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Hi Sooran,If you can run the command:lpad resetthen it means your database connection is configured properly. Give that a try.As for the unit tests, they use the database config files located in:atomate.common.test_filesYou would need to update those test files in the source in order to run the unit tests properly.Best,Anubhav
On Fri, Aug 18, 2017 at 3:01 PM, <lorc...@gmail.com> wrote:
To Whom it may concern,I am trying to install atomate on Stampede using an automated installer.I've signed up with an account at mlab.com. I put every information about MongoDB from mlab in db.json and my_launchpad.yaml.I finished the installation without any error.And then, I went to <<INSTALL_DIR>>/codes/atomate/ and run python setup.py test.There was no error but many skips. While testing, it said "SKIP: Cannot connect to MongoDB! Is the database server running? Are the credentials correct?"I've checked my information several times, and I can login to mlab.com.Could you help me to solve this problem?Thank you for your help.Best,Sooran Kim
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(atomate_env) [skim121@login1 test2]lpad get_wflows
{
"name": "Si--1",
"state": "READY",
"states_list": "REA",
"created_on": "2017-08-19T12:13:14.898000"
}
(atomate_env) [skim121@login1 test2]qlaunch -r rapidfire
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/__init__.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a "PMG_". E.g., "PMG_VASP_PSP_DIR" instead of "VASP_PSP_DIR".
warnings.warn('With effect from pmg 5.0, all pymatgen settings are'
2017-08-19 07:13:37,893 INFO getting queue adapter
2017-08-19 07:13:37,895 INFO Created new dir /work/04049/skim121/atomate_t/test2/block_2017-08-19-12-13-37-894965
2017-08-19 07:13:37,932 INFO The number of jobs currently in the queue is: 0
2017-08-19 07:13:37,933 INFO 0 jobs in queue. Maximum allowed by user: 0
2017-08-19 07:13:38,143 DEBUG FW with id: 1 is unique!
2017-08-19 07:13:38,144 INFO Launching a rocket!
2017-08-19 07:13:38,150 ERROR ----|vvv|----
2017-08-19 07:13:38,152 ERROR Error with queue launcher rapid fire!
2017-08-19 07:13:38,154 ERROR Traceback (most recent call last):
File "/home1/04049/skim121/atomate/codes/fireworks/fireworks/queue/queue_launcher.py", line 221, in rapidfire
strm_lvl, True, fill_mode)
File "/home1/04049/skim121/atomate/codes/fireworks/fireworks/queue/queue_launcher.py", line 68, in launch_rocket_to_queue
raise ValueError('Reservation mode of queue launcher only works for singleshot Rocket Launcher!')
ValueError: Reservation mode of queue launcher only works for singleshot Rocket Launcher!
2017-08-19 07:13:38,155 ERROR ----|^^^|----
=============================================
I've found that rocket_launch in <<intall_dir>>/config/my_qadapter.yaml is
rlaunch -c /home1/04049/skim121/atomate/config rapidfire. I change it as
rlaunch -c /home1/04049/skim121/atomate/config singleshot
With this modification, I ran "qlaunch -r rapidfire" or "qlaunch -r singleshot" successfully. Is this modification a right thing to do?
2. Fort the pymatendb part,
I realized that I didn't insert any data to Mongo database. I followed pymatgendb instruction.
>> mgdb insert -c ~/atomate/config/db.json launcher_2017-08-19-12-46-41-046299
and then I typed =====================
(atomate_env) [skim121@login1 block_2017-08-19-12-46-39-741458]mgdb query -c ~/atomate/config/db.json --props task_id pretty_formula energy_per_atom
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/__init__.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a "PMG_". E.g., "PMG_VASP_PSP_DIR" instead of "VASP_PSP_DIR".
