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Update Colvars library to version 2019-04-26

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The following is list of relevant issues fixed and improvements:

Fix forces and missing output of runtime histogram for histogramRestraint
https://github.com/Colvars/colvars/pull/246

Use fix_modify to add configuration to Colvars:
https://github.com/Colvars/colvars/pull/216

Fix componentCoeff and name not working with orientationAngle components:
https://github.com/Colvars/colvars/issues/213

Fix 1-timestep offset with extendedLagrangian:
https://github.com/Colvars/colvars/pull/210

Changes to improve compiler support:
https://github.com/Colvars/colvars/pull/203

Fix ignored anisotropic cutoff3 for groupCoordNum:
https://github.com/Colvars/colvars/pull/202

New dipoleMagnitude variable:
https://github.com/Colvars/colvars/pull/198

Parser improvements:
https://github.com/Colvars/colvars/pull/196
This commit is contained in:
Giacomo Fiorin
2019-04-30 09:50:12 -04:00
parent 0005ee3e93
commit 7e00acce53
45 changed files with 2378 additions and 1328 deletions
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99
lib/colvars/colvarcomp_protein.cpp
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@ -7,8 +7,6 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <cmath>
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarparse.h"
@ -27,7 +25,7 @@ colvar::alpha_angles::alpha_angles(std::string const &conf)
cvm::log("Initializing alpha_angles object.\n");
function_type = "alpha_angles";
enable(f_cvc_implicit_gradient);
enable(f_cvc_explicit_gradient);
x.type(colvarvalue::type_scalar);
std::string segment_id;
@ -118,7 +116,7 @@ colvar::alpha_angles::alpha_angles()
: cvc()
{
function_type = "alpha_angles";
enable(f_cvc_implicit_gradient);
enable(f_cvc_explicit_gradient);
x.type(colvarvalue::type_scalar);
}
@ -133,6 +131,8 @@ colvar::alpha_angles::~alpha_angles()
delete hb.back();
hb.pop_back();
}
// Our references to atom groups have become invalid now that children cvcs are deleted
atom_groups.clear();
}
@ -191,6 +191,58 @@ void colvar::alpha_angles::calc_gradients()
}
void colvar::alpha_angles::collect_gradients(std::vector<int> const &atom_ids, std::vector<cvm::rvector> &atomic_gradients)
{
cvm::real cvc_coeff = sup_coeff * cvm::real(sup_np) * cvm::integer_power(value().real_value, sup_np-1);
if (theta.size()) {
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;
cvm::real const f = ( (1.0 - (t*t)) /
(1.0 - (t*t*t*t)) );
cvm::real const dfdt =
1.0/(1.0 - (t*t*t*t)) *
( (-2.0 * t) + (-1.0*f)*(-4.0 * (t*t*t)) );
// Coeficient of this CVC's gradient in the colvar gradient, times coefficient of this
// angle's gradient in the CVC's gradient
cvm::real const coeff = cvc_coeff * theta_norm * dfdt * (1.0/theta_tol);
for (size_t j = 0; j < theta[i]->atom_groups.size(); j++) {
cvm::atom_group &ag = *(theta[i]->atom_groups[j]);
for (size_t k = 0; k < ag.size(); k++) {
size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
ag[k].id) - atom_ids.begin();
atomic_gradients[a] += coeff * ag[k].grad;
}
}
}
}
if (hb.size()) {
cvm::real const hb_norm = hb_coeff / cvm::real(hb.size());
for (size_t i = 0; i < hb.size(); i++) {
// Coeficient of this CVC's gradient in the colvar gradient, times coefficient of this
// hbond's gradient in the CVC's gradient
cvm::real const coeff = cvc_coeff * 0.5 * hb_norm;
for (size_t j = 0; j < hb[i]->atom_groups.size(); j++) {
cvm::atom_group &ag = *(hb[i]->atom_groups[j]);
for (size_t k = 0; k < ag.size(); k++) {
size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
ag[k].id) - atom_ids.begin();
atomic_gradients[a] += coeff * ag[k].grad;
}
}
}
}
}
void colvar::alpha_angles::apply_force(colvarvalue const &force)
{
@ -242,7 +294,8 @@ colvar::dihedPC::dihedPC(std::string const &conf)
cvm::log("Initializing dihedral PC object.\n");
function_type = "dihedPC";
enable(f_cvc_implicit_gradient);
// Supported through references to atom groups of children cvcs
enable(f_cvc_explicit_gradient);
x.type(colvarvalue::type_scalar);
std::string segment_id;
@ -372,7 +425,8 @@ colvar::dihedPC::dihedPC()
: cvc()
{
function_type = "dihedPC";
enable(f_cvc_implicit_gradient);
// Supported through references to atom groups of children cvcs
enable(f_cvc_explicit_gradient);
x.type(colvarvalue::type_scalar);
}
@ -383,6 +437,8 @@ colvar::dihedPC::~dihedPC()
delete theta.back();
theta.pop_back();
}
// Our references to atom groups have become invalid now that children cvcs are deleted
atom_groups.clear();
}
@ -392,8 +448,8 @@ void colvar::dihedPC::calc_value()
for (size_t i = 0; i < theta.size(); i++) {
theta[i]->calc_value();
cvm::real const t = (PI / 180.) * theta[i]->value().real_value;
x.real_value += coeffs[2*i ] * std::cos(t)
+ coeffs[2*i+1] * std::sin(t);
x.real_value += coeffs[2*i ] * cvm::cos(t)
+ coeffs[2*i+1] * cvm::sin(t);
}
}
@ -406,12 +462,35 @@ void colvar::dihedPC::calc_gradients()
}
void colvar::dihedPC::collect_gradients(std::vector<int> const &atom_ids, std::vector<cvm::rvector> &atomic_gradients)
{
cvm::real cvc_coeff = sup_coeff * cvm::real(sup_np) * cvm::integer_power(value().real_value, sup_np-1);
for (size_t i = 0; i < theta.size(); i++) {
cvm::real const t = (PI / 180.) * theta[i]->value().real_value;
cvm::real const dcosdt = - (PI / 180.) * cvm::sin(t);
cvm::real const dsindt = (PI / 180.) * cvm::cos(t);
// Coeficient of this dihedPC's gradient in the colvar gradient, times coefficient of this
// dihedral's gradient in the dihedPC's gradient
cvm::real const coeff = cvc_coeff * (coeffs[2*i] * dcosdt + coeffs[2*i+1] * dsindt);
for (size_t j = 0; j < theta[i]->atom_groups.size(); j++) {
cvm::atom_group &ag = *(theta[i]->atom_groups[j]);
for (size_t k = 0; k < ag.size(); k++) {
size_t a = std::lower_bound(atom_ids.begin(), atom_ids.end(),
ag[k].id) - atom_ids.begin();
atomic_gradients[a] += coeff * ag[k].grad;
}
}
}
}
void colvar::dihedPC::apply_force(colvarvalue const &force)
{
for (size_t i = 0; i < theta.size(); i++) {
cvm::real const t = (PI / 180.) * theta[i]->value().real_value;
cvm::real const dcosdt = - (PI / 180.) * std::sin(t);
cvm::real const dsindt = (PI / 180.) * std::cos(t);
cvm::real const dcosdt = - (PI / 180.) * cvm::sin(t);
cvm::real const dsindt = (PI / 180.) * cvm::cos(t);
theta[i]->apply_force((coeffs[2*i ] * dcosdt +
coeffs[2*i+1] * dsindt) * force);