Fix to problems caused by merge

regtest/basic/rt-mpi6/HILLS_rect.reference

@@ -1,5 +1,6 @@
 #! FIELDS time c d sigma_c sigma_d height biasf
 #! SET multivariate false
+#! SET kerneltype gaussian
       0.100000      9.237723      1.097928      0.100000      0.200000      2.496833      1.001000
       0.100000      9.237723      1.097928      0.100000      0.200000      2.743772      1.001000
       0.100000      8.675711      1.162646      0.100000      0.200000      9.977355      1.001000

regtest/basic/rt-mpi6d/HILLSa.0.reference

@@ -1,5 +1,6 @@
 #! FIELDS time c d sigma_c sigma_d height biasf
 #! SET multivariate false
+#! SET kerneltype gaussian
       0.100000      9.237723      1.097928      0.100000      0.200000      2.494339      1.000000
       0.200000      9.327813      1.086855      0.100000      0.200000      1.282241      1.000000
       0.300000      9.157418      1.130546      0.100000      0.200000      1.085108      1.000000

regtest/basic/rt-mpi6d/HILLSa.1.reference

@@ -1,5 +1,6 @@
 #! FIELDS time c d sigma_c sigma_d height biasf
 #! SET multivariate false
+#! SET kerneltype gaussian
       0.100000      9.237723      1.097928      0.100000      0.200000      2.743772      1.100000
       0.200000      8.675711      1.162646      0.100000      0.200000      2.743772      1.100000
       0.300000      9.282739      1.080244      0.100000      0.200000      1.115403      1.100000

regtest/basic/rt-mpi6d/HILLSa.2.reference

@@ -1,5 +1,6 @@
 #! FIELDS time c d sigma_c sigma_d height biasf
 #! SET multivariate false
+#! SET kerneltype gaussian
       0.100000      8.675711      1.162646      0.100000      0.200000      9.977355      4.000000
       0.200000      9.282739      1.080244      0.100000      0.200000      9.977355      4.000000
       0.300000      9.237723      1.097928      0.100000      0.200000      4.056010      4.000000

regtest/basic/rt-mpi6d/HILLSb.reference

@@ -1,5 +1,6 @@
 #! FIELDS time c d sigma_c sigma_d height biasf
 #! SET multivariate false
+#! SET kerneltype gaussian
       0.100000      9.237723      1.097928      0.100000      0.200000      2.494339      1.000000
       0.100000      9.237723      1.097928      0.100000      0.200000      2.743772      1.000000
       0.100000      8.675711      1.162646      0.100000      0.200000      9.977355      1.000000

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

@@ -1,4 +1,4 @@
-FCCUBIC SPECIESA=1-2 SPECIESB=1-1200 SWITCH={CUBIC D_0=1.2 D_MAX=1.5} MEAN LABEL=fcc
+FCCUBIC SPECIESA=1-2 SPECIESB=1-1200 SWITCH={CUBIC D_0=1.2 D_MAX=1.5} MEAN LOWMEM LABEL=fcc
 
 PAMM DATA=fcc CLUSTERS=clusters.dat MEAN REGULARISE=0.0 LABEL=pamm
 # PAMM DATA=fcc CLUSTERS=clusters.dat MEAN NUMERICAL_DERIVATIVES LABEL=pammn

src/crystallization/VectorMultiColvar.cpp

@@ -26,7 +26,7 @@ namespace PLMD {
 namespace crystallization {
 
 void VectorMultiColvar::registerKeywords( Keywords& keys ){
-  MultiColvar::registerKeywords( keys );
+  MultiColvarBase::registerKeywords( keys );
   keys.setComponentsIntroduction("When the label of this action is used as the input for a second you are not referring to a scalar quantity as you are in "
                                  "regular collective variables.  The label is used to reference the full set of vectors calculated by "
                                  "the action.  This is usual when using \\ref multicolvarfunction. Generally when doing this the previously calculated "

src/multicolvar/Torsions.cpp

@@ -85,7 +85,7 @@ PLUMED_REGISTER_ACTION(Torsions,"TORSIONS")
 
 void Torsions::registerKeywords( Keywords& keys ){
   MultiColvarBase::registerKeywords( keys );
-  keys.reserve("numbered","ATOMS","the atoms involved in each of the torsion angles you wish to calculate. "
+  keys.add("numbered","ATOMS","the atoms involved in each of the torsion angles you wish to calculate. "
                              "Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one torsion will be "
                              "calculated for each ATOM keyword you specify (all ATOM keywords should "
                              "provide the indices of four atoms).  The eventual number of quantities calculated by this "

src/pamm/HBPammHydrogens.cpp

@@ -19,7 +19,7 @@
    You should have received a copy of the GNU Lesser General Public License
    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#include "multicolvar/MultiColvar.h"
+#include "multicolvar/MultiColvarBase.h"
 #include "HBPammObject.h"
 #include "tools/NeighborList.h"
 #include "core/ActionRegister.h"
@@ -43,7 +43,7 @@ Number of HBPAMM hydrogen bonds formed by each hydrogen atom in the system
 //+ENDPLUMEDOC
 
