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()); } } } }