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update colvars library to version 2016-06-09

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This commit is contained in:
Axel Kohlmeyer
2016-06-10 05:54:06 -04:00
parent 470cefbba1
commit 48cec4d7d2
34 changed files with 796 additions and 505 deletions
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12
lib/colvars/colvarcomp.cpp
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@ -1,4 +1,4 @@
/// -*- c++ -*-
// -*- c++ -*-
#include "colvarmodule.h"
#include "colvarvalue.h"
@ -134,7 +134,7 @@ void colvar::cvc::read_data()
atoms.reset_atoms_data();
atoms.read_positions();
atoms.calc_required_properties();
// each atom group will take care of its own ref_pos_group, if defined
// each atom group will take care of its own fitting_group, if defined
}
//// Don't try to get atom velocities, as no back-end currently implements it
@ -179,7 +179,7 @@ void colvar::cvc::debug_gradients(cvm::atom_group *group)
// 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_group *group_for_fit = group->fitting_group ? group->fitting_group : group;
cvm::atom_pos fit_gradient_sum, gradient_sum;
// print the values of the fit gradients
@ -190,7 +190,7 @@ void colvar::cvc::debug_gradients(cvm::atom_group *group)
// 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::log((group->fitting_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])) :
@ -231,8 +231,8 @@ void colvar::cvc::debug_gradients(cvm::atom_group *group)
}
}
if ((group->b_fit_gradients) && (group->ref_pos_group != NULL)) {
cvm::atom_group *ref_group = group->ref_pos_group;
if ((group->b_fit_gradients) && (group->fitting_group != NULL)) {
cvm::atom_group *ref_group = group->fitting_group;
group->read_positions();
group->calc_required_properties();