def exercise():
from cctbx import factor_kev_angstrom
w = wavelengths.characteristic("CU")
assert w.label() == "Cu"
assert approx_equal(w.as_angstrom(), 1.5418)
assert approx_equal(w.as_kev(), factor_kev_angstrom / 1.5418)
assert approx_equal(w.as_ev() / 1000, factor_kev_angstrom / 1.5418)
n = 0
for w in wavelengths.characteristic_iterator():
n += 1
uu = wavelengths.characteristic(w.label())
assert uu.label() == w.label()
assert uu.as_ev() == w.as_ev()
assert n == 15
def exercise():
from cctbx import factor_kev_angstrom
w = wavelengths.characteristic("CU")
assert w.label() == "Cu"
assert approx_equal(w.as_angstrom(), 1.5418)
assert approx_equal(w.as_kev(), factor_kev_angstrom / 1.5418)
assert approx_equal(w.as_ev() / 1000, factor_kev_angstrom / 1.5418)
n = 0
for w in wavelengths.characteristic_iterator():
n += 1
uu = wavelengths.characteristic(w.label())
assert uu.label() == w.label()
assert uu.as_ev() == w.as_ev()
assert n == 15
def run (args) :
if (len(args) == 0) or ("--help" in args) :
raise Usage("""
eltbx.show_fp_fdp.py --elements=S,CL --wavelength=1.54
eltbx.show_fp_fdp.py --elements=S,CL --source=CuA1""")
parser = option_parser()
parser.add_option('--elements')
parser.add_option('--xray_source')
parser.add_option('--wavelength')
options, args = parser.parse_args(args)
if (options.xray_source is not None) :
print "Source: %s" % options.xray_source
elif (options.wavelength is not None) :
print "Wavelength: %g Angstrom" % float(options.wavelength)
print
for element in options.elements.split(','):
print "Element: %s" % element
fdp = []
for table_name, table in (('Henke et al.', henke.table),
('Sasaki et al.', sasaki.table)):
inelastic_scattering = table(element)
if (options.xray_source) :
fp_fdp = inelastic_scattering.at_angstrom(
wavelengths.characteristic(options.xray_source).as_angstrom())
elif (options.wavelength) :
fp_fdp = inelastic_scattering.at_angstrom(float(options.wavelength))
else :
raise Sorry("Either --xray_source=... or --wavelength=... required")
print " %-14s: f'=%-9.6g, f''=%-9.6f" % (
table_name, fp_fdp.fp(), fp_fdp.fdp())
fdp.append(fp_fdp.fdp())
print " diff f''=%.2f %%" % ((fdp[1] - fdp[0])/(fdp[1] + fdp[0]) * 100)
def to_diffraction_pattern(crystal_structure, wavelength='Cu'):
"""
Args:
wavelength = (Cr, Fe, Cu, Mo, Ag)
Return structure:
{'wavelength':wavelength, 'meta':['d_spacing', 'two_theta', 'amplitude', 'hkl'], 'data':[]}
Wavelengths from cctbx/eltbx/wavelengths.cpp
// BEGIN_COMPILED_IN_REFERENCE_DATA
{"CrA1", 2.28970}, {"CrA2", 2.29361}, {"Cr", 2.2909},
{"FeA1", 1.93604}, {"FeA2", 1.93998}, {"Fe", 1.9373},
{"CuA1", 1.54056}, {"CuA2", 1.54439}, {"Cu", 1.5418},
{"MoA1", 0.70930}, {"MoA2", 0.71359}, {"Mo", 0.7107},
{"AgA1", 0.55941}, {"AgA2", 0.56380}, {"Ag", 0.5608},
{"", 0}
// END_COMPILED_IN_REFERENCE_DATA
"""
