Anuga-user Digest, Vol 76, Issue 1
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May 17, 2015, 3:11:50 AM5/17/15
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Today's Topics:
1. Anuga sww support in Crayfish - a QGIS plugin (Saber Razmjooei)
2. Applying time-varying stage boundary condition in ANUGA
[SEC=UNCLASSIFIED] (Gareth...@ga.gov.au)
3. Re: Applying time-varying stage boundary condition in ANUGA
[SEC=UNCLASSIFIED] (rudy)
4. Error while running runtests.py (Maikel Issermann)
----------------------------------------------------------------------
Message: 1
Date: Sat, 2 May 2015 09:38:06 +0100
From: "Saber Razmjooei" <saber.r...@lutraconsulting.co.uk>
Subject: [Anuga-user] Anuga sww support in Crayfish - a QGIS plugin
To: <anuga-i...@lists.sourceforge.net>,
<anuga-i...@lists.sourceforge.net>,
<anuga...@lists.sourceforge.net>
Message-ID: <172c01d084b3$50505a00$f0f10e00$@lutraconsulting.co.uk>
Content-Type: text/plain; charset="us-ascii"
Dear Lists,
We are pleased to announce the initial support of SWW in Crayfish, a QGIS
plugin to view time varying grids/vectors, see below for more information
about Crayfish:
http://www.lutraconsulting.co.uk/products/crayfish/
Please note that the support is only available in the latest source code and
not yet from QGIS plugin repository. To test the plugin, you need to compile
the latest code from github:
https://github.com/lutraconsulting/qgis-crayfish-plugin
Instruction for building Crayfish from source are included on the github
page.
Before the final release of Crayfish (version 2.1), would be good to get
some feedback. Feel free to report any bugs or feedback on the github issues
page.
Kind regards,
Saber
Saber Razmjooei
Lutra Consulting
23 Chestnut Close, Burgess Hill, RH15 8HN
<http://www.lutraconsulting.co.uk/> www.lutraconsulting.co.uk
Tel: +44 (0)1444 848012
Mob: +44 (0)7568 129733
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Saber Razmjooei and Peter Wells trading as Lutra Consulting.
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Message: 2
Date: Wed, 13 May 2015 23:12:19 +0000
From: Gareth...@ga.gov.au
Subject: [Anuga-user] Applying time-varying stage boundary condition
in ANUGA [SEC=UNCLASSIFIED]
To: gco...@acor.com.au
Cc: anuga...@lists.sourceforge.net, PMil...@wollongong.nsw.gov.au,
ru...@balancernd.com.au
Message-ID: <9a183a0459024ff1...@WIN-EXCH01.agso.gov.au>
Content-Type: text/plain; charset=iso-8859-1
Hi Greg,
Just replying to your query on setting stage boundaries in ANUGA, in the case that you have a file with time/stage information (I am cc'ing the ANUGA list).
Typically I would proceed like below -- the idea is we use scipy to make an interpolation function from your time/stage data, and then pass this function to the boundary condition, and then pass that to the domain.set_boundary function with the appropriate tag.
Cheers,
Gareth.
------------------------------------
# Here we read a timeseries, and then pass
# that function as a set stage transmissive . boundary
import scipy
import anuga.shallow_water.boundaries as asb
# boundary_data_file should be a csv with 2 columns: time in seconds, stage in m
# In this example we assume it has a single header row which is skipped (see 'skip_header' below).
boundary_data_file = 'myfile.csv'
# Read data
boundary_data = scipy.genfromtxt(
boundary_data_file,
delimiter=',',
skip_header=1)
# Make interpolation function
stage_time_fun = scipy.interpolate.interp1d(
boundary_data[:, 0],
boundary_data[:, 1])
# Make boundary condition
boundary_condition = asb.Transmissive_n_momentum_zero_t_momentum_set_stage_boundary(
domain, stage_time_fun)
