Added new metric and a new multicolvar

The new multicolvar measures the inplanedistance i.e. the
distane from a plane defined by a vector connecting two atoms.
The new refernce distance measures the dot product distance
between two points

src/multicolvar/InPlaneDistances.cpp

+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2013,2014 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed-code.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   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.h"
+#include "tools/SwitchingFunction.h"
+#include "core/ActionRegister.h"
+#include "vesselbase/LessThan.h"
+#include "vesselbase/Between.h"
+#include "tools/Angle.h"
+
+#include <string>
+#include <cmath>
+
+using namespace std;
+
+namespace PLMD{
+namespace multicolvar{
+
+//+PLUMEDOC MCOLVAR INPLANEDISTANCES
+/*
+Calculate distances in the plane perpendicular to an axis
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+class InPlaneDistances : public MultiColvar {
+public:
+  static void registerKeywords( Keywords& keys );
+  InPlaneDistances(const ActionOptions&);
+// active methods:
+  virtual double compute();
+  bool isPeriodic(){ return false; }
+  Vector getCentralAtom();
+};
+
+PLUMED_REGISTER_ACTION(InPlaneDistances,"INPLANEDISTANCES")
+
+void InPlaneDistances::registerKeywords( Keywords& keys ){
+  MultiColvar::registerKeywords( keys );
+  keys.use("MEAN"); keys.use("MIN"); keys.use("MAX"); keys.use("LESS_THAN"); 
+  keys.use("MORE_THAN"); keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MOMENTS");
+  keys.add("atoms","VECTORSTART","The first atom position that is used to define the normal to the plane of interest");
+  keys.add("atoms","VECTOREND","The second atom position that is used to defin the normal to the plane of interest");
+  keys.add("atoms-2","GROUP","The set of atoms for which you wish to calculate the in plane distance ");
+}
+
+InPlaneDistances::InPlaneDistances(const ActionOptions&ao):
+PLUMED_MULTICOLVAR_INIT(ao)
+{
+  // Read in the atoms
+  std::vector<AtomNumber> all_atoms;
+  readThreeGroups("GROUP","VECTORSTART","VECTOREND",false, all_atoms);
+  if( all_atoms.size()>0 ) ActionAtomistic::requestAtoms( all_atoms );
+
+  // Check atoms are OK
+  if( getFullNumberOfTasks()!=getNumberOfAtoms()-2 ) error("you should specify one atom for VECTORSTART and one atom for VECTOREND only");
+
+  // Setup the multicolvar base
+  setupMultiColvarBase(); readVesselKeywords();
+  // And check everything has been read in correctly
+  checkRead();
+
+ // Now check if we can use link cells
+  bool use_link=false; double rcut;
+  if( getNumberOfVessels()>0 ){
+     vesselbase::LessThan* lt=dynamic_cast<vesselbase::LessThan*>( getPntrToVessel(0) );
+     if( lt ){
+         use_link=true; rcut=lt->getCutoff();
+     } else {
+         vesselbase::Between* bt=dynamic_cast<vesselbase::Between*>( getPntrToVessel(0) );
+         if( bt ) use_link=true; rcut=bt->getCutoff();
+     }
+     if( use_link ){
+         for(unsigned i=1;i<getNumberOfVessels();++i){
+            vesselbase::LessThan* lt2=dynamic_cast<vesselbase::LessThan*>( getPntrToVessel(i) );
+            vesselbase::Between* bt=dynamic_cast<vesselbase::Between*>( getPntrToVessel(i) );
+            if( lt2 ){
+                double tcut=lt2->getCutoff();
+                if( tcut>rcut ) rcut=tcut;
+            } else if( bt ){
+                double tcut=bt->getCutoff();
+                if( tcut>rcut ) rcut=tcut;
+            } else {
+               use_link=false;
+            }
+         }
+     }
+     if( use_link ) setLinkCellCutoff( rcut );
+  }
+}
+
+double InPlaneDistances::compute(){
+  Vector normal=getSeparation( getPosition(1), getPosition(2) );
+  Vector dir=getSeparation( getPosition(1), getPosition(0) );
+  PLMD::Angle a; Vector ddij, ddik; double angle=a.compute(normal,dir,ddij,ddik);
+  double sangle=sin(angle), cangle=cos(angle); 
+  double dd=dir.modulo(), invdd=1.0/dd, val=dd*sangle;
+
+  addAtomsDerivatives( 0, dd*cangle*ddik + sangle*invdd*dir );
+  addAtomsDerivatives( 1, -dd*cangle*(ddik+ddij) - sangle*invdd*dir );
+  addAtomsDerivatives( 2, dd*cangle*ddij );
+  addBoxDerivatives( -dd*cangle*(Tensor(normal,ddij)+Tensor(dir,ddik)) - sangle*invdd*Tensor(dir,dir) );
+
+  return val;
+}
+
+Vector InPlaneDistances::getCentralAtom(){
+   addCentralAtomDerivatives( 0, Tensor::identity() );
+   return getPosition(0);
+}
+
+}
+}

src/reference/DotProductDistance.cpp

+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2012-2014 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed-code.org for more information.
+
+   This file is part of plumed, version 2.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   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 "MetricRegister.h"
+#include "ArgumentOnlyDistance.h"
+#include "core/Value.h"
+
+namespace PLMD {
+
+class DotProductDistance : public ArgumentOnlyDistance {
+public:
+  DotProductDistance( const ReferenceConfigurationOptions& ro );
+  void read( const PDB& );
+  double calc( const std::vector<Value*>& vals, const std::vector<double>& arg, const bool& squared );
+};
+
+PLUMED_REGISTER_METRIC(DotProductDistance,"DOTPRODUCT")
+
+DotProductDistance::DotProductDistance( const ReferenceConfigurationOptions& ro ):
+ReferenceConfiguration(ro),
+ArgumentOnlyDistance(ro)
+{
+}
+
+void DotProductDistance::read( const PDB& pdb ){
+  readArgumentsFromPDB( pdb );
+}
+
+double DotProductDistance::calc( const std::vector<Value*>& vals, const std::vector<double>& arg, const bool& squared ){
+  double dot=0.0; 
+  for (unsigned long i=0; i<vals.size(); ++i) dot+=getReferenceArgument(i)*arg[i];
+  return -log(dot);
+}
+
+
+}