qclab 0.3.0a7__tar.gz

qclab-0.3.0a7/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

qclab-0.3.0a7/PKG-INFO

@@ -0,0 +1,297 @@
+Metadata-Version: 2.1
+Name: qclab
+Version: 0.3.0a7
+Summary: QC Lab: a python package for quantum-classical modeling.
+Author-email: Tempelaar Team <roel.tempelaar@northwestern.edu>
+License:                                  Apache License
+                                   Version 2.0, January 2004
+                                http://www.apache.org/licenses/
+        
+           TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+        
+           1. Definitions.
+        
+              "License" shall mean the terms and conditions for use, reproduction,
+              and distribution as defined by Sections 1 through 9 of this document.
+        
+              "Licensor" shall mean the copyright owner or entity authorized by
+              the copyright owner that is granting the License.
+        
+              "Legal Entity" shall mean the union of the acting entity and all
+              other entities that control, are controlled by, or are under common
+              control with that entity. For the purposes of this definition,
+              "control" means (i) the power, direct or indirect, to cause the
+              direction or management of such entity, whether by contract or
+              otherwise, or (ii) ownership of fifty percent (50%) or more of the
+              outstanding shares, or (iii) beneficial ownership of such entity.
+        
+              "You" (or "Your") shall mean an individual or Legal Entity
+              exercising permissions granted by this License.
+        
+              "Source" form shall mean the preferred form for making modifications,
+              including but not limited to software source code, documentation
+              source, and configuration files.
+        
+              "Object" form shall mean any form resulting from mechanical
+              transformation or translation of a Source form, including but
+              not limited to compiled object code, generated documentation,
+              and conversions to other media types.
+        
+              "Work" shall mean the work of authorship, whether in Source or
+              Object form, made available under the License, as indicated by a
+              copyright notice that is included in or attached to the work
+              (an example is provided in the Appendix below).
+        
+              "Derivative Works" shall mean any work, whether in Source or Object
+              form, that is based on (or derived from) the Work and for which the
+              editorial revisions, annotations, elaborations, or other modifications
+              represent, as a whole, an original work of authorship. For the purposes
+              of this License, Derivative Works shall not include works that remain
+              separable from, or merely link (or bind by name) to the interfaces of,
+              the Work and Derivative Works thereof.
+        
+              "Contribution" shall mean any work of authorship, including
+              the original version of the Work and any modifications or additions
+              to that Work or Derivative Works thereof, that is intentionally
+              submitted to Licensor for inclusion in the Work by the copyright owner
+              or by an individual or Legal Entity authorized to submit on behalf of
+              the copyright owner. For the purposes of this definition, "submitted"
+              means any form of electronic, verbal, or written communication sent
+              to the Licensor or its representatives, including but not limited to
+              communication on electronic mailing lists, source code control systems,
+              and issue tracking systems that are managed by, or on behalf of, the
+              Licensor for the purpose of discussing and improving the Work, but
+              excluding communication that is conspicuously marked or otherwise
+              designated in writing by the copyright owner as "Not a Contribution."
+        
+              "Contributor" shall mean Licensor and any individual or Legal Entity
+              on behalf of whom a Contribution has been received by Licensor and
+              subsequently incorporated within the Work.
+        
+           2. Grant of Copyright License. Subject to the terms and conditions of
+              this License, each Contributor hereby grants to You a perpetual,
+              worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+              copyright license to reproduce, prepare Derivative Works of,
+              publicly display, publicly perform, sublicense, and distribute the
+              Work and such Derivative Works in Source or Object form.
+        
+           3. Grant of Patent License. Subject to the terms and conditions of
+              this License, each Contributor hereby grants to You a perpetual,
+              worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+              (except as stated in this section) patent license to make, have made,
+              use, offer to sell, sell, import, and otherwise transfer the Work,
+              where such license applies only to those patent claims licensable
+              by such Contributor that are necessarily infringed by their
+              Contribution(s) alone or by combination of their Contribution(s)
+              with the Work to which such Contribution(s) was submitted. If You
+              institute patent litigation against any entity (including a
+              cross-claim or counterclaim in a lawsuit) alleging that the Work
+              or a Contribution incorporated within the Work constitutes direct
