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;
}
double InterMolecularTorsions::compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const {
Vector v1, v2, dv1, dv2, dconn, conn = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
// Retrieve vectors
std::vector<double> orient0( 5 ), orient1( 5 );
getInputData( 0, true, myatoms, orient0 );
getInputData( 1, true, myatoms, orient1 );
for(unsigned i=0; i<3; ++i) { v1[i]=orient0[2+i]; v2[i]=orient1[2+i]; }
if( getBaseMultiColvar(0)->getNumberOfQuantities()<3 ) return 1.0;
// Evaluate angle
Torsion t; double angle = t.compute( v1, conn, v2, dv1, dconn, dv2 );
for(unsigned i=0; i<3; ++i) { orient0[i+2]=dv1[i]; orient1[i+2]=dv2[i]; }
// And accumulate derivatives
if( !doNotCalculateDerivatives() ) {
MultiValue& myder0=getInputDerivatives( 0, true, myatoms );
mergeInputDerivatives( 1, 2, orient1.size(), 0, orient0, myder0, myatoms );
MultiValue& myder1=getInputDerivatives( 1, true, myatoms );
mergeInputDerivatives( 1, 2, orient0.size(), 1, orient1, myder1, myatoms );
addAtomDerivatives( 1, 0, -dconn, myatoms ); addAtomDerivatives( 1, 1, dconn, myatoms );
myatoms.addBoxDerivatives( 1, -extProduct( conn, dconn ) );
}
return angle;
}
double NumberOfLinks::compute( const unsigned& tindex, AtomValuePack& myatoms ) const {
if( getBaseMultiColvar(0)->getNumberOfQuantities()<3 ) return 1.0;
unsigned ncomp=getBaseMultiColvar(0)->getNumberOfQuantities();
std::vector<double> orient0( ncomp ), orient1( ncomp );
getVectorForTask( myatoms.getIndex(0), true, orient0 );
getVectorForTask( myatoms.getIndex(1), true, orient1 );
double dot=0;
for(unsigned k=2;k<orient0.size();++k){
dot+=orient0[k]*orient1[k];
}
if( !doNotCalculateDerivatives() ){
unsigned nder=myatoms.getNumberOfDerivatives(); //getNumberOfDerivatives();
MultiValue myder0(ncomp,nder), myder1(ncomp,nder);
getVectorDerivatives( myatoms.getIndex(0), true, myder0 );
mergeVectorDerivatives( 1, 2, orient1.size(), myatoms.getIndex(0), orient1, myder0, myatoms );
getVectorDerivatives( myatoms.getIndex(1), true, myder1 );
mergeVectorDerivatives( 1, 2, orient0.size(), myatoms.getIndex(1), orient0, myder1, myatoms );
}
return dot;
}
double DistanceFromContour::compute( const unsigned& tindex, AtomValuePack& myatoms ) const {
Vector distance = getSeparation( getPosition(getNumberOfAtoms()-1), myatoms.getPosition(0) );
std::vector<double> pp(3), der(3,0); for(unsigned j=0;j<3;++j) pp[j] = distance[j];
// Now create the kernel and evaluate
KernelFunctions kernel( pp, bw, kerneltype, false, 1.0, true );
double newval = kernel.evaluate( pval, der, true );
if( mybasemulticolvars[0]->isDensity() ){
if( !doNotCalculateDerivatives() && derivTime ){
MultiValue& myvals=myatoms.getUnderlyingMultiValue();
Vector vder; unsigned basen=myvals.getNumberOfDerivatives() - 12;
for(unsigned i=0;i<3;++i){
vder[i]=der[i]; myvals.addDerivative( 1, basen+i, vder[i] );
}
myatoms.setValue( 2, der[dir] );
addAtomDerivatives( 1, 0, -vder, myatoms );
myatoms.addBoxDerivatives( 1, Tensor(vder,distance) );
}
myatoms.setValue( 0, 1.0 ); return newval;
}
// This does the stuff for averaging
myatoms.setValue( 0, newval );
// This gets the average if we are using a phase field
std::vector<double> cvals( mybasemulticolvars[0]->getNumberOfQuantities() );
mybasedata[0]->retrieveValueWithIndex( tindex, false, cvals );
return newval*cvals[0]*cvals[1];
}
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;
}
void MultiColvarBase::getCentralAtomIndexList( const unsigned& ntotal, const unsigned& jstore, const unsigned& maxder, std::vector<unsigned>& indices ) const {
