def get_geometry(mol):
"""
extract atomlist from block with title 'molecule'
"""
atoms = mol.get("geometry")
atomlist = []
for atom in atoms:
atname = atom.get("atom")
atnumber = AtomicData.atomic_number(str(atname))
coords = atom.get("xyz")
if mol.get("units", "Angstrom") == "Angstrom":
coords = [xyz/AtomicData.bohr_to_angs for xyz in coords]
atomlist.append( (atnumber, coords) )
return atomlist
def load_hotbit_pseudoatom(elmfile):
"""
load description of pseudo atom from a hotbit element (.elm) file
Parameters:
===========
elmfile: path to element description
Returns:
========
atom module with data stored as members
"""
Data = parseHotbitParameters(elmfile)
class Atom:
pass
atom = Atom()
atom.Z = AtomicData.atomic_number(Data["atom_name"])
atom.energies = []
atom.valence_orbitals = []
atom.nshell = []
atom.angular_momenta = []
atom.orbital_occupation = []
atom.r = None
atom.radial_wavefunctions = []
spectr2l = {"s": 0, "p": 1, "d": 2, "f": 3, "g": 4, "h": 5, "i": 6}
for k in Data.keys():
if "orbital_energy" in k:
atom.energies.append(float(Data[k]))
dummy, spectr = k.rsplit("_", 1)
n = int(spectr[0])
l = int(spectr2l[spectr[1]])
occnr = AtomicData.valence_occ_numbers[Data["atom_name"]]
if occnr.has_key(spectr):
atom.orbital_occupation.append(occnr[spectr])
else:
atom.orbital_occupation.append(0)
atom.valence_orbitals.append(len(atom.valence_orbitals))
atom.nshell.append(n)
atom.angular_momenta.append(l)
if Data.has_key("radial_wavefunction_%s" % spectr):
atom.r = Data["radial_wavefunction_%s" % spectr][:, 0]
atom.radial_wavefunctions.append(
Data["radial_wavefunction_%s" % spectr][:, 1])
atom.hubbard_U = Data["hubbard_U"]
return atom
def __init__(self,
symbols,
coordinates,
tstep,
nstates,
charge,
sc_threshold=0.001):
# build list of atoms
atomlist = []
for s, xyz in zip(symbols, coordinates):
Z = AtomicData.atomic_number(s)
atomlist.append((Z, xyz))
self.dt_nuc = tstep # nuclear time step in a.u.
self.nstates = nstates # number of electronic states including the ground state
self.sc_threshold = sc_threshold # threshold for coefficients that are included in the
# computation of the scalar coupling
self.Nat = len(atomlist)
self.masses = AtomicData.atomlist2masses(atomlist)
self.pes = PotentialEnergySurfaces(atomlist, nstates, charge=charge)
# save results from last step
self.last_step = None
def process(self, l):
# Which kind of information should be read?
l = l.strip()
if self.read == None:
if l == "coordinates":
self.read = "C"
return
elif self.read == "C":
if l == "velocities":
self.read = "V"
return
# Read coordinates or velocities line by line
if self.read == "C":
atom, X, Y, Z = l.split()
Zi = AtomicData.atomic_number(atom)
# positions in bohr
pos = float(X), float(Y), float(Z)
self.atomlist.append((Zi, pos))
elif self.read == "V":
vx, vy, vz = l.split()
vel = float(vx), float(vy), float(vz)
self.velocities.append(vel)
def read_slakoformat_par(parfile, atom_order="AB"):
"""
read table for S and H in the format used by hotbit (https://trac.cc.jyu.fi/projects/hotbit)
Paramters:
==========
parfile: path to <atom1>_<atom2>.par
Returns:
========
sk
The Slater Koster data is stored in attributes of sk:
sk.Z1, sk.Z2, sk.d, sk.S, sk.H
"""
from os.path import basename
at1, at2 = basename(parfile).replace(".par", "").split("_")
if atom_order == "BA":
tmp = at1
at1 = at2
at2 = tmp
data_blocks = parseHotbitParameters(parfile)
data_AB = data_blocks["slako_integrals_%s_%s" % (at1, at2)]
