def generate_conformers(self, rotor, cart):
"""
Generate guesses for all of the canonical conformers.
This is a recursive routine to generate them.
rotor: the rotor number in the order it was discovered
"""
if self.cyc_conf == 0:
cycles = 1
else:
cycles = self.cyc_conf
theoretical_confs = np.power(3, len(self.species.conf_dihed)) * cycles
if len(self.species.conf_dihed
) > self.max_dihed or theoretical_confs > self.nconfs:
self.generate_conformers_random_sampling(cart)
return 0
if rotor == len(self.species.conf_dihed):
self.qc.qc_conf(self.species, cart, self.conf)
self.conf += 1
return 0
cart = np.asarray(cart)
zmat_atom, zmat_ref, zmat, zmatorder = zmatrix.make_zmat_from_cart(
self.species, rotor, cart, 1)
rotor += 1
cart0 = zmatrix.make_cart_from_zmat(zmat, zmat_atom, zmat_ref,
self.species.natom,
self.species.atom, zmatorder)
self.generate_conformers(rotor, cart0)
zmat[3][2] += 120.
for i in range(4, self.species.natom):
if zmat_ref[i][2] == 4:
zmat[i][2] += 120.
if zmat_ref[i][2] == 1:
zmat[i][2] += 120.
cart1 = zmatrix.make_cart_from_zmat(zmat, zmat_atom, zmat_ref,
self.species.natom,
self.species.atom, zmatorder)
self.generate_conformers(rotor, cart1)
zmat[3][2] += 120.
for i in range(4, self.species.natom):
if zmat_ref[i][2] == 4:
zmat[i][2] += 120.
if zmat_ref[i][2] == 1:
zmat[i][2] += 120.
cart2 = zmatrix.make_cart_from_zmat(zmat, zmat_atom, zmat_ref,
self.species.natom,
self.species.atom, zmatorder)
self.generate_conformers(rotor, cart2)
return 0
def generate_hir_geoms(self, cart, rigid):
"""
Generate the initial geometries of the points along the scans
"""
# re-initialize the lists in case of a restart of the HIR scans
self.hir_status = []
self.hir_energies = []
self.hir_geoms = []
while len(self.hir_status) < len(self.species.dihed):
self.hir_status.append([-1 for i in range(self.nrotation)])
self.hir_energies.append([-1 for i in range(self.nrotation)])
self.hir_geoms.append([[] for i in range(self.nrotation)])
for rotor in range(len(self.species.dihed)):
if skip_rotor(self.species.name, self.species.dihed[rotor]) == 1:
self.hir_status[rotor] = [2 for i in range(self.nrotation)]
logging.info('For {} rotor {} was skipped in HIR.'.format(
self.species.name, rotor))
continue
cart = np.asarray(cart)
zmat_atom, zmat_ref, zmat, zmatorder = zmatrix.make_zmat_from_cart(
self.species, rotor, cart, 0)
# first element has same geometry
# ( TODO: this shouldn't be recalculated)
cart_new = zmatrix.make_cart_from_zmat(zmat, zmat_atom, zmat_ref,
self.species.natom,
self.species.atom,
zmatorder)
fi = [(zi + 1) for zi in zmatorder[:4]]
self.qc.qc_hir(self.species, cart_new, rotor, 0, [fi], rigid)
for ai in range(1, self.nrotation):
ang = 360. / float(self.nrotation)
zmat[3][2] += ang
for i in range(4, self.species.natom):
if zmat_ref[i][2] == 4:
zmat[i][2] += ang
if zmat_ref[i][2] == 1:
zmat[i][2] += ang
cart_new = zmatrix.make_cart_from_zmat(zmat, zmat_atom,
zmat_ref,
self.species.natom,
self.species.atom,
zmatorder)
self.qc.qc_hir(self.species, cart_new, rotor, ai, [fi], rigid)
return 0
def generate_conformers_random_sampling(self, ini_cart):
"""
Generate a random sampling of each dihedral for a number nconfs of conformers
"""
for ni in range(self.nconfs):
cart = copy.deepcopy(ini_cart)
if ni == 0:
sample = [0. for di in self.species.conf_dihed]
else:
sample = [
random.choice([0., 120., 240.])
