void Value::setGradients(){
gradients.clear();
ActionAtomistic*aa=dynamic_cast<ActionAtomistic*>(action);
ActionWithArguments*aw=dynamic_cast<ActionWithArguments*>(action);
if(aa){
Atoms&atoms((aa->plumed).getAtoms());
for(unsigned j=0;j<aa->getNumberOfAtoms();++j){
AtomNumber an=aa->getAbsoluteIndex(j);
if(atoms.isVirtualAtom(an)){
const ActionWithVirtualAtom* a=atoms.getVirtualAtomsAction(an);
for(std::map<AtomNumber,Tensor>::const_iterator p=a->getGradients().begin();p!=a->getGradients().end();++p){
// controllare l'ordine del matmul:
gradients[(*p).first]+=matmul(Vector(derivatives[3*j],derivatives[3*j+1],derivatives[3*j+2]),(*p).second);
}
} else {
for(unsigned i=0;i<3;i++) gradients[an][i]+=derivatives[3*j+i];
}
}
} else if(aw){
std::vector<Value*> values=aw->getArguments();
for(unsigned j=0;j<derivatives.size();j++){
for(std::map<AtomNumber,Vector>::const_iterator p=values[j]->gradients.begin();p!=values[j]->gradients.end();++p){
AtomNumber iatom=(*p).first;
gradients[iatom]+=(*p).second*derivatives[j];
}
}
} else plumed_error();
}
void Value::setGradients() {
// Can't do gradients if we don't have derivatives
if( !hasDeriv ) return;
gradients.clear();
ActionAtomistic*aa=dynamic_cast<ActionAtomistic*>(action);
ActionWithArguments*aw=dynamic_cast<ActionWithArguments*>(action);
if(aa) {
Atoms&atoms((aa->plumed).getAtoms());
for(unsigned j=0; j<aa->getNumberOfAtoms(); ++j) {
AtomNumber an=aa->getAbsoluteIndex(j);
if(atoms.isVirtualAtom(an)) {
const ActionWithVirtualAtom* a=atoms.getVirtualAtomsAction(an);
for(const auto & p : a->getGradients()) {
// controllare l'ordine del matmul:
gradients[p.first]+=matmul(Vector(derivatives[3*j],derivatives[3*j+1],derivatives[3*j+2]),p.second);
}
} else {
for(unsigned i=0; i<3; i++) gradients[an][i]+=derivatives[3*j+i];
}
}
} else if(aw) {
std::vector<Value*> values=aw->getArguments();
for(unsigned j=0; j<derivatives.size(); j++) {
for(const auto & p : values[j]->gradients) {
AtomNumber iatom=p.first;
gradients[iatom]+=p.second*derivatives[j];
}
}
} else plumed_error();
}
void HistogramBead::set( double l, double h, double w) {
init=true; lowb=l; highb=h; width=w;
const double DP2CUTOFF=6.25;
if( type==gaussian ) cutoff=sqrt(2.0*DP2CUTOFF);
else if( type==triangular ) cutoff=1.;
else plumed_error();
}
void ActionWithInputVessel::readArgument( const std::string& type ) {
std::string mlab;
if( keywords.exists("DATA") && type!="grid" ) parse("DATA",mlab);
ActionWithVessel* mves= plumed.getActionSet().selectWithLabel<ActionWithVessel*>(mlab);
if(!mves) error("action labelled " + mlab + " does not exist or does not have vessels");
addDependency(mves);
ActionWithValue* aval=dynamic_cast<ActionWithValue*>( this );
if(aval) {
if( aval->checkNumericalDerivatives() ) {
ActionWithValue* aval2=dynamic_cast<ActionWithValue*>( mves );
plumed_assert( aval2 ); aval2->useNumericalDerivatives();
}
}
if( type=="bridge" ) {
ActionWithVessel* aves=dynamic_cast<ActionWithVessel*>( this );
plumed_assert(aves); myBridgeVessel = mves->addBridgingVessel( aves );
arguments = dynamic_cast<Vessel*>( myBridgeVessel );
} else if( type=="store" ) {
arguments = dynamic_cast<Vessel*>( mves->buildDataStashes( NULL ) );
} else {
plumed_error();
}
}
void CLTool::parseFlag( const std::string&key, bool&t ){
plumed_massert(keywords.exists(key),"keyword " + key + " has not been registered");
plumed_massert(keywords.style(key,"flag"),"keyword " + key + " has not been registered as a flag");
plumed_assert(inputData.count(key)>0);
if( inputData[key]=="true") t=true;
else if( inputData[key]=="false") t=false;
else plumed_error();
}
void ReferenceArguments::extractArgumentDisplacement( const std::vector<Value*>& vals, const std::vector<double>& arg, std::vector<double>& dirout ) const {
if( hasmetric ) {
plumed_error();
} else {
for(unsigned j=0; j<reference_args.size(); ++j) {
unsigned jk=arg_der_index[j]; dirout[jk]=sqrtweight[j]*vals[jk]->difference( reference_args[j], arg[jk] );
}
}
}
double ReferenceArguments::projectArgDisplacementOnVector( const std::vector<double>& eigv, const std::vector<Value*>& vals, const std::vector<double>& arg, ReferenceValuePack& mypack ) const {
if( hasmetric ) {
plumed_error();
} else {
double proj=0;
for(unsigned j=0; j<reference_args.size(); ++j) {
unsigned jk=arg_der_index[j];
proj += eigv[j]*sqrtweight[j]*vals[jk]->difference( reference_args[j], arg[jk] );
mypack.setArgumentDerivatives( jk, eigv[j]*sqrtweight[j] );
}
return proj;
}
}
double HistogramBead::lboundDerivative( const double& x ) const {
double lowB;
if( type==gaussian ) {
lowB = difference( x, lowb ) / ( sqrt(2.0) * width );
return exp( -lowB*lowB ) / ( sqrt(2*pi)*width );
} else if ( type==triangular ) {
plumed_error();
// lowB = fabs( difference( x, lowb ) / width );
// if( lowB<1 ) return ( 1 - (lowB) ) / 2*width;
// else return 0;
} else {
plumed_merror("function type does not exist");
}
return 0;
}
double HistogramBead::uboundDerivative( const double& x ) const {
plumed_dbg_assert(init && periodicity!=unset );
double upperB;
if( type==gaussian ) {
upperB = difference( x, highb ) / ( sqrt(2.0) * width );
return exp( -upperB*upperB ) / ( sqrt(2*pi)*width );
} else if ( type==triangular ) {
plumed_error();
// upperB = fabs( difference( x, highb ) / width );
// if( upperB<1 ) return ( 1 - (upperB) ) / 2*width;
// else return 0;
} else {
plumed_merror("function type does not exist");
}
return 0;
}
void CLTool::setRemainingToDefault(FILE* out){
std::string def, thiskey;
for(unsigned k=0;k<keywords.size();++k){
thiskey=keywords.get(k);
if( keywords.style(thiskey,"compulsory") ){
if( inputData.count(thiskey)==0 ){
if( keywords.getDefaultValue(thiskey,def) ){
plumed_assert( def.length()>0 );