warnings.warn('With effect from pmg 5.0, all pymatgen settings are'
task_id pretty_formula energy_per_atom
--------- ---------------- -----------------
1 Si -5.4207
============================================
I guess output.energy_per_atom could be a typo in the installation site because when I typed output.energy_get_atom, I couldn't get the information as following=========
(atomate_env) [skim121@login1 block_2017-08-19-12-46-39-741458]mgdb query -c ~/atomate/config/db.json --props task_id pretty_formula output.energy_per_atom
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/__init__.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a "PMG_". E.g., "PMG_VASP_PSP_DIR" instead of "VASP_PSP_DIR".
warnings.warn('With effect from pmg 5.0, all pymatgen settings are'
task_id pretty_formula output.energy_per_atom
--------- ---------------- ------------------------
1 Si
===================================================
Thank you so much for your help.
Best,
Sooran
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--Best,
Anubhav
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--Best,
Anubhav
Hi Anubhav and Bradon,Thank you for your kind reply.0. I've found the change of BSDOSPlotter to BSPlotter in bs-analysis.py in https://hackingmaterials.github.io/atomate/running_workflows.html. Previous bs-analysis.py was that it imported BSDOSPlotter but it use BSPlotterfrom pymatgen.electronic_structure.plotter import DosPlotter, BSDOSPlotter
bs_plotter = BSPlotter(bandstructure)
and it gave the error that BSPlotter is not defined.
1. I didn't use -r option. I only typed "qlaunch rapidfire -m 1 --nlaunches infinite". I couldn't exactly get your point about "if you are using -r, then use the command you wrote." Does it mean that I should type "qlaunch -r rapidfire -m 1 --nlaunches infinite"? Anyway, I will try not to use -r option following your advice.3. I also installed the most recent atomate (0.5.8) and pymatgen (2017.8.16) using install-atomate.sh (https://github.com/PhasesResearchLab/install-atomate). I found the link to this site in https://hackingmaterials.github.io/atomate/installation.html. But I've found that that link has been disappeared in the updated instruction. Is using intall-atomate.sh not recommendable anymore?Back to the error, unfortunately, I've still got the same error even I rerun it using lapd rerun -i <fw_id>.Here is what I did==============================================(atomate_env) [skim121@login1 try6]lpad get_wflows
{
"name": "Si--1",
"state": "READY",
"states_list": "W-W-W-W-W-W-W-W-REA",
"created_on": "2017-08-21T01:05:31.499000"
}
(atomate_env) [skim121@login1 try6]qlaunch rapidfire -m 1 --nlaunches infinite
============================================================Using this, I finished the calculation except the last gibbs energy calculation part. And then, I rerun the job.======================(atomate_env) [skim121@login1 atomate]lpad rerun_fws -i 1
and
(atomate_env) [skim121@login1 launcher_2017-08-21-01-44-51-535123]qlaunch singleshot
===========================================================
Again, I've got the error ==========================================
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/__init__.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a "PMG_". E.g., "PMG_VASP_PSP_DIR" instead of "VASP_PSP_DIR".
warnings.warn('With effect from pmg 5.0, all pymatgen settings are'
Traceback (most recent call last):
File "/home1/04049/skim121/atomate/codes/fireworks/fireworks/core/rocket.py", line 253, in run
m_action = t.run_task(my_spec)
File "/home1/04049/skim121/atomate/codes/atomate/atomate/vasp/firetasks/parse_outputs.py", line 547, in run_task
coll.insert_one(gibbs_dict)
File "/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/pymongo/collection.py", line 670, in insert_one
bypass_doc_val=bypass_document_validation),
File "/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/pymongo/collection.py", line 575, in _insert
check_keys, manipulate, write_concern, op_id, bypass_doc_val)
File "/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/pymongo/collection.py", line 556, in _insert_one
check_keys=check_keys)
File "/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/pymongo/pool.py", line 476, in command
self._raise_connection_failure(error)
File "/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/pymongo/pool.py", line 604, in _raise_connection_failure
raise error
InvalidDocument: Cannot encode object: array([-11.39354489])
====================================================As the second try, I changed rocket_launch in my_qadapter.yaml from singleshot to rapidfire as following=======================================================_fw_name: CommonAdapter
_fw_q_type: SLURM
#rocket_launch: rlaunch -c /home1/04049/skim121/atomate/config singleshot
rocket_launch: rlaunch -c /home1/04049/skim121/atomate/config rapidfire
nodes: 2
ntasks_per_node: 16
walltime: '02:00:00'
queue: development
account: null
job_name: null
pre_rocket: null
post_rocket: null
logdir: /home1/04049/skim121/atomate/logs
======================================================
I ran the job using "qlaunch singleshot" as in the instruction. Unfortunately, I've still got the same error.
