void colvar::distance6::calc_value()
{
group1.reset_atoms_data();
group2.reset_atoms_data();
group1.read_positions();
group2.read_positions();
x.real_value = 0.0;
if (b_no_PBC) {
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++) {
for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
cvm::rvector const dv = ai2->pos - ai1->pos;
cvm::real const d2 = dv.norm2();
x.real_value += 1.0/(d2*d2*d2);
cvm::rvector const dsumddv = -6.0/(d2*d2*d2*d2) * dv;
ai1->grad += -1.0 * dsumddv;
ai2->grad += dsumddv;
}
}
} else {
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++) {
for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
cvm::rvector const dv = cvm::position_distance (ai1->pos, ai2->pos);
cvm::real const d2 = dv.norm2();
x.real_value += 1.0/(d2*d2*d2);
cvm::rvector const dsumddv = -6.0/(d2*d2*d2*d2) * dv;
ai1->grad += -1.0 * dsumddv;
ai2->grad += dsumddv;
}
}
}
x.real_value = std::pow (x.real_value, -1.0/6.0);
}
cvm::real colvar::coordnum::switching_function(cvm::rvector const &r0_vec,
int const &en,
int const &ed,
cvm::atom &A1,
cvm::atom &A2)
{
cvm::rvector const diff = cvm::position_distance(A1.pos, A2.pos);
cvm::rvector const scal_diff(diff.x/r0_vec.x, diff.y/r0_vec.y, diff.z/r0_vec.z);
cvm::real const l2 = scal_diff.norm2();
// Assume en and ed are even integers, and avoid sqrt in the following
int const en2 = en/2;
int const ed2 = ed/2;
cvm::real const xn = std::pow(l2, en2);
cvm::real const xd = std::pow(l2, ed2);
cvm::real const func = (1.0-xn)/(1.0-xd);
if (calculate_gradients) {
cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) - func*ed2*(xd/l2))*(-1.0);
cvm::rvector const dl2dx((2.0/(r0_vec.x*r0_vec.x))*diff.x,
(2.0/(r0_vec.y*r0_vec.y))*diff.y,
(2.0/(r0_vec.z*r0_vec.z))*diff.z);
A1.grad += (-1.0)*dFdl2*dl2dx;
A2.grad += dFdl2*dl2dx;
}
return func;
}
void colvar::distance_pairs::calc_value()
{
x.vector1d_value.resize(group1->size() * group2->size());
if (!is_enabled(f_cvc_pbc_minimum_image)) {
size_t i1, i2;
for (i1 = 0; i1 < group1->size(); i1++) {
for (i2 = 0; i2 < group2->size(); i2++) {
cvm::rvector const dv = (*group2)[i2].pos - (*group1)[i1].pos;
cvm::real const d = dv.norm();
x.vector1d_value[i1*group2->size() + i2] = d;
(*group1)[i1].grad = -1.0 * dv.unit();
(*group2)[i2].grad = dv.unit();
}
}
} else {
size_t i1, i2;
for (i1 = 0; i1 < group1->size(); i1++) {
for (i2 = 0; i2 < group2->size(); i2++) {
cvm::rvector const dv = cvm::position_distance((*group1)[i1].pos,
(*group2)[i2].pos);
cvm::real const d = dv.norm();
x.vector1d_value[i1*group2->size() + i2] = d;
(*group1)[i1].grad = -1.0 * dv.unit();
(*group2)[i2].grad = dv.unit();
}
}
}
}
void colvar::distance_pairs::calc_value()
{
x.vector1d_value.resize(group1.size() * group2.size());
if (b_no_PBC) {
size_t i1, i2;
for (i1 = 0; i1 < group1.size(); i1++) {
for (i2 = 0; i2 < group2.size(); i2++) {
cvm::rvector const dv = group2[i2].pos - group1[i1].pos;
cvm::real const d = dv.norm();
x.vector1d_value[i1*group2.size() + i2] = d;
group1[i1].grad = -1.0 * dv.unit();
group2[i2].grad = dv.unit();
}
}
} else {
size_t i1, i2;
for (i1 = 0; i1 < group1.size(); i1++) {
for (i2 = 0; i2 < group2.size(); i2++) {
cvm::rvector const dv = cvm::position_distance(group1[i1].pos, group2[i2].pos);
cvm::real const d = dv.norm();
x.vector1d_value[i1*group2.size() + i2] = d;
group1[i1].grad = -1.0 * dv.unit();
group2[i2].grad = dv.unit();
}
}
}
}
void colvar::distance_inv::calc_value()
{
x.real_value = 0.0;
if (!is_enabled(f_cvc_pbc_minimum_image)) {
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++) {
for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
cvm::rvector const dv = ai2->pos - ai1->pos;
cvm::real const d2 = dv.norm2();
cvm::real dinv = 1.0;
for (int ne = 0; ne < exponent/2; ne++)
dinv *= 1.0/d2;
x.real_value += dinv;
cvm::rvector const dsumddv = -(cvm::real(exponent)) * dinv/d2 * dv;
ai1->grad += -1.0 * dsumddv;
ai2->grad += dsumddv;
}
}
} else {
for (cvm::atom_iter ai1 = group1->begin(); ai1 != group1->end(); ai1++) {
for (cvm::atom_iter ai2 = group2->begin(); ai2 != group2->end(); ai2++) {
cvm::rvector const dv = cvm::position_distance(ai1->pos, ai2->pos);
cvm::real const d2 = dv.norm2();
cvm::real dinv = 1.0;
for (int ne = 0; ne < exponent/2; ne++)
dinv *= 1.0/d2;
x.real_value += dinv;
cvm::rvector const dsumddv = -(cvm::real(exponent)) * dinv/d2 * dv;
ai1->grad += -1.0 * dsumddv;
ai2->grad += dsumddv;
}
}
}
x.real_value *= 1.0 / cvm::real(group1->size() * group2->size());
x.real_value = std::pow(x.real_value, -1.0/(cvm::real(exponent)));
}
void colvar::distance_pairs::apply_force(colvarvalue const &force)
{
if (b_no_PBC) {
size_t i1, i2;
for (i1 = 0; i1 < group1->size(); i1++) {
for (i2 = 0; i2 < group2->size(); i2++) {
cvm::rvector const dv = (*group2)[i2].pos - (*group1)[i1].pos;
(*group1)[i1].apply_force(force[i1*group2->size() + i2] * (-1.0) * dv.unit());
(*group2)[i2].apply_force(force[i1*group2->size() + i2] * dv.unit());
}
}
} else {
size_t i1, i2;
for (i1 = 0; i1 < group1->size(); i1++) {
for (i2 = 0; i2 < group2->size(); i2++) {
cvm::rvector const dv = cvm::position_distance((*group1)[i1].pos, (*group2)[i2].pos);
(*group1)[i1].apply_force(force[i1*group2->size() + i2] * (-1.0) * dv.unit());
(*group2)[i2].apply_force(force[i1*group2->size() + i2] * dv.unit());
}
}
}
}