Merge pull request #1 from RandomDefaultUser/multi-gpu

Adjustments to multiple GPU implementation

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.0
+current_version = 1.2.1
 commit = True
 tag = True
 sign_tags = True

.github/workflows/cpu-tests.yml

@@ -155,7 +155,7 @@ jobs:
           conda env export -n mala-cpu > env_1.yml
 
           # install mala package
-          pip --no-cache-dir install -e .[opt,test]
+          pip --no-cache-dir install -e .[opt,test] --no-build-isolation
 
       - name: Check if Conda environment meets the specified requirements
         shell: 'bash -c "docker exec -i mala-cpu bash < {0}"'

.pre-commit-config.yaml

@@ -0,0 +1,13 @@
+# https://black.readthedocs.io/en/stable/integrations/source_version_control.html
+
+repos:
+  # Using this mirror lets us use mypyc-compiled black, which is about 2x faster
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.4.0
+    hooks:
+      - id: black
+        # It is recommended to specify the latest version of Python
+        # supported by your project here, or alternatively use
+        # pre-commit's default_language_version, see
+        # https://pre-commit.com/#top_level-default_language_version
+        language_version: python3.12

CITATION.cff

@@ -1,17 +1,21 @@
 # YAML 1.2
-cff-version: 1.1.0
+cff-version: 1.2.1
 message: "If you use this software, please cite it using these metadata."
 authors:
+  - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
+    family-names: Cangi
+    given-names: Attila
+    orcid: https://orcid.org/0000-0001-9162-262X
+  - affiliation: "Sandia National Laboratories (SNL)"
+    family-names: Rajamanickam
+    given-names: Sivasankaran
+    orcid: https://orcid.org/0000-0002-5854-409X
   - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
     family-names: Brzoza
     given-names: Bartosz
   - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
     family-names: Callow
     given-names: Timothy J.
-  - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
-    family-names: Cangi
-    given-names: Attila
-    orcid: https://orcid.org/0000-0001-9162-262X
   - affiliation: "Oak Ridge National Laboratory (ORNL)"
     family-names: Ellis
     given-names: J. Austin
@@ -54,10 +58,6 @@ authors:
   - affiliation: "Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR)"
     family-names: Pöschel
     given-names: Franz
-  - affiliation: "Sandia National Laboratories (SNL)"
-    family-names: Rajamanickam
-    given-names: Sivasankaran
-    orcid: https://orcid.org/0000-0002-5854-409X
   - affiliation: "Nvidia Corporation"
     family-names: Romero
     given-names: Josh
@@ -83,12 +83,12 @@ authors:
     given-names: D. Jon
 
 
-date-released: 2022-10-18
+date-released: 2024-02-01
 keywords:
   - "machine-learning"
   - "dft"
 license: "BSD-3-Clause"
 repository-code: "https://github.com/mala-project/mala"
 title: MALA
 doi: 10.5281/zenodo.5557254 # This DOI represents all versions, and will always resolve to the latest one.
-version: 1.1.0
+version: 1.2.1

Copyright.txt

@@ -1,6 +1,6 @@
  ************************************************************************
 
-                        MALA v. 1.1.0
+                        MALA v. 1.2.1
 
  Under the terms of Contract DE-NA0003525 with NTESS,
  the U.S. Government retains certain rights in this software.

docs/source/CONTRIBUTE.md

@@ -90,6 +90,23 @@ the core development team.
 * If you're adding code that should be tested, add tests
 * If you're adding or modifying examples, make sure to add them to `test_examples.py`
 
+### Formatting code
+
+* MALA uses [`black`](https://github.com/psf/black) for code formatting
+* The `black` configuration is located in `pyproject.toml`, the `black` version
+  is specified in `.pre-commit-config.yaml`
+* Currently, no automatic code reformatting will be done in the CI, thus
+  please ensure that your code is properly formatted before creating a pull
+  request. We suggest to use [`pre-commit`](https://pre-commit.com/). You can
+
+  * manually run `pre-commit run -a` at any given time
+  * configure it to run before each commit by executing `pre-commit install`
+    once locally
+
+  Without `pre-commit`, please install the `black` version named in
+  `.pre-commit-config.yaml` and run `find -name "*.py" | xargs black` or just
+  `black my_modified_file.py`.
+
 ### Adding dependencies
 
 If you add additional dependencies, make sure to add them to `requirements.txt`
@@ -98,7 +115,6 @@ they are not.
 Further, in order for them to be available during the CI tests, make sure to 
 add _required_ dependencies to the appropriate environment files in folder `install/` and _extra_ requirements directly in the `Dockerfile` for the `conda` environment build.
 