I'm not sure if the error is because I installed with "bash install-atomate.sh".
I will try to re-install atomate using updated installation instruction in https://hackingmaterials.github.io/atomate/installation.html not using install-atomate.sh if you think this might cause the problem.
In addition, could you check my "FW_config.yaml" and "my_fworker.yaml"?
====================================================
CONFIG_FILE_DIR: /home1/04049/skim121/atomate/config
QUEUE_UPDATE_INTERVAL: 5
ADD_USER_PACKAGES:
- atomate.vasp.firetasks
- atomate.feff.firetasks
----------------------------------------
name: Stampede
category: ''
query: '{}'
env:
db_file: /home1/04049/skim121/atomate/config/db.json
vasp_cmd: ibrun vasp_std
scratch_dir: /scratch/04049/skim121/
incar_update:
NCORE: 4
========================================================
4. I can't get fw_id with "lpad get_wflows -d more". ==================(atomate_env) [skim121@login1 atomate]lpad get_wflows -d more
{
"name": "Si--1",
"state": "FIZZLED",
"states": {
"Gibbs Free Energy--1": "FIZZLED",
"Si-gibbs group: >>60ada6ae-1605-4210-b7c3-1bd81241acb6<< gibbs deformation 6--2": "COMPLETED",
"Si-gibbs group: >>60ada6ae-1605-4210-b7c3-1bd81241acb6<< gibbs deformation 5--3": "COMPLETED",
"Si-gibbs group: >>60ada6ae-1605-4210-b7c3-1bd81241acb6<< gibbs deformation 4--4": "COMPLETED",
"Si-gibbs group: >>60ada6ae-1605-4210-b7c3-1bd81241acb6<< gibbs deformation 3--5": "COMPLETED",
"Si-gibbs group: >>60ada6ae-1605-4210-b7c3-1bd81241acb6<< gibbs deformation 2--6": "COMPLETED",
"Si-gibbs group: >>60ada6ae-1605-4210-b7c3-1bd81241acb6<< gibbs deformation 1--7": "COMPLETED",
"Si-gibbs group: >>60ada6ae-1605-4210-b7c3-1bd81241acb6<< gibbs deformation 0--8": "COMPLETED",
"Si-gibbs group: >>60ada6ae-1605-4210-b7c3-1bd81241acb6<< structure optimization--9": "COMPLETED"
},
"created_on": "2017-08-21T01:05:31.499000",
"launch_dirs": {
"Gibbs Free Energy--1": [
"/work/04049/skim121/atomate_t/Gibbs/try6/block_2017-08-21-01-11-22-563970/launcher_2017-08-21-01-44-51-535123"
],
"Si-gibbs group: >>60ada6ae-1605-4210-b7c3-1bd81241acb6<< gibbs deformation 6--2": [
"/work/04049/skim121/atomate_t/Gibbs/try6/block_2017-08-21-01-11-22-563970/launcher_2017-08-21-01-40-40-412328"
],
"Si-gibbs group: >>60ada6ae-1605-4210-b7c3-1bd81241acb6<< gibbs deformation 5--3": [
"/work/04049/skim121/atomate_t/Gibbs/try6/block_2017-08-21-01-11-22-563970/launcher_2017-08-21-01-36-29-607684"
],
"Si-gibbs group: >>60ada6ae-1605-4210-b7c3-1bd81241acb6<< gibbs deformation 4--4": [
"/work/04049/skim121/atomate_t/Gibbs/try6/block_2017-08-21-01-11-22-563970/launcher_2017-08-21-01-32-18-564151"
],
"Si-gibbs group: >>60ada6ae-1605-4210-b7c3-1bd81241acb6<< gibbs deformation 3--5": [
