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colvarcomp.C
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Wed, Jul 17, 21:51

colvarcomp.C
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#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvar.h"
#include "colvarcomp.h"
colvar::cvc::cvc()
: sup_coeff (1.0), sup_np (1),
b_periodic (false),
b_debug_gradients (false),
b_inverse_gradients (false),
b_Jacobian_derivative (false)
{}
colvar::cvc::cvc (std::string const &conf)
: sup_coeff (1.0), sup_np (1),
b_periodic (false),
b_debug_gradients (false),
b_inverse_gradients (false),
b_Jacobian_derivative (false)
{
if (cvm::debug())
cvm::log ("Initializing cvc base object.\n");
get_keyval (conf, "name", this->name, std::string (""), parse_silent);
get_keyval (conf, "componentCoeff", sup_coeff, 1.0);
get_keyval (conf, "componentExp", sup_np, 1);
get_keyval (conf, "period", period, 0.0);
get_keyval (conf, "wrapAround", wrap_center, 0.0);
get_keyval (conf, "debugGradients", b_debug_gradients, false, parse_silent);
if (cvm::debug())
cvm::log ("Done initializing cvc base object.\n");
}
void colvar::cvc::parse_group (std::string const &conf,
char const *group_key,
cvm::atom_group &group,
bool optional)
{
if (key_lookup (conf, group_key)) {
group.parse (conf, group_key);
} else {
if (! optional) {
cvm::fatal_error ("Error: definition for atom group \""+
std::string (group_key)+"\" not found.\n");
}
}
}
colvar::cvc::~cvc()
{}
void colvar::cvc::calc_force_invgrads()
{
cvm::fatal_error ("Error: calculation of inverse gradients is not implemented "
"for colvar components of type \""+function_type+"\".\n");
}
void colvar::cvc::calc_Jacobian_derivative()
{
cvm::fatal_error ("Error: calculation of inverse gradients is not implemented "
"for colvar components of type \""+function_type+"\".\n");
}
colvarvalue colvar::cvc::fdiff_change (cvm::atom_group &group)
{
colvarvalue change (x.type());
if (group.old_pos.size()) {
for (size_t i = 0; i < group.size(); i++) {
cvm::rvector const &pold = group.old_pos[i];
cvm::rvector const &p = group[i].pos;
change += group[i].grad * (p - pold);
}
}
// save for next step
group.old_pos = group.positions();
return change;
}

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