LAMMPS: Implement calculate() function #1446

jan-janssen · 2024-06-10T07:09:17Z

Switch the LAMMPS job to the calculate() function as it is introduced in pyiron/pyiron_base#1477 . The pull request is expected to fail until pyiron/pyiron_base#1477 is merged.

With these new changes it is possible to evaluate LAMMPS jobs as functions. For a classical LAMMPS job you would use:

from pyiron_atomistics import Project

pr = Project("test")
job = pr.create.job.Lammps("lmp")
job.structure = pr.create.structure.ase.bulk("Al", cubic=True)
job.run()

This still works, but in addition you can also use an external executor:

from pyiron_atomistics import Project
from concurrent.futures import ProcessPoolExecutor

pr = Project("test")
job = pr.create.job.Lammps("lmp")
job.structure = pr.create.structure.ase.bulk("Al", cubic=True)

with ProcessPoolExecutor() as exe:
    fs = exe.submit(job.get_calculate_function(), **job.calculate_kwargs)
    shell_output, output_dict, job_crashed = fs.result()

job.save_output(output_dict=output_dict, shell_output=shell_output)

…alculate

coveralls · 2024-06-10T07:39:48Z

Pull Request Test Coverage Report for Build 9444291497

Details

13 of 13 (100.0%) changed or added relevant lines in 1 file are covered.
2 unchanged lines in 1 file lost coverage.
Overall coverage increased (+0.002%) to 71.187%

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/potential.py	2	62.5%

Totals
Change from base Build 9438715818:	0.002%
Covered Lines:	10678
Relevant Lines:	15000

💛 - Coveralls

samwaseda · 2024-06-11T19:07:22Z

pyiron_atomistics/lammps/base.py

+            "files_to_copy": files_to_copy,
+        }
+
+    def write_input(self):


Shouldn't this go to AtomisticGenericJob?

Yes, the corresponding pull request is already open on pyiron_base pyiron/pyiron_base#1472 .

Then why is a copy here?

This is primarily for historic reasons, this was the first pull request, before the one in pyiron_base. The copy is removed in #1451

But doesn't it make more sense to not add it in the first place in this PR?

Unless a new version of base is released the tests fail without this temporary function.

I'm ok with it, but it seems to me like a bigger evil to copy and paste lines of code only to be deleted in the next PR if the sole reason to do it is you want to merge it earlier, because it's gonna stay in the commit history and might confuse the future developers. Maybe someone like @pmrv or @liamhuber has an opinion?

@samwaseda, what you are saying sounds perfectly reasonable to me. If this PR ought to depend on a PR in base, unless there is some pressing need to get it merged and released, just wait for what's needed to be available in base.

pyiron_atomistics/lammps/base.py

coveralls · 2024-06-11T19:50:22Z

Pull Request Test Coverage Report for Build 9471820921

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

For more information on this, see Tracking coverage changes with pull request builds.
To avoid this issue with future PRs, see these Recommended CI Configurations.
For a quick fix, rebase this PR at GitHub. Your next report should be accurate.

Details

17 of 17 (100.0%) changed or added relevant lines in 1 file are covered.
217 unchanged lines in 3 files lost coverage.
Overall coverage decreased (-0.001%) to 71.184%

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/potential.py	2	62.5%
pyiron_atomistics/dft/bader.py	4	92.73%
pyiron_atomistics/vasp/base.py	211	66.1%

Totals
Change from base Build 9438715818:	-0.001%
Covered Lines:	10679
Relevant Lines:	15002

💛 - Coveralls

pyiron_atomistics/lammps/base.py

coveralls · 2024-06-12T04:21:59Z

Pull Request Test Coverage Report for Build 9476628334

Details

17 of 17 (100.0%) changed or added relevant lines in 1 file are covered.
2 unchanged lines in 1 file lost coverage.
Overall coverage increased (+0.002%) to 71.184%

