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Update Colvars to version 2021-08-03

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This commit is contained in:
Giacomo Fiorin
2021-08-03 18:03:09 -04:00
parent 50e8d7c36b
commit 2a9be42758
48 changed files with 2557 additions and 527 deletions
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12
lib/colvars/colvarcomp.cpp
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@ -51,7 +51,7 @@ int colvar::cvc::init(std::string const &conf)
std::string const old_name(name);
if (name.size() > 0) {
cvm::log("Updating configuration for component \""+name+"\"");
cvm::log("Updating configuration for component \""+name+"\"\n");
}
if (get_keyval(conf, "name", name, name)) {
@ -112,7 +112,7 @@ int colvar::cvc::init_total_force_params(std::string const &conf)
}
if (get_keyval_feature(this, conf, "oneSiteTotalForce",
f_cvc_one_site_total_force, is_enabled(f_cvc_one_site_total_force))) {
cvm::log("Computing total force on group 1 only");
cvm::log("Computing total force on group 1 only\n");
}
if (! is_enabled(f_cvc_one_site_total_force)) {
@ -426,7 +426,7 @@ void colvar::cvc::collect_gradients(std::vector<int> const &atom_ids, std::vecto
// If necessary, apply inverse rotation to get atomic
// gradient in the laboratory frame
if (ag.b_rotate) {
if (ag.is_enabled(f_ag_rotate)) {
cvm::rotation const rot_inv = ag.rot.inverse();
for (size_t k = 0; k < ag.size(); k++) {
@ -505,7 +505,7 @@ void colvar::cvc::debug_gradients()
cvm::atom_pos fit_gradient_sum, gradient_sum;
// print the values of the fit gradients
if (group->b_rotate || group->b_center) {
if (group->is_enabled(f_ag_center) || group->is_enabled(f_ag_rotate)) {
if (group->is_enabled(f_ag_fit_gradients)) {
size_t j;
@ -514,7 +514,7 @@ void colvar::cvc::debug_gradients()
for (j = 0; j < group_for_fit->fit_gradients.size(); j++) {
cvm::log((group->fitting_group ? std::string("refPosGroup") : group->key) +
"[" + cvm::to_str(j) + "] = " +
(group->b_rotate ?
(group->is_enabled(f_ag_rotate) ?
cvm::to_str(rot_0.rotate(group_for_fit->fit_gradients[j])) :
cvm::to_str(group_for_fit->fit_gradients[j])));
}
@ -525,7 +525,7 @@ void colvar::cvc::debug_gradients()
for (size_t ia = 0; ia < group->size(); ia++) {
// tests are best conducted in the unrotated (simulation) frame
cvm::rvector const atom_grad = (group->b_rotate ?
cvm::rvector const atom_grad = (group->is_enabled(f_ag_rotate) ?
rot_inv.rotate((*group)[ia].grad) :
(*group)[ia].grad);
gradient_sum += atom_grad;