From 25ae27aeed9dcbd72b4c7958dae9de5b051f4c18 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Thu, 16 Jul 2015 19:38:57 +0200
Subject: [PATCH] Fixed masses and charges in NAMD
There was an error in passing masses from NAMD to PLUMED.
Found by Glen Hocky.
Fixes #162
---
patches/namd-2.8.diff | 6 +++---
patches/namd-2.9.diff | 6 +++---
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/patches/namd-2.8.diff b/patches/namd-2.8.diff
index 4fabe2f25..5612e7920 100644
--- a/patches/namd-2.8.diff
+++ b/patches/namd-2.8.diff
@@ -128,8 +128,8 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
+ positions[3*i+0]=coord.x;
+ positions[3*i+1]=coord.y;
+ positions[3*i+2]=coord.z;
-+ masses[i]=Node::Object()->molecule->atommass(i);
-+ charges[i]=Node::Object()->molecule->atommass(i);
++ masses[i]=Node::Object()->molecule->atommass(index[i]);
++ charges[i]=Node::Object()->molecule->atomcharge(index[i]);
+ };
+
+ if(spar->lattice.volume()>0.0){
@@ -141,7 +141,7 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
+
+ for(int i=0;i<forces.size();i++) forces[i]=0.0;
+
-+ cmd("setMasses",&masses[0]);
++ cmd("setMasses",&masses[0]); cmd("setCharges",&charges[0]);
+ cmd("setPositions",&positions[0]);
+ cmd("setForces",&forces[0]);
+
diff --git a/patches/namd-2.9.diff b/patches/namd-2.9.diff
index d4d242cac..73590a2ef 100644
--- a/patches/namd-2.9.diff
+++ b/patches/namd-2.9.diff
@@ -127,8 +127,8 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
+ positions[3*i+0]=coord.x;
+ positions[3*i+1]=coord.y;
+ positions[3*i+2]=coord.z;
-+ masses[i]=Node::Object()->molecule->atommass(i);
-+ charges[i]=Node::Object()->molecule->atommass(i);
++ masses[i]=Node::Object()->molecule->atommass(index[i]);
++ charges[i]=Node::Object()->molecule->atomcharge(index[i]);
+ };
+
+ if(spar->lattice.volume()>0.0){
@@ -140,7 +140,7 @@ patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
+
+ for(int i=0;i<forces.size();i++) forces[i]=0.0;
+
-+ cmd("setMasses",&masses[0]);
++ cmd("setMasses",&masses[0]); cmd("setCharges",&charges[0]);
+ cmd("setPositions",&positions[0]);
+ cmd("setForces",&forces[0]);
+
--
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