svn commit: r479084 - in head/science: . mdynamix

[Yuri Victorovich]

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 at 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/