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pyabacus

README.md

pyabacus: a Python interface for the ABACUS package

pyabacus is a Python interface for the ABACUS package, which provides a high-level Python API for interacting with the ABACUS library.

This project is built using pybind11 and scikit-build-core, so you can easily build the project and use it in your Python environment.

Now, pyabacus provides the following modules:

  • io: a module for input/output in pyabacus.
  • Cell: a module for the cell structure to bridge ModuleNAO in python module with users' input.
  • ModuleBase: a module for basic math functions.
  • ModuleNAO: a module for numerical atomic orbitals (NAO).
  • hsolver: a module for solving the Hamiltonian.

Installation

  • Create and activate a new conda env, e.g. conda create -n myenv python=3.8 & conda activate myenv.
  • Clone ABACUS main repository and cd abacus-develop/python/pyabacus.
  • Build pyabacus by pip install -v . or install test dependencies & build pyabacus by pip install .[test]. (Use pip install -v .[test] -i https://pypi.tuna.tsinghua.edu.cn/simple to accelerate installation process.)

CI Examples

There are examples for CI in .github/workflows. A simple way to produces binary "wheels" for all platforms is illustrated in the "wheels.yml" file, using .

Use pytest -v to run all the unit tests for pyabacus in the local machine.

$ cd tests/
$ pytest -v

Run python vis_nao.py to visualize the numerical orbital.

$ cd examples/
$ python vis_nao.py

Run python ex_s_rotate.py in examples to check the S matrix.

$ cd examples/
$ python ex_s_rotate.py
norm(S_e3 - S_numer) =  3.341208104032616e-15

Run python diago_matrix.py in examples to check the diagonalization of a matrix.

$ cd examples/
$ python diago_matrix.py

====== Calculating eigenvalues using davidson method... ======
eigenvalues calculated by pyabacus-davidson is: 
 [-0.38440611  0.24221155  0.31593272  0.53144616  0.85155108  1.06950154
  1.11142053  1.12462153]
eigenvalues calculated by scipy is: 
 [-0.38440611  0.24221155  0.31593272  0.53144616  0.85155108  1.06950154
  1.11142051  1.12462151]
eigenvalues difference: 
 [4.47258897e-12 5.67104697e-12 8.48299209e-12 1.08900666e-11
 1.87927451e-12 3.15688586e-10 2.11438165e-08 2.68884972e-08]

====== Calculating eigenvalues using dav_subspace method... ======
enter diag... is_subspace = 0, ntry = 0
eigenvalues calculated by pyabacus-dav_subspace is: 
 [-0.38440611  0.24221155  0.31593272  0.53144616  0.85155108  1.06950154
  1.11142051  1.12462153]
eigenvalues calculated by scipy is: 
 [-0.38440611  0.24221155  0.31593272  0.53144616  0.85155108  1.06950154
  1.11142051  1.12462151]
eigenvalues difference: 
 [ 4.64694949e-12  2.14706031e-12  1.09236509e-11  4.66293670e-13
 -8.94295749e-12  4.71351846e-11  5.39378986e-10  1.97244101e-08]

License

pybind11 is provided under a BSD-style license that can be found in the LICENSE file. By using, distributing, or contributing to this project, you agree to the terms and conditions of this license.

Test call

import pyabacus as m
s = m.ModuleBase.Sphbes()
s.sphbesj(1, 0.0)
0.0