plumed_dbg_assert( !doNotCalculateDerivatives() );
indices[jstore]=3*atomsWithCatomDer.getNumberActive();
if( indices[jstore]>maxder ) error("too many derivatives to store. Run with LOWMEM");
unsigned kder = ntotal + jstore*maxder;
for(unsigned jder=0;jder<atomsWithCatomDer.getNumberActive();++jder){
unsigned iatom = 3*atomsWithCatomDer[jder];
for(unsigned icomp=0;icomp<3;++icomp){ indices[ kder ] = iatom+icomp; kder++; }
}
}
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;
}
void DFSClusterDiameter::performTask( const unsigned& task_index, const unsigned& current, MultiValue& myvals ) const {
unsigned iatom=current/getNumberOfNodes(), jatom = current - iatom*getNumberOfNodes();
Vector distance=getSeparation( getPosition(iatom), getPosition(jatom) );
double dd = distance.modulo(), inv = 1.0/dd ; myvals.setValue( 1, dd );
if( !doNotCalculateDerivatives() ){
myvals.addDerivative( 1, 3*iatom + 0, -inv*distance[0] );
myvals.addDerivative( 1, 3*iatom + 1, -inv*distance[1] );
myvals.addDerivative( 1, 3*iatom + 2, -inv*distance[2] );
myvals.addDerivative( 1, 3*jatom + 0, +inv*distance[0] );
myvals.addDerivative( 1, 3*jatom + 1, +inv*distance[1] );
myvals.addDerivative( 1, 3*jatom + 2, +inv*distance[2] );
Tensor vir = -inv*Tensor(distance,distance);
unsigned vbase = myvals.getNumberOfDerivatives() - 9;
for(unsigned i=0;i<3;++i){
for(unsigned j=0;j<3;++j) myvals.addDerivative( 1, vbase+3*i+j, vir(i,j) );
}
}
}
void MultiColvarBase::quotientRule( const unsigned& uder, const unsigned& vder, const unsigned& iout ){
unsigned ustart=uder*getNumberOfDerivatives();
unsigned vstart=vder*getNumberOfDerivatives();
unsigned istart=iout*getNumberOfDerivatives();
double weight = getElementValue( vder ), pref = getElementValue( uder ) / (weight*weight);
if( !doNotCalculateDerivatives() ){
for(unsigned i=0;i<atoms_with_derivatives.getNumberActive();++i){
unsigned n=3*atoms_with_derivatives[i], nx=n, ny=n+1, nz=n+2;
setElementDerivative( istart + nx, getElementDerivative(ustart+nx) / weight - pref*getElementDerivative(vstart+nx) );
setElementDerivative( istart + ny, getElementDerivative(ustart+ny) / weight - pref*getElementDerivative(vstart+ny) );
setElementDerivative( istart + nz, getElementDerivative(ustart+nz) / weight - pref*getElementDerivative(vstart+nz) );
}
unsigned vbase=3*getNumberOfAtoms();
for(unsigned i=0;i<9;++i){
setElementDerivative( istart + vbase + i, getElementDerivative(ustart+vbase+i) / weight - pref*getElementDerivative(vstart+vbase+i) );
}
}
thisval_wasset[iout]=false; setElementValue( iout, getElementValue(uder) / weight );
}
void ActionWithGrid::calculate(){
// Do nothing if derivatives are not required
if( doNotCalculateDerivatives() ) return;
// Clear on every step
if( mygrid ) clearAverage();
// Should not be any reweighting so just set these accordingly
lweight=0; cweight=1.0;
// Prepare to do the averaging
prepareForAveraging();
// Run all the tasks (if required
if( useRunAllTasks ) runAllTasks();
// This the averaging if it is not done using task list
else performOperations( true );
// Update the norm
if( mygrid ) mygrid->setNorm( cweight );
// Finish the averaging
finishAveraging();
// And reset for next step
if( mygrid ) mygrid->reset();
}
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;
}
double OrientationSphere::compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const {
// Make sure derivatives for central atom are only calculated once
VectorMultiColvar* vv = dynamic_cast<VectorMultiColvar*>( getBaseMultiColvar(0) );
