%global _empty_manifest_terminate_build 0 Name: python-pyberny Version: 0.6.3 Release: 1 Summary: Molecular/crystal structure optimizer License: MPL-2.0 URL: https://github.com/jhrmnn/pyberny Source0: https://mirrors.nju.edu.cn/pypi/web/packages/48/22/fa2aa59c294449f13cbbbdc62c6e926bbd0379c6cf1a3d16e51e383f4316/pyberny-0.6.3.tar.gz BuildArch: noarch Requires: python3-numpy Requires: python3-pytest Requires: python3-coverage Requires: python3-sphinx Requires: python3-sphinxcontrib-katex Requires: python3-toml %description # PyBerny [![build](https://img.shields.io/travis/com/jhrmnn/pyberny/master.svg)](https://travis-ci.com/jhrmnn/pyberny) [![coverage](https://img.shields.io/codecov/c/github/jhrmnn/pyberny.svg)](https://codecov.io/gh/jhrmnn/pyberny) ![python](https://img.shields.io/pypi/pyversions/pyberny.svg) [![pypi](https://img.shields.io/pypi/v/pyberny.svg)](https://pypi.org/project/pyberny/) [![commits since](https://img.shields.io/github/commits-since/jhrmnn/pyberny/latest.svg)](https://github.com/jhrmnn/pyberny/releases) [![last commit](https://img.shields.io/github/last-commit/jhrmnn/pyberny.svg)](https://github.com/jhrmnn/pyberny/commits/master) [![license](https://img.shields.io/github/license/jhrmnn/pyberny.svg)](https://github.com/jhrmnn/pyberny/blob/master/LICENSE) [![code style](https://img.shields.io/badge/code%20style-black-202020.svg)](https://github.com/ambv/black) [![doi](https://img.shields.io/badge/doi-10.5281%2Fzenodo.3695037-blue)](http://doi.org/10.5281/zenodo.3695037) PyBerny is an optimizer of molecular geometries with respect to the total energy, using nuclear gradient information. In each step, it takes energy and Cartesian gradients as an input, and returns a new equilibrium structure estimate. The package implements a single optimization algorithm, which is an amalgam of several techniques, comprising the quasi-Newton method, redundant internal coordinates, an iterative Hessian approximation, a trust region scheme, and linear search. The algorithm is described in more detailed in the [documentation](https://jhrmnn.github.io/pyberny/algorithm.html). Several desirable features are missing at the moment but planned, some of them being actively worked on (help is always welcome): [crystal geometries](https://github.com/jhrmnn/pyberny/issues/5), [coordinate constraints](https://github.com/jhrmnn/pyberny/issues/14), [coordinate weighting](https://github.com/jhrmnn/pyberny/issues/32), [transition state search](https://github.com/jhrmnn/pyberny/issues/4). PyBerny is available in [PySCF](https://sunqm.github.io/pyscf/geomopt.html#pyberny), [ASE](https://wiki.fysik.dtu.dk/ase/dev/ase/optimize.html?highlight=berny#pyberny), and [QCEngine](http://docs.qcarchive.molssi.org/projects/QCEngine/en/latest/index.html?highlight=pyberny#backends). ## Installing Install and update using [Pip](https://pip.pypa.io/en/stable/quickstart/): ``` pip install -U pyberny ``` ## Example ```python from berny import Berny, geomlib optimizer = Berny(geomlib.readfile('geom.xyz')) for geom in optimizer: # get energy and gradients for geom optimizer.send((energy, gradients)) ``` ## Links - Documentation: https://jhrmnn.github.io/pyberny %package -n python3-pyberny Summary: Molecular/crystal structure optimizer Provides: python-pyberny BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-pyberny # PyBerny [![build](https://img.shields.io/travis/com/jhrmnn/pyberny/master.svg)](https://travis-ci.com/jhrmnn/pyberny) [![coverage](https://img.shields.io/codecov/c/github/jhrmnn/pyberny.svg)](https://codecov.io/gh/jhrmnn/pyberny) ![python](https://img.shields.io/pypi/pyversions/pyberny.svg) [![pypi](https://img.shields.io/pypi/v/pyberny.svg)](https://pypi.org/project/pyberny/) [![commits since](https://img.shields.io/github/commits-since/jhrmnn/pyberny/latest.svg)](https://github.com/jhrmnn/pyberny/releases) [![last commit](https://img.shields.io/github/last-commit/jhrmnn/pyberny.svg)](https://github.com/jhrmnn/pyberny/commits/master) [![license](https://img.shields.io/github/license/jhrmnn/pyberny.svg)](https://github.com/jhrmnn/pyberny/blob/master/LICENSE) [![code style](https://img.shields.io/badge/code%20style-black-202020.svg)](https://github.com/ambv/black) [![doi](https://img.shields.io/badge/doi-10.5281%2Fzenodo.3695037-blue)](http://doi.org/10.5281/zenodo.3695037) PyBerny is an optimizer of molecular geometries with respect to the total energy, using nuclear gradient information. In each step, it takes energy and Cartesian gradients as an input, and returns a new equilibrium structure estimate. The package implements a single optimization algorithm, which is an amalgam of several techniques, comprising the quasi-Newton method, redundant internal coordinates, an iterative Hessian approximation, a trust region scheme, and