt
M src/coupler/atmosphere/Anomaly.cc
M src/coupler/atmosphere/CosineYearlyCycle.cc
M src/coupler/atmosphere/Delta_P.cc
M src/coupler/atmosphere/Delta_T.cc
M src/coupler/atmosphere/ElevationChange.cc
M src/coupler/atmosphere/Frac_P.cc
M src/coupler/atmosphere/GivenClimate.cc
M src/coupler/atmosphere/PrecipitationScaling.cc
M src/coupler/atmosphere/PrecipitationScaling.hh
M src/coupler/atmosphere/SeariseGreenland.hh
M src/coupler/atmosphere/WeatherStation.cc
M src/coupler/atmosphere/WeatherStation.hh
M src/coupler/frontalmelt/DischargeGiven.cc
M src/coupler/frontalmelt/DischargeRouting.cc
M src/coupler/frontalmelt/Given.cc
M src/coupler/ocean/Anomaly.cc
M src/coupler/ocean/Cache.cc
M src/coupler/ocean/Cache.hh
M src/coupler/ocean/Delta_MBP.cc
M src/coupler/ocean/Delta_SMB.cc
M src/coupler/ocean/Delta_T.cc
M src/coupler/ocean/Frac_MBP.cc
M src/coupler/ocean/Frac_SMB.cc
M src/coupler/ocean/GivenClimate.cc
M src/coupler/ocean/GivenTH.cc
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/Runoff_SMB.cc
M src/coupler/ocean/sea_level/Delta_SL.cc
M src/coupler/ocean/sea_level/Delta_SL_2D.cc
M src/coupler/surface/Anomaly.cc
M src/coupler/surface/Cache.cc
M src/coupler/surface/Cache.hh
M src/coupler/surface/Delta_T.cc
M src/coupler/surface/ElevationChange.cc
M src/coupler/surface/GivenClimate.cc
M src/coupler/surface/ISMIP6Climate.cc
M src/coupler/surface/TemperatureIndex.cc
M src/coupler/surface/TemperatureIndex.hh
R src/coupler/util/ScalarForcing.cc
R src/coupler/util/ScalarForcing.hh
M src/coupler/util/options.cc
M src/coupler/util/options.hh
M src/earth/Given.cc
M src/earth/LingleClark.cc
M src/energy/btutest.cc
M src/frontretreat/PrescribedRetreat.cc
M src/frontretreat/calving/CalvingAtThickness.cc
M src/hydrology/SteadyState.cc
M src/icebin/IBIceModel.cc
M src/icebin/VecBundleWriter.cc
M src/icemodel/IceModel.cc
M src/icemodel/frontretreat.cc
M src/icemodel/initialization.cc
M src/icemodel/output_extra.cc
M src/icemodel/output_save.cc
M src/icemodel/printout.cc
M src/icemodel/utilities.cc
M src/pism_config.cdl
M src/pismv.cc
M src/pythonbindings/CMakeLists.txt
M src/pythonbindings/PISM.i
R src/pythonbindings/pism_Timeseries.i
M src/stressbalance/blatter/util/grid_hierarchy.cc
M src/util/CMakeLists.txt
M src/util/Context.cc
M src/util/Diagnostic.cc
M src/util/Diagnostic.hh
M src/util/IceGrid.cc
A src/util/ScalarForcing.cc
A src/util/ScalarForcing.hh
M src/util/Time.cc
M src/util/Time.hh
R src/util/Time_Calendar.cc
R src/util/Time_Calendar.hh
R src/util/Timeseries.cc
R src/util/Timeseries.hh
M src/util/iceModelVec.cc
M src/util/iceModelVec.hh
M src/util/iceModelVec2T.cc
M src/util/iceModelVec2T.hh
M src/util/interpolation.cc
M src/util/interpolation.hh
M src/util/io/File.cc
M src/util/io/io_helpers.cc
M src/util/io/io_helpers.hh
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh
M test/bed_smoother.py
M test/icemodelvec2t.py
M test/miscellaneous.py
M test/regression/atmosphere_models.py
M test/regression/beddef_given.py
M test/regression/beddef_lc_restart.sh
M test/regression/btu_regression.sh
M test/regression/ocean_models.py
M test/regression/surface_models.py

Log Message:
-----------
Merge branch 'ckhroulev/time' into dev

Commit: 4886c5f3a68b7691ef765e2e4674409e923c9a65
https://github.com/pism/pism/commit/4886c5f3a68b7691ef765e2e4674409e923c9a65
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-09 (Thu, 09 Sep 2021)

Changed paths:
M src/age/AgeModel.cc
M src/coupler/atmosphere/GivenClimate.cc
M src/coupler/atmosphere/OrographicPrecipitation.cc
M src/coupler/atmosphere/YearlyCycle.cc
M src/coupler/frontalmelt/FrontalMelt.cc
M src/coupler/ocean/Initialization.cc
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/sea_level/Initialization.cc
M src/coupler/surface/GivenClimate.cc
M src/coupler/surface/ISMIP6Climate.cc
M src/coupler/surface/StuffAsAnomaly.cc
M src/coupler/surface/SurfaceModel.cc
M src/coupler/surface/TemperatureIndex.cc
A src/coupler/util/ScalarForcing.cc
M src/earth/LingleClark.cc
M src/energy/BTU_Full.cc
M src/energy/BedThermalUnit.cc
M src/energy/CHSystem.cc
M src/energy/EnergyModel.cc
M src/energy/TemperatureModel.cc
M src/fracturedensity/FractureDensity.cc
M src/frontretreat/calving/CalvingAtThickness.cc
M src/geometry/Geometry.cc
M src/hydrology/Distributed.cc
M src/hydrology/Hydrology.cc
M src/hydrology/Routing.cc
M src/hydrology/SteadyState.cc
M src/icemodel/IceModel.cc
M src/icemodel/diagnostics.cc
M src/icemodel/flux_balance.hh
M src/icemodel/initialization.cc
M src/icemodel/output.cc
M src/icemodel/utilities.cc
M src/pythonbindings/pism_VariableMetadata.i
M src/regional/IceRegionalModel.cc
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/StressBalance_diagnostics.cc
M src/stressbalance/sia/SIAFD_diagnostics.cc
M src/stressbalance/ssa/SSA.cc
M src/stressbalance/ssa/SSATestCase.cc
M src/util/Config.cc
M src/util/Diagnostic.cc
M src/util/Diagnostic.hh
M src/util/ScalarForcing.cc
M src/util/Time.cc
A src/util/Time_Calendar.cc
M src/util/VariableMetadata.cc
M src/util/VariableMetadata.hh
M src/util/iceModelVec.cc
M src/util/iceModelVec3.cc
M src/util/io/io_helpers.cc
M src/util/projection.cc
M src/verification/iceCompModel.cc

Log Message:
-----------
Use operator[] to set attributes

Commit: 89d921e426011e59248b3a1fb7759adab04aab49
https://github.com/pism/pism/commit/89d921e426011e59248b3a1fb7759adab04aab49
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-13 (Mon, 13 Sep 2021)

Changed paths:
R src/util/Time_Calendar.cc

Log Message:
-----------
Delete Time_Calendar.cc

Commit: 9c14a28d6c9e2286ee49f6323a4284382d6bef64
https://github.com/pism/pism/commit/9c14a28d6c9e2286ee49f6323a4284382d6bef64
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-13 (Mon, 13 Sep 2021)

Changed paths:
M src/util/IceGrid.cc

Log Message:
-----------
Minor cleanup

Commit: 8c9ee0106279873a0f7f02913b5ba09543ee903f
https://github.com/pism/pism/commit/8c9ee0106279873a0f7f02913b5ba09543ee903f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-13 (Mon, 13 Sep 2021)

Changed paths:
M src/util/Time.cc
M src/util/options.cc
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh

Log Message:
-----------
Add parse_integer() and parse_number()

Commit: eab7835e5345423851f9d198424fbb714999de1e
https://github.com/pism/pism/commit/eab7835e5345423851f9d198424fbb714999de1e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-13 (Mon, 13 Sep 2021)

Changed paths:
M CHANGES.rst
M src/fracturedensity/FractureDensity.cc
M src/pism_config.cdl

Log Message:
-----------
Port Torsten's code to the current dev branch

Commit: bb1227db8d803fc2e8aff3b9a6eadbb8bcad0890
https://github.com/pism/pism/commit/bb1227db8d803fc2e8aff3b9a6eadbb8bcad0890
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-13 (Mon, 13 Sep 2021)

Changed paths:
M src/fracturedensity/FractureDensity.cc

Log Message:
-----------
Remove an unused variable

Commit: ee816f1ec6377cb90c41b3eeac21255ef7df01a6
https://github.com/pism/pism/commit/ee816f1ec6377cb90c41b3eeac21255ef7df01a6
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-14 (Tue, 14 Sep 2021)

Changed paths:
M src/pism_config.cdl
M src/util/Time.cc

Log Message:
-----------
Fix -time_file handling

Commit: 058922f3a6a32ea3a74e246d9c98a0c809e71178
https://github.com/pism/pism/commit/058922f3a6a32ea3a74e246d9c98a0c809e71178
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-14 (Tue, 14 Sep 2021)

Changed paths:
M src/pism_config.cdl
M src/util/Time.cc

Log Message:
-----------
Fix -time_file handling

Commit: 37a9923de2721f8044f42f0e88003e9459484ede
https://github.com/pism/pism/commit/37a9923de2721f8044f42f0e88003e9459484ede
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-09-15 (Wed, 15 Sep 2021)

Changed paths:
M examples/ross/fracture/README.md
M examples/ross/fracture/run_frac.sh
A examples/ross/fracture/run_frac_borstad.sh

Log Message:
-----------
Added bash Ross fracture example with Borstad limit as option

Commit: e0beab31e67ca76e3aee1e0dc568767c7c2ea92d
https://github.com/pism/pism/commit/e0beab31e67ca76e3aee1e0dc568767c7c2ea92d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-15 (Wed, 15 Sep 2021)

Changed paths:
M doc/sphinx/conf.py

Log Message:
-----------
Support both Sphinx 3.x and Sphinx 4.x

Commit: d0be4e0a101b0c6d8c1d3e7793a41d3ecd4577f7
https://github.com/pism/pism/commit/d0be4e0a101b0c6d8c1d3e7793a41d3ecd4577f7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-16 (Thu, 16 Sep 2021)

Changed paths:
M src/geometry/GeometryEvolution.cc
M src/geometry/GeometryEvolution.hh
M src/icemodel/IceModel.cc

Log Message:
-----------
Add GeometryEvolution::reset()

This method sets the conservation error to zero at the beginning of a time step.

Commit: 823efe074551ca29069bbc4adda3c4f85cdefb11
https://github.com/pism/pism/commit/823efe074551ca29069bbc4adda3c4f85cdefb11
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-16 (Thu, 16 Sep 2021)

Changed paths:
M CHANGES.rst
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/diagnostics.cc
M src/icemodel/fracture_density.cc
M src/icemodel/frontretreat.cc
M src/icemodel/initialization.cc
M src/icemodel/timestepping.cc
M src/regional/IceRegionalModel.cc
M src/verification/iceCompModel.cc
M test/test_hydrology/inputforP_regression.nc

Log Message:
-----------
Rename bc_mask -> vel_bc_mask, {u,v}_ssa_bc -> {u,v}_bc

Commit: 1df8546289bba436499efa2ad685c7d944267e09
https://github.com/pism/pism/commit/1df8546289bba436499efa2ad685c7d944267e09
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-16 (Thu, 16 Sep 2021)

Changed paths:
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh

Log Message:
-----------
Add the ice thickness BC mask "thk_bc_mask" to IceModel

Commit: e9bad2f14befb253a0b6c627c2c45966648bff2b
https://github.com/pism/pism/commit/e9bad2f14befb253a0b6c627c2c45966648bff2b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-16 (Thu, 16 Sep 2021)

Changed paths:
M CHANGES.rst
M src/geometry/GeometryEvolution.cc
M src/icemodel/IceModel.cc
M src/icemodel/diagnostics.cc
M src/icemodel/frontretreat.cc
M src/icemodel/initialization.cc
M src/icemodel/timestepping.cc
M src/regional/IceRegionalModel.cc
M src/verification/iceCompModel.cc

Log Message:
-----------
Add the ice thickness BC mask variable thk_bc_mask

This mask is combined with the sliding (SSA) velocity BC mask. In other words: we keep ice
thickness fixed at all the grid points where the sliding velocity is fixed.

Commit: e79da79c2cce40ce32636a89ab006ce6232fb6b0
https://github.com/pism/pism/commit/e79da79c2cce40ce32636a89ab006ce6232fb6b0
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-09-16 (Thu, 16 Sep 2021)

Changed paths:
M examples/ross/fracture/README.md
M examples/ross/fracture/run_frac.sh
M examples/ross/fracture/run_frac_borstad.sh
M src/fracturedensity/FractureDensity.cc
M src/pism_config.cdl

Log Message:
-----------
Added infos to fracture density options in config. Added min criterion for healing. Some clean up in example/ross/fracture

Commit: 9be4c15f18e35b5ad15badf119258697e9a0c5fd
https://github.com/pism/pism/commit/9be4c15f18e35b5ad15badf119258697e9a0c5fd
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-09-16 (Thu, 16 Sep 2021)

Changed paths:
M doc/ice-bib.bib
A doc/sphinx/manual/modeling-choices/marine/damage.rst
M doc/sphinx/manual/modeling-choices/marine/index.rst

Log Message:
-----------
Added some documentation (draft) on fracture density code

Commit: 285a9e93fc56a9ab96b03cfe9e51b6b8cbb41675
https://github.com/pism/pism/commit/285a9e93fc56a9ab96b03cfe9e51b6b8cbb41675
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-09-16 (Thu, 16 Sep 2021)

Changed paths:
M examples/ross/fracture/README.md
M examples/ross/fracture/run_frac.sh
A examples/ross/fracture/run_frac_borstad.sh
M src/fracturedensity/FractureDensity.cc
M src/pism_config.cdl

Log Message:
-----------
Merge branch 'ckhrulev/fracture-density-borstad-limit' of ssh://github.com/pism/pism into fracture-density-borstad-limit

Commit: 9171c336b7ee4ba6b2509980c85b5559b2e204ed
https://github.com/pism/pism/commit/9171c336b7ee4ba6b2509980c85b5559b2e204ed
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-09-16 (Thu, 16 Sep 2021)

Changed paths:
M doc/ice-bib.bib
M doc/sphinx/manual/modeling-choices/marine/damage.rst

Log Message:
-----------
Some clean up on fracture density documentation in manual

Commit: 17f283dd50e372ae47412fac0ff3050b7f24106f
https://github.com/pism/pism/commit/17f283dd50e372ae47412fac0ff3050b7f24106f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-16 (Thu, 16 Sep 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/marine/damage.rst

Log Message:
-----------
Fix rst formatting issues

Commit: a8d14bbfedfe9c56732e5723c77575c72c17f3b1
https://github.com/pism/pism/commit/a8d14bbfedfe9c56732e5723c77575c72c17f3b1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-16 (Thu, 16 Sep 2021)

Changed paths:
M src/geometry/Geometry.cc
M src/geometry/Geometry.hh
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/initialization.cc

Log Message:
-----------
A bit of cleanup

Commit: 34f0afd5ef5a785282bb8fd2b6d8d6c13d64a5be
https://github.com/pism/pism/commit/34f0afd5ef5a785282bb8fd2b6d8d6c13d64a5be
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-16 (Thu, 16 Sep 2021)

Changed paths:
M doc/sphinx/contributing/development-workflow.rst

Log Message:
-----------
Improve the manual section about editing the manual

Commit: e0982de54d24bdd6677bbed9454dfdf96d5e3ae4
https://github.com/pism/pism/commit/e0982de54d24bdd6677bbed9454dfdf96d5e3ae4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-16 (Thu, 16 Sep 2021)

Changed paths:
M doc/sphinx/conf.py

Log Message:
-----------
Support both Sphinx 3.x and Sphinx 4.x

Commit: aa68c39a01e71343ec2380189834cbdaf352ab9e
https://github.com/pism/pism/commit/aa68c39a01e71343ec2380189834cbdaf352ab9e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-16 (Thu, 16 Sep 2021)

Changed paths:
M src/geometry/Geometry.cc
M src/geometry/Geometry.hh
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/initialization.cc

Log Message:
-----------
A bit of cleanup

Commit: 7ad89f2e3a0f4f613426eb217855ec6383470ccf
https://github.com/pism/pism/commit/7ad89f2e3a0f4f613426eb217855ec6383470ccf
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-16 (Thu, 16 Sep 2021)

