ports/179208: science/gromacs: Update to version 4.6.2

[KATO Tsuguru]

>Number:         179208
>Category:       ports
>Synopsis:       science/gromacs: Update to version 4.6.2
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Sun Jun 02 18:10:00 UTC 2013
>Closed-Date:
>Last-Modified:
>Originator:     KATO Tsuguru
>Release:        FreeBSD 8.4-RELEASE i386
>Organization:
>Environment:
>Description:
- Update to version 4.6.2

New file:
files/patch-src__gmxlib__thread_mpi__atomic.c

>How-To-Repeat:
>Fix:

diff -urN /usr/ports/science/gromacs/Makefile science/gromacs/Makefile
--- /usr/ports/science/gromacs/Makefile	2013-04-24 01:03:03.000000000 +0900
+++ science/gromacs/Makefile	2013-06-03 00:00:00.000000000 +0900
@@ -2,7 +2,7 @@
 # $FreeBSD: head/science/gromacs/Makefile 316355 2013-04-23 14:20:25Z bapt $
 
 PORTNAME=	gromacs
-PORTVERSION=	4.6.1
+PORTVERSION=	4.6.2
 CATEGORIES=	science
 MASTER_SITES=	ftp://ftp.gromacs.org/pub/gromacs/
 
diff -urN /usr/ports/science/gromacs/distinfo science/gromacs/distinfo
--- /usr/ports/science/gromacs/distinfo	2013-03-25 04:19:44.000000000 +0900
+++ science/gromacs/distinfo	2013-06-03 00:00:00.000000000 +0900
@@ -1,2 +1,2 @@
-SHA256 (gromacs-4.6.1.tar.gz) = a0514b2a04ecac7461a67fc8edefa2b8eeaf22a25cd61c3348042dd077b077e6
-SIZE (gromacs-4.6.1.tar.gz) = 9975315
+SHA256 (gromacs-4.6.2.tar.gz) = 7bcccd15f02e7163455e1f342fc13e609e9088735b962d96afe0a79aaad92d4c
+SIZE (gromacs-4.6.2.tar.gz) = 10986082
diff -urN /usr/ports/science/gromacs/files/patch-src__gmxlib__thread_mpi__atomic.c science/gromacs/files/patch-src__gmxlib__thread_mpi__atomic.c
--- /usr/ports/science/gromacs/files/patch-src__gmxlib__thread_mpi__atomic.c	1970-01-01 09:00:00.000000000 +0900
+++ science/gromacs/files/patch-src__gmxlib__thread_mpi__atomic.c	2013-06-03 00:00:00.000000000 +0900
@@ -0,0 +1,17 @@
+--- src/gmxlib/thread_mpi/atomic.c.orig
++++ src/gmxlib/thread_mpi/atomic.c
+@@ -35,6 +35,14 @@
+    files.
+  */
+ 
++#ifdef HAVE_TMPI_CONFIG_H
++#include "tmpi_config.h"
++#endif
++
++#ifdef HAVE_CONFIG_H
++#include "config.h"
++#endif
++
+ #include "impl.h"
+ 
+ /* This file is only needed when no intrinsic atomic operations are present. */
diff -urN /usr/ports/science/gromacs/pkg-plist science/gromacs/pkg-plist
--- /usr/ports/science/gromacs/pkg-plist	2013-03-25 04:19:44.000000000 +0900
+++ science/gromacs/pkg-plist	2013-06-03 00:00:00.000000000 +0900
@@ -256,6 +256,8 @@
 include/gromacs/thread_mpi.h
 include/gromacs/thread_mpi/atomic.h
 include/gromacs/thread_mpi/atomic/cycles.h
+include/gromacs/thread_mpi/atomic/derived.h
+include/gromacs/thread_mpi/atomic/fujitsu_sparc64.h
 include/gromacs/thread_mpi/atomic/gcc.h
 include/gromacs/thread_mpi/atomic/gcc_ia64.h
 include/gromacs/thread_mpi/atomic/gcc_intrinsics.h
@@ -985,6 +987,27 @@
 %%DATADIR%%/top/gromos53a6.ff/tip3p.itp
 %%DATADIR%%/top/gromos53a6.ff/tip4p.itp
 %%DATADIR%%/top/gromos53a6.ff/watermodels.dat
+%%DATADIR%%/top/gromos54a7.ff/aminoacids.c.tdb
+%%DATADIR%%/top/gromos54a7.ff/aminoacids.hdb
+%%DATADIR%%/top/gromos54a7.ff/aminoacids.n.tdb
+%%DATADIR%%/top/gromos54a7.ff/aminoacids.r2b
+%%DATADIR%%/top/gromos54a7.ff/aminoacids.rtp
+%%DATADIR%%/top/gromos54a7.ff/aminoacids.vsd
+%%DATADIR%%/top/gromos54a7.ff/atomtypes.atp
+%%DATADIR%%/top/gromos54a7.ff/dppc.itp
+%%DATADIR%%/top/gromos54a7.ff/ff_dum.itp
+%%DATADIR%%/top/gromos54a7.ff/ffbonded.itp
+%%DATADIR%%/top/gromos54a7.ff/ffnonbonded.itp
+%%DATADIR%%/top/gromos54a7.ff/forcefield.doc
+%%DATADIR%%/top/gromos54a7.ff/forcefield.itp
+%%DATADIR%%/top/gromos54a7.ff/ions.itp
+%%DATADIR%%/top/gromos54a7.ff/popc.itp
+%%DATADIR%%/top/gromos54a7.ff/spc.itp
+%%DATADIR%%/top/gromos54a7.ff/spce.itp
+%%DATADIR%%/top/gromos54a7.ff/tip3p.itp
+%%DATADIR%%/top/gromos54a7.ff/tip4p.itp
+%%DATADIR%%/top/gromos54a7.ff/tmcl.itp
+%%DATADIR%%/top/gromos54a7.ff/watermodels.dat
 %%DATADIR%%/top/gurgle.dat
 %%DATADIR%%/top/ha-shift.dat
 %%DATADIR%%/top/highway.dat
@@ -1042,6 +1065,7 @@
 %%DATADIR%%/top/vdwradii.dat
 %%DATADIR%%/top/xlateat.dat
 @dirrm %%DATADIR%%/top/oplsaa.ff
+ at dirrm %%DATADIR%%/top/gromos54a7.ff
 @dirrm %%DATADIR%%/top/gromos53a6.ff
 @dirrm %%DATADIR%%/top/gromos53a5.ff
 @dirrm %%DATADIR%%/top/gromos45a3.ff
>Release-Note:
>Audit-Trail:
>Unformatted: