From: Berk Hess <hess@kth.se>
Date: Fri, 3 Oct 2014 12:00:38 +0000 (+0200)
Subject: Fixes issue with vsiten and Verlet buffers
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=f2007baaf33978684bde92ecc1b43f57d6525666;p=alexxy%2Fgromacs.git

Fixes issue with vsiten and Verlet buffers

Commit 0336ab2d only fixed part of the vsiten issue in the Verlet
buffer calculation code. Parameters were read from incorrect memory
locations, which could lead to a segmentation fault or incorrect
masses for vsiten particles. It unlikely that this affected results.
Part of #1579.

Change-Id: I76cdb94e34194d2f6d49d98a49486ce1df76d91a
---

diff --git a/src/kernel/calc_verletbuf.c b/src/kernel/calc_verletbuf.c
index 64a79f7530..9b1967e44c 100644
--- a/src/kernel/calc_verletbuf.c
+++ b/src/kernel/calc_verletbuf.c
@@ -210,8 +210,8 @@ static void get_vsite_masses(const gmx_moltype_t *moltype,
             for (i = 0; i < il->nr; i += 1+NRAL(ft))
             {
                 const t_iparams *ip;
-                real             cam[5], inv_mass, m_aj;
-                int              a1, j, aj, coeff;
+                real             cam[5], inv_mass, coeff, m_aj;
+                int              a1, j, aj;
 
                 ip = &ffparams->iparams[il->iatoms[i]];
 
@@ -249,10 +249,10 @@ static void get_vsite_masses(const gmx_moltype_t *moltype,
                     case F_VSITEN:
                         /* Exact */
                         inv_mass = 0;
-                        for (j = 0; j < 3*ip->vsiten.n; j += 3)
+                        for (j = 0; j < 3*ffparams->iparams[il->iatoms[i]].vsiten.n; j += 3)
                         {
                             aj    = il->iatoms[i+j+2];
-                            coeff = ip[il->iatoms[i+j]].vsiten.a;
+                            coeff = ffparams->iparams[il->iatoms[i+j]].vsiten.a;
                             if (moltype->atoms.atom[aj].ptype == eptVSite)
                             {
                                 m_aj = vsite_m[aj];