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/ActionWithMatrix.h"
      23             : #include "core/ActionRegister.h"
      24             : 
      25             : //+PLUMEDOC MCOLVAR QUATERNION_PRODUCT_MATRIX
      26             : /*
      27             : Calculate the outer product matrix from two vectors of quaternions
      28             : 
      29             : \par Examples
      30             : 
      31             : */
      32             : //+ENDPLUMEDOC
      33             : 
      34             : namespace PLMD {
      35             : namespace crystdistrib {
      36             : 
      37             : class QuaternionProductMatrix : public ActionWithMatrix {
      38             : private:
      39             :   unsigned nderivatives;
      40             : public:
      41             :   static void registerKeywords( Keywords& keys );
      42             :   explicit QuaternionProductMatrix(const ActionOptions&);
      43             :   unsigned getNumberOfDerivatives();
      44          48 :   unsigned getNumberOfColumns() const override { return getConstPntrToComponent(0)->getShape()[1]; }
      45             :   void setupForTask( const unsigned& task_index, std::vector<unsigned>& indices, MultiValue& myvals ) const ;
      46             :   void performTask( const std::string& controller, const unsigned& index1, const unsigned& index2, MultiValue& myvals ) const override;
      47             :   void runEndOfRowJobs( const unsigned& ival, const std::vector<unsigned> & indices, MultiValue& myvals ) const override ;
      48             : };
      49             : 
      50             : PLUMED_REGISTER_ACTION(QuaternionProductMatrix,"QUATERNION_PRODUCT_MATRIX")
      51             : 
      52           9 : void QuaternionProductMatrix::registerKeywords( Keywords& keys ) {
      53           9 :   ActionWithMatrix::registerKeywords(keys); keys.use("ARG");
      54          18 :   keys.addOutputComponent("w","default","the real component of quaternion");
      55          18 :   keys.addOutputComponent("i","default","the i component of the quaternion");
      56          18 :   keys.addOutputComponent("j","default","the j component of the quaternion");
      57          18 :   keys.addOutputComponent("k","default","the k component of the quaternion");
      58           9 : }
      59             : 
      60           6 : QuaternionProductMatrix::QuaternionProductMatrix(const ActionOptions&ao):
      61             :   Action(ao),
      62           6 :   ActionWithMatrix(ao)
      63             : {
      64           6 :   if( getNumberOfArguments()!=8 ) error("should be eight arguments to this action.  Four quaternions for each set of atoms.  You can repeat actions");
      65           6 :   unsigned nquat = getPntrToArgument(0)->getNumberOfValues();
      66          54 :   for(unsigned i=0; i<8; ++i) {
      67          48 :     Value* myarg=getPntrToArgument(i); if( i==4 ) nquat = getPntrToArgument(i)->getNumberOfValues();
      68          48 :     if( myarg->getRank()!=1 ) error("all arguments to this action should be vectors");
      69          48 :     if( (myarg->getPntrToAction())->getName()!="QUATERNION_VECTOR" ) error("all arguments to this action should be quaternions");
      70          48 :     std::string mylab=getPntrToArgument(i)->getName(); std::size_t dot=mylab.find_first_of(".");
      71          72 :     if( (i==0 || i==4) && mylab.substr(dot+1)!="w" ) error("quaternion arguments are in wrong order");
      72          72 :     if( (i==1 || i==5) && mylab.substr(dot+1)!="i" ) error("quaternion arguments are in wrong order");
      73          72 :     if( (i==2 || i==6) && mylab.substr(dot+1)!="j" ) error("quaternion arguments are in wrong order");
      74          72 :     if( (i==3 || i==7) && mylab.substr(dot+1)!="k" ) error("quaternion arguments are in wrong order");
