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colvarbias.cpp
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Fri, Jul 4, 16:04

colvarbias.cpp
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/// -*- c++ -*-
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarbias.h"
colvarbias::colvarbias (std::string const &conf, char const *key)
: colvarparse(), has_data (false)
{
cvm::log ("Initializing a new \""+std::string (key)+"\" instance.\n");
size_t rank = 1;
std::string const key_str (key);
if (to_lower_cppstr (key_str) == std::string ("abf")) {
rank = cvm::n_abf_biases+1;
}
if (to_lower_cppstr (key_str) == std::string ("harmonic") ||
to_lower_cppstr (key_str) == std::string ("linear")) {
rank = cvm::n_rest_biases+1;
}
if (to_lower_cppstr (key_str) == std::string ("histogram")) {
rank = cvm::n_histo_biases+1;
}
if (to_lower_cppstr (key_str) == std::string ("metadynamics")) {
rank = cvm::n_meta_biases+1;
}
get_keyval (conf, "name", name, key_str+cvm::to_str (rank));
if (cvm::bias_by_name (this->name) != NULL) {
cvm::error ("Error: this bias cannot have the same name, \""+this->name+
"\", as another bias.\n", INPUT_ERROR);
return;
}
// lookup the associated colvars
std::vector<std::string> colvars_str;
if (get_keyval (conf, "colvars", colvars_str)) {
for (size_t i = 0; i < colvars_str.size(); i++) {
add_colvar (colvars_str[i]);
}
}
if (!colvars.size()) {
cvm::error ("Error: no collective variables specified.\n");
return;
}
get_keyval (conf, "outputEnergy", b_output_energy, false);
}
colvarbias::colvarbias()
: colvarparse(), has_data (false)
{}
colvarbias::~colvarbias()
{
// Remove references to this bias from colvars
for (std::vector<colvar *>::iterator cvi = colvars.begin();
cvi != colvars.end();
++cvi) {
for (std::vector<colvarbias *>::iterator bi = (*cvi)->biases.begin();
bi != (*cvi)->biases.end();
++bi) {
if ( *bi == this) {
(*cvi)->biases.erase (bi);
break;
}
}
}
// ...and from the colvars module
for (std::vector<colvarbias *>::iterator bi = cvm::biases.begin();
bi != cvm::biases.end();
++bi) {
if ( *bi == this) {
cvm::biases.erase (bi);
break;
}
}
}
void colvarbias::add_colvar (std::string const &cv_name)
{
if (colvar *cvp = cvm::colvar_by_name (cv_name)) {
cvp->enable (colvar::task_gradients);
if (cvm::debug())
cvm::log ("Applying this bias to collective variable \""+
cvp->name+"\".\n");
colvars.push_back (cvp);
colvar_forces.push_back (colvarvalue (cvp->type()));
cvp->biases.push_back (this); // add back-reference to this bias to colvar
} else {
cvm::error ("Error: cannot find a colvar named \""+
cv_name+"\".\n");
}
}
void colvarbias::communicate_forces()
{
for (size_t i = 0; i < colvars.size(); i++) {
if (cvm::debug()) {
cvm::log ("Communicating a force to colvar \""+
colvars[i]->name+"\", of type \""+
colvarvalue::type_desc[colvars[i]->type()]+"\".\n");
}
colvars[i]->add_bias_force (colvar_forces[i]);
}
}
void colvarbias::change_configuration(std::string const &conf)
{
cvm::error ("Error: change_configuration() not implemented.\n");
}
cvm::real colvarbias::energy_difference(std::string const &conf)
{
cvm::error ("Error: energy_difference() not implemented.\n");
return 0.;
}
std::ostream & colvarbias::write_traj_label (std::ostream &os)
{
os << " ";
if (b_output_energy)
os << " E_"
<< cvm::wrap_string (this->name, cvm::en_width-2);
return os;
}
std::ostream & colvarbias::write_traj (std::ostream &os)
{
os << " ";
if (b_output_energy)
os << " "
<< bias_energy;
return os;
}

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