C++ (Cpp) efp_compute Examples

Example #1

File: energy.c Project: psi4/libefp

/* 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);
}

Example #2

File: energy.c Project: SahanGH/psi4public

/* 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);
}