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 {
      51          98 :     return 0;
      52             :   }
      53             : ///
      54             :   void getMatrixColumnTitles( std::vector<std::string>& argnames ) const override ;
      55             : ///
      56             :   void prepare() override ;
      57             : /// Do the calculation
      58             :   void calculate() override;
      59             : ///
      60             :   void apply() override;
      61             : };
      62             : 
      63             : PLUMED_REGISTER_ACTION(SelectWithMask,"SELECT_WITH_MASK")
      64             : 
      65         178 : void SelectWithMask::registerKeywords( Keywords& keys ) {
      66         178 :   Action::registerKeywords( keys );
      67         178 :   ActionWithValue::registerKeywords( keys );
      68         178 :   ActionWithArguments::registerKeywords( keys );
      69         178 :   keys.use("ARG");
      70         356 :   keys.add("optional","ROW_MASK","an array with ones in the rows of the matrix that you want to discard");
      71         356 :   keys.add("optional","COLUMN_MASK","an array with ones in the columns of the matrix that you want to discard");
      72         356 :   keys.add("compulsory","MASK","an array with ones in the components that you want to discard");
      73         178 :   keys.setValueDescription("a vector/matrix of values that is obtained using a mask to select elements of interest");
      74         178 : }
      75             : 
      76          93 : SelectWithMask::SelectWithMask(const ActionOptions& ao):
      77             :   Action(ao),
      78             :   ActionWithValue(ao),
      79          93 :   ActionWithArguments(ao) {
      80          93 :   if( getNumberOfArguments()!=1 ) {
      81           0 :     error("should only be one argument for this action");
      82             :   }
      83          93 :   getPntrToArgument(0)->buildDataStore();
      84             :   std::vector<unsigned> shape;
      85          93 :   if( getPntrToArgument(0)->getRank()==1 ) {
      86             :     std::vector<Value*> mask;
      87         136 :     parseArgumentList("MASK",mask);
      88          68 :     if( mask.size()!=1 ) {
      89           0 :       error("should only be one input for mask");
      90             :     }
      91          68 :     if( mask[0]->getNumberOfValues()!=getPntrToArgument(0)->getNumberOfValues() ) {
      92           0 :       error("mismatch between size of mask and input vector");
      93             :     }
      94          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() );
      95          68 :     std::vector<Value*> args( getArguments() );
      96          68 :     args.push_back( mask[0] );
      97          68 :     requestArguments( args );
      98          68 :     shape.resize(1,0);
      99          68 :     if( (mask[0]->getPntrToAction())->getName()=="CONSTANT" ) {
     100          57 :       shape[0]=getOutputVectorLength(mask[0]);
     101             :     }
     102          25 :   } else if( getPntrToArgument(0)->getRank()==2 ) {
     103             :     std::vector<Value*> rmask, cmask;
     104          25 :     parseArgumentList("ROW_MASK",rmask);
     105          50 :     parseArgumentList("COLUMN_MASK",cmask);
     106          25 :     if( rmask.size()==0 && cmask.size()==0 ) {
     107           0 :       error("no mask elements have been specified");
     108          25 :     } else if( cmask.size()==0 ) {
     109          11 :       std::string con="0";
     110         144 :       for(unsigned i=1; i<getPntrToArgument(0)->getShape()[1]; ++i) {
     111             :         con += ",0";
     112             :       }
     113          11 :       plumed.readInputWords( Tools::getWords(getLabel() + "_colmask: CONSTANT VALUES=" + con), false );
     114          11 :       std::vector<std::string> labs(1, getLabel() + "_colmask");
     115          11 :       ActionWithArguments::interpretArgumentList( labs, plumed.getActionSet(), this, cmask );
     116          25 :     } else if( rmask.size()==0 ) {
