def get_linear(species,visited,natom):
for j in range(natom):
if j not in visited:
if species.bond[visited[-1]][j] > 0:
if geometry.calc_angle(species.geom[visited[-2]],species.geom[visited[-1]],species.geom[j]) > np.pi * 175. / 180.:
visited.append(j)
return get_linear(species,visited,natom)
if species.bond[visited[0]][j] > 0:
if geometry.calc_angle(species.geom[visited[1]],species.geom[visited[0]],species.geom[j]) > np.pi * 175. / 180.:
visited.insert(0,j)
return get_linear(species,visited,natom)
return visited
def get_linear(species, visited, natom):
for j in range(natom):
if j not in visited:
if species.bond[visited[-1]][j] > 0:
if geometry.calc_angle(species.geom[visited[-2]],
species.geom[visited[-1]],
species.geom[j]) > np.pi * 175. / 180.:
visited.append(j)
return get_linear(species, visited, natom)
if species.bond[visited[0]][j] > 0:
if geometry.calc_angle(species.geom[visited[1]],
species.geom[visited[0]],
species.geom[j]) > np.pi * 175. / 180.:
visited.insert(0, j)
return get_linear(species, visited, natom)
return visited
def testCalcAngle(self):
"""
Test the angle calculation
"""
# calculate a random anle
np.random.seed(1)
a = np.random.uniform(size=3)
b = np.random.uniform(size=3)
c = np.random.uniform(size=3)
cal = geometry.calc_angle(a, b, c)
exp = 1.24358021797
warn = 'Angle calc faild: exp: {}, calc: {}'.format(exp, cal)
self.assertAlmostEqual(exp, cal, places=10, msg=warn)
# calculate an angle between to collinear vectors
np.random.seed(1)
a = np.random.uniform(size=3)
b = np.array([0., 0., 0.])
cal = geometry.calc_angle(a, b, a)
exp = 0.
warn = 'Angle calc faild: exp: {}, calc: {}'.format(exp, cal)
self.assertAlmostEqual(exp, cal, places=10, msg=warn)
# calculate an angle between to inverse vectors
np.random.seed(1)
a = np.random.uniform(size=3)
b = np.array([0., 0., 0.])
c = -a
cal = geometry.calc_angle(a, b, c)
exp = np.pi
warn = 'Angle calc faild: exp: {}, calc: {}'.format(exp, cal)
self.assertAlmostEqual(exp, cal, places=10, msg=warn)
# calculate an angle between to orthogonal vectors
a = np.array([1., 0., 0.])
b = np.array([0., 0., 0.])
c = np.array([0., 1., 0.])
cal = geometry.calc_angle(a, b, c)
exp = np.pi / 2
warn = 'Angle calc faild: exp: {}, calc: {}'.format(exp, cal)
self.assertAlmostEqual(exp, cal, places=10, msg=warn)
def add(j,list,zmat,zmat_atom,zmatorder,zmat_ref,atom,cart):
"""
add an atom on the jth position of the zmat according to the four atoms in the list
"""
zmat_atom[j] = atom[list[0]]
zmatorder[j] = list[0]
zmat_ref[j][0] = zmatorder.index(list[1])+1
zmat[j][0] = np.linalg.norm(cart[list[0]] - cart[list[1]])
zmat_ref[j][1] = zmatorder.index(list[2])+1
zmat[j][1] = np.degrees(geometry.calc_angle(cart[list[0]], cart[list[1]], cart[list[2]]))
zmat_ref[j][2] = zmatorder.index(list[3])+1
zmat[j][2], collin = geometry.calc_dihedral(cart[list[0]], cart[list[1]], cart[list[2]], cart[list[3]])
def add(j, list, zmat, zmat_atom, zmatorder, zmat_ref, atom, cart):
"""
add an atom on the jth position of the zmat according to the four atoms in the list
"""
zmat_atom[j] = atom[list[0]]
zmatorder[j] = list[0]
zmat_ref[j][0] = zmatorder.index(list[1]) + 1
zmat[j][0] = np.linalg.norm(cart[list[0]] - cart[list[1]])
zmat_ref[j][1] = zmatorder.index(list[2]) + 1
zmat[j][1] = np.degrees(geometry.calc_angle(cart[list[0]], cart[list[1]], cart[list[2]]))
zmat_ref[j][2] = zmatorder.index(list[3]) + 1
zmat[j][2], collin = geometry.calc_dihedral(cart[list[0]], cart[list[1]], cart[list[2]], cart[list[3]])
def find_linear(self):
self.linear = []
for ati in range(self.natom):
for atj in range(self.natom):
if self.bonds[0][ati][atj] > 0:
for atk in range(self.natom):
if self.bonds[0][atj][atk] > 0 and atk != ati:
alpha = geometry.calc_angle(
self.geom[ati], self.geom[atj], self.geom[atk])
if alpha > 175. * np.pi / 180.:
if ati < atk:
lin = [ati, atj, atk]
else:
lin = [atk, atj, ati]
if lin not in self.linear:
self.linear.append(lin)
return
def start_linear(species, natom):
"""
Get all the 'neighbors' of i which are connected to i via
one or a set of linear bonds.
This includes
* all direct bonds if they are not part of a linear system
* all sets of consecutive double bonds
* all sets of alternating triple and single bonds
Only look at indices larger than i, as the other bonds have been considered with lower
indices
"""
lin = []
for i in range(natom - 1):
for j in range(i + 1, natom):
if species.bond[i][j] > 0:
if len(get_neighbors(species, j)) == 2:
k = [ni for ni in get_neighbors(species, j) if ni != i][0]
if geometry.calc_angle(
species.geom[i], species.geom[j],
species.geom[k]) > np.pi * 175. / 180.:
new_lin = get_linear(species, [i, j, k], natom)
new = 1
for li in lin:
if all([ni in li for ni in new_lin]):
new = 0
if new:
lin.append(new_lin)
for i in range(natom - 1):
for j in range(i + 1, natom):
if species.bond[i][j] > 0:
new = 1
for li in lin:
if i in li and j in li:
new = 0
if new:
lin.append([i, j])
return lin
def start_linear(species,natom):
"""
Get all the 'neighbors' of i which are connected to i via
one or a set of linear bonds.
