lammps interactive: move functionality to separate class #973

jan-janssen · 2023-02-27T19:23:37Z

No description provided.

jan-janssen · 2023-02-27T19:51:06Z

======================================================================
[1416](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286062890/jobs/7465131158#step:9:1417)
ERROR: test_interactive_positions_setter (lammps.test_interactive.TestLammpsInteractive)
[1417](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286062890/jobs/7465131158#step:9:1418)
----------------------------------------------------------------------
[1418](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286062890/jobs/7465131158#step:9:1419)
Traceback (most recent call last):
[1419](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286062890/jobs/7465131158#step:9:1420)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/tests/lammps/test_interactive.py", line 92, in test_interactive_positions_setter
[1420](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286062890/jobs/7465131158#step:9:1421)
    self.job.interactive_positions_setter(np.arange(6).reshape(2, 3))
[1421](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286062890/jobs/7465131158#step:9:1422)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/lammps/interactive.py", line 107, in interactive_positions_setter
[1422](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286062890/jobs/7465131158#step:9:1423)
    interactive_positions_setter(
[1423](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286062890/jobs/7465131158#step:9:1424)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/lammps/wrapper.py", line 21, in interactive_positions_setter
[1424](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286062890/jobs/7465131158#step:9:1425)
    positions = np.matmul(positions, prism)
[1425](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286062890/jobs/7465131158#step:9:1426)
ValueError: matmul: Input operand 1 does not have enough dimensions (has 0, gufunc core with signature (n?,k),(k,m?)->(n?,m?) requires 1)
[1426](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286062890/jobs/7465131158#step:9:1427)

[1427](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286062890/jobs/7465131158#step:9:1428)
----------------------------------------------------------------------

… lammps_interactive_wrapper

jan-janssen · 2023-02-27T21:41:48Z

======================================================================
[1415](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1416)
ERROR: test_calc_minimize_input (lammps.test_interactive.TestLammpsInteractive)
[1416](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1417)
----------------------------------------------------------------------
[1417](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1418)
Traceback (most recent call last):
[1418](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1419)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/tests/lammps/test_interactive.py", line 117, in test_calc_minimize_input
[1419](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1420)
    self.minimize_control_job._interactive_lammps_input()
[1420](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1421)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/lammps/interactive.py", line 130, in _interactive_lammps_input
[1421](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1422)
    self._interactive_lib_command(
[1422](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1423)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/lammps/interactive.py", line 70, in _interactive_lib_command
[1423](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1424)
    self._interactive_library.interactive_lib_command(command=command)
[1424](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1425)
AttributeError: 'InteractiveLibrary' object has no attribute 'interactive_lib_command'
[1425](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1426)

[1426](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1427)
======================================================================
[1427](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1428)
ERROR: test_interactive_cells_setter (lammps.test_interactive.TestLammpsInteractive)
[1428](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1429)
----------------------------------------------------------------------
[1429](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1430)
Traceback (most recent call last):
[1430](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1431)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/tests/lammps/test_interactive.py", line 69, in test_interactive_cells_setter
[1431](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1432)
    self.job.interactive_cells_setter(self.job._structure_current.cell)
[1432](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1433)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/lammps/interactive.py", line 90, in interactive_cells_setter
[1433](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1434)
    self._interactive_library.interactive_cells_setter(
[1434](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1435)
AttributeError: 'InteractiveLibrary' object has no attribute 'interactive_cells_setter'
[1435](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1436)

[1436](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1437)
======================================================================
[1437](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1438)
ERROR: test_interactive_execute (lammps.test_interactive.TestLammpsInteractive)
[1438](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1439)
----------------------------------------------------------------------
[1439](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1440)
Traceback (most recent call last):
[1440](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1441)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/tests/lammps/test_interactive.py", line 99, in test_interactive_execute
[1441](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1442)
    self.job._interactive_lammps_input()
[1442](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1443)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/lammps/interactive.py", line 130, in _interactive_lammps_input
[1443](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1444)
    self._interactive_lib_command(
[1444](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1445)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/lammps/interactive.py", line 70, in _interactive_lib_command
[1445](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1446)
    self._interactive_library.interactive_lib_command(command=command)
[1446](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1447)
AttributeError: 'InteractiveLibrary' object has no attribute 'interactive_lib_command'
[1447](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1448)

[1448](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1449)
======================================================================
[1449](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1450)
ERROR: test_interactive_positions_setter (lammps.test_interactive.TestLammpsInteractive)
[1450](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1451)
----------------------------------------------------------------------
[1451](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1452)
Traceback (most recent call last):
[1452](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1453)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/tests/lammps/test_interactive.py", line 92, in test_interactive_positions_setter
[1453](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1454)
    self.job.interactive_positions_setter(np.arange(6).reshape(2, 3))
[1454](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1455)
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/lammps/interactive.py", line 79, in interactive_positions_setter
[1455](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1456)
    self._interactive_library.interactive_positions_setter(
[1456](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1457)
AttributeError: 'InteractiveLibrary' object has no attribute 'interactive_positions_setter'
[1457](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1458)

[1458](https://github.com/pyiron/pyiron_atomistics/actions/runs/4286991060/jobs/7467392679#step:9:1459)
----------------------------------------------------------------------

… lammps_interactive_wrapper # Conflicts: # pyiron_atomistics/lammps/wrapper.py

… lammps_interactive_wrapper

jan-janssen · 2023-02-28T05:01:58Z

The PyironLammpsLibrary can be loaded from https://github.com/pyiron/pyiron_lammps

stale · 2023-03-18T12:25:46Z

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

coveralls · 2023-05-14T18:02:59Z

Pull Request Test Coverage Report for Build 6966811085

Warning: This coverage report may be inaccurate.

