def get_e_torsions(mol):
mol.e_torsions = 0.0
for p in range(mol.n_torsions):
tor = mol.torsions[p]
c1 = mol.atoms[tor.at1].coords
c2 = mol.atoms[tor.at2].coords
c3 = mol.atoms[tor.at3].coords
c4 = mol.atoms[tor.at4].coords
tor.t_ijkl = geomcalc.get_t_ijkl(c1, c2, c3, c4)
tor.e = get_e_torsion(tor.t_ijkl, tor.v_n, tor.gam, tor.n, tor.paths)
mol.e_torsions += tor.e
def get_e_torsions(mol):
mol.e_torsions = 0.0
for p in range(mol.n_torsions):
tor = mol.torsions[p]
c1 = mol.atoms[tor.at1].coords
c2 = mol.atoms[tor.at2].coords
c3 = mol.atoms[tor.at3].coords
c4 = mol.atoms[tor.at4].coords
tor.t_ijkl = geomcalc.get_t_ijkl(c1, c2, c3, c4)
tor.e = get_e_torsion(tor.t_ijkl, tor.v_n, tor.gam, tor.n, tor.paths)
mol.e_torsions += tor.e
def get_g_torsions(mol):
mol.g_torsions = np.zeros((mol.n_atoms, 3))
for p in range(mol.n_torsions):
tor = mol.torsions[p]
c1 = mol.atoms[tor.at1].coords
c2 = mol.atoms[tor.at2].coords
c3 = mol.atoms[tor.at3].coords
c4 = mol.atoms[tor.at4].coords
tor.t_ijkl = geomcalc.get_t_ijkl(c1, c2, c3, c4)
tor.g = get_g_torsion(tor.t_ijkl, tor.v_n, tor.gam, tor.n, tor.paths)
dir1, dir2, dir3, dir4 = get_gdir_torsion(c1, c2, c3, c4)
mol.g_torsions[tor.at1] += tor.g * dir1
mol.g_torsions[tor.at2] += tor.g * dir2
mol.g_torsions[tor.at3] += tor.g * dir3
mol.g_torsions[tor.at4] += tor.g * dir4
def get_g_torsions(mol):
mol.g_torsions = np.zeros((mol.n_atoms, 3))
for p in range(mol.n_torsions):
tor = mol.torsions[p]
c1 = mol.atoms[tor.at1].coords
c2 = mol.atoms[tor.at2].coords
c3 = mol.atoms[tor.at3].coords
c4 = mol.atoms[tor.at4].coords
tor.t_ijkl = geomcalc.get_t_ijkl(c1, c2, c3, c4)
tor.g = get_g_torsion(tor.t_ijkl, tor.v_n, tor.gam, tor.n, tor.paths)
dir1, dir2, dir3, dir4 = get_gdir_torsion(c1, c2, c3, c4)
mol.g_torsions[tor.at1] += tor.g * dir1
mol.g_torsions[tor.at2] += tor.g * dir2
mol.g_torsions[tor.at3] += tor.g * dir3
mol.g_torsions[tor.at4] += tor.g * dir4
def get_torsions(mol):
for j in range(mol.n_atoms):
n_jbonds = len(mol.bond_tree[j])
for a in range(n_jbonds):
k = mol.bond_tree[j][a]
if (k < j): continue
n_kbonds = len(mol.bond_tree[k])
for b in range(n_jbonds):
i = mol.bond_tree[j][b]
if (i == k): continue
for c in range(n_kbonds):
l = mol.bond_tree[k][c]
if (l == j or l == i): continue
t_ijkl = geomcalc.get_t_ijkl(mol.atoms[i].coords, mol.atoms[j].coords, mol.atoms[k].coords, mol.atoms[l].coords)
v_n, gamma, nfold, paths = param.get_torsion_param(mol.atoms[i].attype, mol.atoms[j].attype, mol.atoms[k].attype, mol.atoms[l].attype)
if (v_n > 0.0):
mol.torsions.append(molecule.torsion(i, j, k, l, t_ijkl, v_n, gamma, nfold, paths))
mol.n_torsions = len(mol.torsions)