-----------------------------
# Then later on you pass this boundary_condition to the set_boundary function, like in the manual, e.g.
domain.set_boundary({'Ocean': boundary_condition, "...other boundaries here..."})
Gareth Davies
Hydrodynamic Modeller? |? Community Safety Group
Community Safety and Earth Monitoring Division? | ?GEOSCIENCE AUSTRALIA
____________________________________________________________
Phone:? (+61) 0437870552
Email:? Gareth...@ga.gov.au??? Web:? www.ga.gov.au
Cnr Jerrabomberra Avenue and Hindmarsh Drive Symonston ACT
GPO Box 378 Canberra ACT 2601 Australia
Applying geoscience to Australia's most important challenges
Geoscience Australia Disclaimer: This e-mail (and files transmitted with it) is intended only for the person or entity to which it is addressed. If you are not the intended recipient, then you have received this e-mail by mistake and any use, dissemination, forwarding, printing or copying of this e-mail and its file attachments is prohibited. The security of emails transmitted cannot be guaranteed; by forwarding or replying to this email, you acknowledge and accept these risks.
-------------------------------------------------------------------------------------------------------------------------
------------------------------
Message: 3
Date: Thu, 14 May 2015 21:25:02 +1000
From: rudy <ru...@balancernd.com.au>
Subject: Re: [Anuga-user] Applying time-varying stage boundary
condition in ANUGA [SEC=UNCLASSIFIED]
To: Gareth...@ga.gov.au, gco...@acor.com.au
Cc: anuga...@lists.sourceforge.net, PMil...@wollongong.nsw.gov.au
Message-ID: <o9i983nyg9qq8cbdic5...@email.android.com>
Content-Type: text/plain; charset="utf-8"
Thanks Gareth. ...
Sent from Samsung Mobile
-------- Original message --------
From: Gareth...@ga.gov.au
Date:2015/05/14 9:12 AM (GMT+10:00)
To: gco...@acor.com.au
Cc: ru...@balancernd.com.au, stephen...@anu.edu.au, anuga...@lists.sourceforge.net, PMil...@wollongong.nsw.gov.au
Subject: Applying time-varying stage boundary condition in ANUGA [SEC=UNCLASSIFIED]
Hi Greg,
Just replying to your query on setting stage boundaries in ANUGA, in the case that you have a file with time/stage information? (I am cc'ing the ANUGA list).
Typically I would proceed like below -- the idea is we use scipy to make an interpolation function from your time/stage data, and then pass this function to the boundary condition, and then pass that to the domain.set_boundary function with the appropriate tag.
Cheers,
Gareth.
------------------------------------
# Here we read a timeseries, and then pass
# that function as a set stage transmissive . boundary
import scipy
import anuga.shallow_water.boundaries as asb
# boundary_data_file should be a csv with 2 columns: time in seconds, stage in m
# In this example we assume it has a single header row which is skipped (see 'skip_header' below).
boundary_data_file = 'myfile.csv'
????????????
# Read data
boundary_data = scipy.genfromtxt(
??? boundary_data_file,
??? delimiter=',',
??? skip_header=1)
# Make interpolation function
stage_time_fun = scipy.interpolate.interp1d(
??? boundary_data[:, 0],
??? boundary_data[:, 1])
# Make boundary condition
boundary_condition = asb.Transmissive_n_momentum_zero_t_momentum_set_stage_boundary(
??? domain, stage_time_fun)
-----------------------------
# Then later on you pass this boundary_condition to the set_boundary function, like in the manual, e.g.
domain.set_boundary({'Ocean': boundary_condition, "...other boundaries here..."})
Gareth Davies
Hydrodynamic Modeller? |? Community Safety Group
Community Safety and Earth Monitoring Division? | ?GEOSCIENCE AUSTRALIA
____________________________________________________________
Phone:? (+61)? 0437870552
Email:? Gareth...@ga.gov.au??? Web:? www.ga.gov.au
Cnr Jerrabomberra Avenue and Hindmarsh Drive Symonston ACT
GPO Box 378 Canberra ACT 2601 Australia
Applying geoscience to Australia's most important challenges
Geoscience Australia Disclaimer: This e-mail (and files transmitted with it) is intended only for the person or entity to which it is addressed. If you are not the intended recipient, then you have received this e-mail by mistake and any use, dissemination, forwarding, printing or copying of this e-mail and its file attachments is prohibited. The security of emails transmitted cannot be guaranteed; by forwarding or replying to this email, you acknowledge and accept these risks.