      75             :   }
      76           6 :   std::vector<unsigned> shape(2); shape[0]=getPntrToArgument(0)->getShape()[0]; shape[1]=getPntrToArgument(4)->getShape()[0];
      77          12 :   addComponent( "w", shape ); componentIsNotPeriodic("w");
      78          12 :   addComponent( "i", shape ); componentIsNotPeriodic("i");
      79          12 :   addComponent( "j", shape ); componentIsNotPeriodic("j");
      80          12 :   addComponent( "k", shape ); componentIsNotPeriodic("k");
      81           6 :   nderivatives = buildArgumentStore(0);
      82           6 : }
      83             : 
      84          16 : unsigned QuaternionProductMatrix::getNumberOfDerivatives() {
      85          16 :   return nderivatives;
      86             : }
      87             : 
      88          18 : void QuaternionProductMatrix::setupForTask( const unsigned& task_index, std::vector<unsigned>& indices, MultiValue& myvals ) const {
      89          18 :   unsigned start_n = getPntrToArgument(0)->getShape()[0], size_v = getPntrToArgument(4)->getShape()[0];
      90          18 :   if( indices.size()!=size_v+1 ) indices.resize( size_v+1 );
      91          63 :   for(unsigned i=0; i<size_v; ++i) indices[i+1] = start_n + i;
      92             :   myvals.setSplitIndex( size_v + 1 );
      93          18 : }
      94             : 
      95      399598 : void QuaternionProductMatrix::performTask( const std::string& controller, const unsigned& index1, const unsigned& index2, MultiValue& myvals ) const {
      96      399598 :   unsigned ostrn, ind2=index2;
      97      399598 :   if( index2>=getPntrToArgument(0)->getShape()[0] ) ind2 = index2 - getPntrToArgument(0)->getShape()[0];
      98             : 
      99      399598 :   std::vector<double> quat1(4), quat2(4);
     100             : 
     101             :   // Retrieve the first quaternion
     102     1997990 :   for(unsigned i=0; i<4; ++i) quat1[i] = getArgumentElement( i, index1, myvals );
     103             :   // Retrieve the second quaternion
     104     1997990 :   for(unsigned i=0; i<4; ++i) quat2[i] = getArgumentElement( 4+i, ind2, myvals );
     105             : 
     106             :   //make q1 the conjugate
     107      399598 :   quat1[1] *= -1;
     108      399598 :   quat1[2] *= -1;
     109      399598 :   quat1[3] *= -1;
     110             : 
     111             : 
     112             :   double pref=1;
     113             :   double pref2=1;
     114             :   double conj=1;
     115             : //real part of q1*q2
     116     1997990 :   for(unsigned i=0; i<4; ++i) {
     117     1598392 :     if( i>0 ) {pref=-1; pref2=-1;}
     118     1598392 :     myvals.addValue( getConstPntrToComponent(0)->getPositionInStream(), pref*quat1[i]*quat2[i] );
     119     1598392 :     if( doNotCalculateDerivatives() ) continue ;
     120      759240 :     if (i>0) conj=-1;
     121      759240 :     addDerivativeOnVectorArgument( false, 0, i, index1, conj*pref*quat2[i], myvals );
     122      759240 :     addDerivativeOnVectorArgument( false, 0, 4+i, ind2, pref2*quat1[i], myvals );
     123             :   }
     124             :   //i component
     125             :   pref=1;
     126             :   conj=1;
     127             :   pref2=1;
     128     1997990 :   for (unsigned i=0; i<4; i++) {
     129     1598392 :     if(i==3) pref=-1;
     130             :     else pref=1;
     131     1598392 :     if(i==2) pref2=-1;
     132             :     else pref2=1;
     133     1598392 :     myvals.addValue( getConstPntrToComponent(1)->getPositionInStream(), pref*quat1[i]*quat2[(5-i)%4]);
     134     1598392 :     if( doNotCalculateDerivatives() ) continue ;
     135      759240 :     if (i>0) conj=-1;