"/work/04049/skim121/atomate_t/Gibbs/try6/block_2017-08-21-01-11-22-563970/launcher_2017-08-21-01-28-07-268346"
],
"Si-gibbs group: >>60ada6ae-1605-4210-b7c3-1bd81241acb6<< gibbs deformation 2--6": [
"/work/04049/skim121/atomate_t/Gibbs/try6/block_2017-08-21-01-11-22-563970/launcher_2017-08-21-01-23-56-362478"
],
"Si-gibbs group: >>60ada6ae-1605-4210-b7c3-1bd81241acb6<< gibbs deformation 1--7": [
"/work/04049/skim121/atomate_t/Gibbs/try6/block_2017-08-21-01-11-22-563970/launcher_2017-08-21-01-19-45-325511"
],
"Si-gibbs group: >>60ada6ae-1605-4210-b7c3-1bd81241acb6<< gibbs deformation 0--8": [
"/work/04049/skim121/atomate_t/Gibbs/try6/block_2017-08-21-01-11-22-563970/launcher_2017-08-21-01-15-34-158152"
],
"Si-gibbs group: >>60ada6ae-1605-4210-b7c3-1bd81241acb6<< structure optimization--9": [
"/work/04049/skim121/atomate_t/Gibbs/try6/block_2017-08-21-01-11-22-563970/launcher_2017-08-21-01-11-23-185258"
]
},
"updated_on": "2017-08-21T01:45:33.415000"
}
================================
I've found fw_id in FW.json. I guess the last numer of each job name in "states" with lpad get_wflows -d more seems to correspond to fw_id....
Thank you so much for your help. I do appreciate it!Best,
Sooran
2017-08-20 20:20 GMT-04:00 Brandon Bocklund <bock...@psu.edu>:Sooran,Thanks for keeping us aware of how things are going. We are still working to improve the docs for new people and your feedback helps!Anubhav: regarding (0), that was an import error fixed in my most recent PR.Sooran: regarding (3):I have just ran the Gibbs and BS tutorial python code exactly as written in the tutorials. (other than the fixed BSDOSPlotter/BSPlotter import issue above). I ran these with the most recent atomate and pymatgen (from Github, as in the installation guide on the website) and was successful.Try rerunning the job as Anubhav suggested. It might have been a one-off issue?BrandonOn Aug 20, 2017, at 6:21 PM, Anubhav Jain <AJ...@lbl.gov> wrote:0. I prefer BSDOSPlotter, what was the error you got when trying it?1. qlaunch -r rapidfire is correct, but I'll probably rewrite the tutorial to not use -r or at least suggest a non "-r" as an alternate option. But if you are using -r, then use the command you wrote.2. no, not really. I use Cmd+\ which is a bit of a harder stop than Cmd+C (or Ctrl+C). There is also a timeout parameter so you can have it stop after a certain amount of time.3. Not sure, I'll have to talk to Brandon Bocklund who wrote that tutorial. I've cc'ed him here.4. No don't start from the beginning. You need the fw_id of the failed job. You get this using:"lpad get_wflows -d more"which will print the corresponding fw_id for each job. Then type"lpad rerun_fws - i <FW_ID>"which will just rerun the failed job. More in the FireWorks docs on recovering from errors.
