From 1aac39ce8069a8634d93e84b7b70a32f87c72f94 Mon Sep 17 00:00:00 2001 From: samwaseda Date: Wed, 31 Jul 2024 13:59:58 +0000 Subject: [PATCH 01/29] add empty lines --- pyiron_contrib/atomistics/elastic/elastic.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pyiron_contrib/atomistics/elastic/elastic.py b/pyiron_contrib/atomistics/elastic/elastic.py index d81870a397..c847a060fb 100644 --- a/pyiron_contrib/atomistics/elastic/elastic.py +++ b/pyiron_contrib/atomistics/elastic/elastic.py @@ -579,8 +579,10 @@ def collect_output(self): def get_elastic_tensor_by_orientation(self, orientation): """ Get elastic tensor in given orientation. + Args: orientation (numpy.ndarray): 3x3 orientation tensor (e.g. [[1,1,1],[-1,0,1],[1,-2,1]]) + Returns: elastic tensor in the given orientation """ From 28d2da0ded6fcc1508bc2428dedb8265951c9ba7 Mon Sep 17 00:00:00 2001 From: samwaseda Date: Wed, 31 Jul 2024 14:03:30 +0000 Subject: [PATCH 02/29] run black --- pyiron_contrib/jobfactories/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyiron_contrib/jobfactories/__init__.py b/pyiron_contrib/jobfactories/__init__.py index 8ecc2c18a1..36af915a8e 100644 --- a/pyiron_contrib/jobfactories/__init__.py +++ b/pyiron_contrib/jobfactories/__init__.py @@ -355,7 +355,7 @@ def _prepare_job(self, job, structure): try: job.potential[k] = v except AttributeError: - pass # element k does not exist in the current structure + pass # element k does not exist in the current structure if self.storage.nband_nelec_map is not None: # ensure we apply the hack only for structures where we know an NBAND estimate for all elements elems = set(self.storage.nband_nelec_map.keys()) From 1c4a4067971d7df7fabd99ff7bfedb90965164b9 Mon Sep 17 00:00:00 2001 From: pyiron-runner Date: Wed, 31 Jul 2024 19:38:52 +0000 Subject: [PATCH 03/29] [dependabot skip] Update env file --- .binder/environment.yml | 2 +- docs/environment.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.binder/environment.yml b/.binder/environment.yml index 4032b8e71c..1400dc987e 100644 --- a/.binder/environment.yml +++ b/.binder/environment.yml @@ -8,7 +8,7 @@ dependencies: - matplotlib =3.8.3 - numpy =1.26.4 - pyiron_base =0.9.10 -- pyiron_atomistics =0.6.1 +- pyiron_atomistics =0.6.9 - pyiron_snippets =0.1.1 - pyparsing =3.1.2 - scipy =1.12.0 diff --git a/docs/environment.yml b/docs/environment.yml index 9003a0b55e..7aad0b389c 100644 --- a/docs/environment.yml +++ b/docs/environment.yml @@ -13,7 +13,7 @@ dependencies: - matplotlib =3.8.3 - numpy =1.26.4 - pyiron_base =0.9.10 -- pyiron_atomistics =0.6.1 +- pyiron_atomistics =0.6.9 - pyiron_snippets =0.1.1 - pyparsing =3.1.2 - scipy =1.12.0 From 539f106735c1edba81d3f9ebafbc654a4b4b51b7 Mon Sep 17 00:00:00 2001 From: samwaseda Date: Wed, 31 Jul 2024 19:49:44 +0000 Subject: [PATCH 04/29] update environment --- .ci_support/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index 00ac573530..6ffc89a17c 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -9,7 +9,7 @@ dependencies: - numpy =1.26.4 - pyiron_base =0.9.10 - pyiron_atomistics =0.6.9 -- pyiron_snippets =0.1.1 +- pyiron_snippets =0.1.3 - pyparsing =3.1.2 - scipy =1.12.0 - seaborn =0.13.2 From 16b06e354186921eaa9a7c20f88fb2a36fbfe8d4 Mon Sep 17 00:00:00 2001 From: pyiron-runner Date: Wed, 31 Jul 2024 19:52:03 +0000 Subject: [PATCH 05/29] [dependabot skip] Update env file --- .binder/environment.yml | 2 +- docs/environment.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.binder/environment.yml b/.binder/environment.yml index 1400dc987e..b68bc6e349 100644 --- a/.binder/environment.yml +++ b/.binder/environment.yml @@ -9,7 +9,7 @@ dependencies: - numpy =1.26.4 - pyiron_base =0.9.10 - pyiron_atomistics =0.6.9 -- pyiron_snippets =0.1.1 +- pyiron_snippets =0.1.3 - pyparsing =3.1.2 - scipy =1.12.0 - seaborn =0.13.2 diff --git a/docs/environment.yml b/docs/environment.yml index 7aad0b389c..86722adedd 100644 --- a/docs/environment.yml +++ b/docs/environment.yml @@ -14,7 +14,7 @@ dependencies: - numpy =1.26.4 - pyiron_base =0.9.10 - pyiron_atomistics =0.6.9 -- pyiron_snippets =0.1.1 +- pyiron_snippets =0.1.3 - pyparsing =3.1.2 - scipy =1.12.0 - seaborn =0.13.2 From 3d4eb443af668374167d465e59a9cc15ab2e5605 Mon Sep 17 00:00:00 2001 From: samwaseda Date: Wed, 31 Jul 2024 19:55:29 +0000 Subject: [PATCH 06/29] downgrade h5_browser --- .ci_support/environment.yml | 2 +- docs/environment.yml | 2 +- setup.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index 6ffc89a17c..4214a237aa 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -20,6 +20,6 @@ dependencies: - pycp2k =0.2.2 - aws-sam-translator =1.77.0 - distributed =2024.5.2 -- h5io_browser =0.0.17 +- h5io_browser =0.0.16 - pymatgen =2024.5.1 - pympipool =0.8.4 diff --git a/docs/environment.yml b/docs/environment.yml index 86722adedd..aa62a93b84 100644 --- a/docs/environment.yml +++ b/docs/environment.yml @@ -25,6 +25,6 @@ dependencies: - pycp2k =0.2.2 - aws-sam-translator =1.77.0 - distributed =2024.5.2 -- h5io_browser =0.0.17 +- h5io_browser =0.0.16 - pymatgen =2024.5.1 - pympipool =0.8.4 diff --git a/setup.py b/setup.py index 8b82c77d84..892af6f9ca 100644 --- a/setup.py +++ b/setup.py @@ -57,7 +57,7 @@ 'distributed==2024.5.2', 'pymatgen==2024.5.1', 'pympipool==0.8.4', - 'h5io_browser==0.0.17', + 'h5io_browser==0.0.16', ] }, cmdclass=versioneer.get_cmdclass(), From 7701006165c2a66e9b09ec40415dcbabd41fd671 Mon Sep 17 00:00:00 2001 From: pyiron-runner Date: Wed, 31 Jul 2024 19:55:53 +0000 Subject: [PATCH 07/29] [dependabot skip] Update env file --- .binder/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.binder/environment.yml b/.binder/environment.yml index b68bc6e349..cc64ddea58 100644 --- a/.binder/environment.yml +++ b/.binder/environment.yml @@ -20,7 +20,7 @@ dependencies: - pycp2k =0.2.2 - aws-sam-translator =1.77.0 - distributed =2024.5.2 -- h5io_browser =0.0.17 +- h5io_browser =0.0.16 - pymatgen =2024.5.1 - pympipool =0.8.4 - python >= 3.10 From dcc8d4755785981823cd9f4a2e4cebc68f0e09c0 Mon Sep 17 00:00:00 2001 From: samwaseda Date: Wed, 31 Jul 2024 20:27:42 +0000 Subject: [PATCH 08/29] update distributed --- .binder/environment.yml | 2 +- .ci_support/environment.yml | 2 +- docs/environment.yml | 2 +- setup.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.binder/environment.yml b/.binder/environment.yml index cc64ddea58..96d00bead1 100644 --- a/.binder/environment.yml +++ b/.binder/environment.yml @@ -19,7 +19,7 @@ dependencies: - moto =5.0.9 - pycp2k =0.2.2 - aws-sam-translator =1.77.0 -- distributed =2024.5.2 +- distributed =2024.7.1 - h5io_browser =0.0.16 - pymatgen =2024.5.1 - pympipool =0.8.4 diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index 4214a237aa..25a174c221 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -19,7 +19,7 @@ dependencies: - moto =5.0.9 - pycp2k =0.2.2 - aws-sam-translator =1.77.0 -- distributed =2024.5.2 +- distributed =2024.7.1 - h5io_browser =0.0.16 - pymatgen =2024.5.1 - pympipool =0.8.4 diff --git a/docs/environment.yml b/docs/environment.yml index aa62a93b84..1d3e95c013 100644 --- a/docs/environment.yml +++ b/docs/environment.yml @@ -24,7 +24,7 @@ dependencies: - moto =5.0.9 - pycp2k =0.2.2 - aws-sam-translator =1.77.0 -- distributed =2024.5.2 +- distributed =2024.7.1 - h5io_browser =0.0.16 - pymatgen =2024.5.1 - pympipool =0.8.4 diff --git a/setup.py b/setup.py index 892af6f9ca..2c2ac9654a 100644 --- a/setup.py +++ b/setup.py @@ -54,7 +54,7 @@ 'moto==5.0.9' ], 'tinybase': [ - 'distributed==2024.5.2', + 'distributed==2024.7.1', 'pymatgen==2024.5.1', 'pympipool==0.8.4', 'h5io_browser==0.0.16', From de55ad036a0de93306702a726e6d42d19a13223f Mon Sep 17 00:00:00 2001 From: samwaseda Date: Wed, 31 Jul 2024 20:48:29 +0000 Subject: [PATCH 09/29] update daily.yml --- .github/workflows/daily.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/daily.yml b/.github/workflows/daily.yml index d11a2a520f..856f967b1f 100644 --- a/.github/workflows/daily.yml +++ b/.github/workflows/daily.yml @@ -8,5 +8,5 @@ on: jobs: codeql: - uses: pyiron/actions/.github/workflows/tests-and-coverage.yml@actions-1.1.0b - secrets: inherit \ No newline at end of file + uses: pyiron/actions/.github/workflows/tests-and-coverage.yml@actions-3.2.0 + secrets: inherit From f0c30422fc162ae99284d5c570bfefd714891dae Mon Sep 17 00:00:00 2001 From: samwaseda Date: Thu, 1 Aug 2024 06:29:14 +0000 Subject: [PATCH 10/29] Rename push-pull --- .github/workflows/push-pull.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/push-pull.yml b/.github/workflows/push-pull.yml index 4d0b30bb7b..052fb7a8a1 100644 --- a/.github/workflows/push-pull.yml +++ b/.github/workflows/push-pull.yml @@ -9,7 +9,7 @@ on: jobs: pyiron: - uses: pyiron/actions/.github/workflows/push-pull-main.yml@actions-1.1.0b + uses: pyiron/actions/.github/workflows/push-pull.yml@actions-1.1.0b secrets: inherit with: - notebooks-env-files: .ci_support/environment.yml .ci_support/environment-notebooks.yml \ No newline at end of file + notebooks-env-files: .ci_support/environment.yml .ci_support/environment-notebooks.yml From 4618c4f0df06e6bd801072be617bf93a92d68918 Mon Sep 17 00:00:00 2001 From: samwaseda Date: Thu, 1 Aug 2024 06:32:07 +0000 Subject: [PATCH 11/29] ok it looks like it was a mistake --- .github/workflows/push-pull.