data_BA = data_blocks["slako_integrals_%s_%s" % (at2, at1)]
m, n = data_AB.shape
assert data_AB.shape == data_BA.shape
d = data_AB[:, 0]
assert np.all(data_AB[:, 0] == data_BA[:, 0])
sk = SlakoModule()
sk.Z1 = AtomicData.atomic_number(at1)
sk.Z2 = AtomicData.atomic_number(at2)
sk.d = d
sk.S = {}
sk.H = {}
S = sk.S
H = sk.H
for pos, (tausym_AB, tausym_BA) in enumerate(
zip(T.tausymbols_AB[-n:], T.tausymbols_BA[-n:])):
try:
tau_AB = T.symbol2tau[tausym_AB]
tau_BA = T.symbol2tau[tausym_BA]
except KeyError:
continue
# AB
l1, l2 = tau_AB[0], tau_AB[2]
H[(l1, l2, T.tau2index[tau_AB])] = data_AB[:, pos + 1]
S[(l1, l2,
T.tau2index[tau_AB])] = data_AB[:,
len(T.tausymbols_AB) + pos + 1]
# BA
l1, l2 = tau_BA[0], tau_BA[2]
## if sk.Z1 == sk.Z2: # I think this is the right condition
if sk.Z1 > 1 and sk.Z2 > 1: # but with this illogical condition I can reproduce Roland's results for HCNO compounds
orbital_parity = pow(-1, l1 + l2)
else:
orbital_parity = 1
H[(l1, l2, T.tau2index[tau_BA])] = orbital_parity * data_BA[:, pos + 1]
S[(l1, l2, T.tau2index[tau_BA]
)] = orbital_parity * data_BA[:, len(T.tausymbols_BA) + pos + 1]
return sk
def read_slakoformat_skf(skfile, sk=None, atom_order="AB"):
"""
read table for S and H in the format used by DFTB+
see http://www.dftb.org/fileadmin/DFTB/public/misc/slakoformat.pdf
Parameters:
===========
skfile: path to <atom 1>-<atom 2>.skf
sk: slako_module loaded from a different file, to which the data from current table
is appended.
atom_order: Which of the atoms in the SK table is to be treated as the first atom?
"AB": The first orbital belongs to the first atom
"BA": The first orbital belongs to the second atom
Returns:
========
sk
The Slater Koster data is stored in attributes of sk:
sk.Z1, sk.Z2, sk.d, sk.S, sk.H
"""
from os.path import basename
at1, at2 = basename(skfile).replace(".skf", "").split("-")
fh = open(skfile, "r")
# line 1
parts = process_slako_line(fh.readline())
gridDist, nGridPoints = float(parts[0]), int(parts[1])
if at1 == at2:
# line 2
# homonuclear case
Ed, Ep, Es, SPE, Ud, Up, Us, fd, fp, fs = map(
float, process_slako_line(fh.readline()))
# line 2 or 3
mass, c2, c3, c4, c5, c6, c7, c8, c9, rcut, d1, d2, d3, d4, d5, d6, d7, d8, d9, d10 = \
map(float, process_slako_line(fh.readline()))
d = linspace(0.0, gridDist * (nGridPoints - 1), nGridPoints)
if sk == None:
sk = SlakoModule()
sk.Z1 = AtomicData.atomic_number(at1)
sk.Z2 = AtomicData.atomic_number(at2)
sk.d = d
sk.S = {}
sk.H = {}
S = sk.S
H = sk.H
if atom_order == "BA":
tausymbols = T.tausymbols_BA
else:
tausymbols = T.tausymbols_AB
lines = fh.readlines()
parts = process_slako_line(lines[0])
n = len(parts) / 2
assert n == 10 # for orbitals up to d functions there are 10 Slater Koster integrals
for tausym in tausymbols[-n:]:
try:
tau = T.symbol2tau[tausym]
except KeyError:
continue
# print "found %s integrals" % (T.tau2symbol[tau])
H[(tau[0], tau[2], T.tau2index[tau])] = array(
[0.0 for i in range(0, int(nGridPoints))])
S[(tau[0], tau[2], T.tau2index[tau])] = array(
[0.0 for i in range(0, int(nGridPoints))])
# line 4 to (4 + nGridPoints -1)
for i in range(0, nGridPoints):
parts = process_slako_line(lines[i])
#Hdd0 Hdd1 Hdd2 Hpd0 Hpd1 Hpp0 Hpp1 Hsd0 Hsp0 Hss0 Sdd0 Sdd1 Sdd2 Spd0 Spd1 Spp0 Spp1 Ssd0 Ssp0 Sss0
for pos, tausym in enumerate(tausymbols[-n:]):
try:
tau = T.symbol2tau[tausym]
except KeyError:
continue
l1, l2 = tau[0], tau[2]
if atom_order == "BA":
orbital_parity = pow(-1, l1 + l2)
else:
