def exafs_first_shell(S02, energy_shift, absorber,
ignore_elements, edge, neighbor_cutoff, trajectory):
feff_options = {
'RMAX':str(neighbor_cutoff),
'HOLE':'%i %.4f' % (feff_edge_number(edge), S02),
'CORRECTIONS':'%.4f %.4f' % (energy_shift, 0.0),
}
#generate the bulk reference state
atoms = bulk(absorber, orthorhombic=True, cubic=True)
atoms = atoms.repeat((4,4,4))
center = numpy.argmin(numpy.sum((atoms.get_scaled_positions() -
numpy.array( (.5,.5,.5) ))**2.0, axis=1))
#do the bulk reference scattering calculation and get the path
#data from feff
path = run_feff(atoms, center, feff_options, get_path=True)[2]
k = None
chi_total = None
counter = -1
interactions = 0
nl = None
for step, atoms in enumerate(trajectory):
if COMM_WORLD.rank == 0:
print 'step %i/%i' % (step+1, len(trajectory))
atoms = atoms.copy()
if ignore_elements:
ignore_indicies = [atom.index for atom in atoms
if atom.symbol in ignore_elements]
del atoms[ignore_indicies]
if nl == None:
nl = NeighborList(len(atoms)*[neighbor_cutoff], skin=0.3,
self_interaction=False)
nl.update(atoms)
for i in xrange(len(atoms)):
if atoms[i].symbol != absorber:
continue
indicies, offsets = nl.get_neighbors(i)
for j, offset in zip(indicies, offsets):
counter += 1
if counter % COMM_WORLD.size != COMM_WORLD.rank:
continue
r = atoms.get_distance(i,j,True)
if r >= neighbor_cutoff: continue
interactions += 1
k, chi = chi_path(path, r, 0.0, energy_shift, S02, 1)
if chi_total != None:
chi_total += chi
else:
chi_total = chi
chi_total = COMM_WORLD.allreduce(chi_total)
chi_total /= atoms.get_chemical_symbols().count(absorber)
chi_total /= len(trajectory)
chi_total *= 2
return k, chi_total
def exafs_reference_path(z, feff_options):
atoms = bulk(z, orthorhombic=True, cubic=True)
atoms = atoms.repeat((4,4,4))
center = numpy.argmin(numpy.sum((atoms.get_scaled_positions() -
numpy.array( (.5,.5,.5) ))**2.0, axis=1))
#do the bulk reference scattering calculation and get the path
#data from feff
path = run_feff(atoms, center, feff_options, get_path=True)[2]
return path
def exafs_reference_path(z, feff_options):
atoms = bulk(z, orthorhombic=True, cubic=True)
atoms = atoms.repeat((4, 4, 4))
center = numpy.argmin(
numpy.sum((atoms.get_scaled_positions() - numpy.array(
(.5, .5, .5)))**2.0,
axis=1))
#do the bulk reference scattering calculation and get the path
#data from feff
path = run_feff(atoms, center, feff_options, get_path=True)[2]
return path
def exafs_multiple_scattering(S02, energy_shift, absorber, ignore_elements,
edge, rmax, trajectory):
feff_options = {
'RMAX': str(rmax),
'HOLE': '%i %.4f' % (feff_edge_number(edge), S02),
'CORRECTIONS': '%.4f %.4f' % (energy_shift, 0.0),
'NLEG': '4',
}
k = None
chi_total = None
counter = -1
for step, atoms in enumerate(trajectory):
if COMM_WORLD.rank == 0:
time_stamp = strftime("%F %T")
print '[%s] step %i/%i' % (time_stamp, step + 1, len(trajectory))
atoms = atoms.copy()
if ignore_elements:
ignore_indicies = [
atom.index for atom in atoms if atom.symbol in ignore_elements
]
del atoms[ignore_indicies]
for i in xrange(len(atoms)):
counter += 1
if counter % COMM_WORLD.size != COMM_WORLD.rank:
continue
if atoms[i].symbol != absorber:
continue
k, chi = run_feff(atoms, i, feff_options)
if k == None and chi == None:
continue
if chi_total != None:
chi_total += chi
else:
chi_total = chi
#in case too many ranks
k = COMM_WORLD.bcast(k)
if chi_total == None:
chi_total = numpy.zeros(len(k))
chi_total = COMM_WORLD.allreduce(chi_total)
chi_total /= atoms.get_chemical_symbols().count(absorber)
chi_total /= len(trajectory)
return k, chi_total
def exafs_multiple_scattering(S02, energy_shift, absorber,
ignore_elements, edge, rmax, trajectory):
feff_options = {
'RMAX':str(rmax),
'HOLE':'%i %.4f' % (feff_edge_number(edge), S02),
'CORRECTIONS':'%.4f %.4f' % (energy_shift, 0.0),
'NLEG':'4',
}
k = None
chi_total = None
counter = -1
for step, atoms in enumerate(trajectory):
if COMM_WORLD.rank == 0:
time_stamp = strftime("%F %T")
print '[%s] step %i/%i' % (time_stamp, step+1, len(trajectory))
atoms = atoms.copy()
if ignore_elements:
ignore_indicies = [atom.index for atom in atoms
if atom.symbol in ignore_elements]
del atoms[ignore_indicies]
for i in xrange(len(atoms)):
counter += 1
if counter % COMM_WORLD.size != COMM_WORLD.rank:
continue
if atoms[i].symbol != absorber:
continue
k, chi = run_feff(atoms, i, feff_options)
if k is None and chi is None:
continue
if chi_total is not None:
chi_total += chi
else:
chi_total = chi
#in case too many ranks
k = COMM_WORLD.bcast(k)
if chi_total is None:
chi_total = numpy.zeros(len(k))
chi_total = COMM_WORLD.allreduce(chi_total)
chi_total /= atoms.get_chemical_symbols().count(absorber)
chi_total /= len(trajectory)
return k, chi_total
def exafs_multiple_scattering(S02, energy_shift, absorber, ignore_elements, edge, rmax, trajectory):
feff_options = {
"RMAX": str(rmax),
"HOLE": "%i %.4f" % (feff_edge_number(edge), S02),
"CORRECTIONS": "%.4f %.4f" % (energy_shift, 0.0),
"NLEG": "4",
}
k = None
chi_total = None
counter = -1
for step, atoms in enumerate(trajectory):
if COMM_WORLD.rank == 0:
print "step %i/%i" % (step + 1, len(trajectory))
atoms = atoms.copy()
if ignore_elements:
ignore_indicies = [atom.index for atom in atoms if atom.symbol in ignore_elements]
del atoms[ignore_indicies]
for i in xrange(len(atoms)):
counter += 1
if counter % COMM_WORLD.size != COMM_WORLD.rank:
continue
if atoms[i].symbol != absorber:
continue
k, chi = run_feff(atoms, i, feff_options)
if k == None and chi == None:
continue
if chi_total != None:
chi_total += chi
else:
chi_total = chi
chi_total = COMM_WORLD.allreduce(chi_total)
chi_total /= atoms.get_chemical_symbols().count(absorber)
chi_total /= len(trajectory)
return k, chi_total