We've detected an issue with your CI configuration that might affect the accuracy of this pull request's coverage report.
To ensure accuracy in future PRs, please see these guidelines.
A quick fix for this PR: rebase it; your next report should be accurate.

8 of 18 (44.44%) changed or added relevant lines in 1 file are covered.
4 unchanged lines in 1 file lost coverage.
Overall coverage increased (+0.3%) to 68.587%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/lammps/interactive.py	8	18	44.44%

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/lammps/interactive.py	4	45.59%

Totals
Change from base Build 6949127611:	0.3%
Covered Lines:	10716
Relevant Lines:	15624

💛 - Coveralls

…apper # Conflicts: # .ci_support/environment.yml # setup.py

stale · 2023-06-10T05:24:22Z

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

…apper # Conflicts: # .ci_support/environment.yml # setup.py

stale · 2023-09-17T00:57:05Z

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

…apper

lammps interactive: move functionality to separate class

147335b

jan-janssen added the format_black reformat the code using the black standard label Feb 27, 2023

Format black

c8a1088

jan-janssen added 5 commits February 27, 2023 12:58

fix bug

bfef117

Merge remote-tracking branch 'origin/lammps_interactive_wrapper' into…

0da9df4

… lammps_interactive_wrapper

Introduce lammps wrapper

2790ee6

remove unused imports

82ad2ef

minor bugfixes

ad04434

jan-janssen added format_black reformat the code using the black standard and removed format_black reformat the code using the black standard labels Feb 27, 2023

Format black

a6224f7

jan-janssen mentioned this pull request Feb 27, 2023

[Feature] Support for ASE structures pyiron/pylammpsmpi#85

Closed

jan-janssen added 3 commits February 27, 2023 15:36

fix tests

9b030e6

Merge remote-tracking branch 'origin/lammps_interactive_wrapper' into…

8fca3bb

… lammps_interactive_wrapper # Conflicts: # pyiron_atomistics/lammps/wrapper.py

Add library parameter

294534c

jan-janssen added format_black reformat the code using the black standard and removed format_black reformat the code using the black standard labels Feb 27, 2023

pyiron-runner and others added 3 commits February 27, 2023 22:49

Format black

802504e

another bug fix

a8befe6

Merge remote-tracking branch 'origin/lammps_interactive_wrapper' into…

fd649e5

… lammps_interactive_wrapper

jan-janssen added 2 commits March 3, 2023 08:48

Merge branch 'main' into lammps_interactive_wrapper

54c25b3

Update wrapper.py

3d59ea3

stale bot added the stale label Mar 18, 2023

stale bot closed this Apr 2, 2023

jan-janssen reopened this May 14, 2023

stale bot removed the stale label May 14, 2023

jan-janssen and others added 3 commits May 14, 2023 11:05

Use pyiron_lammps

651d806

Merge remote-tracking branch 'origin/main' into lammps_interactive_wr…

87c0604

…apper # Conflicts: # .ci_support/environment.yml # setup.py

Update setup.py

b86f957

stale bot added the stale label Jun 10, 2023

stale bot closed this Aug 12, 2023

jan-janssen reopened this Aug 12, 2023

stale bot removed the stale label Aug 12, 2023

jan-janssen added 4 commits August 16, 2023 22:16

Switch from pyiron_lammps to pylammpsmpi

4fa2238

Merge remote-tracking branch 'origin/main' into lammps_interactive_wr…

6737c1e

…apper # Conflicts: # .ci_support/environment.yml # setup.py

Fixes

fe9c925

update tests but they still require the lammps library

04fd135

stale bot added the stale label Sep 17, 2023

Update environment.yml

d2b06c3

stale bot removed the stale label Nov 20, 2023

jan-janssen and others added 6 commits November 20, 2023 14:27

Update setup.py

d8c6146

Merge branch 'main' into lammps_interactive_wrapper

92988d2

Update environment.yml

d427080

Merge remote-tracking branch 'origin/main' into lammps_interactive_wr…

2c3cc7c

…apper

Update setup.py

0c75837

Update setup.py

9b6d133

jan-janssen merged commit d827caf into main Nov 23, 2023
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lammps interactive: move functionality to separate class #973

lammps interactive: move functionality to separate class #973

jan-janssen commented Feb 27, 2023

jan-janssen commented Feb 27, 2023

jan-janssen commented Feb 27, 2023

jan-janssen commented Feb 28, 2023

stale bot commented Mar 18, 2023

coveralls commented May 14, 2023 •

edited

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stale bot commented Jun 10, 2023

stale bot commented Sep 17, 2023

lammps interactive: move functionality to separate class #973

lammps interactive: move functionality to separate class #973

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jan-janssen commented Feb 27, 2023

jan-janssen commented Feb 27, 2023

jan-janssen commented Feb 27, 2023

jan-janssen commented Feb 28, 2023

stale bot commented Mar 18, 2023

coveralls commented May 14, 2023 • edited Loading

Pull Request Test Coverage Report for Build 6966811085

Warning: This coverage report may be inaccurate.

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stale bot commented Jun 10, 2023

stale bot commented Sep 17, 2023

coveralls commented May 14, 2023 •

edited

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