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 FILE=index.ndx GREATER_THAN_OR_EQUAL=4
      44             : ```
      45             : 
      46             : Obviously, if you want to print the indices of the atoms that have a coordination number that is equal to 4
      47             : you use a command like the one shown below:
      48             : 
      49             : ```plumed
      50             : # These three lines calculate the coordination numbers of 100 atoms
      51             : c1: CONTACT_MATRIX GROUP=1-100 SWITCH={RATIONAL R_0=0.1 NN=6 MM=12}
      52             : ones: ONES SIZE=100
      53             : cc: MATRIX_VECTOR_PRODUCT ARG=c1,ones
      54             : 
      55             : # This command then prints the indices of the atoms that have a coordination number that is equal to 4
      56             : # on every 10th step of the simulation
      57             : PRINT_NDX ...
      58             :    ATOMS=1-100 ARG=cc FILE=index.ndx
      59             :    LESS_THAN_OR_EQUAL=4
      60             :    GREATER_THAN_OR_EQUAL=4
      61             :    STRIDE=10
      62             : ...
      63             : ```
      64             : 
      65             : A command like the one above is used in the [OUTPUT_CLUSTER](OUTPUT_CLUSTER.md) command that you can use to output the indices
      66             : of the atoms that are in a particular cluster.
      67             : 
      68             : ## RESTART, UPDATE_FROM and UPDATE_UNTIL
      69             : 
      70             : Notice that the RESTART, UPDATE_FROM and UPDATE_UNTIL keywords keywords
      71             : can be used in this action in the same way as they are used for [PRINT](PRINT.md).
      72             : Consequently, if you would like to append to an existing file called `index.ndx` instead of backing that
      73             : file up at the start of the calculation and outputting the data from the calculation on a new file called `index.ndx`
      74             : you would use an input like the one shown below:
      75             : 
      76             : ```plumed
      77             : c1: CONTACT_MATRIX GROUP=1-100 SWITCH={RATIONAL R_0=0.1 NN=6 MM=12}
      78             : ones: ONES SIZE=100
      79             : cc: MATRIX_VECTOR_PRODUCT ARG=c1,ones
      80             : 
      81             : PRINT_NDX ...
      82             :   ATOMS=1-100 ARG=cc FILE=index.ndx
      83             :   GREATER_THAN_OR_EQUAL=4 RESTART=YES
      84             : ...
      85             : ```
      86             : 
      87             : Similarly, if you want to only output the `index.ndx` file during the 400 ps time interval after the first
      88             : 100 ps of the simulation you would use an input like the one shown below:
      89             : 
      90             : ```plumed
      91             : c1: CONTACT_MATRIX GROUP=1-100 SWITCH={RATIONAL R_0=0.1 NN=6 MM=12}
      92             : ones: ONES SIZE=100
      93             : cc: MATRIX_VECTOR_PRODUCT ARG=c1,ones
      94             : 
      95             : PRINT_NDX ...
      96             :   ATOMS=1-100 ARG=cc FILE=index.ndx
      97             :   GREATER_THAN_OR_EQUAL=4
      98             :   UPDATE_FROM=100 UPDATE_UNTIL=500
      99             : ...
     100             : ```
     101             : 
     102             : */
     103             : //+ENDPLUMEDOC
     104             : 
     105             : namespace PLMD {
     106             : namespace generic {
     107             : 
     108             : class PrintNDX :
     109             :   public ActionPilot,
     110             :   public ActionAtomistic,
     111             :   public ActionWithArguments {
     112             :   std::string file;
     113             :   OFile ofile;
     114             :   CheckInRange bounds;
     115             : public:
     116           4 :   void calculate() override {}
     117             :   std::string writeInGraph() const override;
     118             :   explicit PrintNDX(const ActionOptions&);
     119             :   static void registerKeywords(Keywords& keys);
     120           0 :   bool actionHasForces() override {
     121           0 :     return false;
     122             :   }
     123           0 :   void calculateNumericalDerivatives( ActionWithValue* a=NULL ) override {
     124           0 :     plumed_error();
     125             :   }
     126             :   void lockRequests() override;
     127             :   void unlockRequests() override;
     128           4 :   void apply() override {}
     129             :   void update() override;
     130          12 :   ~PrintNDX() {}
     131             : };
     132             : 
     133             : PLUMED_REGISTER_ACTION(PrintNDX,"PRINT_NDX")
     134             : 
     135          10 : void PrintNDX::registerKeywords(Keywords& keys) {
     136          10 :   Action::registerKeywords(keys);
     137          10 :   ActionPilot::registerKeywords(keys);
     138          10 :   ActionAtomistic::registerKeywords( keys );
     139          10 :   ActionWithArguments::registerKeywords(keys);
     140          20 :   keys.addInputKeyword("optional","ARG","vector","the labels of vectors that should be used when printind the NDX file");
