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")
// NOTE: this assumes that groups for this cvc are non-overlapping,
// since atom coordinates are modified only within the current group
if (group->b_dummy) return;
cvm::rotation const rot_0 = group->rot;
cvm::rotation const rot_inv = group->rot.inverse();
cvm::real x_0 = x.real_value;
if ((x.type() == colvarvalue::type_vector) && (x.size() == 1)) x_0 = x[0];
// cvm::log("gradients = "+cvm::to_str (gradients)+"\n");
cvm::atom_group *group_for_fit = group->ref_pos_group ? group->ref_pos_group : group;
cvm::atom_pos fit_gradient_sum, gradient_sum;
// print the values of the fit gradients
if (group->b_rotate || group->b_center) {
if (group->b_fit_gradients) {
size_t j;
// fit_gradients are in the simulation frame: we should print them in the rotated frame
cvm::log("Fit gradients:\n");
for (j = 0; j < group_for_fit->fit_gradients.size(); j++) {
cvm::log((group->ref_pos_group ? std::string("refPosGroup") : group->key) +
"[" + cvm::to_str(j) + "] = " +
(group->b_rotate ?
cvm::to_str(rot_0.rotate(group_for_fit->fit_gradients[j])) :
cvm::to_str(group_for_fit->fit_gradients[j])));
}
}
}
// debug the 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 ?
rot_inv.rotate((*group)[ia].grad) :
(*group)[ia].grad);
gradient_sum += atom_grad;
for (size_t id = 0; id < 3; id++) {
// (re)read original positions
group->read_positions();
// change one coordinate
(*group)[ia].pos[id] += cvm::debug_gradients_step_size;
group->calc_required_properties();
calc_value();
cvm::real x_1 = x.real_value;
if ((x.type() == colvarvalue::type_vector) && (x.size() == 1)) 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()) ?
(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,
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");
}
}
if ((group->b_fit_gradients) && (group->ref_pos_group != NULL)) {
cvm::atom_group *ref_group = group->ref_pos_group;
group->read_positions();
group->calc_required_properties();
for (size_t ia = 0; ia < ref_group->size(); ia++) {
// fit gradients are in the unrotated (simulation) frame
cvm::rvector const atom_grad = ref_group->fit_gradients[ia];
fit_gradient_sum += atom_grad;
for (size_t id = 0; id < 3; id++) {
// (re)read original positions
group->read_positions();
ref_group->read_positions();
// change one coordinate
(*ref_group)[ia].pos[id] += cvm::debug_gradients_step_size;
group->calc_required_properties();
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,
21, 14)+"\n");
cvm::real const dx_pred = cvm::debug_gradients_step_size * atom_grad[id];
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("Gradient sum: " + cvm::to_str(gradient_sum) +
" Fit gradient sum: " + cvm::to_str(fit_gradient_sum) +
" Total " + cvm::to_str(gradient_sum + fit_gradient_sum));
return;
}
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")
if (group.b_dummy) return;
cvm::rotation const rot_0 = group.rot;
cvm::rotation const rot_inv = group.rot.inverse();
cvm::real const x_0 = x.real_value;
// 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
if (group.b_rotate || group.b_center)
if (group.b_fit_gradients && (group.ref_pos_group == NULL)) {
group.calc_fit_gradients();
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]);
}
}
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]);
}
}
}
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 ?
rot_inv.rotate (group[ia].grad) :
group[ia].grad;
for (size_t id = 0; id < 3; id++) {
// (re)read original positions
group.read_positions();
// change one coordinate
group[ia].pos[id] += cvm::debug_gradients_step_size;
// (re)do the fit (if defined)
if (group.b_center || group.b_rotate) {
group.calc_apply_roto_translation();
}
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,
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,
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");
}
}
/*
* The code below is WIP
*/
// if (group.ref_pos_group != NULL) {
// cvm::atom_group &ref = *group.ref_pos_group;
// group.calc_fit_gradients();
//
// for (size_t ia = 0; ia < ref.size(); ia++) {
//
// for (size_t id = 0; id < 3; id++) {
// // (re)read original positions
// group.read_positions();
// ref.read_positions();
// // change one coordinate
// ref[ia].pos[id] += cvm::debug_gradients_step_size;
// 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,
// 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,
// 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");
// }
// }
// }
return;
}