-
 ## Pull Requests
 We actively welcome pull requests.
 1. Fork the repo and create your branch from `develop`

docs/source/advanced_usage/descriptors.rst

@@ -3,6 +3,11 @@
 Improved data conversion
 ========================
 
+As a general remark please be reminded that if you have not used LAMMPS
+for your first steps in MALA, and instead used the python-based descriptor
+calculation methods, we highly advise switching to LAMMPS for advanced/more
+involved examples (see  :ref:`installation instructions for LAMMPS <lammpsinstallation>`).
+
 Tuning descriptors
 ******************
 

docs/source/advanced_usage/predictions.rst

@@ -8,6 +8,11 @@ Predictions at scale in principle work just like the predictions shown
 in the basic guide. One has to set a few additional parameters to make
 optimal use of the hardware at hand.
 
+As a general remark please be reminded that if you have not used LAMMPS
+for your first steps in MALA, and instead used the python-based descriptor
+calculation methods, we highly advise switching to LAMMPS for advanced/more
+involved examples (see  :ref:`installation instructions for LAMMPS <lammpsinstallation>`).
+
 MALA ML-DFT models can be used for predictions at system sizes and temperatures
 larger resp. different from the ones they were trained on. If you want to make
 a prediction at a larger length scale then the ML-DFT model was trained on,

docs/source/basic_usage/more_data.rst

@@ -4,7 +4,7 @@ Data generation and conversion
 MALA operates on volumetric data. Volumetric data is stored in binary files.
 By default - and discussed here, in the introductory guide - this
 means ``numpy`` files (``.npy`` files). Advanced data storing techniques
-are :ref:`also available <openpmd data>`
+are :ref:`also available <openpmd data>`.
 
 Data generation
 ###############

docs/source/citing.rst

@@ -67,10 +67,19 @@ range, please cite the respective transferability studies:
 
 
             @article{MALA_temperaturetransfer,
-                title={Machine learning the electronic structure of matter across temperatures},
-                author={Fiedler, Lenz and Modine, Normand A and Miller, Kyle D and Cangi, Attila},
-                journal={arXiv preprint arXiv:2306.06032},
-                year={2023}
+                title = {Machine learning the electronic structure of matter across temperatures},
+                author = {Fiedler, Lenz and Modine, Normand A. and Miller, Kyle D. and Cangi, Attila},
+                journal = {Phys. Rev. B},
+                volume = {108},
+                issue = {12},
+                pages = {125146},
+                numpages = {16},
+                year = {2023},
+                month = {Sep},
+                publisher = {American Physical Society},
+                doi = {10.1103/PhysRevB.108.125146},
+                url = {https://link.aps.org/doi/10.1103/PhysRevB.108.125146}
             }
 
 
+

docs/source/conf.py

@@ -13,25 +13,31 @@
 import os
 import subprocess
 import sys
+
 # sys.path.insert(0, os.path.abspath('.'))
-sys.path.insert(0, os.path.abspath('../../'))
+sys.path.insert(0, os.path.abspath("../../"))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'Materials Learning Algorithms (MALA)'
-copyright = '2021 National Technology & Engineering Solutions of Sandia, ' \
-            'LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, ' \
-            'the U.S. Government retains certain rights in this software. ' \
-            'Attila Cangi, J. Austin Ellis, Lenz Fiedler, Daniel Kotik, ' \
-            'Normand Modine, Sivasankaran Rajamanickam, Steve Schmerler, Aidan Thompson'
+project = "Materials Learning Algorithms (MALA)"
+copyright = (
+    "2021 National Technology & Engineering Solutions of Sandia, "
+    "LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, "
+    "the U.S. Government retains certain rights in this software. "
+    "Attila Cangi, J. Austin Ellis, Lenz Fiedler, Daniel Kotik, "
+    "Normand Modine, Sivasankaran Rajamanickam, Steve Schmerler, Aidan Thompson"
+)
 