Changed paths:
M doc/sphinx/contributing/development-workflow.rst

Log Message:
-----------
Improve the manual section about editing the manual

Commit: cacba1a5fb22be7dc7c3b5dd0667267d43036b60
https://github.com/pism/pism/commit/cacba1a5fb22be7dc7c3b5dd0667267d43036b60
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-16 (Thu, 16 Sep 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/marine/damage.rst
M src/fracturedensity/FractureDensity.cc
M src/pism_config.cdl

Log Message:
-----------
Work on cleaning up the documentation of the fracture density model

Commit: 50464945546af28690956ae6d88307170cfec62e
https://github.com/pism/pism/commit/50464945546af28690956ae6d88307170cfec62e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-17 (Fri, 17 Sep 2021)

Changed paths:
M src/fracturedensity/FractureDensity.cc
M src/pism_config.cdl

Log Message:
-----------
Use configuration parameters instead of command-line options

Commit: 38f895b6e2851e1d62443db63e615fce0032edac
https://github.com/pism/pism/commit/38f895b6e2851e1d62443db63e615fce0032edac
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-17 (Fri, 17 Sep 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/marine/damage.rst

Log Message:
-----------
A few minor edits

Commit: 5d24e5270379d9e0801e4c6587d34e01fd2f09b7
https://github.com/pism/pism/commit/5d24e5270379d9e0801e4c6587d34e01fd2f09b7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-17 (Fri, 17 Sep 2021)

Changed paths:
M examples/ross/fracture/run_frac.sh
M examples/ross/fracture/run_frac_borstad.sh

Log Message:
-----------
Update example scripts

Commit: ea45b370b0261d08f68794820d18c568eb34623e
https://github.com/pism/pism/commit/ea45b370b0261d08f68794820d18c568eb34623e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-17 (Fri, 17 Sep 2021)

Changed paths:
M src/pism_config.cdl

Log Message:
-----------
A couple more edits

Commit: 9d5248f8a5253d6f9336400ac53855609075343d
https://github.com/pism/pism/commit/9d5248f8a5253d6f9336400ac53855609075343d
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-09-18 (Sat, 18 Sep 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/marine/damage.rst

Log Message:
-----------
Minor edits in fracture doc

Commit: 2325f05f9290592db66bccab4d27a5f828be072d
https://github.com/pism/pism/commit/2325f05f9290592db66bccab4d27a5f828be072d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-20 (Mon, 20 Sep 2021)

Changed paths:
M src/util/Time.cc

Log Message:
-----------
Fix the initialization of time units when -time_file is used

Commit: 84374371a430ed982fbbac6b9f6e973a72dec04c
https://github.com/pism/pism/commit/84374371a430ed982fbbac6b9f6e973a72dec04c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-20 (Mon, 20 Sep 2021)

Changed paths:
M src/util/Time.cc

Log Message:
-----------
Fix the initialization of time units when -time_file is used

Commit: 55ae39ec7973d1c099aa44f994df39d1f6372979
https://github.com/pism/pism/commit/55ae39ec7973d1c099aa44f994df39d1f6372979
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-29 (Wed, 29 Sep 2021)

Changed paths:
M src/geometry/GeometryEvolution.cc
M src/geometry/GeometryEvolution.hh

Log Message:
-----------
Include the influence of fixing ice thickness on mass conservation

Commit: d838cf346b387ea3fbe6c60cf365c95d3f5510f3
https://github.com/pism/pism/commit/d838cf346b387ea3fbe6c60cf365c95d3f5510f3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-29 (Wed, 29 Sep 2021)

Changed paths:
M src/coupler/surface/TemperatureIndex.cc
M src/frontretreat/calving/CalvingAtThickness.cc

Log Message:
-----------
Fix metadata set when air_temp_sd and thickness_calving_threshold are constant

Commit: 4c2498d5996670f8a9eb96c8da6eaeab0c6f464e
https://github.com/pism/pism/commit/4c2498d5996670f8a9eb96c8da6eaeab0c6f464e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-29 (Wed, 29 Sep 2021)

Changed paths:
M doc/pismpython/inverse/index.rst
M doc/pismpython/inverse/pism_ssa.rst
M doc/pismpython/inverse/pismi.rst
M doc/sphinx/manual/diagnostics/diagnostics-list.txt
M doc/sphinx/manual/jakobshavn/index.rst
M doc/sphinx/manual/validation/ross.rst
M examples/jako/century.sh
M examples/jako/preprocess.sh
M examples/jako/spinup.sh
M examples/marine/circular/circular_dirichlet.py
M examples/marine/circular/piktests_utils.py
M examples/marine/circular/test_iceberg_removal.py
M examples/marine/flowline/createSetup_flowline.py
M examples/marine/flowline/run_flowline.sh
M examples/marine/tongues/generate_input.py
M examples/nbreen/preprocess.sh
M examples/python/ssa_tests/ssa_test_cfbc.py
M examples/python/ssa_tests/ssa_test_linear.py
M examples/python/ssa_tests/ssa_test_plug.py
M examples/python/ssa_tests/ssa_testi.py
M examples/python/ssa_tests/ssa_testj.py
M examples/ross/fracture/fracture_model.py
M examples/ross/plot.py
M examples/ross/preprocess.py
M site-packages/PISM/invert/ssa.py
M site-packages/PISM/model.py
M site-packages/PISM/ssa.py
M src/icemodel/initialization.cc
M src/inverse/IP_SSAHardavForwardProblem.cc
M src/inverse/IP_SSATaucForwardProblem.cc
M src/verification/tests/exactQ.py
M test/miscellaneous.py
M test/regression/iceberg_remover.py
M test/regression/inverse/build_tiny.py
M test/test_hydrology/runTestP.py

Log Message:
-----------
Rename {u,v}_ssa_bc to {u,v}_bc and bc_mask to vel_bc_mask

Commit: 1d13935e3bd6d468870762f1a07a35b1e78edee6
https://github.com/pism/pism/commit/1d13935e3bd6d468870762f1a07a35b1e78edee6
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-29 (Wed, 29 Sep 2021)

Changed paths:
M examples/marine/circular/piktests_utils.py

Log Message:
-----------
Don't set _FillValue in u_bc, v_bc, and vel_bc_mask

Commit: 0ec72f1981e00a5091e1d06fc5d76c0a440e5bda
https://github.com/pism/pism/commit/0ec72f1981e00a5091e1d06fc5d76c0a440e5bda
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-29 (Wed, 29 Sep 2021)

Changed paths:
M src/icemodel/IceModel.cc

Log Message:
-----------
IceModel::m_ice_thickness_bc_mask needs ghosts

Commit: 94d2ceeb95328570376af6e2606a9d0b994ac7aa
https://github.com/pism/pism/commit/94d2ceeb95328570376af6e2606a9d0b994ac7aa
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-30 (Thu, 30 Sep 2021)

Changed paths:
M examples/ross/preprocess.py

Log Message:
-----------
Update examples/ross/preprocess.py

Commit: e774b3b1a967bc2f930320218f3c33a57421612c
https://github.com/pism/pism/commit/e774b3b1a967bc2f930320218f3c33a57421612c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-30 (Thu, 30 Sep 2021)

Changed paths:
A examples/ross/download.sh

Log Message:
-----------
Add a script that downloads MEaSUREs Antarctica velocity data

Commit: 3961c9d8287ca4fc27c62c62a260080e40d50517
https://github.com/pism/pism/commit/3961c9d8287ca4fc27c62c62a260080e40d50517
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-30 (Thu, 30 Sep 2021)

Changed paths:
M examples/jako/quickjakosetup.sh

Log Message:
-----------
Use python3 instead of python

Commit: 1e8e8d71ffe6581d10d07b63e850641e89a3c0f2
https://github.com/pism/pism/commit/1e8e8d71ffe6581d10d07b63e850641e89a3c0f2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-09-30 (Thu, 30 Sep 2021)

Changed paths:
M CHANGES.rst
M doc/pismpython/inverse/index.rst
M doc/pismpython/inverse/pism_ssa.rst
M doc/pismpython/inverse/pismi.rst
M doc/sphinx/manual/diagnostics/diagnostics-list.txt
M doc/sphinx/manual/jakobshavn/index.rst
M doc/sphinx/manual/validation/ross.rst
M examples/jako/century.sh
M examples/jako/preprocess.sh
M examples/jako/quickjakosetup.sh
M examples/jako/spinup.sh
M examples/marine/circular/circular_dirichlet.py
M examples/marine/circular/piktests_utils.py
M examples/marine/circular/test_iceberg_removal.py
M examples/marine/flowline/createSetup_flowline.py
M examples/marine/flowline/run_flowline.sh
M examples/marine/tongues/generate_input.py
M examples/nbreen/preprocess.sh
M examples/python/ssa_tests/ssa_test_cfbc.py
M examples/python/ssa_tests/ssa_test_linear.py
M examples/python/ssa_tests/ssa_test_plug.py
M examples/python/ssa_tests/ssa_testi.py
M examples/python/ssa_tests/ssa_testj.py
A examples/ross/download.sh
M examples/ross/fracture/fracture_model.py
M examples/ross/plot.py
M examples/ross/preprocess.py
M site-packages/PISM/invert/ssa.py
M site-packages/PISM/model.py
M site-packages/PISM/ssa.py
M src/coupler/surface/TemperatureIndex.cc
M src/frontretreat/calving/CalvingAtThickness.cc
M src/geometry/GeometryEvolution.cc
M src/geometry/GeometryEvolution.hh
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/diagnostics.cc
M src/icemodel/fracture_density.cc
M src/icemodel/frontretreat.cc
M src/icemodel/initialization.cc
M src/icemodel/timestepping.cc
M src/inverse/IP_SSAHardavForwardProblem.cc
M src/inverse/IP_SSATaucForwardProblem.cc
M src/regional/IceRegionalModel.cc
M src/verification/iceCompModel.cc
M src/verification/tests/exactQ.py
M test/miscellaneous.py
M test/regression/iceberg_remover.py
M test/regression/inverse/build_tiny.py
M test/test_hydrology/inputforP_regression.nc
M test/test_hydrology/runTestP.py

Log Message:
-----------
Merge branch 'ckhrulev/thickness-bc-mask' into dev

Commit: 6c5a5b26f1ee4340bdb021b0ff24a56b129a616f
https://github.com/pism/pism/commit/6c5a5b26f1ee4340bdb021b0ff24a56b129a616f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-05 (Tue, 05 Oct 2021)

Changed paths:
M examples/ross/fracture/run_frac.sh
M examples/ross/fracture/run_frac_borstad.sh
M examples/ross/prognostic/run_prog.sh

Log Message:
-----------
Add "-regional" to commands running PISM in examples/ross

Commit: c6d15fc7f9349586ca355b5bccef3ac792bede8a
https://github.com/pism/pism/commit/c6d15fc7f9349586ca355b5bccef3ac792bede8a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-05 (Tue, 05 Oct 2021)

Changed paths:
M CHANGES.rst
M doc/ice-bib.bib
A doc/sphinx/manual/modeling-choices/marine/damage.rst
M doc/sphinx/manual/modeling-choices/marine/index.rst
M examples/ross/fracture/README.md
M examples/ross/fracture/run_frac.sh
A examples/ross/fracture/run_frac_borstad.sh
M examples/ross/prognostic/run_prog.sh
M src/fracturedensity/FractureDensity.cc
M src/pism_config.cdl

Log Message:
-----------
Merge branch 'ckhrulev/fracture-density-borstad-limit' into dev

Commit: 1fcf5472992b41443f1708e3f614bff97dc6e5ab
https://github.com/pism/pism/commit/1fcf5472992b41443f1708e3f614bff97dc6e5ab
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-06 (Wed, 06 Oct 2021)

Changed paths:
M examples/inverse/pismi.py
M site-packages/PISM/invert/ssa.py
M site-packages/PISM/sia.py
M site-packages/PISM/ssa.py
M src/age/AgeModel.cc
M src/coupler/frontalmelt/DischargeGiven.cc
M src/coupler/frontalmelt/DischargeRouting.cc
M src/coupler/frontalmelt/FrontalMelt.cc
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc
M src/energy/BTU_Full.cc
M src/energy/EnergyModel.cc
M src/energy/TemperatureModel.cc
M src/energy/btutest.cc
M src/fracturedensity/FractureDensity.cc
M src/fracturedensity/FractureDensity.hh
M src/frontretreat/FrontRetreat.cc
M src/frontretreat/calving/EigenCalving.cc
M src/frontretreat/calving/HayhurstCalving.cc
M src/frontretreat/calving/StressCalving.cc
M src/frontretreat/calving/StressCalving.hh
M src/frontretreat/calving/vonMisesCalving.cc
M src/frontretreat/util/remove_narrow_tongues.cc
M src/geometry/GeometryEvolution.cc
M src/geometry/grounded_cell_fraction.cc
M src/geometry/part_grid_threshold_thickness.cc
M src/geometry/part_grid_threshold_thickness.hh
M src/hydrology/EmptyingProblem.cc
M src/hydrology/Hydrology.cc
M src/hydrology/Routing.cc
M src/icebin/IBIceModel.cc
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/diagnostics.cc
M src/icemodel/energy.cc
M src/icemodel/frontretreat.cc
M src/icemodel/viewers.cc
M src/inverse/IPTaoTikhonovProblem.hh
M src/inverse/IP_SSATaucTaoTikhonovProblemLCL.cc
M src/inverse/IP_SSATaucTikhonovGNSolver.cc
M src/pythonbindings/IceModelVec2V.py
M src/pythonbindings/PISM.i
M src/pythonbindings/pism_IceModelVec.i
M src/regional/IceRegionalModel.cc
M src/regional/SIAFD_Regional.cc
M src/regional/SSAFD_Regional.cc
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/StressBalance.cc
M src/stressbalance/StressBalance.hh
M src/stressbalance/StressBalance_diagnostics.cc
M src/stressbalance/WeertmanSliding.cc
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/sia/BedSmoother.cc
M src/stressbalance/ssa/SSA.cc
M src/stressbalance/ssa/SSAFD.cc
M src/stressbalance/ssa/SSAFD.hh
M src/stressbalance/ssa/SSAFEM.hh
M src/util/Diagnostic.hh
R src/util/Field.hh
A src/util/IceModelVec2.hh
R src/util/IceModelVec2Struct.hh
M src/util/IceModelVec2V.hh
M src/util/IceModelVec_impl.hh
M src/util/IceModelVec_inline.hh
M src/util/Poisson.cc
R src/util/StarStencil.hh
M src/util/VariableMetadata.cc
M src/util/VariableMetadata.hh
M src/util/iceModelVec.cc
M src/util/iceModelVec.hh
M src/util/iceModelVec2.cc
M src/util/iceModelVec2T.cc
M src/util/iceModelVec2T.hh
M src/util/iceModelVec2V.cc
M src/util/iceModelVec3.cc
M src/util/iceModelVec_helpers.hh
M src/util/io/PNCFile.cc
M src/util/node_types.cc
M src/util/options.cc
M src/util/pism_utilities.cc
A src/util/stencils.hh
M src/verification/iCMthermo.cc
M test/bed_smoother.py
M test/blatter_verification.py
M test/mass_transport.py
M test/miscellaneous.py
M test/regression/hydrology_steady_test.py

Log Message:
-----------
Clean up IceModelVec classes

- Lazy initialization

- to allocate IceModelVec::vec()
- to allocate IceModelVec::dm()

- Rename

- std::dynamic_pointer_cast wrappers to "Cast"
- IceModelVec2Int::int_star() and int_box() to star and box
- IceModelVec2Struct to IceModelVec2 and remove the old IceModelVec2
- copy_2d() and add_2d() to vec::copy() and vec::add()

- Remove

- The second ("special z axis") IceModelVec3 constructor
- IceModelVec::copy_from_vec()
- Field.hh
- IceModelVec::copy_from()
- IceModelVec::update_ghosts(destination)

- Replace

- IceModelVecXX::allocate_copy() with duplicate()
- IceModelVec2S::set_to_magnitude() with stand alone functions
- IceModelVec2S::mask_by() by a stand alone function apply_mask()

- Add

- sum(), min(), max(), absmax() as stand-alone functions
- diff_{x,y} as stand-alone functions

- Clean up IceModelVec3::set_column()

- Don't try to be smart about copying data
The problem is that we don't always know if ghosts of *inputs* are up to date.

- More clarity about begin_access_use_dof (IceModelVec2, Vec2Stag, and Vec3 need this; others do not.)