This includes
* all direct bonds if they are not part of a linear system
* all sets of consecutive double bonds
* all sets of alternating triple and single bonds
Only look at indices larger than i, as the other bonds have been considered with lower
indices
"""
lin = []
for i in range(natom - 1):
for j in range(i+1,natom):
if species.bond[i][j] > 0:
if len(get_neighbors(species,j)) == 2:
k = [ni for ni in get_neighbors(species,j) if ni != i][0]
if geometry.calc_angle(species.geom[i],species.geom[j],species.geom[k]) > np.pi * 175. / 180.:
new_lin = get_linear(species,[i,j,k],natom)
new = 1
for li in lin:
if all([ni in li for ni in new_lin]):
new = 0
if new:
lin.append(new_lin)
for i in range(natom - 1):
for j in range(i+1,natom):
if species.bond[i][j] > 0:
new = 1
for li in lin:
if i in li and j in li:
new = 0
if new:
lin.append([i,j])
return lin
def control_changes(species, name, geom, new_geom, changes, bond):
"""
This method controls three things:
1. the changes are all correct
2. the bonded atom pairs that are not part of the changes have the same bond length
3. the non-bonded atom pairs are far enough from each other
"""
success = 1
gs = '' # initial geomtry string
for i, at in enumerate(species.atom):
x, y, z = geom[i]
gs += '{}, {:.8f}, {:.8f}, {:.8f}, \n'.format(at, x, y, z)
cs = '' # changes list
for ci in changes:
cs += '[{}]\n'.format(', '.join([str(cij) for cij in ci]))
# check if the changes are good
for ci in changes:
if len(ci) == 3:
bond_length = np.linalg.norm(new_geom[ci[0]] - new_geom[ci[1]])
if np.abs(bond_length -
ci[2]) > 0.05: # use a 0.05 Angstrom cutoff
logging.debug("The modified bond length is not correct")
logging.debug("Expected {}, got {}".format(ci[2], bond_length))
logging.debug("Species name: " + name)
logging.debug("For the following initial geometry:\n" + gs)
logging.debug("And the following change list:\n" + cs)
success = 0
if len(ci) == 4:
angle = geometry.calc_angle(new_geom[ci[0]], new_geom[ci[1]],
new_geom[ci[2]])
change_angle = np.radians(ci[3])
if np.abs(angle -
change_angle) > 0.05: # use a 0.05 radians cutoff
logging.debug("The modified angle is not correct")
logging.debug("Expected {}, got {}".format(
change_angle, angle))
logging.debug("Species name: " + name)
logging.debug("For the following initial geometry:\n" + gs)
logging.debug("And the following change list:\n" + cs)
success = 0
# check if the bond lengths are good:
for i in range(species.natom - 1):
for j in range(i + 1, species.natom):
if bond[i][j] > 0:
is_change = 0
for ci in changes:
if i in ci and j in ci:
is_change = 1
if not is_change:
new_bond = np.linalg.norm(new_geom[i] - new_geom[j])
orig_bond = np.linalg.norm(geom[i] - geom[j])
if np.abs(new_bond -
orig_bond) > 0.1: # use a 0.1 Angstrom cutoff
logging.debug(
"The bond length {} {} is not correct after modifications"
.format(i, j))
logging.debug("Expected {}, got {}".format(
orig_bond, new_bond))
logging.debug("Species name: " + name)
logging.debug("For the following initial geometry:\n" +
gs)
logging.debug("And the following change list:\n" + cs)
success = 0
# check if non-bonded atoms are too close:
for i in range(species.natom - 1):
for j in range(i + 1, species.natom):
if bond[i][j] == 0:
dist = np.linalg.norm(new_geom[i] - new_geom[j])
min = constants.st_bond[''.join(
sorted([species.atom[i], species.atom[j]]))]
if dist < min:
logging.debug(
"The atoms {} {} are too close after modifications".
format(i, j))
logging.debug("Species name: " + name)
logging.debug("For the following initial geometry:\n" + gs)
logging.debug("And the following change list:\n" + cs)
success = 0
return success
def modify_coordinates(species, name, geom, changes, bond, write_files=0):
"""
Geom is the geometry (n x 3 matrix with n the number of atoms)
in cartesian coordinates
Changes is a list of lists, each list containing the coordinates
and their new value (atom indices start at 0):
To change a bond length: [atom1, atom2, bond_length]
To change a bond angle: [neighbor1, central_atom, neighbor2,
angle_in_degrees]
To change a dihedral angle: [atom1, atom2, atom3, atom4,
dihedarl_angle_in_degrees]
Bond is the bond matrix of the molecule
"""
start_time = time.time()
logging.debug('Starting coordinate modification for {}'.format(name))
logging.debug('Changes:')
for c in changes:
logging.debug('\t{}'.format('\t'.join([str(ci) for ci in c])))
step = 1
atoms_list = []
count = 0
fname = '{}_{}.xyz'.format(name, count)
while os.path.exists(fname):
count += 1
fname = '{}_{}.xyz'.format(name, count)
f_out = None
if write_files:
f_out = open(fname, 'w')
new_geom = copy.deepcopy(geom)
step = append_geom(species.natom,
step,
0.,
species.atom,
new_geom,
np.zeros((species.natom * 3)),
atoms_list,
f_out=f_out)
# change dihedrals, if necessary
for ci in changes:
if len(ci) == 5:
zmat_atom, zmat_ref, zmat, zmatorder = zmatrix.make_zmat_from_cart(
species, ci[:-1], new_geom, 2)
# write_zmat(zmat_atom, zmat_ref, zmat, new_geom, species.atom)
orig_dih = zmat[3][2]
new_dih = ci[-1]
dih_diff = new_dih - orig_dih
zmat[3][2] += dih_diff
for i in range(4, species.natom):
if zmat_ref[i][2] == 4:
zmat[i][2] += dih_diff
if zmat_ref[i][2] == 1:
zmat[i][2] += dih_diff
new_geom = zmatrix.make_cart_from_zmat(zmat, zmat_atom, zmat_ref,
species.natom, species.atom,
zmatorder)
# write_zmat(zmat_atom, zmat_ref, zmat, new_geom, species.atom)
step = append_geom(species.natom,
step,
0.,
species.atom,
new_geom,
np.zeros((species.natom * 3)),
atoms_list,
f_out=f_out)
# change angles, if necessary
if len(ci) == 4:
# original angle in radians
orig_angle = geometry.calc_angle(new_geom[ci[0]], new_geom[ci[1]],
new_geom[ci[2]])
new_angle = np.radians(ci[-1]) # new angle in radians
v1 = new_geom[ci[0]] - new_geom[ci[1]]
v2 = new_geom[ci[2]] - new_geom[ci[1]]
rot_ax = [0., 0., 0.]
# create a vector perpendicular to v1 and v2
# verify if points are collinear
if np.linalg.norm(np.cross(v1, v2)) == 0:
# rotate around any axis perpendicular to the axis along the three points:
if v1[0] != 0 or v1[1] != 0:
rot_ax = [v1[1], -v1[0], 0.]
elif v1[0] != 0 or v1[2] != 0:
rot_ax = [v1[2], 0., -v1[0]]
else:
rot_ax = [1., 0., 0.]
else:
rot_ax = np.cross(v1, v2)
rot_ax = rot_ax / np.linalg.norm(rot_ax)
# rotate all the atoms on the side of the last atom
st, ats, ats2 = divide_atoms(ci[2], ci[1], bond, species.natom,
species.atom)
if not st:
break
for atj in ats:
new_geom[atj] = perform_rotation(new_geom[atj],
new_geom[ci[1]], rot_ax,
new_angle - orig_angle)
step = append_geom(species.natom,
step,
1.,
species.atom,
new_geom,
np.zeros((species.natom * 3)),
atoms_list,
f_out=f_out)
coords = get_coords(species, bond, new_geom, changes, 0)
# optimize the geometry to meet the coords list
x0 = np.reshape(new_geom, 3 * species.natom)
cost_fct = cost_function(coords)
logging.debug('Starting BFGS')
gs = '' # initial geomtry string
for i, at in enumerate(species.atom):
x, y, z = new_geom[i]
gs += '{}, {:.8f}, {:.8f}, {:.8f}, \n'.format(at, x, y, z)
logging.debug("For the following initial geometry:\n" + gs)
opt = bfgs.BFGS()
x_opt, x_i, g_i = opt.optimize(cost_fct, x0)
new_geom = np.reshape(x_opt, (species.natom, 3))
for i, xi in enumerate(x_i):
geomi = np.reshape(xi, (species.natom, 3))
gradi = np.reshape(g_i[i], (species.natom, 3))
step = append_geom(species.natom,
step,
2.,
species.atom,
geomi,
gradi,
atoms_list,
f_out=f_out)
if write_files:
write(fname.replace('.xyz', '.traj'), atoms_list)
f_out.close()
success = control_changes(species, name, geom, new_geom, changes, bond)
end_time = time.time()
logging.debug(
'Finished coordinate changes after {:.2f} seconds'.format(end_time -
start_time))
return success, new_geom
def make_zmat_from_cart(species, rotor, cart, mode):
"""
Rearrange geometry defined in Cartesian into a Z-matrix,
with references suitable for a 1-D shindered rotor scan.
If mode = 0: all rotatable bonds
If mode = 1: only those bonds, which generate conformers
If mode = 2: suply your one rotor in rotor as a list of atom indices
"""
natom = species.natom
atom = species.atom
if mode == 0:
a = species.dihed[rotor][0]
b = species.dihed[rotor][1]
c = species.dihed[rotor][2]
d = species.dihed[rotor][3]
elif mode == 1:
a = species.conf_dihed[rotor][0]
b = species.conf_dihed[rotor][1]
c = species.conf_dihed[rotor][2]
d = species.conf_dihed[rotor][3]
elif mode == 2:
a = rotor[0]
b = rotor[1]
c = rotor[2]
d = rotor[3]
groupA = np.zeros(natom, dtype=int)
groupB = np.zeros(natom, dtype=int)
groupC = np.zeros(natom, dtype=int)
groupD = np.zeros(natom, dtype=int)
groupA[a] = 1
groupB[b] = 1
groupC[c] = 1
groupD[d] = 1
#get all immediate neighbors of a A, B, C, and D
for i in range(natom):
if species.bond[a][i] > 0 and i != b:
groupA[i] = 1
elif species.bond[b][i] > 0 and i != a and i != c:
groupB[i] = 1
elif species.bond[c][i] > 0 and i != b and i != d:
groupC[i] = 1
elif species.bond[d][i] > 0 and i != c:
groupD[i] = 1
found = 1
while found > 0:
found = 0
for i in range(natom):
if groupA[i] == 1:
for j in range(natom):
if species.bond[i][j] > 0 and j != b and groupA[j] != 1:
groupA[j] = 1
found = 1
elif groupB[i] == 1:
for j in range(natom):
if species.bond[i][j] > 0 and j != a and j != c and groupB[j] != 1:
groupB[j] = 1
found = 1
elif groupC[i] == 1:
for j in range(natom):
if species.bond[i][j] > 0 and j != b and j != d and groupC[j] != 1:
groupC[j] = 1
found = 1
elif groupD[i] == 1:
for j in range(natom):
if species.bond[i][j] > 0 and j != c and groupD[j] != 1:
groupD[j] = 1
found = 1
zmat_atom = ['X' for i in range(natom)]
zmat_ref = np.zeros((natom, 3), dtype=int) - 1
zmat = np.zeros((natom, 3)) - 1
# FIXME need to take care about TS strucutres maybe
zmatorder = [-1 for i in range(natom)]
zmat_atom[0] = atom[a]
zmatorder[0] = a
zmat_atom[1] = atom[b]
zmatorder[1] = b
zmat_ref[1][0] = 1
zmat[1][0] = np.linalg.norm(cart[b] - cart[a])
zmat_atom[2] = atom[c]
zmatorder[2] = c
zmat_ref[2][0] = 2
zmat[2][0] = np.linalg.norm(cart[c] - cart[b])
zmat_ref[2][1] = 1
zmat[2][1] = np.degrees(geometry.calc_angle(cart[c], cart[b], cart[a]))
zmat_atom[3] = atom[d]
zmatorder[3] = d
zmat_ref[3][0] = 3
zmat[3][0] = np.linalg.norm(cart[d] - cart[c])
zmat_ref[3][1] = 2
zmat[3][1] = np.degrees(geometry.calc_angle(cart[d], cart[c], cart[b]))
zmat_ref[3][2] = 1
zmat[3][2], collin = geometry.calc_dihedral(cart[d], cart[c], cart[b], cart[a])
j = 4
for i in range(natom):
if i == a or i == b or i == c or i == d:
continue
zmat_atom[j] = atom[i]
zmatorder[j] = i
if groupA[i] == 1:
zmat_ref[j][0] = 1
zmat[j][0] = np.linalg.norm(cart[i] - cart[a])
zmat_ref[j][1] = 2
zmat[j][1] = np.degrees(geometry.calc_angle(cart[i], cart[a], cart[b]))
zmat_ref[j][2] = 3
zmat[j][2], collin = geometry.calc_dihedral(cart[i], cart[a], cart[b], cart[c])
elif groupB[i] == 1:
zmat_ref[j][0] = 2
zmat[j][0] = np.linalg.norm(cart[i] - cart[b])
zmat_ref[j][1] = 3
zmat[j][1] = np.degrees(geometry.calc_angle(cart[i], cart[b], cart[c]))
zmat_ref[j][2] = 4
zmat[j][2], collin = geometry.calc_dihedral(cart[i], cart[b], cart[c], cart[d])
elif groupC[i] == 1:
zmat_ref[j][0] = 3
zmat[j][0] = np.linalg.norm(cart[i] - cart[c])
zmat_ref[j][1] = 2
zmat[j][1] = np.degrees(geometry.calc_angle(cart[i], cart[c], cart[b]))
zmat_ref[j][2] = 1
zmat[j][2], collin = geometry.calc_dihedral(cart[i], cart[c], cart[b], cart[a])
elif groupD[i] == 1:
zmat_ref[j][0] = 4
zmat[j][0] = np.linalg.norm(cart[i] - cart[d])
zmat_ref[j][1] = 3
zmat[j][1] = np.degrees(geometry.calc_angle(cart[i], cart[d], cart[c]))
zmat_ref[j][2] = 2
zmat[j][2], collin = geometry.calc_dihedral(cart[i], cart[d], cart[c], cart[b])
j += 1
return zmat_atom, zmat_ref, zmat, zmatorder
def make_zmat_from_cart_all_dihedrals(bond, cycle, dihed, conf_dihed, natom, atom, cart, mode):
"""
Rearrange geometry defined in Cartesian into a Z-matrix,
with references suitable for a 1-D hindered rotor scan.
Include all rotors which are:
If mode = 0: all rotatable bonds
If mode = 1: only those bonds, which generate conformers,
i.e. no methyl bonds, t-butyl bonds, etc
bond: bond matrix of the species
cycle: atom list of species with 0 if atom is not in cycle and 1 otherwise
dihed: total list of dihedrals
conf_dihed: list of dihedrals without the symmetrical ones
natom: number of atoms
atom: symbols of all the atoms
cart: cartesian coordinates of the species
"""
rotors = [] #rotors to consider
if mode == 0:
for rotor in dihed:
rotors.append(rotor[:])
if mode == 1:
for rotor in conf_dihed:
rotors.append(rotor[:])
if len(rotors) > 0:
#order in which the atoms will be added:
# 1. First rotor
# 2. Smallest path between first and second rotor (if any)
# 3. Second rotor
# 4. Smallest path between second and third rotor (if any)
# ...
# n. Last rotor
# n+1. All atoms that are not part of a rotor,
# starting by the neighbors of all rotor atoms
#order the rotors as such that the path between subsequent rotors does not
#cross another rotor
rotors, connecting_list, connected_rotor, path_length = order_rotors(rotors,bond,natom, atom)
#Add first rotor:
zmat_atom = ['X' for i in range(natom)]
zmat_ref = np.zeros((natom, 3), dtype=int) - 1
zmat = np.zeros((natom, 3)) - 1
zmatorder = [-1 for i in range(natom)]
zmat_atom[0] = atom[rotors[0][0]]
zmatorder[0] = rotors[0][0]
zmat_atom[1] = atom[rotors[0][1]]
zmatorder[1] = rotors[0][1]
zmat_ref[1][0] = 1
zmat[1][0] = np.linalg.norm(cart[rotors[0][1]] - cart[rotors[0][0]])
zmat_atom[2] = atom[rotors[0][2]]
zmatorder[2] = rotors[0][2]
zmat_ref[2][0] = 2
zmat[2][0] = np.linalg.norm(cart[rotors[0][2]] - cart[rotors[0][1]])
zmat_ref[2][1] = 1
zmat[2][1] = np.degrees(geometry.calc_angle(cart[rotors[0][2]], cart[rotors[0][1]], cart[rotors[0][0]]))
zmat_atom[3] = atom[rotors[0][3]]
zmatorder[3] = rotors[0][3]
zmat_ref[3][0] = 3
zmat[3][0] = np.linalg.norm(cart[rotors[0][3]] - cart[rotors[0][2]])
zmat_ref[3][1] = 2
zmat[3][1] = np.degrees(geometry.calc_angle(cart[rotors[0][3]], cart[rotors[0][2]], cart[rotors[0][1]]))
zmat_ref[3][2] = 1
zmat[3][2], collin = geometry.calc_dihedral(cart[rotors[0][3]], cart[rotors[0][2]], cart[rotors[0][1]], cart[rotors[0][0]])
#Add subsequent rotors:
rot_index = 1
j = 4
while rot_index < len(rotors):
rotor = rotors[rot_index]
chain_length = path_length[rot_index - 1]
chain = connecting_list[rot_index - 1]
conn_rotor = connected_rotor[rot_index - 1]
to_add = []
added = []
for at in rotor:
if not at in zmatorder:
to_add.append(at)
else:
added.append(at)
if len(to_add) == 0:
logging.error("error, all atoms of a rotor have been added, without adding this dihedral explicitly")
elif len(to_add) == 1:
at = to_add[0]
if rotor.index(at) == 1 or rotor.index(at) == 2:
logging.error("error, all atoms except a middle atom have been added, strange...")
