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authorCoprDistGit <infra@openeuler.org>2023-05-31 07:45:42 +0000
committerCoprDistGit <infra@openeuler.org>2023-05-31 07:45:42 +0000
commitd34a68574f928cbb1929e3db3f474fac7add2fa4 (patch)
treea0bfb670cfc92ccb36d81d305841f4e684e87392
parentecbf80ccb47eab00b4aba0e64c102ac7f08df9c6 (diff)
automatic import of python-pyberny
-rw-r--r--.gitignore1
-rw-r--r--python-pyberny.spec210
-rw-r--r--sources1
3 files changed, 212 insertions, 0 deletions
diff --git a/.gitignore b/.gitignore
index e69de29..da25509 100644
--- a/.gitignore
+++ b/.gitignore
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+/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
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+%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 <Python_Bot@openeuler.org> - 0.6.3-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..4be78c6
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+2b9fa70273995451f46d756b9cc5d103 pyberny-0.6.3.tar.gz