Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2014-2017 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 "core/PlumedMain.h"
      26             : #include "core/ActionSet.h"
      27             : 
      28             : //+PLUMEDOC PRINTANALYSIS SELECT_WITH_MASK
      29             : /*
      30             : Use a mask to select elements of an array
      31             : 
      32             : \par Examples
      33             : 
      34             : */
      35             : //+ENDPLUMEDOC
      36             : 
      37             : namespace PLMD {
      38             : namespace valtools {
      39             : 
      40             : class SelectWithMask :
      41             :   public ActionWithValue,
      42             :   public ActionWithArguments {
      43             : private:
      44             :   unsigned getOutputVectorLength( const Value* mask ) const ;
      45             : public:
      46             :   static void registerKeywords( Keywords& keys );
      47             : /// Constructor
      48             :   explicit SelectWithMask(const ActionOptions&);
      49             : /// Get the number of derivatives
      50          98 :   unsigned getNumberOfDerivatives() override { return 0; }
      51             : ///
      52             :   void getMatrixColumnTitles( std::vector<std::string>& argnames ) const override ;
      53             : ///
      54             :   void prepare() override ;
      55             : /// Do the calculation
      56             :   void calculate() override;
      57             : ///
      58             :   void apply() override;
      59             : };
      60             : 
      61             : PLUMED_REGISTER_ACTION(SelectWithMask,"SELECT_WITH_MASK")
      62             : 
      63         178 : void SelectWithMask::registerKeywords( Keywords& keys ) {
      64         178 :   Action::registerKeywords( keys ); ActionWithValue::registerKeywords( keys );
      65         178 :   ActionWithArguments::registerKeywords( keys ); keys.use("ARG");
      66         356 :   keys.add("optional","ROW_MASK","an array with ones in the rows of the matrix that you want to discard");
      67         356 :   keys.add("optional","COLUMN_MASK","an array with ones in the columns of the matrix that you want to discard");
      68         356 :   keys.add("compulsory","MASK","an array with ones in the components that you want to discard");
      69         178 :   keys.setValueDescription("a vector/matrix of values that is obtained using a mask to select elements of interest");
      70         178 : }
      71             : 
      72          93 : SelectWithMask::SelectWithMask(const ActionOptions& ao):
      73             :   Action(ao),
      74             :   ActionWithValue(ao),
      75          93 :   ActionWithArguments(ao)
      76             : {
      77          93 :   if( getNumberOfArguments()!=1 ) error("should only be one argument for this action");
      78          93 :   getPntrToArgument(0)->buildDataStore(); std::vector<unsigned> shape;
      79          93 :   if( getPntrToArgument(0)->getRank()==1 ) {
      80         136 :     std::vector<Value*> mask; parseArgumentList("MASK",mask);
      81          68 :     if( mask.size()!=1 ) error("should only be one input for mask");
      82          68 :     if( mask[0]->getNumberOfValues()!=getPntrToArgument(0)->getNumberOfValues() ) error("mismatch between size of mask and input vector");
      83          68 :     log.printf("  creating vector from elements of %s who have a corresponding element in %s that is zero\n", getPntrToArgument(0)->getName().c_str(), mask[0]->getName().c_str() );
      84          68 :     std::vector<Value*> args( getArguments() ); args.push_back( mask[0] ); requestArguments( args );
      85          68 :     shape.resize(1,0); if( (mask[0]->getPntrToAction())->getName()=="CONSTANT" ) shape[0]=getOutputVectorLength(mask[0]);
      86          25 :   } else if( getPntrToArgument(0)->getRank()==2 ) {
      87          75 :     std::vector<Value*> rmask, cmask; parseArgumentList("ROW_MASK",rmask); parseArgumentList("COLUMN_MASK",cmask);
      88          25 :     if( rmask.size()==0 && cmask.size()==0 ) {
      89           0 :       error("no mask elements have been specified");
      90          25 :     } else if( cmask.size()==0 ) {
      91         144 :       std::string con="0"; for(unsigned i=1; i<getPntrToArgument(0)->getShape()[1]; ++i) con += ",0";
      92          22 :       plumed.readInputLine( getLabel() + "_colmask: CONSTANT VALUES=" + con ); std::vector<std::string> labs(1, getLabel() + "_colmask");
      93          11 :       ActionWithArguments::interpretArgumentList( labs, plumed.getActionSet(), this, cmask );
      94          25 :     } else if( rmask.size()==0 ) {
      95          13 :       std::string con="0"; for(unsigned i=1; i<getPntrToArgument(0)->getShape()[0]; ++i) con += ",0";
      96           2 :       plumed.readInputLine( getLabel() + "_rowmask: CONSTANT VALUES=" + con ); std::vector<std::string> labs(1, getLabel() + "_rowmask");
      97           1 :       ActionWithArguments::interpretArgumentList( labs, plumed.getActionSet(), this, rmask );
      98           1 :     }
      99          25 :     shape.resize(2);
     100          25 :     rmask[0]->buildDataStore(); shape[0] = getOutputVectorLength( rmask[0] );
     101          25 :     cmask[0]->buildDataStore(); shape[1] = getOutputVectorLength( cmask[0] );
     102          25 :     std::vector<Value*> args( getArguments() ); args.push_back( rmask[0] );
     103          25 :     args.push_back( cmask[0] ); requestArguments( args );
     104           0 :   } else error("input should be vector or matrix");
     105             : 
