Merge branch 'master' into local-spahm

Author: YAY-C

.github/workflows/python-package-conda-cache.yml

@@ -11,13 +11,12 @@ on:
   push:
     branches:
       - '*'
-
   pull_request:
     branches:
       - '*'
-
   schedule:
-    - cron: '0 0 * * *'
+    - cron: '0 0 * * 1'
+  workflow_dispatch:
 
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually

README.md

@@ -16,17 +16,16 @@ Q-stack
 
 ## About [↑](#contents)
 
-Q-stack is a stack of codes for dedicated pre- and post-processing tasks for Quantum Machine Learning (QML). It is a work in progress, and will be updated soon.
+Q-stack is a stack of codes for dedicated pre- and post-processing tasks for Quantum Machine Learning (QML). It is a work in progress. Stay tuned for updates!
 
 For now, we link to the relevant packages that will be incorporated (among others):
-- https://github.com/lcmd-epfl/azo-xcite-tools
-- https://github.com/lcmd-epfl/SPAHM
-- https://github.com/lcmd-epfl/RHO-Decomposition
-- https://github.com/lcmd-epfl/ml-density
-- https://github.com/lcmd-epfl/OTPD-basis
-
-Stay tuned for updates!
-
+- [x] https://github.com/lcmd-epfl/azo-xcite-tools
+- [x] https://github.com/lcmd-epfl/SPAHM
+- [x] https://github.com/lcmd-epfl/RHO-Decomposition
+- [ ] https://github.com/lcmd-epfl/ml-density
+- [x] https://github.com/lcmd-epfl/OTPD-basis
+- [x] https://github.com/lcmd-epfl/b2r2-reaction-rep
+      
 ## Install [↑](#contents)
 
 The installation of the library for python use can be done executing the following commands:
@@ -53,34 +52,45 @@ python example_opt.py
 ```
 python example_SPAHM.py
 ```
+- An example for the structure-based reaction representations ($B^2R^2$ and $\mathrm{SLATM}_d$) will follow shortly
 
 
 ## References [↑](#contents)
 
 * A. Fabrizio, A. Grisafi, B. Meyer, M. Ceriotti, and C. Corminboeuf,
-“Electron density learning of non-covalent systems”,
-Chem. Sci. **10**, 9492 (2019)
-[![DOI](https://img.shields.io/badge/DOI-10.1039%2FC9SC02696G-blue)](https://doi.org/10.1039/C9SC02696G)
+  “Electron density learning of non-covalent systems”,
+  Chem. Sci. **10**, 9492 (2019)
+  [![DOI](https://img.shields.io/badge/DOI-10.1039%2FC9SC02696G-blue)](https://doi.org/10.1039/C9SC02696G)
 
 * A. Fabrizio, K. R. Briling, D. D. Girardier, and C. Corminboeuf,
-“Learning on-top: regressing the on-top pair density for real-space visualization of electron correlation”,
-J. Chem. Phys. **153**, 204111 (2020)
-[![DOI](https://img.shields.io/badge/DOI-10.1063%2F5.0033326-blue)](https://doi.org/10.1063/5.0033326)
+  “Learning on-top: regressing the on-top pair density for real-space visualization of electron correlation”,
+  J. Chem. Phys. **153**, 204111 (2020)
+  [![DOI](https://img.shields.io/badge/DOI-10.1063%2F5.0033326-blue)](https://doi.org/10.1063/5.0033326)
 
 * S. Vela, A. Fabrizio, K. R. Briling, and C. Corminboeuf,
-“Machine-learning the transition density of the productive excited states of azo-dyes”
-J. Phys. Chem. Lett. **12**, 5957–5962 (2021).
-[![DOI](https://img.shields.io/badge/DOI-10.1021%2Facs.jpclett.1c01425-blue)](https://doi.org/10.1021/acs.jpclett.1c01425)
+  “Machine-learning the transition density of the productive excited states of azo-dyes”
+  J. Phys. Chem. Lett. **12**, 5957–5962 (2021)
+  [![DOI](https://img.shields.io/badge/DOI-10.1021%2Facs.jpclett.1c01425-blue)](https://doi.org/10.1021/acs.jpclett.1c01425)
 
 * K. R. Briling, A. Fabrizio, and C. Corminboeuf,
-“Impact of quantum-chemical metrics on the machine learning prediction of electron density”,
-J. Chem. Phys. **155**, 024107 (2021)
-[![DOI](https://img.shields.io/badge/DOI-10.1063/5.0055393-blue)](https://doi.org/10.1063/5.0055393)
+  “Impact of quantum-chemical metrics on the machine learning prediction of electron density”,
+  J. Chem. Phys. **155**, 024107 (2021)
+  [![DOI](https://img.shields.io/badge/DOI-10.1063/5.0055393-blue)](https://doi.org/10.1063/5.0055393)
 