vv->firstcall=true;
double d2, sw, value=0, denom=0, dot, f_dot, dot_df, dfunc;
unsigned ncomponents=getBaseMultiColvar(0)->getNumberOfQuantities();
unsigned nder=myatoms.getNumberOfDerivatives();
std::vector<double> catom_orient( ncomponents ), this_orient( ncomponents ), catom_der( ncomponents );
Vector catom_pos = myatoms.getPosition(0);
getVectorForTask( myatoms.getIndex(0), true, catom_orient );
multicolvar::CatomPack atom0; MultiValue myder0(0,0), myder1(0,0);
if( !doNotCalculateDerivatives() ){
myder0.resize( ncomponents,nder ); myder1.resize(ncomponents,nder);
atom0=getCentralAtomPackFromInput( myatoms.getIndex(0) );
getVectorDerivatives( myatoms.getIndex(0), true, myder0 );
}
for(unsigned i=1;i<myatoms.getNumberOfAtoms();++i){
Vector& distance=myatoms.getPosition(i);
if ( (d2=distance[0]*distance[0])<rcut2 &&
(d2+=distance[1]*distance[1])<rcut2 &&
(d2+=distance[2]*distance[2])<rcut2) {
sw = switchingFunction.calculateSqr( d2, dfunc );
getVectorForTask( myatoms.getIndex(i), true, this_orient );
// Calculate the dot product wrt to this position
dot=0; for(unsigned k=2;k<catom_orient.size();++k) dot+=catom_orient[k]*this_orient[k];
f_dot = transformDotProduct( dot, dot_df );
if( !doNotCalculateDerivatives() ){
// N.B. We are assuming here that the imaginary part of the dot product is zero
for(unsigned k=2;k<catom_orient.size();++k){
this_orient[k]*=sw*dot_df; catom_der[k]=sw*dot_df*catom_orient[k];
}
getVectorDerivatives( myatoms.getIndex(i), true, myder1 );
mergeVectorDerivatives( 1, 2, this_orient.size(), myatoms.getIndex(0), this_orient, myder0, myatoms );
mergeVectorDerivatives( 1, 2, catom_der.size(), myatoms.getIndex(i), catom_der, myder1, myatoms );
myatoms.addComDerivatives( 1, f_dot*(-dfunc)*distance, atom0 );
addAtomDerivatives( 1, i, f_dot*(dfunc)*distance, myatoms );
myatoms.addBoxDerivatives( 1, (-dfunc)*f_dot*Tensor(distance,distance) );
myder1.clearAll();
myatoms.addComDerivatives( -1, (-dfunc)*distance, atom0 );
addAtomDerivatives( -1, i, (dfunc)*distance, myatoms );
myatoms.addTemporyBoxDerivatives( (-dfunc)*Tensor(distance,distance) );
}
value += sw*f_dot;
denom += sw;
}
}
double rdenom, df2, pref=calculateCoordinationPrefactor( denom, df2 );
if( fabs(denom)>epsilon ){ rdenom = 1.0 / denom; }
else { plumed_assert(fabs(value)<epsilon); rdenom=1.0; }
// Now divide everything
double rdenom2=rdenom*rdenom;
updateActiveAtoms( myatoms ); MultiValue& myvals=myatoms.getUnderlyingMultiValue();
for(unsigned i=0;i<myvals.getNumberActive();++i){
unsigned ider=myvals.getActiveIndex(i);
double dgd=myvals.getTemporyDerivative(ider);
myvals.setDerivative( 1, ider, rdenom*(pref*myvals.getDerivative(1,ider)+value*df2*dgd) - (value*pref*dgd)*rdenom2 );
}
return pref*rdenom*value;
}
void ClusterProperties::performTask( const unsigned& task_index, const unsigned& current, MultiValue& myvals ) const {
std::vector<double> vals( myvals.getNumberOfValues() ); getPropertiesOfNode( current, vals );
if( !doNotCalculateDerivatives() ) getNodePropertyDerivatives( current, myvals );
for(unsigned k=0; k<vals.size(); ++k) myvals.setValue( k, vals[k] );
}
void TopologyMatrix::calculateForThreeAtoms( const unsigned& iat, const Vector& d1, const double& d1_len,
HistogramBead& bead, multicolvar::AtomValuePack& myatoms ) const {
// Calculate if there are atoms in the cylinder (can use delta here as pbc are done in atom setup)
Vector d2 = getSeparation( myatoms.getPosition(0), myatoms.getPosition(iat) );
// Now calculate projection of d2 on d1
