Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2020 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/ActionWithValue.h"
      23             : #include "core/ActionWithArguments.h"
      24             : #include "core/ActionRegister.h"
      25             : #include "tools/Random.h"
      26             : 
      27             : namespace PLMD {
      28             : namespace generic {
      29             : 
      30             : //+PLUMEDOC DIMRED CREATE_MASK
      31             : /*
      32             : Create a mask vector to use for landmark selection
      33             : 
      34             : \par Examples
      35             : 
      36             : */
      37             : //+ENDPLUMEDOC
      38             : 
      39             : class CreateMask :
      40             :   public ActionWithValue,
      41             :   public ActionWithArguments {
      42             : private:
      43             :   Random r;
      44             :   unsigned nzeros;
      45             :   enum {nomask,stride,random} type;
      46             : public:
      47             :   static void registerKeywords( Keywords& keys );
      48             :   CreateMask( const ActionOptions& );
      49           0 :   unsigned getNumberOfDerivatives() override {
      50           0 :     return 0;
      51             :   }
      52             :   void prepare() override ;
      53             :   void calculate() override ;
      54           6 :   void apply() override {}
      55             : };
      56             : 
      57             : PLUMED_REGISTER_ACTION(CreateMask,"CREATE_MASK")
      58             : 
      59          30 : void CreateMask::registerKeywords( Keywords& keys ) {
      60          30 :   Action::registerKeywords( keys );
      61          30 :   ActionWithValue::registerKeywords( keys );
      62          30 :   ActionWithArguments::registerKeywords( keys );
      63          30 :   keys.use("ARG");
      64          60 :   keys.add("compulsory","TYPE","the way the zeros are supposed to be set");
      65          60 :   keys.add("compulsory","NZEROS","the number of zeros that you want to put in the mask");
      66          60 :   keys.add("optional","SEED","the seed to use for the random number generator");
      67          30 :   keys.setValueDescription("a vector of zeros and ones that is used that can be used to mask some of the elements in a time series");
      68          30 : }
      69             : 
      70             : 
      71          15 : CreateMask::CreateMask( const ActionOptions& ao ) :
      72             :   Action(ao),
      73             :   ActionWithValue(ao),
      74             :   ActionWithArguments(ao),
      75          15 :   nzeros(0) {
      76          15 :   if( getNumberOfArguments()!=1 ) {
      77           0 :     error("should only be one argument to this action");
      78             :   }
      79          15 :   if( getPntrToArgument(0)->getRank()!=1 ) {
      80           0 :     error("argument should be a vector");
      81             :   }
      82             :   std::string stype;
      83          30 :   parse("TYPE",stype);
      84          15 :   if( stype!="nomask" ) {
      85          18 :     parse("NZEROS",nzeros);
      86             :   }
      87             : 
      88          15 :   if( stype=="nomask" ) {
      89           6 :     type=nomask;
      90           6 :     log.printf("  setting all points in output mask to zero \n");
      91           9 :   } else if( stype=="stride" ) {
      92           8 :     type=stride;
      93           8 :     log.printf("  setting every %d equally spaced points in output mask to zero \n", nzeros );
      94           1 :   } else if( stype=="random" ) {
      95           1 :     unsigned seed=230623;
      96           1 :     parse("SEED",seed);
      97           1 :     r.setSeed(-seed);
      98           1 :     getPntrToArgument(0)->buildDataStore();
      99           1 :     type=random;
     100           1 :     log.printf("  choosing %d points to set to non-zero in mask in accordance with input weights \n", nzeros );
     101             :   } else {
     102           0 :     error( stype + " is not a valid way input for TYPE");
     103             :   }
     104          15 :   std::vector<unsigned> shape(1);
     105          15 :   shape[0] = getPntrToArgument(0)->getShape()[0];
     106          15 :   addValue( shape );
     107          15 :   setNotPeriodic();
     108          15 :   getPntrToComponent(0)->buildDataStore();
     109          53 :   for(unsigned i=0; i<shape[0]; ++i) {
     110          38 :     getPntrToComponent(0)->set( i, 1.0 );
     111             :   }
     112          15 : }
     113             : 
     114          25 : void CreateMask::prepare() {
     115          25 :   Value* out=getPntrToComponent(0);
     116             :   Value* arg=getPntrToArgument(0);
     117          25 :   if( out->getShape()[0]!=arg->getShape()[0] ) {
     118          11 :     std::vector<unsigned> shape(1);
     119          11 :     shape[0] = arg->getShape()[0];
     120          11 :     out->setShape( shape );
     121             :   }
     122          25 :   if( type!=nomask ) {
     123         325 :     for(unsigned i=nzeros; i<out->getShape()[0]; ++i) {
     124         306 :       out->set( i, 1 );
     125             :     }
     126             :   }
     127          25 : }
     128             : 
     129          21 : void CreateMask::calculate() {
     130          21 :   Value* out=getPntrToComponent(0);
     131             :   Value* arg=getPntrToArgument(0);
     132          21 :   unsigned ns = arg->getShape()[0];
     133        1171 :   for(unsigned i=0; i<ns; ++i) {
     134        1150 :     out->set( i, 1.0 );
     135             :   }
     136             : 
     137          21 :   if( type==stride ) {
     138          11 :     std::size_t ss = int( std::floor( ns / nzeros ) );
     139         300 :     for(unsigned i=0; i<nzeros; ++i) {
     140         289 :       out->set( i*ss, 0.0 );
     141             :     }
     142          10 :   } else if( type==random ) {
     143          20 :     for(unsigned i=0; i<nzeros; ++i ) {
     144             :       double totweights = 0;
     145         112 :       for(unsigned j=0; j<ns; ++j) {
     146          96 :         if( out->get(j)>0 ) {
     147          72 :           totweights += arg->get(j);
     148             :         }
     149             :       }
     150          16 :       double rr = r.U01()*totweights;
     151             :       double accum=0;
     152          55 :       for(unsigned j=0; j<ns; ++j) {
     153          55 :         if( out->get(j)>0 ) {
     154          46 :           accum += arg->get(j);
     155             :         }
     156          55 :         if( accum<rr ) {
     157             :           continue;
     158             :         }
     159          16 :         out->set( j, 0 );
     160          16 :         break;
     161             :       }
     162             :     }
     163           6 :   } else if( type==nomask ) {
     164         555 :     for(unsigned i=0; i<ns; ++i) {
     165         549 :       out->set( i, 0.0 );
     166             :     }
     167             :   } else {
     168           0 :     error("invalid mask creation type");
     169             :   }
     170          21 : }
     171             : 
     172             : }
     173             : }