On Sun, Aug 20, 2017 at 2:54 PM, Sooran Kim <soo...@seas.harvard.edu> wrote:
Hi Anubhav,Thank you for your comment.Yes, you are right. Only 1/4 calcs are finished. I typed qlaunch singlet again in the same directory after completing the first calculation. I've got an error in *.error file that ===================
raceback (most recent call last):
File "/home1/04049/skim121/atomate/codes/fireworks/fireworks/core/rocket.py", line 253, in runm_action = t.run_task(my_spec)File "/home1/04049/skim121/atomate/codes/atomate/atomate/vasp/firetasks/glue_tasks.py", line 84, in run_taskself.copy_files()File "/home1/04049/skim121/atomate/codes/atomate/atomate/vasp/firetasks/glue_tasks.py", line 113, in copy_filesself.fileclient.copy(prev_path_full + relax_ext + gz_ext, dest_path + gz_ext)File "/home1/04049/skim121/atomate/codes/atomate/atomate/utils/fileio.py", line 112, in copyshutil.copy2(src, dest)File "/opt/apps/intel15/python/2.7.12/lib/python2.7/shutil.py", line 130, in copy2copyfile(src, dst)File "/opt/apps/intel15/python/2.7.12/lib/python2.7/shutil.py", line 69, in copyfileraise Error("`%s` and `%s` are the same file" % (src, dst))Error: `/work/04049/skim121/atomate_t/MgO/option3/try7/POTCAR.gz` and `/work/04049/skim121/atomate_t/MgO/option3/try7/POTCAR.gz` are the same file===========================================================So, I made a new directory for each calculation such as rlx, scf, dos, and band without any input files (except rlx which initially has POSCAR of MgO). I hope this is a right thing to do. And then, I typed "qlaunch singleshot" in each directory after one calculation was finished. I completed 4 calculation without an error. I've got DOS and bandstructure plot with bs-anlalysis.py. Thank you so much.By the way, I guess BSDOSPlotter could be changed to BSPlotter in "bs-analysis.py". After this simple modification, I ran bs-analysis.py successfully.Q1. I wonder if qlaunch option you mentioned for automatic submitting jobs is "qlaunch rapidfire -m 1 --nlaunches infinite". It also worked and it was much easier for me than qlaunch singleshot because I don't have to make a directory myself.Q2. One small thing is that is there a better way to stop infinite mode? I just cut it with ctrl+c.Q3. I moved to the running Gibbs workflows.I typed (gibbs.py is the same as in https://hackingmaterials.github.io/atomate/gibbs_workflow_tutorial.html)>> python gibbs.py>> qlaunch rapidfire -m 1 --nlaunches infinite.It worked until the last calculation.============(atomate_env) [skim121@login1 config]lpad get_wflows{"name": "Si--1","state": "FIZZLED","states_list": "F-C-C-C-C-C-C-C-C","created_on": "2017-08-20T20:49:53.289000"}======================================The error in *.error file is ===================
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/__init__.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a "PMG_". E.g., "PMG_VASP_PSP_DIR" instead of "VASP_PSP_DIR".warnings.warn('With effect from pmg 5.0, all pymatgen settings are'
Traceback (most recent call last):
File "/home1/04049/skim121/atomate/codes/fireworks/fireworks/core/rocket.py", line 253, in runm_action = t.run_task(my_spec)File "/home1/04049/skim121/atomate/codes/atomate/atomate/vasp/firetasks/parse_outputs.py", line 547, in run_taskcoll.insert_one(gibbs_dict)File "/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/pymongo/collection.py", line 670, in insert_onebypass_doc_val=bypass_document_validation),File "/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/pymongo/collection.py", line 575, in _insertcheck_keys, manipulate, write_concern, op_id, bypass_doc_val)File "/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/pymongo/collection.py", line 