def read_slakoformat(filename):
"""
read Slater Koster tables from different file formats, which
are recognized by the file extension.
The following extensions are supported:
*.skf used by DFTB+
*.par used by hotbit
*.py
Paramters:
==========
filename: path to Slater Koster file
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 exists, basename, dirname, join
if ".skf" in filename:
filename_AB = filename
# load Slater Koster integrals for A atom
sk = read_slakoformat_skf(filename_AB, sk=None, atom_order="AB")
at1, at2 = basename(filename).replace(".skf", "").split("-")
# append Slater Koster integrals for B atom
filename_BA = join(dirname(filename), "%s-%s.skf" % (at2, at1))
sk = read_slakoformat_skf(filename_BA, sk=sk, atom_order="BA")
return sk
elif ".par" in filename:
atom_order = "AB"
if not exists(filename):
# file file A_B.par does not exist, look for file B_A.par
at1, at2 = basename(filename).replace(".par", "").split("_")
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
atom_order = "BA"
assert exists(filename)
sk = read_slakoformat_par(filename, atom_order=atom_order)
return sk
elif ".py" in filename:
# access dictionary by .-notation
mod = utils.dotdic()
execfile(filename, mod)
# mod = weird_sign_change(mod)
return mod
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)
xlabel("r / bohr", fontsize=15)
print "Atom %s" % AtomicData.atom_names[atom.Z-1]
print "========"
for i,orb_name in enumerate(atom.orbital_names):
print "Orbital %s: %s %s" % (orb_name, \
("%2.5f Hartree" % atom.energies[i]).rjust(15), \
("%2.5f eV" % (atom.energies[i]*AtomicData.hartree_to_eV)).rjust(20))
plot(atom.r, atom.radial_wavefunctions[i], lw=2.5, label="%s en=%s" % (orb_name, atom.energies[i]))
# compare with hotbit
if elmfile != None and hbdata.has_key("radial_wavefunction_%s" % orb_name):
ru = hbdata["radial_wavefunction_%s" % orb_name]
en = hbdata["orbital_energy_%s" % orb_name]
plot(ru[:,0], ru[:,1], ls="-.", label="%s en=%s (unconfined)" % (orb_name, en))
legend()
show()
# savefig(pngfile)
if __name__ == "__main__":
if len(sys.argv) < 2:
print "Usage: python %s <pseudo atom module>.py [<.elm file for comparison>]" % sys.argv[0]
print "Plots the atomic orbitals of a pseudo atom."
exit(-1)
modfile = sys.argv[1]
if len(sys.argv) > 2:
elmfile = sys.argv[2]
else:
elmfile = None
mod = utils.dotdic()
execfile(modfile, mod)
plot_pseudoatom(mod, "/tmp/%s.png" % AtomicData.atom_names[mod.Z-1], elmfile)