inputData.insert(std::pair<std::string,std::string>(thiskey,def));
} else {
fprintf(out,"ERROR : argument %s is compulsory. Use --help option for help\n",thiskey.c_str() );
plumed_error();
}
}
}
}
}
void Action::parseFlag(const std::string&key,bool & t) {
// Check keyword has been registered
plumed_massert(keywords.exists(key), "keyword " + key + " has not been registered");
// Check keyword is a flag
if(!keywords.style(key,"nohtml")) {
plumed_massert( keywords.style(key,"vessel") || keywords.style(key,"flag") || keywords.style(key,"hidden"), "keyword " + key + " is not a flag");
}
// Read in the flag otherwise get the default value from the keywords object
if(!Tools::parseFlag(line,key,t)) {
if( keywords.style(key,"nohtml") || keywords.style(key,"vessel") ) {
t=false;
} else if ( !keywords.getLogicalDefault(key,t) ) {
log.printf("ERROR in action %s with label %s : flag %s has no default",name.c_str(),label.c_str(),key.c_str() );
plumed_error();
}
}
}
/*! hybrid-36 decoder: converts string s to integer result
width: must be 4 (e.g. for residue sequence numbers)
or 5 (e.g. for atom serial numbers)
s: string to be converted
does not have to be null-terminated
s_size: size of s
must be equal to width, or an error message is
returned otherwise
result: integer holding the conversion result
return value: pointer to error message, if any,
or 0 on success
Example usage (from C++):
int result;
const char* errmsg = hy36decode(width, "A1T5", 4, &result);
if (errmsg) throw std::runtime_error(errmsg);
*/
const char*
hy36decode(unsigned width, const char* s, unsigned s_size, int* result)
{
static const std::vector<int> digits_values_upper_vector([]() {
std::vector<int> ret(128U,-1);
for(unsigned i=0; i<36U; i++) {
int di = digits_upper()[i];
if (di < 0 || di > 127) {
plumed_error()<<"internal error hy36decode: integer value out of range";
}
ret[di] = i;
}
return ret;
}());
static const int* digits_values_upper=digits_values_upper_vector.data();
static const std::vector<int> digits_values_lower_vector([]() {
std::vector<int> ret(128U,-1);
for(unsigned i=0; i<36U; i++) {
int di = digits_lower()[i];
if (di < 0 || di > 127) {
plumed_error()<<"internal error hy36decode: integer value out of range";
}
ret[di] = i;
}
return ret;
}());
static const int* digits_values_lower=digits_values_lower_vector.data();
int di;
const char* errmsg;
if (s_size == width) {
di = s[0];
if (di >= 0 && di <= 127) {
if (digits_values_upper[di] >= 10) {
errmsg = decode_pure(digits_values_upper, 36U, s, s_size, result);
if (errmsg == 0) {
/* result - 10*36**(width-1) + 10**width */
if (width == 4U) (*result) -= 456560;
else if (width == 5U) (*result) -= 16696160;
else {
*result = 0;
return unsupported_width();
}
return 0;
}
}
else if (digits_values_lower[di] >= 10) {
errmsg = decode_pure(digits_values_lower, 36U, s, s_size, result);
if (errmsg == 0) {
/* result + 16*36**(width-1) + 10**width */
if (width == 4U) (*result) += 756496;
else if (width == 5U) (*result) += 26973856;
else {
*result = 0;
return unsupported_width();
}
return 0;
}
}
else {
errmsg = decode_pure(digits_values_upper, 10U, s, s_size, result);
if (errmsg) return errmsg;
if (!(width == 4U || width == 5U)) {
*result = 0;
return unsupported_width();
}
return 0;
}
}
}
*result = 0;
return invalid_number_literal();
}
void MultiColvarBase::setupLinkCells(){
if( !linkcells.enabled() ) return ;
unsigned iblock, jblock;
if( usespecies ){
iblock=0;
} else if( current_atoms.size()<4 ){
iblock=1;
} else {
plumed_error();
}
// Count number of currently active atoms
unsigned nactive_atoms=0;
for(unsigned i=0;i<ablocks[iblock].size();++i){
if( isCurrentlyActive( ablocks[iblock][i] ) ) nactive_atoms++;
}
std::vector<Vector> ltmp_pos( nactive_atoms );
std::vector<unsigned> ltmp_ind( nactive_atoms );
nactive_atoms=0;
if( usespecies ){
ltmp_pos.resize( ablocks[0].size() ); ltmp_ind.resize( ablocks[0].size() );
for(unsigned i=0;i<ablocks[0].size();++i){
if( !isCurrentlyActive( ablocks[0][i] ) ) continue;
ltmp_ind[nactive_atoms]=ablocks[0][i];
ltmp_pos[nactive_atoms]=getPositionOfAtomForLinkCells( ltmp_ind[nactive_atoms] );
nactive_atoms++;
}
} else {
ltmp_pos.resize( ablocks[1].size() ); ltmp_ind.resize( ablocks[1].size() );
for(unsigned i=0;i<ablocks[1].size();++i){
if( !isCurrentlyActive( ablocks[1][i] ) ) continue;
ltmp_ind[nactive_atoms]=i;
ltmp_pos[nactive_atoms]=getPositionOfAtomForLinkCells( ablocks[1][i] );
nactive_atoms++;
}
}
// Build the lists for the link cells
linkcells.buildCellLists( ltmp_pos, ltmp_ind, getPbc() );
if( !usespecies ){
// Get some parallel info
unsigned stride=comm.Get_size();
unsigned rank=comm.Get_rank();
if( serialCalculation() ){ stride=1; rank=0; }
// Ensure we only do tasks where atoms are in appropriate link cells
std::vector<unsigned> linked_atoms( 1+ablocks[1].size() );
std::vector<unsigned> active_tasks( getFullNumberOfTasks(), 0 );
for(unsigned i=rank;i<ablocks[0].size();i+=stride){
if( !isCurrentlyActive( ablocks[0][i] ) ) continue;
natomsper=1; linked_atoms[0]=ltmp_ind[0]; // Note we always check atom 0 because it is simpler than changing LinkCells.cpp
linkcells.retrieveNeighboringAtoms( getPositionOfAtomForLinkCells( ablocks[0][i] ), natomsper, linked_atoms );
for(unsigned j=0;j<natomsper;++j){
for(unsigned k=bookeeping(i,linked_atoms[j]).first;k<bookeeping(i,linked_atoms[j]).second;++k) active_tasks[k]=1;
}
}
if( !serialCalculation() ) comm.Sum( active_tasks );
deactivateAllTasks();
activateTheseTasks( active_tasks );
contributorsAreUnlocked=false;
}
}
void Pbc::test(){
Random r;
r.setSeed(-20);
for(int i=0;i<1000;i++){
// random matrix with some zero element
Tensor box;
for(int j=0;j<3;j++) for(int k=0;k<3;k++) if(r.U01()>0.2){
box[j][k]=2.0*r.U01()-1.0;
}
int boxtype=i%10;