+              or contributory patent infringement, then any patent licenses
+              granted to You under this License for that Work shall terminate
+              as of the date such litigation is filed.
+        
+           4. Redistribution. You may reproduce and distribute copies of the
+              Work or Derivative Works thereof in any medium, with or without
+              modifications, and in Source or Object form, provided that You
+              meet the following conditions:
+        
+              (a) You must give any other recipients of the Work or
+                  Derivative Works a copy of this License; and
+        
+              (b) You must cause any modified files to carry prominent notices
+                  stating that You changed the files; and
+        
+              (c) You must retain, in the Source form of any Derivative Works
+                  that You distribute, all copyright, patent, trademark, and
+                  attribution notices from the Source form of the Work,
+                  excluding those notices that do not pertain to any part of
+                  the Derivative Works; and
+        
+              (d) If the Work includes a "NOTICE" text file as part of its
+                  distribution, then any Derivative Works that You distribute must
+                  include a readable copy of the attribution notices contained
+                  within such NOTICE file, excluding those notices that do not
+                  pertain to any part of the Derivative Works, in at least one
+                  of the following places: within a NOTICE text file distributed
+                  as part of the Derivative Works; within the Source form or
+                  documentation, if provided along with the Derivative Works; or,
+                  within a display generated by the Derivative Works, if and
+                  wherever such third-party notices normally appear. The contents
+                  of the NOTICE file are for informational purposes only and
+                  do not modify the License. You may add Your own attribution
+                  notices within Derivative Works that You distribute, alongside
+                  or as an addendum to the NOTICE text from the Work, provided
+                  that such additional attribution notices cannot be construed
+                  as modifying the License.
+        
+              You may add Your own copyright statement to Your modifications and
+              may provide additional or different license terms and conditions
+              for use, reproduction, or distribution of Your modifications, or
+              for any such Derivative Works as a whole, provided Your use,
+              reproduction, and distribution of the Work otherwise complies with
+              the conditions stated in this License.
+        
+           5. Submission of Contributions. Unless You explicitly state otherwise,
+              any Contribution intentionally submitted for inclusion in the Work
+              by You to the Licensor shall be under the terms and conditions of
+              this License, without any additional terms or conditions.
+              Notwithstanding the above, nothing herein shall supersede or modify
+              the terms of any separate license agreement you may have executed
+              with Licensor regarding such Contributions.
+        
+           6. Trademarks. This License does not grant permission to use the trade
+              names, trademarks, service marks, or product names of the Licensor,
+              except as required for reasonable and customary use in describing the
+              origin of the Work and reproducing the content of the NOTICE file.
+        
+           7. Disclaimer of Warranty. Unless required by applicable law or
+              agreed to in writing, Licensor provides the Work (and each
+              Contributor provides its Contributions) on an "AS IS" BASIS,
+              WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+              implied, including, without limitation, any warranties or conditions
+              of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+              PARTICULAR PURPOSE. You are solely responsible for determining the
+              appropriateness of using or redistributing the Work and assume any
+              risks associated with Your exercise of permissions under this License.
+        
+           8. Limitation of Liability. In no event and under no legal theory,
+              whether in tort (including negligence), contract, or otherwise,
+              unless required by applicable law (such as deliberate and grossly
+              negligent acts) or agreed to in writing, shall any Contributor be
+              liable to You for damages, including any direct, indirect, special,
+              incidental, or consequential damages of any character arising as a
+              result of this License or out of the use or inability to use the
+              Work (including but not limited to damages for loss of goodwill,
+              work stoppage, computer failure or malfunction, or any and all
+              other commercial damages or losses), even if such Contributor
+              has been advised of the possibility of such damages.
+        
+           9. Accepting Warranty or Additional Liability. While redistributing
+              the Work or Derivative Works thereof, You may choose to offer,
+              and charge a fee for, acceptance of support, warranty, indemnity,
+              or other liability obligations and/or rights consistent with this
+              License. However, in accepting such obligations, You may act only
