forked from lijiext/lammps
360 lines
10 KiB
C++
360 lines
10 KiB
C++
#include <cmath>
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#include "colvarmodule.h"
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#include "colvarparse.h"
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#include "colvaratoms.h"
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#include "colvarvalue.h"
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#include "colvar.h"
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#include "colvarcomp.h"
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template<bool calculate_gradients>
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cvm::real colvar::coordnum::switching_function (cvm::real const &r0,
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int const &en,
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int const &ed,
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cvm::atom &A1,
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cvm::atom &A2)
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{
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cvm::rvector const diff = cvm::position_distance (A1.pos, A2.pos);
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cvm::real const l2 = diff.norm2()/(r0*r0);
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// Assume en and ed are even integers, and avoid sqrt in the following
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int const en2 = en/2;
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int const ed2 = ed/2;
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cvm::real const xn = std::pow (l2, en2);
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cvm::real const xd = std::pow (l2, ed2);
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cvm::real const func = (1.0-xn)/(1.0-xd);
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if (calculate_gradients) {
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cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) - func*ed2*(xd/l2))*(-1.0);
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cvm::rvector const dl2dx = (2.0/(r0*r0))*diff;
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A1.grad += (-1.0)*dFdl2*dl2dx;
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A2.grad += dFdl2*dl2dx;
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}
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return func;
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}
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template<bool calculate_gradients>
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cvm::real colvar::coordnum::switching_function (cvm::rvector const &r0_vec,
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int const &en,
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int const &ed,
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cvm::atom &A1,
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cvm::atom &A2)
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{
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cvm::rvector const diff = cvm::position_distance (A1.pos, A2.pos);
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cvm::rvector const scal_diff (diff.x/r0_vec.x, diff.y/r0_vec.y, diff.z/r0_vec.z);
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cvm::real const l2 = scal_diff.norm2();
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// Assume en and ed are even integers, and avoid sqrt in the following
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int const en2 = en/2;
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int const ed2 = ed/2;
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cvm::real const xn = std::pow (l2, en2);
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cvm::real const xd = std::pow (l2, ed2);
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cvm::real const func = (1.0-xn)/(1.0-xd);
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if (calculate_gradients) {
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cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) - func*ed2*(xd/l2))*(-1.0);
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cvm::rvector const dl2dx ((2.0/(r0_vec.x*r0_vec.x))*diff.x,
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(2.0/(r0_vec.y*r0_vec.y))*diff.y,
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(2.0/(r0_vec.z*r0_vec.z))*diff.z);
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A1.grad += (-1.0)*dFdl2*dl2dx;
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A2.grad += dFdl2*dl2dx;
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}
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return func;
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}
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colvar::coordnum::coordnum (std::string const &conf)
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: distance (conf), b_anisotropic (false), b_group2_center_only (false)
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{
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function_type = "coordnum";
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x.type (colvarvalue::type_scalar);
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// group1 and group2 are already initialized by distance()
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if (group1.b_dummy)
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cvm::fatal_error ("Error: only group2 is allowed to be a dummy atom\n");
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// need to specify this explicitly because the distance() constructor
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// has set it to true
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b_inverse_gradients = false;
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bool const b_scale = get_keyval (conf, "cutoff", r0,
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cvm::real (4.0 * cvm::unit_angstrom()));
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if (get_keyval (conf, "cutoff3", r0_vec,
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cvm::rvector (4.0, 4.0, 4.0), parse_silent)) {
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if (b_scale)
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cvm::fatal_error ("Error: cannot specify \"scale\" and "
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"\"scale3\" at the same time.\n");
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b_anisotropic = true;
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// remove meaningless negative signs
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if (r0_vec.x < 0.0) r0_vec.x *= -1.0;
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if (r0_vec.y < 0.0) r0_vec.y *= -1.0;
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if (r0_vec.z < 0.0) r0_vec.z *= -1.0;
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}
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get_keyval (conf, "expNumer", en, int (6) );
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get_keyval (conf, "expDenom", ed, int (12));
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if ( (en%2) || (ed%2) ) {
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cvm::fatal_error ("Error: odd exponents provided, can only use even ones.\n");
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}
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get_keyval (conf, "group2CenterOnly", b_group2_center_only, group2.b_dummy);
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}
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colvar::coordnum::coordnum()
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: b_anisotropic (false), b_group2_center_only (false)
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{
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function_type = "coordnum";
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x.type (colvarvalue::type_scalar);
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}
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void colvar::coordnum::calc_value()
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{
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x.real_value = 0.0;
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if (b_group2_center_only) {
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// create a fake atom to hold the group2 com coordinates
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cvm::atom group2_com_atom;
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group2_com_atom.pos = group2.center_of_mass();
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if (b_anisotropic) {
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for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
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x.real_value += switching_function<false> (r0_vec, en, ed, *ai1, group2_com_atom);
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} else {
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for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
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x.real_value += switching_function<false> (r0, en, ed, *ai1, group2_com_atom);
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}
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} else {
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if (b_anisotropic) {
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for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
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for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
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x.real_value += switching_function<false> (r0_vec, en, ed, *ai1, *ai2);
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}
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} else {
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for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
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for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
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x.real_value += switching_function<false> (r0, en, ed, *ai1, *ai2);
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}
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}
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}
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}
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void colvar::coordnum::calc_gradients()
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{
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if (b_group2_center_only) {
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// create a fake atom to hold the group2 com coordinates
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cvm::atom group2_com_atom;
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group2_com_atom.pos = group2.center_of_mass();
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if (b_anisotropic) {
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for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
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switching_function<true> (r0_vec, en, ed, *ai1, group2_com_atom);
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} else {
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for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
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switching_function<true> (r0, en, ed, *ai1, group2_com_atom);
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}