     136      759240 :     addDerivativeOnVectorArgument( false, 1, i, index1, conj*pref*quat2[(5-i)%4], myvals );
     137      759240 :     addDerivativeOnVectorArgument( false, 1, 4+i, ind2, pref2*quat1[(5-i)%4], myvals );
     138             :   }
     139             : 
     140             :   //j component
     141             :   pref=1;
     142             :   conj=1;
     143             :   pref2=1;
     144     1997990 :   for (unsigned i=0; i<4; i++) {
     145     1598392 :     if(i==1) pref=-1;
     146             :     else pref=1;
     147     1598392 :     if (i==3) pref2=-1;
     148             :     else pref2=1;
     149     1598392 :     myvals.addValue( getConstPntrToComponent(2)->getPositionInStream(), pref*quat1[i]*quat2[(i+2)%4]);
     150     1598392 :     if( doNotCalculateDerivatives() ) continue ;
     151      759240 :     if (i>0) conj=-1;
     152      759240 :     addDerivativeOnVectorArgument( false, 2, i, index1, conj*pref*quat2[(i+2)%4], myvals );
     153      759240 :     addDerivativeOnVectorArgument( false, 2, 4+i, ind2, pref2*quat1[(i+2)%4], myvals );
     154             :   }
     155             : 
     156             :   //k component
     157             :   pref=1;
     158             :   conj=1;
     159             :   pref2=1;
     160     1997990 :   for (unsigned i=0; i<4; i++) {
     161     1598392 :     if(i==2) pref=-1;
     162             :     else pref=1;
     163     1598392 :     if(i==1) pref2=-1;
     164             :     else pref2=1;
     165     1598392 :     myvals.addValue( getConstPntrToComponent(3)->getPositionInStream(), pref*quat1[i]*quat2[(3-i)]);
     166     1598392 :     if( doNotCalculateDerivatives() ) continue ;
     167      759240 :     if (i>0) conj=-1;
     168      759240 :     addDerivativeOnVectorArgument( false, 3, i, index1, conj*pref*quat2[3-i], myvals );
     169      759240 :     addDerivativeOnVectorArgument( false, 3, 4+i, ind2, pref2*quat1[3-i], myvals );
     170             : 
     171             :   }
     172             : 
     173             : 
     174      399598 : }
     175             : 
     176        2028 : void QuaternionProductMatrix::runEndOfRowJobs( const unsigned& ival, const std::vector<unsigned> & indices, MultiValue& myvals ) const {
     177        2028 :   if( doNotCalculateDerivatives() || !matrixChainContinues() ) return ;
     178             : 
     179        3915 :   for(unsigned j=0; j<getNumberOfComponents(); ++j) {
     180        3132 :     unsigned nmat = getConstPntrToComponent(j)->getPositionInMatrixStash(), nmat_ind = myvals.getNumberOfMatrixRowDerivatives( nmat );
     181             :     std::vector<unsigned>& matrix_indices( myvals.getMatrixRowDerivativeIndices( nmat ) ); unsigned ntwo_atoms = myvals.getSplitIndex();
     182             :     // Quaternion for first molecule
     183       15660 :     unsigned base = 0; for(unsigned k=0; k<4; ++k) { matrix_indices[nmat_ind] = base + ival; base += getPntrToArgument(k)->getShape()[0]; nmat_ind++; }
     184             :     // Loop over row of matrix
     185      762372 :     for(unsigned i=1; i<ntwo_atoms; ++i) {
     186      759240 :       unsigned ind2 = indices[i]; if( ind2>=getPntrToArgument(0)->getShape()[0] ) ind2 = indices[i] - getPntrToArgument(0)->getShape()[0];
     187      759240 :       base = 4*getPntrToArgument(0)->getShape()[0];
     188             :       // Quaternion of second molecule
     189     3796200 :       for(unsigned k=0; k<4; ++k) { matrix_indices[nmat_ind] = base + ind2; base += getPntrToArgument(4+k)->getShape()[0]; nmat_ind++; }
     190             :     }
     191             :     myvals.setNumberOfMatrixRowDerivatives( nmat, nmat_ind );
     192             :   }
     193             : 
     194             : }
     195             : 
     196             : }
     197             : }