From nobody Sat Oct 16 23:56:28 2021 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id CC5D717F9491; Sat, 16 Oct 2021 23:56:30 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4HX0R15G5fz4kkH; Sat, 16 Oct 2021 23:56:29 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 88A1122CEE; Sat, 16 Oct 2021 23:56:28 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 19GNuS5O001972; Sat, 16 Oct 2021 23:56:28 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 19GNuSUe001971; Sat, 16 Oct 2021 23:56:28 GMT (envelope-from git) Date: Sat, 16 Oct 2021 23:56:28 GMT Message-Id: <202110162356.19GNuSUe001971@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: b57cde219d58 - main - science/py-pyberny: New port: Optimizer of molecular geometries with respect to the total energy List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: b57cde219d58fc7e96b13f8baa3ffa9860e1c26c Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=b57cde219d58fc7e96b13f8baa3ffa9860e1c26c commit b57cde219d58fc7e96b13f8baa3ffa9860e1c26c Author: Yuri Victorovich AuthorDate: 2021-10-16 23:33:48 +0000 Commit: Yuri Victorovich 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 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