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group2.set_weighted_gradient (group2_com_atom.grad);
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} else {
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if (b_anisotropic) {
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for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
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for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
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switching_function<true> (r0_vec, en, ed, *ai1, *ai2);
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}
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} else {
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for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
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for (cvm::atom_iter ai2 = group2.begin(); ai2 != group2.end(); ai2++) {
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switching_function<true> (r0, en, ed, *ai1, *ai2);
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}
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}
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}
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// if (cvm::debug()) {
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// for (size_t i = 0; i < group1.size(); i++) {
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// cvm::log ("atom["+cvm::to_str (group1[i].id+1)+"] gradient: "+
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// cvm::to_str (group1[i].grad)+"\n");
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// }
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// for (size_t i = 0; i < group2.size(); i++) {
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// cvm::log ("atom["+cvm::to_str (group2[i].id+1)+"] gradient: "+
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// cvm::to_str (group2[i].grad)+"\n");
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// }
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// }
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}
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void colvar::coordnum::apply_force (colvarvalue const &force)
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{
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if (!group1.noforce)
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group1.apply_colvar_force (force.real_value);
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if (!group2.noforce)
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group2.apply_colvar_force (force.real_value);
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}
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// h_bond member functions
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colvar::h_bond::h_bond (std::string const &conf)
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: cvc (conf)
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{
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if (cvm::debug())
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cvm::log ("Initializing h_bond object.\n");
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function_type = "h_bond";
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x.type (colvarvalue::type_scalar);
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int a_num, d_num;
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get_keyval (conf, "acceptor", a_num, -1);
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get_keyval (conf, "donor", d_num, -1);
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if ( (a_num == -1) || (d_num == -1) ) {
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cvm::fatal_error ("Error: either acceptor or donor undefined.\n");
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}
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acceptor = cvm::atom (a_num);
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donor = cvm::atom (d_num);
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atom_groups.push_back (new cvm::atom_group);
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atom_groups[0]->add_atom (acceptor);
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atom_groups[0]->add_atom (donor);
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get_keyval (conf, "cutoff", r0, (3.3 * cvm::unit_angstrom()));
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get_keyval (conf, "expNumer", en, 6);
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get_keyval (conf, "expDenom", ed, 8);
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if ( (en%2) || (ed%2) ) {
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cvm::fatal_error ("Error: odd exponents provided, can only use even ones.\n");
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}
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if (cvm::debug())
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cvm::log ("Done initializing h_bond object.\n");
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}
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colvar::h_bond::h_bond (cvm::atom const &acceptor_i,
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cvm::atom const &donor_i,
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cvm::real r0_i, int en_i, int ed_i)
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: acceptor (acceptor_i),
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donor (donor_i),
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r0 (r0_i), en (en_i), ed (ed_i)
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{
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function_type = "h_bond";
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x.type (colvarvalue::type_scalar);
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atom_groups.push_back (new cvm::atom_group);
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atom_groups[0]->add_atom (acceptor);
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atom_groups[0]->add_atom (donor);
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}
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colvar::h_bond::h_bond()
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: cvc ()
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{
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function_type = "h_bond";
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x.type (colvarvalue::type_scalar);
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}
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colvar::h_bond::~h_bond()
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{
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for (int i=0; i<atom_groups.size(); i++) {
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delete atom_groups[i];
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}
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}
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void colvar::h_bond::calc_value()
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{
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x.real_value = colvar::coordnum::switching_function<false> (r0, en, ed, acceptor, donor);
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}
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void colvar::h_bond::calc_gradients()
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{
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colvar::coordnum::switching_function<true> (r0, en, ed, acceptor, donor);
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(*atom_groups[0])[0].grad = acceptor.grad;
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(*atom_groups[0])[1].grad = donor.grad;
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}
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void colvar::h_bond::apply_force (colvarvalue const &force)
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{
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acceptor.apply_force (force.real_value * acceptor.grad);
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donor.apply_force (force.real_value * donor.grad);
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}
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colvar::selfcoordnum::selfcoordnum (std::string const &conf)
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: distance (conf, false)
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{
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function_type = "selfcoordnum";
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x.type (colvarvalue::type_scalar);
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// group1 is already initialized by distance()
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// need to specify this explicitly because the distance() constructor
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// has set it to true
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b_inverse_gradients = false;
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get_keyval (conf, "cutoff", r0, cvm::real (4.0 * cvm::unit_angstrom()));
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get_keyval (conf, "expNumer", en, int (6) );
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get_keyval (conf, "expDenom", ed, int (12));
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if ( (en%2) || (ed%2) ) {
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cvm::fatal_error ("Error: odd exponents provided, can only use even ones.\n");
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}
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}
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colvar::selfcoordnum::selfcoordnum()
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{
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function_type = "selfcoordnum";
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x.type (colvarvalue::type_scalar);
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}
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void colvar::selfcoordnum::calc_value()
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{
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x.real_value = 0.0;
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for (size_t i = 0; i < group1.size() - 1; i++)
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for (size_t j = i + 1; j < group1.size(); j++)
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x.real_value += colvar::coordnum::switching_function<false> (r0, en, ed, group1[i], group1[j]);
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}
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void colvar::selfcoordnum::calc_gradients()
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{
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for (size_t i = 0; i < group1.size() - 1; i++)
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for (size_t j = i + 1; j < group1.size(); j++)
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colvar::coordnum::switching_function<true> (r0, en, ed, group1[i], group1[j]);
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}
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void colvar::selfcoordnum::apply_force (colvarvalue const &force)
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{
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if (!group1.noforce)
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group1.apply_colvar_force (force.real_value);
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}
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