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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14900 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2016-04-28 14:48:56 +00:00
parent 107e28c77a
commit 17fd5898df
15 changed files with 300 additions and 303 deletions
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77
lib/colvars/colvaratoms.cpp
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@ -297,7 +297,7 @@ int cvm::atom_group::parse(std::string const &conf)
std::string numbers_conf = "";
size_t pos = 0;
while (key_lookup(group_conf, "atomNumbers", numbers_conf, pos)) {
parse_error |= add_atom_numbers(numbers_conf);
cvm::combine_errors(parse_error, add_atom_numbers(numbers_conf));
numbers_conf = "";
}
}
@ -306,7 +306,7 @@ int cvm::atom_group::parse(std::string const &conf)
std::string index_group_name;
if (get_keyval(group_conf, "indexGroup", index_group_name)) {
// use an index group from the index file read globally
parse_error |= add_index_group(index_group_name);
cvm::combine_errors(parse_error, add_index_group(index_group_name));
}
}
@ -315,7 +315,7 @@ int cvm::atom_group::parse(std::string const &conf)
size_t pos = 0;
while (key_lookup(group_conf, "atomNumbersRange",
range_conf, pos)) {
parse_error |= add_atom_numbers_range(range_conf);
cvm::combine_errors(parse_error, add_atom_numbers_range(range_conf));
range_conf = "";
}
}
@ -342,8 +342,8 @@ int cvm::atom_group::parse(std::string const &conf)
cvm::error("Error: more instances of \"atomNameResidueRange\" than "
"values of \"psfSegID\".\n", INPUT_ERROR);
} else {
parse_error |= add_atom_name_residue_range(psf_segids.size() ? *psii : std::string(""),
range_conf);
cvm::combine_errors(parse_error, add_atom_name_residue_range(psf_segids.size() ?
*psii : std::string(""), range_conf));
if (psf_segids.size()) psii++;
}
range_conf = "";
@ -407,7 +407,7 @@ int cvm::atom_group::parse(std::string const &conf)
index = (cvm::proxy)->init_atom_group(atoms_ids);
}
parse_error |= parse_fitting_options(group_conf);
cvm::combine_errors(parse_error, parse_fitting_options(group_conf));
// TODO move this to colvarparse object
check_keywords(group_conf, key.c_str());
@ -612,7 +612,6 @@ int cvm::atom_group::parse_fitting_options(std::string const &group_conf)
// regardless of the configuration, fit gradients must be calculated by refPositionsGroup
ref_pos_group->b_fit_gradients = this->b_fit_gradients;
this->b_fit_gradients = false;
}
atom_group *group_for_fit = ref_pos_group ? ref_pos_group : this;
@ -682,7 +681,7 @@ int cvm::atom_group::parse_fitting_options(std::string const &group_conf)
"If that happens, use refPositionsGroup (or a different definition for it if already defined) "
"to align the coordinates.\n");
// initialize rot member data
rot.request_group1_gradients(this->size());
rot.request_group1_gradients(group_for_fit->size());
}
}
@ -778,13 +777,19 @@ int cvm::atom_group::calc_required_properties()
void cvm::atom_group::calc_apply_roto_translation()
{
// store the laborarory-frame COGs for when they are needed later
cog_orig = this->center_of_geometry();
if (ref_pos_group) {
ref_pos_group->cog_orig = ref_pos_group->center_of_geometry();
}
if (b_center) {
// center on the origin first
cvm::atom_pos const cog = ref_pos_group ?
cvm::atom_pos const rpg_cog = ref_pos_group ?
