diff --git a/.binder/environment.yml b/.binder/environment.yml index 4032b8e71..e69de29bb 100644 --- a/.binder/environment.yml +++ b/.binder/environment.yml @@ -1,29 +0,0 @@ -channels: -- conda-forge -dependencies: -- ase =3.23.0 -- coveralls -- coverage -- codacy-coverage -- matplotlib =3.8.3 -- numpy =1.26.4 -- pyiron_base =0.9.10 -- pyiron_atomistics =0.6.1 -- pyiron_snippets =0.1.1 -- 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 =2024.5.2 -- h5io_browser =0.0.17 -- pymatgen =2024.5.1 -- pympipool =0.8.4 -- python >= 3.10 -- lammps -- nglview >=3.0.8 -- pyiron-data >=0.0.25 diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml index 00ac57353..25a174c22 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 @@ -19,7 +19,7 @@ dependencies: - moto =5.0.9 - pycp2k =0.2.2 - aws-sam-translator =1.77.0 -- distributed =2024.5.2 -- h5io_browser =0.0.17 +- distributed =2024.7.1 +- h5io_browser =0.0.16 - pymatgen =2024.5.1 - pympipool =0.8.4 diff --git a/.github/workflows/daily.yml b/.github/workflows/daily.yml index d11a2a520..a49b18470 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-3.2.1 + secrets: inherit diff --git a/.github/workflows/dependabot-pr.yml b/.github/workflows/dependabot-pr.yml index d38fd9994..3db961f19 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 78c1d79ed..e327f50bf 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 da7c62ed3..ec38f35a5 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/push-pull.yml b/.github/workflows/push-pull.yml index 4d0b30bb7..2c5f75b12 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-3.2.1 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 diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index f5bcdd802..457fada64 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 199412095..a007af3d7 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 diff --git a/docs/environment.yml b/docs/environment.yml index 9003a0b55..41fd99af6 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 @@ -13,8 +14,8 @@ dependencies: - matplotlib =3.8.3 - numpy =1.26.4 - pyiron_base =0.9.10 -- pyiron_atomistics =0.6.1 -- pyiron_snippets =0.1.1 +- pyiron_atomistics =0.6.9 +- pyiron_snippets =0.1.3 - pyparsing =3.1.2 - scipy =1.12.0 - seaborn =0.13.2 @@ -24,7 +25,7 @@ dependencies: - moto =5.0.9 - pycp2k =0.2.2 - aws-sam-translator =1.77.0 -- distributed =2024.5.2 -- h5io_browser =0.0.17 +- distributed =2024.7.1 +- h5io_browser =0.0.16 - pymatgen =2024.5.1 - pympipool =0.8.4 diff --git a/notebooks/tinybase/Lammps.ipynb b/notebooks/tinybase/Lammps.ipynb index 5dfdd8722..1d8188254 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 49c0d35eb..23e413671 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 diff --git a/pyiron_contrib/atomistics/elastic/elastic.py b/pyiron_contrib/atomistics/elastic/elastic.py index d81870a39..c847a060f 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 """ diff --git a/pyiron_contrib/jobfactories/__init__.py b/pyiron_contrib/jobfactories/__init__.py index 8ecc2c18a..36af915a8 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()) diff --git a/setup.py b/setup.py index 8b82c77d8..2c2ac9654 100644 --- a/setup.py +++ b/setup.py @@ -54,10 +54,10 @@ 'moto==5.0.9' ], 'tinybase': [ - 'distributed==2024.5.2', + 'distributed==2024.7.1', 'pymatgen==2024.5.1', 'pympipool==0.8.4', - 'h5io_browser==0.0.17', + 'h5io_browser==0.0.16', ] }, cmdclass=versioneer.get_cmdclass(),