def get_gdir_angle(coords1, coords2, coords3):
r_ji = geomcalc.get_r_ij(coords2, coords1)
r_jk = geomcalc.get_r_ij(coords2, coords3)
u_ji = geomcalc.get_u_ij(coords2, coords1)
u_jk = geomcalc.get_u_ij(coords2, coords3)
cp = geomcalc.get_ucp(u_ji, u_jk)
gdir1 = geomcalc.get_ucp(u_ji, cp) / r_ji
gdir3 = geomcalc.get_ucp(cp, u_jk) / r_jk
gdir2 = -1.0 * (gdir1 + gdir3)
return gdir1, gdir2, gdir3
def get_gdir_angle(coords1, coords2, coords3):
r_ji = geomcalc.get_r_ij(coords2, coords1)
r_jk = geomcalc.get_r_ij(coords2, coords3)
u_ji = geomcalc.get_u_ij(coords2, coords1)
u_jk = geomcalc.get_u_ij(coords2, coords3)
cp = geomcalc.get_ucp(u_ji, u_jk)
gdir1 = geomcalc.get_ucp(u_ji, cp) / r_ji
gdir3 = geomcalc.get_ucp(cp, u_jk) / r_jk
gdir2 = -1.0 * (gdir1 + gdir3)
return gdir1, gdir2, gdir3
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_gdir_inter(coords1, coords2):
gdir1 = geomcalc.get_u_ij(coords2, coords1)
gdir2 = -1.0 * gdir1
return gdir1, gdir2
def get_gdir_inter(coords1, coords2):
gdir1 = geomcalc.get_u_ij(coords2, coords1)
gdir2 = -1.0 * gdir1
return gdir1, gdir2