orbital_parity = 1
H[(l1, l2,
T.tau2index[tau])][i] = orbital_parity * float(parts[pos])
S[(l1, l2, T.tau2index[tau])][i] = orbital_parity * float(
parts[len(tausymbols) + pos])
return sk
def read_repulsive_potential(filename):
"""
read repulsive potential in the format used by Hotbit, DFTBaby or DFTB+
"""
from os.path import exists, basename, dirname, join
if ".par" in filename:
# Hotbit's format
at1, at2 = basename(filename).replace(".par", "").split("_")
if not exists(filename):
# file file A_B.par does not exist, look for file B_A.par
filename_BA = join(dirname(filename), "%s_%s.par" % (at2, at1))
print "parameter file %s does not exist -> try to load %s" % (
filename, filename_BA)
filename = filename_BA
data_blocks = hotbit_format.parseHotbitParameters(filename)
mod = ReppotModule()
mod.d = data_blocks["repulsive_potential"][:, 0]
mod.Vrep = data_blocks["repulsive_potential"][:, 1]
mod.Z1 = AtomicData.atomic_number(at1)
mod.Z2 = AtomicData.atomic_number(at2)
return mod
elif ".py" in filename:
# DFTBaby format
# access dictionary by .-notation
mod = utils.dotdic()
execfile(filename, mod)
return mod
elif ".skf" in filename:
# DFTB+ format, only the Splines part is read
at1, at2 = basename(filename).replace(".skf", "").split("-")
if not exists(filename):
# file file A-B.skf does not exist, look for file B-A.skf
filename_BA = join(dirname(filename), "%s-%s.skf" % (at2, at1))
print "parameter file %s does not exist -> try to load %s" % (
filename, filename_BA)
filename = filename_BA
fh = open(filename)
lines = fh.readlines()
fh.close()
# find section with repulsive potential
for i, l in enumerate(lines):
if l.strip() == "Spline":
break
else:
raise Exception("No 'Spline' section found in parameter file %s" %
filename)
# Line 2:
nInt, cutoff = lines[i + 1].strip().split()
nInt, cutoff = int(nInt), float(cutoff)
# Line 3: V(r < r0) = exp(-a1*r+a2) + a3 is r too small to be covered by the spline
a1, a2, a3 = map(float, lines[i + 2].strip().split())
# Line 4 to 4+nInt-2
rs = np.zeros(nInt)
cs = np.zeros((4, nInt))
for j in range(0, nInt):
# spline for the range [rj=start,r_(j+1)=end]
# V(r_j <= r < r_(j+1)) = c0 + c1*(r-r0) + c2*(r-r0)^2 + c3*(r-r0)^3
start, end, c0, c1, c2, c3 = map(
float, lines[i + 3 + j].strip().split()[:6])
rs[j] = start
cs[:, j] = np.array([c0, c1, c2, c3])
# V(r_nInt < r) = 0.0
assert end == cutoff
# Now we evaluate the spline on a equidistant grid
Npts = 100
d = np.linspace(0.0, cutoff, Npts)
Vrep = np.zeros(Npts)
j = 0
for i, di in enumerate(d):
if (di < rs[0]):
Vrep[i] = np.exp(-a1 * di + a2) + a3
else:
# find interval such that r[j] <= di < r[j+1]
while (di >= rs[j + 1]) and j < nInt - 2:
j += 1
if j < nInt - 2:
assert rs[j] <= di < rs[j + 1]
c0, c1, c2, c3 = cs[:, j]
Vrep[i] = c0 + c1 * (di - rs[j]) + c2 * (
di - rs[j])**2 + c3 * (di - rs[j])**3
else:
Vrep[i] = 0.0
# create python module
mod = ReppotModule()
mod.d = d
mod.Vrep = Vrep
mod.Z1 = AtomicData.atomic_number(at1)
mod.Z2 = AtomicData.atomic_number(at2)
return mod
else:
raise Exception("Format of %s not understood" % filename)
def _create_visualization(self, atomlist):
mlab = self.scene.mlab
# draw atoms as balls
vec = XYZ.atomlist2vector(atomlist)
x, y, z = vec[::3], vec[1::3], vec[2::3]
Zs = np.array([Z for (Z,pos) in atomlist])
atom_names = [AtomicData.atom_names[Z-1] for (Z,pos) in atomlist]
rads = np.array([AtomicData.covalent_radii.get(atname) for atname in atom_names])
atom_radii = np.sqrt(rads)*1.8