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/potential.py	2	62.5%

Totals
Change from base Build 9450521916:	0.002%
Covered Lines:	10679
Relevant Lines:	15002

💛 - Coveralls

coveralls · 2024-06-12T05:08:00Z

Pull Request Test Coverage Report for Build 9476697150

Details

17 of 17 (100.0%) changed or added relevant lines in 1 file are covered.
2 unchanged lines in 1 file lost coverage.
Overall coverage increased (+0.002%) to 71.184%

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/potential.py	2	62.5%

Totals
Change from base Build 9450521916:	0.002%
Covered Lines:	10679
Relevant Lines:	15002

💛 - Coveralls

Merge main

Lammps submit to executor

jan-janssen · 2024-06-12T05:37:49Z

This comment is no longer valid.

jan-janssen · 2024-06-12T05:38:18Z

Waiting for pyiron/pyiron_base#1477

coveralls · 2024-06-12T05:49:37Z

Pull Request Test Coverage Report for Build 9477283041

Details

19 of 19 (100.0%) changed or added relevant lines in 2 files are covered.
50 unchanged lines in 3 files lost coverage.
Overall coverage increased (+0.002%) to 71.201%

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/potential.py	2	62.5%
pyiron_atomistics/lammps/output.py	19	87.18%
pyiron_atomistics/lammps/base.py	29	80.2%

Totals
Change from base Build 9477094720:	0.002%
Covered Lines:	10693
Relevant Lines:	15018

💛 - Coveralls

pmrv

lgtm

…alculate_with_base

…base

…lculate # Conflicts: # pyiron_atomistics/lammps/base.py

…alculate # Conflicts: # pyiron_atomistics/lammps/base.py

coveralls · 2024-06-21T06:13:28Z

Pull Request Test Coverage Report for Build 9609063823

Details

73 of 106 (68.87%) changed or added relevant lines in 2 files are covered.
4 unchanged lines in 3 files lost coverage.
Overall coverage decreased (-0.008%) to 71.18%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/output.py	4	5	80.0%
pyiron_atomistics/lammps/base.py	69	101	68.32%

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/base.py	1	79.85%
pyiron_atomistics/lammps/interactive.py	1	45.14%
pyiron_atomistics/lammps/potential.py	2	62.5%

Totals
Change from base Build 9608395794:	-0.008%
Covered Lines:	10687
Relevant Lines:	15014

💛 - Coveralls

coveralls · 2024-06-21T06:18:17Z

Pull Request Test Coverage Report for Build 9609156113

Details

73 of 106 (68.87%) changed or added relevant lines in 2 files are covered.
4 unchanged lines in 3 files lost coverage.
Overall coverage decreased (-0.008%) to 71.18%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/output.py	4	5	80.0%
pyiron_atomistics/lammps/base.py	69	101	68.32%

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/base.py	1	79.85%
pyiron_atomistics/lammps/interactive.py	1	45.14%
pyiron_atomistics/lammps/potential.py	2	62.5%

Totals
Change from base Build 9608395794:	-0.008%
Covered Lines:	10687
Relevant Lines:	15014

💛 - Coveralls

coveralls · 2024-06-21T06:24:51Z

Pull Request Test Coverage Report for Build 9609216747

Details

73 of 106 (68.87%) changed or added relevant lines in 2 files are covered.
4 unchanged lines in 3 files lost coverage.
Overall coverage decreased (-0.008%) to 71.18%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/output.py	4	5	80.0%
pyiron_atomistics/lammps/base.py	69	101	68.32%

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/base.py	1	79.85%
pyiron_atomistics/lammps/interactive.py	1	45.14%
pyiron_atomistics/lammps/potential.py	2	62.5%

Totals
Change from base Build 9608395794:	-0.008%
Covered Lines:	10687
Relevant Lines:	15014

💛 - Coveralls

jan-janssen added 3 commits June 10, 2024 08:41

LAMMPS: Add get_input_file_dict()

d205a0c

Merge remote-tracking branch 'refs/remotes/origin/main' into lammps_c…

c20e99b

…alculate

LAMMPS: use get_input_file_dict() in write_input()

