git: b57cde219d58 - main - science/py-pyberny: New port: Optimizer of molecular geometries with respect to the total energy

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=b57cde219d58fc7e96b13f8baa3ffa9860e1c26c

commit b57cde219d58fc7e96b13f8baa3ffa9860e1c26c
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2021-10-16 23:33:48 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2021-10-16 23:56:19 +0000

    science/py-pyberny: New port: Optimizer of molecular geometries with respect to the total energy
---
 science/Makefile             |  1 +
 science/py-pyberny/Makefile  | 24 ++++++++++++++++++++++++
 science/py-pyberny/distinfo  |  3 +++
 science/py-pyberny/pkg-descr | 12 ++++++++++++
 4 files changed, 40 insertions(+)

diff --git a/science/Makefile b/science/Makefile
index 76060442c7d4..294fdb4a0b19 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -242,6 +242,7 @@
     SUBDIR += py-asdf
     SUBDIR += py-ase
     SUBDIR += py-avogadrolibs
+    SUBDIR += py-pyberny
     SUBDIR += py-cdo
     SUBDIR += py-chainer
     SUBDIR += py-chainer-chemistry
diff --git a/science/py-pyberny/Makefile b/science/py-pyberny/Makefile
new file mode 100644
index 000000000000..c6a33367dd9c
--- /dev/null
+++ b/science/py-pyberny/Makefile
@@ -0,0 +1,24 @@
+PORTNAME=	pyberny
+DISTVERSION=	0.6.3
+CATEGORIES=	science # chemistry
+MASTER_SITES=	CHEESESHOP
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Optimizer of molecular geometries with respect to the total energy
+
+LICENSE=	MPL20
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+RUN_DEPENDS=	${PYNUMPY}
+TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR}
+
+USES=		python:3.5+
+USE_PYTHON=	distutils concurrent autoplist
+
+NO_ARCH=	yes
+
+do-test: install # no tests run, see https://github.com/jhrmnn/pyberny/issues/36
+	@cd ${WRKSRC} && pytest -rs --pyargs berny
+
+.include <bsd.port.mk>
diff --git a/science/py-pyberny/distinfo b/science/py-pyberny/distinfo
new file mode 100644
index 000000000000..8b9b0eb3b031
--- /dev/null
+++ b/science/py-pyberny/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1634426542
+SHA256 (pyberny-0.6.3.tar.gz) = b4bd9d3d2d58261e8f1d91b8204cc563617044d4b9daf6aae8feee31893cb336
+SIZE (pyberny-0.6.3.tar.gz) = 25628
diff --git a/science/py-pyberny/pkg-descr b/science/py-pyberny/pkg-descr
new file mode 100644
index 000000000000..0de3201f0703
--- /dev/null
+++ b/science/py-pyberny/pkg-descr
@@ -0,0 +1,12 @@
+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.
+
+WWW: https://github.com/jhrmnn/pyberny