556, in _insert_onecheck_keys=check_keys)File "/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/pymongo/pool.py", line 476, in commandself._raise_connection_failure(error)File "/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/pymongo/pool.py", line 604, in _raise_connection_failureraise errorInvalidDocument: Cannot encode object: array([-11.39354489])=======================================It looks like there is a problem when atomate generate gibbs_dict, but I couldn't figure out how to solve this error. Could you help me to solve this issue?Q4. Can I restart from Failed part? For example, in this Gibbs workflow, even if a failure happens at the final calculation, should I start from the first calculation?Thank you so much for your time.Best,Sooran2017-08-19 17:26 GMT-04:00 Anubhav Jain <AJ...@lbl.gov>:Hi SooranI'll probably just rework the tutorial personally and then let you know when it's updated. That should hopefully answer all the questions.Just a quick preview - the band structure workflow has 4 calculations. A qlaunch in reservation mode (singleshot rlaunch) only runs the 1st of 4 calculations, which is the structure optimization. The workflow is still RUNNING because only 1/4 calcs are finished (if you look at the states_list in your output, one calc is completed, one calc is ready to run and 2 calcs are waiting for a dependency). If you see the workflow diagram for the band structure workflow it will show these 4 steps. The bands KPOINTS files are not there because you only ran the structure optimization so far. Only running 1/4 calcs is also why the plotting routines didn't work. You would need to run 4 qlaunches, starting the next one after the previous calc finishes, to finish the entire workflow this way. (qlaunch has some other options so that you can automatically submit jobs when needed, so you only need to type the command once and it will run in a loop, but I won't cover that here)Anyway, when I rework the tutorial all should become much clearer, simpler, and feel smoother. Hopefully I can do it sometime this weekend.Best,AnubhavOn Sat, Aug 19, 2017 at 1:58 PM, Sooran Kim <soo...@seas.harvard.edu> wrote:Hi Anubhav,I'm following the instruction page (http://hackingmaterials.github.io/atomate/installation.html).Yes, I typed >> atwf add -l vasp -s optimize_only.yaml -m mp-149, and as you expect, I have "task.json" file.To keep file-based workflows, I followed the 2nd solution in https://github.com/hackingmaterials/atomate/issues/143 and modified the optimize_only.yaml like below===# Optimize the structure (only)fireworks:- fw: atomate.vasp.fireworks.core.OptimizeFWparams:vasp_cmd: >>vasp_std<<=============================================I've got an error that =============================(atomate_env) [skim121@login1 Si_test]atwf add -l vasp -s optimize_only.yaml -m mp-149
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/__init__.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a "PMG_". E.g., "PMG_VASP_PSP_DIR" instead of "VASP_PSP_DIR".warnings.warn('With effect from pmg 5.0, all pymatgen settings are'
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/ext/matproj.py:108: UserWarning: If you query for structure data encoded using MP's Structure Notation Language (SNL) format and you use `mp_decode=True` (the default) for MPRester queries, you should install dependencies via `pip install pymatgen[matproj.snl]`.warnings.warn("If you query for structure data encoded using MP's "
Traceback (most recent call last):