     141          10 :   keys.add("atoms","ATOMS","the list of atoms that have the corresponding arguments");
     142          10 :   keys.add("compulsory","STRIDE","1","the frequency with which the quantities of interest should be output");
     143          10 :   keys.add("optional","FILE","the name of the file on which to output these quantities");
     144          10 :   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");
     145          10 :   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");
     146          10 :   keys.use("RESTART");
     147          10 :   keys.use("UPDATE_FROM");
     148          10 :   keys.use("UPDATE_UNTIL");
     149          10 : }
     150             : 
     151           4 : PrintNDX::PrintNDX(const ActionOptions&ao):
     152             :   Action(ao),
     153             :   ActionPilot(ao),
     154             :   ActionAtomistic(ao),
     155           4 :   ActionWithArguments(ao) {
     156           4 :   ofile.link(*this);
     157           8 :   parse("FILE",file);
     158           4 :   if(file.length()>0) {
     159           4 :     ofile.open(file);
     160           4 :     log.printf("  on file %s\n",file.c_str());
     161             :   } else {
     162           0 :     log.printf("  on plumed log file\n");
     163           0 :     ofile.link(log);
     164             :   }
     165           4 :   std::vector<AtomNumber> all_atoms;
     166           8 :   parseAtomList("ATOMS",all_atoms);
     167           4 :   std::vector<std::string> argnames( getNumberOfArguments() );
     168           4 :   requestAtoms( all_atoms, false );
     169           8 :   for(unsigned i=0; i<getNumberOfArguments(); ++i) {
     170           4 :     if( getPntrToArgument(i)->getRank()!=1 || getPntrToArgument(i)->hasDerivatives() ) {
     171           0 :       error("arguments for print ndx should be vector");
     172             :     }
     173           4 :     if( getPntrToArgument(i)->getShape()[0]!=all_atoms.size() ) {
     174           0 :       error("mismatch between number of arguments and number of input atoms");
     175             :     }
     176             :     argnames[i] = getPntrToArgument(i)->getName();
     177             :   }
     178           4 :   log.printf("  printing ndx file containing indices of atoms that have arguments in ranges prescribed below \n");
     179           4 :   log.printf("  full set of atom indices investigated are : ");
     180        7988 :   for(unsigned int i=0; i<all_atoms.size(); ++i) {
     181        7984 :     if ( (i+1) % 25 == 0 ) {
     182         316 :       log.printf("  \n");
     183             :     }
     184        7984 :     log.printf("  %d", all_atoms[i].serial());
     185             :   }
     186           4 :   log.printf("\n");
     187           4 :   std::vector<std::string> str_upper, str_lower;
     188             :   std::string errors;
     189           4 :   parseVector("LESS_THAN_OR_EQUAL",str_upper);
     190           4 :   parseVector("GREATER_THAN_OR_EQUAL",str_lower);
     191           4 :   if( !bounds.setBounds( getNumberOfArguments(), str_lower, str_upper, errors ) ) {
     192           0 :     error( errors );
     193             :   }
     194           4 :   if( bounds.wereSet() ) {
     195           8 :     log.printf("  %s \n", bounds.report( argnames ).c_str() );
     196             :   }
     197           4 :   checkRead();
     198           4 : }
     199             : 
     200           0 : std::string PrintNDX::writeInGraph() const {
     201           0 :   return getName() + "\n" + "FILE=" + file;
     202             : }
     203             : 
     204           4 : void PrintNDX::lockRequests() {
     205             :   ActionWithArguments::lockRequests();
     206             :   ActionAtomistic::lockRequests();
     207           4 : }
     208             : 
     209           4 : void PrintNDX::unlockRequests() {
     210             :   ActionWithArguments::unlockRequests();
     211             :   ActionAtomistic::unlockRequests();
     212           4 : }
     213             : 
     214           4 : void PrintNDX::update() {
     215             :   unsigned n=0;
     216           4 :   std::vector<double> argvals( getNumberOfArguments() );
     217           4 :   ofile.printf("[ %s step %lld ] \n", getLabel().c_str(), getStep() );
     218        7988 :   for(unsigned i=0; i<getNumberOfAtoms(); ++i) {
     219       15968 :     for(unsigned j=0; j<getNumberOfArguments(); ++j) {
     220        7984 :       argvals[j] = getPntrToArgument(j)->get(i);
     221             :     }
     222        7984 :     if( bounds.check( argvals ) ) {
     223         156 :       ofile.printf("%6d", getAbsoluteIndexes()[i].serial() );
     224         156 :       n++;
     225         156 :       if( n%15==0 ) {
     226           8 :         ofile.printf("\n");
     227             :       }
     228             :     }
     229             :   }
     230           4 :   ofile.printf("\n");
     231           4 : }
     232             : 
     233             : }
     234             : 
     235             : 
     236             : }