Date: Thu, 6 Sep 2018 05:14:01 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r479084 - in head/science: . mdynamix Message-ID: <201809060514.w865E143027836@repo.freebsd.org>
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Author: yuri Date: Thu Sep 6 05:14:01 2018 New Revision: 479084 URL: https://svnweb.freebsd.org/changeset/ports/479084 Log: New port: science/mdynamix: General purpose molecular dynamics code Added: head/science/mdynamix/ head/science/mdynamix/Makefile (contents, props changed) head/science/mdynamix/distinfo (contents, props changed) head/science/mdynamix/pkg-descr (contents, props changed) Modified: head/science/Makefile Modified: head/science/Makefile ============================================================================== --- head/science/Makefile Thu Sep 6 03:40:36 2018 (r479083) +++ head/science/Makefile Thu Sep 6 05:14:01 2018 (r479084) @@ -124,6 +124,7 @@ SUBDIR += mcstas-comps SUBDIR += mcxtrace SUBDIR += mcxtrace-comps + SUBDIR += mdynamix SUBDIR += medit SUBDIR += meep SUBDIR += mei Added: head/science/mdynamix/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/mdynamix/Makefile Thu Sep 6 05:14:01 2018 (r479084) @@ -0,0 +1,28 @@ +# $FreeBSD$ + +PORTNAME= mdynamix +DISTVERSION= 5.2.8 +CATEGORIES= science +MASTER_SITES= http://www.fos.su.se/~sasha/${PORTNAME}/versions/ +DISTNAME= md${DISTVERSION:S/.//g} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= General purpose molecular dynamics code + +LICENSE= GPLv2+ + +LIB_DEPENDS= libmpich.so:net/mpich2 + +USES= fortran gmake + +ALL_TARGET= default mpi +MAKE_ARGS= FFLAGS="${FFLAGS} -ffast-math" LDFLAGS="${LDFLAGS}" +BINARY_ALIAS= make=gmake gfortran=gfortran${GCC_DEFAULT} + +PLIST_FILES= bin/md bin/mdp + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/md ${STAGEDIR}${PREFIX}/bin + ${INSTALL_PROGRAM} ${WRKSRC}/mdp ${STAGEDIR}${PREFIX}/bin + +.include <bsd.port.mk> Added: head/science/mdynamix/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/mdynamix/distinfo Thu Sep 6 05:14:01 2018 (r479084) @@ -0,0 +1,3 @@ +TIMESTAMP = 1536207685 +SHA256 (md528.tar.gz) = 0031a9c57b5b73072c53d10054b18b09e238b77d3cbc2c6dc54d4ff52df5d745 +SIZE (md528.tar.gz) = 3944145 Added: head/science/mdynamix/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/mdynamix/pkg-descr Thu Sep 6 05:14:01 2018 (r479084) @@ -0,0 +1,16 @@ +MDynaMix is a general purpose molecular dynamics code for simulations of +mixtures of rigid or flexible molecules, interacting by standard +molecular-mechanics force field including electrostatic and Lennard-Jones +potentials for electrostatic interactions as well as terms describing covalent +bonds, angles and dihedral angles. The program is well suited for simulations of +flexible molecules based on the double time step algorithm. Alternatively, rigid +bonds can be treated by the SHAKE algorithm. Algorithms for NVE, NVT, NPT and +anisotropic NPT ensembles are implemented. The long-range electrostatic +interactions are treated by the Ewald summation method, or alternatively by a +reation field or simple cutoff. The program can be run both in sequential and +parallel execution, in the latter case the MPI parallel environment is required. +From v.5.1 possibility for taking into account quantum motion of nuclei using +Path Integral approach is implemented. Expanded ensemble mode of simulations for +calculation of solvation free energies is added in v.5.2. + +WWW: http://www.fos.su.se/~sasha/mdynamix/
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