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Release v0.1.4 (#21)
* update custom pytree node auxdata for safe compare * add fast moleintor vjp, dot_eri_dm vjp * dynamic config * add scipy * add int2e restore * add dfmp2, dfccsd * add iao; update dfmp2 * add rccsd energy * add ccsd symmetry * add _ao2mo * simplify ccsd_t_slow * add optimized ccsd_t * add timer * update eigh; add svd, lowdin jvp * add DF.loop * add df_jk_opt * add ao2mo.nr_e2_opt * avoid df.DF create tmp files * disable jit for ccsd which causes memory leak * update unpack_tril * update pack_tril * add jax scan version of dfmp2 * add boys localization * update implicit_diff, add boys, pipek-mezey * add cphf, mp2 rdm1 * drop support for python 3.7 * drop dependence on jaxopt * add pyscfadlib * add dcsd * add iterative t3 solver * test lo symmetry * update lo, add geomopt * fix basis exp and ctr_coeff derivative * improve eval_gto performance * add eval_gto ctr_coeff gradient * add eval_gto exponent gradient * refactor moleintor
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‎.github/workflows/build_pyscf_linux.sh‎

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@@ -16,7 +16,7 @@ sudo apt-get -qq install \
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cmake
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cd pyscf/pyscf/lib
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curl -L "https://github.com/fishjojo/pyscf-deps/blob/master/pyscf-2.1.0-ad-deps.tar.gz?raw=true" | tar xzf -
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curl -L "https://github.com/fishjojo/pyscf-deps/blob/master/pyscf-2.1.1-ad-deps.tar.gz?raw=true" | tar xzf -
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mkdir build; cd build
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cmake -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF -DBUILD_LIBCINT=OFF ..
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make -j4

‎.github/workflows/install_pyscf.sh‎

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#!/usr/bin/env bash
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python -m pip install --upgrade pip
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python -m pip cache purge
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pip install wheel
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pip install numpy
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pip install 'scipy<1.11'
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pip install 'scipy<1.12'
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pip install h5py
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pip install typing_extensions
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pip install jaxlib jax jaxopt
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pip install pytest pytest-cov
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pip install jaxlib
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pip install jax
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pip install pytest
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pip install pytest-cov
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#pyscf
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git clone https://github.com/fishjojo/pyscf.git
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cd pyscf; git checkout v2.1.1-ad; cd ..
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if [ "$RUNNER_OS" == "Linux" ]; then
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os='linux'
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elif [ "$RUNNER_OS" == "macOS" ]; then
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os='macos'
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else
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echo "$RUNNER_OS not supported"
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exit 1
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fi
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./.github/workflows/build_pyscf_"$os".sh
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pip install 'pyscf==2.3'
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pip install 'pyscfadlib==0.1.4'

‎.github/workflows/lint.sh‎

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export OMP_NUM_THREADS=1
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export PYTHONPATH=$(pwd):$(pwd)/pyscf:$PYTHONPATH
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echo "pyscfad = True" >> $HOME/.pyscf_conf.py
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echo "pyscf_numpy_backend = 'jax'" >> $HOME/.pyscf_conf.py
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echo "pyscf_scipy_linalg_backend = 'pyscfad'" >> $HOME/.pyscf_conf.py
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echo "pyscf_scipy_backend = 'jax'" >> $HOME/.pyscf_conf.py
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pylint pyscfad

‎.github/workflows/pylint.yml‎

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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python 3.7
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- name: Set up Python 3.11
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uses: actions/setup-python@v2
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with:
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python-version: 3.7
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python-version: 3.11
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- name: install pyscf
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run: ./.github/workflows/install_pyscf.sh
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- name: install pylint
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run: pip install pylint
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run: pip install 'pylint==2.17.7'
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- name: style check
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run: ./.github/workflows/lint.sh

