This code is a modification of giorgiodomen/Supplementary_code_for_Quantum_Alchemy developed by Dr. Giorgio Domenichini. Please refer to articles related to the original code:
| Article | Authors | Title |
|---|---|---|
| J. Phys. Chem. 2022 | Giorgio Domenichini, O. Anatole von Lilienfeld | Alchemical geometry relaxation |
| arXiv 2023 | O. Anatole von Lilienfeld, Giorgio Domenichini | Even order contributions to relative energies vanish for antisymmetric perturbations |
| J. Phys. Chem. 2024 | Giorgio Domenichini | Extending the definition of atomic basis sets to atoms with fractional nuclear charge |
For the license, please refer to the LICENSE section.
AQA is also based on PySCF (pyscf/pyscf).
The license and notice files of PySCF is included in ./aqa/.
AQA is still under development and contain bugs.
Analytical alchemical energy derivatives up to the third order in Kohn-Sham density functional theory (KSDFT) as well as quantum alchemy-based rules and analysis methods are added. LDA, GGA, and global hybrid functionals are supported. AQA was used in the following work:
| Article | Authors | Title |
|---|---|---|
| arXiv 2025 | Takafumi Shiraogawa, Simon León Krug, Masahiro Ehara, O. Anatole von Lilienfeld | Antisymmetry rules of response properties in certain chemical spaces |
The following modifications are made for PySCF:
- SCF convergence criteria are modified for APDFT calculations.
- The analytical derivatives are implemented based on the implementation of PySCF.
git clone https://github.com/takafumi-shiraogawa/AQA
Please add a path of aqa/ to PYTHONPATH since the current version of AQA
is not packaged.
Generation of chemical space with unique molecules depends on QML (qmlcode/qml).
Please compile frepresentations.f90 in ./aqa/mini_qml/ with F2PY.
The example of the command can be found in ./aqa/mini_qml/compile.sh.
The license file of QML is included in ./aqa/mini_qml/.
To install the required packages, please use aqa_env.yml or run the following commands:
conda install -c pyscf pyscf
pip install basis_set_exchange
conda install scipy
conda install numpy
conda install matplotlib
conda install pandas
conda install xarray
pip install git+https://github.com/pyscf/properties
Only PySCF ver. 2.2 is tested. The older version of PySCF cannot be used.
Please add a path of properties/ to PYSCF_EXT_PATH.
This software is released under the MIT License and includes the license of the original code
giorgiodomen/Supplementary_code_for_Quantum_Alchemy
in LICENSE.
Jupyter Notebooks and Python files in ./test/aqa include, for example:
- Numerical validation of alchemical derivatives using CO and CH3OH with symmetrized or rotated- and translated- coordinates
(co/co.ipynb, co_rot-trans.ipynb, co_pcx2.ipynb, ch3oh/ch3oh.ipynb, ch3oh_rot-trans.ipynb,
co/hartree-fock/co.ipynb, co_rot-trans.ipynb, ch3oh/hartree-fock/ch3oh.ipynb, ch3oh_rot-trans.ipynb) - Alchemical perturbation density functional theory (APDFT) calculation of CO with reference N2
(n2/n2-co_apdft.ipynb, n2-co_apdft_hf.ipynb) - Alchemical relative energy estimate for N2-CO-BF
(co/co_relative-apdft.ipynb) - Alchemical even energy estimate for N2 with reference CO
(co/co_even_estimate.ipynb) - Alchemical calculator class
(co/co_alch_calc_class.ipynb, co/hartree-fock/co_alch_calc_class.ipynb, n2/n2-co_apdft_hf.ipynb) - Levy's estimate of relative energy E(N2) - E(BF)
(co/co_Levy.ipynb) - Specification of perturbed atoms
(ch3oh/ch3oh_rot-trans_atomlist.ipynb) - Calculations of BN-doped benzene derivatives
(benzene/benzene.ipynb, benzene_pcx2.ipynb, all_derivatives_pc2pcx2/all_benzene.ipynb) - Calculations of BN-doped toluene derivatives
(toluene/calc_aqa.py) - Efficient generation of chemical space of unique molecules
(toluene/efficient_gener_chem_space/efficient_gener_chem_space.py, benzene/efficient_gener_chem_space/gener_ccs.ipynb) - Identifying alchemical enantiomers and diastereomers
(toluene/classify_alchemical_isomers/test_classifier.ipynb, benzene/classify_alchemical_isomers/get_alchemical_enantiomers.py) - Relative energies between alchemical enantiomers and diastereomers
(benzene/relative_energies/calc_rel_ene.py, toluene/relative_energies/calc_rel_ene.py) - SCF calculations of electronic energies of multiple molecules
(co/multiple_scf/co_multiscf.ipynb)