Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2023 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/ActionPilot.h"
      23             : #include "core/ActionWithArguments.h"
      24             : #include "core/ActionAtomistic.h"
      25             : #include "core/ActionRegister.h"
      26             : #include "tools/CheckInRange.h"
      27             : 
      28             : //+PLUMEDOC PRINTANALYSIS PRINT_NDX
      29             : /*
      30             : Print an ndx file
      31             : 
      32             : The following example shows how you can use this command to print out the indices of all the atoms
      33             : that have a coordination number that is greater than or equal to 4.
      34             : 
      35             : ```plumed
      36             : # These three lines calculate the coordination numbers of 100 atoms
      37             : c1: CONTACT_MATRIX GROUP=1-100 SWITCH={RATIONAL R_0=0.1 NN=6 MM=12}
      38             : ones: ONES SIZE=100
      39             : cc: MATRIX_VECTOR_PRODUCT ARG=c1,ones
      40             : 
      41             : # This command then prints the indices of the atoms that have a coordination number that is greater than 4
      42             : # every step
      43             : PRINT_NDX ATOMS=1-100 ARG=cc GREATER_THAN_OR_EQUAL=4
      44             : ```
      45             : 
      46             : This command is used in the [OUTPUT_CLUSTER](OUTPUT_CLUSTER.md) command that you can use to output the indices
      47             : of the atoms that are in a particular cluster.
      48             : 
      49             : */
      50             : //+ENDPLUMEDOC
      51             : 
      52             : namespace PLMD {
      53             : namespace generic {
      54             : 
      55             : class PrintNDX :
      56             :   public ActionPilot,
      57             :   public ActionAtomistic,
      58             :   public ActionWithArguments {
      59             :   std::string file;
      60             :   OFile ofile;
      61             :   CheckInRange bounds;
      62             : public:
      63           4 :   void calculate() override {}
      64             :   std::string writeInGraph() const override;
      65             :   explicit PrintNDX(const ActionOptions&);
      66             :   static void registerKeywords(Keywords& keys);
      67           0 :   bool actionHasForces() override {
      68           0 :     return false;
      69             :   }
      70           0 :   void calculateNumericalDerivatives( ActionWithValue* a=NULL ) override {
      71           0 :     plumed_error();
      72             :   }
      73             :   void lockRequests() override;
      74             :   void unlockRequests() override;
      75           4 :   void apply() override {}
      76             :   void update() override;
      77          12 :   ~PrintNDX() {}
      78             : };
      79             : 
      80             : PLUMED_REGISTER_ACTION(PrintNDX,"PRINT_NDX")
      81             : 
      82           8 : void PrintNDX::registerKeywords(Keywords& keys) {
      83           8 :   Action::registerKeywords(keys);
      84           8 :   ActionPilot::registerKeywords(keys);
      85           8 :   ActionAtomistic::registerKeywords( keys );
      86           8 :   ActionWithArguments::registerKeywords(keys);
      87          16 :   keys.addInputKeyword("optional","ARG","vector","the labels of vectors that should be used when printind the NDX file");
      88           8 :   keys.add("atoms","ATOMS","the list of atoms that have the corresponding arguments");
      89           8 :   keys.add("compulsory","STRIDE","1","the frequency with which the quantities of interest should be output");
      90           8 :   keys.add("optional","FILE","the name of the file on which to output these quantities");
      91           8 :   keys.add("optional","LESS_THAN_OR_EQUAL","when printing with arguments that are vectors only print components of vectors have a value less than or equal to this value");
      92           8 :   keys.add("optional","GREATER_THAN_OR_EQUAL","when printing with arguments that are vectors only print components of vectors have a value greater than or equal to this value");
      93           8 :   keys.use("RESTART");
      94           8 :   keys.use("UPDATE_FROM");
      95           8 :   keys.use("UPDATE_UNTIL");
      96           8 : }
      97             : 
