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colvarcomp_angles.cpp
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Fri, Jul 26, 21:53

colvarcomp_angles.cpp
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// -*- c++ -*-
#include "colvarmodule.h"
#include "colvar.h"
#include "colvarcomp.h"
#include <cmath>
colvar::angle::angle(std::string const &conf)
: cvc(conf)
{
function_type = "angle";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
provide(f_cvc_com_based);
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
group3 = parse_group(conf, "group3");
if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
cvm::log("Computing system force on group 1 only");
}
x.type(colvarvalue::type_scalar);
}
colvar::angle::angle(cvm::atom const &a1,
cvm::atom const &a2,
cvm::atom const &a3)
{
function_type = "angle";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
provide(f_cvc_com_based);
b_1site_force = false;
group1 = new cvm::atom_group(std::vector<cvm::atom>(1, a1));
group2 = new cvm::atom_group(std::vector<cvm::atom>(1, a2));
group3 = new cvm::atom_group(std::vector<cvm::atom>(1, a3));
atom_groups.push_back(group1);
atom_groups.push_back(group2);
atom_groups.push_back(group3);
x.type(colvarvalue::type_scalar);
}
colvar::angle::angle()
{
function_type = "angle";
x.type(colvarvalue::type_scalar);
}
void colvar::angle::calc_value()
{
cvm::atom_pos const g1_pos = group1->center_of_mass();
cvm::atom_pos const g2_pos = group2->center_of_mass();
cvm::atom_pos const g3_pos = group3->center_of_mass();
r21 = cvm::position_distance(g2_pos, g1_pos);
r21l = r21.norm();
r23 = cvm::position_distance(g2_pos, g3_pos);
r23l = r23.norm();
cvm::real const cos_theta = (r21*r23)/(r21l*r23l);
x.real_value = (180.0/PI) * std::acos(cos_theta);
}
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);
}
void colvar::angle::calc_force_invgrads()
{
// This uses a force measurement on groups 1 and 3 only
// to keep in line with the implicit variable change used to
// evaluate the Jacobian term (essentially polar coordinates
// centered on group2, which means group2 is kept fixed
// when propagating changes in the angle)
if (b_1site_force) {
group1->read_system_forces();
cvm::real norm_fact = 1.0 / dxdr1.norm2();
ft.real_value = norm_fact * dxdr1 * group1->system_force();
} else {
group1->read_system_forces();
group3->read_system_forces();
cvm::real norm_fact = 1.0 / (dxdr1.norm2() + dxdr3.norm2());
ft.real_value = norm_fact * ( dxdr1 * group1->system_force()
+ dxdr3 * group3->system_force());
}
return;
}
void colvar::angle::calc_Jacobian_derivative()
{
// det(J) = (2 pi) r^2 * sin(theta)
// hence Jd = cot(theta)
const cvm::real theta = x.real_value * PI / 180.0;
jd = PI / 180.0 * (theta != 0.0 ? std::cos(theta) / std::sin(theta) : 0.0);
}
void colvar::angle::apply_force(colvarvalue const &force)
{
if (!group1->noforce)
group1->apply_colvar_force(force.real_value);
if (!group2->noforce)
group2->apply_colvar_force(force.real_value);
if (!group3->noforce)
group3->apply_colvar_force(force.real_value);
}
colvar::dipole_angle::dipole_angle(std::string const &conf)
: cvc(conf)
{
function_type = "dipole_angle";
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
group3 = parse_group(conf, "group3");
if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
cvm::log("Computing system force on group 1 only");
}
x.type(colvarvalue::type_scalar);
}
colvar::dipole_angle::dipole_angle(cvm::atom const &a1,
cvm::atom const &a2,
cvm::atom const &a3)
{
function_type = "dipole_angle";
b_1site_force = false;
group1 = new cvm::atom_group(std::vector<cvm::atom>(1, a1));
group2 = new cvm::atom_group(std::vector<cvm::atom>(1, a2));
group3 = new cvm::atom_group(std::vector<cvm::atom>(1, a3));
