Merge branch 'v2.2' into v2.3

regtest/multicolvar/rt20-mpi/colvar.reference

-#! FIELDS time d1.lessthan d2.lessthan c1
- 0.000000  3.71160  3.70528  3.63725
- 0.050000  3.65204  3.64568  3.57396
- 0.100000  3.68479  3.67845  3.61408
- 0.150000  3.74173  3.73336  3.66938
- 0.200000  3.80672  3.79754  3.73794
+#! FIELDS time d1.lessthan d2.lessthan d3.lessthan c1
+ 0.000000  3.71160  3.70528  0.02519  3.63725
+ 0.050000  3.65204  3.64568  0.02396  3.57396
+ 0.100000  3.68479  3.67845  0.02281  3.61408
+ 0.150000  3.74173  3.73336  0.02213  3.66938
+ 0.200000  3.80672  3.79754  0.02142  3.73794

regtest/multicolvar/rt20-mpi/plumed.dat

+ce1: CENTER ATOMS=2-10
+ce2: CENTER ATOMS=20-30
+ce3: CENTER ATOMS=40-50
+ce4: CENTER ATOMS=60-70
+
 DISTANCES GROUPA=1 GROUPB=2-100 LESS_THAN={RATIONAL R_0=1.0} LABEL=d1
 DISTANCES GROUPA=1 GROUPB=2-100 LESS_THAN={RATIONAL R_0=1.0} TOL=0.001 LABEL=d2
+DISTANCES GROUP=ce1,ce2,ce3,ce4 LESS_THAN={RATIONAL R_0=1.0} LABEL=d3
 c1: ...
   COORDINATION GROUPA=1 GROUPB=2-100 NLIST NL_CUTOFF=2.5 NL_STRIDE=20
   SWITCH={RATIONAL NN=6 MM=12 R_0=1.0}
 ...
-PRINT ARG=d1.*,d2.*,c1 FILE=colvar FMT=%8.5f STRIDE=1
+PRINT ARG=d1.*,d2.*,d3.*,c1 FILE=colvar FMT=%8.5f STRIDE=1
 COORDINATIONNUMBER SPECIES=1-5 SWITCH={RATIONAL R_0=0.5} MORE_THAN={EXP R_0=4.0} LABEL=c2
 COORDINATIONNUMBER SPECIES=1-5 SWITCH={RATIONAL R_0=0.5} MORE_THAN={EXP R_0=4.0} NUMERICAL_DERIVATIVES LABEL=c2n
 DUMPDERIVATIVES ARG=c2.*,c2n.* FILE=derivatives FMT=%8.4f
+DUMPMULTICOLVAR DATA=d1 FILE=d1.xyz
+DUMPMULTICOLVAR DATA=d3 FILE=d3.xyz

src/multicolvar/DumpMultiColvar.cpp

@@ -163,7 +163,7 @@ void DumpMultiColvar::update(){
     const char* defname="X";
     const char* name=defname;
 
-    Vector apos = mycolv->getCentralAtomPos( mycolv->getTaskCode(i) );
+    Vector apos = mycolv->getCentralAtomPos( mycolv->getPositionInFullTaskList(i) );
     if( getNumberOfAtoms()>0 ) apos=pbcDistance( getPosition(0), apos );
     of.printf(("%s "+fmt_xyz+" "+fmt_xyz+" "+fmt_xyz).c_str(),name,lenunit*apos[0],lenunit*apos[1],lenunit*apos[2]);
     stash->retrieveSequentialValue( i, true, cvals );