- Update to 4.6.2

PR:		179208
Submitted by:	Ports Fury

4 files changed, 44 insertions, 3 deletions

diff --git a/science/gromacs/Makefile b/science/gromacs/Makefile
index b73828e3e11b..740e3387fd38 100644
--- a/science/gromacs/Makefile
+++ b/science/gromacs/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	gromacs
-PORTVERSION=	4.6.1
+PORTVERSION=	4.6.2
 CATEGORIES=	science
 MASTER_SITES=	ftp://ftp.gromacs.org/pub/gromacs/
 
diff --git a/science/gromacs/distinfo b/science/gromacs/distinfo
index 200af9e5de96..cd00132853d0 100644
--- a/science/gromacs/distinfo
+++ b/science/gromacs/distinfo
@@ -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 --git a/science/gromacs/files/patch-src__gmxlib__thread_mpi__atomic.c b/science/gromacs/files/patch-src__gmxlib__thread_mpi__atomic.c
new file mode 100644
index 000000000000..b5be4b19778c
--- /dev/null
+++ b/science/gromacs/files/patch-src__gmxlib__thread_mpi__atomic.c
@@ -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 --git a/science/gromacs/pkg-plist b/science/gromacs/pkg-plist
index 21af82da2853..19f42e3b81fd 100644
--- a/science/gromacs/pkg-plist
+++ b/science/gromacs/pkg-plist
@@ -256,6 +256,8 @@ include/gromacs/tgroup.h
 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 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 %%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 @@ libdata/pkgconfig/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.pc
 %%DATADIR%%/top/vdwradii.dat
 %%DATADIR%%/top/xlateat.dat
 @dirrm %%DATADIR%%/top/oplsaa.ff
+@dirrm %%DATADIR%%/top/gromos54a7.ff
 @dirrm %%DATADIR%%/top/gromos53a6.ff
 @dirrm %%DATADIR%%/top/gromos53a5.ff
 @dirrm %%DATADIR%%/top/gromos45a3.ff