def set_bonds(bonds, atoms, bond_graph):
for bond in bonds:
coords_1 = atoms[bond.at_1].coords
coords_2 = atoms[bond.at_2].coords
bond.set_rij(geometry.get_r_ij(coords_1, coords_2))
bond_graph[bond.at_1][bond.at_2] = bond_graph[bond.at_2][
bond.at_1] = bond.r_ij
def get_all_g_nonbonded(g_vdw, g_elst, atoms, nonints, dielectric, atom_tree,
cutoff):
g_vdw.fill(0.0)
g_elst.fill(0.0)
vdw_cutoff = cutoff[0]
elst_cutoff = cutoff[1]
search_rad = max(6.8 * vdw_cutoff, elst_cutoff)
dont_truncate = cutoff == (0.0, 0.0)
pivot = -1
for i, j in itertools.combinations(range(len(atoms)), 2):
if (i, j) in nonints:
continue
at_1, at_2 = atoms[i], atoms[j]
eps = at_1.at_sreps * at_2.at_sreps
ro = at_1.at_ro + at_2.at_ro
if dont_truncate:
r_ij = geometry.get_r_ij(at_1.coords, at_2.coords)
gdir_1, gdir_2 = get_g_dir_bond(at_1.coords, at_2.coords, r_ij)
grad_elst_mag = get_g_mag_elst(r_ij, at_1.at_charge,
at_2.at_charge, dielectric)
g_elst[i] += grad_elst_mag * gdir_1
g_elst[j] += grad_elst_mag * gdir_2
grad_vdw_mag = get_g_mag_vdw(r_ij, eps, ro)
g_vdw[i] += grad_vdw_mag * gdir_1
g_vdw[j] += grad_vdw_mag * gdir_2
else:
if not i == pivot:
pivot = i
nn_pivot = atom_tree.query_radius(at_1.coords.reshape(1, -1),
r=search_rad,
return_distance=True)
nn_idx = nn_pivot[0][0].tolist()
nn_dist = nn_pivot[1][0]
if j in nn_idx:
r_ij = nn_dist[nn_idx.index(j)]
gdir_1, gdir_2 = get_g_dir_bond(at_1.coords, at_2.coords, r_ij)
if r_ij <= elst_cutoff:
grad_elst_mag = get_g_mag_elst(r_ij,
at_1.at_charge,
at_2.at_charge,
dielectric,
cutoff=elst_cutoff)
g_elst[i] += grad_elst_mag * gdir_1
g_elst[j] += grad_elst_mag * gdir_2
if r_ij <= vdw_cutoff * ro:
grad_vdw_mag = get_g_mag_vdw(r_ij,
eps,
ro,
cutoff=vdw_cutoff)
g_vdw[i] += grad_vdw_mag * gdir_1
g_vdw[j] += grad_vdw_mag * gdir_2
def get_g_dir_angle(coords_1, coords_2, coords_3, r_21=None, r_23=None):
if r_21 is None:
r_21 = geometry.get_r_ij(coords_2, coords_1)
if r_23 is None:
r_23 = geometry.get_r_ij(coords_2, coords_3)
u_21 = geometry.get_u_ij(coords_2, coords_1, r_21)
u_23 = geometry.get_u_ij(coords_2, coords_3, r_23)
ucp_2123 = np.cross(u_21, u_23)
ucp_2123 /= np.linalg.norm(ucp_2123)
gdir_1 = np.cross(u_21, ucp_2123)
gdir_1 /= np.linalg.norm(gdir_1) * r_21
gdir_3 = np.cross(ucp_2123, u_23)
gdir_3 /= np.linalg.norm(gdir_3) * r_23
gdir_2 = -1.0 * (gdir_1 + gdir_3)
return gdir_1, gdir_2, gdir_3
def get_total_e_nonbonded(atoms, nonints, dielectric, atom_tree, cutoff):
e_vdw, e_elst, e_neut = 0.0, 0.0, [0.0, 0.0]
vdw_cutoff = cutoff[0]
elst_cutoff = cutoff[1]
search_rad = max(6.8 * vdw_cutoff, elst_cutoff)
dont_truncate = cutoff == (0.0, 0.0)
pivot = -1
for i, j in itertools.combinations(range(len(atoms)), 2):
if (i, j) in nonints:
continue
at_1, at_2 = atoms[i], atoms[j]
eps = at_1.at_sreps * at_2.at_sreps
ro = at_1.at_ro + at_2.at_ro
if dont_truncate:
r_ij = geometry.get_r_ij(at_1.coords, at_2.coords)
e_elst += get_e_elst(r_ij, at_1.at_charge, at_2.at_charge,
dielectric)
e_vdw += get_e_vdw(r_ij, eps, ro)
else:
if not i == pivot:
pivot = i