switch(boxtype){
case 0:
// cubic
for(int j=0;j<3;j++) for(int k=0;k<3;k++) if(j!=k) box[j][k]=0.0;
for(int j=1;j<3;j++) box[j][j]=box[0][0];
break;
case 1:
// orthorombic
for(int j=0;j<3;j++) for(int k=0;k<3;k++) if(j!=k) box[j][k]=0.0;
break;
case 2:
// hexagonal
{
int perm=r.U01()*100;
Vector a;
a(0)=r.U01()*2-2; a(1)=0.0;a(2)=0.0;
double d=r.U01()*2-2;
Vector b(0.0,d,0.0);
Vector c(0.0,0.5*d,sqrt(3.0)*d*0.5);
box.setRow((perm+0)%3,a);
box.setRow((perm+1)%3,b);
box.setRow((perm+2)%3,c);
}
break;
case 3:
// bcc
{
int perm=r.U01()*100;
double d=r.U01()*2-2;
Vector a(d,d,d);
Vector b(d,-d,d);
Vector c(d,d,-d);
box.setRow((perm+0)%3,a);
box.setRow((perm+1)%3,b);
box.setRow((perm+2)%3,c);
}
break;
case 4:
// fcc
{
int perm=r.U01()*100;
double d=r.U01()*2-2;
Vector a(d,d,0);
Vector b(d,0,d);
Vector c(0,d,d);
box.setRow((perm+0)%3,a);
box.setRow((perm+1)%3,b);
box.setRow((perm+2)%3,c);
}
break;
default:
// triclinic
break;
}
Pbc pbc;
pbc.setBox(box);
std::cerr<<"( "<<boxtype<<" )\n";
std::cerr<<"Box:";
for(int j=0;j<3;j++) for(int k=0;k<3;k++) std::cerr<<" "<<box[j][k];
std::cerr<<"\n";
std::cerr<<"Determinant: "<<determinant(box)<<"\n";
std::cerr<<"Shifts:";
for(int j=0;j<2;j++) for(int k=0;k<2;k++) for(int l=0;l<2;l++) std::cerr<<" "<<pbc.shifts[j][k][l].size();
std::cerr<<"\n";
int nshifts=0;
int ntot=10000;
for(int j=0;j<ntot;j++){
Vector v(r.U01()-0.5,r.U01()-0.5,r.U01()-0.5);
v*=5;
for(int j=0;j<3;j++) if(r.U01()>0.2) v(j)=0.0;
Vector full(v);
Vector fast=pbc.distance(Vector(0,0,0),v,&nshifts);
full=fast;
pbc.fullSearch(full);
if(modulo2(fast-full)>1e-10) {
std::cerr<<"orig "<<v[0]<<" "<<v[1]<<" "<<v[2]<<"\n";
std::cerr<<"fast "<<fast[0]<<" "<<fast[1]<<" "<<fast[2]<<"\n";
std::cerr<<"full "<<full[0]<<" "<<full[1]<<" "<<full[2]<<"\n";
std::cerr<<"diff "<<modulo2(fast)-modulo2(full)<<std::endl;
if(std::fabs(modulo2(fast)-modulo2(full))>1e-15) plumed_error();
}
}
std::cerr<<"Average number of shifts: "<<double(nshifts)/double(ntot)<<"\n";
}
}
void ActionWithAveraging::performOperations( const bool& from_update ) { plumed_error(); }
double FunctionVessel::calcTransform( const double& , double& ) const {
plumed_error(); return 1.0;
}
void IMD::receive(){
if(!connected) return;
if(clientsock){
IMDType type;
int length;
int itype;
while (vmdsock_selread(clientsock,0) > 0) {
type = imd_recv_header(clientsock, &length);
if(type==IMD_MDCOMM){
int32* vmd_atoms = new int32[length];
float* vmd_forces = new float[3*length];
imd_recv_mdcomm(clientsock, length, vmd_atoms, vmd_forces);
for(int i=0;i<length;i++){
forces[3*vmd_atoms[i]+0]=vmd_forces[3*i+0];
forces[3*vmd_atoms[i]+1]=vmd_forces[3*i+1];
forces[3*vmd_atoms[i]+2]=vmd_forces[3*i+2];
}
delete [] vmd_atoms;
delete [] vmd_forces;
itype=0;
comm.Bcast(&itype,1,0);
comm.Bcast(&forces[0],forces.size(),0);
}else if(type==IMD_DISCONNECT){
vmdsock_destroy(clientsock);
clientsock=NULL;
for(unsigned i=0;i<forces.size();i++) forces[i]=0.0;
connected=false;
itype=1;
comm.Bcast(&itype,1,0);
break;
}else if(type==IMD_TRATE){
if(length<1) length=1;
itype=2;
log.printf("IMD: setting transfer rate to %d\n",length);
transferRate=length;
comm.Bcast(&itype,1,0);
comm.Bcast(&transferRate,1,0);
}else if(type==IMD_KILL){
log.printf("IMD: killing simulation\n");
itype=3;
comm.Bcast(&itype,1,0);
plumed.exit();
}
}
itype=-1;
comm.Bcast(&itype,1,0);
}
if(comm.Get_rank()!=0){
int itype;
while(true){
comm.Bcast(&itype,1,0);
if(itype==-1)break;
else if(itype==0) comm.Bcast(&forces[0],forces.size(),0);
else if(itype==1) {
for(unsigned i=0;i<forces.size();i++) forces[i]=0.0;
connected=false;
}
else if(itype==2) comm.Bcast(&transferRate,1,0);
else if(itype==3) plumed.exit();
else plumed_error();
}
}
}
int PREFIX read_alpharmsd(char **word, int count, t_plumed_input *input, FILE *fplog)
{
// Coordinates N CA C O CB (Angstrom) of alpha 6-res block from the representative pdbs of
// each of the 5 architecture entries in class "mainly alpha" of CATH database
// (1oai 1mz9 1jdh 1ppr 1h12)
static rvec ref_alpha[30]={
{ 0.733, 0.519, 5.298}, // N i
{ 1.763, 0.810, 4.301}, // CA
{ 1.527, -0.045, 3.053}, // C
{ 1.646, 0.436, 1.928}, // O
{ 3.166, 0.543, 4.881}, // CB
{ 1.180, -1.312, 3.254}, // N i+1
{ 0.924, -2.203, 2.126}, // CA
{-0.239, -1.711, 1.261}, // C
{-0.190, -1.815, 0.032}, // O
{ 0.650, -3.626, 2.626}, // CB
{-1.280, -1.172, 1.891}, // N i+2
{-2.416, -0.661, 1.127}, // CA
{-1.964, 0.529, 0.276}, // C
{-2.364, 0.659, -0.880}, // O
{-3.548, -0.217, 2.056}, // CB
{-1.130, 1.391, 0.856}, // N i+3
{-0.620, 2.565, 0.148}, // CA
{ 0.231, 2.129, -1.032}, // C
{ 0.179, 2.733, -2.099}, // O
{ 0.228, 3.439, 1.077}, // CB
{ 1.028, 1.084, -0.833}, // N i+4
{ 1.872, 0.593, -1.919}, // CA
{ 1.020, 0.020, -3.049}, // C
{ 1.317, 0.227, -4.224}, // O
{ 2.850, -0.462, -1.397}, // CB
{-0.051, -0.684, -2.696}, // N i+5
{-0.927, -1.261, -3.713}, // CA
{-1.663, -0.171, -4.475}, // C
{-1.916, -0.296, -5.673}, // O
{-1.933, -2.219, -3.074} // CB
};
int i, iw, iat, j, help, ix;
double r_0, d_0, d;
double delta = 0.0;
double angstrom_scale;
char string[400];
real threshold, value;
help=0;
d_0=0.;
colvar.cell_pbc[count]=1; // default is PBC
iw = seek_word(word,"LIST");
if(iw>=0){
j=plumed_get_group(word[iw+1],&colvar.cvatoms[count],colvar.natoms[count],input,fplog);
colvar.natoms[count]+=j;
colvar.list[count][0]=j;
} else{ fprintf(fplog,"|- NEEDED LIST KEYWORD FOR ALPHARMSD\n"); help=1;}
if(colvar.natoms[count]%5!=0){ fprintf(fplog,"|- ERROR: TOTAL NUMBER OF ATOMS MUST BE MULTIPLE OF 5\n"); help=1; }
iw=seek_word(word,"SIGMA");
if(iw>=0){ sscanf(word[iw+1],"%lf", &delta);
colvar.delta_r[count] = (real) delta; }
iw=seek_word(word,"NN");
if(iw>=0) { sscanf(word[iw+1],"%i", &colvar.nn[count]); } else { fprintf(fplog,"|- NEEDED NN KEYWORD FOR ALPHARMSD\n"); help=1;}