atom_groups.push_back(group1);
atom_groups.push_back(group2);
atom_groups.push_back(group3);
x.type(colvarvalue::type_scalar);
}
colvar::dipole_angle::dipole_angle()
{
function_type = "dipole_angle";
x.type(colvarvalue::type_scalar);
}
void colvar::dipole_angle::calc_value()
{
cvm::atom_pos const g1_pos = group1->center_of_mass();
cvm::atom_pos const g2_pos = group2->center_of_mass();
cvm::atom_pos const g3_pos = group3->center_of_mass();
group1->calc_dipole(g1_pos);
r21 = group1->dipole();
r21l = r21.norm();
r23 = cvm::position_distance(g2_pos, g3_pos);
r23l = r23.norm();
cvm::real const cos_theta = (r21*r23)/(r21l*r23l);
x.real_value = (180.0/PI) * std::acos(cos_theta);
}
//to be implemented
//void colvar::dipole_angle::calc_force_invgrads(){}
//void colvar::dipole_angle::calc_Jacobian_derivative(){}
void colvar::dipole_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 );
//this auxiliar variables are to avoid numerical errors inside "for"
double aux1 = group1->total_charge/group1->total_mass;
// double aux2 = group2->total_charge/group2->total_mass;
// double aux3 = group3->total_charge/group3->total_mass;
size_t i;
for (i = 0; i < group1->size(); i++) {
(*group1)[i].grad =((*group1)[i].charge + (-1)* (*group1)[i].mass * aux1) * (dxdr1);
}
for (i = 0; i < group2->size(); i++) {
(*group2)[i].grad = ((*group2)[i].mass/group2->total_mass)* dxdr3 * (-1.0);
}
for (i = 0; i < group3->size(); i++) {
(*group3)[i].grad =((*group3)[i].mass/group3->total_mass) * (dxdr3);
}
}
void colvar::dipole_angle::apply_force(colvarvalue const &force)
{
if (!group1->noforce)
group1->apply_colvar_force(force.real_value);
if (!group2->noforce)
group2->apply_colvar_force(force.real_value);
if (!group3->noforce)
group3->apply_colvar_force(force.real_value);
}
colvar::dihedral::dihedral(std::string const &conf)
: cvc(conf)
{
function_type = "dihedral";
period = 360.0;
b_periodic = true;
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
provide(f_cvc_com_based);
if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
cvm::log("Computing system force on group 1 only");
}
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
group3 = parse_group(conf, "group3");
group4 = parse_group(conf, "group4");
x.type(colvarvalue::type_scalar);
}
colvar::dihedral::dihedral(cvm::atom const &a1,
cvm::atom const &a2,
cvm::atom const &a3,
cvm::atom const &a4)
{
if (cvm::debug())
cvm::log("Initializing dihedral object from atom groups.\n");
function_type = "dihedral";
period = 360.0;
b_periodic = true;
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
provide(f_cvc_com_based);
b_1site_force = false;
group1 = new cvm::atom_group(std::vector<cvm::atom>(1, a1));
group2 = new cvm::atom_group(std::vector<cvm::atom>(1, a2));
group3 = new cvm::atom_group(std::vector<cvm::atom>(1, a3));
group4 = new cvm::atom_group(std::vector<cvm::atom>(1, a4));
atom_groups.push_back(group1);
atom_groups.push_back(group2);
atom_groups.push_back(group3);
atom_groups.push_back(group4);
x.type(colvarvalue::type_scalar);
if (cvm::debug())
cvm::log("Done initializing dihedral object from atom groups.\n");
}
colvar::dihedral::dihedral()
{
function_type = "dihedral";
period = 360.0;
b_periodic = true;
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
x.type(colvarvalue::type_scalar);
}
void colvar::dihedral::calc_value()
{
cvm::atom_pos const g1_pos = group1->center_of_mass();
cvm::atom_pos const g2_pos = group2->center_of_mass();
cvm::atom_pos const g3_pos = group3->center_of_mass();
cvm::atom_pos const g4_pos = group4->center_of_mass();
// Usual sign convention: r12 = r2 - r1
r12 = cvm::position_distance(g1_pos, g2_pos);
r23 = cvm::position_distance(g2_pos, g3_pos);
