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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14703 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2016-03-01 20:40:25 +00:00
parent 6e2893c768
commit 20beaccf0f
16 changed files with 1675 additions and 716 deletions
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17
lib/colvars/colvarcomp.cpp
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@ -46,12 +46,14 @@ colvar::cvc::cvc(std::string const &conf)
void colvar::cvc::parse_group(std::string const &conf,
char const *group_key,
cvm::atom_group &group,
bool optional)
char const *group_key,
cvm::atom_group &group,
bool optional)
{
if (key_lookup(conf, group_key)) {
if (group.parse(conf, group_key) != COLVARS_OK) {
// TODO turn on scalable flag for group objects in cvc init function
group.key = group_key;
if (group.parse(conf) != COLVARS_OK) {
cvm::error("Error parsing definition for atom group \""+
std::string(group_key)+"\".\n");
return;
@ -130,10 +132,7 @@ void colvar::cvc::debug_gradients(cvm::atom_group &group)
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();
}
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];
@ -167,7 +166,7 @@ void colvar::cvc::debug_gradients(cvm::atom_group &group)
// ref.read_positions();
// // change one coordinate
// ref[ia].pos[id] += cvm::debug_gradients_step_size;
// group.calc_apply_roto_translation();
// group.update();
// calc_value();
// cvm::real const x_1 = x.real_value;
// cvm::log("refPosGroup atom "+cvm::to_str(ia)+", component "+cvm::to_str (id)+":\n");