iw=seek_word(word,"MM");
if(iw>=0) { sscanf(word[iw+1],"%i", &colvar.mm[count]);} else { fprintf(fplog,"|- NEEDED MM KEYWORD FOR ALPHARMSD\n"); help=1;}
iw=seek_word(word,"R_0");
if(iw>=0) { sscanf(word[iw+1],"%lf", &r_0); } else { fprintf(fplog,"|- NEEDED R_0 KEYWORD FOR ALPHARMSD\n"); help=1;}
iw=seek_word(word,"D_0");
if(iw>=0) { sscanf(word[iw+1],"%lf", &d_0); }
iw=seek_word(word,"NOPBC");
if(iw>=0) {colvar.cell_pbc[count] = 0;}
iw=seek_word(word,"PBC");
if(iw>=0) {colvar.cell_pbc[count] = 1;}
iw=seek_word(word,"ANGSTROM_SCALE");
if(iw>=0) { sscanf(word[iw+1],"%lf", &angstrom_scale); } else { fprintf(fplog,"|- NEEDED ANGSTROM_SCALE KEYWORD FOR ALPHARMSD\n"); help=1;}
if(help){
fprintf(fplog, "\n-ALPHARMSD CV: WRONG SYNTAX\n");
fprintf(fplog, "e.g.: \n");
fprintf(fplog, "ALPHARMSD LIST <g1> NN 8 MM 12 R_0 0.08 SIGMA 1.0 ANGSTROM_SCALE 0.1 NOPBC\n");
fprintf(fplog, " g1-> \n");
fprintf(fplog, " 7 9 26 27 11 \n");
fprintf(fplog, " 28 30 45 46 32 \n");
fprintf(fplog, " 47 49 56 57 51 \n");
fprintf(fplog, " 58 60 71 72 62 \n");
fprintf(fplog, " 73 75 88 89 77 \n");
fprintf(fplog, " 90 92 100 101 94 \n");
fprintf(fplog, " 102 104 120 121 106 \n");
fprintf(fplog, " 122 124 136 137 126 \n");
fprintf(fplog, " 138 140 147 148 142 \n");
fprintf(fplog, " 149 151 163 164 153 \n");
fprintf(fplog, " 165 167 183 184 169 \n");
fprintf(fplog, " 185 187 190 191 189 \n");
fprintf(fplog, " 192 194 209 210 196 \n");
fprintf(fplog, " g1<- \n");
fprintf(fplog, " \n");
fprintf(fplog, " (where each row contains N CA C O CB of consecutive residues)\n");
fprintf(fplog, " \n");
plumed_error("PluMed dead with errors: check log file");
}
colvar.r_0[count] = (real) r_0;
colvar.d_0[count] = (real) d_0;
colvar.type_s[count] = 37;
fprintf(fplog, "%1i-ALPHARMSD; ATOMS INVOLVED: %i; ", count+1, colvar.natoms[count]);
if(colvar.cell_pbc[count]) fprintf(fplog, " PBC ON");
else fprintf(fplog, " PBC OFF");
if (logical.do_hills) fprintf(fplog," SIGMA %f\n",colvar.delta_r[count]);
else fprintf(fplog,"\n");
fprintf(fplog, "|--FUNCTIONAL FORM: (1-((dist_mat_rmsd-d_0)/r_0)^n) / (1-((dist_mat_rmsd-d_0)/r_0)^m) \n");
fprintf(fplog, "|--PARAMETERS: n= %i m= %i r_0= %f d_0= %f\n", colvar.nn[count], colvar.mm[count], colvar.r_0[count], colvar.d_0[count]);
threshold=pow(0.00001,1./(colvar.nn[count]-colvar.mm[count]));
value=(1.-pow(threshold,colvar.nn[count]))/(1.-pow(threshold,colvar.mm[count]));
fprintf(fplog, "|--CUTOFF VALUE: %f\n",value);
fprintf(fplog, "|--CUTOFF DISTANCE: %f\n",threshold*r_0+d_0);
iat=0;
fprintf(fplog,"|- SET MEMBERS: ");
for(i=0;i<colvar.natoms[count];i++){fprintf(fplog," %d ",colvar.cvatoms[count][i]+1);if((i+1)%20==0)fprintf(fplog,"\n ");}fprintf(fplog,"\n\n");
fprintf(fplog,"|- IMPORTANT NOTE: THIS CV REQUIRES ALIGN_ATOMS (FOR ALL BACKBONE) ON SOME CODES LIKE GROMACS4 !!!\n");
snew(colvar.myder[count], colvar.natoms[count]);
// storing reference distance matrix (converted from angstrom to angstrom*angstrom_scale)
ref_dist_mat.alpha_pairs=0.; // pairs without covalent bond
for (i=0;i<29;i++) {
for (j=i+1;j<30;j++) {
d=0.;
for (ix=0;ix<3;ix++) {
d += pow((ref_alpha[i][ix]-ref_alpha[j][ix]),2);
}
d=sqrt(d);
// here d is in angstrom: covalent bonds among N CA C O CB are maximum 1.54 A
if(d>1.7) {
// convert d in length units of the MD program
d=d*angstrom_scale;
ref_dist_mat.alpha_pairs+=1.;
} else {
// exclude covalent bonds
d=-999.;
}
ref_dist_mat.alpha[i][j]=d;
ref_dist_mat.alpha[j][i]=d;
}
}
return colvar.natoms[count];
}
int PREFIX read_angle(char **word, int count, t_plumed_input *input, FILE *fplog)
{
int i,j, iat, iw, help;
double delta = 0.0;
char string[400];
help = 0;
colvar.doTrig[count]=0; // Default is to do no trigonometry (raw angle)
iw = seek_word(word,"LIST");
if(iw>=0) {
j=plumed_get_group(word[iw+1],&colvar.cvatoms[count],colvar.natoms[count],input,fplog);
colvar.natoms[count]+=j;
colvar.list[count][0]=j;
j=plumed_get_group(word[iw+2],&colvar.cvatoms[count],colvar.natoms[count],input,fplog);
colvar.natoms[count]+=j;
colvar.list[count][1]=j;
j=plumed_get_group(word[iw+3],&colvar.cvatoms[count],colvar.natoms[count],input,fplog);
colvar.natoms[count]+=j;
colvar.list[count][2]=j;
} else { fprintf(fplog,"|- NEEDED LIST KEYWORD FOR ANGLE\n"); help=1;}
iw=seek_word(word,"SIGMA");
if(iw>=0){ sscanf(word[iw+1],"%lf", &delta);
colvar.delta_r[count] = (real) delta; }
if(help){
fprintf(fplog, "\n-ANGLE CV: WRONG SYNTAX\n");
fprintf(fplog, "e.g.: \n");
fprintf(fplog, " ANGLE LIST 12 17 20 SIGMA 1.0 \n");
fprintf(fplog, " \n");
fprintf(fplog, "or in case of group: \n");
fprintf(fplog, " ANGLE LIST <g1> <g2> <g3> SIGMA 1.0 \n");
fprintf(fplog, " g1-> \n");
fprintf(fplog, " 6 10 \n");
fprintf(fplog, " g1<- \n");
fprintf(fplog, " \n");
fprintf(fplog, " g2-> \n");
fprintf(fplog, " 8 15 21 \n");
fprintf(fplog, " g2<- \n");
fprintf(fplog, " \n");
fprintf(fplog, " g3-> \n");
fprintf(fplog, " 23 29 31\n");
fprintf(fplog, " g3<- \n");
fprintf(fplog, " \n");
plumed_error("PluMeD dead with errors: check log file");
}
iw=seek_word(word,"SIN");
if(iw>=0){ colvar.doTrig[count]=1; }
iw=seek_word(word,"COS");
if(iw>=0){ colvar.doTrig[count]=2; }
colvar.type_s[count] = 4;
if(colvar.doTrig[count]==0){
fprintf(fplog, "\n%1i-ANGLE: (1st SET: %i ATOMS), (2nd SET: %i ATOMS), (3rd SET: %i ATOMS); ", count+1,
colvar.list[count][0], colvar.list[count][1], colvar.list[count][2]);
}
if(colvar.doTrig[count]==1){
fprintf(fplog, "\n%1i-SINE OF ANGLE: (1st SET: %i ATOMS), (2nd SET: %i ATOMS), (3rd SET: %i ATOMS); ", count+1,
colvar.list[count][0], colvar.list[count][1], colvar.list[count][2]);
}
if(colvar.doTrig[count]==1){
fprintf(fplog, "\n%1i-COSINE OF ANGLE: (1st SET: %i ATOMS), (2nd SET: %i ATOMS), (3rd SET: %i ATOMS); ", count+1,