-------------------------------------------------------------------------------------------------------------------------
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Message: 4
Date: Sun, 17 May 2015 15:11:14 +0800
From: Maikel Issermann <m.iss...@zoho.com>
Subject: [Anuga-user] Error while running runtests.py
To: anuga...@lists.sourceforge.net
Message-ID: <55583F12...@zoho.com>
Content-Type: text/plain; charset=utf-8; format=flowed
Dear all,
I am running several errors while testing my ANUGA installation. I don't
understand the errors and thus cannot solve them. I hope somebody has a
clue about the error cause and how to fix it.
ANUGA is running on linux mint (ubuntu 14.04). I have netcdf-4.3.3.1 ;
hdf5-1.8.9 zlib-1.2.8 and netCDF4-1.1.7.1 (python).
Here is the error messages:
Building, see build.log...
Build OK
Running unit tests for anuga
NumPy version 1.8.2
NumPy is installed in /usr/lib/python2.7/dist-packages/numpy
Python version 2.7.6 (default, Mar 22 2014, 22:59:56) [GCC 4.8.2]
nose version 1.3.1
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................E..................................................................................................................................................................................................................................................................................................................................................................................................................E.......................................E..........................EE............E..........................E..........................................................................................................................................................................................................
======================================================================
ERROR:
test_simple_interpolation_example_using_direct_interface_and_caching
(test_interpolate.Test_Interpolate)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/tests/test_interpolate.py",
line 270, in
test_simple_interpolation_example_using_direct_interface_and_caching
verbose=False)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/interpolate.py",
line 141, in interpolate
output_centroids=output_centroids)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/interpolate.py",
line 321, in interpolate_block
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 371, in cache
save_args_to_cache(CD,FN,args,kwargs,compression)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 1082, in save_args_to_cache
raise IOError(msg)
IOError: ERROR (caching): Could not open argsfile for writing:
bound_method_Interpolate._build_interpolation_matrix_A_of_Interpolation_object_based_on:_Mesh:_18_vertices,_6_triangles,_18_boundary_segments[732135140967954368]
======================================================================
ERROR: test_get_flow_through_cross_section(self):
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/tests/test_loadsave.py",
line 170, in test_get_flow_through_cross_section_with_geo
verbose=False)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/shallow_water_domain.py",
line 1546, in get_flow_through_cross_section
return cross_section.get_flow_through_cross_section()
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/forcing.py",
line 735, in get_flow_through_cross_section
use_cache=True)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1777, in get_values
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1717, in get_interpolated_values
use_cache=use_cache, verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/interpolate.py",
line 321, in interpolate_block
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 371, in cache
save_args_to_cache(CD,FN,args,kwargs,compression)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 1082, in save_args_to_cache
raise IOError(msg)
IOError: ERROR (caching): Could not open argsfile for writing:
bound_method_Interpolate._build_interpolation_matrix_A_of_Interpolation_object_based_on:_Mesh:_360_vertices,_120_triangles,_360_boundary_segments[9006059791549026239]
======================================================================
ERROR: test_cross_section_class(self):
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/tests/test_shallow_water_domain.py",
line 1985, in test_cross_section_class
Q = cross_section.get_flow_through_cross_section()
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/forcing.py",
line 735, in get_flow_through_cross_section
use_cache=True)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1777, in get_values
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1717, in get_interpolated_values
use_cache=use_cache, verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/interpolate.py",
line 321, in interpolate_block
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 371, in cache
save_args_to_cache(CD,FN,args,kwargs,compression)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 1082, in save_args_to_cache
raise IOError(msg)
IOError: ERROR (caching): Could not open argsfile for writing:
bound_method_Interpolate._build_interpolation_matrix_A_of_Interpolation_object_based_on:_Mesh:_360_vertices,_120_triangles,_360_boundary_segments[9006059791549026239]
======================================================================
ERROR: test_get_energy_through_cross_section(self):