- Move stencil structs into util/stencils.hh

Commit: a109d85c40dca3519eaa8aee1ee4ee2fa6591cd2
https://github.com/pism/pism/commit/a109d85c40dca3519eaa8aee1ee4ee2fa6591cd2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-06 (Wed, 06 Oct 2021)

Changed paths:
M examples/inverse/pismi.py
M site-packages/PISM/invert/ssa.py
M site-packages/PISM/sia.py
M site-packages/PISM/ssa.py
M src/age/AgeModel.cc
M src/coupler/frontalmelt/DischargeGiven.cc
M src/coupler/frontalmelt/DischargeRouting.cc
M src/coupler/frontalmelt/FrontalMelt.cc
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc
M src/energy/BTU_Full.cc
M src/energy/EnergyModel.cc
M src/energy/TemperatureModel.cc
M src/energy/btutest.cc
M src/fracturedensity/FractureDensity.cc
M src/fracturedensity/FractureDensity.hh
M src/frontretreat/FrontRetreat.cc
M src/frontretreat/calving/EigenCalving.cc
M src/frontretreat/calving/HayhurstCalving.cc
M src/frontretreat/calving/StressCalving.cc
M src/frontretreat/calving/StressCalving.hh
M src/frontretreat/calving/vonMisesCalving.cc
M src/frontretreat/util/remove_narrow_tongues.cc
M src/geometry/GeometryEvolution.cc
M src/geometry/grounded_cell_fraction.cc
M src/geometry/part_grid_threshold_thickness.cc
M src/geometry/part_grid_threshold_thickness.hh
M src/hydrology/EmptyingProblem.cc
M src/hydrology/Hydrology.cc
M src/hydrology/Routing.cc
M src/icebin/IBIceModel.cc
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/diagnostics.cc
M src/icemodel/energy.cc
M src/icemodel/frontretreat.cc
M src/icemodel/viewers.cc
M src/inverse/IPTaoTikhonovProblem.hh
M src/inverse/IP_SSATaucTaoTikhonovProblemLCL.cc
M src/inverse/IP_SSATaucTikhonovGNSolver.cc
M src/pythonbindings/IceModelVec2V.py
M src/pythonbindings/PISM.i
M src/pythonbindings/pism_IceModelVec.i
M src/regional/IceRegionalModel.cc
M src/regional/SIAFD_Regional.cc
M src/regional/SSAFD_Regional.cc
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/StressBalance.cc
M src/stressbalance/StressBalance.hh
M src/stressbalance/StressBalance_diagnostics.cc
M src/stressbalance/WeertmanSliding.cc
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/sia/BedSmoother.cc
M src/stressbalance/ssa/SSA.cc
M src/stressbalance/ssa/SSAFD.cc
M src/stressbalance/ssa/SSAFD.hh
M src/stressbalance/ssa/SSAFEM.hh
M src/util/Diagnostic.hh
R src/util/Field.hh
A src/util/IceModelVec2.hh
R src/util/IceModelVec2Struct.hh
M src/util/IceModelVec2V.hh
M src/util/IceModelVec_impl.hh
M src/util/IceModelVec_inline.hh
M src/util/Poisson.cc
R src/util/StarStencil.hh
M src/util/VariableMetadata.cc
M src/util/VariableMetadata.hh
M src/util/iceModelVec.cc
M src/util/iceModelVec.hh
M src/util/iceModelVec2.cc
M src/util/iceModelVec2T.cc
M src/util/iceModelVec2T.hh
M src/util/iceModelVec2V.cc
M src/util/iceModelVec3.cc
M src/util/iceModelVec_helpers.hh
M src/util/io/PNCFile.cc
M src/util/node_types.cc
M src/util/options.cc
M src/util/pism_utilities.cc
A src/util/scatters.cc
A src/util/stencils.hh
M src/verification/iCMthermo.cc
M test/bed_smoother.py
M test/blatter_verification.py
M test/mass_transport.py
M test/miscellaneous.py
M test/regression/hydrology_steady_test.py

Log Message:
-----------
Merge branch 'ckhrulev/vec-cleanup' into dev

Commit: 7b6fb4a00f9681046b5c495d2e108075c41dec46
https://github.com/pism/pism/commit/7b6fb4a00f9681046b5c495d2e108075c41dec46
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-10-06 (Wed, 06 Oct 2021)

Changed paths:
M src/hydrology/Hydrology.cc
M src/pism_config.cdl

Log Message:
-----------
Added option -set_tillwat_ocean to set tillwat_max also in ocean area. This reduces friction at the advancing grounding line.

Commit: 738ad9a425b67580fc40ce8e6bca3f682f758a7f
https://github.com/pism/pism/commit/738ad9a425b67580fc40ce8e6bca3f682f758a7f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-06 (Wed, 06 Oct 2021)

Changed paths:
M src/hydrology/Distributed.cc
M src/hydrology/Hydrology.cc
M src/hydrology/Hydrology.hh
M src/hydrology/NullTransport.cc
M src/hydrology/Routing.cc
M src/pism_config.cdl

Log Message:
-----------
Remove configuration parameter hydrology.set_tillwat_ocean

Commit: f5d18c9d28bff7a0e073027bcd86e122497b213a
https://github.com/pism/pism/commit/f5d18c9d28bff7a0e073027bcd86e122497b213a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-06 (Wed, 06 Oct 2021)

Changed paths:
M src/hydrology/Hydrology.cc
M src/icemodel/diagnostics.cc

Log Message:
-----------
Minor cleanup

Commit: ec0af003feef74a3897e5d22ec792308985e0a72
https://github.com/pism/pism/commit/ec0af003feef74a3897e5d22ec792308985e0a72
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-06 (Wed, 06 Oct 2021)

Changed paths:
M CHANGES.rst

Log Message:
-----------
Update the change log

Commit: 3ecac975380b1a19b632de2cc98d2d5f0b53e404
https://github.com/pism/pism/commit/3ecac975380b1a19b632de2cc98d2d5f0b53e404
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-06 (Wed, 06 Oct 2021)

Changed paths:
M CHANGES.rst
M src/hydrology/Distributed.cc
M src/hydrology/Hydrology.cc
M src/hydrology/Hydrology.hh
M src/hydrology/NullTransport.cc
M src/hydrology/Routing.cc
M src/icemodel/diagnostics.cc

Log Message:
-----------
Merge branch 'pik/tillwat_ocean' into dev

Commit: 34faa1d5b591c776e64aa6659db1dbb91abf8e17
https://github.com/pism/pism/commit/34faa1d5b591c776e64aa6659db1dbb91abf8e17
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-08 (Fri, 08 Oct 2021)

Changed paths:
M src/frontretreat/calving/StressCalving.cc

Log Message:
-----------
Fix a bug in stress-based calving models

Probably introduced by a109d85c40dca3519eaa8aee1ee4ee2fa6591cd2

Commit: efb48c47cda7714a90e7538c57a60e92092336bc
https://github.com/pism/pism/commit/efb48c47cda7714a90e7538c57a60e92092336bc
Author: Andy <andy.as...@gmail.com>
Date: 2021-10-18 (Mon, 18 Oct 2021)

Changed paths:
M util/adjust_timeline.py
M util/create_timeline.py

Log Message:
-----------
Updated python scripts that use "cftime".

The "utime" function was removed in newer versions of "cftime".
Also added a command line option for the calendar.

Commit: 190ab6fd95f3bba7c6d344ec5d4eed13efaf8a8e
https://github.com/pism/pism/commit/190ab6fd95f3bba7c6d344ec5d4eed13efaf8a8e
Author: Andy <andy.as...@gmail.com>
Date: 2021-10-18 (Mon, 18 Oct 2021)

Changed paths:
M util/adjust_timeline.py

Log Message:
-----------
Fixed a typo

Commit: 2ef62f387da108adcd2c577a07db8e3b365c2279
https://github.com/pism/pism/commit/2ef62f387da108adcd2c577a07db8e3b365c2279
Author: Andy <andy.as...@gmail.com>
Date: 2021-10-18 (Mon, 18 Oct 2021)

Changed paths:
M util/adjust_timeline.py

Log Message:
-----------
Fixed another typo

Commit: a81ab48b932414c2c9295185b85ee9e783abab64
https://github.com/pism/pism/commit/a81ab48b932414c2c9295185b85ee9e783abab64
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-19 (Tue, 19 Oct 2021)

Changed paths:
M src/util/iceModelVec3.cc

Log Message:
-----------
Add #if...#endif to remove a compiler warning

Commit: ae34fcd8f7dde9d750ff1484b253f2f6e5fe2ae5
https://github.com/pism/pism/commit/ae34fcd8f7dde9d750ff1484b253f2f6e5fe2ae5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-19 (Tue, 19 Oct 2021)

Changed paths:
M src/basalstrength/MohrCoulombYieldStress.cc
M src/basalstrength/MohrCoulombYieldStress.hh

Log Message:
-----------
Forward-declare IceModelVec2T in MohrCoulombYieldStress.hh

Commit: d19340b1096e5da08f8327c6d10c7ed40f5352a7
https://github.com/pism/pism/commit/d19340b1096e5da08f8327c6d10c7ed40f5352a7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-19 (Tue, 19 Oct 2021)

Changed paths:
R src/coupler/util/ScalarForcing.cc

Log Message:
-----------
Delete an old file (must have missed it when merging branches)

Commit: 9bc8456c3007774ecb1b83179c12dc510253437b
https://github.com/pism/pism/commit/9bc8456c3007774ecb1b83179c12dc510253437b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-19 (Tue, 19 Oct 2021)

Changed paths:
M src/basalstrength/ConstantYieldStress.cc
M src/basalstrength/ConstantYieldStress.hh
M src/basalstrength/MohrCoulombYieldStress.cc
M src/basalstrength/MohrCoulombYieldStress.hh
M src/basalstrength/YieldStress.cc
M src/basalstrength/YieldStress.hh
M src/basalstrength/basal_resistance.cc
M src/basalstrength/basal_resistance.hh
M src/coupler/AtmosphereModel.hh
M src/coupler/FrontalMelt.hh
M src/coupler/OceanModel.hh
M src/coupler/SeaLevel.hh
M src/coupler/SurfaceModel.hh
M src/coupler/atmosphere/Anomaly.cc
M src/coupler/atmosphere/Anomaly.hh
M src/coupler/atmosphere/AtmosphereModel.cc
M src/coupler/atmosphere/CosineYearlyCycle.cc
M src/coupler/atmosphere/CosineYearlyCycle.hh
M src/coupler/atmosphere/Delta_P.cc
M src/coupler/atmosphere/Delta_P.hh
M src/coupler/atmosphere/ElevationChange.cc
M src/coupler/atmosphere/ElevationChange.hh
M src/coupler/atmosphere/Factory.cc
M src/coupler/atmosphere/Factory.hh
M src/coupler/atmosphere/Frac_P.cc
M src/coupler/atmosphere/Frac_P.hh
M src/coupler/atmosphere/GivenClimate.cc
M src/coupler/atmosphere/GivenClimate.hh
M src/coupler/atmosphere/OrographicPrecipitation.hh
M src/coupler/atmosphere/PIK.cc
M src/coupler/atmosphere/PIK.hh
M src/coupler/atmosphere/PrecipitationScaling.cc
M src/coupler/atmosphere/PrecipitationScaling.hh
M src/coupler/atmosphere/WeatherStation.cc
M src/coupler/atmosphere/WeatherStation.hh
M src/coupler/atmosphere/YearlyCycle.cc
M src/coupler/atmosphere/YearlyCycle.hh
M src/coupler/frontalmelt/Constant.cc
M src/coupler/frontalmelt/Constant.hh
M src/coupler/frontalmelt/DischargeGiven.cc
M src/coupler/frontalmelt/DischargeGiven.hh
M src/coupler/frontalmelt/DischargeRouting.cc
M src/coupler/frontalmelt/DischargeRouting.hh
M src/coupler/frontalmelt/Factory.cc
M src/coupler/frontalmelt/Factory.hh
M src/coupler/frontalmelt/FrontalMelt.cc
M src/coupler/frontalmelt/Given.cc
M src/coupler/frontalmelt/Given.hh
M src/coupler/ocean/Anomaly.cc
M src/coupler/ocean/Anomaly.hh
M src/coupler/ocean/CompleteOceanModel.cc
M src/coupler/ocean/CompleteOceanModel.hh
M src/coupler/ocean/Constant.cc
M src/coupler/ocean/Constant.hh
M src/coupler/ocean/ConstantPIK.cc
M src/coupler/ocean/ConstantPIK.hh
M src/coupler/ocean/Factory.cc
M src/coupler/ocean/Factory.hh
M src/coupler/ocean/GivenClimate.cc
M src/coupler/ocean/GivenClimate.hh
M src/coupler/ocean/GivenTH.cc
M src/coupler/ocean/GivenTH.hh
M src/coupler/ocean/OceanModel.cc
M src/coupler/ocean/Runoff_SMB.hh
M src/coupler/ocean/sea_level/Delta_SL.hh
M src/coupler/ocean/sea_level/Delta_SL_2D.cc
M src/coupler/ocean/sea_level/Delta_SL_2D.hh
M src/coupler/ocean/sea_level/Factory.cc
M src/coupler/ocean/sea_level/Factory.hh
M src/coupler/ocean/sea_level/SeaLevel.cc
M src/coupler/surface/Anomaly.cc
M src/coupler/surface/Anomaly.hh
M src/coupler/surface/EISMINTII.cc
M src/coupler/surface/EISMINTII.hh
M src/coupler/surface/ElevationChange.cc
M src/coupler/surface/ElevationChange.hh
M src/coupler/surface/Factory.cc
M src/coupler/surface/Factory.hh
M src/coupler/surface/ForceThickness.cc
M src/coupler/surface/ForceThickness.hh
M src/coupler/surface/Formulas.cc
M src/coupler/surface/Formulas.hh
M src/coupler/surface/GivenClimate.cc
M src/coupler/surface/GivenClimate.hh
M src/coupler/surface/ISMIP6Climate.cc
M src/coupler/surface/ISMIP6Climate.hh
M src/coupler/surface/StuffAsAnomaly.cc
M src/coupler/surface/SurfaceModel.cc
M src/coupler/surface/TemperatureIndex.cc
M src/coupler/surface/TemperatureIndex.hh
M src/coupler/surface/localMassBalance.cc
M src/coupler/surface/localMassBalance.hh
M src/earth/BedDef.cc
M src/earth/BedDef.hh
M src/earth/Given.cc
M src/earth/Given.hh
M src/earth/LingleClark.hh
M src/earth/LingleClarkSerial.hh
M src/earth/PointwiseIsostasy.cc
M src/energy/BTU_Full.cc
M src/energy/BTU_Full.hh
M src/energy/BedThermalUnit.cc
M src/energy/BedThermalUnit.hh
M src/energy/BedrockColumn.cc
M src/energy/BedrockColumn.hh
M src/energy/CHSystem.cc
M src/energy/CHSystem.hh
M src/fracturedensity/FractureDensity.cc
M src/fracturedensity/FractureDensity.hh
M src/frontretreat/FrontRetreat.cc
M src/frontretreat/FrontRetreat.hh
M src/frontretreat/PrescribedRetreat.cc
M src/frontretreat/PrescribedRetreat.hh
M src/frontretreat/calving/CalvingAtThickness.cc
M src/frontretreat/calving/CalvingAtThickness.hh
M src/frontretreat/calving/EigenCalving.cc
M src/frontretreat/calving/EigenCalving.hh
M src/frontretreat/calving/FloatKill.cc
M src/frontretreat/calving/FloatKill.hh
M src/frontretreat/calving/HayhurstCalving.cc
M src/frontretreat/calving/HayhurstCalving.hh
M src/frontretreat/calving/StressCalving.cc
M src/frontretreat/calving/StressCalving.hh
M src/frontretreat/calving/vonMisesCalving.cc
M src/frontretreat/calving/vonMisesCalving.hh
M src/frontretreat/util/IcebergRemover.cc
M src/frontretreat/util/IcebergRemover.hh
M src/hydrology/Distributed.cc
M src/hydrology/Distributed.hh
M src/hydrology/EmptyingProblem.cc
M src/hydrology/EmptyingProblem.hh
M src/hydrology/Hydrology.cc
M src/hydrology/Hydrology.hh
M src/hydrology/NullTransport.cc
M src/hydrology/NullTransport.hh
M src/hydrology/Routing.cc
M src/hydrology/Routing.hh
M src/hydrology/SteadyState.cc
M src/hydrology/SteadyState.hh
M src/icebin/IBIceModel.cc
M src/inverse/IPTwoBlockVec.cc
M src/inverse/IPTwoBlockVec.hh
M src/inverse/IP_SSAHardavForwardProblem.cc
M src/inverse/IP_SSAHardavForwardProblem.hh
M src/inverse/IP_SSATaucForwardProblem.cc
M src/inverse/IP_SSATaucForwardProblem.hh
M src/inverse/IP_SSATaucTaoTikhonovProblemLCL.cc
M src/inverse/IP_SSATaucTaoTikhonovProblemLCL.hh
M src/inverse/IP_SSATaucTikhonovGNSolver.cc
M src/inverse/IP_SSATaucTikhonovGNSolver.hh
M src/regional/RegionalYieldStress.cc
M src/regional/RegionalYieldStress.hh
M src/regional/SIAFD_Regional.cc
M src/regional/SIAFD_Regional.hh
M src/regional/SSAFD_Regional.cc
M src/regional/SSAFD_Regional.hh
M src/rheology/FlowLaw.cc
M src/rheology/FlowLaw.hh
M src/rheology/FlowLawFactory.cc
M src/rheology/FlowLawFactory.hh
M src/rheology/Hooke.cc
M src/rheology/Hooke.hh
M src/rheology/PatersonBudd.cc
M src/rheology/PatersonBudd.hh
M src/rheology/PatersonBuddCold.cc
M src/rheology/PatersonBuddCold.hh
M src/rheology/PatersonBuddWarm.cc
M src/rheology/PatersonBuddWarm.hh
M src/stressbalance/SSB_Modifier.cc
M src/stressbalance/SSB_Modifier.hh
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/ShallowStressBalance.hh
M src/stressbalance/WeertmanSliding.cc
M src/stressbalance/WeertmanSliding.hh
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/BlatterMod.cc
M src/stressbalance/blatter/BlatterMod.hh
M src/stressbalance/sia/BedSmoother.cc
M src/stressbalance/sia/BedSmoother.hh
M src/stressbalance/ssa/SSAFD.cc
M src/stressbalance/ssa/SSAFD.hh
M src/stressbalance/ssa/SSAFEM.cc
M src/stressbalance/ssa/SSAFEM.hh
M src/util/Component.cc
M src/util/Component.hh
M src/util/Config.cc
M src/util/Config.hh
M src/util/Diagnostic.cc
M src/util/Diagnostic.hh
M src/util/EnthalpyConverter.cc
M src/util/EnthalpyConverter.hh
M src/util/error_handling.cc
M src/util/error_handling.hh
M src/util/fem/Element.cc
M src/util/fem/Element.hh
M src/util/io/NC4File.cc
M src/util/io/NC4File.hh
M src/util/io/NC4_Serial.cc
M src/util/io/NC4_Serial.hh
M src/util/io/NCFile.cc
M src/util/io/NCFile.hh
M src/util/io/ParallelIO.cc
M src/util/io/ParallelIO.hh
M src/verification/BTU_Verification.cc
M src/verification/BTU_Verification.hh
M src/verification/PSVerification.cc
M src/verification/PSVerification.hh