s = atom_radii
if self.show_flags["atoms"] == False:
# make atoms so small that one does not see them
scale_factor = 0.01
self.shown_atoms = False
else:
scale_factor = 0.45
self.shown_atoms = True
atoms = mlab.quiver3d(x,y,z, s,s,s, scalars=Zs.astype(float),
mode="sphere", scale_factor=scale_factor, resolution=20,
figure=self.scene.mayavi_scene)
# atoms are coloured by their atomic number
atoms.glyph.color_mode = "color_by_scalar"
atoms.glyph.glyph_source.glyph_source.center = [0,0,0]
self.lut = atoms.module_manager.scalar_lut_manager.lut.table.to_array()
for atname in set(atom_names):
Z = AtomicData.atomic_number(atname)
self.lut[Z,0:3] = ( np.array( atom_colours_rgb.get(atname, (0.0, 0.75, 0.75)) )*255.0 ).astype('uint8')
atoms.module_manager.scalar_lut_manager.lut.table = self.lut
atoms.module_manager.scalar_lut_manager.data_range = (0.0, 255.0)
# draw bonds
C = XYZ.connectivity_matrix(atomlist)
Nat = len(atomlist)
connections = []
bonds = mlab.points3d(x,y,z, scale_factor=0.15, resolution=20,
figure=self.scene.mayavi_scene)
for i in range(0, Nat):
Zi, posi = atomlist[i]
for j in range(i+1,Nat):
if C[i,j] == 1:
Zj, posj = atomlist[j]
connections.append( (i,j) )
bonds.mlab_source.dataset.lines = np.array(connections)
bonds.mlab_source.dataset.modified()
tube = mlab.pipeline.tube(bonds, tube_radius=0.15, #tube_radius=0.05,
figure=self.scene.mayavi_scene)
tube.filter.radius_factor = 1.0
surface = mlab.pipeline.surface(tube, color=(0.8,0.8,0.0),
opacity=0.7,
figure=self.scene.mayavi_scene)
self.atoms = atoms
self.bonds = bonds
# self.tube = tube
# self.surface = surface
self.atom_radii = s
self.Zs = Zs.astype(float)
self.primitives.append(atoms)
self.primitives.append(bonds)
self.primitives.append(tube)
self.primitives.append(surface)
# Lewis structure
if self.show_flags["Lewis structure"] == True:
bondsTuples, bond_orders, lone_pairs, formal_charges = BondOrders.assign_bond_orders(atomlist, C, charge=0)
# plot DOUBLE bonds
double_bonds = mlab.points3d(x,y,z, scale_factor=0.15, resolution=20, figure=self.scene.mayavi_scene)
connections_double = []
for i,bond in enumerate(bondsTuples):
if bond_orders[i] == 2:
# double bond between atoms I and J
connections_double.append( bond )
double_bonds.mlab_source.dataset.lines = np.array(connections_double)
double_bonds.mlab_source.dataset.modified()
tube = mlab.pipeline.tube(double_bonds, tube_radius=0.35, figure=self.scene.mayavi_scene)
tube.filter.radius_factor = 1.0
surface = mlab.pipeline.surface(tube, color=(0.8,0.8,0.0), figure=self.scene.mayavi_scene)
#
self.double_bonds = double_bonds
self.primitives.append(double_bonds)
self.primitives.append(tube)
self.primitives.append(surface)
#
# plot TRIPLE bonds
triple_bonds = mlab.points3d(x,y,z, scale_factor=0.15, resolution=20, figure=self.scene.mayavi_scene)
connections_triple = []
for i,bond in enumerate(bondsTuples):
if bond_orders[i] == 3:
# triple bond between atoms I and J
connections_triple.append( bond )
triple_bonds.mlab_source.dataset.lines = np.array(connections_triple)
triple_bonds.mlab_source.dataset.modified()
tube = mlab.pipeline.tube(triple_bonds, tube_radius=0.35, figure=self.scene.mayavi_scene)
tube.filter.radius_factor = 1.0
surface = mlab.pipeline.surface(tube, color=(0.8,0.8,0.0), figure=self.scene.mayavi_scene)
#
self.triple_bonds = triple_bonds
self.primitives.append(triple_bonds)
self.primitives.append(tube)
self.primitives.append(surface)
self.shown_lewis_structure = True