‎.github/workflows/run_test.sh‎

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#!/usr/bin/env bash
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export OMP_NUM_THREADS=1
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export PYTHONPATH=$(pwd):$(pwd)/pyscf:$PYTHONPATH
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# preload MKL
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#if [[ -n "${MKLROOT}" ]]; then
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# export LD_PRELOAD=$MKLROOT/lib/intel64/libmkl_avx2.so:$MKLROOT/lib/intel64/libmkl_sequential.so:$MKLROOT/lib/intel64/libmkl_core.so
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#fi
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echo "pyscfad = True" >> $HOME/.pyscf_conf.py
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echo "pyscf_numpy_backend = 'jax'" >> $HOME/.pyscf_conf.py
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echo "pyscf_scipy_linalg_backend = 'pyscfad'" >> $HOME/.pyscf_conf.py
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echo "pyscf_scipy_backend = 'jax'" >> $HOME/.pyscf_conf.py
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echo "pyscfad_scf_implicit_diff = True" >> $HOME/.pyscf_conf.py
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echo "pyscfad_ccsd_implicit_diff = True" >> $HOME/.pyscf_conf.py
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#echo "pyscf_numpy_backend = 'jax'" >> $HOME/.pyscf_conf.py
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#echo "pyscf_scipy_linalg_backend = 'pyscfad'" >> $HOME/.pyscf_conf.py
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#echo "pyscf_scipy_backend = 'jax'" >> $HOME/.pyscf_conf.py
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cd pyscfad
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pytest --cov-report xml --cov=. --verbosity=1 --durations=10
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pytest ./pyscfad --cov-report xml --cov=. --verbosity=1 --durations=10

‎.pylintrc‎

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deprecated-method,
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arguments-out-of-order,
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consider-using-in,
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invalid-unary-operand-type,
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[REPORTS]

‎LICENSE‎

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MIT License
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Copyright (c) 2021-2023 Xing Zhang
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Copyright (c) 2021-2024 Xing Zhang
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal

‎MANIFEST.in‎

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include MANIFEST.in
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include README.md setup.py LICENSE
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prune pyscfad/lib/build
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include pyscfad/geomopt/log.ini
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include pyscfad/lib/*.so
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include pyscfad/lib/*.dylib
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recursive-include pyscfad/lib *.c *.h
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global-exclude *.py[cod]

‎README.md‎

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Installation
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------------
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---
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* To install the latest release, run:
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```
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pip install pyscfad
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```
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---
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* To install the development version, use the following command instead:
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* To install the development version, run:
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```
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pip install git+https://github.com/fishjojo/pyscfad.git
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```
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This should also install all the dependencies.
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Alternatively, the dependencies can be installed via a predefined conda environment:
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```
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conda env create -f environment.yml
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conda activate pyscfad_env
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```
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OpenMP is not required, but is recommended:
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```
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# install OpenMP runtime used with clang
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# On Linux:
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sudo apt update
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sudo apt install libomp-dev
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# On OSX:
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brew install libomp
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```
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---
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* One can also run PySCFAD inside a docker container:
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```
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docker pull fishjojo/pyscfad:latest
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docker run -rm -t -i fishjojo/pyscfad:latest /bin/bash
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```
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`pyscfad` depends on `pyscf==2.3.0`.
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Other dependencies include
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`numpy>=1.17`, `scipy<1.12`, `h5py`,
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`pyscfadlib`,
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`jax>=0.3.25` and `jaxlib>=0.3.25`.
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Running examples
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----------------
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the PySCF configure file ($HOME/.pyscf\_conf.py)
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```
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pyscfad = True
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pyscf_numpy_backend = 'jax'
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pyscf_scipy_linalg_backend = 'pyscfad'
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pyscf_scipy_backend = 'jax'
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# The followings turn on implicit differentiations
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# for SCF and CC amplitude solvers
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pyscfad_scf_implicit_diff = True
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pyscfad_ccsd_implicit_diff = True
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```
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Citing PySCFAD

‎environment.yml‎

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