Log Message:
-----------
Use C++11 "= default" to mark destructors as default (empty)

Commit: 6fd430dcc1f16b98cb375ad4c106395fcc6e82c4
https://github.com/pism/pism/commit/6fd430dcc1f16b98cb375ad4c106395fcc6e82c4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-19 (Tue, 19 Oct 2021)

Changed paths:
M CHANGES.rst

Log Message:
-----------
Fix a typo in the change log

Commit: 7438ea4d5572fcd237bb8138e6fb30ccf50111e3
https://github.com/pism/pism/commit/7438ea4d5572fcd237bb8138e6fb30ccf50111e3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-19 (Tue, 19 Oct 2021)

Changed paths:
M src/util/ConfigInterface.cc
M src/util/IceGrid.cc

Log Message:
-----------
Remove some outdated code

Commit: ab46a6cd883eee504d5715325586c2213a5ebf2d
https://github.com/pism/pism/commit/ab46a6cd883eee504d5715325586c2213a5ebf2d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-19 (Tue, 19 Oct 2021)

Changed paths:
M src/basalstrength/YieldStress.cc

Log Message:
-----------
Fix a message printed to stdout

Commit: 731517ec2dc8826f6cd74eea3194a00443435f1b
https://github.com/pism/pism/commit/731517ec2dc8826f6cd74eea3194a00443435f1b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-28 (Thu, 28 Oct 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/marine/melange.rst

Log Message:
-----------
Fix a typo in the manual

Commit: 5ea0ed1e3f84a3684f78cf1090dc4056900b5e37
https://github.com/pism/pism/commit/5ea0ed1e3f84a3684f78cf1090dc4056900b5e37
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-28 (Thu, 28 Oct 2021)

Changed paths:
M test/vnreport.py

Log Message:
-----------
Update vnreport.py

Commit: d88c7093e5348b603fb3acc7a0bc6ffe3ff8e2bd
https://github.com/pism/pism/commit/d88c7093e5348b603fb3acc7a0bc6ffe3ff8e2bd
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-28 (Thu, 28 Oct 2021)

Changed paths:
M src/stressbalance/ssa/SSATestCase.cc

Log Message:
-----------
SSATestCase: save exact velocity in m/s

Commit: df869ba74099135c0b671e0c8ae8ccae354da67f
https://github.com/pism/pism/commit/df869ba74099135c0b671e0c8ae8ccae354da67f
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-28 (Thu, 28 Oct 2021)

Changed paths:
M src/stressbalance/ssa/SSATestCase.cc

Log Message:
-----------
SSATestCase: fix NetCDF error reporting

Commit: a708fd613094eee31f8996bd39aee86c8b1a35f4
https://github.com/pism/pism/commit/a708fd613094eee31f8996bd39aee86c8b1a35f4
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-10-28 (Thu, 28 Oct 2021)

Changed paths:
A examples/mismip/check_taud_flowline/README.md
A examples/mismip/check_taud_flowline/plot_diff.py
A examples/mismip/check_taud_flowline/prepare_iceshelf.py
A examples/mismip/check_taud_flowline/run_test.sh
M src/pism_config.cdl
M src/stressbalance/ssa/SSA.cc

Log Message:
-----------
Added test to fix driving stress scheme at ice margin

Commit: 0459cef20b27ae42a667aeddc7d66d7c8bb0eec7
https://github.com/pism/pism/commit/0459cef20b27ae42a667aeddc7d66d7c8bb0eec7
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-28 (Thu, 28 Oct 2021)

Changed paths:
M examples/mismip/check_taud_flowline/plot_diff.py
M examples/mismip/check_taud_flowline/run_test.sh

Log Message:
-----------
Clean up the scripts in examples/mismip/check_taud_flowline/

Commit: 6982a5a530d5b0e03cb9ed86fd09a4464a3ca692
https://github.com/pism/pism/commit/6982a5a530d5b0e03cb9ed86fd09a4464a3ca692
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-28 (Thu, 28 Oct 2021)

Changed paths:
M examples/mismip/check_taud_flowline/prepare_iceshelf.py

Log Message:
-----------
Restore Python 3 compatibility

Commit: 2a28a7c21ab93b5e292d8d69c390ea92a47657d9
https://github.com/pism/pism/commit/2a28a7c21ab93b5e292d8d69c390ea92a47657d9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-29 (Fri, 29 Oct 2021)

Changed paths:
M src/pism_config.cdl
M src/stressbalance/ssa/SSA.cc

Log Message:
-----------
Remove stress_balance.fix_taud_at_margin

Commit: aa371185b55041544c19b50a0b901185ebea0950
https://github.com/pism/pism/commit/aa371185b55041544c19b50a0b901185ebea0950
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-29 (Fri, 29 Oct 2021)

Changed paths:
M test/regression/ssa/ssa_test_cfbc_fd.sh

Log Message:
-----------
Update the SSAFD-CFBC regression test

Commit: 57ee39cf6815f6336e9c6223690b252d881bdb72
https://github.com/pism/pism/commit/57ee39cf6815f6336e9c6223690b252d881bdb72
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-29 (Fri, 29 Oct 2021)

Changed paths:
M doc/sphinx/technical/index.rst
A doc/sphinx/technical/ssafd-flow-line.rst

Log Message:
-----------
Add notes about the flow line SSA

Commit: a3ac8c2ce276e782c18f5c50b8956c65d80e7295
https://github.com/pism/pism/commit/a3ac8c2ce276e782c18f5c50b8956c65d80e7295
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-29 (Fri, 29 Oct 2021)

Changed paths:
M examples/mismip/check_taud_flowline/run_test.sh

Log Message:
-----------
Remove "scheme" from the test script

... now that the new method is the default.

Commit: 2a9bbdb9631e354198bc8d7913bb048a94581205
https://github.com/pism/pism/commit/2a9bbdb9631e354198bc8d7913bb048a94581205
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-29 (Fri, 29 Oct 2021)

Changed paths:
M examples/mismip/check_taud_flowline/prepare_iceshelf.py

Log Message:
-----------
Silence NumPy warnings

Commit: 14388a818c2a828b2626cb8b9e8c665548670913
https://github.com/pism/pism/commit/14388a818c2a828b2626cb8b9e8c665548670913
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-29 (Fri, 29 Oct 2021)

Changed paths:
M examples/mismip/check_taud_flowline/plot_diff.py

Log Message:
-----------
Edit the plotting script

- plot ice thickness instead of its change
- compare to the unperturbed run instead of u_ssa_bc in the input file

Commit: d5f3a6978f799796c0ddb7a2b89b1c568e82dc40
https://github.com/pism/pism/commit/d5f3a6978f799796c0ddb7a2b89b1c568e82dc40
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-29 (Fri, 29 Oct 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/authorship.rst

Log Message:
-----------
Update the change log

Commit: c764a415ca9c7f01edcbdefabc79b9351e53a629
https://github.com/pism/pism/commit/c764a415ca9c7f01edcbdefabc79b9351e53a629
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-29 (Fri, 29 Oct 2021)

Changed paths:
M examples/mismip/check_taud_flowline/run_test.sh
M src/pism_config.cdl

Log Message:
-----------
Revert an unnecessary change to pism_config.cdl

Commit: 2bf22a839a55337e8b834de8eb5a88ea7a7d36e3
https://github.com/pism/pism/commit/2bf22a839a55337e8b834de8eb5a88ea7a7d36e3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-29 (Fri, 29 Oct 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/authorship.rst
M doc/sphinx/technical/index.rst
A doc/sphinx/technical/ssafd-flow-line.rst
A examples/mismip/check_taud_flowline/README.md
A examples/mismip/check_taud_flowline/plot_diff.py
A examples/mismip/check_taud_flowline/prepare_iceshelf.py
A examples/mismip/check_taud_flowline/run_test.sh
M src/stressbalance/ssa/SSA.cc
M test/regression/ssa/ssa_test_cfbc_fd.sh

Log Message:
-----------
Merge pull request #493 from pism/pik/fix_taud_margins

Fix the driving stress approximation at ice shelf fronts

Commit: 70ad22e7c719173da805f6bc9bde1f1b24d3da14
https://github.com/pism/pism/commit/70ad22e7c719173da805f6bc9bde1f1b24d3da14
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-29 (Fri, 29 Oct 2021)

Changed paths:
M src/stressbalance/ssa/SSA.cc

Log Message:
-----------
The fix from #493 should not be used at grounded margins

Commit: 1528e2e8d8401beb739288a9007e3efe2f2f3f8d
https://github.com/pism/pism/commit/1528e2e8d8401beb739288a9007e3efe2f2f3f8d
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-30 (Sat, 30 Oct 2021)

Changed paths:
M doc/ice-bib.bib
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst
M doc/sphinx/manual/practical-usage/mass-conservation.rst
M doc/sphinx/math-definitions.tex
M src/CMakeLists.txt
M src/basalstrength/MohrCoulombYieldStress.cc
M src/basalstrength/MohrCoulombYieldStress.hh
A src/basalstrength/OptTillphiYieldStress.cc
A src/basalstrength/OptTillphiYieldStress.hh
M src/geometry/GeometryEvolution.cc
M src/geometry/GeometryEvolution.hh
M src/icemodel/initialization.cc
M src/pism_config.cdl
M src/util/ConfigInterface.cc

Log Message:
-----------
Add the till phi optimization code from the other branch

Commit: 4e84983792dbf9e11b73ff71e078724e8ae23739
https://github.com/pism/pism/commit/4e84983792dbf9e11b73ff71e078724e8ae23739
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-30 (Sat, 30 Oct 2021)

Changed paths:
M src/basalstrength/OptTillphiYieldStress.cc
M src/geometry/GeometryEvolution.cc

Log Message:
-----------
Run clang-format (and clean up a bit)

Commit: 939ac041569475b41f61a10cdc084326f61e3bf8
https://github.com/pism/pism/commit/939ac041569475b41f61a10cdc084326f61e3bf8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-30 (Sat, 30 Oct 2021)

Changed paths:
M src/geometry/GeometryEvolution.cc
M src/geometry/GeometryEvolution.hh
M src/pism_config.cdl

Log Message:
-----------
Remove GeometryEvolution::ensure_grounded_icearea() and related code

Commit: f123ea203c99abe21eccc5bdceaaf6b32cd50562
https://github.com/pism/pism/commit/f123ea203c99abe21eccc5bdceaaf6b32cd50562
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-30 (Sat, 30 Oct 2021)

Changed paths:
M src/coupler/CMakeLists.txt
M src/coupler/surface/Factory.cc
A src/coupler/surface/NoGLRetreat.cc
A src/coupler/surface/NoGLRetreat.hh

Log Message:
-----------
Implement -surface ...,no_gl_retreat

Commit: 5daa9d6dc7126a1eef96af2f6a4a3907e3b550a4
https://github.com/pism/pism/commit/5daa9d6dc7126a1eef96af2f6a4a3907e3b550a4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-30 (Sat, 30 Oct 2021)

Changed paths:
M src/basalstrength/OptTillphiYieldStress.cc

Log Message:
-----------
Convert basal_yield_stress.mohr_coulomb.iterative_phi.dh_conv to m/s before use

Commit: e91b58a8b711dbddac89cd2a7997e2458ec8fe96
https://github.com/pism/pism/commit/e91b58a8b711dbddac89cd2a7997e2458ec8fe96
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-30 (Sat, 30 Oct 2021)

Changed paths:
M src/basalstrength/OptTillphiYieldStress.cc
M src/basalstrength/OptTillphiYieldStress.hh

Log Message:
-----------
Remove an unused variable and fix a variable name

Commit: 2c4ec51faa714cd48debd4aaa187059df900bb75
https://github.com/pism/pism/commit/2c4ec51faa714cd48debd4aaa187059df900bb75
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-30 (Sat, 30 Oct 2021)

Changed paths:
M src/basalstrength/MohrCoulombYieldStress.cc
M src/basalstrength/OptTillphiYieldStress.cc

Log Message:
-----------
Undo unnecessary changes to MohrCoulombYieldStress

Commit: 1f6a89617c0469f6c517e142a9d3d808d77b2a75
https://github.com/pism/pism/commit/1f6a89617c0469f6c517e142a9d3d808d77b2a75
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-30 (Sat, 30 Oct 2021)

Changed paths:
M src/basalstrength/OptTillphiYieldStress.hh

Log Message:
-----------
Remove unnecessary #includes

Commit: 869374afc40071827a1762743d36a9dc4ab02500
https://github.com/pism/pism/commit/869374afc40071827a1762743d36a9dc4ab02500
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-30 (Sat, 30 Oct 2021)

Changed paths:
M src/basalstrength/MohrCoulombYieldStress.hh
M src/basalstrength/OptTillphiYieldStress.cc
M src/basalstrength/OptTillphiYieldStress.hh

Log Message:
-----------
Clean up

Commit: 30651981414ab802f3d57225fc99be2808b25755
https://github.com/pism/pism/commit/30651981414ab802f3d57225fc99be2808b25755
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-30 (Sat, 30 Oct 2021)

Changed paths:
M src/util/ConfigInterface.cc

Log Message:
-----------
Remove the command-line option setting 9 numbers at once

Commit: 2dfa5b1d41490aa38c2aa9f3928866a72ce93e92
https://github.com/pism/pism/commit/2dfa5b1d41490aa38c2aa9f3928866a72ce93e92
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-30 (Sat, 30 Oct 2021)

Changed paths:
M doc/sphinx/climate_forcing/surface.rst
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst
M doc/sphinx/math-definitions.tex
M src/basalstrength/OptTillphiYieldStress.cc
M src/basalstrength/OptTillphiYieldStress.hh
M src/icemodel/initialization.cc
M src/pism_config.cdl

Log Message:
-----------
Clean up and document the new till friction optimization code

Commit: 1991eed37cd19bc59dcfd327c1184f8a8be05371
https://github.com/pism/pism/commit/1991eed37cd19bc59dcfd327c1184f8a8be05371
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-10-30 (Sat, 30 Oct 2021)

Changed paths:
M CHANGES.rst

Log Message:
-----------
Update the change log

Commit: c63387274054cbe0d716e3f59a0f8349ed41178b
https://github.com/pism/pism/commit/c63387274054cbe0d716e3f59a0f8349ed41178b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-01 (Mon, 01 Nov 2021)

Changed paths:
M src/basalstrength/OptTillphiYieldStress.cc
M src/basalstrength/OptTillphiYieldStress.hh

Log Message:
-----------
Fix the time step restriction in OptTillphiYieldStress

This makes it possible to stop and re-start iterations.

Commit: 8ef1497951216090db9dccb0492852732ad679d9
https://github.com/pism/pism/commit/8ef1497951216090db9dccb0492852732ad679d9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-01 (Mon, 01 Nov 2021)

Changed paths:
M src/earth/LingleClark.cc

Log Message:
-----------
Use time_stepping.resolution in the LingleClark bed deformation model

Commit: ee3795126e1e90aafa4bc7700e9af72c6b54f376
https://github.com/pism/pism/commit/ee3795126e1e90aafa4bc7700e9af72c6b54f376
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-01 (Mon, 01 Nov 2021)

Changed paths:
M CHANGES.rst
M doc/ice-bib.bib
M doc/sphinx/climate_forcing/surface.rst
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst
M doc/sphinx/manual/practical-usage/mass-conservation.rst
M doc/sphinx/math-definitions.tex
M src/CMakeLists.txt
M src/basalstrength/MohrCoulombYieldStress.hh
A src/basalstrength/OptTillphiYieldStress.cc
A src/basalstrength/OptTillphiYieldStress.hh
M src/coupler/CMakeLists.txt
M src/coupler/surface/Factory.cc
A src/coupler/surface/NoGLRetreat.cc
A src/coupler/surface/NoGLRetreat.hh
M src/icemodel/initialization.cc
M src/pism_config.cdl

Log Message:
-----------
Merge pull request #496 from pism/ckhrulev/till-phi-optimization

Implement till friction angle optimization

As far as I can tell this PR is in good enough shape to merge right now. The changes it contains are isolated and so mistakes in the implementation will not affect the rest of the model.

Commit: 0a8470eb49a25996cd3e5e43901bbe15df6d6ec8
https://github.com/pism/pism/commit/0a8470eb49a25996cd3e5e43901bbe15df6d6ec8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-02 (Tue, 02 Nov 2021)

Changed paths:
M CHANGES.rst
M doc/sphinx/climate_forcing/atmosphere.rst
M src/coupler/atmosphere/ElevationChange.cc
M src/coupler/atmosphere/ElevationChange.hh
M src/pism_config.cdl
M test/regression/atmosphere_models.py

Log Message:
-----------
Add atmosphere.elevation_change.precipitation.temp_lapse_rate

This new parameter make it possible to use "-atmosphere ...,lapse_rate" with a model that
already includes a temperature lapse rate. (For example: now "-atmosphere pik,lapse_rate"
can be used to adjust precipitation in response to changing ice geometry *without* messing
up the near-surface air temperature coming from "-atmosphere pik".)

This takes care of the issue #492 tried to address.

Commit: 4d59b4830f49fca985ace3bd84cf84d70a1059eb
https://github.com/pism/pism/commit/4d59b4830f49fca985ace3bd84cf84d70a1059eb
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-03 (Wed, 03 Nov 2021)

Changed paths:
M doc/sphinx/logo/pism-logo.png

Log Message:
-----------
Replace the PISM logo in the manual

Commit: f9b9d14812fa2cb393c3bebc68aea24b0d4f9b1c
https://github.com/pism/pism/commit/f9b9d14812fa2cb393c3bebc68aea24b0d4f9b1c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-03 (Wed, 03 Nov 2021)

Changed paths:
M test/miscellaneous.py

Log Message:
-----------
Add a regression test checking the grounding line flux approximation

The flux through the grounding line should be zero when the flux direction is parallel to
the grounding line.

Commit: 72b819ba04221a529e6054b0be35636ad3fd661e
https://github.com/pism/pism/commit/72b819ba04221a529e6054b0be35636ad3fd661e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-03 (Wed, 03 Nov 2021)

Changed paths:
M src/geometry/GeometryEvolution.cc

Log Message:
-----------
Fix the grounding line flux approximation

Commit: 60d6417486e561aaebda8254377b2fb45a75d1c4
https://github.com/pism/pism/commit/60d6417486e561aaebda8254377b2fb45a75d1c4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-03 (Wed, 03 Nov 2021)

Changed paths:
M CHANGES.rst

Log Message:
-----------
Update the change log

Commit: a3f295c3c218b0bbaa8fc7f29649be3b22f34004
https://github.com/pism/pism/commit/a3f295c3c218b0bbaa8fc7f29649be3b22f34004
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-03 (Wed, 03 Nov 2021)

Changed paths:
M CHANGES.rst
M src/geometry/GeometryEvolution.cc
M test/miscellaneous.py

Log Message:
-----------
Merge branch 'ckhrulev/grounding-line-flux' into dev

Commit: b6cfdad6390a14dfde8db7d37b4e627440a6e105
https://github.com/pism/pism/commit/b6cfdad6390a14dfde8db7d37b4e627440a6e105
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-08 (Mon, 08 Nov 2021)

Changed paths:
M CHANGES.rst

Log Message:
-----------
Fix the change log entry

The changes in 72b819ba04221a529e6054b0be35636ad3fd661e do not *fix* the issue, they just
improve the approximation a little bit.

Commit: 3379d09ce3a6c9c437ffe74015d8dc8bfdc5792a
https://github.com/pism/pism/commit/3379d09ce3a6c9c437ffe74015d8dc8bfdc5792a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-09 (Tue, 09 Nov 2021)

Changed paths:
M src/icemodel/timestepping.cc

Log Message:
-----------
A bit of cleanup

Commit: b38d62b748818d0076690f52e7962402931d3980
https://github.com/pism/pism/commit/b38d62b748818d0076690f52e7962402931d3980
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-09 (Tue, 09 Nov 2021)

Changed paths:
M src/icemodel/timestepping.cc

Log Message:
-----------
Fix the "time step skipping" mechanism

Commit: 7d607abf728579b2a4a6f685a59382f5e6e98c46
https://github.com/pism/pism/commit/7d607abf728579b2a4a6f685a59382f5e6e98c46
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-10 (Wed, 10 Nov 2021)

Changed paths:
M src/external/calcalcs/calcalcs.c
M src/external/calcalcs/calcalcs.h

Log Message:
-----------
Fix a bug in CalCalcs

"errno" in errno.h (part of the C99 standard) may be defined as a macro (appears to be the
case in the GNU C library), so CalCalcs' use of "errno" as a variable name is a bad idea.

Commit: 64f0830735bb98996d543f9a6820eab05df8eed2
https://github.com/pism/pism/commit/64f0830735bb98996d543f9a6820eab05df8eed2
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-10 (Wed, 10 Nov 2021)

Changed paths:
M src/util/Time.cc

Log Message:
-----------
Fix a bug in pism::increment_date() and add more sanity checks

- Disallow negative years with calendars other than 360_day and 365_day. "Real-life"
calendars do not have a year zero (year jumps from -1 to 1) and handling this properly
would require writing more code we don't really need.
- Stop if the run length is negative (-ys A -ye B with A > B or -y C with C < 0).

Commit: a21c55ff63a5b9c18e81551dd94d3e5012a6ae08
https://github.com/pism/pism/commit/a21c55ff63a5b9c18e81551dd94d3e5012a6ae08
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-10 (Wed, 10 Nov 2021)

Changed paths:
M doc/sphinx/logo/pism-logo.png

Log Message:
-----------
Update the PISM logo

Commit: f1014540955a17980f5f4c4683ccbeba4ddc3510
https://github.com/pism/pism/commit/f1014540955a17980f5f4c4683ccbeba4ddc3510
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-11 (Thu, 11 Nov 2021)

Changed paths:
M src/external/calcalcs/calcalcs.c

Log Message:
-----------
Fix a bug in CalCalcs

ccs_isleap() should always give "false" for 360_day and 365_day calendars. The check
"if (year < -4714)" is not appropriate here.

Commit: 408abdec2ffeaf614e00732ba0aa1bb4bb0bc977
https://github.com/pism/pism/commit/408abdec2ffeaf614e00732ba0aa1bb4bb0bc977
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-11 (Thu, 11 Nov 2021)

Changed paths:
M src/coupler/atmosphere/YearlyCycle.cc
M src/util/Time.cc
M src/util/Time.hh

Log Message:
-----------
Minor cleanup in Time.{cc,hh}

Commit: 08d08a636fe892d1905e82736415b870420caee8
https://github.com/pism/pism/commit/08d08a636fe892d1905e82736415b870420caee8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-11 (Thu, 11 Nov 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/computational/time.rst

Log Message:
-----------
Update and improve the manual section about time management and calendars

Commit: dabf44f67614c5e677d37ddfaf732b16ba9da320
https://github.com/pism/pism/commit/dabf44f67614c5e677d37ddfaf732b16ba9da320
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-11 (Thu, 11 Nov 2021)

Changed paths:
M doc/sphinx/manual/modeling-choices/computational/time.rst

Log Message:
-----------
Minor formatting fix in the manual

Commit: 1cffeb305c38e2e7bbfee86cb4a933aaac21508a
https://github.com/pism/pism/commit/1cffeb305c38e2e7bbfee86cb4a933aaac21508a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-11 (Thu, 11 Nov 2021)

Changed paths:
M ACKNOWLEDGE.rst
M CHANGES.rst
M CONTRIBUTING.rst
M README.rst
M doc/citing-pism.bib
M examples/labgum/README.md
M src/util/pism_options.cc

Log Message:
-----------
Replace almost all mentions of pism-docs.org with pism.io

Commit: c800298ff506e70f1b777fb3612f8406005cdc5a
https://github.com/pism/pism/commit/c800298ff506e70f1b777fb3612f8406005cdc5a
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-11 (Thu, 11 Nov 2021)

Changed paths:
R util/pism_config_editor
R util/pism_config_editor.py

Log Message:
-----------
Delete old scripts that no one needs

Commit: bc9033574ef0c6ef89fac21c3b0f632c2918db79
https://github.com/pism/pism/commit/bc9033574ef0c6ef89fac21c3b0f632c2918db79
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-11 (Thu, 11 Nov 2021)

Changed paths:
M doc/sphinx/contributing/development-workflow.rst
M doc/sphinx/contributing/git-branches.rst
M doc/sphinx/contributing/git-introduction.rst
M doc/sphinx/installation/code/parallelio.sh
M release.sh

Log Message:
-----------
Replace all references to the "master" branch with "main"

See https://sfconservancy.org/news/2020/jun/23/gitbranchname/ (for example) if you want to
know why.

Commit: 09ab76bc179b595d1cac61567a6c1d4b087c3ec4
https://github.com/pism/pism/commit/09ab76bc179b595d1cac61567a6c1d4b087c3ec4
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-11 (Thu, 11 Nov 2021)

Changed paths:
M src/util/Time.cc

Log Message:
-----------
Fix Time::increment_date() for fractional increments and the 360_day calendar

Commit: 637d72836ec50cd32325025800356d70ed402164
https://github.com/pism/pism/commit/637d72836ec50cd32325025800356d70ed402164
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-12 (Fri, 12 Nov 2021)

Changed paths:
M src/energy/enthSystem.cc
M src/stressbalance/blatter/Blatter.cc
M src/stressbalance/blatter/Blatter.hh
M src/stressbalance/blatter/BlatterMod.cc
M src/stressbalance/blatter/jacobian.cc
M src/stressbalance/blatter/residual.cc
M src/stressbalance/sia/SIAFD.cc
M src/stressbalance/sia/SIAFD.hh
M src/util/ColumnInterpolation.cc
M src/util/ColumnSystem.cc
M src/util/ColumnSystem.hh
M src/util/ConfigInterface.cc
M src/util/ConfigInterface.hh
M src/util/EnthalpyConverter.cc
M src/util/EnthalpyConverter.hh
M src/util/IceGrid.cc
M src/util/Logger.cc
M src/util/MaxTimestep.cc
M src/util/MaxTimestep.hh
M src/util/Profiling.cc
M src/util/Profiling.hh
M src/util/ScalarForcing.cc
M src/util/Time.cc
M src/util/VariableMetadata.cc
M src/util/VariableMetadata.hh
M src/util/Vars.cc
M src/util/Vector2.hh
M src/util/connected_components.cc
M src/util/error_handling.cc
M src/util/fem/Element.cc
M src/util/fem/Element.hh
M src/util/fem/FEM.hh
M src/util/fftw_utilities.cc
M src/util/iceModelVec.cc
M src/util/iceModelVec.hh
M src/util/iceModelVec2.cc
M src/util/iceModelVec2T.cc
M src/util/iceModelVec2V.cc
M src/util/iceModelVec3.cc
M src/util/interpolation.hh
M src/util/io/File.cc
M src/util/label_components.cc
M src/util/node_types.cc
M src/util/options.cc
M src/util/pism_options.cc
M src/util/pism_options.hh
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh
M src/util/projection.cc

Log Message:
-----------
Minor cleanup inspired by clang-tidy

Commit: 9b9a7f6336ec1d5a2403bb274229ea7f4b8dc906
https://github.com/pism/pism/commit/9b9a7f6336ec1d5a2403bb274229ea7f4b8dc906
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-12 (Fri, 12 Nov 2021)

Changed paths:
A doc/sphinx/contributing/code/tidy.sh
M doc/sphinx/contributing/development-workflow.rst

Log Message:
-----------
Document how I use clang-tidy

Commit: 56c2d6b362188397d770b323b110a1979aa72224
https://github.com/pism/pism/commit/56c2d6b362188397d770b323b110a1979aa72224
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-12 (Fri, 12 Nov 2021)

Changed paths:
M doc/sphinx/global.txt
M doc/sphinx/installation/arch.rst

Log Message:
-----------
Update Julien Seguinot's e-mail address in the manual

Commit: 42aa34fde65ee4f80e735238801be6181ecf7848
https://github.com/pism/pism/commit/42aa34fde65ee4f80e735238801be6181ecf7848
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-15 (Mon, 15 Nov 2021)

Changed paths:
M src/geometry/grounded_cell_fraction.cc

Log Message:
-----------
More cleanup inspired by clang-tidy

Commit: 84ade1297c8416a2788e0bdcfdb5818acc9c036c
https://github.com/pism/pism/commit/84ade1297c8416a2788e0bdcfdb5818acc9c036c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-16 (Tue, 16 Nov 2021)

Changed paths:
M src/icemodel/output_extra.cc
M src/icemodel/output_save.cc
M src/icemodel/utilities.cc

Log Message:
-----------
Try to avoid using spaces in file names

This affects file names that include "dates":
- -extra_split (output.extra.split)
- -save_split (output.snapshot.split)
- state saved if PISM received the USR1 signal

Commit: d82e4970403efd6004e2b82c080b026b2e7ccd69
https://github.com/pism/pism/commit/d82e4970403efd6004e2b82c080b026b2e7ccd69
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-16 (Tue, 16 Nov 2021)

Changed paths:
M CMakeLists.txt

Log Message:
-----------
Set CMAKE_BUILD_TYPE to "Release" if not specified

Commit: 6cc74d380f20b378e59ee0bc0481906c70739fa3
https://github.com/pism/pism/commit/6cc74d380f20b378e59ee0bc0481906c70739fa3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-16 (Tue, 16 Nov 2021)

Changed paths:
M test/CMakeLists.txt

Log Message:
-----------
Always enable all regression tests

Commit: 122a729943b205a179f85e7ed169899e37ec38a6
https://github.com/pism/pism/commit/122a729943b205a179f85e7ed169899e37ec38a6
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-16 (Tue, 16 Nov 2021)

Changed paths:
M src/geometry/grounded_cell_fraction.cc

Log Message:
-----------
Add three more sanity checks to grounded_area_fraction()

Commit: 1b6772d2a5c2ee422fb20dd24bc0b93d82da0d1b
https://github.com/pism/pism/commit/1b6772d2a5c2ee422fb20dd24bc0b93d82da0d1b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-16 (Tue, 16 Nov 2021)

Changed paths:
M doc/sphinx/global.txt
M doc/sphinx/installation/code/install_docu_libraries.sh
M doc/sphinx/installation/code/petsc.sh
M doc/sphinx/installation/common-problems.rst
M doc/sphinx/installation/documentation.rst
M doc/sphinx/installation/petsc.rst
M doc/sphinx/installation/pism.rst
M doc/sphinx/installation/quick-tests.rst
M doc/sphinx/manual/index.rst
M doc/sphinx/manual/std-greenland/parameter-study.rst

Log Message:
-----------
Update part of the manual

Commit: c286cf0dd3483204ea0a9815e154a1145832cdfa
https://github.com/pism/pism/commit/c286cf0dd3483204ea0a9815e154a1145832cdfa
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-17 (Wed, 17 Nov 2021)

Changed paths:
M doc/sphinx/climate_forcing/atmosphere.rst
M doc/sphinx/climate_forcing/ocean.rst
M doc/sphinx/climate_forcing/surface.rst
M doc/sphinx/manual/modeling-choices/dynamics/rheology.rst
M doc/sphinx/manual/modeling-choices/dynamics/sia.rst
M doc/sphinx/manual/modeling-choices/dynamics/ssa.rst
M doc/sphinx/manual/modeling-choices/dynamics/weertman.rst
M doc/sphinx/manual/modeling-choices/marine/calving.rst
M doc/sphinx/manual/modeling-choices/marine/damage.rst
M doc/sphinx/manual/modeling-choices/subglacier/bed-deformation.rst
M doc/sphinx/pism_config.py

Log Message:
-----------
Clean up lists of parameters in the manual

Commit: 19b400eccdfde8d57321170e2816e3c2a9fdf8d1
https://github.com/pism/pism/commit/19b400eccdfde8d57321170e2816e3c2a9fdf8d1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-17 (Wed, 17 Nov 2021)

Changed paths:
M src/geometry/Geometry.cc

Log Message:
-----------
Save ice geometry that led to a failure in compute_grounded_cell_fraction()

Commit: 2afb5a5ee7eb63b4d54aad8b73641d92634ac506
https://github.com/pism/pism/commit/2afb5a5ee7eb63b4d54aad8b73641d92634ac506
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-17 (Wed, 17 Nov 2021)

Changed paths:
M src/geometry/grounded_cell_fraction.cc

Log Message:
-----------
"std::isfinite()" is more appropriate than "not std::isnan()"

Commit: 1137648170ce3d29b96433e84548abfe9a5c585c
https://github.com/pism/pism/commit/1137648170ce3d29b96433e84548abfe9a5c585c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-18 (Thu, 18 Nov 2021)

Changed paths:
M src/coupler/ocean/Pico.cc

Log Message:
-----------
Work around a bug in PICO

This commit ensures that we don't divide by zero and so allows PISM to continue running,
but it *does not* fix the real bug: for some reason sometimes (depending on the number of
processes and the parallel domain decomposition) n_shelf_cells[s] is zero. This is not
right.