elif rotor.index(at) == 0:
add(j,[at,rotor[1],rotor[2],rotor[3]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif rotor.index(at) == 3:
add(j,[at,rotor[2],rotor[1],rotor[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif len(to_add) == 2:
at1 = to_add[0]
at2 = to_add[1]
if sorted([rotor.index(at1),rotor.index(at2)]) == [0,1]:
neighbor_list = get_neighbors(rotor[2],bond,natom,rotors,zmatorder)
#add rotor[1]
add(j,[rotor[1],rotor[2],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
#add rotor[0]
add(j,[rotor[0],rotor[1],rotor[2],rotor[3]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif sorted([rotor.index(at1),rotor.index(at2)]) == [2,3]:
neighbor_list = get_neighbors(rotor[1],bond,natom,rotors,zmatorder)
#add rotor[2]
add(j,[rotor[2],rotor[1],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
#add rotor[3]
add(j,[rotor[3],rotor[2],rotor[1],rotor[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif sorted([rotor.index(at1),rotor.index(at2)]) == [0,3]:
r1,pos1 = middle_atom(rotors,rotor[1])
r2,pos2 = middle_atom(rotors,rotor[2])
if r1 and pos1[0] in zmatorder and pos1[1] in zmatorder:
#add rotor[0]
add(j,[rotor[0],rotor[1],pos1[0],pos1[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
#add rotor[3]
add(j,[rotor[3],rotor[2],rotor[1],rotor[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif r2 and pos2[0] in zmatorder and pos2[1] in zmatorder:
#add rotor[3]
add(j,[rotor[3],rotor[2],pos2[0],pos2[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
#add rotor[0]
add(j,[rotor[0],rotor[1],rotor[2],rotor[3]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
else:
if cycle[rotor[2]] == 1:
neighbor_list = get_neighbors(rotor[2],bond,natom,rotors,zmatorder)
#add rotor[3]
add(j,[rotor[3],rotor[2],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
#add rotor[0]
add(j,[rotor[0],rotor[1],rotor[2],rotor[3]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
else:
neighbor_list = get_neighbors(rotor[1],bond,natom,rotors,zmatorder)
#add rotor[0]
add(j,[rotor[0],rotor[1],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
#add rotor[3]
add(j,[rotor[3],rotor[2],rotor[1],rotor[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif sorted([rotor.index(at1),rotor.index(at2)]) == [0,2]:
neighbor_list = get_neighbors(rotor[1],bond,natom,rotors,zmatorder)
#add rotor[2]
add(j,[rotor[2],rotor[1],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
#add rotor[0]
add(j,[rotor[0],rotor[1],rotor[2],rotor[3]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif sorted([rotor.index(at1),rotor.index(at2)]) == [1,3]:
neighbor_list = get_neighbors(rotor[0],bond,natom,rotors,zmatorder)
#add rotor[1]
add(j,[rotor[1],rotor[0],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
#add rotor[3]
add(j,[rotor[3],rotor[2],rotor[1],rotor[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
else:
logging.error("error, two atoms that need to be added are not the outer atoms of a rotor, strange...")
elif len(to_add) == 3:
if added[0] == rotor[0]:
neighbor_list = get_neighbors(rotor[0],bond,natom,rotors,zmatorder)
add(j,[rotor[1],rotor[0],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[2],rotor[1],rotor[0],neighbor_list[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[3],rotor[2],rotor[1],rotor[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif added[0] == rotor[1]:
neighbor_list = get_neighbors(rotor[1],bond,natom,rotors,zmatorder)
if cycle[rotor[3]] == 1 or cycle[rotor[2]] == 1:
add(j,[rotor[2],rotor[1],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[3],rotor[2],rotor[1],neighbor_list[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[0],rotor[1],rotor[2],rotor[3]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
else:
add(j,[rotor[0],rotor[1],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[2],rotor[1],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[3],rotor[2],rotor[1],rotor[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif added[0] == rotor[2]:
neighbor_list = get_neighbors(rotor[2],bond,natom,rotors,zmatorder)
if cycle[rotor[3]] == 1 or cycle[rotor[2]] == 1:
add(j,[rotor[3],rotor[2],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[1],rotor[2],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[0],rotor[1],rotor[2],rotor[3]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
else:
add(j,[rotor[1],rotor[2],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[0],rotor[1],rotor[2],neighbor_list[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[3],rotor[2],rotor[1],rotor[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif added[0] == rotor[3]:
neighbor_list = get_neighbors(rotor[3],bond,natom,rotors,zmatorder)
add(j,[rotor[2],rotor[3],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[1],rotor[2],rotor[3],neighbor_list[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[0],rotor[1],rotor[2],rotor[3]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
else:
logging.error('error')
else:
if len(chain) == 2: #this is the minimum chain length
neighbor_list=get_neighbors(chain[1],bond,natom,rotors,zmatorder)
if chain[0] == rotor[0]:
add(j,[rotor[0],chain[1],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[1],rotor[0],chain[1],neighbor_list[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[2],rotor[1],rotor[0],chain[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[3],rotor[2],rotor[1],rotor[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif chain[0] == rotor[1]:
if cycle[rotor[3]] == 1 or cycle[rotor[2]] == 1:
add(j,[rotor[1],chain[1],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[2],rotor[1],chain[1],neighbor_list[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[3],rotor[2],rotor[1],chain[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[0],rotor[1],rotor[2],rotor[3]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
else:
add(j,[rotor[1],chain[1],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[0],rotor[1],chain[1],neighbor_list[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[2],rotor[1],chain[1],neighbor_list[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[3],rotor[2],rotor[1],rotor[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif chain[0] == rotor[2]:
if cycle[rotor[3]] == 1 or cycle[rotor[2]] == 1:
add(j,[rotor[2],chain[1],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[1],rotor[2],chain[1],neighbor_list[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[3],rotor[2],chain[1],neighbor_list[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[0],rotor[1],rotor[2],rotor[3]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
else:
add(j,[rotor[2],chain[1],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[1],rotor[2],chain[1],neighbor_list[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[0],rotor[1],rotor[2],chain[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[3],rotor[2],rotor[1],rotor[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif chain[0] == rotor[3]:
add(j,[rotor[3],chain[1],neighbor_list[0],neighbor_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[2],rotor[3],chain[1],neighbor_list[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[1],rotor[2],rotor[3],chain[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[0],rotor[1],rotor[2],rotor[3]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif len(chain) > 2:
neighbor_list=get_neighbors(chain[-1],bond,natom,rotors,zmatorder)
#add the chain of atoms between this rotor and the closest rotor that is already in the zmatrix
for i in range(1,len(chain)-1): #do not consider two outer atoms, which are part of a rotor
ref_list = []
if i == 1:
ref_list = [chain[-1],neighbor_list[0],neighbor_list[1]]
elif i == 2:
ref_list = [chain[-2],chain[-1],neighbor_list[0]]
else:
ref_list = [chain[-i],chain[-(i-1)],chain[-(i-2)]]
add(j,[chain[-(i+1)],ref_list[0],ref_list[1],ref_list[2]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
#add the rotor itself:
ref_list = []
if len(chain) == 3: #only one atom connects the two rotors:
ref_list = [chain[1],chain[2],neighbor_list[0]]
else:
ref_list = [chain[1],chain[2],chain[3]]
if chain[0] == rotor[0]:
add(j,[rotor[0],ref_list[0],ref_list[1],ref_list[2]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[1],rotor[0],ref_list[0],ref_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[2],rotor[1],rotor[0],ref_list[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[3],rotor[2],rotor[1],rotor[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif chain[0] == rotor[1]:
if cycle[rotor[3]] == 1 or cycle[rotor[2]] == 1:
add(j,[rotor[1],ref_list[0],ref_list[1],ref_list[2]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[2],rotor[1],ref_list[0],ref_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[3],rotor[2],rotor[1],ref_list[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[0],rotor[1],rotor[2],rotor[3]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
else:
add(j,[rotor[1],ref_list[0],ref_list[1],ref_list[2]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[0],rotor[1],ref_list[0],ref_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[2],rotor[1],ref_list[0],ref_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[3],rotor[2],rotor[1],rotor[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif chain[0] == rotor[2]:
if cycle[rotor[3]] == 1 or cycle[rotor[2]] == 1:
add(j,[rotor[2],ref_list[0],ref_list[1],ref_list[2]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[1],rotor[2],ref_list[0],ref_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[3],rotor[2],ref_list[0],ref_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[0],rotor[1],rotor[2],rotor[3]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
else:
add(j,[rotor[2],ref_list[0],ref_list[1],ref_list[2]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[1],rotor[2],ref_list[0],ref_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[0],rotor[1],rotor[2],ref_list[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[3],rotor[2],rotor[1],rotor[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
elif chain[0] == rotor[3]:
add(j,[rotor[3],ref_list[0],ref_list[1],ref_list[2]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[2],rotor[3],ref_list[0],ref_list[1]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[1],rotor[2],rotor[3],ref_list[0]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
add(j,[rotor[0],rotor[1],rotor[2],rotor[3]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
else:
logging.error('error, chain length too small')
rot_index += 1
else:
# no rotors here, add the first four atoms of the molecule
zmat_atom = ['X' for i in range(natom)]
zmat_ref = np.zeros((natom, 3), dtype=int) - 1
zmat = np.zeros((natom, 3)) - 1
zmatorder = [-1 for i in range(natom)]
if len(atom) == 1:
zmat_atom[0] = atom[0]
zmatorder[0] = 0
elif len(atom) == 2:
zmat_atom[0] = atom[0]
zmatorder[0] = 0
zmat_atom[1] = atom[1]
zmatorder[1] = 1
zmat_ref[1][0] = 1
zmat[1][0] = np.linalg.norm(cart[1] - cart[0])
else:
# get three atoms that are bonded to one another
motif = ['X','X','X']
ins = start_motif(motif, natom, bond, atom, -1, [[k] for k in range(natom)])[0]
zmat_atom[0] = atom[ins[0]]
zmatorder[0] = ins[0]
zmat_atom[1] = atom[ins[1]]
zmatorder[1] = ins[1]
zmat_ref[1][0] = 1
zmat[1][0] = np.linalg.norm(cart[ins[1]] - cart[ins[0]])
zmat_atom[2] = atom[ins[2]]
zmatorder[2] = ins[2]
zmat_ref[2][0] = 2
zmat[2][0] = np.linalg.norm(cart[ins[2]] - cart[ins[1]])
zmat_ref[2][1] = 1
zmat[2][1] = np.degrees(geometry.calc_angle(cart[ins[2]], cart[ins[1]], cart[ins[0]]))
j = 3
#add all the remaining atoms
while -1 in zmatorder:
for i in range(natom):
if not i in zmatorder:
neighbor_list = get_three_neighbors(i,bond,natom,rotors,zmatorder)
if len(neighbor_list) > 2:
add(j,[i,neighbor_list[0],neighbor_list[1],neighbor_list[2]],zmat,zmat_atom,zmatorder,zmat_ref,atom,cart)
j += 1
return zmat_atom, zmat_ref, zmat, zmatorder
def make_zmat_from_cart(species, rotor, cart, mode):
"""
Rearrange geometry defined in Cartesian into a Z-matrix,
with references suitable for a 1-D hindered rotor scan.
If mode = 0: all rotatable bonds
If mode = 1: only those bonds, which generate conformers
If mode = 2: suply your one rotor in rotor as a list of atom indices
"""
natom = species.natom
atom = species.atom
if mode == 0:
a = species.dihed[rotor][0]
b = species.dihed[rotor][1]
c = species.dihed[rotor][2]
d = species.dihed[rotor][3]
elif mode == 1:
a = species.conf_dihed[rotor][0]
b = species.conf_dihed[rotor][1]
c = species.conf_dihed[rotor][2]
d = species.conf_dihed[rotor][3]
elif mode == 2:
a = rotor[0]
b = rotor[1]
c = rotor[2]
d = rotor[3]
groupA = np.zeros(natom, dtype=int)
groupB = np.zeros(natom, dtype=int)
groupC = np.zeros(natom, dtype=int)
groupD = np.zeros(natom, dtype=int)
groupA[a] = 1
groupB[b] = 1
groupC[c] = 1
groupD[d] = 1
# get all immediate neighbors of a A, B, C, and D
for i in range(natom):
if species.bond[a][i] > 0 and i != b:
groupA[i] = 1
elif species.bond[b][i] > 0 and i != a and i != c:
groupB[i] = 1
elif species.bond[c][i] > 0 and i != b and i != d:
groupC[i] = 1
elif species.bond[d][i] > 0 and i != c:
groupD[i] = 1
found = 1
while found > 0:
found = 0
for i in range(natom):
if groupA[i] == 1:
for j in range(natom):
if species.bond[i][j] > 0 and j != b and groupA[j] != 1:
groupA[j] = 1
found = 1
elif groupB[i] == 1:
for j in range(natom):
if species.bond[i][j] > 0 and j != a and j != c and groupB[j] != 1:
groupB[j] = 1
found = 1
elif groupC[i] == 1:
for j in range(natom):
if species.bond[i][j] > 0 and j != b and j != d and groupC[j] != 1:
groupC[j] = 1
found = 1
elif groupD[i] == 1:
for j in range(natom):
if species.bond[i][j] > 0 and j != c and groupD[j] != 1:
groupD[j] = 1
found = 1
zmat_atom = ['X' for i in range(natom)]
zmat_ref = np.zeros((natom, 3), dtype=int) - 1
zmat = np.zeros((natom, 3)) - 1
# FIXME need to take care about TS structures maybe
zmatorder = [-1 for i in range(natom)]
zmat_atom[0] = atom[a]
zmatorder[0] = a
zmat_atom[1] = atom[b]
zmatorder[1] = b
zmat_ref[1][0] = 1
zmat[1][0] = np.linalg.norm(cart[b] - cart[a])
zmat_atom[2] = atom[c]
zmatorder[2] = c
zmat_ref[2][0] = 2
zmat[2][0] = np.linalg.norm(cart[c] - cart[b])
zmat_ref[2][1] = 1
zmat[2][1] = np.degrees(geometry.calc_angle(cart[c], cart[b], cart[a]))
zmat_atom[3] = atom[d]
zmatorder[3] = d
zmat_ref[3][0] = 3
zmat[3][0] = np.linalg.norm(cart[d] - cart[c])
zmat_ref[3][1] = 2
zmat[3][1] = np.degrees(geometry.calc_angle(cart[d], cart[c], cart[b]))
zmat_ref[3][2] = 1
zmat[3][2], collin = geometry.calc_dihedral(cart[d], cart[c], cart[b], cart[a])
j = 4
for i in range(natom):
if i == a or i == b or i == c or i == d:
continue
zmat_atom[j] = atom[i]
zmatorder[j] = i
if groupA[i] == 1:
zmat_ref[j][0] = 1
zmat[j][0] = np.linalg.norm(cart[i] - cart[a])
zmat_ref[j][1] = 2
zmat[j][1] = np.degrees(geometry.calc_angle(cart[i], cart[a], cart[b]))
zmat_ref[j][2] = 3
zmat[j][2], collin = geometry.calc_dihedral(cart[i], cart[a], cart[b], cart[c])
elif groupB[i] == 1:
zmat_ref[j][0] = 2
zmat[j][0] = np.linalg.norm(cart[i] - cart[b])
zmat_ref[j][1] = 3
zmat[j][1] = np.degrees(geometry.calc_angle(cart[i], cart[b], cart[c]))
zmat_ref[j][2] = 4
zmat[j][2], collin = geometry.calc_dihedral(cart[i], cart[b], cart[c], cart[d])
elif groupC[i] == 1:
zmat_ref[j][0] = 3
zmat[j][0] = np.linalg.norm(cart[i] - cart[c])
zmat_ref[j][1] = 2
zmat[j][1] = np.degrees(geometry.calc_angle(cart[i], cart[c], cart[b]))
zmat_ref[j][2] = 1
zmat[j][2], collin = geometry.calc_dihedral(cart[i], cart[c], cart[b], cart[a])
elif groupD[i] == 1:
zmat_ref[j][0] = 4
zmat[j][0] = np.linalg.norm(cart[i] - cart[d])
zmat_ref[j][1] = 3
zmat[j][1] = np.degrees(geometry.calc_angle(cart[i], cart[d], cart[c]))
zmat_ref[j][2] = 2
zmat[j][2], collin = geometry.calc_dihedral(cart[i], cart[d], cart[c], cart[b])
j += 1
return zmat_atom, zmat_ref, zmat, zmatorder
def make_zmat_from_cart_all_dihedrals(bond, cycle, dihed, conf_dihed, natom, atom, cart, mode):
"""
Rearrange geometry defined in Cartesian into a Z-matrix,
with references suitable for a 1-D hindered rotor scan.