colvar.list[count][0], colvar.list[count][1], colvar.list[count][2]);
}
if (logical.do_hills) fprintf(fplog," SIGMA %f\n",colvar.delta_r[count]);
else fprintf(fplog,"\n");
iat=0;
fprintf(fplog,"|- 1st SET MEMBERS: ");
for(i=0;i<colvar.list[count][0];i++){fprintf(fplog," %d ",colvar.cvatoms[count][iat++]+1);if((i+1)%20==0)fprintf(fplog,"\n ");}fprintf(fplog,"\n");
fprintf(fplog,"|- 2nd SET MEMBERS: ");
for(i=0;i<colvar.list[count][1];i++){fprintf(fplog," %d ",colvar.cvatoms[count][iat++]+1);if((i+1)%20==0)fprintf(fplog,"\n ");}fprintf(fplog,"\n");
fprintf(fplog,"|- 3rd SET MEMBERS: ");
for(i=0;i<colvar.list[count][2];i++){fprintf(fplog," %d ",colvar.cvatoms[count][iat++]+1);if((i+1)%20==0)fprintf(fplog,"\n ");}fprintf(fplog,"\n\n");
snew(colvar.myder[count], colvar.natoms[count]);
return colvar.natoms[count];
}
void CLTool::error( const std::string& msg ){
fprintf(stderr,"ERROR : in input for command line tool %s : %s\n",name.c_str(),msg.c_str());
plumed_error();
}
void PREFIX angle_restraint(int i_c, struct mtd_data_s *mtd_data)
{
int i, j, iat, k, ix;
real myp[3][3], totmasse[3], d[3][3];
rvec rij, sij, tij;
real mod_rij, mod_sij;
real eps, sign0;
real caa, cbb, cab, ccc, sab;
real ac, Vac, bc, dVac, cos_psi, sin_psi;
totmasse[0] = totmasse[1] = totmasse[2] = 0.;
myp[0][0] = myp[0][1] = myp[0][2] = 0.;
myp[1][0] = myp[1][1] = myp[1][2] = 0.;
myp[2][0] = myp[2][1] = myp[2][2] = 0.;
k = 0;
for(j=0;j<3;j++) {
for(i=0;i<colvar.list[i_c][j];i++){
iat = colvar.cvatoms[i_c][k];
myp[j][0] += mtd_data->mass[iat]*mtd_data->pos[iat][0];
myp[j][1] += mtd_data->mass[iat]*mtd_data->pos[iat][1];
myp[j][2] += mtd_data->mass[iat]*mtd_data->pos[iat][2];
totmasse[j] += mtd_data->mass[iat];
k++;
}
myp[j][0] /= totmasse[j];
myp[j][1] /= totmasse[j];
myp[j][2] /= totmasse[j];
}
minimal_image(myp[1], myp[0], &mod_rij, rij);
minimal_image(myp[1], myp[2], &mod_sij, sij);
caa = norm2(rij);
cab = iprod(rij,sij);
cbb = norm2(sij);
oprod(rij,sij,tij);
sab = norm(tij);
ccc = 1.0/sqrt(caa*cbb);
ac = cab*ccc; // cosine of teta
Vac = acos(ac);
dVac = -ccc/sqrt(1.-ac*ac);
for(ix=0;ix<3;ix++) {
d[0][ix] = -dVac*(-cab/caa*rij[ix]+sij[ix]);
d[1][ix] = dVac*(-cab/caa*rij[ix]-cab/cbb*sij[ix]+rij[ix]+sij[ix]);
d[2][ix] = dVac*(cab/cbb*sij[ix]-rij[ix]);
}
// Now we do appropriate multiplication of the derivatives to get what we are interested in
if( colvar.doTrig[i_c]==0 ){ colvar.ss0[i_c] = Vac; }
else if( colvar.doTrig[i_c]==1 ){
cos_psi=cos( Vac );
for(i=0;i<3;++i){d[0][i]*= cos_psi; d[1][i]*= cos_psi; d[2][i]*= cos_psi;}
colvar.ss0[i_c] = sin( Vac );
}
else if( colvar.doTrig[i_c]==2 ){
sin_psi=-sin( Vac );
for(i=0;i<3;++i){d[0][i]*= sin_psi; d[1][i]*= sin_psi; d[2][i]*= sin_psi;}
colvar.ss0[i_c] = cos( Vac );
}
else{ plumed_error("No trigonometric mode defined in torsion restraint"); }
k=0;
for(j=0;j<3;j++) {
for(i=0;i<colvar.list[i_c][j];i++){
iat = colvar.cvatoms[i_c][k];
for(ix=0;ix<3;ix++) colvar.myder[i_c][k][ix] = d[j][ix]*mtd_data->mass[iat]/totmasse[j];
k++;
}
}
//colvar.ss0[i_c] = Vac;
}
int PREFIX read_position(char **word, int count, t_plumed_input *input, FILE *fplog)
{
int i, iw, j;
double delta = 0.0;
char string[400];
char chr[3];
int help;
int i1, i2, i3;
double rtmp;
help=0;
chr[0]=chr[1]=chr[2]=' ';
iw = seek_word(word,"LIST");
if(iw>=0){
j=plumed_get_group(word[iw+1],&colvar.cvatoms[count],colvar.natoms[count],input,fplog);
colvar.natoms[count]+=j;
colvar.list[count][0]=j;
} else{ fprintf(fplog,"|- NEEDED LIST KEYWORD FOR POSITION\n"); help=1;}
iw=seek_word(word,"SIGMA");
if(iw>=0){ sscanf(word[iw+1],"%lf", &delta);
colvar.delta_r[count] = (real) delta; }
iw=seek_word(word,"DIR");
if(iw>=0) {
sscanf(word[iw+1],"%s", chr);
if(!strcmp(chr,"X") || !strcmp(chr,"x"))
colvar.intpar[count][0] = 0;
else if(!strcmp(chr,"Y") || !strcmp(chr,"y"))
colvar.intpar[count][0] = 1;
else if(!strcmp(chr,"Z") || !strcmp(chr,"z"))
colvar.intpar[count][0] = 2;
}
iw=seek_word(word,"LINE_POS");
if(iw>=0) {
colvar.intpar[count][0] = 3;
sscanf(word[++iw],"%s", chr);
if (!strcmp(chr,"X")){
colvar.intpar[count][1] = 0;
colvar.intpar[count][2] = 1;
colvar.intpar[count][3] = 1;
}else if(!strcmp(chr,"Y")){
colvar.intpar[count][1] = 1;
colvar.intpar[count][2] = 2;
colvar.intpar[count][3] = 1;
}else if(!strcmp(chr,"Z")){
colvar.intpar[count][1] = 2;
colvar.intpar[count][2] = 3;
colvar.intpar[count][3] = 1;
}else if(!strcmp(chr,"XY")){
colvar.intpar[count][1] = 0;
colvar.intpar[count][2] = 2;
colvar.intpar[count][3] = 1;
}else if(!strcmp(chr,"XZ")){
colvar.intpar[count][1] = 0;
colvar.intpar[count][2] = 3;
colvar.intpar[count][3] = 2;
}else if(!strcmp(chr,"YZ")){
colvar.intpar[count][1] = 1;
colvar.intpar[count][2] = 3;
colvar.intpar[count][3] = 1;
}else if(!strcmp(chr,"XYZ")){
colvar.intpar[count][1] = 0;
colvar.intpar[count][2] = 3;
colvar.intpar[count][3] = 1;
}else{
help=1;
}
i1=colvar.intpar[count][1];
i2=colvar.intpar[count][2];
i3=colvar.intpar[count][3];
for(i=i1;i<i2;i+=i3){
sscanf(word[++iw],"%lf", &rtmp);
colvar.vecpar[count][0][i]= (real) rtmp;
}
for(i=i1;i<i2;i+=i3){
sscanf(word[++iw],"%lf", &rtmp);
colvar.vecpar[count][1][i]= (real) rtmp;
}
}
iw=seek_word(word,"LINE_DIST");
if(iw>=0) {
colvar.intpar[count][0] = 4;
sscanf(word[++iw],"%s", chr);
if (!strcmp(chr,"X")){
colvar.intpar[count][1] = 0;
colvar.intpar[count][2] = 1;
colvar.intpar[count][3] = 1;
}else if(!strcmp(chr,"Y")){
colvar.intpar[count][1] = 1;
colvar.intpar[count][2] = 2;
colvar.intpar[count][3] = 1;
}else if(!strcmp(chr,"Z")){
colvar.intpar[count][1] = 2;
colvar.intpar[count][2] = 3;
colvar.intpar[count][3] = 1;
}else if(!strcmp(chr,"XY")){
colvar.intpar[count][1] = 0;
colvar.intpar[count][2] = 2;
colvar.intpar[count][3] = 1;
}else if(!strcmp(chr,"XZ")){