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/push-pull.yml b/.github/workflows/push-pull.yml index 052fb7a8a1..43db0a7a9e 100644 --- a/.github/workflows/push-pull.yml +++ b/.github/workflows/push-pull.yml @@ -9,7 +9,7 @@ on: jobs: pyiron: - uses: pyiron/actions/.github/workflows/push-pull.yml@actions-1.1.0b + uses: pyiron/actions/.github/workflows/push-pull-all.yml@actions-1.1.0b secrets: inherit with: notebooks-env-files: .ci_support/environment.yml .ci_support/environment-notebooks.yml From 5f927d047e4de9a105a57ffd850cd111d5ff57ae Mon Sep 17 00:00:00 2001 From: samwaseda Date: Thu, 1 Aug 2024 06:33:12 +0000 Subject: [PATCH 12/29] I'm a loss --- .github/workflows/push-pull.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/push-pull.yml b/.github/workflows/push-pull.yml index 43db0a7a9e..e6dcaf7657 100644 --- a/.github/workflows/push-pull.yml +++ b/.github/workflows/push-pull.yml @@ -9,7 +9,7 @@ on: jobs: pyiron: - uses: pyiron/actions/.github/workflows/push-pull-all.yml@actions-1.1.0b + uses: pyiron/actions/.github/workflows/push-pull-main.yml@actions-1.1.0b secrets: inherit with: notebooks-env-files: .ci_support/environment.yml .ci_support/environment-notebooks.yml From 5f95ba28c5d1d3f086d46e5ec1b41c041bd54366 Mon Sep 17 00:00:00 2001 From: samwaseda Date: Thu, 1 Aug 2024 06:34:42 +0000 Subject: [PATCH 13/29] ok it was a version problem --- .github/workflows/push-pull.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/push-pull.yml b/.github/workflows/push-pull.yml index e6dcaf7657..e5d0d85ac1 100644 --- a/.github/workflows/push-pull.yml +++ b/.github/workflows/push-pull.yml @@ -9,7 +9,7 @@ on: jobs: pyiron: - uses: pyiron/actions/.github/workflows/push-pull-main.yml@actions-1.1.0b + uses: pyiron/actions/.github/workflows/push-pull.yml@actions-3.2.0b secrets: inherit with: notebooks-env-files: .ci_support/environment.yml .ci_support/environment-notebooks.yml From ae228b0ac734f13c6eb09b2953d115c8edc612cf Mon Sep 17 00:00:00 2001 From: samwaseda Date: Thu, 1 Aug 2024 06:37:12 +0000 Subject: [PATCH 14/29] there was no b --- .github/workflows/push-pull.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/push-pull.yml b/.github/workflows/push-pull.yml index e5d0d85ac1..85e3e6ccc7 100644 --- a/.github/workflows/push-pull.yml +++ b/.github/workflows/push-pull.yml @@ -9,7 +9,7 @@ on: jobs: pyiron: - uses: pyiron/actions/.github/workflows/push-pull.yml@actions-3.2.0b + uses: pyiron/actions/.github/workflows/push-pull.yml@actions-3.2.1 secrets: inherit with: notebooks-env-files: .ci_support/environment.yml .ci_support/environment-notebooks.yml From 3e7c3cb0d24869c3bcf1c9610f66e02c963bd7f4 Mon Sep 17 00:00:00 2001 From: pyiron-runner Date: Thu, 1 Aug 2024 06:38:00 +0000 Subject: [PATCH 15/29] [dependabot skip] Update env file --- docs/environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/environment.yml b/docs/environment.yml index 1d3e95c013..41fd99af66 100644 --- a/docs/environment.yml +++ b/docs/environment.yml @@ -6,6 +6,7 @@ dependencies: - nbsphinx - sphinx-gallery - sphinx-rtd-theme +- versioneer - ase =3.23.0 - coveralls - coverage From 923a711166d1db5f641f1544e6a6f314fabe5a4d Mon Sep 17 00:00:00 2001 From: samwaseda Date: Thu, 1 Aug 2024 06:42:16 +0000 Subject: [PATCH 16/29] update all yml files --- .github/workflows/daily.yml | 2 +- .github/workflows/dependabot-pr.yml | 4 ++-- .github/workflows/pr-labeled.yml | 4 ++-- .github/workflows/pr-target-opened.yml | 4 ++-- .github/workflows/release.yml | 4 ++-- .github/workflows/weekly.yml | 4 ++-- 6 files changed, 11 insertions(+), 11 deletions(-) diff --git a/.github/workflows/daily.yml b/.github/workflows/daily.yml index 856f967b1f..a49b18470c 100644 --- a/.github/workflows/daily.yml +++ b/.github/workflows/daily.yml @@ -8,5 +8,5 @@ on: jobs: codeql: - uses: pyiron/actions/.github/workflows/tests-and-coverage.yml@actions-3.2.0 + uses: pyiron/actions/.github/workflows/tests-and-coverage.yml@actions-3.2.1 secrets: inherit diff --git a/.github/workflows/dependabot-pr.yml b/.github/workflows/dependabot-pr.yml index d38fd99946..3db961f199 100644 --- a/.github/workflows/dependabot-pr.yml +++ b/.github/workflows/dependabot-pr.yml @@ -6,5 +6,5 @@ on: jobs: pyiron: - uses: pyiron/actions/.github/workflows/dependabot-pr.yml@actions-1.1.0b - secrets: inherit \ No newline at end of file + uses: pyiron/actions/.github/workflows/dependabot-pr.yml@actions-3.2.1 + secrets: inherit diff --git a/.github/workflows/pr-labeled.yml b/.github/workflows/pr-labeled.yml index 78c1d79ed5..e327f50bfa 100644 --- a/.github/workflows/pr-labeled.yml +++ b/.github/workflows/pr-labeled.yml @@ -8,5 +8,5 @@ on: jobs: pyiron: - uses: pyiron/actions/.github/workflows/pr-labeled.yml@actions-1.1.0b - secrets: inherit \ No newline at end of file + uses: pyiron/actions/.github/workflows/pr-labeled.yml@actions-3.2.1 + secrets: inherit diff --git a/.github/workflows/pr-target-opened.yml b/.github/workflows/pr-target-opened.yml index da7c62ed30..ec38f35a5c 100644 --- a/.github/workflows/pr-target-opened.yml +++ b/.github/workflows/pr-target-opened.yml @@ -8,5 +8,5 @@ on: jobs: pyiron: - uses: pyiron/actions/.github/workflows/pr-target-opened.yml@actions-1.1.0b - secrets: inherit \ No newline at end of file + uses: pyiron/actions/.github/workflows/pr-target-opened.yml@actions-3.2.1 + secrets: inherit diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index f5bcdd8028..457fada64c 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -7,5 +7,5 @@ on: jobs: pyiron: - uses: pyiron/actions/.github/workflows/release.yml@actions-1.1.0b - secrets: inherit \ No newline at end of file + uses: pyiron/actions/.github/workflows/release.yml@actions-3.2.1 + secrets: inherit diff --git a/.github/workflows/weekly.yml b/.github/workflows/weekly.yml index 199412095e..a007af3d73 100644 --- a/.github/workflows/weekly.yml +++ b/.github/workflows/weekly.yml @@ -8,5 +8,5 @@ on: jobs: codeql: - uses: pyiron/actions/.github/workflows/codeql.yml@actions-1.1.0b - secrets: inherit \ No newline at end of file + uses: pyiron/actions/.github/workflows/codeql.yml@actions-3.2.1 + secrets: inherit From 791533a522bae7fc998033626fa9ef9fc56580f3 Mon Sep 17 00:00:00 2001 From: samwaseda Date: Thu, 1 Aug 2024 06:53:10 +0000 Subject: [PATCH 17/29] downgrade pycp2k to see what happens --- .ci_support/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index 25a174c221..eea7c24ae1 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -17,7 +17,7 @@ dependencies: - randspg =0.0.1 - boto3 =1.34.122 - moto =5.0.9 -- pycp2k =0.2.2 +- pycp2k =0.2.1 - aws-sam-translator =1.77.0 - distributed =2024.7.1 - h5io_browser =0.0.16 From fe460729d032c670cf636ba2aab13b2210bb276e Mon Sep 17 00:00:00 2001 From: pyiron-runner Date: Thu, 1 Aug 2024 06:53:32 +0000 Subject: [PATCH 18/29] [dependabot skip] Update env file --- .binder/environment.yml | 2 +- docs/environment.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.binder/environment.yml b/.binder/environment.yml index 96d00bead1..04b9255b5e 100644 --- a/.binder/environment.yml +++ b/.binder/environment.yml @@ -17,7 +17,7 @@ dependencies: - randspg =0.0.1 - boto3 =1.34.122 - moto =5.0.9 -- pycp2k =0.2.2 +- pycp2k =0.2.1 - aws-sam-translator =1.77.0 - distributed =2024.7.1 - h5io_browser =0.0.16 diff --git a/docs/environment.yml b/docs/environment.yml index 41fd99af66..0e51539800 100644 --- a/docs/environment.yml +++ b/docs/environment.yml @@ -23,7 +23,7 @@ dependencies: - randspg =0.0.1 - boto3 =1.34.122 - moto =5.0.9 -- pycp2k =0.2.2 +- pycp2k =0.2.1 - aws-sam-translator =1.77.0 - distributed =2024.7.1 - h5io_browser =0.0.16 From 8e9ddf2a7e77a27ef8de5c04a9126149fc1d3c5a Mon Sep 17 00:00:00 2001 From: samwaseda Date: Thu, 1 Aug 2024 06:55:14 +0000 Subject: [PATCH 19/29] set back because this cannot have been the reason --- .ci_support/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index eea7c24ae1..25a174c221 100644 --- a/.ci_support/environment.yml +++ b/.ci_support/environment.yml @@ -17,7 +17,7 @@ dependencies: - randspg =0.0.1 - boto3 =1.34.122 - moto =5.0.9 -- pycp2k =0.2.1 +- pycp2k =0.2.2 - aws-sam-translator =1.77.0 - distributed =2024.7.1 - h5io_browser =0.0.16 From 46a29cca00a6171552cdb4b6828e7ab5bf74e534 Mon Sep 17 00:00:00 2001 From: pyiron-runner Date: Thu, 1 Aug 2024 06:58:35 +0000 Subject: [PATCH 20/29] [dependabot skip] Update env file --- .binder/environment.yml | 2 +- docs/environment.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.binder/environment.yml b/.binder/environment.yml index 04b9255b5e..96d00bead1 100644 --- a/.binder/environment.yml +++ b/.binder/environment.yml @@ -17,7 +17,7 @@ dependencies: - randspg =0.0.1 - boto3 =1.34.122 - moto =5.0.9 -- pycp2k =0.2.1 +- pycp2k =0.2.2 - aws-sam-translator =1.77.0 - distributed =2024.7.1 - h5io_browser =0.0.16 diff --git a/docs/environment.yml b/docs/environment.yml index 0e51539800..41fd99af66 100644 --- a/docs/environment.yml +++ b/docs/environment.yml @@ -23,7 +23,7 @@ dependencies: - randspg =0.0.1 - boto3 =1.34.122 - moto =5.0.9 -- pycp2k =0.2.1 +- pycp2k =0.2.2 - aws-sam-translator =1.77.0 - distributed =2024.7.1 - h5io_browser =0.0.16 From d675eacc06f4f85cd5c1e5e4fca1015a5d753d55 Mon Sep 17 00:00:00 2001 From: Marvin Poul Date: Thu, 1 Aug 2024 22:01:28 +0200 Subject: [PATCH 21/29] Update lammps notebook The example resource wants to use lmp, but lammps conda package provides lmp_mpi only. Maybe that changed recently? Also updated the notebook to not hard code my own filesystem paths