nn_pivot = atom_tree.query_radius(at_1.coords.reshape(1, -1),
r=search_rad,
return_distance=True)
nn_idx = nn_pivot[0][0].tolist()
nn_dist = nn_pivot[1][0]
if j in nn_idx:
r_ij = nn_dist[nn_idx.index(j)]
if r_ij <= elst_cutoff:
d_e_elst = get_e_elst(r_ij,
at_1.at_charge,
at_2.at_charge,
dielectric,
cutoff=elst_cutoff,
return_neut=False)
e_elst += d_e_elst
if r_ij <= vdw_cutoff * ro:
d_e_vdw = get_e_vdw(r_ij,
eps,
ro,
cutoff=vdw_cutoff,
return_neut=False)
e_vdw += d_e_vdw
return e_vdw, e_elst, e_neut
def get_g_dir_outofplane(coords_1,
coords_2,
coords_3,
coords_4,
o_ijkl,
r_31=None,
r_32=None,
r_34=None):
if r_31 is None:
r_31 = geometry.get_r_ij(coords_3, coords_1)
if r_32 is None:
r_32 = geometry.get_r_ij(coords_3, coords_2)
if r_34 is None:
r_34 = geometry.get_r_ij(coords_3, coords_4)
u_31 = geometry.get_u_ij(coords_3, coords_1, r_31)
u_32 = geometry.get_u_ij(coords_3, coords_2, r_32)
u_34 = geometry.get_u_ij(coords_3, coords_4, r_34)
cp_3234 = np.cross(u_32, u_34)
cp_3431 = np.cross(u_34, u_31)
cp_3132 = np.cross(u_31, u_32)
a_132 = geometry.get_a_ijk(coords_1, coords_3, coords_2, r_31, r_34)
s_132 = np.sin(const.DEG2RAD * a_132)
c_132 = np.cos(const.DEG2RAD * a_132)
c_o_ijkl = np.cos(const.DEG2RAD * o_ijkl)
t_o_ijkl = np.tan(const.DEG2RAD * o_ijkl)
gdir_1 = ((1.0 / r_31) * (cp_3234 / (c_o_ijkl * s_132) -
(t_o_ijkl / s_132**2) * (u_31 - c_132 * u_32)))
gdir_2 = ((1.0 / r_32) * (cp_3431 / (c_o_ijkl * s_132) -
(t_o_ijkl / s_132**2) * (u_32 - c_132 * u_31)))
gdir_4 = ((1.0 / r_34) * (cp_3132 / (c_o_ijkl * s_132) -
(t_o_ijkl * u_34)))
gdir_3 = -1.0 * (gdir_1 + gdir_2 + gdir_4)
return gdir_1, gdir_2, gdir_3, gdir_4
def get_g_dir_torsion(coords_1,
coords_2,
coords_3,
coords_4,
r_12=None,
r_23=None,
r_34=None):
if r_12 is None:
r_12 = geometry.get_r_ij(coords_1, coords_2)
if r_23 is None:
r_23 = geometry.get_r_ij(coords_2, coords_3)
if r_34 is None:
r_34 = geometry.get_r_ij(coords_3, coords_4)
u_21 = geometry.get_u_ij(coords_2, coords_1, r_12)
u_34 = geometry.get_u_ij(coords_3, coords_4, r_34)
u_23 = geometry.get_u_ij(coords_2, coords_3, r_23)
u_32 = -1.0 * u_23
a_123 = geometry.get_a_ijk(coords_1, coords_2, coords_3, r_12, r_23)
a_432 = geometry.get_a_ijk(coords_4, coords_3, coords_2, r_34, r_23)
s_123 = np.sin(const.DEG2RAD * a_123)
s_432 = np.sin(const.DEG2RAD * a_432)
c_123 = np.cos(const.DEG2RAD * a_123)
c_432 = np.cos(const.DEG2RAD * a_432)
gdir_1 = np.cross(u_21, u_23)
gdir_1 /= np.linalg.norm(gdir_1) * r_12 * s_123
gdir_4 = np.cross(u_34, u_32)
gdir_4 /= np.linalg.norm(gdir_4) * r_34 * s_432
gdir_2 = (r_12 * c_123 / r_23 - 1.0) * gdir_1 - (r_34 * c_432 /
r_23) * gdir_4
gdir_3 = (r_34 * c_432 / r_23 - 1.0) * gdir_4 - (r_12 * c_123 /
r_23) * gdir_1
return gdir_1, gdir_2, gdir_3, gdir_4
def get_bond_from_prm(record, atoms):
at_1, at_2 = (i - 1 for i in map(int, record[1:3]))
k_b, r_eq = tuple(map(float, record[3:5]))
coords_1, coords_2 = (atoms[i].coords for i in (at_1, at_2))
r_ij = geometry.get_r_ij(coords_1, coords_2)
return molecule.Bond(at_1, at_2, r_ij, r_eq, k_b)