Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2019 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 "ActionWithVirtualAtom.h"
      23             : #include "ActionRegister.h"
      24             : #include "core/PlumedMain.h"
      25             : #include "core/Atoms.h"
      26             : #include <cmath>
      27             : 
      28             : using namespace std;
      29             : 
      30             : namespace PLMD {
      31             : namespace vatom {
      32             : 
      33             : //+PLUMEDOC VATOM COM
      34             : /*
      35             : Calculate the center of mass for a group of atoms.
      36             : 
      37             : The computed
      38             : center of mass is stored as a virtual atom that can be accessed in
      39             : an atom list through the label for the COM action that creates it.
      40             : 
      41             : For arbitrary weights (e.g. geometric center) see \ref CENTER.
      42             : 
      43             : When running with periodic boundary conditions, the atoms should be
      44             : in the proper periodic image. This is done automatically since PLUMED 2.2,
      45             : by considering the ordered list of atoms and rebuilding PBCs with a procedure
      46             : that is equivalent to that done in \ref WHOLEMOLECULES . Notice that
      47             : rebuilding is local to this action. This is different from \ref WHOLEMOLECULES
      48             : which actually modifies the coordinates stored in PLUMED.
      49             : 
      50             : In case you want to recover the old behavior you should use the NOPBC flag.
      51             : In that case you need to take care that atoms are in the correct
      52             : periodic image.
      53             : 
      54             : \par Examples
      55             : 
      56             : The following input instructs plumed to print the distance between the
      57             : center of mass for atoms 1,2,3,4,5,6,7 and that for atoms 15,20:
      58             : \plumedfile
      59             : c1: COM ATOMS=1-7
      60             : c2: COM ATOMS=15,20
      61             : d1: DISTANCE ATOMS=c1,c2
      62             : PRINT ARG=d1
      63             : \endplumedfile
      64             : 
      65             : */
      66             : //+ENDPLUMEDOC
      67             : 
      68             : 
      69          58 : class COM:
      70             :   public ActionWithVirtualAtom
      71             : {
      72             :   bool nopbc;
      73             :   bool first;
      74             : public:
      75             :   explicit COM(const ActionOptions&ao);
      76             :   void calculate();
      77             :   static void registerKeywords( Keywords& keys );
      78             : };
      79             : 
      80        6510 : PLUMED_REGISTER_ACTION(COM,"COM")
      81             : 
      82          59 : void COM::registerKeywords(Keywords& keys) {
      83          59 :   ActionWithVirtualAtom::registerKeywords(keys);
      84         177 :   keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
      85          59 : }
      86             : 
      87          58 : COM::COM(const ActionOptions&ao):
      88             :   Action(ao),
      89             :   ActionWithVirtualAtom(ao),
      90             :   nopbc(false),
      91          58 :   first(true)
      92             : {
      93             :   vector<AtomNumber> atoms;
      94         116 :   parseAtomList("ATOMS",atoms);
      95          58 :   if(atoms.size()==0) error("at least one atom should be specified");
      96         116 :   parseFlag("NOPBC",nopbc);
      97          58 :   checkRead();
      98          58 :   log.printf("  of atoms");
      99        2423 :   for(unsigned i=0; i<atoms.size(); ++i) {
     100         769 :     if(i%25==0) log<<"\n";
     101        1538 :     log.printf(" %d",atoms[i].serial());
     102             :   }
     103          58 :   log.printf("\n");
     104          58 :   if(nopbc) {
     105          23 :     log<<"  PBC will be ignored\n";
     106             :   } else {
     107          35 :     log<<"  broken molecules will be rebuilt assuming atoms are in the proper order\n";
     108             :   }
     109          58 :   requestAtoms(atoms);
     110          58 : }
     111             : 
     112        2427 : void COM::calculate() {
     113        2427 :   Vector pos;
     114        2427 :   if(!nopbc) makeWhole();
     115             :   double mass(0.0);
     116        2427 :   if( first ) {
     117         496 :     for(unsigned i=0; i<getNumberOfAtoms(); i++) {
     118         496 :       if(std::isnan(getMass(i))) {
     119           0 :         error(
     120             :           "You are trying to compute a COM but masses are not known.\n"
     121             :           "        If you are using plumed driver, please use the --mc option"
     122             :         );
     123             :       }
     124             :     }
     125          49 :     first=false;
     126             :   }
     127        2427 :   vector<Tensor> deriv(getNumberOfAtoms());
     128       39153 :   for(unsigned i=0; i<getNumberOfAtoms(); i++) mass+=getMass(i);
     129        4854 :   if( plumed.getAtoms().chargesWereSet() ) {
     130             :     double charge(0.0);
     131        4175 :     for(unsigned i=0; i<getNumberOfAtoms(); i++) charge+=getCharge(i);
     132             :     setCharge(charge);
     133             :   } else {
     134             :     setCharge(0.0);
     135             :   }
     136       39153 :   for(unsigned i=0; i<getNumberOfAtoms(); i++) {
     137       36726 :     pos+=(getMass(i)/mass)*getPosition(i);
     138       55089 :     deriv[i]=(getMass(i)/mass)*Tensor::identity();
     139             :   }
     140             :   setPosition(pos);
     141             :   setMass(mass);
     142             :   setAtomsDerivatives(deriv);
     143        2427 : }
     144             : 
     145             : }
     146        4839 : }