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             : #include "tools/Torsion.h"
      25             : 
      26             : //+PLUMEDOC MCOLVAR TORSIONS_MATRIX
      27             : /*
      28             : Calculate the matrix of torsions between two vectors of molecules
      29             : 
      30             : \par Examples
      31             : 
      32             : */
      33             : //+ENDPLUMEDOC
      34             : 
      35             : namespace PLMD {
      36             : namespace adjmat {
      37             : 
      38             : class TorsionsMatrix : public ActionWithMatrix {
      39             : private:
      40             :   unsigned nderivatives;
      41             :   bool stored_matrix1, stored_matrix2;
      42             : public:
      43             :   static void registerKeywords( Keywords& keys );
      44             :   explicit TorsionsMatrix(const ActionOptions&);
      45             :   unsigned getNumberOfDerivatives();
      46           0 :   unsigned getNumberOfColumns() const override { return getConstPntrToComponent(0)->getShape()[1]; }
      47             :   void setupForTask( const unsigned& task_index, std::vector<unsigned>& indices, MultiValue& myvals ) const ;
      48             :   void performTask( const std::string& controller, const unsigned& index1, const unsigned& index2, MultiValue& myvals ) const override;
      49             :   void runEndOfRowJobs( const unsigned& ival, const std::vector<unsigned> & indices, MultiValue& myvals ) const override ;
      50             : };
      51             : 
      52             : PLUMED_REGISTER_ACTION(TorsionsMatrix,"TORSIONS_MATRIX")
      53             : 
      54          14 : void TorsionsMatrix::registerKeywords( Keywords& keys ) {
      55          14 :   ActionWithMatrix::registerKeywords(keys);
      56          28 :   keys.addInputKeyword("compulsory","ARG","matrix","an Nx3 and a 3xN matrix that contain the bond vectors that you would like to determine the torsion angles between");
      57          28 :   keys.add("atoms","POSITIONS1","the positions to use for the molecules specified using the first argument");
      58          28 :   keys.add("atoms","POSITIONS2","the positions to use for the molecules specified using the second argument");
      59          28 :   keys.setValueDescription("matrix","the matrix of torsions between the two vectors of input directors");
      60          14 : }
      61             : 
      62           7 : TorsionsMatrix::TorsionsMatrix(const ActionOptions&ao):
      63             :   Action(ao),
      64           7 :   ActionWithMatrix(ao)
      65             : {
      66           7 :   if( getNumberOfArguments()!=2 ) error("should be two arguments to this action, a matrix and a vector");
      67           7 :   if( getPntrToArgument(0)->getRank()!=2 || getPntrToArgument(0)->hasDerivatives() ) error("first argument to this action should be a matrix");
      68           7 :   if( getPntrToArgument(1)->getRank()!=2 || getPntrToArgument(1)->hasDerivatives() ) error("second argument to this action should be a matrix");
      69           7 :   if( getPntrToArgument(0)->getShape()[1]!=3 || getPntrToArgument(1)->getShape()[0]!=3 ) error("number of columns in first matrix and number of rows in second matrix should equal 3");
      70             : 
      71          14 :   std::vector<AtomNumber> atoms_a; parseAtomList("POSITIONS1", atoms_a );
      72           7 :   if( atoms_a.size()!=getPntrToArgument(0)->getShape()[0] ) error("mismatch between number of atoms specified using POSITIONS1 and number of arguments in vector input");
      73           7 :   log.printf("  using positions of these atoms for vectors in first matrix \n");
      74         933 :   for(unsigned int i=0; i<atoms_a.size(); ++i) {
      75         926 :     if ( (i+1) % 25 == 0 ) log.printf("  \n");
      76         926 :     log.printf("  %d", atoms_a[i].serial());
      77             :   }
      78          14 :   log.printf("\n"); std::vector<AtomNumber> atoms_b; parseAtomList("POSITIONS2", atoms_b );
      79           7 :   if( atoms_b.size()!=getPntrToArgument(1)->getShape()[1] ) error("mismatch between number of atoms specified using POSITIONS2 and number of arguments in vector input");
      80           7 :   log.printf("  using positions of these atoms for vectors in second matrix \n");
      81        1225 :   for(unsigned i=0; i<atoms_b.size(); ++i) {
      82        1218 :     if ( (i+1) % 25 == 0 ) log.printf("  \n");
      83        1218 :     log.printf("  %d", atoms_b[i].serial()); atoms_a.push_back( atoms_b[i] );
      84             :   }
      85           7 :   log.printf("\n"); requestAtoms( atoms_a, false );
      86             : 
      87           7 :   std::vector<unsigned> shape(2); shape[0]=getPntrToArgument(0)->getShape()[0]; shape[1]=getPntrToArgument(1)->getShape()[1];
      88          14 :   addValue( shape ); setPeriodic("-pi","pi"); nderivatives = buildArgumentStore(0) + 3*getNumberOfAtoms() + 9;
      89           7 :   std::string headstr=getFirstActionInChain()->getLabel();
      90           7 :   stored_matrix1 = getPntrToArgument(0)->ignoreStoredValue( headstr );
      91           7 :   stored_matrix2 = getPntrToArgument(1)->ignoreStoredValue( headstr );