Include all rotors which are:
If mode = 0: all rotatable bonds
If mode = 1: only those bonds, which generate conformers,
i.e. no methyl bonds, t-butyl bonds, etc
bond: bond matrix of the species
cycle: atom list of species with 0 if atom is not in cycle and 1 otherwise
dihed: total list of dihedrals
conf_dihed: list of dihedrals without the symmetrical ones
natom: number of atoms
atom: symbols of all the atoms
cart: cartesian coordinates of the species
"""
rotors = [] # rotors to consider
if mode == 0:
for rotor in dihed:
rotors.append(rotor[:])
if mode == 1:
for rotor in conf_dihed:
rotors.append(rotor[:])
if len(rotors) > 0:
# order in which the atoms will be added:
# 1. First rotor
# 2. Smallest path between first and second rotor (if any)
# 3. Second rotor
# 4. Smallest path between second and third rotor (if any)
# ...
# n. Last rotor
# n+1. All atoms that are not part of a rotor,
# starting by the neighbors of all rotor atoms
# order the rotors as such that the path between subsequent rotors does not
# cross another rotor
rotors, connecting_list, connected_rotor, path_length = order_rotors(rotors, bond, natom, atom)
# Add first rotor:
zmat_atom = ['X' for i in range(natom)]
zmat_ref = np.zeros((natom, 3), dtype=int) - 1
zmat = np.zeros((natom, 3)) - 1
zmatorder = [-1 for i in range(natom)]
zmat_atom[0] = atom[rotors[0][0]]
zmatorder[0] = rotors[0][0]
zmat_atom[1] = atom[rotors[0][1]]
zmatorder[1] = rotors[0][1]
zmat_ref[1][0] = 1
zmat[1][0] = np.linalg.norm(cart[rotors[0][1]] - cart[rotors[0][0]])
zmat_atom[2] = atom[rotors[0][2]]
zmatorder[2] = rotors[0][2]
zmat_ref[2][0] = 2
zmat[2][0] = np.linalg.norm(cart[rotors[0][2]] - cart[rotors[0][1]])
zmat_ref[2][1] = 1
zmat[2][1] = np.degrees(geometry.calc_angle(cart[rotors[0][2]], cart[rotors[0][1]], cart[rotors[0][0]]))
zmat_atom[3] = atom[rotors[0][3]]
zmatorder[3] = rotors[0][3]
zmat_ref[3][0] = 3
zmat[3][0] = np.linalg.norm(cart[rotors[0][3]] - cart[rotors[0][2]])
zmat_ref[3][1] = 2
zmat[3][1] = np.degrees(geometry.calc_angle(cart[rotors[0][3]], cart[rotors[0][2]], cart[rotors[0][1]]))
zmat_ref[3][2] = 1
zmat[3][2], collin = geometry.calc_dihedral(cart[rotors[0][3]], cart[rotors[0][2]], cart[rotors[0][1]], cart[rotors[0][0]])
# Add subsequent rotors:
rot_index = 1
j = 4
while rot_index < len(rotors):
rotor = rotors[rot_index]
chain_length = path_length[rot_index - 1]
chain = connecting_list[rot_index - 1]
conn_rotor = connected_rotor[rot_index - 1]
to_add = []
added = []
for at in rotor:
if at not in zmatorder:
to_add.append(at)
else:
added.append(at)
if len(to_add) == 0:
logging.error("error, all atoms of a rotor have been added, without adding this dihedral explicitly")
elif len(to_add) == 1:
at = to_add[0]
if rotor.index(at) == 1 or rotor.index(at) == 2:
logging.error("error, all atoms except a middle atom have been added, strange...")
elif rotor.index(at) == 0:
add(j, [at, rotor[1], rotor[2], rotor[3]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif rotor.index(at) == 3:
add(j, [at, rotor[2], rotor[1], rotor[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif len(to_add) == 2:
at1 = to_add[0]
at2 = to_add[1]
if sorted([rotor.index(at1), rotor.index(at2)]) == [0, 1]:
neighbor_list = get_neighbors(rotor[2], bond, natom, rotors, zmatorder)
# add rotor[1]
add(j, [rotor[1], rotor[2], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
# add rotor[0]
add(j, [rotor[0], rotor[1], rotor[2], rotor[3]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif sorted([rotor.index(at1), rotor.index(at2)]) == [2, 3]:
neighbor_list = get_neighbors(rotor[1], bond, natom, rotors, zmatorder)
# add rotor[2]
add(j, [rotor[2], rotor[1], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
# add rotor[3]
add(j, [rotor[3], rotor[2], rotor[1], rotor[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif sorted([rotor.index(at1), rotor.index(at2)]) == [0, 3]:
r1, pos1 = middle_atom(rotors, rotor[1])
r2, pos2 = middle_atom(rotors, rotor[2])
if r1 and pos1[0] in zmatorder and pos1[1] in zmatorder:
# add rotor[0]
add(j, [rotor[0], rotor[1], pos1[0], pos1[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
# add rotor[3]
add(j, [rotor[3], rotor[2], rotor[1], rotor[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif r2 and pos2[0] in zmatorder and pos2[1] in zmatorder:
# add rotor[3]
add(j, [rotor[3], rotor[2], pos2[0], pos2[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
# add rotor[0]
add(j, [rotor[0], rotor[1], rotor[2], rotor[3]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
else:
if cycle[rotor[2]] == 1:
neighbor_list = get_neighbors(rotor[2], bond, natom, rotors, zmatorder)
# add rotor[3]
add(j, [rotor[3], rotor[2], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
# add rotor[0]
add(j, [rotor[0], rotor[1], rotor[2], rotor[3]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
else:
neighbor_list = get_neighbors(rotor[1], bond, natom, rotors, zmatorder)
# add rotor[0]
add(j, [rotor[0], rotor[1], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
# add rotor[3]
add(j, [rotor[3], rotor[2], rotor[1], rotor[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif sorted([rotor.index(at1), rotor.index(at2)]) == [0, 2]:
neighbor_list = get_neighbors(rotor[1], bond, natom, rotors, zmatorder)
# add rotor[2]
add(j, [rotor[2], rotor[1], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
# add rotor[0]
add(j, [rotor[0], rotor[1], rotor[2], rotor[3]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif sorted([rotor.index(at1), rotor.index(at2)]) == [1, 3]:
neighbor_list = get_neighbors(rotor[0], bond, natom, rotors, zmatorder)
# add rotor[1]
add(j, [rotor[1], rotor[0], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
# add rotor[3]
add(j, [rotor[3], rotor[2], rotor[1], rotor[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
else:
logging.error("error, two atoms that need to be added are not the outer atoms of a rotor, strange...")
