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formatting update for colvars library

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This commit is contained in:
Axel Kohlmeyer
2014-10-24 17:09:06 -04:00
parent ca928af3bd
commit 0e550d0e27
33 changed files with 3081 additions and 3081 deletions
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88
lib/colvars/colvarcomp.cpp
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@ -8,54 +8,54 @@
colvar::cvc::cvc()
: sup_coeff (1.0), sup_np (1),
b_periodic (false),
b_inverse_gradients (false),
b_Jacobian_derivative (false),
b_debug_gradients (false)
: sup_coeff(1.0), sup_np(1),
b_periodic(false),
b_inverse_gradients(false),
b_Jacobian_derivative(false),
b_debug_gradients(false)
{}
colvar::cvc::cvc (std::string const &conf)
: sup_coeff (1.0), sup_np (1),
b_periodic (false),
b_inverse_gradients (false),
b_Jacobian_derivative (false),
b_debug_gradients (false)
colvar::cvc::cvc(std::string const &conf)
: sup_coeff(1.0), sup_np(1),
b_periodic(false),
b_inverse_gradients(false),
b_Jacobian_derivative(false),
b_debug_gradients(false)
{
if (cvm::debug())
cvm::log ("Initializing cvc base object.\n");
cvm::log("Initializing cvc base object.\n");
get_keyval (conf, "name", this->name, std::string (""), parse_silent);
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, "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, "period", period, 0.0);
get_keyval(conf, "wrapAround", wrap_center, 0.0);
get_keyval (conf, "debugGradients", b_debug_gradients, false, parse_silent);
get_keyval(conf, "debugGradients", b_debug_gradients, false, parse_silent);
if (cvm::debug())
cvm::log ("Done initializing cvc base object.\n");
cvm::log("Done initializing cvc base object.\n");
}
void colvar::cvc::parse_group (std::string const &conf,
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)) {
if (group.parse (conf, group_key) != COLVARS_OK) {
cvm::error ("Error parsing definition for atom group \""+
std::string (group_key)+"\".\n");
if (key_lookup(conf, group_key)) {
if (group.parse(conf, group_key) != COLVARS_OK) {
cvm::error("Error parsing definition for atom group \""+
std::string(group_key)+"\".\n");
return;
}
} else {
if (! optional) {
cvm::error ("Error: definition for atom group \""+
std::string (group_key)+"\" not found.\n");
cvm::error("Error: definition for atom group \""+
std::string(group_key)+"\" not found.\n");
return;
}
}
@ -68,19 +68,19 @@ colvar::cvc::~cvc()
void colvar::cvc::calc_force_invgrads()
{
cvm::fatal_error ("Error: calculation of inverse gradients is not implemented "
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 "
cvm::fatal_error("Error: calculation of inverse gradients is not implemented "
"for colvar components of type \""+function_type+"\".\n");
}
void colvar::cvc::debug_gradients (cvm::atom_group &group)
void colvar::cvc::debug_gradients(cvm::atom_group &group)
{
// this function should work for any scalar variable:
// the only difference will be the name of the atom group (here, "group")
@ -92,7 +92,7 @@ void colvar::cvc::debug_gradients (cvm::atom_group &group)
cvm::real const x_0 = x.real_value;
// cvm::log ("gradients = "+cvm::to_str (gradients)+"\n");
// cvm::log("gradients = "+cvm::to_str (gradients)+"\n");
// it only makes sense to debug the fit gradients
// when the fitting group is the same as this group
@ -102,13 +102,13 @@ void colvar::cvc::debug_gradients (cvm::atom_group &group)
if (group.b_rotate) {
// fit_gradients are in the original frame, we should print them in the rotated frame
for (size_t j = 0; j < group.fit_gradients.size(); j++) {
group.fit_gradients[j] = rot_0.rotate (group.fit_gradients[j]);
group.fit_gradients[j] = rot_0.rotate(group.fit_gradients[j]);
}
}
cvm::log ("fit_gradients = "+cvm::to_str (group.fit_gradients)+"\n");
cvm::log("fit_gradients = "+cvm::to_str(group.fit_gradients)+"\n");
if (group.b_rotate) {
for (size_t j = 0; j < group.fit_gradients.size(); j++) {
group.fit_gradients[j] = rot_inv.rotate (group.fit_gradients[j]);
group.fit_gradients[j] = rot_inv.rotate(group.fit_gradients[j]);
}
}
}
@ -117,7 +117,7 @@ void colvar::cvc::debug_gradients (cvm::atom_group &group)
// tests are best conducted in the unrotated (simulation) frame
cvm::rvector const atom_grad = group.b_rotate ?
