/* current coordinates from efp struct are used */
void compute_energy(struct state *state, bool do_grad)
{
struct efp_atom *atoms;
struct efp_energy efp_energy;
double xyz[3], xyzabc[6], *grad;
size_t ifrag, nfrag, iatom, natom;
int itotal;
/* EFP part */
check_fail(efp_compute(state->efp, do_grad));
check_fail(efp_get_energy(state->efp, &efp_energy));
check_fail(efp_get_frag_count(state->efp, &nfrag));
if (do_grad) {
check_fail(efp_get_gradient(state->efp, state->grad));
check_fail(efp_get_point_charge_gradient(state->efp,
state->grad + 6 * nfrag));
}
state->energy = efp_energy.total;
/* constraints */
for (ifrag = 0; ifrag < nfrag; ifrag++) {
const struct frag *frag = state->sys->frags + ifrag;
check_fail(efp_get_frag_xyzabc(state->efp, ifrag, xyzabc));
if (frag->constraint_enable) {
double dr2, drx, dry, drz;
drx = xyzabc[0] - frag->constraint_xyz.x;
dry = xyzabc[1] - frag->constraint_xyz.y;
drz = xyzabc[2] - frag->constraint_xyz.z;
dr2 = drx * drx + dry * dry + drz * drz;
state->energy += 0.5 * frag->constraint_k * dr2;
if (do_grad) {
grad = state->grad + 6 * ifrag;
grad[0] += frag->constraint_k * drx;
grad[1] += frag->constraint_k * dry;
grad[2] += frag->constraint_k * drz;
}
}
}
/* MM force field part */
if (state->ff == NULL)
return;
for (ifrag = 0, itotal = 0; ifrag < nfrag; ifrag++) {
check_fail(efp_get_frag_atom_count(state->efp, ifrag, &natom));
atoms = malloc(natom * sizeof(struct efp_atom));
check_fail(efp_get_frag_atoms(state->efp, ifrag, natom, atoms));
for (iatom = 0; iatom < natom; iatom++, itotal++)
ff_set_atom_xyz(state->ff, itotal, &atoms[iatom].x);
free(atoms);
}
ff_compute(state->ff, do_grad);
if (do_grad) {
for (ifrag = 0, itotal = 0, grad = state->grad; ifrag < nfrag; ifrag++, grad += 6) {
check_fail(efp_get_frag_xyzabc(state->efp, ifrag, xyzabc));
check_fail(efp_get_frag_atom_count(state->efp, ifrag, &natom));
atoms = malloc(natom * sizeof(struct efp_atom));
check_fail(efp_get_frag_atoms(state->efp, ifrag, natom, atoms));
for (iatom = 0; iatom < natom; iatom++, itotal++) {
ff_get_atom_gradient(state->ff, itotal, xyz);
grad[0] += xyz[0];
grad[1] += xyz[1];
grad[2] += xyz[2];
grad[3] += (atoms[iatom].y - xyzabc[1]) * xyz[2] -
(atoms[iatom].z - xyzabc[2]) * xyz[1];
grad[4] += (atoms[iatom].z - xyzabc[2]) * xyz[0] -
(atoms[iatom].x - xyzabc[0]) * xyz[2];
grad[5] += (atoms[iatom].x - xyzabc[0]) * xyz[1] -
(atoms[iatom].y - xyzabc[1]) * xyz[0];
}
free(atoms);
}
}
state->energy += ff_get_energy(state->ff);
}
/* current coordinates from efp struct are used */
void compute_energy(struct state *state, bool do_grad)
{
struct efp_atom *atoms;
struct efp_energy efp_energy;
double xyz[3], xyzabc[6], *grad;
size_t ifrag, nfrag, iatom, natom;
int itotal;
check_fail(efp_compute(state->efp, do_grad));
check_fail(efp_get_energy(state->efp, &efp_energy));
check_fail(efp_get_frag_count(state->efp, &nfrag));
if (do_grad) {
check_fail(efp_get_gradient(state->efp, state->grad));
check_fail(efp_get_point_charge_gradient(state->efp, state->grad + 6 * nfrag));
}
state->energy = efp_energy.total;
if (state->ff == NULL)
return;
for (ifrag = 0, itotal = 0; ifrag < nfrag; ifrag++) {
check_fail(efp_get_frag_atom_count(state->efp, ifrag, &natom));
atoms = malloc(natom * sizeof(struct efp_atom));
check_fail(efp_get_frag_atoms(state->efp, ifrag, natom, atoms));
for (iatom = 0; iatom < natom; iatom++, itotal++)
ff_set_atom_xyz(state->ff, itotal, &atoms[iatom].x);
free(atoms);
}
ff_compute(state->ff, do_grad);
if (do_grad) {
for (ifrag = 0, itotal = 0, grad = state->grad; ifrag < nfrag; ifrag++, grad += 6) {
check_fail(efp_get_frag_xyzabc(state->efp, ifrag, xyzabc));
check_fail(efp_get_frag_atom_count(state->efp, ifrag, &natom));
atoms = malloc(natom * sizeof(struct efp_atom));
check_fail(efp_get_frag_atoms(state->efp, ifrag, natom, atoms));
for (iatom = 0; iatom < natom; iatom++, itotal++) {
ff_get_atom_gradient(state->ff, itotal, xyz);
grad[0] += xyz[0];
grad[1] += xyz[1];
grad[2] += xyz[2];
grad[3] += (atoms[iatom].y - xyzabc[1]) * xyz[2] -
(atoms[iatom].z - xyzabc[2]) * xyz[1];
grad[4] += (atoms[iatom].z - xyzabc[2]) * xyz[0] -
(atoms[iatom].x - xyzabc[0]) * xyz[2];
grad[5] += (atoms[iatom].x - xyzabc[0]) * xyz[1] -
(atoms[iatom].y - xyzabc[1]) * xyz[0];
}
free(atoms);
}
}
state->energy += ff_get_energy(state->ff);
}