colvar.intpar[count][1] = 0;
colvar.intpar[count][2] = 3;
colvar.intpar[count][3] = 2;
}else if(!strcmp(chr,"YZ")){
colvar.intpar[count][1] = 1;
colvar.intpar[count][2] = 3;
colvar.intpar[count][3] = 1;
}else if(!strcmp(chr,"XYZ")){
colvar.intpar[count][1] = 0;
colvar.intpar[count][2] = 3;
colvar.intpar[count][3] = 1;
}else{
help=1;
}
i1=colvar.intpar[count][1];
i2=colvar.intpar[count][2];
i3=colvar.intpar[count][3];
for(i=i1;i<i2;i+=i3){
sscanf(word[++iw],"%lf", &rtmp);
colvar.vecpar[count][0][i]= (real) rtmp;
}
for(i=i1;i<i2;i+=i3){
sscanf(word[++iw],"%lf", &rtmp);
colvar.vecpar[count][1][i]= (real) rtmp;
}
}
if(chr[0]==' ')help=1;
if(help){
fprintf(fplog, "\n-POSIION CV: WRONG SYNTAX\n");
fprintf(fplog, "e.g.: \n");
fprintf(fplog, " POSITION LIST 42 {TYPE} SIGMA 1.0 \n");
fprintf(fplog, "or in case of groups \n");
fprintf(fplog, " POSITION LIST <g1> {TYPE} SIGMA 1.0 \n");
fprintf(fplog, " g1-> \n");
fprintf(fplog, " 6 10 \n");
fprintf(fplog, " g1<- \n");
fprintf(fplog, " \n");
fprintf(fplog, " TYPE can be either DIR, LINE_POS or LINE_DIST\n");
fprintf(fplog, " possible flags for DIR are X, Y and Z\n");
fprintf(fplog, " possible flags for LINE_POS and LINE_DIST are X, Y, Z, XY, XZ, YZ or XYZ\n");
plumed_error("PluMeD dead with errors: check log file");
}
colvar.type_s[count] = 32;
snew(colvar.myder[count], colvar.natoms[count]);
fprintf(fplog, "%i-%1s POSITION OF %i ATOMS; ", count+1,chr,colvar.natoms[count]);
if (logical.do_hills) fprintf(fplog," SIGMA %f\n",colvar.delta_r[count]);
else fprintf(fplog,"\n");
fprintf(fplog,"|- SET MEMBERS: ");
for(i=0;i<colvar.natoms[count];i++){fprintf(fplog," %d ",colvar.cvatoms[count][i]+1);if((i+1)%20==0)fprintf(fplog,"\n ");}fprintf(fplog,"\n\n");
return 0;
}
int PREFIX read_histogram( char **word, int count, t_plumed_input *input, FILE *fplog ) {
int i, j, k, iw, ncolvar, ngrid, nspline; int* cvlist;
double smooth, delta = 0.0; int help=0;
ncolvar=0; cvlist=NULL;
// This reads in all the CVs used for histogram collective coordinates
iw = seek_word(word,"CV_LIST");
if(iw>=0){ ncolvar=plumed_get_group(word[iw+1],&cvlist,0,input,fplog);
if( ncolvar>count ){ plumed_error("NUMBER OF CVS USED TO CALCULATE HISTOGRAM"); }
}
else{ fprintf(fplog,"|- NEEDED CV_LIST KEYWORD FOR HISTOGRAM\n"); help=1;}
colvar.histo_ncv[count]=ncolvar;
snew( colvar.histo_cvlist[count], colvar.histo_ncv[count] );
for(i=0;i<colvar.histo_ncv[count];++i){ colvar.histo_cvlist[count][i]=cvlist[i]; }
// This is the sanity check for CV_LIST ( part 2 : check all the cvs used to construct histogram cvs are declared before any BESPOKE cvs)
for(i=0;i<colvar.histo_ncv[count];i++){
if( colvar.histo_cvlist[count][i]>count ){fprintf(fplog,"HISTOGRAM COMMAND MUST COME AFTER ALL CVS USED TO CREATE HISTOGRAM CV \n"); help=1; }
// Number of atoms involved in this CV (sum of number of atoms involved in all other cvs)
colvar.natoms[count]+=colvar.natoms[ colvar.histo_cvlist[count][i] ];
}
iw = seek_word(word,"RANGE");
if(iw>=0) {
sscanf(word[iw+1], "%lf", &delta ); colvar.histo_low[count] = (real) delta;
sscanf(word[iw+2], "%lf", &delta ); colvar.histo_high[count] = (real) delta;
}
else{ fprintf(fplog,"|- NEEDED RANGE KEYWORD FOR HISTOGRAM\n"); help=1; }
iw = seek_word(word,"WIDTH");
if(iw>=0) { sscanf(word[iw+1], "%lf", &delta ); colvar.histo_width[count] = (real) delta; }
else{ fprintf(fplog,"|- NEEDED WIDTH KEYWORD FOR HISTOGRAM\n"); help=1; }
// Setup array of atoms involved in this cv
snew( colvar.cvatoms[count], colvar.natoms[count] ); k=0;
for(i=0;i<colvar.histo_ncv[count];i++){
for(j=0;j<colvar.natoms[ colvar.histo_cvlist[count][i] ];j++){
colvar.cvatoms[count][k]=colvar.cvatoms[ colvar.histo_cvlist[count][i] ][j];
k++;
}
}
// Setup derivatives array
snew( colvar.myder[count], colvar.natoms[count] );
if(help){
fprintf(fplog,"\n-HISTOGRAM CV: WRONG SYNTAX\n");
fprintf(fplog,"e.g.: \n");
fprintf(fplog,"TORSION LIST <g1> <g2> <g3> <g4> \n");
fprintf(fplog,"TORSION LIST <g2> <g3> <g4> <g5> \n");
fprintf(fplog,"TORSION LIST <g3> <g4> <g5> <g6> \n");
fprintf(fplog,"TORSION LIST <g4> <g5> <g6> <g7> \n");
fprintf(fplog,"HISTOGRAM CV_LIST <cv_list> RANGE 2.0 3.0 WIDTH 0.5\n");
fprintf(fplog,"cvlist-> \n");
fprintf(fplog,"1 2 3 4 \n");
fprintf(fplog,"cvlist<- \n");
fprintf(fplog," \n");
plumed_error("PluMed dead with errors: check log file");
}
iw=seek_word(word,"SIGMA");
if(iw>=0){ sscanf(word[iw+1],"%lf", &delta);
colvar.delta_r[count] = (real) delta; }
fprintf(fplog, "%1i-HISTOGRAM COLLECTIVE COORDINATE CREATED FROM %i OTHER CVS \n", count+1, colvar.histo_ncv[count]);
fprintf(fplog, "|--PARAMETERS: RANGE OF DESIRED VALUE = %f %f. WIDTH OF GAUSSIAN FOR SMOOTHING %f. \n", colvar.histo_low[count], colvar.histo_high[count],colvar.histo_width[count] );
fprintf(fplog,"|- COLVARS USED IN HISTOGRAM CV:");
for(i=0;i<colvar.histo_ncv[count];i++){fprintf(fplog," %d ",colvar.histo_cvlist[count][i]+1);if((i+1)%20==0)fprintf(fplog,"\n ");}fprintf(fplog,"\n\n");
return colvar.natoms[count];
}
void MultiColvarBase::setupLinkCells(){
if( !linkcells.enabled() ) return ;
unsigned iblock;
if( usespecies ){
iblock=0;
} else if( ablocks.size()<4 ){
iblock=1;
} else {
plumed_error();
}
// Count number of currently active atoms
unsigned nactive_atoms=0;
for(unsigned i=0;i<ablocks[iblock].size();++i){
if( isCurrentlyActive( iblock, ablocks[iblock][i] ) ) nactive_atoms++;
}
std::vector<Vector> ltmp_pos( nactive_atoms );
std::vector<unsigned> ltmp_ind( nactive_atoms );
nactive_atoms=0;
if( usespecies ){
for(unsigned i=0;i<ablocks[0].size();++i){
if( !isCurrentlyActive( 0, ablocks[0][i] ) ) continue;
ltmp_ind[nactive_atoms]=ablocks[0][i];
ltmp_pos[nactive_atoms]=getPositionOfAtomForLinkCells( ltmp_ind[nactive_atoms] );
nactive_atoms++;
}
} else {
