Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2020 The plumed team
       3             :    (see the PEOPLE file at the root of the distribution for a list of names)
       4             : 
       5             :    See http://www.plumed.org for more information.
       6             : 
       7             :    This file is part of plumed, version 2.
       8             : 
       9             :    plumed is free software: you can redistribute it and/or modify
      10             :    it under the terms of the GNU Lesser General Public License as published by
      11             :    the Free Software Foundation, either version 3 of the License, or
      12             :    (at your option) any later version.
      13             : 
      14             :    plumed is distributed in the hope that it will be useful,
      15             :    but WITHOUT ANY WARRANTY; without even the implied warranty of
      16             :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
      17             :    GNU Lesser General Public License for more details.
      18             : 
      19             :    You should have received a copy of the GNU Lesser General Public License
      20             :    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
      21             : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
      22             : #include "AdjacencyMatrixBase.h"
      23             : #include "tools/SwitchingFunction.h"
      24             : #include "core/ActionRegister.h"
      25             : 
      26             : #include <string>
      27             : #include <cmath>
      28             : 
      29             : namespace PLMD {
      30             : namespace adjmat {
      31             : 
      32             : //+PLUMEDOC MCOLVAR BRIDGE_MATRIX
      33             : /*
      34             : Calculate the number of atoms that bridge two parts of a structure
      35             : 
      36             : This quantity calculates:
      37             : 
      38             : \f[
      39             :  f(x) = \sum_{ijk} s_A(r_{ij})s_B(r_{ik})
      40             : \f]
      41             : 
      42             : where the sum over \f$i\f$ is over all the ``bridging atoms" and
      43             : \f$s_A\f$ and \f$s_B\f$ are \ref switchingfunction.
      44             : 
      45             : \par Examples
      46             : 
      47             : The following example instructs plumed to calculate the number of water molecules
      48             : that are bridging between atoms 1-10 and atoms 11-20 and to print the value
      49             : to a file
      50             : 
      51             : \plumedfile
      52             : w1: BRIDGE BRIDGING_ATOMS=100-200 GROUPA=1-10 GROUPB=11-20 SWITCH={RATIONAL R_0=0.2}
      53             : PRINT ARG=w1 FILE=colvar
      54             : \endplumedfile
      55             : 
      56             : */
      57             : //+ENDPLUMEDOC
      58             : 
      59             : class BridgeMatrix : public AdjacencyMatrixBase {
      60             : private:
      61             :   Vector dij, dik;
      62             :   SwitchingFunction sf1;
      63             :   SwitchingFunction sf2;
      64             : public:
      65             :   static void registerKeywords( Keywords& keys );
      66             :   explicit BridgeMatrix(const ActionOptions&);
      67             : // active methods:
      68             :   double calculateWeight( const Vector& pos1, const Vector& pos2, const unsigned& natoms, MultiValue& myvals ) const override;
      69             : };
      70             : 
      71             : PLUMED_REGISTER_ACTION(BridgeMatrix,"BRIDGE_MATRIX")
      72             : 
      73          18 : void BridgeMatrix::registerKeywords( Keywords& keys ) {
      74          18 :   AdjacencyMatrixBase::registerKeywords( keys );
      75          36 :   keys.add("atoms","BRIDGING_ATOMS","The list of atoms that can form the bridge between the two interesting parts "
      76             :            "of the structure.");
      77          36 :   keys.add("optional","SWITCH","The parameters of the two switchingfunction in the above formula");
      78          36 :   keys.add("optional","SWITCHA","The switchingfunction on the distance between bridging atoms and the atoms in "
      79             :            "group A");
      80          36 :   keys.add("optional","SWITCHB","The switchingfunction on the distance between the bridging atoms and the atoms in "
      81             :            "group B");
      82          18 : }
      83             : 
      84           8 : BridgeMatrix::BridgeMatrix(const ActionOptions&ao):
      85             :   Action(ao),
      86           8 :   AdjacencyMatrixBase(ao)
      87             : {
      88          16 :   bool oneswitch; std::string sfinput,errors; parse("SWITCH",sfinput);
      89           8 :   if( sfinput.length()>0 ) {
      90           8 :     sf1.set(sfinput,errors); oneswitch=true;
      91           8 :     if( errors.length()!=0 ) error("problem reading SWITCH keyword : " + errors );
      92           8 :     sf2.set(sfinput,errors);
      93           8 :     if( errors.length()!=0 ) error("problem reading SWITCH keyword : " + errors );
      94             :   } else {
      95           0 :     parse("SWITCHA",sfinput);
      96           0 :     if(sfinput.length()>0) {
      97           0 :       sf1.set(sfinput,errors); oneswitch=false;
      98           0 :       if( errors.length()!=0 ) error("problem reading SWITCHA keyword : " + errors );
      99           0 :       sfinput.clear(); parse("SWITCHB",sfinput);
     100           0 :       if(sfinput.length()==0) error("found SWITCHA keyword without SWITCHB");
     101           0 :       sf2.set(sfinput,errors);
     102           0 :       if( errors.length()!=0 ) error("problem reading SWITCHB keyword : " + errors );
     103             :     } else {
     104           0 :       error("missing definition of switching functions");
     105             :     }
     106             :   }
     107           8 :   log.printf("  distance between bridging atoms and atoms in GROUPA must be less than %s\n",sf1.description().c_str());
     108           8 :   log.printf("  distance between bridging atoms and atoms in GROUPB must be less than %s\n",sf2.description().c_str());
     109             : 
     110             :   // Setup link cells
     111           8 :   setLinkCellCutoff( oneswitch, sf1.get_dmax() + sf2.get_dmax() );
     112             : 
     113             :   // And check everything has been read in correctly
     114           8 :   checkRead();
     115           8 : }
     116             : 
     117         537 : double BridgeMatrix::calculateWeight( const Vector& pos1, const Vector& pos2, const unsigned& natoms, MultiValue& myvals ) const {
     118         537 :   double tot=0; if( pos2.modulo2()<epsilon ) return 0.0;
     119       21359 :   for(unsigned i=0; i<natoms; ++i) {
     120       20822 :     Vector dij= getPosition(i,myvals); double dijm = dij.modulo2();
     121       20822 :     double dw1, w1=sf1.calculateSqr( dijm, dw1 ); if( dijm<epsilon ) { w1=0.0; dw1=0.0; }
     122       20822 :     Vector dik=pbcDistance( getPosition(i,myvals), pos2 ); double dikm=dik.modulo2();
     123       20822 :     double dw2, w2=sf2.calculateSqr( dikm, dw2 ); if( dikm<epsilon ) { w2=0.0; dw2=0.0; }
     124             : 
     125       20822 :     tot += w1*w2;
     126             :     // And finish the calculation
     127       20822 :     addAtomDerivatives( 0,  -w2*dw1*dij, myvals );
     128       20822 :     addAtomDerivatives( 1,  w1*dw2*dik, myvals );
     129       20822 :     addThirdAtomDerivatives( i, -w1*dw2*dik+w2*dw1*dij, myvals );
     130       20822 :     addBoxDerivatives( w1*(-dw2)*Tensor(dik,dik)+w2*(-dw1)*Tensor(dij,dij), myvals );
     131             :   }
     132         537 :   return tot;
     133             : }
     134             : 
     135             : }
     136             : }