linear search. The algorithm is described in more detailed in the [documentation](https://jhrmnn.github.io/pyberny/algorithm.html). Several desirable features are missing at the moment but planned, some of them being actively worked on (help is always welcome): [crystal geometries](https://github.com/jhrmnn/pyberny/issues/5), [coordinate constraints](https://github.com/jhrmnn/pyberny/issues/14), [coordinate weighting](https://github.com/jhrmnn/pyberny/issues/32), [transition state search](https://github.com/jhrmnn/pyberny/issues/4). PyBerny is available in [PySCF](https://sunqm.github.io/pyscf/geomopt.html#pyberny), [ASE](https://wiki.fysik.dtu.dk/ase/dev/ase/optimize.html?highlight=berny#pyberny), and [QCEngine](http://docs.qcarchive.molssi.org/projects/QCEngine/en/latest/index.html?highlight=pyberny#backends). ## Installing Install and update using [Pip](https://pip.pypa.io/en/stable/quickstart/): ``` pip install -U pyberny ``` ## Example ```python from berny import Berny, geomlib optimizer = Berny(geomlib.readfile('geom.xyz')) for geom in optimizer: # get energy and gradients for geom optimizer.send((energy, gradients)) ``` ## Links - Documentation: https://jhrmnn.github.io/pyberny %package help Summary: Development documents and examples for pyberny Provides: python3-pyberny-doc %description help # PyBerny [![build](https://img.shields.io/travis/com/jhrmnn/pyberny/master.svg)](https://travis-ci.com/jhrmnn/pyberny) [![coverage](https://img.shields.io/codecov/c/github/jhrmnn/pyberny.svg)](https://codecov.io/gh/jhrmnn/pyberny) ![python](https://img.shields.io/pypi/pyversions/pyberny.svg) [![pypi](https://img.shields.io/pypi/v/pyberny.svg)](https://pypi.org/project/pyberny/) [![commits since](https://img.shields.io/github/commits-since/jhrmnn/pyberny/latest.svg)](https://github.com/jhrmnn/pyberny/releases) [![last commit](https://img.shields.io/github/last-commit/jhrmnn/pyberny.svg)](https://github.com/jhrmnn/pyberny/commits/master) [![license](https://img.shields.io/github/license/jhrmnn/pyberny.svg)](https://github.com/jhrmnn/pyberny/blob/master/LICENSE) [![code style](https://img.shields.io/badge/code%20style-black-202020.svg)](https://github.com/ambv/black) [![doi](https://img.shields.io/badge/doi-10.5281%2Fzenodo.3695037-blue)](http://doi.org/10.5281/zenodo.3695037) PyBerny is an optimizer of molecular geometries with respect to the total energy, using nuclear gradient information. In each step, it takes energy and Cartesian gradients as an input, and returns a new equilibrium structure estimate. The package implements a single optimization algorithm, which is an amalgam of several techniques, comprising the quasi-Newton method, redundant internal coordinates, an iterative Hessian approximation, a trust region scheme, and linear search. The algorithm is described in more detailed in the [documentation](https://jhrmnn.github.io/pyberny/algorithm.html). Several desirable features are missing at the moment but planned, some of them being actively worked on (help is always welcome): [crystal geometries](https://github.com/jhrmnn/pyberny/issues/5), [coordinate constraints](https://github.com/jhrmnn/pyberny/issues/14), [coordinate weighting](https://github.com/jhrmnn/pyberny/issues/32), [transition state search](https://github.com/jhrmnn/pyberny/issues/4). PyBerny is available in [PySCF](https://sunqm.github.io/pyscf/geomopt.html#pyberny), [ASE](https://wiki.fysik.dtu.dk/ase/dev/ase/optimize.html?highlight=berny#pyberny), and [QCEngine](http://docs.qcarchive.molssi.org/projects/QCEngine/en/latest/index.html?highlight=pyberny#backends). ## Installing Install and update using [Pip](https://pip.pypa.io/en/stable/quickstart/): ``` pip install -U pyberny ``` ## Example ```python from berny import Berny, geomlib optimizer = Berny(geomlib.readfile('geom.xyz')) for geom in optimizer: # get energy and gradients for geom optimizer.send((energy, gradients)) ``` ## Links - Documentation: https://jhrmnn.github.io/pyberny %prep %autosetup -n pyberny-0.6.3 %build %py3_build %install %py3_install install -d -m755 %{buildroot}/%{_pkgdocdir} if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi pushd %{buildroot} if [ -d usr/lib ]; then find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/lib64 ]; then find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/bin ]; then find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/sbin ]; then find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst fi touch doclist.lst if [ -d usr/share/man ]; then find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst fi popd mv %{buildroot}/filelist.lst . mv %{buildroot}/doclist.lst . %files -n python3-pyberny -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Wed May 31 2023 Python_Bot - 0.6.3-1 - Package Spec generated