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author | CoprDistGit <infra@openeuler.org> | 2023-05-31 07:45:42 +0000 |
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committer | CoprDistGit <infra@openeuler.org> | 2023-05-31 07:45:42 +0000 |
commit | d34a68574f928cbb1929e3db3f474fac7add2fa4 (patch) | |
tree | a0bfb670cfc92ccb36d81d305841f4e684e87392 | |
parent | ecbf80ccb47eab00b4aba0e64c102ac7f08df9c6 (diff) |
automatic import of python-pyberny
-rw-r--r-- | .gitignore | 1 | ||||
-rw-r--r-- | python-pyberny.spec | 210 | ||||
-rw-r--r-- | sources | 1 |
3 files changed, 212 insertions, 0 deletions
@@ -0,0 +1 @@ +/pyberny-0.6.3.tar.gz diff --git a/python-pyberny.spec b/python-pyberny.spec new file mode 100644 index 0000000..1d323cd --- /dev/null +++ b/python-pyberny.spec @@ -0,0 +1,210 @@ +%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 + +[](https://travis-ci.com/jhrmnn/pyberny) +[](https://codecov.io/gh/jhrmnn/pyberny) + +[](https://pypi.org/project/pyberny/) +[](https://github.com/jhrmnn/pyberny/releases) +[](https://github.com/jhrmnn/pyberny/commits/master) +[](https://github.com/jhrmnn/pyberny/blob/master/LICENSE) +[](https://github.com/ambv/black) +[](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 + +[](https://travis-ci.com/jhrmnn/pyberny) +[](https://codecov.io/gh/jhrmnn/pyberny) + +[](https://pypi.org/project/pyberny/) +[](https://github.com/jhrmnn/pyberny/releases) +[](https://github.com/jhrmnn/pyberny/commits/master) +[](https://github.com/jhrmnn/pyberny/blob/master/LICENSE) +[](https://github.com/ambv/black) +[](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 + +[](https://travis-ci.com/jhrmnn/pyberny) +[](https://codecov.io/gh/jhrmnn/pyberny) + +[](https://pypi.org/project/pyberny/) +[](https://github.com/jhrmnn/pyberny/releases) +[](https://github.com/jhrmnn/pyberny/commits/master) +[](https://github.com/jhrmnn/pyberny/blob/master/LICENSE) +[](https://github.com/ambv/black) +[](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 <Python_Bot@openeuler.org> - 0.6.3-1 +- Package Spec generated @@ -0,0 +1 @@ +2b9fa70273995451f46d756b9cc5d103 pyberny-0.6.3.tar.gz |