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Minor changes and fixes not relevant to LAMMPS

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This commit is contained in:
Giacomo Fiorin
2016-10-24 17:08:36 -04:00
parent c243093980
commit be2d155cef
9 changed files with 85 additions and 37 deletions
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45
lib/colvars/colvaratoms.cpp
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@ -367,6 +367,7 @@ int cvm::atom_group::parse(std::string const &conf)
cvm::error("Error: atomsColValue, if provided, must be non-zero.\n", INPUT_ERROR);
}
// NOTE: calls to add_atom() and/or add_atom_id() are in the proxy-implemented function
cvm::load_atoms(atoms_file_name.c_str(), *this, atoms_col, atoms_col_value);
}
}
@ -403,11 +404,21 @@ int cvm::atom_group::parse(std::string const &conf)
}
}
// We need to know the fitting options to decide whether the group is scalable
parse_error |= parse_fitting_options(group_conf);
if (is_available(f_ag_scalable_com) && !b_rotate) {
enable(f_ag_scalable_com);
enable(f_ag_scalable);
}
if (is_enabled(f_ag_scalable) && !b_dummy) {
cvm::log("Enabling scalable calculation for group \""+this->key+"\".\n");
index = (cvm::proxy)->init_atom_group(atoms_ids);
}
parse_error |= parse_fitting_options(group_conf);
bool b_print_atom_ids = false;
get_keyval(group_conf, "printAtomIDs", b_print_atom_ids, false, colvarparse::parse_silent);
// TODO move this to colvarparse object
check_keywords(group_conf, key.c_str());
@ -427,6 +438,10 @@ int cvm::atom_group::parse(std::string const &conf)
cvm::to_str(total_mass)+", total charge = "+
cvm::to_str(total_charge)+".\n");
if (b_print_atom_ids) {
cvm::log("Internal definition of the atom group:\n");
}
cvm::decrease_depth();
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
@ -583,6 +598,21 @@ int cvm::atom_group::add_atom_name_residue_range(std::string const &psf_segid,
}
std::string const cvm::atom_group::print_atom_ids() const
{
size_t line_count = 0;
std::ostringstream os("");
for (size_t i = 0; i < atoms_ids.size(); i++) {
os << " " << std::setw(9) << atoms_ids[i];
if (++line_count == 7) {
os << "\n";
line_count = 0;
}
}
return os.str();
}
int cvm::atom_group::parse_fitting_options(std::string const &group_conf)
{
bool b_defined_center = get_keyval(group_conf, "centerReference", b_center, false);
@ -1118,8 +1148,7 @@ void cvm::atom_group::apply_colvar_force(cvm::real const &force)
log("Communicating a colvar force from atom group to the MD engine.\n");
}
if (b_dummy)
return;
if (b_dummy) return;
if (noforce) {
cvm::error("Error: sending a force to a group that has "
@ -1161,17 +1190,21 @@ void cvm::atom_group::apply_colvar_force(cvm::real const &force)
void cvm::atom_group::apply_force(cvm::rvector const &force)
{
if (b_dummy)
return;
if (cvm::debug()) {
log("Communicating a colvar force from atom group to the MD engine.\n");
}
if (b_dummy) return;
if (noforce) {
cvm::error("Error: sending a force to a group that has "
"\"disableForces\" defined.\n");
"\"enableForces\" set to off.\n");
return;
}
if (is_enabled(f_ag_scalable)) {
(cvm::proxy)->apply_atom_group_force(index, force);
return;
}
if (b_rotate) {