ref_pos_group->center_of_geometry() : this->center_of_geometry();
apply_translation(-1.0 * cog);
apply_translation(-1.0 * rpg_cog);
if (ref_pos_group) {
ref_pos_group->apply_translation(-1.0 * cog);
ref_pos_group->apply_translation(-1.0 * rpg_cog);
}
}
@ -945,26 +950,23 @@ void cvm::atom_group::calc_fit_gradients()
{
if (b_dummy) return;
if ((!b_center) && (!b_rotate)) return; // no fit
if (cvm::debug())
cvm::log("Calculating fit gradients.\n");
atom_group *group_for_fit = ref_pos_group ? ref_pos_group : this;
group_for_fit->fit_gradients.assign(group_for_fit->size(), cvm::rvector(0.0, 0.0, 0.0));
if (b_center) {
// add the center of geometry contribution to the gradients
cvm::rvector atom_grad;
for (size_t i = 0; i < this->size(); i++) {
// need to bring the gradients in original frame first
cvm::rvector const atom_grad = b_rotate ?
(rot.inverse()).rotate(atoms[i].grad) :
atoms[i].grad;
for (size_t j = 0; j < group_for_fit->size(); j++) {
group_for_fit->fit_gradients[j] +=
(-1.0)/(cvm::real(group_for_fit->size())) *
atom_grad;
}
atom_grad += atoms[i].grad;
}
if (b_rotate) atom_grad = (rot.inverse()).rotate(atom_grad);
atom_grad *= (-1.0)/(cvm::real(group_for_fit->size()));
for (size_t j = 0; j < group_for_fit->size(); j++) {
group_for_fit->fit_gradients[j] = atom_grad;
}
}
@ -972,23 +974,26 @@ void cvm::atom_group::calc_fit_gradients()
// add the rotation matrix contribution to the gradients
cvm::rotation const rot_inv = rot.inverse();
cvm::atom_pos const cog = center_of_geometry();
for (size_t i = 0; i < this->size(); i++) {
cvm::atom_pos const pos_orig = rot_inv.rotate((b_center ? (atoms[i].pos - cog) : (atoms[i].pos)));
// compute centered, unrotated position
cvm::atom_pos const pos_orig =
rot_inv.rotate((b_center ? (atoms[i].pos - ref_pos_cog) : (atoms[i].pos)));
// calculate \partial(R(q) \vec{x}_i)/\partial q) \cdot \partial\xi/\partial\vec{x}_i
cvm::quaternion const dxdq =
rot.q.position_derivative_inner(pos_orig, atoms[i].grad);
for (size_t j = 0; j < group_for_fit->size(); j++) {
// calculate \partial(R(q) \vec{x}_i)/\partial q) \cdot \partial\xi/\partial\vec{x}_i
cvm::quaternion const dxdq =
rot.q.position_derivative_inner(pos_orig, atoms[i].grad);
// multiply by \cdot {\partial q}/\partial\vec{x}_j and add it to the fit gradients
// multiply by {\partial q}/\partial\vec{x}_j and add it to the fit gradients
for (size_t iq = 0; iq < 4; iq++) {
group_for_fit->fit_gradients[j] += dxdq[iq] * rot.dQ0_1[j][iq];
}
}
}
}
if (cvm::debug())
cvm::log("Done calculating fit gradients.\n");
}
@ -1138,17 +1143,9 @@ void cvm::atom_group::apply_colvar_force(cvm::real const &force)
atom_group *group_for_fit = ref_pos_group ? ref_pos_group : this;
// add the contribution from the roto-translational fit to the gradients
if (b_rotate) {
// rotate forces back to the original frame
cvm::rotation const rot_inv = rot.inverse();
for (size_t j = 0; j < group_for_fit->size(); j++) {
(*group_for_fit)[j].apply_force(rot_inv.rotate(force * group_for_fit->fit_gradients[j]));
}
} else {
for (size_t j = 0; j < group_for_fit->size(); j++) {
(*group_for_fit)[j].apply_force(force * group_for_fit->fit_gradients[j]);
}
// Fit gradients are already calculated in "laboratory" frame
for (size_t j = 0; j < group_for_fit->size(); j++) {
(*group_for_fit)[j].apply_force(force * group_for_fit->fit_gradients[j]);
}
}