Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2014-2023 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 "core/ActionAtomistic.h"
      23             : #include "core/ActionWithValue.h"
      24             : #include "core/ActionRegister.h"
      25             : 
      26             : //+PLUMEDOC MCOLVAR CHARGE
      27             : /*
      28             : Get the charges of one or multiple atoms
      29             : 
      30             : The following example shows how you can print the charge of atom one:
      31             : 
      32             : ```plumed
      33             : q: CHARGE ATOMS=1
      34             : PRINT ARG=q FILE=colvar
      35             : ```
      36             : 
      37             : If you want to output the charges of multiple atoms you would use an input similar to the one below:
      38             : 
      39             : ```plumed
      40             : q: CHARGE ATOMS=1-10
      41             : PRINT ARG=q FILE=colvar
      42             : ```
      43             : 
      44             : This input outputs a 10 dimensional vector that contains the charges of the first 10 atoms.
      45             : 
      46             : */
      47             : //+ENDPLUMEDOC
      48             : 
      49             : //+PLUMEDOC MCOLVAR MASS
      50             : /*
      51             : Get the mass of one or multiple atoms
      52             : 
      53             : The following example shows how you can print the mass of atom one:
      54             : 
      55             : ```plumed
      56             : m: MASS ATOMS=1
      57             : PRINT ARG=m FILE=colvar
      58             : ```
      59             : 
      60             : If you want to output the masses of multiple atoms you would use an input similar to the one below:
      61             : 
      62             : ```plumed
      63             : m: MASS ATOMS=1-10
      64             : PRINT ARG=m FILE=colvar
      65             : ```
      66             : 
      67             : This input outputs a 10 dimensional vector that contains the masses of the first 10 atoms.
      68             : 
      69             : */
      70             : //+ENDPLUMEDOC
      71             : 
      72             : namespace PLMD {
      73             : namespace colvar {
      74             : 
      75             : class SelectMassCharge :
      76             :   public ActionAtomistic,
      77             :   public ActionWithValue {
      78             : public:
      79             :   static void registerKeywords( Keywords& keys );
      80             :   explicit SelectMassCharge(const ActionOptions&);
      81             : // active methods:
      82          36 :   unsigned getNumberOfDerivatives() override {
      83          36 :     return 0;
      84             :   }
      85             :   void calculate() override;
      86          18 :   void apply() override {}
      87             : };
      88             : 
      89             : PLUMED_REGISTER_ACTION(SelectMassCharge,"MASS")
      90             : PLUMED_REGISTER_ACTION(SelectMassCharge,"CHARGE")
      91             : 
      92          40 : void SelectMassCharge::registerKeywords( Keywords& keys ) {
      93          40 :   Action::registerKeywords( keys );
      94          40 :   ActionAtomistic::registerKeywords( keys );
      95          40 :   ActionWithValue::registerKeywords( keys );
      96          40 :   keys.add("atoms","ATOMS","the atom numbers that you would like to store the masses and charges of");
      97          40 :   keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log");
      98          40 :   keys.remove("NUMERICAL_DERIVATIVES");
      99          80 :   keys.setValueDescription("scalar/vector","the " + keys.getDisplayName() + " of the atom/s");
     100          40 : }
     101             : 
     102          18 : SelectMassCharge::SelectMassCharge(const ActionOptions&ao):
     103             :   Action(ao),
     104             :   ActionAtomistic(ao),
     105          18 :   ActionWithValue(ao) {
     106             :   std::vector<AtomNumber> atoms;
     107          18 :   parseAtomList("ATOMS",atoms);
     108          18 :   log.printf("  getting %s of atoms : ", getName().c_str() );
     109        5162 :   for(unsigned i=0; i<atoms.size(); ++i) {
     110        5144 :     std::pair<std::size_t,std::size_t> p = getValueIndices( atoms[i] );
     111        5144 :     if( getName()=="MASS" && !masv[p.first]->isConstant() ) {
     112           0 :       error("cannot deal with non-constant " + getName() + " values");
     113             :     }
     114        5144 :     if( getName()=="CHARGE" && !chargev[p.first]->isConstant() ) {
     115           0 :       error("cannot deal with non-constant " + getName() + " values");
     116             :     }
     117        5144 :     log.printf("%d ", atoms[i].serial() );
     118             :   }
     119          18 :   log.printf("\n");
     120          18 :   requestAtoms(atoms);
     121          18 :   std::vector<std::size_t> shape(1);
     122          18 :   if(atoms.size()==1) {
     123           0 :     shape.resize(0);
     124             :   } else {
     125          18 :     shape[0] = atoms.size();
     126             :   }
     127          18 :   addValue( shape );
     128          18 :   setNotPeriodic();
     129          18 :   getPntrToComponent(0)->setConstant();
     130          18 : }
     131             : 
     132             : // calculator
     133          18 : void SelectMassCharge::calculate() {
     134          18 :   Value* myval = getPntrToComponent(0);
     135          18 :   if( getName()=="CHARGES" ) {
     136           0 :     if( !chargesWereSet ) {
     137           0 :       error("cannot determine charges are charges were not set");
     138             :     }
     139           0 :     for(unsigned i=0; i<getNumberOfAtoms(); ++i) {
     140           0 :       myval->set( i, getCharge(i) );
     141             :     }
     142             :   } else {
     143        5162 :     for(unsigned i=0; i<getNumberOfAtoms(); ++i) {
     144        5144 :       myval->set( i, getMass(i) );
     145             :     }
     146             :   }
     147          18 : }
     148             : 
     149             : }
     150             : }
     151             : 
     152             : 
     153             :