anymore. Oops. --- notebooks/tinybase/Lammps.ipynb | 352 +++++++++++++++--- .../lammps/bin/run_lammps_default.sh | 2 +- 2 files changed, 308 insertions(+), 46 deletions(-) diff --git a/notebooks/tinybase/Lammps.ipynb b/notebooks/tinybase/Lammps.ipynb index 5dfdd87225..1d8188254f 100644 --- a/notebooks/tinybase/Lammps.ipynb +++ b/notebooks/tinybase/Lammps.ipynb @@ -8,18 +8,10 @@ "tags": [] }, "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/home/poul/pyiron/contrib/pyiron_contrib/__init__.py:9: UserWarning: pyiron module not found, importing Project from pyiron_base\n", - " warnings.warn(\"pyiron module not found, importing Project from pyiron_base\")\n" - ] - }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "49e565b4cb784276848f55d7ada29e56", + "model_id": "43a6621164964abab0c96113e4b9d35d", "version_major": 2, "version_minor": 0 }, @@ -66,13 +58,30 @@ { "cell_type": "code", "execution_count": 4, + "id": "aedb78ac-e1a9-499d-a8b6-d02326076655", + "metadata": {}, + "outputs": [], + "source": [ + "from pathlib import Path\n", + "cwd = Path.cwd()\n", + "if cwd.name == \"tinybase\":\n", + " # Then the notebook was started locally\n", + " notebook_dir = cwd\n", + "else:\n", + " # We are probably executing from papermill on the CI\n", + " notebook_dir = cwd / \"notebooks\" / \"tinybase\"" + ] + }, + { + "cell_type": "code", + "execution_count": 5, "id": "8c340f6c-c687-4461-9c33-f98b768773d6", "metadata": { "tags": [] }, "outputs": [], "source": [ - "state.settings.resource_paths.insert(0, '/home/poul/pyiron/contrib/notebooks/tinybase/resources')" + "state.settings.resource_paths.insert(0, str(notebook_dir / \"resources\"))" ] }, { @@ -85,7 +94,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 6, "id": "64c9b3d4-e6e1-4e21-86fc-318940c4c8e8", "metadata": { "tags": [] @@ -97,7 +106,7 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 7, "id": "df4de500-24f5-4160-933d-57cf3d0f15a6", "metadata": { "tags": [] @@ -109,7 +118,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 8, "id": "4e5c69d6-fee8-4166-8e06-ba8a2e58e707", "metadata": { "tags": [] @@ -129,7 +138,7 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 9, "id": "1056c4b6-603c-4603-8021-a89c64f84255", "metadata": { "scrolled": true, @@ -146,7 +155,7 @@ " '2003--Mendelev-M-I--Fe-2--LAMMPS--ipr3']" ] }, - "execution_count": 22, + "execution_count": 9, "metadata": {}, "output_type": "execute_result" } @@ -157,7 +166,7 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 10, "id": "a6af7f64-5435-40b1-b44c-960528fc0cc5", "metadata": { "tags": [] @@ -169,19 +178,66 @@ }, { "cell_type": "code", - "execution_count": 27, + "execution_count": 11, "id": "8a699e68-ad89-4d52-bdff-3b86d9624a4b", "metadata": { "tags": [] }, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n" + ] + } + ], "source": [ "ret, out = lmp.execute()" ] }, { "cell_type": "code", - "execution_count": 28, + "execution_count": 12, + "id": "c4e2d57f-9def-4ab4-a003-95bc4e245a1f", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "LammpsStaticOutput(forces=array([[-0.02987269, -0.00282932, -0.12843858],\n", + " [-0.15820356, 0.0453781 , -0.03744197],\n", + " [-0.18450471, -0.08204103, 0.07020649],\n", + " [-0.06351491, 0.03401585, 0.00719245],\n", + " [-0.0037588 , 0.1333546 , 0.1740541 ],\n", + " [ 0.05387634, -0.00118085, -0.09480989],\n", + " [ 0.07405356, 0.11763504, -0.20276011],\n", + " [ 0.02384882, -0.05766377, 0.10891183],\n", + " [ 0.04153901, -0.08675459, 0.09708118],\n", + " [ 0.00966064, 0.03839169, -0.03484355],\n", + " [ 0.11122156, -0.23955637, -0.05193921],\n", + " [ 0.10710042, -0.19785464, 0.08232861],\n", + " [-0.03485634, 0.2108871 , 0.10971198],\n", + " [-0.01956278, -0.10410639, -0.02254802],\n", + " [ 0.0187732 , 0.08581792, 0.07211624],\n", + " [ 0.05420023, 0.10650667, -0.14882155]]), energy_kin=0.0, energy_pot=-69.0339463780543)" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "out" + ] + }, + { + "cell_type": "code", + "execution_count": 13, "id": "8b837b3d-7bd0-4930-817b-d497e8ae1ead", "metadata": { "tags": [] @@ -193,7 +249,7 @@ "ReturnStatus(Code.DONE, None)" ] }, - "execution_count": 28, + "execution_count": 13, "metadata": {}, "output_type": "execute_result" } @@ -212,7 +268,7 @@ }, { "cell_type": "code", - "execution_count": 29, + "execution_count": 14, "id": "c4793e9e-b7f1-476f-807c-c313718ed49b", "metadata": { "tags": [] @@ -224,7 +280,7 @@ "-69.0339463780543" ] }, - "execution_count": 29, + "execution_count": 14, "metadata": {}, "output_type": "execute_result" } @@ -235,7 +291,7 @@ }, { "cell_type": "code", - "execution_count": 30, + "execution_count": 15, "id": "afe5c4a1-08ae-4e3a-bb0a-f501dacf4be4", "metadata": { "tags": [] @@ -247,7 +303,7 @@ "0.0" ] }, - "execution_count": 30, + "execution_count": 15, "metadata": {}, "output_type": "execute_result" } @@ -258,7 +314,7 @@ }, { "cell_type": "code", - "execution_count": 31, + "execution_count": 16, "id": "6b48188a-b84c-482a-9add-26d61a4e65f2", "metadata": { "tags": [] @@ -285,7 +341,7 @@ " [ 0.05420023, 0.10650667, -0.14882155]])" ] }, - "execution_count": 31, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" } @@ -306,7 +362,7 @@ }, { "cell_type": "code", - "execution_count": 34, + "execution_count": 17, "id": "cc50f529-e3bc-4f36-af63-f496f6c1405f", "metadata": { "tags": [] @@ -319,7 +375,7 @@ }, { "cell_type": "code", - "execution_count": 33, + "execution_count": 18, "id": "1fb9a556-d882-4b21-99fa-0fd30023d3f4", "metadata": { "tags": [] @@ -331,7 +387,7 @@ }, { "cell_type": "code", - "execution_count": 36, + "execution_count": 19, "id": "cab52837-17eb-4f33-8182-cb5e917d02ec", "metadata": { "tags": [] @@ -343,7 +399,7 @@ }, { "cell_type": "code", - "execution_count": 37, + "execution_count": 20, "id": "c95da0c4-fbdb-48d7-8086-f890f82c7725", "metadata": { "tags": [] @@ -357,7 +413,7 @@ }, { "cell_type": "code", - "execution_count": 38, + "execution_count": 21, "id": "edb93bf2-9e70-4717-9929-101a3101599b", "metadata": { "tags": [] @@ -369,18 +425,224 @@ }, { "cell_type": "code", - "execution_count": 39, + "execution_count": 22, "id": "9eab17d8-380a-4199-88b0-50910b5e5296", "metadata": { "tags": [] }, "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:186: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " df = pd.read_csv(StringIO(\"\".join(lines)), delim_whitespace=True)\n", + "/home/poul/micromamba/envs/pyiron_contrib/lib/python3.11/site-packages/pymatgen/io/lammps/outputs.py:75: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\\s+'`` instead\n", + " data = pd.read_csv(StringIO(\"\\n\".join(lines[9:])), names=data_head, delim_whitespace=True)\n" + ] + }, { "name": "stdout", "output_type": "stream", "text": [ - "CPU times: user 256 ms, sys: 634 ms, total: 890 ms\n", - "Wall time: 8.49 s\n" + "CPU times: user 559 ms, sys: 1.02 s, total: 1.57 s\n", + "Wall time: 19.9 s\n" ] } ], @@ -395,7 +657,7 @@ }, { "cell_type": "code", - "execution_count": 41, + "execution_count": 23, "id": "44ffaf29-f35c-451f-a3fd-9f342035569b", "metadata": { "tags": [] @@ -418,17 +680,17 @@ }, { "cell_type": "code", - "execution_count": 42, + "execution_count": 24, "id": "c6d3f82b-7acb-47f1-ab0c-c0380382e7a7", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "93594.71816845893" + "94700.42445783262" ] }, - "execution_count": 42, + "execution_count": 24, "metadata": {}, "output_type": "execute_result" } @@ -439,17 +701,17 @@ }, { "cell_type": "code", - "execution_count": 43, + "execution_count": 25, "id": "f8911ebd-bcc6-4696-89f4-498c60aad544", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "93594.71816845887" + "94700.42445783273" ] }, - "execution_count": 43, + "execution_count": 25, "metadata": {}, "output_type": "execute_result" } @@ -460,17 +722,17 @@ }, { "cell_type": "code", - "execution_count": 44, + "execution_count": 26, "id": "620c128d-fcd4-4842-8f49-cd6f7052b4c3", "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "Atoms(symbols='Fe8000', pbc=True, cell=[[-28.602047036763544, 28.602047036763544, 28.602047036763544], [28.602047036763544, -28.602047036763544, 28.602047036763544], [28.602047036763544, 28.602047036763544, -28.602047036763544]])" + "Atoms(symbols='Fe8000', pbc=True, cell=[[-28.71423903603843, 28.71423903603843, 28.71423903603843], [28.71423903603843, -28.71423903603843, 28.71423903603843], [28.71423903603843, 28.71423903603843, -28.71423903603843]])" ] }, - "execution_count": 44, + "execution_count": 26, "metadata": {}, "output_type": "execute_result" } @@ -496,7 +758,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.7" + "version": "3.11.8" } }, "nbformat": 4, diff --git a/notebooks/tinybase/resources/lammps/bin/run_lammps_default.sh b/notebooks/tinybase/resources/lammps/bin/run_lammps_default.sh index 49c0d35ebe..23e4136718 100755 --- a/notebooks/tinybase/resources/lammps/bin/run_lammps_default.sh +++ b/notebooks/tinybase/resources/lammps/bin/run_lammps_default.sh @@ -1,3 +1,3 @@ #!/usr/bin/env bash -lmp -in control.inp +lmp_mpi -in control.inp From 8d9c3b300729374881cf9b855004b0c90046134f Mon Sep 17 00:00:00 2001 From: samwaseda Date: Fri, 2 Aug 2024 06:01:11 +0000 Subject: [PATCH 22/29] follow chatgpt recommendation --- .github/workflows/push-pull.