rot_inv.rotate (group[ia].grad) :
rot_inv.rotate(group[ia].grad) :
group[ia].grad;
for (size_t id = 0; id < 3; id++) {
@ -131,18 +131,18 @@ void colvar::cvc::debug_gradients (cvm::atom_group &group)
}
calc_value();
cvm::real const x_1 = x.real_value;
cvm::log ("Atom "+cvm::to_str (ia)+", component "+cvm::to_str (id)+":\n");
cvm::log ("dx(actual) = "+cvm::to_str (x_1 - x_0,
cvm::log("Atom "+cvm::to_str(ia)+", component "+cvm::to_str(id)+":\n");
cvm::log("dx(actual) = "+cvm::to_str(x_1 - x_0,
21, 14)+"\n");
//cvm::real const dx_pred = (group.fit_gradients.size() && (group.ref_pos_group == NULL)) ?
cvm::real const dx_pred = (group.fit_gradients.size()) ?
(cvm::debug_gradients_step_size * (atom_grad[id] + group.fit_gradients[ia][id])) :
(cvm::debug_gradients_step_size * atom_grad[id]);
cvm::log ("dx(interp) = "+cvm::to_str (dx_pred,
cvm::log("dx(interp) = "+cvm::to_str(dx_pred,
21, 14)+"\n");
cvm::log ("|dx(actual) - dx(interp)|/|dx(actual)| = "+
cvm::to_str (std::fabs (x_1 - x_0 - dx_pred) /
std::fabs (x_1 - x_0), 12, 5)+"\n");
cvm::log("|dx(actual) - dx(interp)|/|dx(actual)| = "+
cvm::to_str(std::fabs(x_1 - x_0 - dx_pred) /
std::fabs(x_1 - x_0), 12, 5)+"\n");
}
}
@ -164,18 +164,18 @@ void colvar::cvc::debug_gradients (cvm::atom_group &group)
// group.calc_apply_roto_translation();
// calc_value();
// cvm::real const x_1 = x.real_value;
// cvm::log ("refPosGroup atom "+cvm::to_str (ia)+", component "+cvm::to_str (id)+":\n");
// cvm::log ("dx(actual) = "+cvm::to_str (x_1 - x_0,
// cvm::log("refPosGroup atom "+cvm::to_str(ia)+", component "+cvm::to_str (id)+":\n");
// cvm::log("dx(actual) = "+cvm::to_str (x_1 - x_0,
// 21, 14)+"\n");
// //cvm::real const dx_pred = (group.fit_gradients.size() && (group.ref_pos_group == NULL)) ?
// // cvm::real const dx_pred = (group.fit_gradients.size()) ?
// // (cvm::debug_gradients_step_size * (atom_grad[id] + group.fit_gradients[ia][id])) :
// // (cvm::debug_gradients_step_size * atom_grad[id]);
// cvm::real const dx_pred = cvm::debug_gradients_step_size * ref.fit_gradients[ia][id];
// cvm::log ("dx(interp) = "+cvm::to_str (dx_pred,
// cvm::log("dx(interp) = "+cvm::to_str (dx_pred,
// 21, 14)+"\n");
// cvm::log ("|dx(actual) - dx(interp)|/|dx(actual)| = "+
// cvm::to_str (std::fabs (x_1 - x_0 - dx_pred) /
// cvm::to_str(std::fabs (x_1 - x_0 - dx_pred) /
// std::fabs (x_1 - x_0),
// 12, 5)+
// ".\n");