+              on Your own behalf and on Your sole responsibility, not on behalf
+              of any other Contributor, and only if You agree to indemnify,
+              defend, and hold each Contributor harmless for any liability
+              incurred by, or claims asserted against, such Contributor by reason
+              of your accepting any such warranty or additional liability.
+        
+           END OF TERMS AND CONDITIONS
+        
+           APPENDIX: How to apply the Apache License to your work.
+        
+              To apply the Apache License to your work, attach the following
+              boilerplate notice, with the fields enclosed by brackets "[]"
+              replaced with your own identifying information. (Don't include
+              the brackets!)  The text should be enclosed in the appropriate
+              comment syntax for the file format. We also recommend that a
+              file or class name and description of purpose be included on the
+              same "printed page" as the copyright notice for easier
+              identification within third-party archives.
+        
+           Copyright [yyyy] [name of copyright owner]
+        
+           Licensed under the Apache License, Version 2.0 (the "License");
+           you may not use this file except in compliance with the License.
+           You may obtain a copy of the License at
+        
+               http://www.apache.org/licenses/LICENSE-2.0
+        
+           Unless required by applicable law or agreed to in writing, software
+           distributed under the License is distributed on an "AS IS" BASIS,
+           WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+           See the License for the specific language governing permissions and
+           limitations under the License.
+        
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Education
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX :: Linux
+Classifier: License :: OSI Approved :: Apache Software License
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: tqdm
+Requires-Dist: h5py
+Requires-Dist: numba
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: mpi4py; extra == "tests"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: pydata-sphinx-theme; extra == "docs"
+Requires-Dist: sphinx-design; extra == "docs"
+Requires-Dist: sphinx-togglebutton; extra == "docs"
+Requires-Dist: sphinxcontrib-mermaid; extra == "docs"
+Requires-Dist: graphviz; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
+
+QC Lab: A package for quantum-classical modeling
+================================================
+
+
+**QC Lab** is a Python package designed for implementing and executing quantum-classical (QC) dynamics simulations.
+It offers an environment for developing physical models and QC algorithms which enables algorithms and models to be combined arbitrarily.
+QC Lab comes with a variety of already implemented models and algorithms which we hope will encourage new researchers to explore the field of quantum-classical dynamics. Users that implement their own models and algorithms will have the opportunity to contribute them to QC Lab to form a growing library of quantum-classical dynamics tools.
+
+
+**QC Lab** is developed and maintained by the Tempelaar Team in the Chemistry Department of Northwestern University in Evanston, Illinois, USA.
+
+
+The documentation for QC Lab can be found at https://tempelaar-team.github.io/qclab/.
+
+
+Capabilities
+------------
+
+Dynamics Algorithms
+```````````````````
+
+The following algorithms are implemented making use of the complex-classical coordinate formalism established in [1].
+
+
+* Mean-field (Ehrenfest) dynamics [2]
+* Fewest-switches surface hopping (FSSH) dynamics [3]
+
+Model Systems
+`````````````
+
+* Spin-boson model [4]
+* Holstein lattice model [5]
+* Fenna-Matthews-Olson (FMO) complex [6, 7]
+
+
+Installing qclab
+-----------------
+
+QC Lab can be installed from the Python Package Index (PyPI) by executing::
+
+   pip install qclab
+
+To install QC Lab without h5py or numba support, execute::
+
+   pip install qclab --no-deps
+   pip install numpy tqdm
+
+QC Lab can be installed from source by downloading the repository and executing::
+
+   pip install ./
+
+from inside its topmost directory (where the `pyproject.toml` file is located).
+
+
+Bibliography
+------------
+
+1. Miyazaki, K.; Krotz, A.; Tempelaar, R. Mixed Quantum-Classical Dynamics under Arbitrary Unitary Basis Transformations. J. Chem. Theory Comput. 2024, 20 (15), 6500-6509. https://doi.org/10.1021/acs.jctc.4c00555
+2. Tully, J. C. Mixed Quantum–Classical Dynamics. Faraday Discuss. 1998, 110 (0), 407–419. https://doi.org/10.1039/A801824C.
+3. Hammes‐Schiffer, S.; Tully, J. C. Proton Transfer in Solution: Molecular Dynamics with Quantum Transitions. J. Chem. Phys. 1994, 101 (6), 4657–4667. https://doi.org/10.1063/1.467455.
+4. Tempelaar, R.; Reichman, D. R. Generalization of Fewest-Switches Surface Hopping for Coherences. The Journal of Chemical Physics 2018, 148 (10), 102309. https://doi.org/10.1063/1.5000843.
+5. Krotz, A.; Provazza, J.; Tempelaar, R. A Reciprocal-Space Formulation of Mixed Quantum–Classical Dynamics. J. Chem. Phys. 2021, 154 (22), 224101. https://doi.org/10.1063/5.0053177.
+6. Fenna, R. E. & Matthews, B. W. Chlorophyll arrangement in a bacteriochlorophyll protein from Chlorobium limicola. Nature 258, 573–577 (1975). https://doi.org/10.1038/258573a0.
+7. Mulvihill, E.; Lenn, K. M.; Gao, X.; Schubert, A.; Dunietz, B. D.; Geva, E. Simulating Energy Transfer Dynamics in the Fenna–Matthews–Olson Complex via the Modified Generalized Quantum Master Equation. The Journal of Chemical Physics 2021, 154 (20), 204109. https://doi.org/10.1063/5.0051101.

