void colvar::distance_z::calc_gradients()
{
main.set_weighted_gradient( axis );
if (fixed_axis) {
ref1.set_weighted_gradient(-1.0 * axis);
} else {
if (b_no_PBC) {
ref1.set_weighted_gradient( 1.0 / axis_norm * (main.center_of_mass() - ref2.center_of_mass() -
x.real_value * axis ));
ref2.set_weighted_gradient( 1.0 / axis_norm * (ref1.center_of_mass() - main.center_of_mass() +
x.real_value * axis ));
} else {
ref1.set_weighted_gradient( 1.0 / axis_norm * (
cvm::position_distance(ref2.center_of_mass(), main.center_of_mass()) - x.real_value * axis ));
ref2.set_weighted_gradient( 1.0 / axis_norm * (
cvm::position_distance(main.center_of_mass(), ref1.center_of_mass()) + x.real_value * axis ));
}
}
if (b_debug_gradients) {
cvm::log("Debugging gradients for group main:\n");
debug_gradients(main);
cvm::log("Debugging gradients for group ref1:\n");
debug_gradients(ref1);
cvm::log("Debugging gradients for group ref2:\n");
debug_gradients(ref2);
}
}
void colvar::distance_pairs::calc_gradients()
{
// will be calculated on the fly in apply_force()
if (b_debug_gradients) {
cvm::log("Debugging gradients:\n");
debug_gradients(group1);
}
}
void colvar::inertia_z::calc_gradients()
{
for (cvm::atom_iter ai = atoms.begin(); ai != atoms.end(); ai++) {
ai->grad = 2.0 * (ai->pos * axis) * axis;
}
if (b_debug_gradients) {
cvm::log ("Debugging gradients:\n");
debug_gradients (atoms);
}
}
void colvar::eigenvector::calc_gradients()
{
for (size_t ia = 0; ia < atoms.size(); ia++) {
atoms[ia].grad = eigenvec[ia];
}
if (b_debug_gradients) {
cvm::log ("Debugging gradients:\n");
debug_gradients (atoms);
}
}
void colvar::orientation_proj::calc_gradients()
{
cvm::real const dxdq0 = 2.0 * 2.0 * (rot.q).q0;
for (size_t ia = 0; ia < atoms.size(); ia++) {
atoms[ia].grad = (dxdq0 * (rot.dQ0_2[ia])[0]);
}
if (b_debug_gradients) {
cvm::log("Debugging orientationProj component gradients:\n");
debug_gradients(atoms);
}
}
void colvar::gyration::calc_gradients()
{
cvm::real const drdx = 1.0/(cvm::real (atoms.size()) * x.real_value);
for (cvm::atom_iter ai = atoms.begin(); ai != atoms.end(); ai++) {
ai->grad = drdx * ai->pos;
}
if (b_debug_gradients) {
cvm::log ("Debugging gradients:\n");
debug_gradients (atoms);
}
}
void colvar::angle::calc_gradients()
{
cvm::real const cos_theta = (r21*r23)/(r21l*r23l);
cvm::real const dxdcos = -1.0 / std::sqrt(1.0 - cos_theta*cos_theta);
dxdr1 = (180.0/PI) * dxdcos *
(1.0/r21l) * ( r23/r23l + (-1.0) * cos_theta * r21/r21l );
dxdr3 = (180.0/PI) * dxdcos *
(1.0/r23l) * ( r21/r21l + (-1.0) * cos_theta * r23/r23l );
group1->set_weighted_gradient(dxdr1);
group2->set_weighted_gradient((dxdr1 + dxdr3) * (-1.0));
group3->set_weighted_gradient(dxdr3);
if (is_enabled(f_cvc_debug_gradient)) {
debug_gradients(group1);
debug_gradients(group2);
debug_gradients(group3);
}
}
void colvar::rmsd::calc_gradients()
{
cvm::real const drmsddx2 = (x.real_value > 0.0) ?
0.5 / (x.real_value * cvm::real (atoms.size())) :
0.0;
for (size_t ia = 0; ia < atoms.size(); ia++) {
atoms[ia].grad = (drmsddx2 * 2.0 * (atoms[ia].pos - ref_pos[ia]));
}
if (b_debug_gradients) {
cvm::log ("Debugging gradients:\n");
debug_gradients (atoms);
}
}
void colvar::orientation_angle::calc_gradients()
{
cvm::real const dxdq0 =
( ((rot.q).q0 * (rot.q).q0 < 1.0) ?
((180.0 / PI) * (-2.0) / std::sqrt(1.0 - ((rot.q).q0 * (rot.q).q0))) :
0.0 );
for (size_t ia = 0; ia < atoms.size(); ia++) {
atoms[ia].grad = (dxdq0 * (rot.dQ0_2[ia])[0]);
}
if (b_debug_gradients) {
cvm::log("Debugging orientationAngle component gradients:\n");
debug_gradients(atoms);
}
}
void colvar::tilt::calc_gradients()
{
cvm::quaternion const dxdq = rot.dcos_theta_dq(axis);
for (size_t ia = 0; ia < atoms.size(); ia++) {
atoms[ia].grad = cvm::rvector(0.0, 0.0, 0.0);
for (size_t iq = 0; iq < 4; iq++) {
atoms[ia].grad += (dxdq[iq] * (rot.dQ0_2[ia])[iq]);
}
}
if (b_debug_gradients) {
cvm::log("Debugging tilt component gradients:\n");
debug_gradients(atoms);
}
}