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/push-pull.yml b/.github/workflows/push-pull.yml index 85e3e6ccc7..3897434a58 100644 --- a/.github/workflows/push-pull.yml +++ b/.github/workflows/push-pull.yml @@ -10,6 +10,6 @@ on: jobs: pyiron: uses: pyiron/actions/.github/workflows/push-pull.yml@actions-3.2.1 - secrets: inherit with: - notebooks-env-files: .ci_support/environment.yml .ci_support/environment-notebooks.yml + notebooks-env-files: ".ci_support/environment.yml .ci_support/environment-notebooks.yml" + secrets: inherit From ce2932a3a583966eef1ae0e5d98d14ce11ed01ce Mon Sep 17 00:00:00 2001 From: samwaseda Date: Fri, 2 Aug 2024 06:18:19 +0000 Subject: [PATCH 23/29] revert last change because it didn't work --- .github/workflows/push-pull.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/push-pull.yml b/.github/workflows/push-pull.yml index 3897434a58..2c5f75b129 100644 --- a/.github/workflows/push-pull.yml +++ b/.github/workflows/push-pull.yml @@ -10,6 +10,6 @@ on: jobs: pyiron: uses: pyiron/actions/.github/workflows/push-pull.yml@actions-3.2.1 - with: - notebooks-env-files: ".ci_support/environment.yml .ci_support/environment-notebooks.yml" secrets: inherit + with: + notebooks-env-files: ci_support/environment.yml .ci_support/environment-notebooks.yml From 030a9475101bfce0c9c0984d606f37144068fd86 Mon Sep 17 00:00:00 2001 From: samwaseda Date: Fri, 2 Aug 2024 06:19:31 +0000 Subject: [PATCH 24/29] See what happens if there's only one env file --- .ci_support/environment-notebooks.yml | 22 ++++++++++++++++++++++ .github/workflows/push-pull.yml | 2 +- 2 files changed, 23 insertions(+), 1 deletion(-) diff --git a/.ci_support/environment-notebooks.yml b/.ci_support/environment-notebooks.yml index 7ec09ee166..5861e44c0e 100644 --- a/.ci_support/environment-notebooks.yml +++ b/.ci_support/environment-notebooks.yml @@ -5,3 +5,25 @@ dependencies: - lammps - nglview >=3.0.8 - pyiron-data >=0.0.25 + - ase =3.23.0 + - coveralls + - coverage + - codacy-coverage + - matplotlib =3.8.3 + - numpy =1.26.4 + - pyiron_base =0.9.10 + - pyiron_atomistics =0.6.9 + - pyiron_snippets =0.1.3 + - pyparsing =3.1.2 + - scipy =1.12.0 + - seaborn =0.13.2 + - scikit-image =0.24.0 + - randspg =0.0.1 + - boto3 =1.34.122 + - moto =5.0.9 + - pycp2k =0.2.2 + - aws-sam-translator =1.77.0 + - distributed =2024.7.1 + - h5io_browser =0.0.16 + - pymatgen =2024.5.1 + - pympipool =0.8.4 diff --git a/.github/workflows/push-pull.yml b/.github/workflows/push-pull.yml index 2c5f75b129..5adfcdedc5 100644 --- a/.github/workflows/push-pull.yml +++ b/.github/workflows/push-pull.yml @@ -12,4 +12,4 @@ jobs: uses: pyiron/actions/.github/workflows/push-pull.yml@actions-3.2.1 secrets: inherit with: - notebooks-env-files: ci_support/environment.yml .ci_support/environment-notebooks.yml + notebooks-env-files: .ci_support/environment-notebooks.yml From 0bb72bc8ea14f943c8b7cc79ac1c82a8e00b0fd9 Mon Sep 17 00:00:00 2001 From: pyiron-runner Date: Fri, 2 Aug 2024 06:19:54 +0000 Subject: [PATCH 25/29] [dependabot skip] Update env file --- .binder/environment.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.binder/environment.yml b/.binder/environment.yml index 96d00bead1..dc799a07a9 100644 --- a/.binder/environment.yml +++ b/.binder/environment.yml @@ -1,6 +1,10 @@ channels: - conda-forge dependencies: +- python >= 3.10 +- lammps +- nglview >=3.0.8 +- pyiron-data >=0.0.25 - ase =3.23.0 - coveralls - coverage @@ -23,7 +27,3 @@ dependencies: - h5io_browser =0.0.16 - pymatgen =2024.5.1 - pympipool =0.8.4 -- python >= 3.10 -- lammps -- nglview >=3.0.8 -- pyiron-data >=0.0.25 From dfb4ce53f95e6300f3cb774e51ec6abde584043e Mon Sep 17 00:00:00 2001 From: samwaseda Date: Fri, 2 Aug 2024 06:37:23 +0000 Subject: [PATCH 26/29] Revert "See what happens if there's only one env file" This reverts commit 030a9475101bfce0c9c0984d606f37144068fd86. --- .ci_support/environment-notebooks.yml | 22 ---------------------- .github/workflows/push-pull.yml | 2 +- 2 files changed, 1 insertion(+), 23 deletions(-) diff --git a/.ci_support/environment-notebooks.yml b/.ci_support/environment-notebooks.yml index 5861e44c0e..7ec09ee166 100644 --- a/.ci_support/environment-notebooks.yml +++ b/.ci_support/environment-notebooks.yml @@ -5,25 +5,3 @@ dependencies: - lammps - nglview >=3.0.8 - pyiron-data >=0.0.25 - - ase =3.23.0 - - coveralls - - coverage - - codacy-coverage - - matplotlib =3.8.3 - - numpy =1.26.4 - - pyiron_base =0.9.10 - - pyiron_atomistics =0.6.9 - - pyiron_snippets =0.1.3 - - pyparsing =3.1.2 - - scipy =1.12.0 - - seaborn =0.13.2 - - scikit-image =0.24.0 - - randspg =0.0.1 - - boto3 =1.34.122 - - moto =5.0.9 - - pycp2k =0.2.2 - - aws-sam-translator =1.77.0 - - distributed =2024.7.1 - - h5io_browser =0.0.16 - - pymatgen =2024.5.1 - - pympipool =0.8.4 diff --git a/.github/workflows/push-pull.yml b/.github/workflows/push-pull.yml index 