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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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69
lib/colvars/colvarcomp_distances.cpp
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@ -167,7 +167,7 @@ colvar::distance_z::distance_z(std::string const &conf)
// this group is optional
ref2 = parse_group(conf, "ref2", true);
if (ref2->size()) {
if (ref2 && ref2->size()) {
cvm::log("Using axis joining the centers of mass of groups \"ref\" and \"ref2\"");
fixed_axis = false;
if (key_lookup(conf, "axis"))
@ -249,15 +249,6 @@ void colvar::distance_z::calc_gradients()
cvm::position_distance(main->center_of_mass(), ref1->center_of_mass()) + x.real_value * axis ));
}
}
if (is_enabled(f_cvc_debug_gradient)) {
cvm::log("Debugging gradients for group main:\n");
debug_gradients(main);
cvm::log("Debugging gradients for group ref1:\n");
debug_gradients(ref1);
cvm::log("Debugging gradients for group ref2:\n");
debug_gradients(ref2);
}
}
void colvar::distance_z::calc_force_invgrads()
@ -282,7 +273,7 @@ void colvar::distance_z::apply_force(colvarvalue const &force)
if (!ref1->noforce)
ref1->apply_colvar_force(force.real_value);
if (ref2->size() && !ref2->noforce)
if (ref2 && ref2->size() && !ref2->noforce)
ref2->apply_colvar_force(force.real_value);
if (!main->noforce)
@ -382,7 +373,7 @@ void colvar::distance_xy::apply_force(colvarvalue const &force)
if (!ref1->noforce)
ref1->apply_colvar_force(force.real_value);
if (ref2->size() && !ref2->noforce)
if (ref2 && ref2->size() && !ref2->noforce)
ref2->apply_colvar_force(force.real_value);
if (!main->noforce)
@ -593,10 +584,6 @@ void colvar::distance_pairs::calc_value()
void colvar::distance_pairs::calc_gradients()
{
// will be calculated on the fly in apply_force()
if (is_enabled(f_cvc_debug_gradient)) {
cvm::log("Debugging gradients:\n");
debug_gradients(group1);
}
}
void colvar::distance_pairs::apply_force(colvarvalue const &force)
@ -667,11 +654,6 @@ void colvar::gyration::calc_gradients()
for (cvm::atom_iter ai = atoms->begin(); ai != atoms->end(); ai++) {
ai->grad = drdx * ai->pos;
}
if (is_enabled(f_cvc_debug_gradient)) {
cvm::log("Debugging gradients:\n");
debug_gradients(atoms);
}
}
@ -731,11 +713,6 @@ void colvar::inertia::calc_gradients()
for (cvm::atom_iter ai = atoms->begin(); ai != atoms->end(); ai++) {
ai->grad = 2.0 * ai->pos;
}
if (is_enabled(f_cvc_debug_gradient)) {
cvm::log("Debugging gradients:\n");
debug_gradients(atoms);
}
}
@ -786,11 +763,6 @@ void colvar::inertia_z::calc_gradients()
for (cvm::atom_iter ai = atoms->begin(); ai != atoms->end(); ai++) {
ai->grad = 2.0 * (ai->pos * axis) * axis;
}
if (is_enabled(f_cvc_debug_gradient)) {
cvm::log("Debugging gradients:\n");
debug_gradients(atoms);
}
}
@ -811,7 +783,7 @@ colvar::rmsd::rmsd(std::string const &conf)
atoms = parse_group(conf, "atoms");
if (atoms->size() == 0) {
if (!atoms || atoms->size() == 0) {
cvm::error("Error: \"atoms\" must contain at least 1 atom to compute RMSD.");
return;
}
@ -891,18 +863,11 @@ colvar::rmsd::rmsd(std::string const &conf)
cvm::log("This is a standard minimum RMSD, derivatives of the optimal rotation "
"will not be computed as they cancel out in the gradients.");
atoms->b_fit_gradients = false;
}
if (atoms->b_rotate) {
// TODO: finer-grained control of this would require exposing a
// "request_Jacobian_derivative()" method to the colvar, and the same
// from the colvar to biases
// TODO: this should not be enabled here anyway, as it is not specific of the
// component - instead it should be decided in a generic way by the atom group
// request the calculation of the derivatives of the rotation defined by the atom group
atoms->rot.request_group1_gradients(atoms->size());
// request derivatives of optimal rotation wrt reference coordinates for Jacobian:
// this is only required for ABF, but we do both groups here for better caching
atoms->rot.request_group2_gradients(atoms->size());
}
}
@ -930,11 +895,6 @@ void colvar::rmsd::calc_gradients()
for (size_t ia = 0; ia < atoms->size(); ia++) {
(*atoms)[ia].grad = (drmsddx2 * 2.0 * ((*atoms)[ia].pos - ref_pos[ia]));
}
if (is_enabled(f_cvc_debug_gradient)) {
cvm::log("Debugging gradients:\n");
debug_gradients(atoms);
}
}
@ -1031,7 +991,7 @@ colvar::eigenvector::eigenvector(std::string const &conf)
cvm::log("Using reference positions from input file.\n");
if (ref_pos.size() != atoms->size()) {
cvm::error("Error: reference positions do not "
"match the number of requested atoms->\n");
"match the number of requested atoms.\n");
return;
}
}
@ -1064,9 +1024,14 @@ colvar::eigenvector::eigenvector(std::string const &conf)
}
}
if (ref_pos.size() == 0) {
cvm::error("Error: reference positions were not provided.\n", INPUT_ERROR);
return;
}
if (ref_pos.size() != atoms->size()) {
cvm::error("Error: reference positions were not provided, or do not "
"match the number of requested atoms->\n");
cvm::error("Error: reference positions do not "
"match the number of requested atoms.\n", INPUT_ERROR);
return;
}
@ -1087,6 +1052,8 @@ colvar::eigenvector::eigenvector(std::string const &conf)
atoms->b_rotate = true;
atoms->ref_pos = ref_pos;
atoms->center_ref_pos();
atoms->b_fit_gradients = false; // cancel out if group is fitted on itself
// and cvc is translationally invariant
// request the calculation of the derivatives of the rotation defined by the atom group
atoms->rot.request_group1_gradients(atoms->size());
@ -1216,11 +1183,6 @@ void colvar::eigenvector::calc_gradients()
for (size_t ia = 0; ia < atoms->size(); ia++) {
(*atoms)[ia].grad = eigenvec[ia];
}
if (is_enabled(f_cvc_debug_gradient)) {
cvm::log("Debugging gradients:\n");
debug_gradients(atoms);
}
}
@ -1313,6 +1275,7 @@ colvar::cartesian::cartesian(std::string const &conf)
if (axes.size() == 0) {
cvm::error("Error: a \"cartesian\" component was defined with all three axes disabled.\n");
return;
}
x.type(colvarvalue::type_vector);