[Debichem-commits] r1558 - in /unstable/gromacs/debian: changelog patches/00list patches/50_type2bonds.dpatch

[nbreen-guest at users.alioth.debian.org]

Author: nbreen-guest
Date: Wed Nov 26 22:04:22 2008
New Revision: 1558

URL: http://svn.debian.org/wsvn/debichem/?sc=1&rev=1558
Log:
debian/patches/50_type2bonds.dpatch: Fix grompp freeze when using type 2 bonds (G96) and all-angle constraints.  (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=261)


Added:
    unstable/gromacs/debian/patches/50_type2bonds.dpatch   (with props)
Modified:
    unstable/gromacs/debian/changelog
    unstable/gromacs/debian/patches/00list

Modified: unstable/gromacs/debian/changelog
URL: http://svn.debian.org/wsvn/debichem/unstable/gromacs/debian/changelog?rev=1558&op=diff
==============================================================================
--- unstable/gromacs/debian/changelog (original)
+++ unstable/gromacs/debian/changelog Wed Nov 26 22:04:22 2008
@@ -1,8 +1,11 @@
-gromacs (4.0.2-2) unstable; urgency=low
+gromacs (4.0.2-2) UNRELEASED; urgency=low
 
   * debian/*.postinst: Resort update-alternatives priorities for the MPI
     packages to follow the newly proposed priorities of the individual
     MPI implementations themselves, OpenMPI > MPICH > LAM.
+  * debian/patches/50_type2bonds.dpatch: Fix grompp freeze when using
+    type 2 bonds (G96) and all-angle constraints.
+    (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=261)
 
  -- Nicholas Breen <nbreen at ofb.net>  Wed, 19 Nov 2008 10:07:34 -0800
 

Modified: unstable/gromacs/debian/patches/00list
URL: http://svn.debian.org/wsvn/debichem/unstable/gromacs/debian/patches/00list?rev=1558&op=diff
==============================================================================
--- unstable/gromacs/debian/patches/00list (original)
+++ unstable/gromacs/debian/patches/00list Wed Nov 26 22:04:22 2008
@@ -1,2 +1,3 @@
 04_autoconf_mpisuffix.dpatch
 11_readme.dpatch
+50_type2bonds.dpatch

Added: unstable/gromacs/debian/patches/50_type2bonds.dpatch
URL: http://svn.debian.org/wsvn/debichem/unstable/gromacs/debian/patches/50_type2bonds.dpatch?rev=1558&op=file
==============================================================================
--- unstable/gromacs/debian/patches/50_type2bonds.dpatch (added)
+++ unstable/gromacs/debian/patches/50_type2bonds.dpatch Wed Nov 26 22:04:22 2008
@@ -1,0 +1,21 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 11_readme.dpatch by Nicholas Breen <nbreen at ofb.net>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Fix freeze when using type 2 bonds (G96) and constraints=all-angles.
+## DP: cf. http://bugzilla.gromacs.org/show_bug.cgi?id=261
+
+ at DPATCH@
+
+diff -Nru gromacs-4.0.2-orig/src/kernel/topshake.c gromacs-4.0.2/src/kernel/topshake.c
+--- gromacs-4.0.2-orig/src/kernel/topshake.c	2008-11-07 09:16:02.000000000 -0800
++++ gromacs-4.0.2/src/kernel/topshake.c	2008-11-26 14:00:21.000000000 -0800
+@@ -124,7 +124,7 @@
+ 	if (interaction_function[ftype].flags & IF_BTYPE) {
+ 	  bonds=&(plist[ftype]);
+ 
+-	  for(ftype_a = 0; (ftype_a < F_NRE); ftype_a++) {
++	  for(ftype_a = 0; (bonds->nr > 0 && ftype_a < F_NRE); ftype_a++) {
+ 	    if (interaction_function[ftype_a].flags & IF_ATYPE) {
+ 	      pr = &(plist[ftype_a]);
+ 	      

Propchange: unstable/gromacs/debian/patches/50_type2bonds.dpatch
------------------------------------------------------------------------------
    svn:executable = *