Commit: 34ea20521c766c43f58bcca8bda9cf85c109b99f
https://github.com/pism/pism/commit/34ea20521c766c43f58bcca8bda9cf85c109b99f
Author: Andy <andy.as...@gmail.com>
Date: 2021-11-19 (Fri, 19 Nov 2021)

Changed paths:
M doc/funding.csv

Log Message:
-----------
Updated US funding

For some new grants, we don't have the grant no. yet.

Commit: cce57d05ccb26bc37516438ff172dcc26d5c0bd1
https://github.com/pism/pism/commit/cce57d05ccb26bc37516438ff172dcc26d5c0bd1
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-19 (Fri, 19 Nov 2021)

Changed paths:
M doc/funding.csv

Log Message:
-----------
Minor edits in funding.csv

Commit: 9304da61dc28b224a49c8088338c4c88987de714
https://github.com/pism/pism/commit/9304da61dc28b224a49c8088338c4c88987de714
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-19 (Fri, 19 Nov 2021)

Changed paths:
M ACKNOWLEDGE.rst
M doc/sphinx/funding.txt

Log Message:
-----------
Update funding acknowledgments

Commit: 53b742a41b4dca9a05dea1fd656fb826a8925e87
https://github.com/pism/pism/commit/53b742a41b4dca9a05dea1fd656fb826a8925e87
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-19 (Fri, 19 Nov 2021)

Changed paths:
M ACKNOWLEDGE.rst
M doc/acknowledge.py
M doc/funding.csv
M doc/sphinx/funding.txt

Log Message:
-----------
Skip grants for which we don't have a number (yet)

Commit: 254216f632c893446f3a5418652a7a9d9725d451
https://github.com/pism/pism/commit/254216f632c893446f3a5418652a7a9d9725d451
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-19 (Fri, 19 Nov 2021)

Changed paths:
M doc/sphinx/contributing/development-workflow.rst

Log Message:
-----------
Document using PETSc's option -fp_trap for debugging

Commit: 5828701c7b25ea471981354eea73c4b2965aa325
https://github.com/pism/pism/commit/5828701c7b25ea471981354eea73c4b2965aa325
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-19 (Fri, 19 Nov 2021)

Changed paths:
M src/coupler/ocean/Pico.cc

Log Message:
-----------
Remove one more place where PICO was dividing by zero

(This instance was harmless because the resulting NaN was never used.)

Commit: a879134c582d39d40338c6e23cacd951c07719a5
https://github.com/pism/pism/commit/a879134c582d39d40338c6e23cacd951c07719a5
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-19 (Fri, 19 Nov 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc

Log Message:
-----------
Fix a variable name

Commit: 9767cba0f9556100e6663dc9adcc1511ec254f9c
https://github.com/pism/pism/commit/9767cba0f9556100e6663dc9adcc1511ec254f9c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-23 (Tue, 23 Nov 2021)

Changed paths:
M .dir-locals.el

Log Message:
-----------
Fix Emacs settings for indenting C++11 lambdas

Commit: 897cdc91afc3c13fc2acf9a8087a4a9e06f83134
https://github.com/pism/pism/commit/897cdc91afc3c13fc2acf9a8087a4a9e06f83134
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-23 (Tue, 23 Nov 2021)

Changed paths:
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh

Log Message:
-----------
Add GlobalMax(MPI_Comm, int*, int*, int)

Commit: f20e53faf4a7e1286f65dba99ccd3b1fa7b5e758
https://github.com/pism/pism/commit/f20e53faf4a7e1286f65dba99ccd3b1fa7b5e758
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-23 (Tue, 23 Nov 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
Fix #497

... by re-writing the code that identifies basin neighbors.

Commit: b427f74614d0f9199e051d49cf73643ab59a1cd1
https://github.com/pism/pism/commit/b427f74614d0f9199e051d49cf73643ab59a1cd1
Author: Torsten Albrecht <albr...@pik-potsdam.de>
Date: 2021-11-24 (Wed, 24 Nov 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc

Log Message:
-----------
detect PICO basin neighbors along the ice front only

Commit: f8dd8c833263a01cb3c3a819d0e0627f6a8f43c9
https://github.com/pism/pism/commit/f8dd8c833263a01cb3c3a819d0e0627f6a8f43c9
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-24 (Wed, 24 Nov 2021)

Changed paths:
M src/coupler/ocean/PicoGeometry.cc

Log Message:
-----------
Minor cleanup in PicoGeometry::basin_neighbors()

Commit: e55a283827dc1758305ff66f1a1f5f68e14f126e
https://github.com/pism/pism/commit/e55a283827dc1758305ff66f1a1f5f68e14f126e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-29 (Mon, 29 Nov 2021)

Changed paths:
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh

Log Message:
-----------
Update basin adjacency in PicoGeometry::update() instead of init()

In our current interpretation basin adjacency depends on the ice extent. This means that
we cannot pre-compute it during initialization.

Commit: 6599658ce9127654f065976cdb83c180d9762a19
https://github.com/pism/pism/commit/6599658ce9127654f065976cdb83c180d9762a19
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-11-30 (Tue, 30 Nov 2021)

Changed paths:
M src/util/iceModelVec.cc
M src/util/iceModelVec.hh

Log Message:
-----------
Add IceModelVec::fletcher64_serial()

This checksum makes it easier to find bugs that result in differences between simulations
using different numbers of MPI processes, different domain decompositions, etc.

Commit: 7d79cfbc40ad49028979f2bacfb70e5ae03aebca
https://github.com/pism/pism/commit/7d79cfbc40ad49028979f2bacfb70e5ae03aebca
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-12-02 (Thu, 02 Dec 2021)

Changed paths:
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh

Log Message:
-----------
Add pism::print_checksum()

Commit: 69d7ca2df9e5be896d48f65321f3585df18d9c42
https://github.com/pism/pism/commit/69d7ca2df9e5be896d48f65321f3585df18d9c42
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-12-02 (Thu, 02 Dec 2021)

Changed paths:
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh

Log Message:
-----------
Add pism::print_vector()

Commit: 36e8d5ae8b82fdc8d8915c3d7e520c36bf2397dd
https://github.com/pism/pism/commit/36e8d5ae8b82fdc8d8915c3d7e520c36bf2397dd
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-12-02 (Thu, 02 Dec 2021)

Changed paths:
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh

Log Message:
-----------
Add pism::replace_character()

This utility function replaces all occurrences of a character in a string with a
replacement and returns the result.

std::regex_replace() can do this, but I'm running into strange compilation issues...

Commit: 8c1158d8dd352eb150d95dc9027b47466b0c85f3
https://github.com/pism/pism/commit/8c1158d8dd352eb150d95dc9027b47466b0c85f3
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-12-02 (Thu, 02 Dec 2021)

Changed paths:
M src/icemodel/output_extra.cc
M src/icemodel/output_save.cc
M src/icemodel/utilities.cc

Log Message:
-----------
Replace std::regex_replace() with pism::replace_character()

Commit: 9643721dcaa3965b6b84ceec458a1baf1115c723
https://github.com/pism/pism/commit/9643721dcaa3965b6b84ceec458a1baf1115c723
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-12-02 (Thu, 02 Dec 2021)

Changed paths:
M test/miscellaneous.py

Log Message:
-----------
Fix a regression test

Commit: bece6733be47f48a7782e3d35796ab8b3780791c
https://github.com/pism/pism/commit/bece6733be47f48a7782e3d35796ab8b3780791c
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-12-02 (Thu, 02 Dec 2021)

Changed paths:
M src/pythonbindings/PISM.i

Log Message:
-----------
Remove two debugging functions from Python bindings

Commit: ef4964e42c6e717a2a40074dfae9098dee0ab83b
https://github.com/pism/pism/commit/ef4964e42c6e717a2a40074dfae9098dee0ab83b
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-12-02 (Thu, 02 Dec 2021)

Changed paths:
M src/coupler/ocean/Pico.cc

Log Message:
-----------
Fix a bug in PICO

We need to update ghosts of the basal melt rate field before we compute an average over
floating *neighbors* of a cell.

Commit: 90b55caca389118647b585764735b9578b1b9180
https://github.com/pism/pism/commit/90b55caca389118647b585764735b9578b1b9180
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-12-02 (Thu, 02 Dec 2021)

Changed paths:
M src/coupler/ocean/Pico.cc

Log Message:
-----------
Minor cleanup in PICO

Commit: 8c3e4b397d09302e5726955975a8c836793e3334
https://github.com/pism/pism/commit/8c3e4b397d09302e5726955975a8c836793e3334
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-12-02 (Thu, 02 Dec 2021)

Changed paths:
M release.sh

Log Message:
-----------
Fix release.sh

Commit: 534337bf88fc47d8d884c1693cc562a5879f7d5e
https://github.com/pism/pism/commit/534337bf88fc47d8d884c1693cc562a5879f7d5e
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-12-02 (Thu, 02 Dec 2021)

Changed paths:
M .circleci/config.yml

Log Message:
-----------
Deploy the "main" branch manual and code browser

... instead of the "dev" branch version.

Commit: 67885791fed037be7577cf51b3c70c676bf47d04
https://github.com/pism/pism/commit/67885791fed037be7577cf51b3c70c676bf47d04
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-12-02 (Thu, 02 Dec 2021)

Changed paths:
M doc/ice-bib.bib
M doc/sphinx/global.txt
M doc/sphinx/manual/jakobshavn/index.rst

Log Message:
-----------
Fix some broken links

Commit: 976efe1230c9296004ca3a4d51991f313d229ccf
https://github.com/pism/pism/commit/976efe1230c9296004ca3a4d51991f313d229ccf
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-12-03 (Fri, 03 Dec 2021)