qclab-0.3.0a7/README.rst

@@ -0,0 +1,64 @@
+QC Lab: A package for quantum-classical modeling
+================================================
+
+
+**QC Lab** is a Python package designed for implementing and executing quantum-classical (QC) dynamics simulations.
+It offers an environment for developing physical models and QC algorithms which enables algorithms and models to be combined arbitrarily.
+QC Lab comes with a variety of already implemented models and algorithms which we hope will encourage new researchers to explore the field of quantum-classical dynamics. Users that implement their own models and algorithms will have the opportunity to contribute them to QC Lab to form a growing library of quantum-classical dynamics tools.
+
+
+**QC Lab** is developed and maintained by the Tempelaar Team in the Chemistry Department of Northwestern University in Evanston, Illinois, USA.
+
+
+The documentation for QC Lab can be found at https://tempelaar-team.github.io/qclab/.
+
+
+Capabilities
+------------
+
+Dynamics Algorithms
+```````````````````
+
+The following algorithms are implemented making use of the complex-classical coordinate formalism established in [1].
+
+
+* Mean-field (Ehrenfest) dynamics [2]
+* Fewest-switches surface hopping (FSSH) dynamics [3]
+
+Model Systems
+`````````````
+
+* Spin-boson model [4]
+* Holstein lattice model [5]
+* Fenna-Matthews-Olson (FMO) complex [6, 7]
+
+
+Installing qclab
+-----------------
+
+QC Lab can be installed from the Python Package Index (PyPI) by executing::
+
+   pip install qclab
+
+To install QC Lab without h5py or numba support, execute::
+
+   pip install qclab --no-deps
+   pip install numpy tqdm
+
+QC Lab can be installed from source by downloading the repository and executing::
+
+   pip install ./
+
+from inside its topmost directory (where the `pyproject.toml` file is located).
+
+
+Bibliography
+------------
+
+1. Miyazaki, K.; Krotz, A.; Tempelaar, R. Mixed Quantum-Classical Dynamics under Arbitrary Unitary Basis Transformations. J. Chem. Theory Comput. 2024, 20 (15), 6500-6509. https://doi.org/10.1021/acs.jctc.4c00555
+2. Tully, J. C. Mixed Quantum–Classical Dynamics. Faraday Discuss. 1998, 110 (0), 407–419. https://doi.org/10.1039/A801824C.
+3. Hammes‐Schiffer, S.; Tully, J. C. Proton Transfer in Solution: Molecular Dynamics with Quantum Transitions. J. Chem. Phys. 1994, 101 (6), 4657–4667. https://doi.org/10.1063/1.467455.
+4. Tempelaar, R.; Reichman, D. R. Generalization of Fewest-Switches Surface Hopping for Coherences. The Journal of Chemical Physics 2018, 148 (10), 102309. https://doi.org/10.1063/1.5000843.
+5. Krotz, A.; Provazza, J.; Tempelaar, R. A Reciprocal-Space Formulation of Mixed Quantum–Classical Dynamics. J. Chem. Phys. 2021, 154 (22), 224101. https://doi.org/10.1063/5.0053177.
+6. Fenna, R. E. & Matthews, B. W. Chlorophyll arrangement in a bacteriochlorophyll protein from Chlorobium limicola. Nature 258, 573–577 (1975). https://doi.org/10.1038/258573a0.
+7. Mulvihill, E.; Lenn, K. M.; Gao, X.; Schubert, A.; Dunietz, B. D.; Geva, E. Simulating Energy Transfer Dynamics in the Fenna–Matthews–Olson Complex via the Modified Generalized Quantum Master Equation. The Journal of Chemical Physics 2021, 154 (20), 204109. https://doi.org/10.1063/5.0051101.

