def get_gdir_torsion(coords1, coords2, coords3, coords4):
r_kl = geomcalc.get_r_ij(coords3, coords4)
r_ij = geomcalc.get_r_ij(coords1, coords2)
u_ji = geomcalc.get_u_ij(coords2, coords1)
u_jk = geomcalc.get_u_ij(coords2, coords3)
u_kj = geomcalc.get_u_ij(coords3, coords2)
u_kl = geomcalc.get_u_ij(coords3, coords4)
a_ijk = geomcalc.get_a_ijk(coords1, coords2, coords3)
a_lkj = geomcalc.get_a_ijk(coords4, coords3, coords2)
gdir1 = geomcalc.get_ucp(u_ji, u_jk)
gdir4 = geomcalc.get_ucp(u_kl, u_kj)
gdir1 /= r_ij * math.sin(geomcalc.deg2rad() * a_ijk)
gdir4 /= r_kl * math.sin(geomcalc.deg2rad() * a_lkj)
gdir2 = -0.5 * (gdir1 + gdir4)
gdir3 = 1.0 * gdir2
return gdir1, gdir2, gdir3, gdir4
def get_gdir_torsion(coords1, coords2, coords3, coords4):
r_kl = geomcalc.get_r_ij(coords3, coords4)
r_ij = geomcalc.get_r_ij(coords1, coords2)
u_ji = geomcalc.get_u_ij(coords2, coords1)
u_jk = geomcalc.get_u_ij(coords2, coords3)
u_kj = geomcalc.get_u_ij(coords3, coords2)
u_kl = geomcalc.get_u_ij(coords3, coords4)
a_ijk = geomcalc.get_a_ijk(coords1, coords2, coords3)
a_lkj = geomcalc.get_a_ijk(coords4, coords3, coords2)
gdir1 = geomcalc.get_ucp(u_ji, u_jk)
gdir4 = geomcalc.get_ucp(u_kl, u_kj)
gdir1 /= r_ij * math.sin(geomcalc.deg2rad() * a_ijk)
gdir4 /= r_kl * math.sin(geomcalc.deg2rad() * a_lkj)
gdir2 = -0.5 * (gdir1 + gdir4)
gdir3 = 1.0 * gdir2
return gdir1, gdir2, gdir3, gdir4
def get_e_angles(mol):
mol.e_angles = 0.0
for p in range(mol.n_angles):
ang = mol.angles[p]
c1 = mol.atoms[ang.at1].coords
c2 = mol.atoms[ang.at2].coords
c3 = mol.atoms[ang.at3].coords
ang.a_ijk = geomcalc.get_a_ijk(c1, c2, c3)
ang.e = get_e_angle(ang.a_ijk, ang.a_eq, ang.k_a)
mol.e_angles += ang.e
def get_e_angles(mol):
mol.e_angles = 0.0
for p in range(mol.n_angles):
ang = mol.angles[p]
c1 = mol.atoms[ang.at1].coords
c2 = mol.atoms[ang.at2].coords
c3 = mol.atoms[ang.at3].coords
ang.a_ijk = geomcalc.get_a_ijk(c1, c2, c3)
ang.e = get_e_angle(ang.a_ijk, ang.a_eq, ang.k_a)
mol.e_angles += ang.e
def get_angles(mol):
for j in range(mol.n_atoms):
n_jbonds = len(mol.bond_tree[j])
for a in range(n_jbonds):
i = mol.bond_tree[j][a]
for b in range(a+1, n_jbonds):
k = mol.bond_tree[j][b]
a_ijk = geomcalc.get_a_ijk(mol.atoms[i].coords, mol.atoms[j].coords, mol.atoms[k].coords)
k_a, a_eq = param.get_angle_param(mol.atoms[i].attype, mol.atoms[j].attype, mol.atoms[k].attype)
if (k_a > 0.0):
mol.angles.append(molecule.angle(i, j, k, a_ijk, a_eq, k_a))
mol.n_angles = len(mol.angles)
def get_g_angles(mol):
mol.g_angles = np.zeros((mol.n_atoms, 3))
for p in range(mol.n_angles):
ang = mol.angles[p]
c1 = mol.atoms[ang.at1].coords
c2 = mol.atoms[ang.at2].coords
c3 = mol.atoms[ang.at3].coords
ang.a_ijk = geomcalc.get_a_ijk(c1, c2, c3)
ang.g = get_g_angle(ang.a_ijk, ang.a_eq, ang.k_a)
dir1, dir2, dir3 = get_gdir_angle(c1, c2, c3)
mol.g_angles[ang.at1] += ang.g * dir1
mol.g_angles[ang.at2] += ang.g * dir2
mol.g_angles[ang.at3] += ang.g * dir3
def get_g_angles(mol):
mol.g_angles = np.zeros((mol.n_atoms, 3))
for p in range(mol.n_angles):
ang = mol.angles[p]
c1 = mol.atoms[ang.at1].coords
c2 = mol.atoms[ang.at2].coords
c3 = mol.atoms[ang.at3].coords
ang.a_ijk = geomcalc.get_a_ijk(c1, c2, c3)
ang.g = get_g_angle(ang.a_ijk, ang.a_eq, ang.k_a)
dir1, dir2, dir3 = get_gdir_angle(c1, c2, c3)
mol.g_angles[ang.at1] += ang.g * dir1
mol.g_angles[ang.at2] += ang.g * dir2
mol.g_angles[ang.at3] += ang.g * dir3