r34 = cvm::position_distance(g3_pos, g4_pos);
cvm::rvector const n1 = cvm::rvector::outer(r12, r23);
cvm::rvector const n2 = cvm::rvector::outer(r23, r34);
cvm::real const cos_phi = n1 * n2;
cvm::real const sin_phi = n1 * r34 * r23.norm();
x.real_value = (180.0/PI) * std::atan2(sin_phi, cos_phi);
this->wrap(x);
}
void colvar::dihedral::calc_gradients()
{
cvm::rvector A = cvm::rvector::outer(r12, r23);
cvm::real rA = A.norm();
cvm::rvector B = cvm::rvector::outer(r23, r34);
cvm::real rB = B.norm();
cvm::rvector C = cvm::rvector::outer(r23, A);
cvm::real rC = C.norm();
cvm::real const cos_phi = (A*B)/(rA*rB);
cvm::real const sin_phi = (C*B)/(rC*rB);
cvm::rvector f1, f2, f3;
rB = 1.0/rB;
B *= rB;
if (std::fabs(sin_phi) > 0.1) {
rA = 1.0/rA;
A *= rA;
cvm::rvector const dcosdA = rA*(cos_phi*A-B);
cvm::rvector const dcosdB = rB*(cos_phi*B-A);
rA = 1.0;
cvm::real const K = (1.0/sin_phi) * (180.0/PI);
f1 = K * cvm::rvector::outer(r23, dcosdA);
f3 = K * cvm::rvector::outer(dcosdB, r23);
f2 = K * (cvm::rvector::outer(dcosdA, r12)
+ cvm::rvector::outer(r34, dcosdB));
}
else {
rC = 1.0/rC;
C *= rC;
cvm::rvector const dsindC = rC*(sin_phi*C-B);
cvm::rvector const dsindB = rB*(sin_phi*B-C);
rC = 1.0;
cvm::real const K = (-1.0/cos_phi) * (180.0/PI);
f1.x = K*((r23.y*r23.y + r23.z*r23.z)*dsindC.x
- r23.x*r23.y*dsindC.y
- r23.x*r23.z*dsindC.z);
f1.y = K*((r23.z*r23.z + r23.x*r23.x)*dsindC.y
- r23.y*r23.z*dsindC.z
- r23.y*r23.x*dsindC.x);
f1.z = K*((r23.x*r23.x + r23.y*r23.y)*dsindC.z
- r23.z*r23.x*dsindC.x
- r23.z*r23.y*dsindC.y);
f3 = cvm::rvector::outer(dsindB, r23);
f3 *= K;
f2.x = K*(-(r23.y*r12.y + r23.z*r12.z)*dsindC.x
+(2.0*r23.x*r12.y - r12.x*r23.y)*dsindC.y
+(2.0*r23.x*r12.z - r12.x*r23.z)*dsindC.z
+dsindB.z*r34.y - dsindB.y*r34.z);
f2.y = K*(-(r23.z*r12.z + r23.x*r12.x)*dsindC.y
+(2.0*r23.y*r12.z - r12.y*r23.z)*dsindC.z
+(2.0*r23.y*r12.x - r12.y*r23.x)*dsindC.x
+dsindB.x*r34.z - dsindB.z*r34.x);
f2.z = K*(-(r23.x*r12.x + r23.y*r12.y)*dsindC.z
+(2.0*r23.z*r12.x - r12.z*r23.x)*dsindC.x
+(2.0*r23.z*r12.y - r12.z*r23.y)*dsindC.y
+dsindB.y*r34.x - dsindB.x*r34.y);
}
group1->set_weighted_gradient(-f1);
group2->set_weighted_gradient(-f2 + f1);
group3->set_weighted_gradient(-f3 + f2);
group4->set_weighted_gradient(f3);
}
void colvar::dihedral::calc_force_invgrads()
{
cvm::rvector const u12 = r12.unit();
cvm::rvector const u23 = r23.unit();
cvm::rvector const u34 = r34.unit();
cvm::real const d12 = r12.norm();
cvm::real const d34 = r34.norm();
cvm::rvector const cross1 = (cvm::rvector::outer(u23, u12)).unit();
cvm::rvector const cross4 = (cvm::rvector::outer(u23, u34)).unit();
cvm::real const dot1 = u23 * u12;
cvm::real const dot4 = u23 * u34;
cvm::real const fact1 = d12 * std::sqrt(1.0 - dot1 * dot1);
cvm::real const fact4 = d34 * std::sqrt(1.0 - dot4 * dot4);
group1->read_system_forces();
if ( b_1site_force ) {
// This is only measuring the force on group 1
ft.real_value = PI/180.0 * fact1 * (cross1 * group1->system_force());
} else {
// Default case: use groups 1 and 4
group4->read_system_forces();
ft.real_value = PI/180.0 * 0.5 * (fact1 * (cross1 * group1->system_force())
+ fact4 * (cross4 * group4->system_force()));
}
}
void colvar::dihedral::calc_Jacobian_derivative()
{
// With this choice of inverse gradient ("internal coordinates"), Jacobian correction is 0
jd = 0.0;
}
void colvar::dihedral::apply_force(colvarvalue const &force)
{
if (!group1->noforce)
group1->apply_colvar_force(force.real_value);
if (!group2->noforce)
group2->apply_colvar_force(force.real_value);
if (!group3->noforce)
group3->apply_colvar_force(force.real_value);
if (!group4->noforce)
group4->apply_colvar_force(force.real_value);
}

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