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_e_bonds(mol):
mol.e_bonds = 0.0
for p in range(mol.n_bonds):
bond = mol.bonds[p]
c1 = mol.atoms[bond.at1].coords
c2 = mol.atoms[bond.at2].coords
bond.r_ij = geomcalc.get_r_ij(c1, c2)
bond.e = get_e_bond(bond.r_ij, bond.r_eq, bond.k_b)
mol.e_bonds += bond.e
def get_e_bonds(mol):
mol.e_bonds = 0.0
for p in range(mol.n_bonds):
bond = mol.bonds[p]
c1 = mol.atoms[bond.at1].coords
c2 = mol.atoms[bond.at2].coords
bond.r_ij = geomcalc.get_r_ij(c1, c2)
bond.e = get_e_bond(bond.r_ij, bond.r_eq, bond.k_b)
mol.e_bonds += bond.e
def get_bonds(mol):
for i in range(mol.n_atoms):
for a in range(len(mol.bond_tree[i])):
j = mol.bond_tree[i][a]
if (i < j):
r_ij = geomcalc.get_r_ij(mol.atoms[i].coords, mol.atoms[j].coords)
k_b, r_eq = param.get_bond_param(mol.atoms[i].attype, mol.atoms[j].attype)
if (k_b > 0.0):
mol.bonds.append(molecule.bond(i, j, r_ij, r_eq, k_b))
mol.n_bonds = len(mol.bonds)
def get_g_bonds(mol):
mol.g_bonds = np.zeros((mol.n_atoms, 3))
for p in range(mol.n_bonds):
bond = mol.bonds[p]
c1 = mol.atoms[bond.at1].coords
c2 = mol.atoms[bond.at2].coords
bond.r_ij = geomcalc.get_r_ij(c1, c2)
bond.g = get_g_bond(bond.r_ij, bond.r_eq, bond.k_b)
dir1, dir2 = get_gdir_inter(c1, c2)
mol.g_bonds[bond.at1] += bond.g * dir1
mol.g_bonds[bond.at2] += bond.g * dir2
def get_g_bonds(mol):
mol.g_bonds = np.zeros((mol.n_atoms, 3))
for p in range(mol.n_bonds):
bond = mol.bonds[p]
c1 = mol.atoms[bond.at1].coords
c2 = mol.atoms[bond.at2].coords
bond.r_ij = geomcalc.get_r_ij(c1, c2)
bond.g = get_g_bond(bond.r_ij, bond.r_eq, bond.k_b)
dir1, dir2 = get_gdir_inter(c1, c2)
mol.g_bonds[bond.at1] += bond.g * dir1
mol.g_bonds[bond.at2] += bond.g * dir2
def get_e_nonbonded(mol):
mol.e_nonbonded, mol.e_vdw, mol.e_elst = 0.0, 0.0, 0.0
# van der waals and electrostatic energy
for i in range(mol.n_atoms):
atom1 = mol.atoms[i]
for j in range(i+1, mol.n_atoms):
atom2 = mol.atoms[j]
if (j in mol.nonints[i]): continue
r_ij = geomcalc.get_r_ij(atom1.coords, atom2.coords)
eps_ij = atom1.sreps * atom2.sreps
ro_ij = atom1.ro + atom2.ro
mol.e_elst += get_e_elst_ij(r_ij, atom1.charge, atom2.charge, mol.dielectric)
mol.e_vdw += get_e_vdw_ij(r_ij, eps_ij, ro_ij)
def get_e_nonbonded(mol):
mol.e_nonbonded, mol.e_vdw, mol.e_elst = 0.0, 0.0, 0.0
# van der waals and electrostatic energy
for i in range(mol.n_atoms):
atom1 = mol.atoms[i]
for j in range(i + 1, mol.n_atoms):
atom2 = mol.atoms[j]
if (j in mol.nonints[i]): continue
r_ij = geomcalc.get_r_ij(atom1.coords, atom2.coords)
eps_ij = atom1.sreps * atom2.sreps
ro_ij = atom1.ro + atom2.ro
mol.e_elst += get_e_elst_ij(r_ij, atom1.charge, atom2.charge,
mol.dielectric)
mol.e_vdw += get_e_vdw_ij(r_ij, eps_ij, ro_ij)
def get_g_nonbonded(mol):
mol.g_nonbonded = np.zeros((mol.n_atoms, 3))
mol.g_vdw = np.zeros((mol.n_atoms, 3))
mol.g_elst = np.zeros((mol.n_atoms, 3))
# van der waals and electrostatic energy
for i in range(mol.n_atoms):
atom1 = mol.atoms[i]
for j in range(i+1, mol.n_atoms):
if (j in mol.nonints[i]): continue
atom2 = mol.atoms[j]
dir1, dir2 = get_gdir_inter(atom1.coords, atom2.coords)
r_ij = geomcalc.get_r_ij(atom1.coords, atom2.coords)
eps_ij = atom1.sreps * atom2.sreps
ro_ij = atom1.ro + atom2.ro
g_elst = get_g_elst_ij(r_ij, atom1.charge, atom2.charge, mol.dielectric)
g_vdw = get_g_vdw_ij(r_ij, eps_ij, ro_ij)
mol.g_vdw[i] += g_vdw * dir1
mol.g_vdw[j] += g_vdw * dir2
mol.g_elst[i] += g_elst * dir1
mol.g_elst[j] += g_elst * dir2
def get_g_nonbonded(mol):
mol.g_nonbonded = np.zeros((mol.n_atoms, 3))
mol.g_vdw = np.zeros((mol.n_atoms, 3))
mol.g_elst = np.zeros((mol.n_atoms, 3))
# van der waals and electrostatic energy
for i in range(mol.n_atoms):
atom1 = mol.atoms[i]
for j in range(i + 1, mol.n_atoms):
if (j in mol.nonints[i]): continue
atom2 = mol.atoms[j]
dir1, dir2 = get_gdir_inter(atom1.coords, atom2.coords)
r_ij = geomcalc.get_r_ij(atom1.coords, atom2.coords)
eps_ij = atom1.sreps * atom2.sreps
ro_ij = atom1.ro + atom2.ro
g_elst = get_g_elst_ij(r_ij, atom1.charge, atom2.charge,
mol.dielectric)
g_vdw = get_g_vdw_ij(r_ij, eps_ij, ro_ij)
mol.g_vdw[i] += g_vdw * dir1
mol.g_vdw[j] += g_vdw * dir2
mol.g_elst[i] += g_elst * dir1
mol.g_elst[j] += g_elst * dir2