File "/home1/04049/skim121/atomate/atomate_env/bin/atwf", line 6, in <module>exec(compile(open(__file__).read(), __file__, 'exec'))File "/home1/04049/skim121/atomate/codes/atomate/scripts/atwf", line 238, in <module>args.func(args)File "/home1/04049/skim121/atomate/codes/atomate/scripts/atwf", line 95, in add_wfwf = _get_wf(args, s)File "/home1/04049/skim121/atomate/codes/atomate/scripts/atwf", line 69, in _get_wfd = loadfn(spec_path)File "/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/monty/serialization.py", line 78, in loadfnreturn yaml.load(fp, *args, **kwargs)File "/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/ruamel/yaml/main.py", line 633, in loadreturn loader._constructor.get_single_data() # type: ignoreFile "/home1/04049/skim121/atomate/atomate_env/lib/python2.7/site-packages/ruamel/yaml/constructor.py", line 102, in get_single_datanode = self.composer.get_single_node()File "_ruamel_yaml.pyx", line 706, in _ruamel_yaml.CParser.get_single_node (ext/_ruamel_yaml.c:9612)File "_ruamel_yaml.pyx", line 724, in _ruamel_yaml.CParser._compose_document (ext/_ruamel_yaml.c:9922)File "_ruamel_yaml.pyx", line 775, in _ruamel_yaml.CParser._compose_node (ext/_ruamel_yaml.c:10814)File "_ruamel_yaml.pyx", line 889, in _ruamel_yaml.CParser._compose_mapping_node (ext/_ruamel_yaml.c:12609)File "_ruamel_yaml.pyx", line 773, in _ruamel_yaml.CParser._compose_node (ext/_ruamel_yaml.c:10784)File "_ruamel_yaml.pyx", line 850, in _ruamel_yaml.CParser._compose_sequence_node (ext/_ruamel_yaml.c:12011)File "_ruamel_yaml.pyx", line 775, in _ruamel_yaml.CParser._compose_node (ext/_ruamel_yaml.c:10814)File "_ruamel_yaml.pyx", line 889, in _ruamel_yaml.CParser._compose_mapping_node (ext/_ruamel_yaml.c:12609)File "_ruamel_yaml.pyx", line 775, in _ruamel_yaml.CParser._compose_node (ext/_ruamel_yaml.c:10814)File "_ruamel_yaml.pyx", line 889, in _ruamel_yaml.CParser._compose_mapping_node (ext/_ruamel_yaml.c:12609)File "_ruamel_yaml.pyx", line 731, in _ruamel_yaml.CParser._compose_node (ext/_ruamel_yaml.c:10027)File "_ruamel_yaml.pyx", line 904, in _ruamel_yaml.CParser._parse_next_event (ext/_ruamel_yaml.c:12818)ruamel.yaml.scanner.ScannerError: while scanning a block scalarin "/home1/04049/skim121/atomate/codes/atomate/scripts/../atomate/vasp/workflows/base/library/optimize_only.yaml", line 5, column 15did not find expected comment or line breakin "/home1/04049/skim121/atomate/codes/atomate/scripts/../atomate/vasp/workflows/base/library/optimize_only.yaml", line 5, column 16========================================================When I followed the 3rd solution, I've also got an error that============(atomate_env) [skim121@login1 Si_test]atwf add -l vasp -s optimize_only.yaml -m mp-149 --common_params vasp_cmd=">>vasp_std<<"
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/__init__.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a "PMG_". E.g., "PMG_VASP_PSP_DIR" instead of "VASP_PSP_DIR".warnings.warn('With effect from pmg 5.0, all pymatgen settings are'
usage: atwf [-h] {add,test,verify,powerup} ...atwf: error: unrecognized arguments: --common_params vasp_cmd=>>vasp_std<<========================================================So, I moved to the preset function based workflows by typing ==========>> atwf add -l vasp -p wf_bandstructure -m mp-149>> qlaunch singleshot=========================================================After finishing the caculation, I checked wheather the information inserted to database, and it worked! ====(atomate_env) [skim121@login1 Si_test]mgdb query -c ~/atomate/config/db.json --props task_id formula_pretty output.energy_per_atom /home1/04049/skim121/atomate/codes/pymatgen/pymatgen/__init__.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a "PMG_". E.g., "PMG_VASP_PSP_DIR" instead of "VASP_PSP_DIR".