for di in self.species.conf_dihed
]
for rotor in range(len(self.species.conf_dihed)):
zmat_atom, zmat_ref, zmat, zmatorder = zmatrix.make_zmat_from_cart(
self.species, rotor, cart, 1)
zmat[3][2] += sample[rotor]
for i in range(4, self.species.natom):
if zmat_ref[i][2] == 4:
zmat[i][2] += sample[rotor]
if zmat_ref[i][2] == 1:
zmat[i][2] += sample[rotor]
cart = zmatrix.make_cart_from_zmat(zmat, zmat_atom, zmat_ref,
self.species.natom,
self.species.atom,
zmatorder)
self.qc.qc_conf(self.species, cart, self.conf)
self.conf += 1
return 0
def generate_hir_geoms(self, cart):
"""
Generate the initial geometries of the points along the scans
"""
# re-initialize the lists incase of a restart of the HIR scans
self.hir_status = []
self.hir_energies = []
self.hir_geoms = []
while len(self.hir_status) < len(self.species.dihed):
self.hir_status.append([-1 for i in range(self.nrotation)])
self.hir_energies.append([-1 for i in range(self.nrotation)])
self.hir_geoms.append([[] for i in range(self.nrotation)])
for rotor in range(len(self.species.dihed)):
cart = np.asarray(cart)
zmat_atom, zmat_ref, zmat, zmatorder = zmatrix.make_zmat_from_cart(self.species, rotor, cart, 0)
# first element has same geometry
# ( TODO: this shouldn't be recalculated)
cart_new = zmatrix.make_cart_from_zmat(zmat,
zmat_atom,
zmat_ref,
self.species.natom,
self.species.atom,
zmatorder)
fi = [(zi+1) for zi in zmatorder[:4]]
self.qc.qc_hir(self.species, cart_new, rotor, 0, [fi])
for ai in range(1, self.nrotation):
ang = 360. / float(self.nrotation)
zmat[3][2] += ang
for i in range(4, self.species.natom):
if zmat_ref[i][2] == 4:
zmat[i][2] += ang
if zmat_ref[i][2] == 1:
zmat[i][2] += ang
cart_new = zmatrix.make_cart_from_zmat(zmat,
zmat_atom,
zmat_ref,
self.species.natom,
self.species.atom,
zmatorder)
self.qc.qc_hir(self.species, cart_new, rotor, ai, [fi])
return 0
def generate_conformers(self, rotor, cart):
"""
Generate guesses for all of the canonical conformers.
This is a recursive routine to generate them.
rotor: the rotor number in the order it was discovered
"""
if len(self.species.conf_dihed) > self.max_dihed:
self.generate_conformers_random_sampling(cart)
return 0
if rotor == len(self.species.conf_dihed):
self.qc.qc_conf(self.species, cart, self.conf)
self.conf += 1
return 0
cart = np.asarray(cart)
zmat_atom, zmat_ref, zmat, zmatorder = zmatrix.make_zmat_from_cart(self.species, rotor, cart, 1)
rotor += 1
cart0 = zmatrix.make_cart_from_zmat(zmat, zmat_atom, zmat_ref, self.species.natom, self.species.atom, zmatorder)
self.generate_conformers(rotor, cart0)
zmat[3][2] += 120.
for i in range(4, self.species.natom):
if zmat_ref[i][2] == 4:
zmat[i][2] += 120.
if zmat_ref[i][2] == 1:
zmat[i][2] += 120.
cart1 = zmatrix.make_cart_from_zmat(zmat, zmat_atom, zmat_ref, self.species.natom, self.species.atom, zmatorder)
self.generate_conformers(rotor, cart1)
zmat[3][2] += 120.
for i in range(4, self.species.natom):
if zmat_ref[i][2] == 4:
zmat[i][2] += 120.
if zmat_ref[i][2] == 1:
zmat[i][2] += 120.
