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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10118 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-06-27 22:48:27 +00:00
parent 38112d0063
commit 4da20dce99
30 changed files with 883 additions and 571 deletions
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16
lib/colvars/colvarcomp_protein.cpp
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@ -122,7 +122,7 @@ void colvar::alpha_angles::calc_value()
if (theta.size()) {
cvm::real const theta_norm =
cvm::real const theta_norm =
(1.0-hb_coeff) / cvm::real (theta.size());
for (size_t i = 0; i < theta.size(); i++) {
@ -162,7 +162,7 @@ void colvar::alpha_angles::calc_value()
void colvar::alpha_angles::calc_gradients()
{
for (size_t i = 0; i < theta.size(); i++)
for (size_t i = 0; i < theta.size(); i++)
(theta[i])->calc_gradients();
for (size_t i = 0; i < hb.size(); i++)
@ -175,9 +175,9 @@ void colvar::alpha_angles::apply_force (colvarvalue const &force)
if (theta.size()) {
cvm::real const theta_norm =
cvm::real const theta_norm =
(1.0-hb_coeff) / cvm::real (theta.size());
for (size_t i = 0; i < theta.size(); i++) {
cvm::real const t = ((theta[i])->value().real_value-theta_ref)/theta_tol;
@ -185,10 +185,10 @@ void colvar::alpha_angles::apply_force (colvarvalue const &force)
(1.0 - std::pow (t, (int) 4)) );
cvm::real const dfdt =
1.0/(1.0 - std::pow (t, (int) 4)) *
1.0/(1.0 - std::pow (t, (int) 4)) *
( (-2.0 * t) + (-1.0*f)*(-4.0 * std::pow (t, (int) 3)) );
(theta[i])->apply_force (theta_norm *
(theta[i])->apply_force (theta_norm *
dfdt * (1.0/theta_tol) *
force.real_value );
}
@ -216,7 +216,7 @@ void colvar::alpha_angles::apply_force (colvarvalue const &force)
// of this cvc (alpha)
// This is true of all cvcs with sub-cvcs, and those
// that do not calculate explicit gradients
// SO: we need a flag giving the availability of
// SO: we need a flag giving the availability of
// atomic gradients
colvar::dihedPC::dihedPC (std::string const &conf)
: cvc (conf)
@ -260,7 +260,7 @@ colvar::dihedPC::dihedPC (std::string const &conf)
std::string vecFileName;
int vecNumber;
if (get_keyval (conf, "vectorFile", vecFileName, vecFileName)) {
get_keyval (conf, "vectorNumber", vecNumber, 0);
get_keyval (conf, "vectorNumber", vecNumber, 0);
if (vecNumber < 1)
cvm::fatal_error ("A positive value of vectorNumber is required.");