Changed paths:
M .circleci/config.yml
M .dir-locals.el
M .mailmap
M ACKNOWLEDGE.rst
M CHANGES.rst
M CMake/PISM_CMake_macros.cmake
M CMakeLists.txt
M CONTRIBUTING.rst
M README.rst
M doc/CMakeLists.txt
M doc/Makefile
M doc/acknowledge.py
M doc/browser/CMakeLists.txt
R doc/browser/doxybib.bst
R doc/browser/doxybib.dbj
R doc/browser/doxybib.py
M doc/browser/doxyfile
R doc/browser/figures/ssastencil.png
A doc/browser/list_references.py
M doc/browser/mainpage.md
R doc/browser/petsc.md
R doc/browser/pism.sty
M doc/citing-pism.bib
M doc/funding.csv
M doc/ice-bib.bib
M doc/sphinx/CMakeLists.txt
M doc/sphinx/Makefile
M doc/sphinx/authorship.rst
M doc/sphinx/climate_forcing/atmosphere.rst
A doc/sphinx/climate_forcing/delta_T.cdl
M doc/sphinx/climate_forcing/index.rst
M doc/sphinx/climate_forcing/ocean.rst
M doc/sphinx/climate_forcing/surface.rst
M doc/sphinx/climate_forcing/testing.rst
A doc/sphinx/climate_forcing/time-dependent.rst
R doc/sphinx/climate_forcing/time.rst
M doc/sphinx/conf.py
A doc/sphinx/contributing/code/tidy.sh
M doc/sphinx/contributing/development-workflow.rst
M doc/sphinx/contributing/git-branches.rst
M doc/sphinx/contributing/git-introduction.rst
M doc/sphinx/funding.txt
M doc/sphinx/global.txt
M doc/sphinx/installation/arch.rst
M doc/sphinx/installation/code/hdf5.sh
M doc/sphinx/installation/code/install_docu_libraries.sh
M doc/sphinx/installation/code/install_libraries.sh
M doc/sphinx/installation/code/io_libraries.sh
M doc/sphinx/installation/code/netcdf.sh
M doc/sphinx/installation/code/parallelio.sh
A doc/sphinx/installation/code/petsc-mkl-mumps-hypre.sh
A doc/sphinx/installation/code/petsc-mumps-hypre.sh
A doc/sphinx/installation/code/petsc.sh
A doc/sphinx/installation/code/pism.sh
M doc/sphinx/installation/common-problems.rst
M doc/sphinx/installation/debian-packages.csv
M doc/sphinx/installation/debian.rst
M doc/sphinx/installation/documentation.rst
M doc/sphinx/installation/petsc.rst
M doc/sphinx/installation/pism.rst
M doc/sphinx/installation/quick-tests.rst
R doc/sphinx/list_parameters.py
M doc/sphinx/logo/pism-logo.png
M doc/sphinx/manual/diagnostics/diagnostics-list.txt
M doc/sphinx/manual/highlevelview/climate-inputs.rst
M doc/sphinx/manual/highlevelview/figures/stressbalance.dot
M doc/sphinx/manual/highlevelview/figures/stressbalance.png
M doc/sphinx/manual/highlevelview/model-hierarchy.rst
M doc/sphinx/manual/highlevelview/stress-balance-models.rst
M doc/sphinx/manual/index.rst
M doc/sphinx/manual/initialization/bootstrapping.rst
M doc/sphinx/manual/initialization/index.rst
M doc/sphinx/manual/initialization/restarting.rst
M doc/sphinx/manual/jakobshavn/index.rst
M doc/sphinx/manual/modeling-choices/computational/box.rst
A doc/sphinx/manual/modeling-choices/computational/figures/grid-vertical-pism.png
A doc/sphinx/manual/modeling-choices/computational/figures/grid-vertical-sigma.png
A doc/sphinx/manual/modeling-choices/computational/figures/grid-vertical.svg
M doc/sphinx/manual/modeling-choices/computational/grid.rst
M doc/sphinx/manual/modeling-choices/computational/time.rst
M doc/sphinx/manual/modeling-choices/dynamics/age.rst
A doc/sphinx/manual/modeling-choices/dynamics/blatter.rst
R doc/sphinx/manual/modeling-choices/dynamics/figures/.DS_Store
M doc/sphinx/manual/modeling-choices/dynamics/index.rst
M doc/sphinx/manual/modeling-choices/dynamics/rheology.rst
A doc/sphinx/manual/modeling-choices/dynamics/sia.rst
A doc/sphinx/manual/modeling-choices/dynamics/ssa.rst
M doc/sphinx/manual/modeling-choices/dynamics/stress-balance.rst
R doc/sphinx/manual/modeling-choices/dynamics/surface-gradient.rst
A doc/sphinx/manual/modeling-choices/dynamics/weertman.rst
M doc/sphinx/manual/modeling-choices/marine/calving.rst
A doc/sphinx/manual/modeling-choices/marine/damage.rst
M doc/sphinx/manual/modeling-choices/marine/index.rst
M doc/sphinx/manual/modeling-choices/marine/melange.rst
M doc/sphinx/manual/modeling-choices/marine/pik.rst
M doc/sphinx/manual/modeling-choices/regional/index.rst
M doc/sphinx/manual/modeling-choices/subglacier/basal-strength.rst
M doc/sphinx/manual/modeling-choices/subglacier/bed-deformation.rst
R doc/sphinx/manual/modeling-choices/subglacier/bed-roughness.rst
M doc/sphinx/manual/modeling-choices/subglacier/hydrology.rst
M doc/sphinx/manual/modeling-choices/subglacier/index.rst
M doc/sphinx/manual/parameters/index.rst
R doc/sphinx/manual/parameters/parameter-list.txt
M doc/sphinx/manual/practical-usage/diagnostic-viewers.rst
M doc/sphinx/manual/practical-usage/flowline.rst
M doc/sphinx/manual/practical-usage/index.rst
M doc/sphinx/manual/practical-usage/input-output.rst
M doc/sphinx/manual/practical-usage/mass-conservation.rst
M doc/sphinx/manual/practical-usage/modifying-pism.rst
M doc/sphinx/manual/practical-usage/regridding.rst
M doc/sphinx/manual/practical-usage/saving-diagnostics.rst
M doc/sphinx/manual/practical-usage/saving-snapshots.rst
M doc/sphinx/manual/practical-usage/saving-time-series.rst
M doc/sphinx/manual/practical-usage/time-stepping.rst
M doc/sphinx/manual/simplified-geometry/eismint-2.rst
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-a.png
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-b.png
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-c.png
A doc/sphinx/manual/simplified-geometry/figures/ismiphom-d.png
A doc/sphinx/manual/simplified-geometry/figures/uvel_no_slip.png
A doc/sphinx/manual/simplified-geometry/figures/uvel_sliding.png
A doc/sphinx/manual/simplified-geometry/figures/uvelsurf.png
M doc/sphinx/manual/simplified-geometry/index.rst
A doc/sphinx/manual/simplified-geometry/ismip-hom.rst
M doc/sphinx/manual/simplified-geometry/mismip3d.rst
M doc/sphinx/manual/std-greenland/grid-sequencing.rst
M doc/sphinx/manual/std-greenland/index.rst
M doc/sphinx/manual/std-greenland/parameter-study.rst
M doc/sphinx/manual/validation/ross.rst
M doc/sphinx/manual/verification/index.rst
A doc/sphinx/math-definitions.tex
R doc/sphinx/math-definitions.txt
A doc/sphinx/pism_config.py
A doc/sphinx/technical/blatter-pattyn.rst
M doc/sphinx/technical/bombproof.rst
M doc/sphinx/technical/index.rst
A doc/sphinx/technical/ocean-th.rst
M doc/sphinx/technical/release_checklist.rst
M doc/sphinx/technical/ssafd-cfbc.rst
A doc/sphinx/technical/ssafd-flow-line.rst
M doc/sphinx/technical/steady-hydrology.rst
M doc/sphinx/technical/vertchange.rst
M docker/CMakeLists.txt
A docker/ubuntu-ci/CMakeLists.txt
A docker/ubuntu-ci/Dockerfile.in
A docker/ubuntu-ci/README.rst
A docker/ubuntu-minimal/CMakeLists.txt
A docker/ubuntu-minimal/Dockerfile.in
A docker/ubuntu-minimal/README.rst
R examples/bedmap2/README.md
R examples/bedmap2/readgeom.py
M examples/eismintII/runexp.sh
M examples/inverse/make_synth_ssa.py
M examples/inverse/pismi.py
A examples/ismip-hom/README.rst
A examples/ismip-hom/abcd/Makefile
A examples/ismip-hom/abcd/README.rst
A examples/ismip-hom/abcd/convert-ismiphom.py
A examples/ismip-hom/abcd/plot-ismiphom.py
A examples/ismip-hom/abcd/run-ismiphom.py
A examples/ismip-hom/e-arolla/Makefile
A examples/ismip-hom/e-arolla/README.md
A examples/ismip-hom/e-arolla/convert.py
A examples/ismip-hom/e-arolla/plot.py
A examples/ismip-hom/e-arolla/run.sh
M examples/jako/century.sh
M examples/jako/preprocess.sh
M examples/jako/quickjakosetup.sh
M examples/jako/spinup.sh
M examples/labgum/README.md
M examples/labgum/preprocess.py
M examples/labgum/rungum.sh
M examples/marine/circular/circular_dirichlet.py
M examples/marine/circular/piktests_utils.py
M examples/marine/circular/test_iceberg_removal.py
M examples/marine/flood/Makefile
M examples/marine/flood/README.md
M examples/marine/flowline/createSetup_flowline.py
M examples/marine/flowline/run_flowline.sh
M examples/marine/tongues/generate_input.py
A examples/mismip/check_taud_flowline/README.md
A examples/mismip/check_taud_flowline/plot_diff.py
A examples/mismip/check_taud_flowline/prepare_iceshelf.py
A examples/mismip/check_taud_flowline/run_test.sh
M examples/mismip/mismip2d/run.py
M examples/mismip/mismip3d/preprocess.py
M examples/nbreen/README.md
M examples/nbreen/fake-inputtobed.py
M examples/nbreen/preprocess.sh
M examples/nbreen/run.sh
A examples/python/orographic_precipitation.py
M examples/python/ssa_tests/ssa_test_cfbc.py
M examples/python/ssa_tests/ssa_test_linear.py
M examples/python/ssa_tests/ssa_test_plug.py
M examples/python/ssa_tests/ssa_testi.py
M examples/python/ssa_tests/ssa_testj.py
A examples/ross/download.sh
M examples/ross/fracture/README.md
M examples/ross/fracture/fracture_model.py
M examples/ross/fracture/run_frac.sh
A examples/ross/fracture/run_frac_borstad.sh
M examples/ross/plot.py
M examples/ross/preprocess.py
M examples/ross/prognostic/run_prog.sh
M examples/std-greenland/spinup.sh
M examples/storglaciaren/create_warming_climate.py
A release.sh
M site-packages/PISM/invert/sipletools.py
M site-packages/PISM/invert/ssa.py
M site-packages/PISM/invert/ssa_siple.py
M site-packages/PISM/model.py
M site-packages/PISM/sia.py
M site-packages/PISM/ssa.py
M site-packages/PISM/testing.py
M site-packages/PISM/util.py
M src/CMakeLists.txt
M src/age/AgeModel.cc
M src/basalstrength/ConstantYieldStress.cc
M src/basalstrength/ConstantYieldStress.hh
M src/basalstrength/MohrCoulombYieldStress.cc
M src/basalstrength/MohrCoulombYieldStress.hh
A src/basalstrength/OptTillphiYieldStress.cc
A src/basalstrength/OptTillphiYieldStress.hh
M src/basalstrength/YieldStress.cc
M src/basalstrength/YieldStress.hh
M src/basalstrength/basal_resistance.cc
M src/basalstrength/basal_resistance.hh
M src/coupler/AtmosphereModel.hh
M src/coupler/CMakeLists.txt
M src/coupler/FrontalMelt.hh
M src/coupler/OceanModel.hh
M src/coupler/SeaLevel.hh
M src/coupler/SurfaceModel.hh
M src/coupler/atmosphere/Anomaly.cc
M src/coupler/atmosphere/Anomaly.hh
M src/coupler/atmosphere/AtmosphereModel.cc
M src/coupler/atmosphere/CosineYearlyCycle.cc
M src/coupler/atmosphere/CosineYearlyCycle.hh
M src/coupler/atmosphere/Delta_P.cc
M src/coupler/atmosphere/Delta_P.hh
M src/coupler/atmosphere/Delta_T.cc
M src/coupler/atmosphere/ElevationChange.cc
M src/coupler/atmosphere/ElevationChange.hh
M src/coupler/atmosphere/Factory.cc
M src/coupler/atmosphere/Factory.hh
M src/coupler/atmosphere/Frac_P.cc
M src/coupler/atmosphere/Frac_P.hh
M src/coupler/atmosphere/GivenClimate.cc
M src/coupler/atmosphere/GivenClimate.hh
M src/coupler/atmosphere/OrographicPrecipitation.cc
M src/coupler/atmosphere/OrographicPrecipitation.hh
M src/coupler/atmosphere/OrographicPrecipitationSerial.cc
M src/coupler/atmosphere/OrographicPrecipitationSerial.hh
M src/coupler/atmosphere/PIK.cc
M src/coupler/atmosphere/PIK.hh
M src/coupler/atmosphere/PrecipitationScaling.cc
M src/coupler/atmosphere/PrecipitationScaling.hh
M src/coupler/atmosphere/SeariseGreenland.hh
M src/coupler/atmosphere/WeatherStation.cc
M src/coupler/atmosphere/WeatherStation.hh
M src/coupler/atmosphere/YearlyCycle.cc
M src/coupler/atmosphere/YearlyCycle.hh
M src/coupler/frontalmelt/Constant.cc
M src/coupler/frontalmelt/Constant.hh
M src/coupler/frontalmelt/DischargeGiven.cc
M src/coupler/frontalmelt/DischargeGiven.hh
M src/coupler/frontalmelt/DischargeRouting.cc
M src/coupler/frontalmelt/DischargeRouting.hh
M src/coupler/frontalmelt/Factory.cc
M src/coupler/frontalmelt/Factory.hh
M src/coupler/frontalmelt/FrontalMelt.cc
M src/coupler/frontalmelt/Given.cc
M src/coupler/frontalmelt/Given.hh
M src/coupler/ocean/Anomaly.cc
M src/coupler/ocean/Anomaly.hh
M src/coupler/ocean/Cache.cc
M src/coupler/ocean/Cache.hh
M src/coupler/ocean/CompleteOceanModel.cc
M src/coupler/ocean/CompleteOceanModel.hh
M src/coupler/ocean/Constant.cc
M src/coupler/ocean/Constant.hh
M src/coupler/ocean/ConstantPIK.cc
M src/coupler/ocean/ConstantPIK.hh
A src/coupler/ocean/Delta_MBP.cc
A src/coupler/ocean/Delta_MBP.hh
M src/coupler/ocean/Delta_SMB.cc
M src/coupler/ocean/Delta_T.cc
M src/coupler/ocean/Factory.cc
M src/coupler/ocean/Factory.hh
M src/coupler/ocean/Frac_MBP.cc
M src/coupler/ocean/Frac_MBP.hh
M src/coupler/ocean/Frac_SMB.cc
M src/coupler/ocean/GivenClimate.cc
M src/coupler/ocean/GivenClimate.hh
M src/coupler/ocean/GivenTH.cc
M src/coupler/ocean/GivenTH.hh
M src/coupler/ocean/Initialization.cc
M src/coupler/ocean/Initialization.hh
M src/coupler/ocean/OceanModel.cc
M src/coupler/ocean/Pico.cc
M src/coupler/ocean/Pico.hh
M src/coupler/ocean/PicoGeometry.cc
M src/coupler/ocean/PicoGeometry.hh
M src/coupler/ocean/PicoPhysics.cc
A src/coupler/ocean/Runoff_SMB.cc
A src/coupler/ocean/Runoff_SMB.hh
M src/coupler/ocean/sea_level/Delta_SL.cc
M src/coupler/ocean/sea_level/Delta_SL.hh
M src/coupler/ocean/sea_level/Delta_SL_2D.cc
M src/coupler/ocean/sea_level/Delta_SL_2D.hh
M src/coupler/ocean/sea_level/Factory.cc
M src/coupler/ocean/sea_level/Factory.hh
M src/coupler/ocean/sea_level/Initialization.cc
M src/coupler/ocean/sea_level/SeaLevel.cc
M src/coupler/surface/Anomaly.cc
M src/coupler/surface/Anomaly.hh
M src/coupler/surface/Cache.cc
M src/coupler/surface/Cache.hh
M src/coupler/surface/Delta_T.cc
M src/coupler/surface/EISMINTII.cc
M src/coupler/surface/EISMINTII.hh
M src/coupler/surface/ElevationChange.cc
M src/coupler/surface/ElevationChange.hh
M src/coupler/surface/Factory.cc
M src/coupler/surface/Factory.hh
M src/coupler/surface/ForceThickness.cc
M src/coupler/surface/ForceThickness.hh
M src/coupler/surface/Formulas.cc
M src/coupler/surface/Formulas.hh
M src/coupler/surface/GivenClimate.cc
M src/coupler/surface/GivenClimate.hh
M src/coupler/surface/ISMIP6Climate.cc
M src/coupler/surface/ISMIP6Climate.hh
M src/coupler/surface/Initialization.cc
A src/coupler/surface/NoGLRetreat.cc
A src/coupler/surface/NoGLRetreat.hh
M src/coupler/surface/StuffAsAnomaly.cc
M src/coupler/surface/SurfaceModel.cc
M src/coupler/surface/TemperatureIndex.cc
M src/coupler/surface/TemperatureIndex.hh
M src/coupler/surface/localMassBalance.cc
M src/coupler/surface/localMassBalance.hh
M src/coupler/util/PCFactory.hh
R src/coupler/util/ScalarForcing.cc
R src/coupler/util/ScalarForcing.hh
M src/coupler/util/options.cc
M src/coupler/util/options.hh
M src/earth/BedDef.cc
M src/earth/BedDef.hh
M src/earth/CMakeLists.txt
A src/earth/Given.cc
A src/earth/Given.hh
M src/earth/LingleClark.cc
M src/earth/LingleClark.hh
M src/earth/LingleClarkSerial.cc
M src/earth/LingleClarkSerial.hh
M src/earth/PointwiseIsostasy.cc
M src/energy/BTU_Full.cc
M src/energy/BTU_Full.hh
M src/energy/BedThermalUnit.cc
M src/energy/BedThermalUnit.hh
M src/energy/BedrockColumn.cc
M src/energy/BedrockColumn.hh
M src/energy/CHSystem.cc
M src/energy/CHSystem.hh
M src/energy/EnergyModel.cc
M src/energy/EnthalpyModel.cc
M src/energy/TemperatureModel.cc
M src/energy/btutest.cc
M src/energy/enthSystem.cc
M src/energy/enthSystem.hh
M src/energy/utilities.cc
M src/external/calcalcs/calcalcs.c
M src/external/calcalcs/calcalcs.h
M src/fracturedensity/FractureDensity.cc