cart2 = zmatrix.make_cart_from_zmat(zmat, zmat_atom, zmat_ref, self.species.natom, self.species.atom, zmatorder)
self.generate_conformers(rotor, cart2)
return 0
def generate_conformers_random_sampling(self, ini_cart):
"""
Generate a random sampling of each dihedral for a number nconfs of conformers
"""
for ni in range(self.nconfs):
cart = copy.deepcopy(ini_cart)
if ni == 0:
sample = [0. for di in self.species.conf_dihed]
else:
sample = [random.choice([0., 120., 240.]) for di in self.species.conf_dihed]
for rotor in range(len(self.species.conf_dihed)):
zmat_atom, zmat_ref, zmat, zmatorder = zmatrix.make_zmat_from_cart(self.species, rotor, cart, 1)
zmat[3][2] += sample[rotor]
for i in range(4, self.species.natom):
if zmat_ref[i][2] == 4:
zmat[i][2] += sample[rotor]
if zmat_ref[i][2] == 1:
zmat[i][2] += sample[rotor]
cart = zmatrix.make_cart_from_zmat(zmat, zmat_atom, zmat_ref, self.species.natom, self.species.atom, zmatorder)
self.qc.qc_conf(self.species, cart, self.conf)
self.conf += 1
return 0
def generate_conformers(self, rotor, cart, print_warning=False):
"""
Generate guesses for all of the canonical conformers.
This is a recursive routine to generate them.
rotor: the rotor number in the order it was discovered
if -999, then just do a single calculation at the given geometry
"""
if self.cyc_conf == 0:
cycles = 1
else:
cycles = self.cyc_conf
name = self.get_name()
# what is the value of cycles
# what is value of all things associated w/ conf generation
# what is length of conf_dihed?
theoretical_confs = np.power(self.grid, len(
self.species.conf_dihed)) * cycles
if rotor != -999:
if len(self.species.conf_dihed
) > self.max_dihed or theoretical_confs > self.nconfs:
if rotor == 0:
if self.info:
logging.info(
'Random conformer search is carried out for {}.'.
format(name))
self.info = False
# skipping generation if done
if self.cyc_conf > 1:
nrandconf = int(round(self.nconfs / self.cyc_conf) + 2)
else:
nrandconf = self.nconfs
if os.path.exists('{}.log'.format(
self.get_job_name(nrandconf - 1)
)) and os.path.exists('conf/{}_low.log'.format(name)):
rows = self.db.select(
name=self.get_job_name(nrandconf - 1))
for row in rows:
self.conf = nrandconf
logging.info(
'Last conformer was found in kinbot.db, generation is skipped for {}.'
.format(self.get_job_name(nrandconf)))
logging.info(
'Make sure the files are correct, you can reactivate calcs by deleting the last log file.'
)
return 1
self.generate_conformers_random_sampling(cart)
return 0
# retraction from the recursion
if rotor == len(self.species.conf_dihed) or rotor == -999:
self.qc.qc_conf(self.species,
cart,
self.conf,
semi_emp=self.semi_emp)
if self.conf == 0:
logging.info(
'Theoretical number of conformers is {} for {}.'.format(
theoretical_confs, name))
self.conf += 1
return 0
# skipping generation if done
if os.path.exists('{}.log'.format(
self.get_job_name(theoretical_confs - 1))) and os.path.exists(
'conf/{}_low.log'.format(name)):
rows = self.db.select(name=self.get_job_name(theoretical_confs -
1))
for row in rows:
self.conf = theoretical_confs
if print_warning:
logging.info(
'Theoretical number of conformers is {} for {}.'.
format(theoretical_confs, name))
logging.info(
'Last conformer was found in kinbot.db, generation is skipped for {}.'
.format(name))
logging.info(
'Make sure the files are correct, you can reactivate calcs by deleting the last log file.'
)
return 1
cart = np.asarray(cart)
zmat_atom, zmat_ref, zmat, zmatorder = zmatrix.make_zmat_from_cart(
self.species, rotor, cart, 1)
rotor += 1
for gr in range(self.grid):
zmat[3][2] += 360. / self.grid
for i in range(4, self.species.natom):
if zmat_ref[i][2] == 4:
zmat[i][2] += 360. / self.grid
if zmat_ref[i][2] == 1:
zmat[i][2] += 360. / self.grid
cartmod = zmatrix.make_cart_from_zmat(zmat, zmat_atom, zmat_ref,
self.species.natom,
self.species.atom, zmatorder)
self.generate_conformers(rotor, cartmod)
return 0
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 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