for(unsigned i=0;i<ablocks[1].size();++i){
if( !isCurrentlyActive( 1, ablocks[1][i] ) ) continue;
ltmp_ind[nactive_atoms]=i;
ltmp_pos[nactive_atoms]=getPositionOfAtomForLinkCells( ablocks[1][i] );
nactive_atoms++;
}
}
// Build the lists for the link cells
linkcells.buildCellLists( ltmp_pos, ltmp_ind, getPbc() );
if( !usespecies ){
// Get some parallel info
unsigned stride=comm.Get_size();
unsigned rank=comm.Get_rank();
if( serialCalculation() ){ stride=1; rank=0; }
// Ensure we only do tasks where atoms are in appropriate link cells
std::vector<unsigned> linked_atoms( 1+ablocks[1].size() );
std::vector<unsigned> active_tasks( getFullNumberOfTasks(), 0 );
for(unsigned i=rank;i<ablocks[0].size();i+=stride){
if( !isCurrentlyActive( 0, ablocks[0][i] ) ) continue;
unsigned natomsper=1; linked_atoms[0]=ltmp_ind[0]; // Note we always check atom 0 because it is simpler than changing LinkCells.cpp
linkcells.retrieveNeighboringAtoms( getPositionOfAtomForLinkCells( ablocks[0][i] ), natomsper, linked_atoms );
for(unsigned j=0;j<natomsper;++j){
for(unsigned k=bookeeping(i,linked_atoms[j]).first;k<bookeeping(i,linked_atoms[j]).second;++k) active_tasks[k]=1;
}
}
if( !serialCalculation() ) comm.Sum( active_tasks );
deactivateAllTasks();
activateTheseTasks( active_tasks );
contributorsAreUnlocked=false;
} else {
// Now check for calculating volumes (currently this is only done for usespecies style commands
// as it is difficult to do with things like DISTANCES or ANGLES and I think pointless
bool justVolumes=true;
for(unsigned i=0;i<getNumberOfVessels();++i){
vesselbase::BridgeVessel* myb=dynamic_cast<vesselbase::BridgeVessel*>( getPntrToVessel(i) );
if( !myb ){ justVolumes=false; break; }
ActionVolume* myv=dynamic_cast<ActionVolume*>( myb->getOutputAction() );
if( !myv ){ justVolumes=false; break; }
}
// Now ensure that we only do calculations for those atoms in the relevant volume
if( justVolumes ){
bool justVolumes=true;
// Setup the regions in the action volume objects
for(unsigned i=0;i<getNumberOfVessels();++i){
vesselbase::BridgeVessel* myb=dynamic_cast<vesselbase::BridgeVessel*>( getPntrToVessel(i) );
ActionVolume* myv=dynamic_cast<ActionVolume*>( myb->getOutputAction() );
myv->retrieveAtoms(); myv->setupRegions();
}
unsigned stride=comm.Get_size();
unsigned rank=comm.Get_rank();
if( serialCalculation() ){ stride=1; rank=0; }
unsigned nactive=0;
std::vector<unsigned> active_tasks( getFullNumberOfTasks(), 0 );
for(unsigned i=rank;i<getFullNumberOfTasks();i+=stride){
bool invol=false;
for(unsigned j=0;j<getNumberOfVessels();++j){
vesselbase::BridgeVessel* myb=dynamic_cast<vesselbase::BridgeVessel*>( getPntrToVessel(j) );
ActionVolume* myv=dynamic_cast<ActionVolume*>( myb->getOutputAction() );
if( myv->inVolumeOfInterest(i) ){ invol=true; }
}
if( invol ){ nactive++; active_tasks[i]=1; }
}
if( !serialCalculation() ) comm.Sum( active_tasks );
deactivateAllTasks();
activateTheseTasks( active_tasks );
contributorsAreUnlocked=false;
}
}
}
int PREFIX read_adf( char **word, int count, t_plumed_input *input, FILE *fplog ) {
int i, iw, j, iat, k, help, rdflab, checkLists, natoms1, natoms2;
double delta = 0.0, upBound, lowBound, width, r_0, d_0;
help=0; d_0=0;
// Deal with periodic boundary conditions
colvar.cell_pbc[count]=1; // default is PBC
iw=seek_word(word,"NOPBC");
if(iw>=0) {colvar.cell_pbc[count] = 0;}
iw=seek_word(word,"PBC");
if(iw>=0) {colvar.cell_pbc[count] = 1;}
// This is the label for which rdf this bead is from
iw = seek_word(word,"RDF_LABEL");
if(iw>=0){ sscanf(word[iw+1],"%d",&rdflab); colvar.rdflab[count]=rdflab; }
else{ fprintf(fplog,"|- NEEDED RDF_LABEL KEYWORD FOR ANGLE RDF\n"); help=1; }
// Now we check whether there are other beads from this rdf that have been read in
checkLists=-1; for(i=0;i<count;i++){ if( colvar.type_s[i]==52 && colvar.rdflab[i]==rdflab ){ checkLists=i; break; } }
// Get atoms involved in the rdf
iw = seek_word(word,"LIST");
if(iw>=0){
j=plumed_get_group(word[iw+1],&colvar.cvatoms[count],colvar.natoms[count],input,fplog);
colvar.natoms[count]+=j;
colvar.list[count][0]=j;
j=plumed_get_group(word[iw+2],&colvar.cvatoms[count],colvar.natoms[count],input,fplog);
colvar.natoms[count]+=j;
colvar.list[count][1]=j;
j=plumed_get_group(word[iw+3],&colvar.cvatoms[count],colvar.natoms[count],input,fplog);
colvar.natoms[count]+=j;
colvar.list[count][2]=j;
} else{ fprintf(fplog,"|- NEEDED LIST KEYWORD FOR ADF\n"); help=1; }
// Get the parameters for the switching function
iw=seek_word(word,"NN");
if(iw>=0) { sscanf(word[iw+1],"%i", &colvar.nn[count]); } else { fprintf(fplog,"|- NEEDED NN KEYWORD FOR ADF\n"); help=1;}
iw=seek_word(word,"MM");
if(iw>=0) { sscanf(word[iw+1],"%i", &colvar.mm[count]);} else { fprintf(fplog,"|- NEEDED MM KEYWORD FOR ADF\n"); help=1;}
iw=seek_word(word,"R_0");
if(iw>=0) { sscanf(word[iw+1],"%lf", &r_0); } else { fprintf(fplog,"|- NEEDED R_0 KEYWORD FOR ADF\n"); help=1;}
iw=seek_word(word,"D_0");
if(iw>=0) { sscanf(word[iw+1],"%lf", &d_0); }
// Store the values
colvar.r_0[count] = (real) r_0;
colvar.d_0[count] = (real) d_0;
// Check that the everything is consistent with other rdfs of this type
if( checkLists!=-1){
// Check the lists
if( colvar.natoms[count]!=colvar.natoms[checkLists] ){
fprintf(fplog,"|- MISLABELED ADF: ATOM LIST SIZES DO NOT MATCH\n"); help=1;
} else{
for(i=0;i<colvar.natoms[count];i++){
if( colvar.cvatoms[count][i]!=colvar.cvatoms[checkLists][i] ){
fprintf(fplog,"|- MISLABELED ADF: ATOM LISTS DO NOT MATCH\n"); help=1;
}
}
}
// Now check the parameters for the switching functions
if( colvar.nn[count]!=colvar.nn[checkLists] ){
fprintf(fplog,"|- MISLABELED ADF: NN VALUES DO NOT MATCH\n"); help=1;
}
if( colvar.mm[count]!=colvar.mm[checkLists] ){