M src/fracturedensity/FractureDensity.hh
M src/frontretreat/CMakeLists.txt
M src/frontretreat/FrontRetreat.cc
M src/frontretreat/FrontRetreat.hh
M src/frontretreat/PrescribedRetreat.cc
M src/frontretreat/PrescribedRetreat.hh
M src/frontretreat/calving/CalvingAtThickness.cc
M src/frontretreat/calving/CalvingAtThickness.hh
M src/frontretreat/calving/EigenCalving.cc
M src/frontretreat/calving/EigenCalving.hh
M src/frontretreat/calving/FloatKill.cc
M src/frontretreat/calving/FloatKill.hh
M src/frontretreat/calving/HayhurstCalving.cc
M src/frontretreat/calving/HayhurstCalving.hh
M src/frontretreat/calving/StressCalving.cc
M src/frontretreat/calving/StressCalving.hh
M src/frontretreat/calving/vonMisesCalving.cc
M src/frontretreat/calving/vonMisesCalving.hh
M src/frontretreat/util/IcebergRemover.cc
M src/frontretreat/util/IcebergRemover.hh
A src/frontretreat/util/IcebergRemoverFEM.cc
A src/frontretreat/util/IcebergRemoverFEM.hh
M src/frontretreat/util/remove_narrow_tongues.cc
M src/geometry/Geometry.cc
M src/geometry/Geometry.hh
M src/geometry/GeometryEvolution.cc
M src/geometry/GeometryEvolution.hh
M src/geometry/grounded_cell_fraction.cc
M src/geometry/part_grid_threshold_thickness.cc
M src/geometry/part_grid_threshold_thickness.hh
M src/hydrology/Distributed.cc
M src/hydrology/Distributed.hh
M src/hydrology/EmptyingProblem.cc
M src/hydrology/EmptyingProblem.hh
M src/hydrology/Hydrology.cc
M src/hydrology/Hydrology.hh
M src/hydrology/NullTransport.cc
M src/hydrology/NullTransport.hh
M src/hydrology/Routing.cc
M src/hydrology/Routing.hh
M src/hydrology/SteadyState.cc
M src/hydrology/SteadyState.hh
M src/icebin/IBIceModel.cc
M src/icebin/IBIceModel.hh
M src/icebin/IBSurfaceModel.cc
M src/icebin/MassEnergyBudget.cc
M src/icebin/MassEnergyBudget.hh
M src/icebin/VecBundleWriter.cc
M src/icemodel/IceEISModel.cc
M src/icemodel/IceEISModel.hh
M src/icemodel/IceModel.cc
M src/icemodel/IceModel.hh
M src/icemodel/diagnostics.cc
M src/icemodel/energy.cc
M src/icemodel/flux_balance.hh
M src/icemodel/fracture_density.cc
M src/icemodel/frontretreat.cc
M src/icemodel/initialization.cc
M src/icemodel/output.cc
M src/icemodel/output_extra.cc
M src/icemodel/output_save.cc
M src/icemodel/output_ts.cc
M src/icemodel/printout.cc
M src/icemodel/timestepping.cc
M src/icemodel/utilities.cc
M src/icemodel/viewers.cc
M src/inverse/IPDesignVariableParameterization.cc
M src/inverse/IPDesignVariableParameterization.hh
M src/inverse/IPTaoTikhonovProblem.hh
M src/inverse/IPTwoBlockVec.cc
M src/inverse/IPTwoBlockVec.hh
M src/inverse/IP_SSAHardavForwardProblem.cc
M src/inverse/IP_SSAHardavForwardProblem.hh
M src/inverse/IP_SSATaucForwardProblem.cc
M src/inverse/IP_SSATaucForwardProblem.hh
M src/inverse/IP_SSATaucTaoTikhonovProblemLCL.cc
M src/inverse/IP_SSATaucTaoTikhonovProblemLCL.hh
M src/inverse/IP_SSATaucTikhonovGNSolver.cc
M src/inverse/IP_SSATaucTikhonovGNSolver.hh
M src/inverse/functional/IPFunctional.cc
M src/inverse/functional/IPFunctional.hh
M src/inverse/functional/IPGroundedIceH1NormFunctional.cc
M src/inverse/functional/IPLogRatioFunctional.cc
M src/inverse/functional/IPLogRelativeFunctional.cc
M src/inverse/functional/IPMeanSquareFunctional.cc
M src/inverse/functional/IPMeanSquareFunctional.hh
M src/inverse/functional/IPTotalVariationFunctional.cc
M src/inverse/functional/IP_H1NormFunctional.cc
M src/inverse/functional/IP_H1NormFunctional.hh
M src/inverse/functional/IP_L2NormFunctional.cc
M src/pism_config.cdl
A src/pism_config.py
M src/pismr.cc
R src/pisms.cc
M src/pismv.cc
M src/pythonbindings/CMakeLists.txt
M src/pythonbindings/IceModelVec.py
M src/pythonbindings/IceModelVec2V.py
M src/pythonbindings/PISM.i
M src/pythonbindings/pism_BedDef.i
M src/pythonbindings/pism_IceModelVec.i
M src/pythonbindings/pism_SIA.i
M src/pythonbindings/pism_SSA.i
R src/pythonbindings/pism_Timeseries.i
M src/pythonbindings/pism_VariableMetadata.i
A src/pythonbindings/pism_blatter.i
M src/pythonbindings/pism_calving.i
M src/pythonbindings/pism_energy.i
M src/pythonbindings/pism_ocean.i
M src/regional/EnthalpyModel_Regional.cc
M src/regional/IceGrid_Regional.cc
M src/regional/IceGrid_Regional.hh
M src/regional/IceRegionalModel.cc
M src/regional/IceRegionalModel.hh
M src/regional/RegionalYieldStress.cc
M src/regional/RegionalYieldStress.hh
M src/regional/SIAFD_Regional.cc
M src/regional/SIAFD_Regional.hh
M src/regional/SSAFD_Regional.cc
M src/regional/SSAFD_Regional.hh
M src/rheology/FlowLaw.cc
M src/rheology/FlowLaw.hh
M src/rheology/FlowLawFactory.cc
M src/rheology/FlowLawFactory.hh
M src/rheology/GPBLD.cc
M src/rheology/GPBLD.hh
M src/rheology/GoldsbyKohlstedt.cc
M src/rheology/GoldsbyKohlstedt.hh
M src/rheology/Hooke.cc
M src/rheology/Hooke.hh
M src/rheology/PatersonBudd.cc
M src/rheology/PatersonBudd.hh
M src/rheology/PatersonBuddCold.cc
M src/rheology/PatersonBuddCold.hh
M src/rheology/PatersonBuddWarm.cc
M src/rheology/PatersonBuddWarm.hh
M src/stressbalance/CMakeLists.txt
M src/stressbalance/SSB_Modifier.cc
M src/stressbalance/SSB_Modifier.hh
M src/stressbalance/ShallowStressBalance.cc
M src/stressbalance/ShallowStressBalance.hh
M src/stressbalance/StressBalance.cc
M src/stressbalance/StressBalance.hh
M src/stressbalance/StressBalance_diagnostics.cc
M src/stressbalance/WeertmanSliding.cc
M src/stressbalance/WeertmanSliding.hh
A src/stressbalance/blatter/Blatter.cc
A src/stressbalance/blatter/Blatter.hh
A src/stressbalance/blatter/BlatterMod.cc
A src/stressbalance/blatter/BlatterMod.hh
A src/stressbalance/blatter/CMakeLists.txt
A src/stressbalance/blatter/README.org
A src/stressbalance/blatter/ismip-hom/BlatterISMIPHOM.cc
A src/stressbalance/blatter/ismip-hom/BlatterISMIPHOM.hh
A src/stressbalance/blatter/jacobian.cc
A src/stressbalance/blatter/residual.cc
A src/stressbalance/blatter/util/DataAccess.hh
A src/stressbalance/blatter/util/grid_hierarchy.cc
A src/stressbalance/blatter/util/grid_hierarchy.hh
A src/stressbalance/blatter/verification/BlatterTestCFBC.cc
A src/stressbalance/blatter/verification/BlatterTestCFBC.hh
A src/stressbalance/blatter/verification/BlatterTestHalfar.cc
A src/stressbalance/blatter/verification/BlatterTestHalfar.hh
A src/stressbalance/blatter/verification/BlatterTestXY.cc
A src/stressbalance/blatter/verification/BlatterTestXY.hh
A src/stressbalance/blatter/verification/BlatterTestXZ.cc
A src/stressbalance/blatter/verification/BlatterTestXZ.hh
A src/stressbalance/blatter/verification/BlatterTestvanderVeen.cc
A src/stressbalance/blatter/verification/BlatterTestvanderVeen.hh
A src/stressbalance/blatter/verification/Makefile
A src/stressbalance/blatter/verification/blatter.py
A src/stressbalance/blatter/verification/blatter_codegen.py
A src/stressbalance/blatter/verification/manufactured_solutions.cc
A src/stressbalance/blatter/verification/manufactured_solutions.hh
A src/stressbalance/blatter/verification/manufactured_solutions.py
A src/stressbalance/blatter/verification/test_xy.py
A src/stressbalance/blatter/verification/test_xz.py
A src/stressbalance/blatter/verification/test_xz_cfbc.py
A src/stressbalance/blatter/verification/test_xz_halfar.py
A src/stressbalance/blatter/verification/test_xz_vanderveen.py
A src/stressbalance/blatter/verification/wiggles.py
M src/stressbalance/factory.cc
M src/stressbalance/sia/BedSmoother.cc
M src/stressbalance/sia/BedSmoother.hh
M src/stressbalance/sia/SIAFD.cc
M src/stressbalance/sia/SIAFD.hh
M src/stressbalance/sia/SIAFD_diagnostics.cc
M src/stressbalance/sia/siafd_test.cc
M src/stressbalance/ssa/SSA.cc
M src/stressbalance/ssa/SSA.hh
M src/stressbalance/ssa/SSAFD.cc
M src/stressbalance/ssa/SSAFD.hh
M src/stressbalance/ssa/SSAFEM.cc
M src/stressbalance/ssa/SSAFEM.hh
M src/stressbalance/ssa/SSATestCase.cc
M src/stressbalance/ssa/SSATestCase.hh
M src/stressbalance/ssa/doc/fem_p1.mac
A src/stressbalance/ssa/doc/fem_p1_boundary.mac
A src/stressbalance/ssa/doc/fem_q1.mac
A src/stressbalance/ssa/doc/fem_q1_boundary.mac
M src/stressbalance/ssa/tests/ssa_test_cfbc.cc
M src/stressbalance/ssa/tests/ssa_test_const.cc
M src/stressbalance/ssa/tests/ssa_test_linear.cc
M src/stressbalance/ssa/tests/ssa_test_plug.cc
M src/stressbalance/ssa/tests/ssa_testi.cc
M src/stressbalance/ssa/tests/ssa_testj.cc
M src/stressbalance/timestepping.cc
M src/util/CMakeLists.txt
M src/util/ColumnInterpolation.cc
M src/util/ColumnSystem.cc
M src/util/ColumnSystem.hh
M src/util/Component.cc
M src/util/Component.hh
M src/util/Config.cc
M src/util/Config.hh
M src/util/ConfigInterface.cc
M src/util/ConfigInterface.hh
M src/util/Context.cc
M src/util/Context.hh
M src/util/Diagnostic.cc
M src/util/Diagnostic.hh
M src/util/EnthalpyConverter.cc
M src/util/EnthalpyConverter.hh
R src/util/FETools.cc
R src/util/FETools.hh
R src/util/Field.hh
M src/util/IceGrid.cc
M src/util/IceGrid.hh
A src/util/IceModelVec2.hh
M src/util/IceModelVec2CellType.hh
A src/util/IceModelVec2V.hh
A src/util/IceModelVec_impl.hh
M src/util/IceModelVec_inline.hh
M src/util/Logger.cc
M src/util/Mask.hh
M src/util/MaxTimestep.cc
M src/util/MaxTimestep.hh
M src/util/Poisson.cc
M src/util/Poisson.hh
M src/util/Profiling.cc
M src/util/Profiling.hh
A src/util/ScalarForcing.cc
A src/util/ScalarForcing.hh
R src/util/StarStencil.hh
M src/util/Time.cc
M src/util/Time.hh
R src/util/Time_Calendar.cc
R src/util/Time_Calendar.hh
R src/util/Timeseries.cc
R src/util/Timeseries.hh
M src/util/Units.cc
M src/util/Units.hh
M src/util/VariableMetadata.cc
M src/util/VariableMetadata.hh
M src/util/Vars.cc
M src/util/Vector2.hh
M src/util/connected_components.cc
M src/util/connected_components.hh
M src/util/error_handling.cc
M src/util/error_handling.hh
A src/util/fem/DirichletData.cc
A src/util/fem/DirichletData.hh
A src/util/fem/Element.cc
A src/util/fem/Element.hh
A src/util/fem/ElementIterator.cc
A src/util/fem/ElementIterator.hh
A src/util/fem/FEM.cc
A src/util/fem/FEM.hh
A src/util/fem/Quadrature.cc
A src/util/fem/Quadrature.hh
A src/util/fem/q1_3d_boundary.mac
M src/util/fftw_utilities.cc
M src/util/fftw_utilities.hh
M src/util/iceModelVec.cc
M src/util/iceModelVec.hh
M src/util/iceModelVec2.cc
M src/util/iceModelVec2T.cc
M src/util/iceModelVec2T.hh
M src/util/iceModelVec2V.cc
M src/util/iceModelVec3.cc
R src/util/iceModelVec3Custom.cc
R src/util/iceModelVec3Custom.hh
M src/util/iceModelVec_helpers.hh
M src/util/interpolation.cc
M src/util/interpolation.hh
M src/util/io/File.cc
M src/util/io/File.hh
M src/util/io/IO_Flags.hh
M src/util/io/LocalInterpCtx.cc
R src/util/io/NC3File.cc
R src/util/io/NC3File.hh
M src/util/io/NC4File.cc
M src/util/io/NC4File.hh
M src/util/io/NC4_Par.cc
M src/util/io/NC4_Par.hh
M src/util/io/NC4_Serial.cc
M src/util/io/NC4_Serial.hh
M src/util/io/NCFile.cc
M src/util/io/NCFile.hh
A src/util/io/NC_Serial.cc
A src/util/io/NC_Serial.hh
M src/util/io/PNCFile.cc
M src/util/io/PNCFile.hh
M src/util/io/ParallelIO.cc
M src/util/io/ParallelIO.hh
M src/util/io/io_helpers.cc
M src/util/io/io_helpers.hh
M src/util/label_components.cc
M src/util/node_types.cc
M src/util/options.cc
M src/util/pism_options.cc
M src/util/pism_options.hh
M src/util/pism_utilities.cc
M src/util/pism_utilities.hh
M src/util/projection.cc
M src/util/projection.hh
A src/util/scatters.cc
A src/util/stencils.hh
M src/verification/BTU_Verification.cc
M src/verification/BTU_Verification.hh
M src/verification/PSVerification.cc
M src/verification/PSVerification.hh
M src/verification/TemperatureModel_Verification.cc
M src/verification/iCMthermo.cc
M src/verification/iceCompModel.cc
M src/verification/iceCompModel.hh
M src/verification/tests/exactQ.py
M test/CMakeLists.txt
M test/bed_smoother.py
A test/blatter_flowline.py
A test/blatter_verification.py
A test/grounded_cell_fraction.py
R test/grounded_cell_fraction/grounded_cell_fraction.mac
R test/grounded_cell_fraction/grounded_cell_fraction.py
M test/icemodelvec2t.py
M test/mass_transport.py
M test/miscellaneous.py
M test/regression/CMakeLists.txt
M test/regression/atmosphere_models.py
A test/regression/beddef_given.py
M test/regression/beddef_lc_restart.sh
M test/regression/btu_regression.sh
M test/regression/file.py
M test/regression/hydrology_steady_test.py
A test/regression/iceberg_remover.py
M test/regression/inverse/build_tiny.py
M test/regression/inverse/tiny_nlcg.sh
M test/regression/inverse/tiny_tikhonov_lmvm.sh
M test/regression/ocean_models.py
M test/regression/orographic_precipitation.py
A test/regression/pico_split/bedmap2_schmidtko14_50km.nc
A test/regression/pico_split/run_test.sh
A test/regression/sorted_parameters.sh
M test/regression/ssa/ssa_test_cfbc_fd.sh
M test/regression/ssa/ssa_test_cfbc_fem.sh
M test/regression/ssa/ssa_testi_fd.sh
M test/regression/ssa/ssa_testi_fem.sh
M test/regression/ssa/ssa_testj_fd.sh
M test/regression/ssa/ssa_testj_fem.sh
A test/regression/ssa/ssafem.py
M test/regression/ssa/ssafem_test_linear.sh
M test/regression/ssa/ssafem_test_plug.sh
M test/regression/surface_models.py
M test/regression/temp_continuity.py
M test/regression/test_01.sh
M test/regression/test_03.sh
M test/regression/test_05.sh
M test/regression/test_08.sh
M test/regression/test_09.sh
M test/regression/test_10.sh
M test/regression/test_13.sh
M test/regression/test_15.sh
M test/regression/test_16.sh
M test/regression/test_17.sh
M test/regression/test_18.sh
M test/regression/test_23.sh
M test/regression/test_27.sh
M test/regression/test_28.sh
M test/regression/test_29.py
M test/regression/test_31.sh
M test/regression/test_32.sh
M test/regression/test_33.sh
M test/regression/test_epsg_processing.py
M test/regression/vertical_grid_expansion.sh
M test/test_hydrology/inputforP_regression.nc
M test/test_hydrology/runTestP.py
M test/vnreport.py
M util/adjust_timeline.py
M util/create_timeline.py
M util/fill_missing_petsc.py
M util/nc2cdo.py
R util/pism_config_editor
R util/pism_config_editor.py

Log Message:
-----------
Merge branch 'dev' into main

Commit: 5b67393cbc16e661ccc49096d738dc17129494b8
https://github.com/pism/pism/commit/5b67393cbc16e661ccc49096d738dc17129494b8
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-12-03 (Fri, 03 Dec 2021)

Changed paths:
R .deepsource.toml
M CMake/PISM_CMake_macros.cmake
M README.rst
R docker/ubuntu/CMakeLists.txt
R docker/ubuntu/Dockerfile.in
R docker/ubuntu/README.rst
M src/coupler/CMakeLists.txt

Log Message:
-----------
Clean up the merge

Commit: bfcc2a9ded9efc16a161952dc983d3eb916a3411
https://github.com/pism/pism/commit/bfcc2a9ded9efc16a161952dc983d3eb916a3411
Author: Constantine Khrulev <ckhr...@alaska.edu>
Date: 2021-12-03 (Fri, 03 Dec 2021)

Changed paths:
M CMake/PISM_CMake_macros.cmake
M CMakeLists.txt
M doc/sphinx/conf.py

Log Message:
-----------
Update PISM version to 2.0

Compare: https://github.com/pism/pism/compare/dad024795dc2...bfcc2a9ded9e

Reply all

Reply to author

Forward

0 new messages