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/tests/test_shallow_water_domain.py",
line 1886, in test_get_energy_through_cross_section_with_geo
verbose=False)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/shallow_water_domain.py",
line 1580, in get_energy_through_cross_section
return cross_section.get_energy_through_cross_section(kind)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/forcing.py",
line 780, in get_energy_through_cross_section
w = stage.get_values(interpolation_points=self.midpoints,
use_cache=True)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1777, in get_values
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1717, in get_interpolated_values
use_cache=use_cache, verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/interpolate.py",
line 321, in interpolate_block
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 371, in cache
save_args_to_cache(CD,FN,args,kwargs,compression)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 1082, in save_args_to_cache
raise IOError(msg)
IOError: ERROR (caching): Could not open argsfile for writing:
bound_method_Interpolate._build_interpolation_matrix_A_of_Interpolation_object_based_on:_Mesh:_360_vertices,_120_triangles,_360_boundary_segments[9006059791549026239]
======================================================================
ERROR: test_get_flow_through_cross_section(self):
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/tests/test_shallow_water_domain.py",
line 1801, in test_get_flow_through_cross_section_with_geo
verbose=False)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/shallow_water_domain.py",
line 1546, in get_flow_through_cross_section
return cross_section.get_flow_through_cross_section()
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/forcing.py",
line 735, in get_flow_through_cross_section
use_cache=True)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1777, in get_values
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1717, in get_interpolated_values
use_cache=use_cache, verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/interpolate.py",
line 321, in interpolate_block
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 371, in cache
save_args_to_cache(CD,FN,args,kwargs,compression)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 1082, in save_args_to_cache
raise IOError(msg)
IOError: ERROR (caching): Could not open argsfile for writing:
bound_method_Interpolate._build_interpolation_matrix_A_of_Interpolation_object_based_on:_Mesh:_360_vertices,_120_triangles,_360_boundary_segments[9006059791549026239]
======================================================================
ERROR: test_inflow_using_flowline
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/tests/test_shallow_water_domain.py",
line 7952, in test_inflow_using_flowline
[200.0, 20.0]])
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/shallow_water_domain.py",
line 1546, in get_flow_through_cross_section
return cross_section.get_flow_through_cross_section()
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/forcing.py",
line 735, in get_flow_through_cross_section
use_cache=True)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1777, in get_values
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1717, in get_interpolated_values
use_cache=use_cache, verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/interpolate.py",
line 321, in interpolate_block
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 371, in cache
save_args_to_cache(CD,FN,args,kwargs,compression)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 1082, in save_args_to_cache
raise IOError(msg)
IOError: ERROR (caching): Could not open argsfile for writing:
bound_method_Interpolate._build_interpolation_matrix_A_of_Interpolation_object_based_on:_Mesh:_2400_vertices,_800_triangles,_2400_boundary_segments[1280555080918628026]
======================================================================
ERROR: test_volumetric_balance_computation
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/tests/test_shallow_water_domain.py",
line 7410, in test_volumetric_balance_computation
[200.0, 20.0]])
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/shallow_water_domain.py",
line 1546, in get_flow_through_cross_section
return cross_section.get_flow_through_cross_section()
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/forcing.py",
line 735, in get_flow_through_cross_section
use_cache=True)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1777, in get_values
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1717, in get_interpolated_values
use_cache=use_cache, verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/interpolate.py",
line 321, in interpolate_block
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 371, in cache
save_args_to_cache(CD,FN,args,kwargs,compression)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 1082, in save_args_to_cache
raise IOError(msg)
IOError: ERROR (caching): Could not open argsfile for writing:
bound_method_Interpolate._build_interpolation_matrix_A_of_Interpolation_object_based_on:_Mesh:_2880_vertices,_960_triangles,_2880_boundary_segments[1280555080918628026]
----------------------------------------------------------------------
Ran 1250 tests in 541.061s
FAILED (errors=7)
Very hint is deeply appreciate!
with best regards!
Maikel
------------------------------
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than "Re: Contents of Anuga-user digest..."