elif len(to_add) == 3:
if added[0] == rotor[0]:
neighbor_list = get_neighbors(rotor[0], bond, natom, rotors, zmatorder)
add(j, [rotor[1], rotor[0], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[2], rotor[1], rotor[0], neighbor_list[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[3], rotor[2], rotor[1], rotor[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif added[0] == rotor[1]:
neighbor_list = get_neighbors(rotor[1], bond, natom, rotors, zmatorder)
if cycle[rotor[3]] == 1 or cycle[rotor[2]] == 1:
add(j, [rotor[2], rotor[1], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[3], rotor[2], rotor[1], neighbor_list[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[0], rotor[1], rotor[2], rotor[3]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
else:
add(j, [rotor[0], rotor[1], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[2], rotor[1], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[3], rotor[2], rotor[1], rotor[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif added[0] == rotor[2]:
neighbor_list = get_neighbors(rotor[2], bond, natom, rotors, zmatorder)
if cycle[rotor[3]] == 1 or cycle[rotor[2]] == 1:
add(j, [rotor[3], rotor[2], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[1], rotor[2], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[0], rotor[1], rotor[2], rotor[3]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
else:
add(j, [rotor[1], rotor[2], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[0], rotor[1], rotor[2], neighbor_list[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[3], rotor[2], rotor[1], rotor[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif added[0] == rotor[3]:
neighbor_list = get_neighbors(rotor[3], bond, natom, rotors, zmatorder)
add(j, [rotor[2], rotor[3], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[1], rotor[2], rotor[3], neighbor_list[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[0], rotor[1], rotor[2], rotor[3]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
else:
logging.error('error')
else:
if len(chain) == 2: # this is the minimum chain length
neighbor_list = get_neighbors(chain[1], bond, natom, rotors, zmatorder)
if chain[0] == rotor[0]:
add(j, [rotor[0], chain[1], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[1], rotor[0], chain[1], neighbor_list[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[2], rotor[1], rotor[0], chain[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[3], rotor[2], rotor[1], rotor[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif chain[0] == rotor[1]:
if cycle[rotor[3]] == 1 or cycle[rotor[2]] == 1:
add(j, [rotor[1], chain[1], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[2], rotor[1], chain[1], neighbor_list[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[3], rotor[2], rotor[1], chain[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[0], rotor[1], rotor[2], rotor[3]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
else:
add(j, [rotor[1], chain[1], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[0], rotor[1], chain[1], neighbor_list[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[2], rotor[1], chain[1], neighbor_list[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[3], rotor[2], rotor[1], rotor[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif chain[0] == rotor[2]:
if cycle[rotor[3]] == 1 or cycle[rotor[2]] == 1:
add(j, [rotor[2], chain[1], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[1], rotor[2], chain[1], neighbor_list[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[3], rotor[2], chain[1], neighbor_list[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[0], rotor[1], rotor[2], rotor[3]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
else:
add(j, [rotor[2], chain[1], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[1], rotor[2], chain[1], neighbor_list[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[0], rotor[1], rotor[2], chain[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[3], rotor[2], rotor[1], rotor[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif chain[0] == rotor[3]:
add(j, [rotor[3], chain[1], neighbor_list[0], neighbor_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[2], rotor[3], chain[1], neighbor_list[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[1], rotor[2], rotor[3], chain[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[0], rotor[1], rotor[2], rotor[3]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif len(chain) > 2:
neighbor_list = get_neighbors(chain[-1], bond, natom, rotors, zmatorder)
# add the chain of atoms between this rotor and the closest rotor that is already in the zmatrix
for i in range(1, len(chain) - 1): # do not consider two outer atoms, which are part of a rotor
ref_list = []
if i == 1:
ref_list = [chain[-1], neighbor_list[0], neighbor_list[1]]
elif i == 2:
ref_list = [chain[-2], chain[-1], neighbor_list[0]]
else:
ref_list = [chain[-i], chain[-(i - 1)], chain[-(i - 2)]]
add(j, [chain[-(i + 1)], ref_list[0], ref_list[1], ref_list[2]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
# add the rotor itself:
ref_list = []
if len(chain) == 3: # only one atom connects the two rotors:
ref_list = [chain[1], chain[2], neighbor_list[0]]
else:
ref_list = [chain[1], chain[2], chain[3]]
if chain[0] == rotor[0]:
add(j, [rotor[0], ref_list[0], ref_list[1], ref_list[2]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[1], rotor[0], ref_list[0], ref_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[2], rotor[1], rotor[0], ref_list[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[3], rotor[2], rotor[1], rotor[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif chain[0] == rotor[1]:
if cycle[rotor[3]] == 1 or cycle[rotor[2]] == 1:
add(j, [rotor[1], ref_list[0], ref_list[1], ref_list[2]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[2], rotor[1], ref_list[0], ref_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[3], rotor[2], rotor[1], ref_list[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[0], rotor[1], rotor[2], rotor[3]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
else:
add(j, [rotor[1], ref_list[0], ref_list[1], ref_list[2]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[0], rotor[1], ref_list[0], ref_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[2], rotor[1], ref_list[0], ref_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[3], rotor[2], rotor[1], rotor[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif chain[0] == rotor[2]:
if cycle[rotor[3]] == 1 or cycle[rotor[2]] == 1:
add(j, [rotor[2], ref_list[0], ref_list[1], ref_list[2]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[1], rotor[2], ref_list[0], ref_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[3], rotor[2], ref_list[0], ref_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[0], rotor[1], rotor[2], rotor[3]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
else:
add(j, [rotor[2], ref_list[0], ref_list[1], ref_list[2]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[1], rotor[2], ref_list[0], ref_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[0], rotor[1], rotor[2], ref_list[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[3], rotor[2], rotor[1], rotor[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
elif chain[0] == rotor[3]:
add(j, [rotor[3], ref_list[0], ref_list[1], ref_list[2]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[2], rotor[3], ref_list[0], ref_list[1]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[1], rotor[2], rotor[3], ref_list[0]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
add(j, [rotor[0], rotor[1], rotor[2], rotor[3]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
else:
logging.error('error, chain length too small')
rot_index += 1
else:
# no rotors here, add the first four atoms of the molecule
zmat_atom = ['X' for i in range(natom)]
zmat_ref = np.zeros((natom, 3), dtype=int) - 1
zmat = np.zeros((natom, 3)) - 1