fprintf(fplog,"|- MISLABELED ADF: MM VALUES DO NOT MATCH\n"); help=1;
}
if( colvar.r_0[count]!=colvar.r_0[checkLists] ){
fprintf(fplog,"|- MISLABELED ADF: R_0 VALUES DO NOT MATCH\n"); help=1;
}
if( colvar.d_0[count]!=colvar.d_0[checkLists] ){
fprintf(fplog,"|- MISLABELED ADF: D_0 VALUES DO NOT MATCH\n"); help=1;
}
}
// Check whether or not lists 2 and 3 are the same
colvar.rdfNorm[count]=1;
natoms2=colvar.list[count][1] - colvar.list[count][0];
natoms1=colvar.list[count][1] - colvar.list[count][0];
if( natoms1==natoms2 ){
for(i=0;i<natoms1;i++){
j=colvar.cvatoms[count][colvar.list[count][0]+i]; k=colvar.cvatoms[count][colvar.list[count][1]+i];
if( j!=k ){ colvar.rdfNorm[count]=0; break; }
}
} else{ colvar.rdfNorm[count]=0; }
// Get the start and end of this particular bead
iw = seek_word(word,"RANGE");
if(iw>=0){ sscanf(word[iw+1],"%lf",&lowBound); sscanf(word[iw+2],"%lf", &upBound);
colvar.rdfBeadLower[count]=lowBound; colvar.rdfBeadUpper[count]=upBound;
} else{ fprintf(fplog,"|- NEEDED RANGE KEYWORD FOR RDF\n"); help=1;}
// Get the width of this bead
iw = seek_word(word,"WIDTH");
if(iw>=0){ sscanf(word[iw+1],"%lf",&width);
colvar.rdfBeadWidth[count]=width;
} else{ fprintf(fplog,"|- NEEDED WIDTH KEYWORD FOR RDF\n"); help=1;}
if(help){
fprintf(fplog,"\n-ADF CV: WRONG SYNTAX\n");
fprintf(fplog,"e.g.: \n");
fprintf(fplog,"ADF RDF_LABEL 1 LIST <gr1> <gr2> <gr2> RANGE 2.0 3.0 WIDTH 1.5 R_0 1.0 D_0 0.0 NN 6 MM 12 \n");
fprintf(fplog,"ADF RDF_LABEL 1 LIST <gr1> <gr2> <gr2> RANGE 2.0 3.0 WIDTH 1.5 R_0 1.0 D_0 0.0 NN 6 MM 12 \n");
fprintf(fplog,"gr1-> \n");
fprintf(fplog,"1 2 3 4 \n");
fprintf(fplog,"gr1<- \n");
fprintf(fplog,"gr2-> \n");
fprintf(fplog,"1 2 3 4 \n");
fprintf(fplog,"gr2<- \n");
fprintf(fplog,"gr3-> \n");
fprintf(fplog,"1 2 3 4 \n");
fprintf(fplog,"gr3<- \n");
fprintf(fplog," \n");
plumed_error("PluMed dead with errors: check log file");
}
// Resize derivatives array
snew(colvar.myder[count], colvar.natoms[count]);
iw=seek_word(word,"SIGMA");
if(iw>=0){ sscanf(word[iw+1],"%lf", &delta);
colvar.delta_r[count] = (real) delta; }
fprintf(fplog, "%1i-BEAD FROM DISTRIBUTION OF ANGLES ABOUT (1st SET: %i ATOMS) ANGLES ARE BETWEEN (2nd SET: %i ATOMS) AND (3rd SET: %i ATOMS); \n", count+1, colvar.list[count][0], colvar.list[count][1], colvar.list[count][2]);
if( colvar.rdfNorm[count]==1 ){ fprintf(fplog, "|--LISTS 2 AND 3 ARE IDENTICAL\n"); }
fprintf(fplog, "|--LOWER BOUND %f, UPPER BOUND %f, WIDTH %f \n", colvar.rdfBeadLower[count], colvar.rdfBeadUpper[count], colvar.rdfBeadWidth[count]);
fprintf(fplog, "|--PARAMETERS FOR SWITCHING FUNCTION : R_0 %f, D_0 %f, NN %d, MM %d \n", colvar.r_0[count], colvar.d_0[count], colvar.nn[count], colvar.mm[count] );
iat=0;
fprintf(fplog,"|- 1st SET MEMBERS: ");
for(i=0;i<colvar.list[count][0];i++){fprintf(fplog," %d ",colvar.cvatoms[count][iat++]+1);if((i+1)%20==0)fprintf(fplog,"\n ");}fprintf(fplog,"\n");
fprintf(fplog,"|- 2nd SET MEMBERS: ");
for(i=0;i<colvar.list[count][1];i++){fprintf(fplog," %d ",colvar.cvatoms[count][iat++]+1);if((i+1)%20==0)fprintf(fplog,"\n ");}fprintf(fplog,"\n");
fprintf(fplog,"|- 3rd SET MEMBERS: ");
for(i=0;i<colvar.list[count][2];i++){fprintf(fplog," %d ",colvar.cvatoms[count][iat++]+1);if((i+1)%20==0)fprintf(fplog,"\n ");}fprintf(fplog,"\n\n");
return colvar.natoms[count];
}
void MultiDomainRMSD::setReferenceAtoms( const std::vector<Vector>& conf, const std::vector<double>& align_in, const std::vector<double>& displace_in ) {
plumed_error();
}
void ActionWithVessel::transformBridgedDerivatives( const unsigned& current, MultiValue& invals, MultiValue& outvals ) const {
plumed_error();
}
int PREFIX read_cmap(char **word, int count,t_plumed_input *input,FILE *fplog)
{
int i,iw;
double sigma = 0.0;
char file_maps[129];
char file_group[129];
struct sz_data *my_sz;
int help;
help=0;
colvar.cell_pbc[count]=1; // default is PBC
my_sz=&(my_sz_list[nsz]);
ic_to_sz[count]=nsz;
my_sz->my_cmap_pack.logical_group = 0; // no GROUP
iw=seek_word(word,"SIGMA");
if(iw>=0){ sscanf(word[iw+1],"%lf", &sigma);
colvar.delta_r[count] = (real) sigma; }
iw = seek_word(word,"INDEX");
if(iw>=0) { sscanf(word[iw+1],"%s", file_maps);
} else {
fprintf(fplog,"|- NEEDED INDEX KEYWORD FOR CMAP\n");
help=1;
}
iw=seek_word(word,"GROUP");
if(iw>=0) {
sscanf(word[iw+1],"%s",file_group);
my_sz->my_cmap_pack.logical_group = 1;
}
iw=seek_word(word,"NOPBC");
if(iw>=0) {colvar.cell_pbc[count] = 0;}
iw=seek_word(word,"PBC");
if(iw>=0) {colvar.cell_pbc[count] = 1;}
if(help){
fprintf(fplog,"|- CMAP SYNTAX:\n");
fprintf(fplog,"|- INDEX : contact definition file \n");
fprintf(fplog,"|- GROUP : group definition file \n");
fprintf(fplog,"|- SIGMA : hills width for this cv\n");
fprintf(fplog,"|- e.g.\n");
fprintf(fplog,"|- \n");
fprintf(fplog,"|- CMAP INDEX cmap.index { GROUP cmap.group } { NOPBC } SIGMA 1.0 \n");
fprintf(fplog,"|- \n");
plumed_error("PluMeD dead with errors: check log file");
}
fprintf(fplog, "\n%1i-CMAP: INDEX file %s ", count+1, file_maps);
if(my_sz->my_cmap_pack.logical_group) fprintf(fplog, " GROUP file %s ", file_group);
if(colvar.cell_pbc[count]) fprintf(fplog, " PBC ON ");
else fprintf(fplog, " PBC OFF ");
if (logical.do_hills){
if (colvar.delta_r[count]>0){
fprintf(fplog," SIGMA %f\n",colvar.delta_r[count]);
}
}
else fprintf(fplog,"\n");
read_sz_map(my_sz,file_maps,file_maps,file_group,0,fplog);
colvar.natoms[count] = my_sz->my_cmap_pack.atoms;
snew(colvar.myder[count], colvar.natoms[count]);
snew(colvar.cvatoms[count], colvar.natoms[count]);
for(i=0;i<colvar.natoms[count];i++)
colvar.cvatoms[count][i] = my_sz->my_cmap_pack.list[i];
nsz++;
if(nsz==NMAX_PATH) plumed_error("TOO MANY PATH CVS. Increase NMAX_PATH in metadyn.h and recompile");
fprintf(fplog,"\n");
return colvar.natoms[count];
}