double proj=dotProduct(d2,d1);
// This tells us if we are outside the end of the cylinder
double excess = proj - d1_len;
// Return if we are outside of the cylinder as calculated based on excess
if( excess>low_sf( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) ).get_dmax() ) return;
// Find the length of the cylinder
double binw = binw_mat( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) );
double lcylinder = (std::floor( d1_len / binw ) + 1)*binw;
// Return if the projection is outside the length of interest
if( proj<-bead.getCutoff() || proj>(lcylinder+bead.getCutoff()) ) return;
// Calculate the excess swiching function
double edf, eval = low_sf( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) ).calculate( excess, edf );
// Calculate the projection on the perpendicular distance from the center of the tube
double cm = d2.modulo2() - proj*proj;
// Now calculate the density in the cylinder
if( cm<cylinder_sw( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) ).get_dmax2() ) {
double dfuncr, val = cylinder_sw( getBaseColvarNumber( myatoms.getIndex(0) ),
getBaseColvarNumber( myatoms.getIndex(1) ) ).calculateSqr( cm, dfuncr );
double cellv = cell_volume( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) );
Vector dc1, dc2, dc3, dd1, dd2, dd3, de1, de2, de3;
if( !doNotCalculateDerivatives() ) {
Tensor d1_a1;
// Derivative of director connecting atom1 - atom2 wrt the position of atom 1
d1_a1(0,0) = ( -(d1[1]*d1[1]+d1[2]*d1[2])/d1_len ); // dx/dx
d1_a1(0,1) = ( d1[0]*d1[1]/d1_len ); // dx/dy
d1_a1(0,2) = ( d1[0]*d1[2]/d1_len ); // dx/dz
d1_a1(1,0) = ( d1[1]*d1[0]/d1_len ); // dy/dx
d1_a1(1,1) = ( -(d1[0]*d1[0]+d1[2]*d1[2])/d1_len ); // dy/dy
d1_a1(1,2) = ( d1[1]*d1[2]/d1_len );
d1_a1(2,0) = ( d1[2]*d1[0]/d1_len );
d1_a1(2,1) = ( d1[2]*d1[1]/d1_len );
d1_a1(2,2) = ( -(d1[1]*d1[1]+d1[0]*d1[0])/d1_len );
// Calculate derivatives of dot product
dd1 = matmul(d2, d1_a1) - d1;
dd2 = matmul(d2, -d1_a1);
dd3 = d1;
// Calculate derivatives of cross product
dc1 = dfuncr*( -d2 - proj*dd1 );
dc2 = dfuncr*( -proj*dd2 );
dc3 = dfuncr*( d2 - proj*dd3 );
// Calculate derivatives of excess
de1 = edf*excess*( dd1 + d1 );
de2 = edf*excess*( dd2 - d1 );
de3 = edf*excess*dd3;
}
Vector pos1 = myatoms.getPosition(0) + d1_len*d1;
Vector pos2 = myatoms.getPosition(0) + d2;
Vector g1derivf,g2derivf,lderivf; Tensor vir;
for(unsigned bin=0; bin<maxbins; ++bin) {
bead.set( bin*binw, (bin+1)*binw, sigma );
if( proj<(bin*binw-bead.getCutoff()) || proj>binw*(bin+1)+bead.getCutoff() ) continue;
double der, contr=bead.calculateWithCutoff( proj, der ) / cellv; der /= cellv;
myatoms.addValue( 2+bin, contr*val*eval );
if( !doNotCalculateDerivatives() ) {
g1derivf=contr*eval*dc1 + val*eval*der*dd1 + contr*val*de1;
addAtomDerivatives( 2+bin, 0, g1derivf, myatoms );
g2derivf=contr*eval*dc2 + val*eval*der*dd2 + contr*val*de2;
addAtomDerivatives( 2+bin, 1, g2derivf, myatoms );
lderivf=contr*eval*dc3 + val*eval*der*dd3 + contr*val*de3;
addAtomDerivatives( 2+bin, iat, lderivf, myatoms );
// Virial
vir = -Tensor( myatoms.getPosition(0), g1derivf ) - Tensor( pos1, g2derivf ) - Tensor( pos2, lderivf );
myatoms.addBoxDerivatives( 2+bin, vir );
}
}
}
}
void DFSBasic::performTask( const unsigned& task_index, const unsigned& current, MultiValue& myvals ) const {
std::vector<double> vals( myvals.getNumberOfValues() ); getVectorForTask( current, false, vals );
if( !doNotCalculateDerivatives() ) getVectorDerivatives( current, false, myvals );
for(unsigned k=0;k<vals.size();++k) myvals.setValue( k, vals[k] );
}
