double ContactAlignedMatrix::compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const {
  double f_dot, dot_df; 

  std::vector<double> orient0(ncomp), orient1(ncomp);
  getOrientationVector( myatoms.getIndex(0), true, orient0 );
  getOrientationVector( myatoms.getIndex(1), true, orient1 );
  double dot=0; for(unsigned k=2;k<orient0.size();++k) dot+=orient0[k]*orient1[k];
  f_dot=0.5*( 1 + dot ); dot_df=0.5; 

  // Retrieve the weight of the connection
  double weight = myatoms.getValue(0); myatoms.setValue(0,1.0); 

  if( !doNotCalculateDerivatives() ){
      Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
      double dfunc, sw = switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) ).calculate( distance.modulo(), dfunc );
      addAtomDerivatives( 1, 0, (-dfunc)*f_dot*distance, myatoms );
      addAtomDerivatives( 1, 1, (+dfunc)*f_dot*distance, myatoms ); 
      myatoms.addBoxDerivatives( 1, (-dfunc)*f_dot*Tensor(distance,distance) ); 

      // Add derivatives of orientation 
      for(unsigned k=2;k<orient0.size();++k){ orient0[k]*=sw*dot_df; orient1[k]*=sw*dot_df; }
      addOrientationDerivatives( 1, 0, orient1, myatoms );
      addOrientationDerivatives( 1, 1, orient0, myatoms );
  }
  return weight*f_dot;
}
Example #2
0
double TopologyMatrix::compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const {
  HistogramBead bead; bead.isNotPeriodic(); bead.setKernelType( kerneltype );

  // Initialise to zero density on all bins
  for(unsigned bin=0; bin<maxbins; ++bin) myatoms.setValue(bin+1,0);
  // Calculate whether or not atoms 1 and 2 are within cutoff (can use delta here as pbc are done in atom setup)
  Vector d1 = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) ); double d1_len = d1.modulo();
  d1 = d1 / d1_len;  // Convert vector into director
  AtomNumber a1 = myatoms.getAbsoluteIndex( 0 );
  AtomNumber a2 = myatoms.getAbsoluteIndex( 1 );
  for(unsigned i=2; i<myatoms.getNumberOfAtoms(); ++i) {
    AtomNumber a3 = myatoms.getAbsoluteIndex( i );
    if( a3!=a1 && a3!=a2 ) calculateForThreeAtoms( i, d1, d1_len, bead, myatoms );
  }
  // std::vector<double> binvals( 1+maxbins ); for(unsigned i=1;i<maxbins;++i) binvals[i]=myatoms.getValue(i);
  // unsigned ii; double fdf;
  //std::cout<<"HELLO DENSITY "<<myatoms.getIndex(0)<<" "<<myatoms.getIndex(1)<<" "<<transformStoredValues( binvals, ii, fdf )<<std::endl;

  // Now find the element for which the density is maximal
  unsigned vout=2; double max=myatoms.getValue( 2 );
  for(unsigned i=3; i<myatoms.getUnderlyingMultiValue().getNumberOfValues()-1; ++i) {
    if( myatoms.getValue(i)>max ) { max=myatoms.getValue(i); vout=i; }
  }
  // Calculate value and derivative of switching function between atoms 1 and 2
  double dfuncl, sw = switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ),
                                         getBaseColvarNumber( myatoms.getIndex(1) ) ).calculate( d1_len, dfuncl );
  // Transform the density
  double df, tsw = threshold_switch.calculate( max, df );
  if( !doNotCalculateDerivatives() ) {
    // Factor of d1_len is required here because d1 is normalized
    d1 *= d1_len;
    addAtomDerivatives( 2+maxbins, 0, -dfuncl*d1, myatoms );
    addAtomDerivatives( 2+maxbins, 1, dfuncl*d1, myatoms );
    myatoms.addBoxDerivatives( 2+maxbins, (-dfuncl)*Tensor(d1,d1) );
    // Update active atoms so that next bit works
    updateActiveAtoms( myatoms );
    // Now finish caclulation of derivatives
    MultiValue& myvals=myatoms.getUnderlyingMultiValue();
    for(unsigned jd=0; jd<myvals.getNumberActive(); ++jd) {
      unsigned ider=myvals.getActiveIndex(jd);
      myvals.addDerivative( 1, ider, sw*df*max*myvals.getDerivative( vout, ider ) + tsw*myvals.getDerivative( 2+maxbins, ider ) );
    }
  }
  return sw*tsw;
}
Example #3
0
double ContactMatrix::compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const {
  if( !doNotCalculateDerivatives() ){
      Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
      double dfunc, sw = switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) - ncol_t ).calculate( distance.modulo(), dfunc );
      addAtomDerivatives( 1, 0, (-dfunc)*distance, myatoms );
      addAtomDerivatives( 1, 1, (+dfunc)*distance, myatoms ); 
      myatoms.addBoxDerivatives( 1, (-dfunc)*Tensor(distance,distance) ); 
  }
  double val=myatoms.getValue(0); myatoms.setValue(0,1.0);
  return val;
}
Example #4
0
double VectorMultiColvar::doCalculation( const unsigned& taskIndex, multicolvar::AtomValuePack& myatoms ) const {
  // Now calculate the vector
  calculateVector( myatoms );
  // Sort out the active derivatives
  updateActiveAtoms( myatoms );

  // Now calculate the norm of the vector (this is what we return here)
  double norm=0; 
  for(unsigned i=0;i<ncomponents;++i) norm += myatoms.getValue(2+i)*myatoms.getValue(2+i); 
  norm=sqrt(norm);
 
  if( !doNotCalculateDerivatives() ){
      double inorm = 1.0 / norm; std::vector<double> dervec( ncomponents );
      for(unsigned i=0;i<ncomponents;++i) dervec[i] = inorm*myatoms.getValue(2+i);
 
      MultiValue& myvals=myatoms.getUnderlyingMultiValue();
      for(unsigned j=0;j<myvals.getNumberActive();++j){
          unsigned jder=myvals.getActiveIndex(j);
          for(unsigned i=0;i<ncomponents;++i) myvals.addDerivative( 1, jder, dervec[i]*myvals.getDerivative( 2+i, jder ) );
      }
  }
  
  return norm;
}