Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2012-2023 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 "Colvar.h"
      23             : #include "ActionRegister.h"
      24             : 
      25             : namespace PLMD {
      26             : namespace colvar {
      27             : 
      28             : //+PLUMEDOC COLVAR DIPOLE
      29             : /*
      30             : Calculate the dipole moment for a group of atoms.
      31             : 
      32             : When running with periodic boundary conditions, the atoms should be
      33             : in the proper periodic image. This is done automatically since PLUMED 2.5,
      34             : by considering the ordered list of atoms and rebuilding the molecule with a procedure
      35             : that is equivalent to that done in \ref WHOLEMOLECULES . Notice that
      36             : rebuilding is local to this action. This is different from \ref WHOLEMOLECULES
      37             : which actually modifies the coordinates stored in PLUMED.
      38             : 
      39             : In case you want to recover the old behavior you should use the NOPBC flag.
      40             : In that case you need to take care that atoms are in the correct
      41             : periodic image.
      42             : 
      43             : \par Examples
      44             : 
      45             : The following tells plumed to calculate the dipole of the group of atoms containing
      46             : the atoms from 1-10 and print it every 5 steps
      47             : \plumedfile
      48             : d: DIPOLE GROUP=1-10
      49             : PRINT FILE=output STRIDE=5 ARG=d
      50             : \endplumedfile
      51             : 
      52             : \attention
      53             : If the total charge Q of the group in non zero, then a charge Q/N will be subtracted to every atom,
      54             : where N is the number of atoms. This implies that the dipole (which for a charged system depends
      55             : on the position) is computed on the geometric center of the group.
      56             : 
      57             : 
      58             : */
      59             : //+ENDPLUMEDOC
      60             : 
      61             : class Dipole : public Colvar {
      62             :   std::vector<AtomNumber> ga_lista;
      63             :   bool components;
      64             :   bool nopbc;
      65             : public:
      66             :   explicit Dipole(const ActionOptions&);
      67             :   void calculate() override;
      68             :   static void registerKeywords(Keywords& keys);
      69             : };
      70             : 
      71       13893 : PLUMED_REGISTER_ACTION(Dipole,"DIPOLE")
      72             : 
      73          58 : void Dipole::registerKeywords(Keywords& keys) {
      74          58 :   Colvar::registerKeywords(keys);
      75         116 :   keys.add("atoms","GROUP","the group of atoms we are calculating the dipole moment for");
      76         116 :   keys.addFlag("COMPONENTS",false,"calculate the x, y and z components of the dipole separately and store them as label.x, label.y and label.z");
      77         116 :   keys.addOutputComponent("x","COMPONENTS","the x-component of the dipole");
      78         116 :   keys.addOutputComponent("y","COMPONENTS","the y-component of the dipole");
      79         116 :   keys.addOutputComponent("z","COMPONENTS","the z-component of the dipole");
      80          58 : }
      81             : 
      82          54 : Dipole::Dipole(const ActionOptions&ao):
      83             :   PLUMED_COLVAR_INIT(ao),
      84          54 :   components(false) {
      85          54 :   parseAtomList("GROUP",ga_lista);
      86          54 :   parseFlag("COMPONENTS",components);
      87          54 :   parseFlag("NOPBC",nopbc);
      88          54 :   checkRead();
      89          54 :   if(components) {
      90           2 :     addComponentWithDerivatives("x");
      91           2 :     componentIsNotPeriodic("x");
      92           2 :     addComponentWithDerivatives("y");
      93           2 :     componentIsNotPeriodic("y");
      94           2 :     addComponentWithDerivatives("z");
      95           4 :     componentIsNotPeriodic("z");
      96             :   } else {
      97          52 :     addValueWithDerivatives();
      98          52 :     setNotPeriodic();
      99             :   }
     100             : 
     101          54 :   log.printf("  of %u atoms\n",static_cast<unsigned>(ga_lista.size()));
     102         379 :   for(unsigned int i=0; i<ga_lista.size(); ++i) {
     103         325 :     log.printf("  %d", ga_lista[i].serial());
     104             :   }
     105          54 :   log.printf("  \n");
     106          54 :   if(nopbc) {
     107          38 :     log.printf("  without periodic boundary conditions\n");
     108             :   } else {
     109          16 :     log.printf("  using periodic boundary conditions\n");
     110             :   }
     111             : 
     112          54 :   requestAtoms(ga_lista);
     113          54 : }
     114             : 
     115             : // calculator
     116         923 : void Dipole::calculate() {
     117         923 :   if(!nopbc) {
     118         541 :     makeWhole();
     119             :   }
     120             :   double ctot=0.;
     121             :   unsigned N=getNumberOfAtoms();
     122         923 :   std::vector<double> charges(N);
     123         923 :   Vector dipje;
     124             : 
     125        7258 :   for(unsigned i=0; i<N; ++i) {
     126        6335 :     charges[i]=getCharge(i);
     127        6335 :     ctot+=charges[i];
     128             :   }
     129         923 :   ctot/=(double)N;
     130             : 
     131        7258 :   for(unsigned i=0; i<N; ++i) {
     132        6335 :     charges[i]-=ctot;
     133        6335 :     dipje += charges[i]*getPosition(i);
     134             :   }
     135             : 
     136         923 :   if(!components) {
     137         778 :     double dipole = dipje.modulo();
     138         778 :     double idip = 1./dipole;
     139             : 
     140        6243 :     for(unsigned i=0; i<N; i++) {
     141        5465 :       double dfunc=charges[i]*idip;
     142        5465 :       setAtomsDerivatives(i,dfunc*dipje);
     143             :     }
     144         778 :     setBoxDerivativesNoPbc();
     145         778 :     setValue(dipole);
     146             :   } else {
     147         145 :     Value* valuex=getPntrToComponent("x");
     148         145 :     Value* valuey=getPntrToComponent("y");
     149         145 :     Value* valuez=getPntrToComponent("z");
     150        1015 :     for(unsigned i=0; i<N; i++) {
     151         870 :       setAtomsDerivatives(valuex,i,charges[i]*Vector(1.0,0.0,0.0));
     152         870 :       setAtomsDerivatives(valuey,i,charges[i]*Vector(0.0,1.0,0.0));
     153         870 :       setAtomsDerivatives(valuez,i,charges[i]*Vector(0.0,0.0,1.0));
     154             :     }
     155         145 :     setBoxDerivativesNoPbc(valuex);
     156         145 :     setBoxDerivativesNoPbc(valuey);
     157         145 :     setBoxDerivativesNoPbc(valuez);
     158         145 :     valuex->set(dipje[0]);
     159         145 :     valuey->set(dipje[1]);
     160         145 :     valuez->set(dipje[2]);
     161             :   }
     162         923 : }
     163             : 
     164             : }
     165             : }