qclab-0.3.0a7/pyproject.toml

@@ -0,0 +1,42 @@
+[build-system]
+requires = ["setuptools>=64,<75", "wheel", "build"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "qclab"
+version = "0.3.0a7"
+description = "QC Lab: a python package for quantum-classical modeling."
+readme = "README.rst"
+requires-python = ">=3.8"
+license = { file = "LICENSE" }
+authors = [{ name = "Tempelaar Team", email = "roel.tempelaar@northwestern.edu" }]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Education",
+    "Programming Language :: Python :: 3",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX :: Linux",
+    "License :: OSI Approved :: Apache Software License",
+]
+dependencies = [
+    "numpy",
+    "tqdm",
+    "h5py",
+    "numba",
+]
+
+[project.optional-dependencies]
+tests = [
+    "pytest",
+    "mpi4py",
+]
+docs = [
+    "sphinx",
+    "pydata-sphinx-theme",
+    "sphinx-design",
+    "sphinx-togglebutton",
+    "sphinxcontrib-mermaid",
+    "graphviz",
+    "sphinx-autodoc-typehints",
+]

qclab-0.3.0a7/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

qclab-0.3.0a7/src/qclab/__init__.py

@@ -0,0 +1,13 @@
+"""
+This module contains the QC Lab package initialization.
+"""
+
+from qclab.simulation import Simulation
+from qclab.variable import Variable
+from qclab.data import Data
+from qclab.model import Model
+from qclab.algorithm import Algorithm
+from qclab.constants import Constants
+from qclab.utils import configure_memory_logger
+
+configure_memory_logger()

qclab-0.3.0a7/src/qclab/algorithm.py

@@ -0,0 +1,43 @@
+"""
+This module contains the Algorithm class.
+"""
+
+import copy
+from qclab.constants import Constants
+
+
+class Algorithm:
+    """
+    Algorithm class for defining and executing algorithm recipes.
+    """
+
+    def __init__(self, default_settings=None, settings=None):
+        if settings is None:
+            settings = {}
+        if default_settings is None:
+            default_settings = {}
+        # Merge default settings with user-provided settings.
+        settings = {**default_settings, **settings}
+        # Construct a Constants object to hold settings.
+        self.settings = Constants()
+        # Put settings from the dictionary into the Constants object.
+        for key, val in settings.items():
+            setattr(self.settings, key, val)
+        # Copy the recipes and output variables to ensure they are not shared
+        # across instances.
+        self.initialization_recipe = copy.deepcopy(self.initialization_recipe)
+        self.update_recipe = copy.deepcopy(self.update_recipe)
+        self.collect_recipe = copy.deepcopy(self.collect_recipe)
+
+    initialization_recipe = []
+    update_recipe = []
+    collect_recipe = []
+
+    def execute_recipe(self, sim, state, parameters, recipe):
+        """
+        Carry out the given recipe for the simulation by running
+        each task in the recipe.
+        """
+        for func in recipe:
+            state, parameters = func(sim, state, parameters)
+        return state, parameters