     117           1 :       std::string con="0";
     118          13 :       for(unsigned i=1; i<getPntrToArgument(0)->getShape()[0]; ++i) {
     119             :         con += ",0";
     120             :       }
     121           1 :       plumed.readInputWords( Tools::getWords(getLabel() + "_rowmask: CONSTANT VALUES=" + con), false );
     122           1 :       std::vector<std::string> labs(1, getLabel() + "_rowmask");
     123           1 :       ActionWithArguments::interpretArgumentList( labs, plumed.getActionSet(), this, rmask );
     124           1 :     }
     125          25 :     shape.resize(2);
     126          25 :     rmask[0]->buildDataStore();
     127          25 :     shape[0] = getOutputVectorLength( rmask[0] );
     128          25 :     cmask[0]->buildDataStore();
     129          25 :     shape[1] = getOutputVectorLength( cmask[0] );
     130          25 :     std::vector<Value*> args( getArguments() );
     131          25 :     args.push_back( rmask[0] );
     132          25 :     args.push_back( cmask[0] );
     133          25 :     requestArguments( args );
     134             :   } else {
     135           0 :     error("input should be vector or matrix");
     136             :   }
     137             : 
     138          93 :   addValue( shape );
     139          93 :   getPntrToComponent(0)->buildDataStore();
     140          93 :   if( getPntrToArgument(0)->isPeriodic() ) {
     141             :     std::string min, max;
     142           7 :     getPntrToArgument(0)->getDomain( min, max );
     143           7 :     setPeriodic( min, max );
     144             :   } else {
     145          86 :     setNotPeriodic();
     146             :   }
     147          93 :   if( getPntrToComponent(0)->getRank()==2 ) {
     148          25 :     getPntrToComponent(0)->reshapeMatrixStore( shape[1] );
     149             :   }
     150          93 : }
     151             : 
     152       10693 : unsigned SelectWithMask::getOutputVectorLength( const Value* mask ) const  {
     153             :   unsigned l=0;
     154      154139 :   for(unsigned i=0; i<mask->getNumberOfValues(); ++i) {
     155      143446 :     if( fabs(mask->get(i))>0 ) {
     156       10011 :       continue;
     157             :     }
     158      133435 :     l++;
     159             :   }
     160       10693 :   return l;
     161             : }
     162             : 
     163          18 : void SelectWithMask::getMatrixColumnTitles( std::vector<std::string>& argnames ) const {
     164             :   std::vector<std::string> alltitles;
     165          18 :   (getPntrToArgument(0)->getPntrToAction())->getMatrixColumnTitles( alltitles );
     166         103 :   for(unsigned i=0; i<alltitles.size(); ++i) {
     167          85 :     if( fabs(getPntrToArgument(2)->get(i))>0 ) {
     168          34 :       continue;
     169             :     }
     170          51 :     argnames.push_back( alltitles[i] );
     171             :   }
     172          18 : }
     173             : 
     174       10551 : void SelectWithMask::prepare() {
     175             :   Value* arg = getPntrToArgument(0);
     176       10551 :   Value* out = getPntrToComponent(0);
     177       10551 :   if( arg->getRank()==1 ) {
     178             :     Value* mask = getPntrToArgument(1);
     179       10516 :     std::vector<unsigned> shape(1);
     180       10516 :     shape[0]=getOutputVectorLength( mask );
     181       10516 :     if( out->getNumberOfValues()!=shape[0] ) {
     182          19 :       if( shape[0]==1 ) {
     183           0 :         shape.resize(0);
     184             :       }
     185          19 :       out->setShape(shape);
     186             :     }
     187          35 :   } else if( arg->getRank()==2 ) {
     188          35 :     std::vector<unsigned> outshape(2);
     189             :     Value* rmask = getPntrToArgument(1);
     190          35 :     outshape[0] = getOutputVectorLength( rmask );
     191             :     Value* cmask = getPntrToArgument(2);
     192          35 :     outshape[1] = getOutputVectorLength( cmask );
