def get_e_outofplanes(mol):
mol.e_outofplanes = 0.0
for p in range(mol.n_outofplanes):
oop = mol.outofplanes[p]
c1 = mol.atoms[oop.at1].coords
c2 = mol.atoms[oop.at2].coords
c3 = mol.atoms[oop.at3].coords
c4 = mol.atoms[oop.at4].coords
oop.o_ijkl = geomcalc.get_o_ijkl(c1, c2, c3, c4)
oop.e = get_e_outofplane(oop.o_ijkl, oop.v_n, oop.gam, oop.n)
mol.e_outofplanes += oop.e
def get_e_outofplanes(mol):
mol.e_outofplanes = 0.0
for p in range(mol.n_outofplanes):
oop = mol.outofplanes[p]
c1 = mol.atoms[oop.at1].coords
c2 = mol.atoms[oop.at2].coords
c3 = mol.atoms[oop.at3].coords
c4 = mol.atoms[oop.at4].coords
oop.o_ijkl = geomcalc.get_o_ijkl(c1, c2, c3, c4)
oop.e = get_e_outofplane(oop.o_ijkl, oop.v_n, oop.gam, oop.n)
mol.e_outofplanes += oop.e
def get_g_outofplanes(mol):
mol.g_outofplanes = np.zeros((mol.n_atoms, 3))
for p in range(mol.n_outofplanes):
oop = mol.outofplanes[p]
c1 = mol.atoms[oop.at1].coords
c2 = mol.atoms[oop.at2].coords
c3 = mol.atoms[oop.at3].coords
c4 = mol.atoms[oop.at4].coords
oop.o_ijkl = geomcalc.get_o_ijkl(c1, c2, c3, c4)
tor.g = get_g_outofplane(oop.o_ijkl, oop.v_n, oop.gam, oop.n)
dir1, dir2, dir3, dir4 = get_gdir_torsion(c1, c2, c3, c4)
mol.g_torsions[oop.at1] += oop.g * dir1
mol.g_torsions[oop.at2] += oop.g * dir2
mol.g_torsions[oop.at3] += oop.g * dir3
mol.g_torsions[oop.at4] += oop.g * dir4
def get_g_outofplanes(mol):
mol.g_outofplanes = np.zeros((mol.n_atoms, 3))
for p in range(mol.n_outofplanes):
oop = mol.outofplanes[p]
c1 = mol.atoms[oop.at1].coords
c2 = mol.atoms[oop.at2].coords
c3 = mol.atoms[oop.at3].coords
c4 = mol.atoms[oop.at4].coords
oop.o_ijkl = geomcalc.get_o_ijkl(c1, c2, c3, c4)
tor.g = get_g_outofplane(oop.o_ijkl, oop.v_n, oop.gam, oop.n)
dir1, dir2, dir3, dir4 = get_gdir_torsion(c1, c2, c3, c4)
mol.g_torsions[oop.at1] += oop.g * dir1
mol.g_torsions[oop.at2] += oop.g * dir2
mol.g_torsions[oop.at3] += oop.g * dir3
mol.g_torsions[oop.at4] += oop.g * dir4
def get_outofplanes(mol):
for l in range(mol.n_atoms):
n_lbonds = len(mol.bond_tree[l])
for a in range(n_lbonds):
i = mol.bond_tree[l][a]
for b in range(n_lbonds):
j = mol.bond_tree[l][b]
if (i == j): continue
for c in range(b+1, n_lbonds):
k = mol.bond_tree[l][c]
if (i == k): continue
o_ijkl = geomcalc.get_o_ijkl(mol.atoms[i].coords, mol.atoms[j].coords, mol.atoms[k].coords, mol.atoms[l].coords)
v_n, gamma, nfold = param.get_outofplane_param(mol.atoms[i].coords, mol.atoms[j].coords, mol.atoms[k].coords, mol.atoms[l].coords)
if (v_n > 0.0):
mol.outofplanes.append(molecule.outofplane(i, j, k, l, o_ijkl, v_n, gamma, nfold))
mol.n_outofplanes = len(mol.outofplanes)