zmatorder = [-1 for i in range(natom)]
if len(atom) == 1:
zmat_atom[0] = atom[0]
zmatorder[0] = 0
elif len(atom) == 2:
zmat_atom[0] = atom[0]
zmatorder[0] = 0
zmat_atom[1] = atom[1]
zmatorder[1] = 1
zmat_ref[1][0] = 1
zmat[1][0] = np.linalg.norm(cart[1] - cart[0])
else:
# get three atoms that are bonded to one another
motif = ['X', 'X', 'X']
ins = start_motif(motif, natom, bond, atom, -1, [[k] for k in range(natom)])[0]
zmat_atom[0] = atom[ins[0]]
zmatorder[0] = ins[0]
zmat_atom[1] = atom[ins[1]]
zmatorder[1] = ins[1]
zmat_ref[1][0] = 1
zmat[1][0] = np.linalg.norm(cart[ins[1]] - cart[ins[0]])
zmat_atom[2] = atom[ins[2]]
zmatorder[2] = ins[2]
zmat_ref[2][0] = 2
zmat[2][0] = np.linalg.norm(cart[ins[2]] - cart[ins[1]])
zmat_ref[2][1] = 1
zmat[2][1] = np.degrees(geometry.calc_angle(cart[ins[2]], cart[ins[1]], cart[ins[0]]))
j = 3
# add all the remaining atoms
while -1 in zmatorder:
for i in range(natom):
if i not in zmatorder:
neighbor_list = get_three_neighbors(i, bond, natom, rotors, zmatorder)
if len(neighbor_list) > 2:
add(j, [i, neighbor_list[0], neighbor_list[1], neighbor_list[2]], zmat, zmat_atom, zmatorder, zmat_ref, atom, cart)
j += 1
return zmat_atom, zmat_ref, zmat, zmatorder
def control_changes(species, name, geom, new_geom, changes, bond):
"""
This method controls three things:
1. the changes are all correct
2. the bonded atom pairs that are not part of the changes have the same bond length
3. the non-bonded atom pairs are far enough from each other
"""
success = 1
gs = '' # initial geomtry string
for i, at in enumerate(species.atom):
x, y, z = geom[i]
gs += '{}, {:.8f}, {:.8f}, {:.8f}, \n'.format(at, x, y, z)
cs = '' # changes list
for ci in changes:
cs += '[{}]\n'.format(', '.join([str(cij) for cij in ci]))
# check if the changes are good
for ci in changes:
if len(ci) == 3:
bond_length = np.linalg.norm(new_geom[ci[0]] - new_geom[ci[1]])
if np.abs(bond_length - ci[2]) > 0.05: # use a 0.05 Angstrom cutoff
logging.debug("The modified bond length is not correct")
logging.debug("Expected {}, got {}".format(ci[2], bond_length))
logging.debug("Species name: " + name)
logging.debug("For the following initial geometry:\n" + gs)
logging.debug("And the following change list:\n" + cs)
success = 0
if len(ci) == 4:
angle = geometry.calc_angle(new_geom[ci[0]], new_geom[ci[1]], new_geom[ci[2]])
change_angle = np.radians(ci[3])
if np.abs(angle - change_angle) > 0.05: # use a 0.05 radians cutoff
logging.debug("The modified angle is not correct")
logging.debug("Expected {}, got {}".format(change_angle, angle))
logging.debug("Species name: " + name)
logging.debug("For the following initial geometry:\n" + gs)
logging.debug("And the following change list:\n" + cs)
success = 0
# check if the bond lengths are good:
for i in range(species.natom - 1):
for j in range(i+1, species.natom):
if bond[i][j] > 0:
is_change = 0
for ci in changes:
if i in ci and j in ci:
is_change = 1
if not is_change:
new_bond = np.linalg.norm(new_geom[i] - new_geom[j])
orig_bond = np.linalg.norm(geom[i] - geom[j])
if np.abs(new_bond - orig_bond) > 0.1: # use a 0.1 Angstrom cutoff
logging.debug("The bond length {} {} is not correct after modifications".format(i, j))
logging.debug("Expected {}, got {}".format(orig_bond, new_bond))
logging.debug("Species name: " + name)
logging.debug("For the following initial geometry:\n" + gs)
logging.debug("And the following change list:\n" + cs)
success = 0
# check if non-bonded atoms are too close:
for i in range(species.natom - 1):
for j in range(i+1, species.natom):
if bond[i][j] == 0:
dist = np.linalg.norm(new_geom[i] - new_geom[j])
min = constants.st_bond[''.join(sorted([species.atom[i], species.atom[j]]))]
if dist < min:
logging.debug("The atoms {} {} are too close after modifications".format(i, j))
logging.debug("Species name: " + name)
logging.debug("For the following initial geometry:\n" + gs)
logging.debug("And the following change list:\n" + cs)
success = 0
return success
def modify_coordinates(species, name, geom, changes, bond, write_files=0):
"""
Geom is the geometry (n x 3 matrix with n the number of atoms)
in cartesian coordinates
Changes is a list of lists, each list containing the coordinates
and their new value (atom indices start at 0):
To change a bond length: [atom1, atom2, bond_length]
To change a bond angle: [neighbor1, central_atom, neighbor2,
angle_in_degrees]
To change a dihedral angle: [atom1, atom2, atom3, atom4,
dihedarl_angle_in_degrees]
Bond is the bond matrix of the molecule
"""
start_time = time.time()
logging.debug('Starting coordinate modification for {}'.format(name))
logging.debug('Changes:')
for c in changes:
logging.debug('\t{}'.format('\t'.join([str(ci) for ci in c])))
step = 1
atoms_list = []
count = 0
fname = '{}_{}.xyz'.format(name, count)
while os.path.exists(fname):
count += 1
fname = '{}_{}.xyz'.format(name, count)
f_out = None
if write_files:
f_out = open(fname, 'w')
new_geom = copy.deepcopy(geom)
step = append_geom(species.natom, step, 0., species.atom, new_geom, np.zeros((species.natom*3)), atoms_list, f_out=f_out)
# change dihedrals, if necessary
for ci in changes:
if len(ci) == 5:
zmat_atom, zmat_ref, zmat, zmatorder = zmatrix.make_zmat_from_cart(species, ci[:-1], new_geom, 2)
# write_zmat(zmat_atom, zmat_ref, zmat, new_geom, species.atom)
orig_dih = zmat[3][2]
new_dih = ci[-1]
dih_diff = new_dih - orig_dih
zmat[3][2] += dih_diff
for i in range(4, species.natom):
if zmat_ref[i][2] == 4:
zmat[i][2] += dih_diff
if zmat_ref[i][2] == 1:
zmat[i][2] += dih_diff
new_geom = zmatrix.make_cart_from_zmat(zmat, zmat_atom, zmat_ref, species.natom, species.atom, zmatorder)
# write_zmat(zmat_atom, zmat_ref, zmat, new_geom, species.atom)
step = append_geom(species.natom, step, 0., species.atom, new_geom, np.zeros((species.natom*3)), atoms_list, f_out=f_out)
# change angles, if necessary
if len(ci) == 4:
# original angle in radians
orig_angle = geometry.calc_angle(new_geom[ci[0]], new_geom[ci[1]], new_geom[ci[2]])
new_angle = np.radians(ci[-1]) # new angle in radians
v1 = new_geom[ci[0]] - new_geom[ci[1]]
v2 = new_geom[ci[2]] - new_geom[ci[1]]
rot_ax = [0., 0., 0.]
# create a vector perpendicular to v1 and v2
# verify if points are collinear
if np.linalg.norm(np.cross(v1, v2)) == 0:
# rotate around any axis perpendicular to the axis along the three points:
if v1[0] != 0 or v1[1] != 0:
rot_ax = [v1[1], -v1[0], 0.]
elif v1[0] != 0 or v1[2] != 0:
rot_ax = [v1[2], 0., -v1[0]]
else:
rot_ax = [1., 0., 0.]
else:
rot_ax = np.cross(v1, v2)
rot_ax = rot_ax/np.linalg.norm(rot_ax)
# rotate all the atoms on the side of the last atom
st, ats, ats2 = divide_atoms(ci[2], ci[1], bond, species.natom, species.atom)
if not st:
break
for atj in ats:
new_geom[atj] = perform_rotation(new_geom[atj], new_geom[ci[1]], rot_ax, new_angle-orig_angle)
step = append_geom(species.natom, step, 1., species.atom, new_geom, np.zeros((species.natom*3)), atoms_list, f_out=f_out)
coords = get_coords(species, bond, new_geom, changes, 0)
# optimize the geometry to meet the coords list
x0 = np.reshape(new_geom, 3*species.natom)
cost_fct = cost_function(coords)
logging.debug('Starting BFGS')
gs = '' # initial geomtry string
for i, at in enumerate(species.atom):
x, y, z = new_geom[i]
gs += '{}, {:.8f}, {:.8f}, {:.8f}, \n'.format(at, x, y, z)
logging.debug("For the following initial geometry:\n" + gs)
opt = bfgs.BFGS()
x_opt, x_i, g_i = opt.optimize(cost_fct, x0)
new_geom = np.reshape(x_opt, (species.natom, 3))
for i, xi in enumerate(x_i):
geomi = np.reshape(xi, (species.natom, 3))
gradi = np.reshape(g_i[i], (species.natom, 3))
step = append_geom(species.natom, step, 2., species.atom, geomi, gradi, atoms_list, f_out=f_out)
if write_files:
write(fname.replace('.xyz', '.traj'), atoms_list)
f_out.close()
success = control_changes(species, name, geom, new_geom, changes, bond)
end_time = time.time()
logging.debug('Finished coordinate changes after {:.2f} seconds'.format(end_time - start_time))
return success, new_geom