Merge branch 'v2.1' into v2.2

CHANGES/v2.1.txt

@@ -221,6 +221,12 @@ Unreleased changes (will be included in 2.1.4)
 See branch \branch{v2.1} on git repository.
 
 For users:
+- Fixed NAMD patch. Masses and charges were not passed correctly, thus resulting in wrong
+  \ref COM or \ref CENTER with MASS.
+  This fix required repatching NAMD.
+  Notice that this bug was present also in v2.0 but in a different form.
+  More information here (\issue{162}), including a workaround that allows masses to be fixed
+  without repatching.
 - Fixed erroneously reported message about MPI at the end of ./configure.
 - Changed warning message about undocumented components.
 - PLUMED now says in the log file if it was compiled from a dirty git repository.

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]);
 +

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]);
 +