Today's Topics:
1. Anuga sww support in Crayfish - a QGIS plugin (Saber Razmjooei)
2. Applying time-varying stage boundary condition in ANUGA
[SEC=UNCLASSIFIED] (Gareth...@ga.gov.au)
3. Re: Applying time-varying stage boundary condition in ANUGA
[SEC=UNCLASSIFIED] (rudy)
4. Error while running runtests.py (Maikel Issermann)
----------------------------------------------------------------------
Message: 1
Date: Sat, 2 May 2015 09:38:06 +0100
From: "Saber Razmjooei" <saber.r...@lutraconsulting.co.uk>
Subject: [Anuga-user] Anuga sww support in Crayfish - a QGIS plugin
To: <anuga-i...@lists.sourceforge.net>,
<anuga-i...@lists.sourceforge.net>,
<anuga...@lists.sourceforge.net>
Message-ID: <172c01d084b3$50505a00$f0f10e00$@lutraconsulting.co.uk>
Content-Type: text/plain; charset="us-ascii"
Dear Lists,
We are pleased to announce the initial support of SWW in Crayfish, a QGIS
plugin to view time varying grids/vectors, see below for more information
about Crayfish:
http://www.lutraconsulting.co.uk/products/crayfish/
Please note that the support is only available in the latest source code and
not yet from QGIS plugin repository. To test the plugin, you need to compile
the latest code from github:
https://github.com/lutraconsulting/qgis-crayfish-plugin
Instruction for building Crayfish from source are included on the github
page.
Before the final release of Crayfish (version 2.1), would be good to get
some feedback. Feel free to report any bugs or feedback on the github issues
page.
Kind regards,
Saber
Saber Razmjooei
Lutra Consulting
23 Chestnut Close, Burgess Hill, RH15 8HN
<http://www.lutraconsulting.co.uk/> www.lutraconsulting.co.uk
Tel: +44 (0)1444 848012
Mob: +44 (0)7568 129733
--
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Saber Razmjooei and Peter Wells trading as Lutra Consulting.
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Message: 2
Date: Wed, 13 May 2015 23:12:19 +0000
From: Gareth...@ga.gov.au
Subject: [Anuga-user] Applying time-varying stage boundary condition
in ANUGA [SEC=UNCLASSIFIED]
To: gco...@acor.com.au
Cc: anuga...@lists.sourceforge.net, PMil...@wollongong.nsw.gov.au,
ru...@balancernd.com.au
Message-ID: <9a183a0459024ff1...@WIN-EXCH01.agso.gov.au>
Content-Type: text/plain; charset=iso-8859-1
Hi Greg,
Just replying to your query on setting stage boundaries in ANUGA, in the case that you have a file with time/stage information (I am cc'ing the ANUGA list).
Typically I would proceed like below -- the idea is we use scipy to make an interpolation function from your time/stage data, and then pass this function to the boundary condition, and then pass that to the domain.set_boundary function with the appropriate tag.
Cheers,
Gareth.
------------------------------------
# Here we read a timeseries, and then pass
# that function as a set stage transmissive . boundary
import scipy
import anuga.shallow_water.boundaries as asb
# boundary_data_file should be a csv with 2 columns: time in seconds, stage in m
# In this example we assume it has a single header row which is skipped (see 'skip_header' below).
boundary_data_file = 'myfile.csv'
# Read data
boundary_data = scipy.genfromtxt(
boundary_data_file,
delimiter=',',
skip_header=1)
# Make interpolation function
stage_time_fun = scipy.interpolate.interp1d(
boundary_data[:, 0],
boundary_data[:, 1])
# Make boundary condition
boundary_condition = asb.Transmissive_n_momentum_zero_t_momentum_set_stage_boundary(
domain, stage_time_fun)
-----------------------------
# Then later on you pass this boundary_condition to the set_boundary function, like in the manual, e.g.
domain.set_boundary({'Ocean': boundary_condition, "...other boundaries here..."})
Gareth Davies
Hydrodynamic Modeller? |? Community Safety Group
Community Safety and Earth Monitoring Division? | ?GEOSCIENCE AUSTRALIA
____________________________________________________________
Phone:? (+61) 0437870552
Email:? Gareth...@ga.gov.au??? Web:? www.ga.gov.au
Cnr Jerrabomberra Avenue and Hindmarsh Drive Symonston ACT
GPO Box 378 Canberra ACT 2601 Australia
Applying geoscience to Australia's most important challenges
Geoscience Australia Disclaimer: This e-mail (and files transmitted with it) is intended only for the person or entity to which it is addressed. If you are not the intended recipient, then you have received this e-mail by mistake and any use, dissemination, forwarding, printing or copying of this e-mail and its file attachments is prohibited. The security of emails transmitted cannot be guaranteed; by forwarding or replying to this email, you acknowledge and accept these risks.
-------------------------------------------------------------------------------------------------------------------------
------------------------------
Message: 3
Date: Thu, 14 May 2015 21:25:02 +1000
From: rudy <ru...@balancernd.com.au>
Subject: Re: [Anuga-user] Applying time-varying stage boundary
condition in ANUGA [SEC=UNCLASSIFIED]
To: Gareth...@ga.gov.au, gco...@acor.com.au
Cc: anuga...@lists.sourceforge.net, PMil...@wollongong.nsw.gov.au
Message-ID: <o9i983nyg9qq8cbdic5...@email.android.com>
Content-Type: text/plain; charset="utf-8"
Thanks Gareth. ...
Sent from Samsung Mobile
-------- Original message --------
From: Gareth...@ga.gov.au
Date:2015/05/14 9:12 AM (GMT+10:00)
To: gco...@acor.com.au
Cc: ru...@balancernd.com.au, stephen...@anu.edu.au, anuga...@lists.sourceforge.net, PMil...@wollongong.nsw.gov.au
Subject: Applying time-varying stage boundary condition in ANUGA [SEC=UNCLASSIFIED]
Hi Greg,
Just replying to your query on setting stage boundaries in ANUGA, in the case that you have a file with time/stage information? (I am cc'ing the ANUGA list).
Typically I would proceed like below -- the idea is we use scipy to make an interpolation function from your time/stage data, and then pass this function to the boundary condition, and then pass that to the domain.set_boundary function with the appropriate tag.
Cheers,
Gareth.
------------------------------------
# Here we read a timeseries, and then pass
# that function as a set stage transmissive . boundary
import scipy
import anuga.shallow_water.boundaries as asb
# boundary_data_file should be a csv with 2 columns: time in seconds, stage in m
# In this example we assume it has a single header row which is skipped (see 'skip_header' below).
boundary_data_file = 'myfile.csv'
????????????
# Read data
boundary_data = scipy.genfromtxt(
??? boundary_data_file,
??? delimiter=',',
??? skip_header=1)
# Make interpolation function
stage_time_fun = scipy.interpolate.interp1d(
??? boundary_data[:, 0],
??? boundary_data[:, 1])
# Make boundary condition
boundary_condition = asb.Transmissive_n_momentum_zero_t_momentum_set_stage_boundary(
??? domain, stage_time_fun)
-----------------------------
# Then later on you pass this boundary_condition to the set_boundary function, like in the manual, e.g.
domain.set_boundary({'Ocean': boundary_condition, "...other boundaries here..."})
Gareth Davies
Hydrodynamic Modeller? |? Community Safety Group
Community Safety and Earth Monitoring Division? | ?GEOSCIENCE AUSTRALIA
____________________________________________________________
Phone:? (+61)? 0437870552
Email:? Gareth...@ga.gov.au??? Web:? www.ga.gov.au
Cnr Jerrabomberra Avenue and Hindmarsh Drive Symonston ACT
GPO Box 378 Canberra ACT 2601 Australia
Applying geoscience to Australia's most important challenges
Geoscience Australia Disclaimer: This e-mail (and files transmitted with it) is intended only for the person or entity to which it is addressed. If you are not the intended recipient, then you have received this e-mail by mistake and any use, dissemination, forwarding, printing or copying of this e-mail and its file attachments is prohibited. The security of emails transmitted cannot be guaranteed; by forwarding or replying to this email, you acknowledge and accept these risks.