     193          35 :     if( out->getShape()[0]!=outshape[0] || out->getShape()[1]!=outshape[1] ) {
     194          20 :       out->setShape(outshape);
     195          20 :       out->reshapeMatrixStore( outshape[1] );
     196             :     }
     197             :   }
     198       10551 : }
     199             : 
     200       10543 : void SelectWithMask::calculate() {
     201             :   Value* arg = getPntrToArgument(0);
     202       10543 :   Value* out = getPntrToComponent(0);
     203       10543 :   if( arg->getRank()==1 ) {
     204             :     Value* mask = getPntrToArgument(1);
     205             :     unsigned n=0;
     206      149144 :     for(unsigned i=0; i<mask->getNumberOfValues(); ++i) {
     207      138632 :       if( fabs(mask->get(i))>0 ) {
     208        7434 :         continue;
     209             :       }
     210      131198 :       out->set(n, arg->get(i) );
     211      131198 :       n++;
     212             :     }
     213          31 :   } else if ( arg->getRank()==2 ) {
     214          31 :     std::vector<unsigned> outshape( out->getShape() );
     215             :     unsigned n = 0;
     216          31 :     std::vector<unsigned> inshape( arg->getShape() );
     217             :     Value* rmask = getPntrToArgument(1);
     218             :     Value* cmask = getPntrToArgument(2);
     219        1774 :     for(unsigned i=0; i<inshape[0]; ++i) {
     220        1743 :       if( fabs(rmask->get(i))>0 ) {
     221         592 :         continue;
     222             :       }
     223             :       unsigned m = 0;
     224      378651 :       for(unsigned j=0; j<inshape[1]; ++j) {
     225      377500 :         if( fabs(cmask->get(j))>0 ) {
     226      188095 :           continue;
     227             :         }
     228      189405 :         out->set( n*outshape[1] + m, arg->get(i*inshape[1] + j) );
     229      189405 :         m++;
     230             :       }
     231        1151 :       n++;
     232             :     }
     233             :   }
     234       10543 : }
     235             : 
     236       10505 : void SelectWithMask::apply() {
     237       10505 :   if( doNotCalculateDerivatives() || !getPntrToComponent(0)->forcesWereAdded() ) {
     238          62 :     return ;
     239             :   }
     240             : 
     241             :   Value* arg = getPntrToArgument(0);
     242       10443 :   Value* out = getPntrToComponent(0);
     243       10443 :   if( arg->getRank()==1 ) {
     244             :     unsigned n=0;
     245             :     Value* mask = getPntrToArgument(1);
     246      145276 :     for(unsigned i=0; i<mask->getNumberOfValues(); ++i) {
     247      134833 :       if( fabs(mask->get(i))>0 ) {
     248        4153 :         continue;
     249             :       }
     250      130680 :       arg->addForce(i, out->getForce(n) );
     251      130680 :       n++;
     252             :     }
     253           0 :   } else if( arg->getRank()==2 ) {
     254             :     unsigned n = 0;
     255           0 :     std::vector<unsigned> inshape( arg->getShape() );
     256           0 :     std::vector<unsigned> outshape( out->getShape() );
     257             :     Value* rmask = getPntrToArgument(1);
     258             :     Value* cmask = getPntrToArgument(2);
     259           0 :     for(unsigned i=0; i<inshape[0]; ++i) {
     260           0 :       if( fabs(rmask->get(i))>0 ) {
     261           0 :         continue;
     262             :       }
     263             :       unsigned m = 0;
     264           0 :       for(unsigned j=0; j<inshape[1]; ++j) {
     265           0 :         if( fabs(cmask->get(j))>0 ) {
     266           0 :           continue;
     267             :         }
     268           0 :         arg->addForce( i*inshape[1] + j, out->getForce(n*outshape[1] + m) );
     269           0 :         m++;
     270             :       }
     271           0 :       n++;
     272             :     }
     273             :   }
     274             : }
     275             : 
     276             : 
     277             : 
     278             : }
     279             : }