Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2018 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             : 
      27             : using namespace std;
      28             : 
      29             : namespace PLMD {
      30             : namespace vatom {
      31             : 
      32             : //+PLUMEDOC VATOM COM
      33             : /*
      34             : Calculate the center of mass for a group of atoms.
      35             : 
      36             : The computed
      37             : center of mass is stored as a virtual atom that can be accessed in
      38             : an atom list through the label for the COM action that creates it.
      39             : 
      40             : For arbitrary weights (e.g. geometric center) see \ref CENTER.
      41             : 
      42             : When running with periodic boundary conditions, the atoms should be
      43             : in the proper periodic image. This is done automatically since PLUMED 2.2,
      44             : by considering the ordered list of atoms and rebuilding PBCs with a procedure
      45             : that is equivalent to that done in \ref WHOLEMOLECULES . Notice that
      46             : rebuilding is local to this action. This is different from \ref WHOLEMOLECULES
      47             : which actually modifies the coordinates stored in PLUMED.
      48             : 
      49             : In case you want to recover the old behavior you should use the NOPBC flag.
      50             : In that case you need to take care that atoms are in the correct
      51             : periodic image.
      52             : 
      53             : \par Examples
      54             : 
      55             : The following input instructs plumed to print the distance between the
      56             : center of mass for atoms 1,2,3,4,5,6,7 and that for atoms 15,20:
      57             : \verbatim
      58             : COM ATOMS=1-7         LABEL=c1
      59             : COM ATOMS=15,20       LABEL=c2
      60             : DISTANCE ATOMS=c1,c2  LABEL=d1
      61             : PRINT ARG=d1
      62             : \endverbatim
      63             : (See also \ref DISTANCE and \ref PRINT).
      64             : 
      65             : */
      66             : //+ENDPLUMEDOC
      67             : 
      68             : 
      69          76 : class COM:
      70             :   public ActionWithVirtualAtom
      71             : {
      72             :   bool nopbc;
      73             : public:
      74             :   explicit COM(const ActionOptions&ao);
      75             :   void calculate();
      76             :   static void registerKeywords( Keywords& keys );
      77             : };
      78             : 
      79        2561 : PLUMED_REGISTER_ACTION(COM,"COM")
      80             : 
      81          39 : void COM::registerKeywords(Keywords& keys) {
      82          39 :   ActionWithVirtualAtom::registerKeywords(keys);
      83          39 :   keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
      84          39 : }
      85             : 
      86          38 : COM::COM(const ActionOptions&ao):
      87             :   Action(ao),
      88             :   ActionWithVirtualAtom(ao),
      89          38 :   nopbc(false)
      90             : {
      91          38 :   vector<AtomNumber> atoms;
      92          38 :   parseAtomList("ATOMS",atoms);
      93          38 :   if(atoms.size()==0) error("at least one atom should be specified");
      94          38 :   parseFlag("NOPBC",nopbc);
      95          38 :   checkRead();
      96          38 :   log.printf("  of atoms");
      97          38 :   for(unsigned i=0; i<atoms.size(); ++i) log.printf(" %d",atoms[i].serial());
      98          38 :   log.printf("\n");
      99          38 :   if(nopbc) {
     100          17 :     log<<"  PBC will be ignored\n";
     101             :   } else {
     102          21 :     log<<"  broken molecules will be rebuilt assuming atoms are in the proper order\n";
     103             :   }
     104          38 :   requestAtoms(atoms);
     105          38 : }
     106             : 
     107        2355 : void COM::calculate() {
     108        2355 :   Vector pos;
     109        2355 :   if(!nopbc) makeWhole();
     110        2355 :   double mass(0.0);
     111        2355 :   vector<Tensor> deriv(getNumberOfAtoms());
     112        2355 :   for(unsigned i=0; i<getNumberOfAtoms(); i++) mass+=getMass(i);
     113        2355 :   if( plumed.getAtoms().chargesWereSet() ) {
     114         300 :     double charge(0.0);
     115         300 :     for(unsigned i=0; i<getNumberOfAtoms(); i++) charge+=getCharge(i);
     116         300 :     setCharge(charge);
     117             :   } else {
     118        2055 :     setCharge(0.0);
     119             :   }
     120       19926 :   for(unsigned i=0; i<getNumberOfAtoms(); i++) {
     121       17571 :     pos+=(getMass(i)/mass)*getPosition(i);
     122       17571 :     deriv[i]=(getMass(i)/mass)*Tensor::identity();
     123             :   }
     124        2355 :   setPosition(pos);
     125        2355 :   setMass(mass);
     126        2355 :   setAtomsDerivatives(deriv);
     127        2355 : }
     128             : 
     129             : }
     130        2523 : }