-------------------------------------------------------------------------------------------------------------------------
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Message: 4
Date: Sun, 17 May 2015 15:11:14 +0800
From: Maikel Issermann <m.iss...@zoho.com>
Subject: [Anuga-user] Error while running runtests.py
To: anuga...@lists.sourceforge.net
Message-ID: <55583F12...@zoho.com>
Content-Type: text/plain; charset=utf-8; format=flowed
Dear all,
I am running several errors while testing my ANUGA installation. I don't
understand the errors and thus cannot solve them. I hope somebody has a
clue about the error cause and how to fix it.
ANUGA is running on linux mint (ubuntu 14.04). I have netcdf-4.3.3.1 ;
hdf5-1.8.9 zlib-1.2.8 and netCDF4-1.1.7.1 (python).
Here is the error messages:
Building, see build.log...
Build OK
Running unit tests for anuga
NumPy version 1.8.2
NumPy is installed in /usr/lib/python2.7/dist-packages/numpy
Python version 2.7.6 (default, Mar 22 2014, 22:59:56) [GCC 4.8.2]
nose version 1.3.1
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................E..................................................................................................................................................................................................................................................................................................................................................................................................................E.......................................E..........................EE............E..........................E..........................................................................................................................................................................................................
======================================================================
ERROR:
test_simple_interpolation_example_using_direct_interface_and_caching
(test_interpolate.Test_Interpolate)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/tests/test_interpolate.py",
line 270, in
test_simple_interpolation_example_using_direct_interface_and_caching
verbose=False)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/interpolate.py",
line 141, in interpolate
output_centroids=output_centroids)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/interpolate.py",
line 321, in interpolate_block
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 371, in cache
save_args_to_cache(CD,FN,args,kwargs,compression)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 1082, in save_args_to_cache
raise IOError(msg)
IOError: ERROR (caching): Could not open argsfile for writing:
bound_method_Interpolate._build_interpolation_matrix_A_of_Interpolation_object_based_on:_Mesh:_18_vertices,_6_triangles,_18_boundary_segments[732135140967954368]
======================================================================
ERROR: test_get_flow_through_cross_section(self):
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/tests/test_loadsave.py",
line 170, in test_get_flow_through_cross_section_with_geo
verbose=False)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/shallow_water_domain.py",
line 1546, in get_flow_through_cross_section
return cross_section.get_flow_through_cross_section()
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/forcing.py",
line 735, in get_flow_through_cross_section
use_cache=True)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1777, in get_values
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1717, in get_interpolated_values
use_cache=use_cache, verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/interpolate.py",
line 321, in interpolate_block
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 371, in cache
save_args_to_cache(CD,FN,args,kwargs,compression)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 1082, in save_args_to_cache
raise IOError(msg)
IOError: ERROR (caching): Could not open argsfile for writing:
bound_method_Interpolate._build_interpolation_matrix_A_of_Interpolation_object_based_on:_Mesh:_360_vertices,_120_triangles,_360_boundary_segments[9006059791549026239]
======================================================================
ERROR: test_cross_section_class(self):
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/tests/test_shallow_water_domain.py",
line 1985, in test_cross_section_class
Q = cross_section.get_flow_through_cross_section()
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/forcing.py",
line 735, in get_flow_through_cross_section
use_cache=True)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1777, in get_values
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1717, in get_interpolated_values
use_cache=use_cache, verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/interpolate.py",
line 321, in interpolate_block
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 371, in cache
save_args_to_cache(CD,FN,args,kwargs,compression)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 1082, in save_args_to_cache
raise IOError(msg)
IOError: ERROR (caching): Could not open argsfile for writing:
bound_method_Interpolate._build_interpolation_matrix_A_of_Interpolation_object_based_on:_Mesh:_360_vertices,_120_triangles,_360_boundary_segments[9006059791549026239]
======================================================================
ERROR: test_get_energy_through_cross_section(self):
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/tests/test_shallow_water_domain.py",