5adfcdedc5..2c5f75b129 100644 --- a/.github/workflows/push-pull.yml +++ b/.github/workflows/push-pull.yml @@ -12,4 +12,4 @@ jobs: uses: pyiron/actions/.github/workflows/push-pull.yml@actions-3.2.1 secrets: inherit with: - notebooks-env-files: .ci_support/environment-notebooks.yml + notebooks-env-files: ci_support/environment.yml .ci_support/environment-notebooks.yml From b5288d336f0e2e27554f8c433bbba683db7711dd Mon Sep 17 00:00:00 2001 From: samwaseda Date: Fri, 2 Aug 2024 06:37:30 +0000 Subject: [PATCH 27/29] Revert "Revert "See what happens if there's only one env file"" This reverts commit dfb4ce53f95e6300f3cb774e51ec6abde584043e. --- .ci_support/environment-notebooks.yml | 22 ++++++++++++++++++++++ .github/workflows/push-pull.yml | 2 +- 2 files changed, 23 insertions(+), 1 deletion(-) diff --git a/.ci_support/environment-notebooks.yml b/.ci_support/environment-notebooks.yml index 7ec09ee166..5861e44c0e 100644 --- a/.ci_support/environment-notebooks.yml +++ b/.ci_support/environment-notebooks.yml @@ -5,3 +5,25 @@ dependencies: - lammps - nglview >=3.0.8 - pyiron-data >=0.0.25 + - ase =3.23.0 + - coveralls + - coverage + - codacy-coverage + - matplotlib =3.8.3 + - numpy =1.26.4 + - pyiron_base =0.9.10 + - pyiron_atomistics =0.6.9 + - pyiron_snippets =0.1.3 + - pyparsing =3.1.2 + - scipy =1.12.0 + - seaborn =0.13.2 + - scikit-image =0.24.0 + - randspg =0.0.1 + - boto3 =1.34.122 + - moto =5.0.9 + - pycp2k =0.2.2 + - aws-sam-translator =1.77.0 + - distributed =2024.7.1 + - h5io_browser =0.0.16 + - pymatgen =2024.5.1 + - pympipool =0.8.4 diff --git a/.github/workflows/push-pull.yml b/.github/workflows/push-pull.yml index 2c5f75b129..5adfcdedc5 100644 --- a/.github/workflows/push-pull.yml +++ b/.github/workflows/push-pull.yml @@ -12,4 +12,4 @@ jobs: uses: pyiron/actions/.github/workflows/push-pull.yml@actions-3.2.1 secrets: inherit with: - notebooks-env-files: ci_support/environment.yml .ci_support/environment-notebooks.yml + notebooks-env-files: .ci_support/environment-notebooks.yml From ea3c5f41db814032ae23aec7e6200a2668fafe21 Mon Sep 17 00:00:00 2001 From: samwaseda Date: Fri, 2 Aug 2024 06:38:21 +0000 Subject: [PATCH 28/29] Revert "Revert "Revert "See what happens if there's only one env file""" This reverts commit b5288d336f0e2e27554f8c433bbba683db7711dd. --- .ci_support/environment-notebooks.yml | 22 ---------------------- .github/workflows/push-pull.yml | 2 +- 2 files changed, 1 insertion(+), 23 deletions(-) diff --git a/.ci_support/environment-notebooks.yml b/.ci_support/environment-notebooks.yml index 5861e44c0e..7ec09ee166 100644 --- a/.ci_support/environment-notebooks.yml +++ b/.ci_support/environment-notebooks.yml @@ -5,25 +5,3 @@ dependencies: - lammps - nglview >=3.0.8 - pyiron-data >=0.0.25 - - ase =3.23.0 - - coveralls - - coverage - - codacy-coverage - - matplotlib =3.8.3 - - numpy =1.26.4 - - pyiron_base =0.9.10 - - pyiron_atomistics =0.6.9 - - pyiron_snippets =0.1.3 - - pyparsing =3.1.2 - - scipy =1.12.0 - - seaborn =0.13.2 - - scikit-image =0.24.0 - - randspg =0.0.1 - - boto3 =1.34.122 - - moto =5.0.9 - - pycp2k =0.2.2 - - aws-sam-translator =1.77.0 - - distributed =2024.7.1 - - h5io_browser =0.0.16 - - pymatgen =2024.5.1 - - pympipool =0.8.4 diff --git a/.github/workflows/push-pull.yml b/.github/workflows/push-pull.yml index 5adfcdedc5..2c5f75b129 100644 --- a/.github/workflows/push-pull.yml +++ b/.github/workflows/push-pull.yml @@ -12,4 +12,4 @@ jobs: uses: pyiron/actions/.github/workflows/push-pull.yml@actions-3.2.1 secrets: inherit with: - notebooks-env-files: .ci_support/environment-notebooks.yml + notebooks-env-files: ci_support/environment.yml .ci_support/environment-notebooks.yml From b1ca4207687ad4950f9f1cb97315c73e24e6d3d5 Mon Sep 17 00:00:00 2001 From: pyiron-runner Date: Fri, 2 Aug 2024 06:39:05 +0000 Subject: [PATCH 29/29] [dependabot skip] Update env file --- .binder/environment.yml | 29 ----------------------------- 1 file changed, 29 deletions(-) diff --git a/.binder/environment.yml b/.binder/environment.yml index dc799a07a9..e69de29bb2 100644 --- a/.binder/environment.yml +++ b/.binder/environment.yml @@ -1,29 +0,0 @@ -channels: -- conda-forge -dependencies: -- python >= 3.10 -- lammps -- nglview >=3.0.8 -- pyiron-data >=0.0.25 -- ase =3.23.0 -- coveralls -- coverage -- codacy-coverage -- matplotlib =3.8.3 -- numpy =1.26.4 -- pyiron_base =0.9.10 -- pyiron_atomistics =0.6.9 -- pyiron_snippets =0.1.3 -- pyparsing =3.1.2 -- scipy =1.12.0 -- seaborn =0.13.2 -- scikit-image =0.24.0 -- randspg =0.0.1 -- boto3 =1.34.122 -- moto =5.0.9 -- pycp2k =0.2.2 -- aws-sam-translator =1.77.0 -- distributed =2024.7.1 -- h5io_browser =0.0.16 -- pymatgen =2024.5.1 -- pympipool =0.8.4