Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2023 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/ActionPilot.h"
      24             : #include "core/ActionRegister.h"
      25             : #include "tools/File.h"
      26             : #include "core/PlumedMain.h"
      27             : 
      28             : namespace PLMD {
      29             : namespace generic {
      30             : 
      31             : //+PLUMEDOC PRINTANALYSIS DUMPMASSCHARGE
      32             : /*
      33             : Dump masses and charges on a selected file.
      34             : 
      35             : This command dumps a file containing charges and masses.
      36             : It does so only once in the simulation (at first step).
      37             : File can be recycled in the \ref driver tool.
      38             : 
      39             : Notice that masses and charges are only written once at the beginning
      40             : of the simulation. In case no atom list is provided, charges and
      41             : masses for all atoms are written.
      42             : 
      43             : \par Examples
      44             : 
      45             : You can add the DUMPMASSCHARGE action at the end of the plumed.dat
      46             : file that you use during an MD simulations:
      47             : 
      48             : \plumedfile
      49             : c1: COM ATOMS=1-10
      50             : c2: COM ATOMS=11-20
      51             : DUMPATOMS ATOMS=c1,c2 FILE=coms.xyz STRIDE=100
      52             : 
      53             : DUMPMASSCHARGE FILE=mcfile
      54             : \endplumedfile
      55             : 
      56             : In this way, you will be able to use the same masses while processing
      57             : a trajectory from the \ref driver . To do so, you need to
      58             : add the --mc flag on the driver command line, e.g.
      59             : \verbatim
      60             : plumed driver --mc mcfile --plumed plumed.dat --ixyz traj.xyz
      61             : \endverbatim
      62             : 
      63             : With the following input you can dump only the charges for a specific
      64             : group:
      65             : 
      66             : \plumedfile
      67             : solute_ions: GROUP ATOMS=1-121,200-2012
      68             : DUMPATOMS FILE=traj.gro ATOMS=solute_ions STRIDE=100
      69             : DUMPMASSCHARGE FILE=mcfile ATOMS=solute_ions
      70             : \endplumedfile
      71             : 
      72             : */
      73             : //+ENDPLUMEDOC
      74             : 
      75             : class DumpMassCharge:
      76             :   public ActionAtomistic,
      77             :   public ActionPilot {
      78             :   std::string file;
      79             :   bool first;
      80             :   bool second;
      81             :   bool print_masses;
      82             :   bool print_charges;
      83             : public:
      84             :   explicit DumpMassCharge(const ActionOptions&);
      85             :   ~DumpMassCharge();
      86             :   static void registerKeywords( Keywords& keys );
      87           0 :   bool actionHasForces() override {
      88           0 :     return false;
      89             :   }
      90             :   void prepare() override;
      91          94 :   void calculate() override {}
      92          94 :   void apply() override {}
      93             :   void update() override;
      94             : };
      95             : 
      96             : PLUMED_REGISTER_ACTION(DumpMassCharge,"DUMPMASSCHARGE")
      97             : 
      98          18 : void DumpMassCharge::registerKeywords( Keywords& keys ) {
      99          18 :   Action::registerKeywords( keys );
     100          18 :   ActionPilot::registerKeywords( keys );
     101          18 :   ActionAtomistic::registerKeywords( keys );
     102          36 :   keys.add("compulsory","STRIDE","1","the frequency with which the atoms should be output");
     103          36 :   keys.add("atoms", "ATOMS", "the atom indices whose charges and masses you would like to print out");
     104          36 :   keys.add("compulsory", "FILE", "file on which to output charges and masses.");
     105          36 :   keys.addFlag("ONLY_MASSES",false,"Only output masses to file");
     106          36 :   keys.addFlag("ONLY_CHARGES",false,"Only output charges to file");
     107          18 : }
     108             : 
     109          14 : DumpMassCharge::DumpMassCharge(const ActionOptions&ao):
     110             :   Action(ao),
     111             :   ActionAtomistic(ao),
     112             :   ActionPilot(ao),
     113          14 :   first(true),
     114          14 :   second(true),
     115          14 :   print_masses(true),
     116          14 :   print_charges(true) {
     117             :   std::vector<AtomNumber> atoms;
     118          28 :   parse("FILE",file);
     119          14 :   if(file.length()==0) {
     120           0 :     error("name of output file was not specified");
     121             :   }
     122          14 :   log.printf("  output written to file %s\n",file.c_str());
     123             : 
     124          28 :   parseAtomList("ATOMS",atoms);
     125             : 
     126          14 :   if(atoms.size()==0) {
     127          10 :     std::vector<std::string> strvec(1);
     128             :     strvec[0]="@mdatoms";
     129          10 :     interpretAtomList( strvec,atoms );
     130          10 :   }
     131             : 
     132          14 :   bool only_masses = false;
     133          14 :   parseFlag("ONLY_MASSES",only_masses);
     134          14 :   if(only_masses) {
     135           1 :     print_charges = false;
     136           1 :     log.printf("  only masses will be written to file\n");
     137             :   }
     138             : 
     139          14 :   bool only_charges = false;
     140          14 :   parseFlag("ONLY_CHARGES",only_charges);
     141          14 :   if(only_charges) {
     142           1 :     print_masses = false;
     143           1 :     log.printf("  only charges will be written to file\n");
     144             :   }
     145             : 
     146             : 
     147          14 :   checkRead();
     148             : 
     149          14 :   log.printf("  printing the following atoms:" );
     150        1224 :   for(unsigned i=0; i<atoms.size(); ++i) {
     151        1210 :     log.printf(" %d",atoms[i].serial() );
     152             :   }
     153          14 :   log.printf("\n");
     154          14 :   requestAtoms(atoms);
     155             : 
     156          14 :   if(only_masses && only_charges) {
     157           0 :     plumed_merror("using both ONLY_MASSES and ONLY_CHARGES doesn't make sense");
     158             :   }
     159             : 
     160          14 : }
     161             : 
     162          94 : void DumpMassCharge::prepare() {
     163          94 :   if(!first && second) {
     164          14 :     requestAtoms(std::vector<AtomNumber>());
     165          14 :     second=false;
     166             :   }
     167          94 : }
     168             : 
     169          94 : void DumpMassCharge::update() {
     170          94 :   if(!first) {
     171          80 :     return;
     172             :   }
     173          14 :   first=false;
     174             : 
     175          14 :   OFile of;
     176          14 :   of.link(*this);
     177          14 :   of.open(file);
     178             : 
     179        1224 :   for(unsigned i=0; i<getNumberOfAtoms(); i++) {
     180        1210 :     int ii=getAbsoluteIndex(i).index();
     181        1210 :     of.printField("index",ii);
     182        1210 :     if(print_masses) {
     183        2204 :       of.printField("mass",getMass(i));
     184             :     }
     185        1210 :     if(print_charges) {
     186        2204 :       of.printField("charge",getCharge(i));
     187             :     }
     188        1210 :     of.printField();
     189             :   }
     190          14 : }
     191             : 
     192          28 : DumpMassCharge::~DumpMassCharge() {
     193          28 : }
     194             : 
     195             : 
     196             : }
     197             : }