      98           4 : PrintNDX::PrintNDX(const ActionOptions&ao):
      99             :   Action(ao),
     100             :   ActionPilot(ao),
     101             :   ActionAtomistic(ao),
     102           4 :   ActionWithArguments(ao) {
     103           4 :   ofile.link(*this);
     104           8 :   parse("FILE",file);
     105           4 :   if(file.length()>0) {
     106           4 :     ofile.open(file);
     107           4 :     log.printf("  on file %s\n",file.c_str());
     108             :   } else {
     109           0 :     log.printf("  on plumed log file\n");
     110           0 :     ofile.link(log);
     111             :   }
     112             :   std::vector<AtomNumber> all_atoms;
     113           8 :   parseAtomList("ATOMS",all_atoms);
     114           4 :   std::vector<std::string> argnames( getNumberOfArguments() );
     115           4 :   requestAtoms( all_atoms, false );
     116           8 :   for(unsigned i=0; i<getNumberOfArguments(); ++i) {
     117           4 :     if( getPntrToArgument(i)->getRank()!=1 || getPntrToArgument(i)->hasDerivatives() ) {
     118           0 :       error("arguments for print ndx should be vector");
     119             :     }
     120           4 :     if( getPntrToArgument(i)->getShape()[0]!=all_atoms.size() ) {
     121           0 :       error("mismatch between number of arguments and number of input atoms");
     122             :     }
     123           4 :     getPntrToArgument(i)->buildDataStore(true);
     124             :     argnames[i] = getPntrToArgument(i)->getName();
     125             :   }
     126           4 :   log.printf("  printing ndx file containing indices of atoms that have arguments in ranges prescribed below \n");
     127           4 :   log.printf("  full set of atom indices investigated are : ");
     128        7988 :   for(unsigned int i=0; i<all_atoms.size(); ++i) {
     129        7984 :     if ( (i+1) % 25 == 0 ) {
     130         316 :       log.printf("  \n");
     131             :     }
     132        7984 :     log.printf("  %d", all_atoms[i].serial());
     133             :   }
     134           4 :   log.printf("\n");
     135             :   std::vector<std::string> str_upper, str_lower;
     136             :   std::string errors;
     137           4 :   parseVector("LESS_THAN_OR_EQUAL",str_upper);
     138           8 :   parseVector("GREATER_THAN_OR_EQUAL",str_lower);
     139           4 :   if( !bounds.setBounds( getNumberOfArguments(), str_lower, str_upper, errors ) ) {
     140           0 :     error( errors );
     141             :   }
     142           4 :   if( bounds.wereSet() ) {
     143           8 :     log.printf("  %s \n", bounds.report( argnames ).c_str() );
     144             :   }
     145           4 :   checkRead();
     146           8 : }
     147             : 
     148           0 : std::string PrintNDX::writeInGraph() const {
     149           0 :   return getName() + "\n" + "FILE=" + file;
     150             : }
     151             : 
     152           4 : void PrintNDX::lockRequests() {
     153             :   ActionWithArguments::lockRequests();
     154             :   ActionAtomistic::lockRequests();
     155           4 : }
     156             : 
     157           4 : void PrintNDX::unlockRequests() {
     158             :   ActionWithArguments::unlockRequests();
     159             :   ActionAtomistic::unlockRequests();
     160           4 : }
     161             : 
     162           4 : void PrintNDX::update() {
     163             :   unsigned n=0;
     164           4 :   std::vector<double> argvals( getNumberOfArguments() );
     165           4 :   ofile.printf("[ %s step %d ] \n", getLabel().c_str(), getStep() );
     166        7988 :   for(unsigned i=0; i<getNumberOfAtoms(); ++i) {
     167       15968 :     for(unsigned j=0; j<getNumberOfArguments(); ++j) {
     168        7984 :       argvals[j] = getPntrToArgument(j)->get(i);
     169             :     }
     170        7984 :     if( bounds.check( argvals ) ) {
     171         156 :       ofile.printf("%6d", getAbsoluteIndexes()[i].serial() );
     172         156 :       n++;
     173         156 :       if( n%15==0 ) {
     174           8 :         ofile.printf("\n");
     175             :       }
     176             :     }
     177             :   }
     178           4 :   ofile.printf("\n");
     179           4 : }
     180             : 
     181             : }
     182             : 
     183             : 
     184             : }