 * A. Fabrizio, K. R. Briling, and C. Corminboeuf,
-“SPAHM: the Spectrum of Approximated Hamiltonian Matrices representations”,
-Digital Discovery, *1*, 286–294 (2022)
-[![DOI](https://img.shields.io/badge/DOI-10.1039/D1DD00050K-blue)](https://doi.org/10.1039/D1DD00050K)
+  “SPAHM: the Spectrum of Approximated Hamiltonian Matrices representations”,
+  Digital Discovery **1**, 286–294 (2022)
+  [![DOI](https://img.shields.io/badge/DOI-10.1039/D1DD00050K-blue)](https://doi.org/10.1039/D1DD00050K)
+
+* K. R. Briling, Y. Calvino Alonso, A. Fabrizio, and C. Corminboeuf,
+  “SPAHM(a,b): Encoding the Density Information from Guess Hamiltonian in Quantum Machine Learning Representations”,
+  J. Chem. Theory Comput. **20**, 1108–1117 (2024)
+  [![DOI](https://img.shields.io/badge/DOI-10.1021/acs.jctc.3c01040-blue)](https://doi.org/10.1021/acs.jctc.3c01040)
+
+* P. van Gerwen, A. Fabrizio, M. Wodrich, and C. Corminboeuf,
+  “Physics-based representations for machine learning properties of chemical reactions”,
+  Mach. Learn.: Sci. Technol. **3**, 045005 (2022)
+  [![DOI](https://img.shields.io/badge/DOI-10.1088/2632--2153/ac8f1a-blue)](https://doi.org/10.1088/2632-2153/ac8f1a)
 
 
 ## Acknowledgements [↑](#contents)

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/build/doctrees/environment.pickle

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 450e7a1e3bad33915566791df8961235
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/doctrees/index.doctree

@@ -0,0 +1,30 @@
+.. Q-stack documentation master file, created by
+   sphinx-quickstart on Wed Feb  1 16:22:53 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Q-stack's documentation!
+===================================
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
+
+   modules
+
+.. include:: ../../README.md
+   :parser: myst_parser.sphinx_
+
+
+To do List
+==========
+
+.. todolist::
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

docs/build/doctrees/modules.doctree

@@ -0,0 +1,7 @@
+qstack
+======
+
+.. toctree::
+   :maxdepth: 4
+
+   qstack

docs/build/doctrees/qstack.basis_opt.doctree

@@ -0,0 +1,29 @@
+qstack.basis\_opt package
+=========================
+
+Submodules
+----------
+
+qstack.basis\_opt.basis\_tools module
+-------------------------------------
+
+.. automodule:: qstack.basis_opt.basis_tools
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+qstack.basis\_opt.opt module
+----------------------------
+
+.. automodule:: qstack.basis_opt.opt
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: qstack.basis_opt
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/build/doctrees/qstack.doctree

@@ -0,0 +1,69 @@
+qstack.fields package
+=====================
+
+Submodules
+----------
+
+qstack.fields.decomposition module
+----------------------------------
+
+.. automodule:: qstack.fields.decomposition
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+qstack.fields.density2file module
+---------------------------------
+
+.. automodule:: qstack.fields.density2file
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+qstack.fields.dm module
+-----------------------
+
+.. automodule:: qstack.fields.dm
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+qstack.fields.excited module
+----------------------------
+
+.. automodule:: qstack.fields.excited
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+qstack.fields.hf\_otpd module
+-----------------------------
+
+.. automodule:: qstack.fields.hf_otpd
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+qstack.fields.hirshfeld module
+------------------------------
+
+.. automodule:: qstack.fields.hirshfeld
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+qstack.fields.moments module
+----------------------------
+
+.. automodule:: qstack.fields.moments
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: qstack.fields
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/build/doctrees/qstack.fields.doctree

@@ -0,0 +1,69 @@
+qstack.regression package
+=========================
+
+Submodules
+----------
+
+qstack.regression.condition module
+----------------------------------
+
+.. automodule:: qstack.regression.condition
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+qstack.regression.final\_error module
+-------------------------------------
+
+.. automodule:: qstack.regression.final_error
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+qstack.regression.hyperparameters module
+----------------------------------------
+
+.. automodule:: qstack.regression.hyperparameters
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+qstack.regression.kernel module
+-------------------------------
+
+.. automodule:: qstack.regression.kernel
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+qstack.regression.kernel\_utils module
+--------------------------------------
+
+.. automodule:: qstack.regression.kernel_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+qstack.regression.oos module
+----------------------------
+
+.. automodule:: qstack.regression.oos
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+qstack.regression.regression module
+-----------------------------------
+
+.. automodule:: qstack.regression.regression
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: qstack.regression
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/build/doctrees/qstack.regression.doctree

@@ -0,0 +1,56 @@
+qstack package
+==============
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   qstack.basis_opt
+   qstack.fields
+   qstack.regression
+   qstack.spahm
+
+Submodules
+----------
+
+qstack.compound module
+----------------------
+
+.. automodule:: qstack.compound
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+qstack.constants module
+-----------------------
+
+.. automodule:: qstack.constants
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+qstack.equio module
+-------------------
+
+.. automodule:: qstack.equio
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+qstack.tools module
+-------------------
+
+.. automodule:: qstack.tools
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: qstack
+   :members:
+   :undoc-members:
+   :show-inheritance: