void SecondaryStructureRMSD::performTask( const unsigned& task_index, const unsigned& current, MultiValue& myvals ) const {
// Retrieve the positions
std::vector<Vector> pos( references[0]->getNumberOfAtoms() );
const unsigned n=pos.size();
for(unsigned i=0;i<n;++i) pos[i]=ActionAtomistic::getPosition( getAtomIndex(current,i) );
// This does strands cutoff
Vector distance=pbcDistance( pos[align_atom_1],pos[align_atom_2] );
if( s_cutoff2>0 ){
if( distance.modulo2()>s_cutoff2 ){
myvals.setValue( 0, 0.0 );
return;
}
}
// This aligns the two strands if this is required
if( alignType!="DRMSD" && align_strands ){
Vector origin_old, origin_new; origin_old=pos[align_atom_2];
origin_new=pos[align_atom_1]+distance;
for(unsigned i=15;i<30;++i){
pos[i]+=( origin_new - origin_old );
}
}
// Create a holder for the derivatives
ReferenceValuePack mypack( 0, pos.size(), myvals ); mypack.setValIndex( 1 );
for(unsigned i=0;i<n;++i) mypack.setAtomIndex( i, getAtomIndex(current,i) );
// And now calculate the RMSD
const Pbc& pbc=getPbc();
unsigned closest=0;
double r = references[0]->calculate( pos, pbc, mypack, false );
const unsigned rs = references.size();
for(unsigned i=1;i<rs;++i){
mypack.setValIndex( i+1 );
double nr=references[i]->calculate( pos, pbc, mypack, false );
if( nr<r ){ closest=i; r=nr; }
}
// Transfer everything to the value
myvals.setValue( 0, 1.0 ); myvals.setValue( 1, r );
if( closest>0 ) mypack.moveDerivatives( closest+1, 1 );
if( !mypack.virialWasSet() ){
Tensor vir;
const unsigned cacs = colvar_atoms[current].size();
for(unsigned i=0;i<cacs;++i){
vir+=(-1.0*Tensor( pos[i], mypack.getAtomDerivative(i) ));
}
mypack.setValIndex(1); mypack.addBoxDerivatives( vir );
}
return;
}
double DRMSD::calc( const std::vector<Vector>& pos, const Pbc& pbc, ReferenceValuePack& myder, const bool& squared ) const {
plumed_dbg_assert(!targets.empty());
Vector distance;
myder.clear();
double drmsd=0.;
for(std::map< std::pair <unsigned,unsigned> , double>::const_iterator it=targets.begin();it!=targets.end();++it){
const unsigned i=getAtomIndex( it->first.first );
const unsigned j=getAtomIndex( it->first.second );
if(nopbc) distance=delta( pos[i] , pos[j] );
else distance=pbc.distance( pos[i] , pos[j] );
const double len = distance.modulo();
const double diff = len - it->second;
const double der = diff / len;
drmsd += diff * diff;
myder.addAtomDerivatives( i, -der * distance );
myder.addAtomDerivatives( j, der * distance );
myder.addBoxDerivatives( - der * Tensor(distance,distance) );
}
const double inpairs = 1./static_cast<double>(targets.size());
double idrmsd;
if(squared){
drmsd = drmsd * inpairs;
idrmsd = 2.0 * inpairs;
} else {
drmsd = sqrt( drmsd * inpairs );
idrmsd = inpairs / drmsd ;
}
myder.scaleAllDerivatives( idrmsd );
return drmsd;
}
double DRMSD::calc( const std::vector<Vector>& pos, const Pbc& pbc, const bool& squared ){
plumed_dbg_assert( !targets.empty() );
Vector distance;
double drmsd=0.;
for(std::map< std::pair <unsigned,unsigned> , double>::const_iterator it=targets.begin();it!=targets.end();++it){
unsigned i=getAtomIndex( it->first.first );
unsigned j=getAtomIndex( it->first.second );
if(nopbc){ distance=delta( pos[i] , pos[j] ); }
else{ distance=pbc.distance( pos[i] , pos[j] ); }
double len = distance.modulo();
double diff = len - it->second;
drmsd += diff * diff;
addAtomicDerivatives( i, -( diff / len ) * distance );
addAtomicDerivatives( j, ( diff / len ) * distance );
addBoxDerivatives( -( diff / len ) * Tensor(distance,distance) );
}
double npairs = static_cast<double>(targets.size());
double idrmsd;
if(squared){
drmsd = drmsd / npairs;
idrmsd = 2.0 / npairs;
} else {
drmsd = sqrt( drmsd / npairs );
idrmsd = 1.0/( drmsd * npairs );
}
virial *= idrmsd;
for(unsigned i=0;i<getNumberOfAtoms();++i){atom_ders[i] *= idrmsd;}
return drmsd;
}
void Steinhardt::calculateVector(){
double dfunc, dpoly_ass, md, tq6, itq6, real_z, imag_z;
Vector distance, dz, myrealvec, myimagvec, real_dz, imag_dz;
// The square root of -1
std::complex<double> ii( 0.0, 1.0 ), dp_x, dp_y, dp_z;
double sw, poly_ass, dlen, nbond=0.0; std::complex<double> powered;
for(unsigned i=1;i<getNAtoms();++i){
distance=getSeparation( getPosition(0), getPosition(i) );
dlen=distance.modulo(); sw = switchingFunction.calculate( dlen, dfunc );
if( sw>=getTolerance() ){
nbond += sw; // Accumulate total number of bonds
double dlen3 = dlen*dlen*dlen;
// Store derivatives of weight
MultiColvarBase::addAtomsDerivatives( 0, getAtomIndex(0), (-dfunc)*distance );
MultiColvarBase::addAtomsDerivatives( 0, getAtomIndex(i), (+dfunc)*distance );
MultiColvarBase::addBoxDerivatives( 0, (-dfunc)*Tensor( distance,distance ) );
// Do stuff for m=0
poly_ass=deriv_poly( 0, distance[2]/dlen, dpoly_ass );
// Derivatives of z/r wrt x, y, z
dz = -( distance[2] / dlen3 )*distance; dz[2] += (1.0 / dlen);
// Derivative wrt to the vector connecting the two atoms
myrealvec = (+sw)*dpoly_ass*dz + poly_ass*(+dfunc)*distance;
// Accumulate the derivatives
addAtomsDerivative( tmom, 0, -myrealvec );
addAtomsDerivative( tmom, i, myrealvec );
addBoxDerivatives( tmom, Tensor( -myrealvec,distance ) );
// And store the vector function
addComponent( tmom, sw*poly_ass );
// The complex number of which we have to take powers
std::complex<double> com1( distance[0]/dlen ,distance[1]/dlen );
// Do stuff for all other m values
for(unsigned m=1;m<=tmom;++m){
// Calculate Legendre Polynomial
poly_ass=deriv_poly( m, distance[2]/dlen, dpoly_ass );
// Calculate powe of complex number
powered=pow(com1,m-1); md=static_cast<double>(m);
// Real and imaginary parts of z
real_z = real(com1*powered); imag_z = imag(com1*powered );
// Calculate steinhardt parameter
tq6=poly_ass*real_z; // Real part of steinhardt parameter
itq6=poly_ass*imag_z; // Imaginary part of steinhardt parameter
// Derivatives wrt ( x/r + iy )^m
dp_x = md*powered*( (1.0/dlen)-(distance[0]*distance[0])/dlen3-ii*(distance[0]*distance[1])/dlen3 );
dp_y = md*powered*( ii*(1.0/dlen)-(distance[0]*distance[1])/dlen3-ii*(distance[1]*distance[1])/dlen3 );
dp_z = md*powered*( -(distance[0]*distance[2])/dlen3-ii*(distance[1]*distance[2])/dlen3 );
// Derivatives of real and imaginary parts of above
real_dz[0] = real( dp_x ); real_dz[1] = real( dp_y ); real_dz[2] = real( dp_z );
imag_dz[0] = imag( dp_x ); imag_dz[1] = imag( dp_y ); imag_dz[2] = imag( dp_z );
// Complete derivative of steinhardt parameter
myrealvec = (+sw)*dpoly_ass*real_z*dz + (+dfunc)*distance*tq6 + (+sw)*poly_ass*real_dz;
myimagvec = (+sw)*dpoly_ass*imag_z*dz + (+dfunc)*distance*itq6 + (+sw)*poly_ass*imag_dz;
// Real part
addComponent( tmom+m, sw*tq6 );
addAtomsDerivative( tmom+m, 0, -myrealvec );
addAtomsDerivative( tmom+m, i, myrealvec );
addBoxDerivatives( tmom+m, Tensor( -myrealvec,distance ) );
// Imaginary part
addImaginaryComponent( tmom+m, sw*itq6 );
addImaginaryAtomsDerivative( tmom+m, 0, -myimagvec );
addImaginaryAtomsDerivative( tmom+m, i, myimagvec );
addImaginaryBoxDerivatives( tmom+m, Tensor( -myimagvec,distance ) );
// Store -m part of vector
double pref=pow(-1.0,m);
// -m part of vector is just +m part multiplied by (-1.0)**m and multiplied by complex
// conjugate of Legendre polynomial
// Real part
addComponent( tmom-m, pref*sw*tq6 );
addAtomsDerivative( tmom-m, 0, -pref*myrealvec );
addAtomsDerivative( tmom-m, i, pref*myrealvec );
addBoxDerivatives( tmom-m, pref*Tensor( -myrealvec,distance ) );
// Imaginary part
addImaginaryComponent( tmom-m, -pref*sw*itq6 );
addImaginaryAtomsDerivative( tmom-m, 0, pref*myimagvec );
addImaginaryAtomsDerivative( tmom-m, i, -pref*myimagvec );
addImaginaryBoxDerivatives( tmom-m, pref*Tensor( myimagvec,distance ) );
}
} else {
removeAtomRequest( i, sw );
}
}
// Normalize
setElementValue(0, nbond ); updateActiveAtoms();
for(unsigned i=0;i<2*getNumberOfComponentsInVector();++i) quotientRule( 5+i, 0, 5+i );
// Clear tempory stuff
clearDerivativesAfterTask(0);
}
str
malAtomProperty(MalBlkPtr mb, InstrPtr pci)
{
str name;
int tpe;
(void)mb; /* fool compilers */
assert(pci != 0);
name = getFunctionId(pci);
tpe = getAtomIndex(getModuleId(pci), (int)strlen(getModuleId(pci)), TYPE_any);
if (tpe < 0 || tpe >= GDKatomcnt || tpe >= MAXATOMS)
return MAL_SUCCEED;
assert(pci->fcn != NULL);
switch (name[0]) {
case 'd':
if (idcmp("del", name) == 0 && pci->argc == 1) {
BATatoms[tpe].atomDel = (void (*)(Heap *, var_t *))pci->fcn;
setAtomName(pci);
return MAL_SUCCEED;
}
break;
case 'c':
if (idcmp("cmp", name) == 0 && pci->argc == 1) {
BATatoms[tpe].atomCmp = (int (*)(const void *, const void *))pci->fcn;
BATatoms[tpe].linear = true;
setAtomName(pci);
return MAL_SUCCEED;
}
break;
case 'f':
if (idcmp("fromstr", name) == 0 && pci->argc == 1) {
BATatoms[tpe].atomFromStr = (ssize_t (*)(const char *, size_t *, ptr *, bool))pci->fcn;
setAtomName(pci);
return MAL_SUCCEED;
}
if (idcmp("fix", name) == 0 && pci->argc == 1) {
BATatoms[tpe].atomFix = (int (*)(const void *))pci->fcn;
setAtomName(pci);
return MAL_SUCCEED;
}
break;
case 'h':
if (idcmp("heap", name) == 0 && pci->argc == 1) {
/* heap function makes an atom varsized */
BATatoms[tpe].size = sizeof(var_t);
assert_shift_width(ATOMelmshift(ATOMsize(tpe)), ATOMsize(tpe));
BATatoms[tpe].atomHeap = (void (*)(Heap *, size_t))pci->fcn;
setAtomName(pci);
return MAL_SUCCEED;
}
if (idcmp("hash", name) == 0 && pci->argc == 1) {
BATatoms[tpe].atomHash = (BUN (*)(const void *))pci->fcn;
setAtomName(pci);
return MAL_SUCCEED;
}
break;
case 'l':
if (idcmp("length", name) == 0 && pci->argc == 1) {
BATatoms[tpe].atomLen = (size_t (*)(const void *))pci->fcn;
setAtomName(pci);
return MAL_SUCCEED;
}
break;
case 'n':
if (idcmp("null", name) == 0 && pci->argc == 1) {
const void *atmnull = ((const void *(*)(void))pci->fcn)();
BATatoms[tpe].atomNull = atmnull;
setAtomName(pci);
return MAL_SUCCEED;
}
if (idcmp("nequal", name) == 0 && pci->argc == 1) {
BATatoms[tpe].atomCmp = (int (*)(const void *, const void *))pci->fcn;
setAtomName(pci);
return MAL_SUCCEED;
}
break;
case 'p':
if (idcmp("put", name) == 0 && pci->argc == 1) {
BATatoms[tpe].atomPut = (var_t (*)(Heap *, var_t *, const void *))pci->fcn;
setAtomName(pci);
return MAL_SUCCEED;
}
break;
case 's':
if (idcmp("storage", name) == 0 && pci->argc == 1) {
BATatoms[tpe].storage = (*(int (*)(void))pci->fcn)();
setAtomName(pci);
return MAL_SUCCEED;
}
break;
case 't':
if (idcmp("tostr", name) == 0 && pci->argc == 1) {
BATatoms[tpe].atomToStr = (ssize_t (*)(str *, size_t *, const void *, bool))pci->fcn;
setAtomName(pci);
return MAL_SUCCEED;
}
break;
case 'u':
if (idcmp("unfix", name) == 0 && pci->argc == 1) {
BATatoms[tpe].atomUnfix = (int (*)(const void *))pci->fcn;
setAtomName(pci);
return MAL_SUCCEED;
}
break;
case 'r':
if (idcmp("read", name) == 0 && pci->argc == 1) {
BATatoms[tpe].atomRead = (void *(*)(void *, stream *, size_t))pci->fcn;
setAtomName(pci);
return MAL_SUCCEED;
}
break;
case 'w':
if (idcmp("write", name) == 0 && pci->argc == 1) {
BATatoms[tpe].atomWrite = (gdk_return (*)(const void *, stream *, size_t))pci->fcn;
setAtomName(pci);
return MAL_SUCCEED;
}
break;
}
return MAL_SUCCEED;
}