warnings.warn('With effect from pmg 5.0, all pymatgen settings are'
task_id formula_pretty output.energy_per_atom--------- ---------------- ------------------------10 Si -5.4207===============================================================================Unfortunately, I've also met some difficulties to understand.1. Even the calculation was completed, when I checked workflows using lpad get_wflows, the state is still "RUNNING". It didn't happen when I used file-based workflows.=============================================================(atomate_env) [skim121@login1 Si_test]squeue -u skim121JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)(atomate_env) [skim121@login1 Si_test]lpad get_wflows{"name": "Si--1","state": "RUNNING","states_list": "W-W-REA-C","created_on": "2017-08-19T19:59:49.403000"}======================================================2. I wonder if I cannot see the band structure data in the working directory. I found the band gap and kpoints in mlab database. but I cannot see INCAR and KPOINTS for the band calculation in the working directory. All the files I have in the directory seem to be related to the structural optimization.<image.png>3. To analysis the band structure, I made the file "bs-analysis.py" according to the running workflow tutorial (https://hackingmaterials.github.io/atomate/running_workflows.html)Here is my "bs-analysis.py" ==============from atomate.vasp.database import VaspCalcDbfrom pymatgen.electronic_structure.plotter import DosPlotter, BSDOSPlotter# create the atomate db from your db.jsonPATH_TO_MY_DB_JSON = '/home1/04049/skim121/atomate/config/db.json'atomate_db = VaspCalcDb.from_db_file(PATH_TO_MY_DB_JSON)# get the entry from the database and# use the get_band_structure method of the database to get the pymatgen BandStructureSymmLine for that task idline_bs_entry = atomate_db.collection.find_one({'task_label': 'nscf line', 'formula_pretty': 'Si'})bandstructure = atomate_db.get_band_structure(line_bs_entry['task_id'])# Instatiate a bandstructure plotter and plot the bandstructure.# You can uncomment out the get_plot if you have a GUI frontend to plot to.bs_plotter = BSPlotter(bandstructure)# bs_plotter.get_plot()bs_plotter.save_plot('Si-bandstructure.pdf', img_format='pdf')========================================Again, I've got an error below =======================(atomate_env) [skim121@login1 Si_test]python bs-analysis.py
/home1/04049/skim121/atomate/codes/pymatgen/pymatgen/__init__.py:33: UserWarning: With effect from pmg 5.0, all pymatgen settings are prefixed with a "PMG_". E.g., "PMG_VASP_PSP_DIR" instead of "VASP_PSP_DIR".warnings.warn('With effect from pmg 5.0, all pymatgen settings are'
Traceback (most recent call last):
File "bs-analysis.py", line 11, in <module>bandstructure = atomate_db.get_band_structure(line_bs_entry['task_id'])TypeError: 'NoneType' object has no attribute '__getitem__'==========================================I've got the same errors of bs-analysis.py with MgO test following the option 3 in https://hackingmaterials.github.io/atomate/running_workflows.html.I do appreciate your help.Best,Sooran2017-08-19 14:54 GMT-04:00 Anubhav Jain <AJ...@lbl.gov>:I'm looking at some of the instructions and code now and it's also possible there is an issue with the "atwf" command when using file workflows.Can you check if you have a file called "task.json" in the directory where your VASP calculation ran? If that is the case, then atwf did not detect your db.json correctly. Let me know if this is the case. You can do a temporary fix by replacing the atwf command in the tutorial with the one listed here:If it fixes it I will also update the docs and ask the proponents of atwf to resolve that issue.On Sat, Aug 19, 2017 at 11:48 AM, Anubhav Jain <AJ...@lbl.gov> wrote:Hi SooranIf you have set up atomate correctly (using exactly the instructions in http://hackingmaterials.github.io/atomate/installation.html), and you have successfully executed workflows with atomate (using the instruction on running workflows in those docs), those workflows will have automatically inserted data into the MongoDB database (the one with credentials defined in your db.json). You can then find that data either with standard MongoDB tools or with the mgdb command.If this is not working, please describe exactly what you did, what you are seeing etc. e.g., if you are following a tutorial, report what tutorial you're following, how far you got, and whether you did anything different than the standard instructions (e.g., tried some kind of automated installer, skipped steps, etc).Anubhav
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--------Best,
AnubhavBest,
AnubhavSooran KimPostdoctoral FellowHarvard John A. Paulson School of Engineering and Applied SciencesBest,
Anubhav--Sooran KimPostdoctoral FellowHarvard John A. Paulson School of Engineering and Applied Sciences--Best,
Anubhav--Sooran KimPostdoctoral FellowHarvard John A. Paulson School of Engineering and Applied Sciences
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