      92           7 : }
      93             : 
      94          10 : unsigned TorsionsMatrix::getNumberOfDerivatives() {
      95          10 :   return nderivatives;
      96             : }
      97             : 
      98           2 : void TorsionsMatrix::setupForTask( const unsigned& task_index, std::vector<unsigned>& indices, MultiValue& myvals ) const {
      99             :   unsigned start_n = getPntrToArgument(0)->getShape()[0], size_v = getPntrToArgument(1)->getShape()[1];
     100           2 :   if( indices.size()!=size_v+1 ) indices.resize( size_v+1 );
     101           6 :   for(unsigned i=0; i<size_v; ++i) indices[i+1] = start_n + i;
     102             :   myvals.setSplitIndex( size_v + 1 );
     103           2 : }
     104             : 
     105     1240496 : void TorsionsMatrix::performTask( const std::string& controller, const unsigned& index1, const unsigned& index2, MultiValue& myvals ) const {
     106     1240496 :   unsigned ostrn = getConstPntrToComponent(0)->getPositionInStream(), ind2=index2;
     107     1240496 :   if( index2>=getPntrToArgument(0)->getShape()[0] ) ind2 = index2 - getPntrToArgument(0)->getShape()[0];
     108             : 
     109     1240496 :   Vector v1, v2, dv1, dv2, dconn;
     110             :   // Compute the distance connecting the two centers
     111     1240496 :   Vector conn=pbcDistance( getPosition(index1), getPosition(index2) );
     112     2479668 :   if( conn.modulo2()<epsilon ) return;
     113             : 
     114             :   // Get the two vectors
     115     4961624 :   for(unsigned i=0; i<3; ++i) {
     116     3721218 :     v1[i] = getElementOfMatrixArgument( 0, index1, i, myvals );
     117     3721218 :     v2[i] = getElementOfMatrixArgument( 1, i, ind2, myvals );
     118             :   }
     119             :   // Evaluate angle
     120     1240406 :   Torsion t; double angle = t.compute( v1, conn, v2, dv1, dconn, dv2 );
     121     1240406 :   myvals.addValue( ostrn, angle );
     122             : 
     123     1240406 :   if( doNotCalculateDerivatives() ) return;
     124             : 
     125             :   // Add the derivatives on the matrices
     126        4936 :   for(unsigned i=0; i<3; ++i) {
     127        3702 :     addDerivativeOnMatrixArgument( stored_matrix1, 0, 0, index1, i, dv1[i], myvals );
     128        3702 :     addDerivativeOnMatrixArgument( stored_matrix2, 0, 1, i, ind2, dv2[i], myvals );
     129             :   }
     130             :   // And derivatives on positions
     131        1234 :   unsigned narg_derivatives = getPntrToArgument(0)->getNumberOfValues() + getPntrToArgument(1)->getNumberOfValues();
     132        4936 :   for(unsigned i=0; i<3; ++i) {
     133        3702 :     myvals.addDerivative( ostrn, narg_derivatives + 3*index1+i, -dconn[i] ); myvals.addDerivative( ostrn, narg_derivatives + 3*index2+i, dconn[i] );
     134        3702 :     myvals.updateIndex( ostrn, narg_derivatives + 3*index1+i ); myvals.updateIndex( ostrn, narg_derivatives + 3*index2+i );
     135             :   }
     136             :   //And virial
     137        1234 :   Tensor vir( -extProduct( conn, dconn ) ); unsigned virbase = narg_derivatives + 3*getNumberOfAtoms();
     138       16042 :   for(unsigned i=0; i<3; ++i) for(unsigned j=0; j<3; ++j ) { myvals.addDerivative( ostrn, virbase+3*i+j, vir(i,j) ); myvals.updateIndex( ostrn, virbase+3*i+j ); }
     139             : }
     140             : 
     141        5366 : void TorsionsMatrix::runEndOfRowJobs( const unsigned& ival, const std::vector<unsigned> & indices, MultiValue& myvals ) const {
     142        5366 :   if( doNotCalculateDerivatives() || !matrixChainContinues() ) return ;
     143             : 
     144         178 :   unsigned mat1s = 3*ival, ss = getPntrToArgument(1)->getShape()[1];
     145         178 :   unsigned nmat = getConstPntrToComponent(0)->getPositionInMatrixStash(), nmat_ind = myvals.getNumberOfMatrixRowDerivatives( nmat );
     146         178 :   unsigned narg_derivatives = getPntrToArgument(0)->getNumberOfValues() + getPntrToArgument(1)->getNumberOfValues();
     147             :   std::vector<unsigned>& matrix_indices( myvals.getMatrixRowDerivativeIndices( nmat ) ); unsigned ntwo_atoms = myvals.getSplitIndex();
     148         712 :   for(unsigned j=0; j<3; ++j) {
     149         534 :     matrix_indices[nmat_ind] = mat1s + j; nmat_ind++;
     150         534 :     matrix_indices[nmat_ind] = narg_derivatives + mat1s + j; nmat_ind++;
     151        4242 :     for(unsigned i=1; i<ntwo_atoms; ++i) {
     152        3708 :       unsigned ind2 = indices[i]; if( ind2>=getPntrToArgument(0)->getShape()[0] ) ind2 = indices[i] - getPntrToArgument(0)->getShape()[0];
     153        3708 :       matrix_indices[nmat_ind] = arg_deriv_starts[1] + j*ss + ind2; nmat_ind++;
     154        3708 :       matrix_indices[nmat_ind] = narg_derivatives + 3*indices[i] + j; nmat_ind++;
     155             :     }
     156             :   }
     157        1780 :   unsigned base = narg_derivatives + 3*getNumberOfAtoms(); for(unsigned j=0; j<9; ++j) { matrix_indices[nmat_ind] = base + j; nmat_ind++; }
     158             :   myvals.setNumberOfMatrixRowDerivatives( nmat, nmat_ind );
     159             : }
     160             : 
     161             : }
     162             : }