Merge branch 'pr-madqc' of github.com:m-a-d-n-e-s-s/madness

.gitignore

@@ -1,6 +1,8 @@
 build*
 cmake-build-debug*
 .history*
+output_dir
+
 
 # Compiled Object files
 *.slo

src/apps/CMakeLists.txt

@@ -13,6 +13,7 @@ add_subdirectory(dirac)
 add_subdirectory(mp2)
 add_subdirectory(cc2)
 add_subdirectory(oep)
+add_subdirectory(madqc)
 add_subdirectory(znemo)
 add_subdirectory(zcis)
 #add_subdirectory(hf)

src/apps/madqc/CMakeLists.txt

@@ -0,0 +1,6 @@
+# src/apps/moldft
+
+add_mad_executable(madqc madqc.cc "MADchem")
+add_dependencies(applications-madness madqc)
+
+install(TARGETS madqc DESTINATION "${MADNESS_INSTALL_BINDIR}")

src/apps/madqc/doc/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 = .
+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)

src/apps/madqc/doc/conf.py

@@ -0,0 +1,62 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "maddft"
+copyright = "2024, Adrian Hurtado"
+author = "Adrian Hurtado"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+ "myst_parser",
+ "sphinx_copybutton",
+ "sphinxcontrib.bibtex",
+ "sphinx.ext.mathjax",
+]
+latex_engine = 'xelatex'
+latex_elements = {
+ 'preamble': r'''
+ \usepackage{physics},
+ '''
+}
+latex_additional_files = ['mra.sty']
+
+
+
+myst_enable_extensions = [
+ "dollarmath", # Allows $ symbols for math expressions
+ "amsmath", # Enables support for amsmath LaTeX environments
+ "deflist", # Enables definition lists
+
+ # add other extensions as needed
+]
+
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+source_suffix = {
+ ".rst": "restructuredtext",
+ ".md": "markdown",
+}
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+# html_theme = "alabaster"
+#html_theme = "pydata_sphinx_theme"
+html_theme = "sphinx_rtd_theme"
+
+
+#html_static_path = ["_static"]
+
+bibtex_bibfiles = ["references.bib"]
+bibtex_default_style = "plain"
+bibtex_reference_style = "label"

src/apps/madqc/doc/index.rst

@@ -0,0 +1,74 @@
+.. maddft documentation master file, created by
+ sphinx-quickstart on Tue Apr 30 14:32:26 2024.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+Welcome to madqc's documentation!
+==================================
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+
+ installation.rst
+ quickstart.rst
+ references.rst
+ usage/calculation_structure.rst
+ usage/qcengine_interface.rst
+ usage/response_properties.rst
+ usage/property_examples.rst
+
+Multiresolution Quantum Chemistry Interface
+-----------------------------------------------
+
+The goal of this project is to provide a unified interface for computing with the various quantum chemistry applications available within MADNESS.
+The motivation for this project is make MADNESS more accessible to the quantum chemistry community, providing them a platform to compute
+benchmark quality results with minimal effort. Towards easy access, we aim to make this interface compatible with QCEngine, given 
+users the ability define and run their computations from python jupyter notebooks.
+
+Currently, the interface is designed to work with :code:`moldft` and :code:`molresponse` in order to compute Hartree-Fock and DFT ground and response properties including excited states.
+Future work will include additional quantum chemistry methods.
+
+Why we need MADQCEngine?
+------------------------
+
+In the currently implemtation, all quantum chemistry methods are seperate executables, even though many of them depend on
+each other. For example, in order to compute a response property, which depends both on ground and response states, the current procedure
+is to first compute the ground state using :code:`moldft` and then compute the response property using :code:`molresponse`.
+To do this properly, a user necessarily needs to manage details such as
+where to place the response calculation in relation the ground state calculation, and how to pass the ground state calculation.
+Further complications arise when trying to compute response states at multiple frequencies, or higher order response properties which 
+depend on a mixture of multiple ground and response states. Currently the locations of all files where managed outside of the
+code base which can be a cumbersome process.
+
+Instead, MADQCEngine aims to provide a unified interface to manage all of these details for the user. The user can simply define their
+calculation, and the interface will manage the details of where to place the files in a consistent manner. Additionally, the interface
+will contain logic to manage the restart of files as well as whether or not to overwrite files during restarts. For ease of use,
+all outputs will be stored json files and will include a :code:`calc_paths.json` file which will contain the paths to all of the
+files generated during the calculation. 
+
+
+Getting Started
+---------------
+
+This documentation will guide you through the features, setup, and use of MADQCEngine. Here's how to get started:
+
+1. **Installation**: Learn how to install MyProject on your machine. See :doc:`installation`.
+2. **Quick Start**: Jump straight into using MyProject with our Quick Start guide. See :doc:`quickstart`.
+3. **Reponse Properties** Learn how to compute HF/DFT response properties. See :doc:`usage/response_properties`.
+4. **Calculation Structure** Learn how :code:`madqce` manages calculations and where to find the output files. See :doc:`usage/calculation_structure`.
+5. **Interfacing with QCEngine** Learn how to interface with QCEngine. See :doc:`usage/qcengine_interface`.
+6. **Property Examples** Learn how to compute specific properties using MADQCEngine. See :doc:`usage/property_examples`.
+
+Navigate through the documentation using the sidebar. Each section is designed to help you understand and use MyProject effectively.
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+
+

src/apps/madqc/doc/installation.rst

@@ -0,0 +1,4 @@
+Installation
+=============
+
+

src/apps/madqc/doc/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+ set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+ echo.
+ echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+ echo.installed, then set the SPHINXBUILD environment variable to point
+ echo.to the full path of the 'sphinx-build' executable. Alternatively you
+ echo.may add the Sphinx directory to PATH.
+ echo.
+ echo.If you don't have Sphinx installed, grab it from
+ echo.https://www.sphinx-doc.org/
+ exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd