def __init__(self, atomlist):
# convert the list of atoms into a list of 3d points
nat = len(atomlist)
pos = XYZ.atomlist2vector(atomlist)
points = []
for i in range(0, nat):
points.append(pos[3 * i:3 * (i + 1)])
# QHull needs at least 4 point to construct the initial
# simplex.
if nat < 4:
# If there are less than 4 atoms,
# we add the center of mass as an additional point
masses = AtomicData.atomlist2masses(atomlist)
com = MolCo.center_of_mass(masses, pos)
points.append(com)
if nat < 3:
# If there are less than 3 atoms we add
# an arbitrary point on the x-axis
points.append(com + np.array([0.0005, 0.0, 0.0]))
if nat < 2:
# If there is only one atom, we add another arbitrary
# point on the y-axis
points.append(com + np.array([0.0, 0.0005, 0.0]))
# We add small random numbers to the input coordinates, so that
# we get a 3D convex hull even if the molecule is planar
points = np.array(points) + 0.0001 * np.random.rand(len(points), 3)
# find the convex hull using the qhull code
hull = ConvexHull(points, qhull_options="QbB Qt")
# call the constructor of the parent class (MinimalEnclosingBox)
super(MoleculeBox, self).__init__(hull)
def molecular_frame_transformation(atomlist):
"""
The molecule is shifted to the center of mass and its principle axes of inertia are aligned
with the coordinate axes. This standard orientation defines the molecular frame.
The translation vector and Euler angles needed to transform the geometry from the
molecular frame to the original frame are also returned.
Returns:
========
atomlist_std: molecular geometry in standard orientation
(a,b,g): Euler angles in z-y-z convention
cm: 3D vector with center of mass
"""
pos = XYZ.atomlist2vector(atomlist)
masses = AtomicData.atomlist2masses(atomlist)
# shift center of mass to origin
Nat = len(atomlist)
pos_std = np.zeros(pos.shape)
cm = center_of_mass(masses, pos)
for i in range(0, Nat):
pos_std[3*i:3*i+3] = pos[3*i:3*i+3] - cm
(a,b,g) = euler_angles_inertia(masses, pos_std)
R = EulerAngles2Rotation(a,b,g)
for i in range(0, Nat):
pos_std[3*i:3*i+3] = np.dot(R, pos_std[3*i:3*i+3])
atomlist_std = XYZ.vector2atomlist(pos_std, atomlist)
# The MolecularCoord module uses a strange convention for Euler angles.
# Therefore we extract the Euler angles in z-y-z convention directly
# from the rotation matrix, that rotates the molecule from the standard
# orientation into the original orientation
Rinv = R.transpose()
a,b,g = rotation2EulerAngles(Rinv, convention="z-y-z")
return atomlist_std, (a,b,g), cm
def partition_kinetic_energy(atomlists, dt):
Nt = len(atomlists)
# determine the indeces of the molecular fragments at the first
# time-step.
fragments_graph = MolecularGraph.atomlist2graph(atomlists[0])
fragments_indeces = [
MolecularGraph.graph2indeces(g) for g in fragments_graph
]
fragment_atomlists = [[[atomlist[ii] for ii in I]
for atomlist in atomlists]
for I in fragments_indeces]
# compute vibrational and center of mass kinetic energy for each fragment
Nfrag = len(fragment_atomlists)
ekin_com = np.zeros((Nt, Nfrag))
ekin_tot = np.zeros((Nt, Nfrag))
for f in range(0, Nfrag):
masses = AtomicData.atomlist2masses(fragment_atomlists[f][0])
print((fragment_atomlists[f][0]))
# total mass
M = np.sum(masses) / 3.0
positions, velocities = velocities_finite_diff(fragment_atomlists[f],
dt)
for i in range(0, Nt):
vm = velocities[i] * masses
vel_com = np.array(
[np.sum(vm[0::3]),
np.sum(vm[1::3]),
np.sum(vm[2::3])]) / M
ekin_com_f = 1.0 / 2.0 * M * np.sum(vel_com**2)
ekin_tot_f = 1.0 / 2.0 * np.sum(masses * velocities[i]**2)
ekin_com[i, f] += ekin_com_f
ekin_tot[i, f] += ekin_tot_f
return ekin_com, ekin_tot
def wigner_from_G09_hessian(g09_file, Nsample=100, zero_threshold=1.0e-9):
"""
create Wigner ensemble based on hessian matrix from Gaussian 09 calculation
"""
suffix = g09_file.split(".")[-1]
if suffix in ["out", "log"]:
print("Reading Gaussian 09 log file %s" % g09_file)
atomlist = Gaussian.read_geometry(g09_file)
forces = Gaussian.read_forces(g09_file)
hess = Gaussian.read_force_constants(g09_file)
elif suffix in ["fchk"]:
print("Reading formatted Gaussian 09 checkpoint file %s" % g09_file)
Data = Checkpoint.parseCheckpointFile(g09_file)
# cartesian coordinates
pos = Data["_Current_cartesian_coordinates"]
atnos = Data["_Atomic_numbers"]
# forces
frc = -Data["_Cartesian_Gradient"]
atomlist = []
forces = []
for i, Zi in enumerate(atnos):
atomlist.append((Zi, tuple(pos[3 * i:3 * (i + 1)])))
forces.append((Zi, tuple(frc[3 * i:3 * (i + 1)])))
# Hessian
hess = Data["_Cartesian_Force_Constants"]
masses = np.array(AtomicData.atomlist2masses(atomlist))
x0 = XYZ.atomlist2vector(atomlist)
x0 = shift_to_com(x0, masses)
grad = -XYZ.atomlist2vector(forces)
grad_nrm = la.norm(grad)
print(" gradient norm = %s" % grad_nrm)
# assert grad_nrm < 1.0e-3, "Gradient norm too large for minimum!"
vib_freq, vib_modes = vibrational_analysis(hess,
masses,
zero_threshold=zero_threshold)
Aw, Bw = wigner_distribution(x0,
hess,
masses,
zero_threshold=zero_threshold)
gw = GaussianWavepacket.Gaussian(Aw, Bw)
qs, ps = gw.sample(Nsample)
mx = np.outer(masses, np.ones(Nsample)) * qs
avg_com = np.mean(np.sum(mx[::3, :], axis=0)), np.mean(
np.sum(mx[1::3, :], axis=0)), np.mean(np.sum(mx[2::3, :], axis=0))
print(avg_com)
geometries = [
XYZ.vector2atomlist(qs[:, i], atomlist) for i in range(0, Nsample)
]
return geometries
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 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 dynamics_in_format(atomlist, q, p, fname):
atomlist_q = XYZ.vector2atomlist(q, atomlist)
masses = AtomicData.atomlist2masses(atomlist)
Nat = len(atomlist_q)
txt = "%d\n" % Nat
# positions in bohr
for Zi, (x, y, z) in atomlist_q:
atname = AtomicData.atom_names[Zi - 1]
txt += "%4s %+10.15f %+10.15f %+10.15f\n" % (atname, x, y, z)
# velocities in bohr/s
vel = p / masses
for i in range(0, Nat):
vx, vy, vz = vel[3 * i:3 * (i + 1)]
txt += " %+10.15f %+10.15f %+10.15f\n" % (vx, vy, vz)
return txt
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 cut_sphere(atomlist, R=20.0):
"""
remove all atoms outside sphere
Parameters:
===========
atomlist
R: radius of sphere in bohr
Returns:
========
atomlist with atoms inside sphere
"""
# shift to center of mass
masses = AtomicData.atomlist2masses(atomlist)
pos = XYZ.atomlist2vector(atomlist)
pos_shifted = MolecularCoords.shift_to_com(pos, masses)
atomlist = XYZ.vector2atomlist(pos_shifted, atomlist)
Con = connectivity(atomlist)
print("recursively remove connected atoms...")
removed = [] # list of removed indeces
for i,(Zi,posi) in enumerate(atomlist):
print("i = %s" % i)
if la.norm(posi) > R:
if not (i in removed):
print("remove %s%d" % (AtomicData.atom_names[Zi-1], i))
removed.append(i)
# remove connect atoms
connected = find_connected(Con, i)
print("and connected atoms %s" % connected)
removed += connected
removed = set(removed)
cut_atomlist = []
for i,(Zi,posi) in enumerate(atomlist):
if i in removed:
pass
else:
cut_atomlist.append( (Zi, posi) )
return cut_atomlist
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 qmf3_in_format(atomlist, q, p, fname):
"""
Save initial conditions in the format expected by Matthias' QMF3 program
"""
atomlist_q = XYZ.vector2atomlist(q, atomlist)
masses = AtomicData.atomlist2masses(atomlist)
Nat = len(atomlist_q)
txt = "$coordinates [\n"
# positions in bohr
for Zi, (x, y, z) in atomlist_q:
atname = AtomicData.atom_names[Zi - 1]
txt += "%4s %+10.15f %+10.15f %+10.15f\n" % (atname, x, y, z)
txt += "]\n"
# velocities in bohr/s
vel = p / masses
txt += "$velocities [\n"
for i in range(0, Nat):
vx, vy, vz = vel[3 * i:3 * (i + 1)]
txt += " %+10.15f %+10.15f %+10.15f\n" % (vx, vy, vz)
txt += "]\n"
txt += "$end\n"
return txt
xyz_file = args[0]
# ... Hessian of energy
hessian_file = args[1]
# output file
state_file = args[2]
# load minimum geometry and Hessian
atomlist = XYZ.read_xyz(xyz_file)[-1]
hess = np.loadtxt(hessian_file)
print "optimized geometry read from '%s'" % xyz_file
print "Hessian read from '%s'" % hessian_file
# compute normal modes and frequencies
xopt = XYZ.atomlist2vector(atomlist)
masses = AtomicData.atomlist2masses(atomlist)
# setting zero_threshold to -0.1 makes sure that all frequencies are returned
# even if some of them are imaginary
vib_freq, vib_modes = HarmonicApproximation.vibrational_analysis(xopt, hess, masses, \
zero_threshold=-0.1, is_molecule=True)
# sort frequencies in ascending order
vib_freq = vib_freq.real
sort_index = np.argsort(abs(vib_freq)**2)
vib_freq = vib_freq[sort_index]
vib_modes = vib_modes[:, sort_index]
# remove lowest 6 vibrations (3 translation + 3 rotation) assuming the molecule
# is not linear
nat = len(atomlist)
nvib = 3 * nat - 6
def minimize(self):
I = self.state
# convert geometry to a vector
x0 = XYZ.atomlist2vector(self.atomlist)
# This member variable holds the last energy of the state
# of interest.
self.enI = 0.0
# last available energies of all electronic states that were
# calculated
self.energies = None
# FIND ENERGY MINIMUM
# f is the objective function that should be minimized
# it returns (f(x), f'(x))
def f_cart(x):
#
if I == 0 and type(self.pes.tddftb.XmY) != type(None):
# Only ground state is needed. However, at the start
# a single TD-DFT calculation is performed to initialize
# all variables (e.g. X-Y), so that the program does not
# complain about non-existing variables.
enI, gradI = self.pes.getEnergyAndGradient_S0(x)
energies = np.array([enI])
else:
energies, gradI = self.pes.getEnergiesAndGradient(x, I)
enI = energies[I]
self.enI = enI
self.energies = energies
print("E = %2.7f |grad| = %2.7f" % (enI, la.norm(gradI)))
#
# also save geometries from line searches
save_xyz(x)
return enI, gradI
print("Intermediate geometries will be written to %s" % self.xyz_opt)
# This is a callback function that is executed for each optimization step.
# It appends the current geometry to an xyz-file.
def save_xyz(x, mode="a"):
self.atomlist = XYZ.vector2atomlist(x, self.atomlist)
XYZ.write_xyz(self.xyz_opt, [self.atomlist], \
title="charge=%s energy= %s" % (self.geom_kwds.get("charge",0), self.enI),\
mode=mode)
return x
Nat = len(self.atomlist)
if self.coord_system == "cartesian":
print(
"optimization is performed directly in cartesian coordinates")
q0 = x0
objective_func = f_cart
save_geometry = save_xyz
max_steplen = None
elif self.coord_system == "internal":
print(
"optimization is performed in redundant internal coordinates")
# transform cartesian to internal coordinates, x0 ~ q0
q0 = self.IC.cartesian2internal(x0)
# define functions that wrap the cartesian<->internal transformations
def objective_func(q):
# transform back from internal to cartesian coordinates
x = self.IC.internal2cartesian(q)
self.IC.cartesian2internal(x)
# compute energy and gradient in cartesian coordinates
en, grad_cart = f_cart(x)
# transform gradient to internal coordinates
grad = self.IC.transform_gradient(x, grad_cart)
return en, grad
def save_geometry(q, **kwds):
# transform back from internal to cartesian coordinates
x = self.IC.internal2cartesian(q)
# save cartesian coordinates
save_xyz(x, **kwds)
return x
def max_steplen(q0, v):
"""
find a step size `a` such that the internal->cartesian
transformation converges for the point q = q0+a*v
"""
a = 1.0
for i in range(0, 7):
q = q0 + a * v
try:
x = self.IC.internal2cartesian(q)
except NotConvergedError as e:
# reduce step size by factor of 1/2
a /= 2.0
continue
break
else:
raise RuntimeError(
"Could not find a step size for which the transformation from internal to cartesian coordinates would work for q=q0+a*v! Last step size a= %e |v|= %e |a*v|= %e"
% (a, la.norm(v), la.norm(a * v)))
return a
else:
raise ValueError("Unknown coordinate system '%s'!" %
self.coord_system)
# save initial energy and geometry
objective_func(q0)
save_geometry(q0, mode="w")
options = {
'gtol': self.grad_tol,
'maxiter': self.maxiter,
'gtol': self.grad_tol,
'norm': 2
}
if self.method == 'CG':
# The "BFGS" method is probably better than "CG", but the line search in BFGS is expensive.
res = optimize.minimize(objective_func,
q0,
method="CG",
jac=True,
callback=save_geometry,
options=options)
#res = optimize.minimize(objective_func, q0, method="BFGS", jac=True, callback=save_geometry, options=options)
elif self.method in ['Steepest Descent', 'Newton', 'BFGS']:
# My own implementation of optimization algorithms
res = minimize(
objective_func,
q0,
method=self.method,
#line_search_method="largest",
callback=save_geometry,
max_steplen=max_steplen,
maxiter=self.maxiter,
gtol=self.grad_tol,
ftol=self.func_tol)
else:
raise ValueError("Unknown optimization algorithm '%s'!" %
self.method)
# save optimized geometry
qopt = res.x
Eopt = res.fun
xopt = save_geometry(qopt)
print("Optimized geometry written to %s" % self.xyz_opt)
if self.calc_hessian == 1:
# COMPUTE HESSIAN AND VIBRATIONAL MODES
# The hessian is calculated by numerical differentiation of the
# analytical cartesian gradients
def grad(x):
en, grad_cart = f_cart(x)
return grad_cart
print("Computing Hessian")
hess = HarmonicApproximation.numerical_hessian_G(grad, xopt)
np.savetxt("hessian.dat", hess)
masses = AtomicData.atomlist2masses(atomlist)
vib_freq, vib_modes = HarmonicApproximation.vibrational_analysis(xopt, hess, masses, \
zero_threshold=1.0e-9, is_molecule=True)
# compute thermodynamic quantities and write summary
thermo = Thermochemistry.Thermochemistry(
atomlist, Eopt, vib_freq,
self.pes.tddftb.dftb2.getSymmetryGroup())
thermo.calculate()
# write vibrational modes to molden file
molden = MoldenExporterSectioned(self.pes.tddftb.dftb2)
atomlist_opt = XYZ.vector2atomlist(xopt, atomlist)
molden.addVibrations(atomlist_opt, vib_freq.real,
vib_modes.transpose())
molden.export("vib.molden")
## It's better to use the script initial_conditions.py for sampling from the Wigner
## distribution
"""
(opts, args) = parser.parse_args()
if len(args) < 2:
print usage
exit(-1)
xyz_file = args[0]
hess_file = args[1]
# should be options
# optimized geometry
atomlist = XYZ.read_xyz(xyz_file)[-1]
xopt = XYZ.atomlist2vector(atomlist)
# load hessian
hess = np.loadtxt(hess_file)
masses = AtomicData.atomlist2masses(atomlist)
vib_freq, vib_modes = HarmonicApproximation.vibrational_analysis(xopt, hess, masses, \
zero_threshold=opts.zero_threshold, is_molecule=True)
# SAMPLE INITIAL CONDITIONS FROM WIGNER DISTRIBUTION
qs, ps = HarmonicApproximation.initial_conditions_wigner(
xopt,
hess,
masses,
Nsample=opts.Nsample,
zero_threshold=opts.zero_threshold)
# make hydrogens slower
for i in range(0, opts.Nsample):
for A, (Z, pos) in enumerate(atomlist):
if Z == 1:
ps[3 * A:3 * (A + 1), i] *= 0.001
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 __init__(self, atomlist, freeze=[], explicit_bonds=[], verbose=0):
"""
setup system of internal coordinates using
valence bonds, angles and dihedrals
Parameters
----------
atomlist : list of tuples (Z,[x,y,z]) with molecular
geometry, connectivity defines the valence
coordinates
Optional
--------
freeze : list of tuples of atom indices (starting at 0) corresponding
to internal coordinates that should be frozen
explicit_bonds : list of pairs of atom indices (starting at 0) between which artificial
bonds should be inserted, i.e. [(0,1), (10,20)].
This allows to connect separate fragments.
verbose : write out additional information if > 0
"""
self.verbose = verbose
self.atomlist = atomlist
self.masses = AtomicData.atomlist2masses(self.atomlist)
# Bonds, angles and torsions are constructed by the force field.
# Atom types, partial charges and lattice vectors
# all don't matter, so we assign atom type 6 (C_R, carbon in resonance)
# to all atoms.
atomtypes = [6 for atom in atomlist]
partial_charges = [0.0 for atom in atomlist]
lattice_vectors = [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0]]
# But since the covalent radii are wrong, we have to provide
# the connectivity matrix
conmat = XYZ.connectivity_matrix(atomlist, hydrogen_bonds=True)
# insert artificial bonds
for (I, J) in explicit_bonds:
print("explicit bond between atoms %d-%d" % (I + 1, J + 1))
conmat[I, J] = 1
# Internal coordinates only work if the molecule does not
# contain disconnected fragments, since there is no way how the
# interfragment distance could be expressed in terms of internal coordinates.
# We need to check that there is only a single fragment.
fragment_graphs = MolecularGraph.atomlist2graph(self.atomlist,
conmat=conmat)
nr_fragments = len(fragment_graphs)
error_msg = "The molecule consists of %d disconnected fragments.\n" % nr_fragments
error_msg += "Internal coordinates only work if all atoms in the molecular graph are connected.\n"
error_msg += "Disconnected fragments may be joined via an artificial bond using the\n"
error_msg += "`explicit_bonds` option.\n"
assert nr_fragments == 1, error_msg
# Frozen degrees of freedom do not necessarily correspond to physical bonds
# or angles. For instance we can freeze the H-H distance in water although there
# is no bond between the hydrogens. To allow the definition of such 'unphysical'
# internal coordinates, we have to modify the connectivity matrix and introduce
# artificial bonds.
for IJKL in freeze:
if len(IJKL) == 2:
I, J = IJKL
# create artificial bond between atoms I and J
conmat[I, J] = 1
elif len(IJKL) == 3:
I, J, K = IJKL
# create artifical bonds I-J and J-K so that the valence angle I-J-K exists
conmat[I, J] = 1
conmat[J, K] = 1
elif len(IJKL) == 4:
I, J, K, L = IJKL
# create artifical bonds I-J, J-K and K-L so that the dihedral angle I-J-K-L
# exists
conmat[I, J] = 1
conmat[J, K] = 1
conmat[K, L] = 1
# cutoff for small singular values when solving the
# linear system of equations B.dx = dq in a least square
# sense.
self.cond_threshold = 1.0e-10
self.force_field = PeriodicForceField(atomlist,
atomtypes,
partial_charges,
lattice_vectors, [],
connectivity_matrix=conmat,
verbose=1)
x0 = XYZ.atomlist2vector(atomlist)
# shift molecule to center of mass
self.x0 = MolCo.shift_to_com(x0, self.masses)
self._selectActiveInternals(freeze=freeze)
def __init__(self, xyz_file, dyson_file=None):
super(Main, self).__init__()
self.settings = Settings({
"Continuum Orbital": {
"Ionization transitions":
[0, ["only intra-atomic", "inter-atomic"]]
},
"Averaging": {
"Euler angle grid points": 5,
"polar angle grid points": 1000,
"sphere radius Rmax": 300.0,
},
"Scan": {
"nr. points": 20
},
"Cube": {
"extra space / bohr": 15.0,
"points per bohr": 3.0
}
})
# perform DFTB calculation
# BOUND ORBITAL = H**O
self.atomlist = XYZ.read_xyz(xyz_file)[0]
# shift molecule to center of mass
print "shift molecule to center of mass"
pos = XYZ.atomlist2vector(self.atomlist)
masses = AtomicData.atomlist2masses(self.atomlist)
pos_com = MolCo.shift_to_com(pos, masses)
self.atomlist = XYZ.vector2atomlist(pos_com, self.atomlist)
self.tddftb = LR_TDDFTB(self.atomlist)
self.tddftb.setGeometry(self.atomlist, charge=0)
options = {"nstates": 1}
try:
self.tddftb.getEnergies(**options)
except DFTB.Solver.ExcitedStatesNotConverged:
pass
self.valorbs, radial_val = load_pseudo_atoms(self.atomlist)
if dyson_file == None:
# Kohn-Sham orbitals are taken as Dyson orbitals
self.H**O, self.LUMO = self.tddftb.dftb2.getFrontierOrbitals()
self.bound_orbs = self.tddftb.dftb2.getKSCoefficients()
self.orbe = self.tddftb.dftb2.getKSEnergies()
orbital_names = []
norb = len(self.orbe)
for o in range(0, norb):
if o < self.H**O:
name = "occup."
elif o == self.H**O:
name = "H**O"
elif o == self.LUMO:
name = "LUMO "
else:
name = "virtual"
name = name + " " + str(o).rjust(4) + (
" %+10.3f eV" % (self.orbe[o] * 27.211))
orbital_names.append(name)
initially_selected = self.H**O
else:
# load coefficients of Dyson orbitals from file
names, ionization_energies, self.bound_orbs = load_dyson_orbitals(
dyson_file)
self.orbe = np.array(ionization_energies) / 27.211
orbital_names = []
norb = len(self.orbe)
for o in range(0, norb):
name = names[o] + " " + str(o).rjust(4) + (
" %4.2f eV" % (self.orbe[o] * 27.211))
orbital_names.append(name)
initially_selected = 0
self.photo_kinetic_energy = slako_tables_scattering.energies[0]
self.epol = np.array([15.0, 0.0, 0.0])
# Build Graphical User Interface
main = QtGui.QWidget()
mainLayout = QtGui.QHBoxLayout(main)
#
selectionFrame = QtGui.QFrame()
selectionFrame.setSizePolicy(QtGui.QSizePolicy.Fixed,
QtGui.QSizePolicy.Preferred)
mainLayout.addWidget(selectionFrame)
selectionLayout = QtGui.QVBoxLayout(selectionFrame)
#
label = QtGui.QLabel(selectionFrame)
label.setText("Select bound MO:")
selectionLayout.addWidget(label)
# bound orbitals
self.orbitalSelection = QtGui.QListWidget(selectionFrame)
self.orbitalSelection.itemSelectionChanged.connect(
self.selectBoundOrbital)
norb = len(self.orbe)
self.orbital_dict = {}
for o in range(0, norb):
name = orbital_names[o]
self.orbital_dict[name] = o
item = QtGui.QListWidgetItem(name, self.orbitalSelection)
if o == initially_selected:
selected_orbital_item = item
selectionLayout.addWidget(self.orbitalSelection)
### VIEWS
center = QtGui.QWidget()
mainLayout.addWidget(center)
centerLayout = QtGui.QGridLayout(center)
#
boundFrame = QtGui.QFrame()
centerLayout.addWidget(boundFrame, 1, 1)
boundLayout = QtGui.QVBoxLayout(boundFrame)
# "Bound Orbital"
label = QtGui.QLabel(boundFrame)
label.setText("Bound Orbital")
boundLayout.addWidget(label)
#
self.boundOrbitalViewer = QCubeViewerWidget(boundFrame)
boundLayout.addWidget(self.boundOrbitalViewer)
# continuum orbital
continuumFrame = QtGui.QFrame()
centerLayout.addWidget(continuumFrame, 1, 2)
continuumLayout = QtGui.QVBoxLayout(continuumFrame)
# "Dipole-Prepared Continuum Orbital"
label = QtGui.QLabel(continuumFrame)
label.setText("Dipole-Prepared Continuum Orbital")
continuumLayout.addWidget(label)
self.continuumOrbitalViewer = QCubeViewerWidget(continuumFrame)
continuumLayout.addWidget(self.continuumOrbitalViewer)
self.efield_objects = []
self.efield_actors = []
self.selected = None
# picker
self.picker = self.continuumOrbitalViewer.visualization.scene.mayavi_scene.on_mouse_pick(
self.picker_callback)
self.picker.tolerance = 0.01
# PHOTO KINETIC ENERGY
sliderFrame = QtGui.QFrame(continuumFrame)
continuumLayout.addWidget(sliderFrame)
sliderLayout = QtGui.QHBoxLayout(sliderFrame)
# label
self.pke_label = QtGui.QLabel()
self.pke_label.setText("PKE: %6.4f eV" %
(self.photo_kinetic_energy * 27.211))
sliderLayout.addWidget(self.pke_label)
# Slider for changing the PKE
self.pke_slider = QtGui.QSlider(QtCore.Qt.Horizontal)
self.pke_slider.setMinimum(0)
self.pke_slider.setMaximum(len(slako_tables_scattering.energies) - 1)
self.pke_slider.setValue(0)
self.pke_slider.sliderReleased.connect(self.changePKE)
self.pke_slider.valueChanged.connect(self.searchPKE)
sliderLayout.addWidget(self.pke_slider)
#
# molecular frame photoangular distribution
mfpadFrame = QtGui.QFrame()
centerLayout.addWidget(mfpadFrame, 2, 1)
mfpadLayout = QtGui.QVBoxLayout(mfpadFrame)
mfpadLayout.addWidget(QtGui.QLabel("Molecular Frame PAD"))
mfpadTabs = QtGui.QTabWidget()
mfpadLayout.addWidget(mfpadTabs)
# 2D map
mfpadFrame2D = QtGui.QFrame()
mfpadTabs.addTab(mfpadFrame2D, "2D")
mfpadLayout2D = QtGui.QVBoxLayout(mfpadFrame2D)
self.MFPADfig2D = Figure()
self.MFPADCanvas2D = FigureCanvas(self.MFPADfig2D)
mfpadLayout2D.addWidget(self.MFPADCanvas2D)
self.MFPADCanvas2D.draw()
NavigationToolbar(self.MFPADCanvas2D, mfpadFrame2D, coordinates=True)
# 3D
mfpadFrame3D = QtGui.QFrame()
mfpadTabs.addTab(mfpadFrame3D, "3D")
mfpadLayout3D = QtGui.QVBoxLayout(mfpadFrame3D)
self.MFPADfig3D = Figure()
self.MFPADCanvas3D = FigureCanvas(self.MFPADfig3D)
mfpadLayout3D.addWidget(self.MFPADCanvas3D)
self.MFPADCanvas3D.draw()
NavigationToolbar(self.MFPADCanvas3D, mfpadFrame3D, coordinates=True)
# orientation averaged photoangular distribution
avgpadFrame = QtGui.QFrame()
centerLayout.addWidget(avgpadFrame, 2, 2)
avgpadLayout = QtGui.QVBoxLayout(avgpadFrame)
self.activate_average = QtGui.QCheckBox("Orientation Averaged PAD")
self.activate_average.setToolTip(
"Check this box to start averaging of the molecular frame PADs over all orientations. This can take a while."
)
self.activate_average.setCheckState(QtCore.Qt.Unchecked)
self.activate_average.stateChanged.connect(self.activateAveragedPAD)
avgpadLayout.addWidget(self.activate_average)
avgpadTabs = QtGui.QTabWidget()
avgpadLayout.addWidget(avgpadTabs)
# 1D map
avgpadFrame1D = QtGui.QFrame()
avgpadTabs.addTab(avgpadFrame1D, "1D")
avgpadLayout1D = QtGui.QVBoxLayout(avgpadFrame1D)
self.AvgPADfig1D = Figure()
self.AvgPADCanvas1D = FigureCanvas(self.AvgPADfig1D)
avgpadLayout1D.addWidget(self.AvgPADCanvas1D)
self.AvgPADCanvas1D.draw()
NavigationToolbar(self.AvgPADCanvas1D, avgpadFrame1D, coordinates=True)
# 2D map
avgpadFrame2D = QtGui.QFrame()
avgpadFrame2D.setToolTip(
"The averaged PAD should have no phi-dependence anymore. A phi-dependence is a sign of incomplete averaging."
)
avgpadTabs.addTab(avgpadFrame2D, "2D")
avgpadLayout2D = QtGui.QVBoxLayout(avgpadFrame2D)
self.AvgPADfig2D = Figure()
self.AvgPADCanvas2D = FigureCanvas(self.AvgPADfig2D)
avgpadLayout2D.addWidget(self.AvgPADCanvas2D)
self.AvgPADCanvas2D.draw()
NavigationToolbar(self.AvgPADCanvas2D, avgpadFrame2D, coordinates=True)
# Table
avgpadFrameTable = QtGui.QFrame()
avgpadTabs.addTab(avgpadFrameTable, "Table")
avgpadLayoutTable = QtGui.QVBoxLayout(avgpadFrameTable)
self.avgpadTable = QtGui.QTableWidget(0, 6)
self.avgpadTable.setToolTip(
"Activate averaging and move the PKE slider above to add a new row with beta values. After collecting betas for different energies you can save the table or plot a curve beta(PKE) for the selected orbital."
)
self.avgpadTable.setHorizontalHeaderLabels(
["PKE / eV", "sigma", "beta1", "beta2", "beta3", "beta4"])
avgpadLayoutTable.addWidget(self.avgpadTable)
# Buttons
buttonFrame = QtGui.QFrame()
avgpadLayoutTable.addWidget(buttonFrame)
buttonLayout = QtGui.QHBoxLayout(buttonFrame)
deleteButton = QtGui.QPushButton("Delete")
deleteButton.setToolTip("clear table")
deleteButton.clicked.connect(self.deletePADTable)
buttonLayout.addWidget(deleteButton)
buttonLayout.addSpacing(3)
scanButton = QtGui.QPushButton("Scan")
scanButton.setToolTip(
"fill table by scanning automatically through all PKE values")
scanButton.clicked.connect(self.scanPADTable)
buttonLayout.addWidget(scanButton)
saveButton = QtGui.QPushButton("Save")
saveButton.setToolTip("save table as a text file")
saveButton.clicked.connect(self.savePADTable)
buttonLayout.addWidget(saveButton)
plotButton = QtGui.QPushButton("Plot")
plotButton.setToolTip("plot beta2 column as a function of PKE")
plotButton.clicked.connect(self.plotPADTable)
buttonLayout.addWidget(plotButton)
"""
# DOCKS
self.setDockOptions(QtGui.QMainWindow.AnimatedDocks | QtGui.QMainWindow.AllowNestedDocks)
#
selectionDock = QtGui.QDockWidget(self)
selectionDock.setWidget(selectionFrame)
selectionDock.setFeatures(QtGui.QDockWidget.DockWidgetFloatable | QtGui.QDockWidget.DockWidgetMovable)
self.addDockWidget(QtCore.Qt.DockWidgetArea(1), selectionDock)
#
boundDock = QtGui.QDockWidget(self)
boundDock.setWidget(boundFrame)
boundDock.setFeatures(QtGui.QDockWidget.DockWidgetFloatable | QtGui.QDockWidget.DockWidgetMovable)
boundDock.setSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Preferred)
self.addDockWidget(QtCore.Qt.DockWidgetArea(2), boundDock)
#
continuumDock = QtGui.QDockWidget(self)
continuumDock.setWidget(continuumFrame)
continuumDock.setFeatures(QtGui.QDockWidget.DockWidgetFloatable | QtGui.QDockWidget.DockWidgetMovable)
continuumDock.setSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Preferred)
self.addDockWidget(QtCore.Qt.DockWidgetArea(2), continuumDock)
"""
self.setCentralWidget(main)
self.status_bar = QtGui.QStatusBar(main)
self.setStatusBar(self.status_bar)
self.default_message = "Click on the tip of the green arrow in the top right figure to change the orientation of the E-field"
self.statusBar().showMessage(self.default_message)
# Menu bar
menubar = self.menuBar()
exitAction = QtGui.QAction('&Exit', self)
exitAction.setShortcut('Ctrl+Q')
exitAction.setStatusTip('Exit program')
exitAction.triggered.connect(exit)
fileMenu = menubar.addMenu('&File')
fileMenu.addAction(exitAction)
settingsMenu = menubar.addMenu('&Edit')
settingsAction = QtGui.QAction('&Settings...', self)
settingsAction.setStatusTip('Edit settings')
settingsAction.triggered.connect(self.editSettings)
settingsMenu.addAction(settingsAction)
self.loadContinuum()
# select H**O
selected_orbital_item.setSelected(True)
def __init__(self,
atomlist,
E0,
vib_freq,
symmetry_group,
pressure=AtomicData.atm_pressure,
temperature=AtomicData.satp_temperature):
"""
temperature in Kelvin
"""
self.E0 = E0
self.P = pressure
self.T = temperature
self.vib_freq = vib_freq
self.symmetry_group = symmetry_group
self.atomlist = atomlist
Nat = len(atomlist)
self.masses = AtomicData.atomlist2masses(self.atomlist)
# compute rotational constants from tensor of inertia
x0 = XYZ.atomlist2vector(atomlist)
# shift the origin to the center of mass
x0_shift = MolCo.shift_to_com(x0, self.masses)
# diagonalize the tensor of inertia to obtain the principal moments and
# the normalized eigenvectors of I
Inert = MolCo.inertial_tensor(self.masses, x0_shift)
principle_moments, X = la.eigh(Inert)
Iaa, Ibb, Icc = np.sort(abs(principle_moments))
print("principle moments of inertia (in a.u.): %s %s %s" %
(Iaa, Ibb, Icc))
# In a linear triatomic molecule we have Icc = Ibb > Iaa = 0
self.is_linear = False
if abs(Icc - Ibb) / abs(Icc) < 1.0e-6 and abs(Iaa) / abs(Icc) < 1.0e-6:
self.is_linear = True
print("Molecule is linear")
# Determine the type of rotor
if self.is_linear == True:
self.rotor_type = "linear rotor"
else:
if abs(Icc - Ibb) / abs(Icc) < 1.0e-4 and abs(Icc - Iaa) / abs(
Icc) < 1.0e-4:
# three equal moments of inertia
self.rotor_type = "spherical rotor"
elif abs(Icc - Ibb) / abs(Icc) < 1.0e-4 or abs(Ibb - Iaa) / abs(
Icc) < 1.0e-4:
# two equal moments of inertia
self.rotor_type = "symmetric rotor"
else:
self.rotor_type = "asymmetric rotor"
# rotational constants
self.rotational_constants = 1.0 / (
2.0 * principle_moments + 1.0e-20
) # avoid division by zero error for a linear molecule, the invalid values are not actually used
# symmetry number
if symmetry_group == None:
print(
"Symmetry group unknown, setting rotational symmetry number to 1"
)
self.sigma_rot = 1
else:
self.sigma_rot = symmetry_group.rotational_symmetry_number()
# beta = 1/(kB*T)
kB = AtomicData.kBoltzmann
self.beta = 1.0 / (kB * self.T)
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
def _update_visualization(self, atomlist, charges, fragments):
"""
only change the underlying data but do not recreate visualization.
This is faster and avoids jerky animations.
"""
mlab = self.scene.mlab
if self.show_flags["charges"] == True:
i = 0
for q,(Z,pos) in zip(charges, atomlist):
x,y,z = pos
if q < 0.0:
color = (0.,0.,1.)
elif q > 0.0:
color = (1.,0.,0.)
else:
color = (1.,1.,1.)
# color does not work so far
txt = "%+2.3f" % q
if self.show_flags["labels"] == True:
# maybe charges should not overlap with labels
txt = "%s" % txt
# update label position and text
label = self.charge_labels[i]
label.remove()
label = mlab.text(x,y, txt, z=z, figure=self.scene.mayavi_scene)
self.charge_labels[i] = label
label.actor.set(text_scale_mode='none', width=0.05, height=0.1)
label.property.set(justification='centered', vertical_justification='centered')
i += 1
if self.show_flags["frag. charges"] == True:
i = 0
for ifrag,(fragment_indeces, fragment_atomlist) in enumerate(fragments):
# compute the charges on fragment
qfrag = np.sum(charges[fragment_indeces])
print "Fragment charges: %s" % charges[fragment_indeces]
# compute the center of the molecule,
pos_frag = XYZ.atomlist2vector(fragment_atomlist)
masses_frag = AtomicData.atomlist2masses(fragment_atomlist)
com = MolCo.center_of_mass(masses_frag, pos_frag)
#
print "Fragment %d charge = %s" % (ifrag, qfrag)
txt = "%+2.3f" % qfrag
label = self.frag_charge_labels[i]
label.remove()
label = mlab.text(com[0],com[1], txt, z=com[2], line_width=0.8, figure=self.scene.mayavi_scene)
self.frag_charge_labels[i] = label
label.actor.set(text_scale_mode='none', width=0.05, height=0.1)
label.property.set(justification='centered', vertical_justification='centered')
i += 1
if self.show_flags["charge clouds"] == True:
vec = XYZ.atomlist2vector(atomlist)
x, y, z = vec[::3], vec[1::3], vec[2::3]
s = abs(charges)
# The charge clouds represent surfaces of equal charge density around each atoms.
# In DFTB the charge fluctuations are modelled by a Gaussian:
# F(r) = 1/(2*pi*sA^2)^(3/2) * exp(-r^2/(2*sA^2))
# The radii of the charge clouds are scaled by the charge on the atom:
# r = q * r0
# The radius r0 belongs to a charge cloud containing exactly 1 electron, it depends
# on the hubbard parameter through sA and on the isoValue:
# F(r0) = F(0) * isoValue
#
r0s = self.charge_cloud_radii.getRadii(atomlist)
s *= r0s
self.cloud.mlab_source.set(x=x,y=y,z=z,u=s,v=s,w=s, scalars=charges, scale_factor=1.0)
# atoms are coloured by their atomic number
self.cloud.glyph.color_mode = "color_by_scalar"
self.cloud.glyph.glyph_source.glyph_source.center = [0,0,0]
self.cloud.module_manager.scalar_lut_manager.lut.table = self.lut
self.cloud.module_manager.scalar_lut_manager.data_range = (-1.0, 1.0)
def _create_visualization(self, atomlist, charges, fragments):
mlab = self.scene.mlab
if self.show_flags["charges"] == True and type(charges) != type(None):
self.charge_labels = []
for q,(Z,pos) in zip(charges, atomlist):
x,y,z = pos
if q < 0.0:
color = (0.,0.,1.)
elif q > 0.0:
color = (1.,0.,0.)
else:
color = (1.,1.,1.)
# color does not work so far
txt = "%+2.3f" % q
if self.show_flags["labels"] == True:
# maybe charges should not overlap with labels
txt = "%s" % txt
label = mlab.text(x,y, txt, z=z, figure=self.scene.mayavi_scene)
label.actor.set(text_scale_mode='none', width=0.05, height=0.1)
label.property.set(justification='centered', vertical_justification='centered')
self.charge_labels.append( label )
self.shown_charges = True
else:
self.shown_charges = False
if self.show_flags["frag. charges"] == True and type(charges) != type(None):
self.frag_charge_labels = []
for ifrag,(fragment_indeces, fragment_atomlist, fragment_box) in enumerate(fragments):
# compute the charges on fragment
qfrag = np.sum(charges[fragment_indeces])
print "Fragment charges: %s" % charges[fragment_indeces]
# compute the center of the molecule,
pos_frag = XYZ.atomlist2vector(fragment_atomlist)
masses_frag = AtomicData.atomlist2masses(fragment_atomlist)
com = MolCo.center_of_mass(masses_frag, pos_frag)
#
print "Fragment %d charge = %s" % (ifrag, qfrag)
txt = "%+2.3f" % qfrag
label = mlab.text(com[0],com[1], txt, z=com[2], line_width=0.8, figure=self.scene.mayavi_scene)
label.actor.set(text_scale_mode='none', width=0.05, height=0.1)
label.property.set(justification='centered', vertical_justification='centered')
self.frag_charge_labels.append( label )
self.shown_frag_charges = True
else:
self.shown_frag_charges = False
if self.show_flags["charge clouds"] == True and type(charges) != type(None):
self.charge_clouds = []
vec = XYZ.atomlist2vector(atomlist)
x, y, z = vec[::3], vec[1::3], vec[2::3]
s = abs(charges)
# The charge clouds represent surfaces of equal charge density around each atoms.
# In DFTB the charge fluctuations are modelled by a Gaussian:
# F(r) = 1/(2*pi*sA^2)^(3/2) * exp(-r^2/(2*sA^2))
# The radii of the charge clouds are scaled by the charge on the atom:
# r = q * r0
# The radius r0 belongs to a charge cloud containing exactly 1 electron, it depends
# on the hubbard parameter through sA and on the isoValue:
# F(r0) = F(0) * isoValue
#
r0s = self.charge_cloud_radii.getRadii(atomlist)
s *= r0s
cloud = mlab.quiver3d(x,y,z,s,s,s, scalars=charges,
mode="sphere", scale_factor=1.0, resolution=20,
opacity = 0.4,
figure=self.scene.mayavi_scene)
# atoms are coloured by their atomic number
cloud.glyph.color_mode = "color_by_scalar"
cloud.glyph.glyph_source.glyph_source.center = [0,0,0]
self.lut = cloud.module_manager.scalar_lut_manager.lut.table.to_array()
red = np.array((255.0, 0.0, 0.0)).astype('uint8')
blue = np.array((0.0, 0.0, 255.0)).astype('uint8')
for i in range(0, 255):
if i < 128:
color = blue
else:
color = red
self.lut[i,0:3] = color
cloud.module_manager.scalar_lut_manager.lut.table = self.lut
cloud.module_manager.scalar_lut_manager.data_range = (-1.0, 1.0)
self.cloud = cloud
self.charge_clouds.append( cloud )
self.shown_charge_clouds = True
else:
self.shown_charge_clouds = False
if self.show_flags["dipole moment"] == True and type(charges) != type(None):
self.dipole_vectors = []
# The dipole vector is placed at the center of mass
pos = XYZ.atomlist2vector(atomlist)
masses = AtomicData.atomlist2masses(atomlist)
com = MolCo.center_of_mass(masses, pos)
# compute dipole moment from charge distribution
dipole = np.zeros(3)
for i,q in enumerate(charges):
dipole += q * pos[3*i:3*(i+1)]
print "Dipole moment D = %s a.u." % dipole
# For plotting the dipole vector is converted to Debye
dipole *= AtomicData.ebohr_to_debye
print "Dipole moment D = %s Debye" % dipole
print "Length of dipole moment |D| = %s Debye" % la.norm(dipole)
quiver3d = mlab.quiver3d(com[0],com[1],com[2],
dipole[0], dipole[1], dipole[2], line_width=5.0,
scale_mode='vector',
color=(0,0,1),
scale_factor=1.0)
self.dipole_vectors.append(quiver3d)
else:
self.shown_dipole_moment = False
if self.show_flags["enclosing box"] == True:
self.frag_enclosing_boxes = []
for ifrag,(fragment_indeces, fragment_atomlist, fragment_box) in enumerate(fragments):
box = fragment_box
# plot edges of the enclosing box
for edge in box.edges:
l = mlab.plot3d(box.vertices[edge,0], box.vertices[edge,1], box.vertices[edge,2],
color=(1,0,0),
figure=self.scene.mayavi_scene)
self.frag_enclosing_boxes.append(l)
# plot axes
for axis, color in zip(box.axes, [(1.,0.,0.),(0.,1.,0.), (0.,0.,1.)]):
ax = mlab.quiver3d(float(box.center[0]), float(box.center[1]), float(box.center[2]),
float(axis[0]), float(axis[1]), float(axis[2]),
color=color, scale_factor=3.0, mode='arrow', resolution=20,
figure=self.scene.mayavi_scene)
self.frag_enclosing_boxes.append(ax)
self.shown_enclosing_boxes = True
else:
self.shown_enclosing_boxes = False
if self.show_flags["screening charges (COSMO)"] == True:
# read parameter for solvent model from command line
# or configuration file
parser = OptionParserFuncWrapper([ImplicitSolvent.SolventCavity.__init__], "",
unknown_options="ignore")
# extract only arguments for constructor of solvent cavity
(solvent_options, args) = parser.parse_args(ImplicitSolvent.SolventCavity.__init__)
#
cavity = ImplicitSolvent.SolventCavity(**solvent_options)
cavity.constructSAS(atomlist)
area = cavity.getSurfaceArea()
print "solvent accessible surface area: %8.6f bohr^2 %8.6f Ang^2" % (area, area*AtomicData.bohr_to_angs**2)
points = cavity.getSurfacePoints()
x,y,z = points[:,0], points[:,1], points[:,2]
if type(charges) != type(None):
# If there are Mulliken charges we can compute the
# induced charges on the surface of the cavity
# according to COSMO
cavity.constructCOSMO()
induced_charges = cavity.getInducedCharges(charges)
screening_energy = cavity.getScreeningEnergy(charges)
print "screening energy: %10.6f Hartree %10.6f kcal/mol" \
% (screening_energy, screening_energy * AtomicData.hartree_to_kcalmol)
# The surface points are colored and scaled
# according to their charge
# negative -> blue positive -> red
points3d = mlab.points3d(x,y,z,induced_charges,
colormap="blue-red",
mode='2dcross',
scale_factor=10)
# mode='2dvertex')
points3d.glyph.color_mode = "color_by_scalar"
else:
#
points3d = mlab.points3d(x,y,z,color=(0.0,0.0,0.8), mode='2dvertex')
self.sas_points.append( points3d )
else:
self.shown_solvent_screening_charges = False
if self.show_flags["non-adiab. coupling vectors"] == True:
vec = XYZ.atomlist2vector(atomlist)
x, y, z = vec[::3], vec[1::3], vec[2::3]
# assume that charges are transition charges
transition_charges = charges
# Because we don't know the energy here, the energy difference
# in the denominator is set to 1, so only the direction and relative
# lengths are correct.
nac = NACsApprox.coupling_vector(atomlist, transition_charges, 1.0)
# directions of NAC vectors
u,v,w = nac[0,:], nac[1,:], nac[2,:]
# Add a NAC vector at each atom
quiver3d = mlab.quiver3d(x,y,z, u,v,w, line_width=5.0)
self.nac_vectors.append(quiver3d)
else:
self.shown_nacs = False
def averaged_pad_scan(xyz_file, dyson_file,
selected_orbitals, npts_euler, npts_theta, nskip, inter_atomic, sphere_radius):
molecule_name = os.path.basename(xyz_file).replace(".xyz", "")
atomlist = XYZ.read_xyz(xyz_file)[-1]
# shift molecule to center of mass
print "shift molecule to center of mass"
pos = XYZ.atomlist2vector(atomlist)
masses = AtomicData.atomlist2masses(atomlist)
pos_com = MolCo.shift_to_com(pos, masses)
atomlist = XYZ.vector2atomlist(pos_com, atomlist)
# compute molecular orbitals with DFTB
tddftb = LR_TDDFTB(atomlist)
tddftb.setGeometry(atomlist, charge=0)
options={"nstates": 1}
try:
tddftb.getEnergies(**options)
except DFTB.Solver.ExcitedStatesNotConverged:
pass
valorbs, radial_val = load_pseudo_atoms(atomlist)
if dyson_file == None:
print "tight-binding Kohn-Sham orbitals are taken as Dyson orbitals"
H**O, LUMO = tddftb.dftb2.getFrontierOrbitals()
bound_orbs = tddftb.dftb2.getKSCoefficients()
if selected_orbitals == None:
# all orbitals
selected_orbitals = range(0,bound_orbs.shape[1])
else:
selected_orbitals = eval(selected_orbitals, {}, {"H**O": H**O+1, "LUMO": LUMO+1})
print "Indeces of selected orbitals (counting from 1): %s" % selected_orbitals
orbital_names = ["orb_%s" % o for o in selected_orbitals]
selected_orbitals = np.array(selected_orbitals, dtype=int)-1 # counting from 0
dyson_orbs = bound_orbs[:,selected_orbitals]
ionization_energies = -tddftb.dftb2.getKSEnergies()[selected_orbitals]
else:
print "coeffients for Dyson orbitals are read from '%s'" % dyson_file
orbital_names, ionization_energies, dyson_orbs = load_dyson_orbitals(dyson_file)
ionization_energies = np.array(ionization_energies) / AtomicData.hartree_to_eV
print ""
print "*******************************************"
print "* PHOTOELECTRON ANGULAR DISTRIBUTIONS *"
print "*******************************************"
print ""
# determine the radius of the sphere where the angular distribution is calculated. It should be
# much larger than the extent of the molecule
(xmin,xmax),(ymin,ymax),(zmin,zmax) = Cube.get_bbox(atomlist, dbuff=0.0)
dx,dy,dz = xmax-xmin,ymax-ymin,zmax-zmin
Rmax = max([dx,dy,dz]) + sphere_radius
Npts = max(int(Rmax),1) * 50
print "Radius of sphere around molecule, Rmax = %s bohr" % Rmax
print "Points on radial grid, Npts = %d" % Npts
nr_dyson_orbs = len(orbital_names)
# compute PADs for all selected orbitals
for iorb in range(0, nr_dyson_orbs):
print "computing photoangular distribution for orbital %s" % orbital_names[iorb]
data_file = "betas_" + molecule_name + "_" + orbital_names[iorb] + ".dat"
pad_data = []
print " SCAN"
nskip = max(1, nskip)
# save table
fh = open(data_file, "w")
print " Writing table with betas to %s" % data_file
print>>fh, "# ionization from orbital %s IE = %6.3f eV" % (orbital_names[iorb], ionization_energies[iorb]*AtomicData.hartree_to_eV)
print>>fh, "# inter_atomic: %s npts_euler: %s npts_theta: %s rmax: %s" % (inter_atomic, npts_euler, npts_theta, Rmax)
print>>fh, "# PKE/eV sigma beta1 beta2 beta3 beta4"
for i,E in enumerate(slako_tables_scattering.energies):
if i % nskip != 0:
continue
print " PKE = %6.6f Hartree (%4.4f eV)" % (E, E*AtomicData.hartree_to_eV)
k = np.sqrt(2*E)
wavelength = 2.0 * np.pi/k
bs_free = AtomicScatteringBasisSet(atomlist, E, rmin=0.0, rmax=Rmax+2*wavelength, Npts=Npts)
SKT_bf, SKT_ff = load_slako_scattering(atomlist, E)
Dipole = ScatteringDipoleMatrix(atomlist, valorbs, SKT_bf, inter_atomic=inter_atomic).real
orientation_averaging = PAD.OrientationAveraging_small_memory(Dipole, bs_free, Rmax, E, npts_euler=npts_euler, npts_theta=npts_theta)
pad,betasE = orientation_averaging.averaged_pad(dyson_orbs[:,iorb])
pad_data.append( [E*AtomicData.hartree_to_eV] + list(betasE) )
# save PAD for this energy
print>>fh, "%10.6f %10.6e %+10.6e %+10.6f %+10.6e %+10.6e" % tuple(pad_data[-1])
fh.flush()
fh.close()
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)