line 1886, in test_get_energy_through_cross_section_with_geo
verbose=False)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/shallow_water_domain.py",
line 1580, in get_energy_through_cross_section
return cross_section.get_energy_through_cross_section(kind)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/forcing.py",
line 780, in get_energy_through_cross_section
w = stage.get_values(interpolation_points=self.midpoints,
use_cache=True)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1777, in get_values
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1717, in get_interpolated_values
use_cache=use_cache, verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/interpolate.py",
line 321, in interpolate_block
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 371, in cache
save_args_to_cache(CD,FN,args,kwargs,compression)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 1082, in save_args_to_cache
raise IOError(msg)
IOError: ERROR (caching): Could not open argsfile for writing:
bound_method_Interpolate._build_interpolation_matrix_A_of_Interpolation_object_based_on:_Mesh:_360_vertices,_120_triangles,_360_boundary_segments[9006059791549026239]
======================================================================
ERROR: test_get_flow_through_cross_section(self):
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/tests/test_shallow_water_domain.py",
line 1801, in test_get_flow_through_cross_section_with_geo
verbose=False)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/shallow_water_domain.py",
line 1546, in get_flow_through_cross_section
return cross_section.get_flow_through_cross_section()
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/forcing.py",
line 735, in get_flow_through_cross_section
use_cache=True)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1777, in get_values
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1717, in get_interpolated_values
use_cache=use_cache, verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/interpolate.py",
line 321, in interpolate_block
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 371, in cache
save_args_to_cache(CD,FN,args,kwargs,compression)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 1082, in save_args_to_cache
raise IOError(msg)
IOError: ERROR (caching): Could not open argsfile for writing:
bound_method_Interpolate._build_interpolation_matrix_A_of_Interpolation_object_based_on:_Mesh:_360_vertices,_120_triangles,_360_boundary_segments[9006059791549026239]
======================================================================
ERROR: test_inflow_using_flowline
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/tests/test_shallow_water_domain.py",
line 7952, in test_inflow_using_flowline
[200.0, 20.0]])
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/shallow_water_domain.py",
line 1546, in get_flow_through_cross_section
return cross_section.get_flow_through_cross_section()
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/forcing.py",
line 735, in get_flow_through_cross_section
use_cache=True)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1777, in get_values
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1717, in get_interpolated_values
use_cache=use_cache, verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/interpolate.py",
line 321, in interpolate_block
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 371, in cache
save_args_to_cache(CD,FN,args,kwargs,compression)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 1082, in save_args_to_cache
raise IOError(msg)
IOError: ERROR (caching): Could not open argsfile for writing:
bound_method_Interpolate._build_interpolation_matrix_A_of_Interpolation_object_based_on:_Mesh:_2400_vertices,_800_triangles,_2400_boundary_segments[1280555080918628026]
======================================================================
ERROR: test_volumetric_balance_computation
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/tests/test_shallow_water_domain.py",
line 7410, in test_volumetric_balance_computation
[200.0, 20.0]])
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/shallow_water_domain.py",
line 1546, in get_flow_through_cross_section
return cross_section.get_flow_through_cross_section()
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/shallow_water/forcing.py",
line 735, in get_flow_through_cross_section
use_cache=True)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1777, in get_values
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/abstract_2d_finite_volumes/quantity.py",
line 1717, in get_interpolated_values
use_cache=use_cache, verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/fit_interpolate/interpolate.py",
line 321, in interpolate_block
verbose=verbose)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 371, in cache
save_args_to_cache(CD,FN,args,kwargs,compression)
File
"/home/scrox/anuga_core/build/testenv/lib/python2.7/site-packages/anuga/caching/caching.py",
line 1082, in save_args_to_cache
raise IOError(msg)
IOError: ERROR (caching): Could not open argsfile for writing:
bound_method_Interpolate._build_interpolation_matrix_A_of_Interpolation_object_based_on:_Mesh:_2880_vertices,_960_triangles,_2880_boundary_segments[1280555080918628026]
----------------------------------------------------------------------
Ran 1250 tests in 541.061s
FAILED (errors=7)
Very hint is deeply appreciate!
with best regards!
Maikel
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