 
-class HBPammHydrogens : public multicolvar::MultiColvar {
+class HBPammHydrogens : public multicolvar::MultiColvarBase {
 private:
   double rcut2;
   unsigned block1upper,block2lower;
@@ -60,7 +60,7 @@ class HBPammHydrogens : public multicolvar::MultiColvar {
 PLUMED_REGISTER_ACTION(HBPammHydrogens,"HBPAMM_SH")
 
 void HBPammHydrogens::registerKeywords( Keywords& keys ){
-  multicolvar::MultiColvar::registerKeywords( keys );
+  multicolvar::MultiColvarBase::registerKeywords( keys );
   keys.add("atoms-1","HYDROGENS","The list of hydrogen atoms that can form part of a hydrogen bond.  The atoms must be specified using a comma separated list.");
   keys.add("atoms-1","SITES","The list of atoms which can be part of a hydrogen bond.  When this command is used the set of atoms that can donate a "
                              "hydrogen bond is assumed to be the same as the set of atoms that can form hydrogen bonds.  The atoms involved must be specified"
@@ -88,7 +88,8 @@ void HBPammHydrogens::registerKeywords( Keywords& keys ){
 }
 
 HBPammHydrogens::HBPammHydrogens(const ActionOptions&ao):
-PLUMED_MULTICOLVAR_INIT(ao)
+Action(ao),
+MultiColvarBase(ao)
 {
   // Read in the atoms
   usespecies=true; weightHasDerivatives=false;

src/pamm/PAMM.cpp

@@ -22,7 +22,8 @@
 #include "core/ActionRegister.h"
 #include "tools/KernelFunctions.h"
 #include "tools/IFile.h"
-#include "multicolvar/MultiColvarFunction.h"
+#include "multicolvar/MultiColvarBase.h"
+#include "multicolvar/AtomValuePack.h"
 #include "PammObject.h"
 
 //+PLUMEDOC MCOLVARF PAMM
@@ -107,7 +108,7 @@ and compute these PAMM variables and we can transform the PAMM variables themsel
 namespace PLMD {
 namespace pamm {
 
-class PAMM : public multicolvar::MultiColvarFunction {
+class PAMM : public multicolvar::MultiColvarBase {
 private:
   PammObject mypamm;
 public:
@@ -128,7 +129,8 @@ class PAMM : public multicolvar::MultiColvarFunction {
 PLUMED_REGISTER_ACTION(PAMM,"PAMM")
 
 void PAMM::registerKeywords( Keywords& keys ){
-  MultiColvarFunction::registerKeywords( keys ); 
+  MultiColvarBase::registerKeywords( keys ); 
+  keys.add("compulsory","DATA","the multicolvars from which the pamm coordinates are calculated");
   keys.add("compulsory","CLUSTERS","the name of the file that contains the definitions of all the clusters");
   keys.add("compulsory","REGULARISE","0.001","don't allow the denominator to be smaller then this value");
   keys.use("MEAN"); keys.use("MORE_THAN"); keys.use("SUM"); keys.use("LESS_THAN"); keys.use("HISTOGRAM"); keys.use("HISTOGRAM");
@@ -153,8 +155,10 @@ void PAMM::registerKeywords( Keywords& keys ){
 
 PAMM::PAMM(const ActionOptions& ao):
 Action(ao),
-MultiColvarFunction(ao)
+MultiColvarBase(ao)
 {
+   // This builds the lists
+   buildSets();
    // Check for reasonable input
    for(unsigned i=0;i<getNumberOfBaseMultiColvars();++i){
      if( getBaseMultiColvar(i)->getNumberOfQuantities()!=2 ) error("cannot use PAMM with " + getBaseMultiColvar(i)->getName() );
@@ -175,8 +179,6 @@ MultiColvarFunction(ao)
    std::string errorstr, filename; parse("CLUSTERS",filename); 
    mypamm.setup( filename, regulariser, valnames, pbc, min, max, errorstr );
    if( errorstr.length()>0 ) error( errorstr );
-   // This builds the lists
-   buildSets();
 }
 
 unsigned PAMM::getNumberOfQuantities() const {