-author = 'Attila Cangi, J. Austin Ellis, Lenz Fiedler, Daniel Kotik, ' \
-         'Normand Modine, Sivasankaran Rajamanickam, Steve Schmerler, Aidan Thompson'
+author = (
+    "Attila Cangi, J. Austin Ellis, Lenz Fiedler, Daniel Kotik, "
+    "Normand Modine, Sivasankaran Rajamanickam, Steve Schmerler, Aidan Thompson"
+)
 
 # The version info for the project
-tag = subprocess.run(['git', 'describe', '--tags'], capture_output=True,
-                        text=True)
+tag = subprocess.run(
+    ["git", "describe", "--tags"], capture_output=True, text=True
+)
 version = tag.stdout.strip()
 
 
@@ -41,46 +47,47 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'myst_parser',
-    'sphinx_markdown_tables',
-    'sphinx_copybutton',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.githubpages',
+    "myst_parser",
+    "sphinx_markdown_tables",
+    "sphinx_copybutton",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
 ]
 
 napoleon_google_docstring = False
 napoleon_numpy_docstring = True
 
 autodoc_mock_imports = [
-    'ase',
-    'optuna',
-    'mpmath',
-    'torch',
-    'numpy',
-    'scipy',
-    'oapackage',
-    'matplotlib',
-    'horovod',
-    'lammps',
-    'total_energy',
-    'pqkmeans',
-    'dftpy',
-    'asap3',
-    'openpmd_io'
+    "ase",
+    "optuna",
+    "mpmath",
+    "torch",
+    "numpy",
+    "scipy",
+    "oapackage",
+    "matplotlib",
+    "horovod",
+    "lammps",
+    "total_energy",
+    "pqkmeans",
+    "dftpy",
+    "asap3",
+    "openpmd_io",
+    "skspatial",
 ]
 
 myst_heading_anchors = 3
 
-autodoc_member_order = 'groupwise'
+autodoc_member_order = "groupwise"
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['templates']
+templates_path = ["templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -93,30 +100,30 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_logo = "./img/logos/mala_horizontal_white.png"
 
 html_context = {
-  'display_github': True,
-  'github_repo': 'mala-project/mala',
-  'github_version': 'develop',
-  'conf_py_path': '/docs/source/',
+    "display_github": True,
+    "github_repo": "mala-project/mala",
+    "github_version": "develop",
+    "conf_py_path": "/docs/source/",
 }
 
 html_theme_options = {
-    'logo_only': True,
-    'display_version': False,
+    "logo_only": True,
+    "display_version": False,
 }
-html_static_path = ['_static']
+html_static_path = ["_static"]
 # html_static_path = []
 html_css_files = ["css/custom.css"]
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = "./img/logos/mala_vertical.png"
+# html_logo = "./img/logos/mala_vertical.png"
 
 # The name of an image file (relative to this directory) to use as a favicon of
 # the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
@@ -125,12 +132,9 @@
 
 # The suffix of source file names.
 source_suffix = {
-    '.rst': 'restructuredtext',
-    '.txt': 'markdown',
-    '.md': 'markdown',
+    ".rst": "restructuredtext",
+    ".txt": "markdown",
+    ".md": "markdown",
 }
 
 add_module_names = False
-
-
-

docs/source/index.md

@@ -93,11 +93,12 @@ MALA has been employed in various publications, showcasing its versatility and e
     data calculated for hundreds of atoms, MALA can predict the electronic
     structure of up to 100'000 atoms.
 
-- [Machine learning the electronic structure of matter across temperatures](https://doi.org/10.48550/arXiv.2306.06032) (arXiv preprint)
+- [Machine learning the electronic structure of matter across temperatures](https://doi.org/10.1103/PhysRevB.108.125146) (Phys. Rev. B)
   by L. Fiedler, N. A. Modine, K. D. Miller, A. Cangi
 
-  - Currently in the preprint stage. Shown here is the temperature 
-    tranferability of MALA models.
+  - This publication shows how MALA models can be employed across temperature 
+    ranges. It is demonstrated how such models account for both ionic and
+    electronic temperature effects of materials.
 
 
 

docs/source/install/installing_lammps.rst

@@ -1,3 +1,5 @@
+.. _lammpsinstallation:
+
 Installing LAMMPS
 ==================