Added test of aperiodic pamm and added warning for mixed periodic/aperiodic

regtest/crystallization/rt-pamm-aperiodic/Makefile

+include ../../scripts/test.make

regtest/crystallization/rt-pamm-aperiodic/clusters.dat

+#! FIELDS weight center-fcc width-fcc-fcc
+      4.13163724E-0001      1.44833887E-0002      2.52246630E-0002 
+      5.86836276E-0001      8.72359830E-0001      1.71959514E-0002 

regtest/crystallization/rt-pamm-aperiodic/colvar.reference

+#! FIELDS time pamm.mean
+ 0.000000   0.5677
+ 1.000000   0.5380
+ 2.000000   0.5791
+ 3.000000   0.6325
+ 4.000000   0.6342

regtest/crystallization/rt-pamm-aperiodic/config

+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz ncub.xyz"

regtest/crystallization/rt-pamm-aperiodic/plumed.dat

+FCCUBIC SPECIES=1-1200 SWITCH={CUBIC D_0=1.2 D_MAX=1.5} MEAN LABEL=fcc
+
+PAMM DATA=fcc CLUSTERS=clusters.dat MEAN LABEL=pamm
+# PAMM DATA=fcc CLUSTERS=clusters.dat MEAN NUMERICAL_DERIVATIVES LABEL=pammn
+
+PRINT ARG=pamm.* FILE=colvar FMT=%8.4f
+DUMPDERIVATIVES ARG=pamm.* FILE=deriv FMT=%8.4f

src/multicolvar/PAMM.cpp

@@ -30,6 +30,8 @@ Probabilistic analysis of molecular mofifs.
 
 This is an implementation of the methods discussed in \cite{pamm}
 
+\warning Mixing periodic and aperiodic variables in input has not been tested
+
 \par Examples
 
 */
@@ -79,8 +81,10 @@ MultiColvarFunction(ao)
    // This builds the lists
    buildSets(); 
 
+   bool mixed=getBaseMultiColvar(0)->isPeriodic();
    for(unsigned i=0;i<getNumberOfBaseMultiColvars();++i){
        pos.push_back( new Value() );
+       if( getBaseMultiColvar(i)->isPeriodic()!=mixed ) warning("mixing of periodic and aperiodic base variables in pamm is untested");
        if( !getBaseMultiColvar(i)->isPeriodic() ){
            pos[i]->setNotPeriodic();
        } else {