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colvarcomp_angles.cpp
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Wed, Nov 6, 08:18

colvarcomp_angles.cpp
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#include "colvarmodule.h"
#include "colvar.h"
#include "colvarcomp.h"
#include <cmath>
colvar::angle::angle (std::string const &conf)
: cvc (conf)
{
function_type = "angle";
b_inverse_gradients = true;
b_Jacobian_derivative = true;
parse_group (conf, "group1", group1);
parse_group (conf, "group2", group2);
parse_group (conf, "group3", group3);
atom_groups.push_back (&group1);
atom_groups.push_back (&group2);
atom_groups.push_back (&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)
: group1 (std::vector<cvm::atom> (1, a1)),
group2 (std::vector<cvm::atom> (1, a2)),
group3 (std::vector<cvm::atom> (1, a3))
{
function_type = "angle";
b_inverse_gradients = true;
b_Jacobian_derivative = true;
b_1site_force = false;
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()
{
group1.read_positions();
group2.read_positions();
group3.read_positions();
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 );
for (size_t i = 0; i < group1.size(); i++) {
group1[i].grad = (group1[i].mass/group1.total_mass) *
(dxdr1);
}
for (size_t i = 0; i < group2.size(); i++) {
group2[i].grad = (group2[i].mass/group2.total_mass) *
(dxdr1 + dxdr3) * (-1.0);
}
for (size_t i = 0; i < group3.size(); i++) {
group3[i].grad = (group3[i].mass/group3.total_mass) *
(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::dihedral::dihedral (std::string const &conf)
: cvc (conf)
{
function_type = "dihedral";
period = 360.0;
b_periodic = true;
b_inverse_gradients = true;
b_Jacobian_derivative = true;
if (get_keyval (conf, "oneSiteSystemForce", b_1site_force, false)) {
cvm::log ("Computing system force on group 1 only");
}
parse_group (conf, "group1", group1);
parse_group (conf, "group2", group2);
parse_group (conf, "group3", group3);
parse_group (conf, "group4", group4);
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);
}
colvar::dihedral::dihedral (cvm::atom const &a1,
cvm::atom const &a2,
cvm::atom const &a3,
cvm::atom const &a4)
: group1 (std::vector<cvm::atom> (1, a1)),
group2 (std::vector<cvm::atom> (1, a2)),
group3 (std::vector<cvm::atom> (1, a3)),
group4 (std::vector<cvm::atom> (1, a4))
{
if (cvm::debug())
cvm::log ("Initializing dihedral object from atom groups.\n");
function_type = "dihedral";
period = 360.0;
b_periodic = true;
b_inverse_gradients = true;
b_Jacobian_derivative = true;
b_1site_force = false;
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;
b_inverse_gradients = true;
b_Jacobian_derivative = true;
x.type (colvarvalue::type_scalar);
}
void colvar::dihedral::calc_value()
{
group1.read_positions();
group2.read_positions();
group3.read_positions();
group4.read_positions();
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);
}
for (size_t i = 0; i < group1.size(); i++)
group1[i].grad = (group1[i].mass/group1.total_mass) * (-f1);
for (size_t i = 0; i < group2.size(); i++)
group2[i].grad = (group2[i].mass/group2.total_mass) * (-f2 + f1);
for (size_t i = 0; i < group3.size(); i++)
group3[i].grad = (group3[i].mass/group3.total_mass) * (-f3 + f2);
for (size_t i = 0; i < group4.size(); i++)
group4[i].grad = (group4[i].mass/group4.total_mass) * (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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