619d5e3

jan-janssen added the format_black reformat the code using the black standard label Jun 10, 2024

pyiron-runner and others added 3 commits June 10, 2024 07:15

Format black

79b7173

Update base.py

9c8f747

Update base.py

e09eca5

jan-janssen and others added 4 commits June 10, 2024 13:02

Use input file dict from base

34c930b

Add _store_output()

8a1c535

Format black

19ea6e0

Remove write_input() and use write_input() from base

e377501

jan-janssen mentioned this pull request Jun 11, 2024

Add get_input_file_dict() in GenericJob pyiron/pyiron_base#1472

Merged

jan-janssen requested a review from samwaseda June 11, 2024 18:39

samwaseda reviewed Jun 11, 2024

View reviewed changes

pyiron_atomistics/lammps/base.py Outdated Show resolved Hide resolved

Add docstring

17ec7a8

jan-janssen commented Jun 11, 2024

View reviewed changes

pyiron_atomistics/lammps/base.py Show resolved Hide resolved

samwaseda approved these changes Jun 11, 2024

View reviewed changes

Update pyiron_atomistics/lammps/base.py

8b5ae63

jan-janssen mentioned this pull request Jun 11, 2024

VASP: Implement get_input_file_dict() #1447

Merged

jan-janssen closed this Jun 12, 2024

jan-janssen reopened this Jun 12, 2024

jan-janssen added format_black reformat the code using the black standard and removed format_black reformat the code using the black standard labels Jun 12, 2024

Format black

7b524f7

Merge pull request #1455 from pyiron/main

e5e9e1d

Merge main

jan-janssen added 3 commits June 12, 2024 07:33

Merge pull request #1456 from pyiron/main

36ac077

Merge main

Merge branch 'lammps_calculate' into lammps_calculate_with_base

26de0f8

Merge pull request #1451 from pyiron/lammps_calculate_with_base

89a5a09

Lammps submit to executor

jan-janssen marked this pull request as draft June 12, 2024 05:37

jan-janssen mentioned this pull request Jun 12, 2024

Introduce calculate() function pyiron/pyiron_base#1477

Merged

pmrv approved these changes Jun 12, 2024

View reviewed changes

jan-janssen added 4 commits June 20, 2024 11:27

Merge remote-tracking branch 'refs/remotes/origin/main' into lammps_c…

4995d40

…alculate_with_base

Update LAMMPS interface to be compatible to latest changes in pyiron_…

2edc692

…base

Merge remote-tracking branch 'origin/lammps_calculate' into lammps_ca…

1a0fc0a

…lculate # Conflicts: # pyiron_atomistics/lammps/base.py

fix pandas import

e50a801

jan-janssen changed the title ~~LAMMPS: Implement get_input_file_dict()~~ LAMMPS: Implement calculate() function Jun 20, 2024

jan-janssen added format_black reformat the code using the black standard and removed format_black reformat the code using the black standard labels Jun 20, 2024

pyiron-runner and others added 2 commits June 20, 2024 10:36

Format black

638274f

Merge remote-tracking branch 'refs/remotes/origin/main' into lammps_c…

762fa8d

…alculate # Conflicts: # pyiron_atomistics/lammps/base.py

jan-janssen marked this pull request as ready for review June 21, 2024 04:46

Fix bugs

470f2af

jan-janssen added format_black reformat the code using the black standard and removed format_black reformat the code using the black standard labels Jun 21, 2024

pyiron-runner and others added 2 commits June 21, 2024 06:04

Format black

bc4f428

Update environment-old.yml

86e398e

Update environment-old.yml

1920be2

jan-janssen merged commit 00177f7 into main Jun 21, 2024
23 of 24 checks passed

jan-janssen deleted the lammps_calculate branch June 21, 2024 06:37

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