     106          93 :   addValue( shape ); getPntrToComponent(0)->buildDataStore();
     107          93 :   if( getPntrToArgument(0)->isPeriodic() ) {
     108           7 :     std::string min, max; getPntrToArgument(0)->getDomain( min, max ); setPeriodic( min, max );
     109          86 :   } else setNotPeriodic();
     110          93 :   if( getPntrToComponent(0)->getRank()==2 ) getPntrToComponent(0)->reshapeMatrixStore( shape[1] );
     111          93 : }
     112             : 
     113       10693 : unsigned SelectWithMask::getOutputVectorLength( const Value* mask ) const  {
     114             :   unsigned l=0;
     115      154139 :   for(unsigned i=0; i<mask->getNumberOfValues(); ++i) {
     116      143446 :     if( fabs(mask->get(i))>0 ) continue;
     117      133435 :     l++;
     118             :   }
     119       10693 :   return l;
     120             : }
     121             : 
     122          18 : void SelectWithMask::getMatrixColumnTitles( std::vector<std::string>& argnames ) const {
     123          18 :   std::vector<std::string> alltitles; (getPntrToArgument(0)->getPntrToAction())->getMatrixColumnTitles( alltitles );
     124         103 :   for(unsigned i=0; i<alltitles.size(); ++i) {
     125          85 :     if( fabs(getPntrToArgument(2)->get(i))>0 ) continue;
     126          51 :     argnames.push_back( alltitles[i] );
     127             :   }
     128          18 : }
     129             : 
     130       10551 : void SelectWithMask::prepare() {
     131       10551 :   Value* arg = getPntrToArgument(0); Value* out = getPntrToComponent(0);
     132       10551 :   if( arg->getRank()==1 ) {
     133             :     Value* mask = getPntrToArgument(1);
     134       10516 :     std::vector<unsigned> shape(1); shape[0]=getOutputVectorLength( mask );
     135       10516 :     if( out->getNumberOfValues()!=shape[0] ) {
     136          19 :       if( shape[0]==1 ) shape.resize(0);
     137          19 :       out->setShape(shape);
     138             :     }
     139          35 :   } else if( arg->getRank()==2 ) {
     140          35 :     std::vector<unsigned> outshape(2);
     141          35 :     Value* rmask = getPntrToArgument(1); outshape[0] = getOutputVectorLength( rmask );
     142          35 :     Value* cmask = getPntrToArgument(2); outshape[1] = getOutputVectorLength( cmask );
     143          35 :     if( out->getShape()[0]!=outshape[0] || out->getShape()[1]!=outshape[1] ) {
     144          20 :       out->setShape(outshape); out->reshapeMatrixStore( outshape[1] );
     145             :     }
     146             :   }
     147       10551 : }
     148             : 
     149       10543 : void SelectWithMask::calculate() {
     150       10543 :   Value* arg = getPntrToArgument(0); Value* out = getPntrToComponent(0);
     151       10543 :   if( arg->getRank()==1 ) {
     152             :     Value* mask = getPntrToArgument(1); unsigned n=0;
     153      149144 :     for(unsigned i=0; i<mask->getNumberOfValues(); ++i) {
     154      138632 :       if( fabs(mask->get(i))>0 ) continue;
     155      131198 :       out->set(n, arg->get(i) ); n++;
     156             :     }
     157          31 :   } else if ( arg->getRank()==2 ) {
     158          31 :     std::vector<unsigned> outshape( out->getShape() );
     159          31 :     unsigned n = 0; std::vector<unsigned> inshape( arg->getShape() );
     160             :     Value* rmask = getPntrToArgument(1); Value* cmask = getPntrToArgument(2);
     161        1774 :     for(unsigned i=0; i<inshape[0]; ++i) {
     162        1743 :       if( fabs(rmask->get(i))>0 ) continue;
     163             :       unsigned m = 0;
     164      378651 :       for(unsigned j=0; j<inshape[1]; ++j) {
     165      377500 :         if( fabs(cmask->get(j))>0 ) continue;
     166      189405 :         out->set( n*outshape[1] + m, arg->get(i*inshape[1] + j) );
     167      189405 :         m++;
     168             :       }
     169        1151 :       n++;
     170             :     }
     171             :   }
     172       10543 : }
     173             : 
     174       10505 : void SelectWithMask::apply() {
     175       10505 :   if( doNotCalculateDerivatives() || !getPntrToComponent(0)->forcesWereAdded() ) return ;
     176             : 
     177       10443 :   Value* arg = getPntrToArgument(0); Value* out = getPntrToComponent(0);
     178       10443 :   if( arg->getRank()==1 ) {
     179             :     unsigned n=0; Value* mask = getPntrToArgument(1);
     180      145276 :     for(unsigned i=0; i<mask->getNumberOfValues(); ++i) {
     181      134833 :       if( fabs(mask->get(i))>0 ) continue;
     182      130680 :       arg->addForce(i, out->getForce(n) ); n++;
     183             :     }
     184           0 :   } else if( arg->getRank()==2 ) {
     185             :     unsigned n = 0;
     186           0 :     std::vector<unsigned> inshape( arg->getShape() );
     187           0 :     std::vector<unsigned> outshape( out->getShape() );
     188             :     Value* rmask = getPntrToArgument(1); Value* cmask = getPntrToArgument(2);
     189           0 :     for(unsigned i=0; i<inshape[0]; ++i) {
     190           0 :       if( fabs(rmask->get(i))>0 ) continue;
     191             :       unsigned m = 0;
     192           0 :       for(unsigned j=0; j<inshape[1]; ++j) {
     193           0 :         if( fabs(cmask->get(j))>0 ) continue;
     194           0 :         arg->addForce( i*inshape[1] + j, out->getForce(n*outshape[1] + m) );
     195           0 :         m++;
     196             :       }
     197           0 :       n++;
     198             :     }
     199             :   }
     200             : }
     201             : 
     202             : 
     203             : 
     204             : }
     205             : }