#d_min = 3
# f_calc is the intensity?
# Need to sanatize the Site labels !!
miller_indices = crystal_structure.build_miller_set(anomalous_flag=False,
d_min=1,
d_max=20)
wavelength_in_ang = wavelengths.characteristic(wavelength).as_angstrom()
unit_cell = crystal_structure.unit_cell()
pattern = []
f_calc = crystal_structure.structure_factors(d_min=1,
algorithm="direct").f_calc()
for hkl, j in zip(f_calc.indices(), f_calc.data()):
two_theta = unit_cell.two_theta(hkl, wavelength_in_ang, deg=True)
d = unit_cell.d(hkl)
#print hkl, d, abs(j), two_theta
#xrds.append({"hkl":list(hkl), "amplitude":abs(j), "d-spacing":d, "two_theta":two_theta})
pattern.append([abs(j), list(hkl), two_theta, d])
#return xrds
'''
f_calc = crystal_structure.structure_factors(d_min=d_min).f_calc()
millers = crystal_structure.structure_factors(d_min=d_min).miller_set()
miller_indices = millers.indices()
wavelength = wavelengths.characteristic('CU').as_angstrom()
two_thetas = crystal_structure.unit_cell().two_theta(millers.indices(), wavelength, deg=True)
d_spacings = f_calc.d_spacings()
unit_cell = c.crystal_structure.unit_cell()
'''
d = {
'wavelength': {
'element': wavelength,
'in_angstroms': wavelength_in_ang
},
'meta': ['amplitude', 'hkl', 'two_theta', 'd_spacing'],
'pattern': pattern
}
return d
def run(args):
two_thetas_obs = flex.double()
miller_indices = flex.miller_index()
for line in two_theta_and_index_list:
fields = line.split()
assert len(fields) == 4
two_thetas_obs.append(float(fields[0]))
miller_indices.append([int(s) for s in fields[1:]])
wavelength = wavelengths.characteristic("CU").as_angstrom()
unit_cell_start = uctbx.unit_cell((10, 10, 10, 80, 100, 80))
show_fit(two_thetas_obs, miller_indices, wavelength, unit_cell_start)
refined_accu = []
assert len(args) in [0, 1]
if (len(args) != 0):
arg = args[0]
if (arg.find(",") > 0):
modes = eval("[" + arg + "]")
elif (arg.find(":") > 0):
modes = eval("range(" + arg.replace(":", ",") + "+1)")
else:
modes = [eval(arg)]
else:
modes = range(8)
print "modes:", modes
print
for mode in modes:
refined = refinery(two_thetas_obs,
miller_indices,
wavelength,
unit_cell_start,
mode=mode)
refined_accu.append(refined)
print
p = open("tmp.xy", "w")
print >> p, "@with g0"
print >> p, '@ title "%s"' % "\\n".join(
[platform.platform(), platform.node()])
for i, r in enumerate(refined_accu):
print >> p, '@ s%d legend "%s"' % (i, r.plot_legend)
print >> p, '@ s%d symbol 1' % i
for refined in refined_accu:
for x, y in enumerate(refined.functionals):
if (x > 15): break
print >> p, x, y
print >> p, "&"
del p
if (0):
show_fit(two_thetas_obs, miller_indices, wavelength,
refined.unit_cell())
print refined.unit_cell()
print
print libtbx.utils.format_cpu_times()
def rietveld_refine_structure(
crystalstructure,
wavelength=wavelengths.characteristic("CU").as_angstrom(),
I_obs=None,
Profile=None,
ProfileFile=None):
"""This function tries to rietveld refine a structure using FullProf.
If I_obs is given neither a Profile or a ProfileFile may be specified.
'Profile' and 'ProfileFile' are also exclusive.
:param crystalstructure: the starting model for the refinement
:type crystalstructure: cctbx.xray.structure
:param wavelength: the x-ray wavelength for the given intensity data
:type wavelength: float
:param I_obs: observed Intensities
:type I_obs: cctbx.miller
:param Profile: a XRD profile given as a list/tuple of (2-theta, intensity)-tuples
:type Profile: list/tuple(tuple(2theta,I))
:param ProfileFile: path to a XRD profile as FullProf .prf file
:type ProfileFile: string
"""
# Check preconditions
if [I_obs, Profile, ProfileFile].count(None) != 2:
raise ValueError(
"You may only pass one of I_obs, Profile and ProfileFile")
# start work
from iotbx.write_pcr import write_pcr
import tempfile
import shutil
import os
# write pcr file and execute FullProf
try:
f = tempfile.NamedTemporaryFile(suffix=".pcr", delete=False)
except IOError:
raise
pcrfile = f.name
basepath = os.path.splitext(pcrfile)[0]
write_pcr(f,
crystalstructure,
jobtype=0,
wavelength=wavelength,
I_obs=I_obs)
f.close()
try:
if ProfileFile is not None:
shutil.copyfile(ProfileFile, basepath + ".dat")
elif Profile is not None:
# write out profile file for FullProf
# XXX: todo implement
pass
except IOError:
raise
run_fullprof(pcrfile, verbose=0)
# XXX Todo: extract refined structure from resulting .pcr/.new
# XXX Todo: extract Rwp of refined structure from resulting .pcr/.new
return None, None
def run(args):
two_thetas_obs = flex.double()
miller_indices = flex.miller_index()
for line in two_theta_and_index_list:
fields = line.split()
assert len(fields) == 4
two_thetas_obs.append(float(fields[0]))
miller_indices.append([int(s) for s in fields[1:]])
wavelength = wavelengths.characteristic("CU").as_angstrom()
unit_cell_start = uctbx.unit_cell((10,10,10,80,100,80))
show_fit(
two_thetas_obs, miller_indices, wavelength, unit_cell_start)
refined_accu = []
assert len(args) in [0,1]
if (len(args) != 0):
arg = args[0]
if (arg.find(",") > 0):
modes = eval("["+arg+"]")
elif (arg.find(":") > 0):
modes = eval("range("+arg.replace(":",",")+"+1)")
else:
modes = [eval(arg)]
else:
modes = range(8)
print "modes:", modes
print
for mode in modes:
refined = refinery(
two_thetas_obs, miller_indices, wavelength, unit_cell_start, mode=mode)
refined_accu.append(refined)
print
p = open("tmp.xy", "w")
print >> p, "@with g0"
print >> p, '@ title "%s"' % "\\n".join([
platform.platform(),
platform.node()])
for i,r in enumerate(refined_accu):
print >> p, '@ s%d legend "%s"' % (i, r.plot_legend)
print >> p, '@ s%d symbol 1' % i
for refined in refined_accu:
for x,y in enumerate(refined.functionals):
if (x > 15): break
print >> p, x,y
print >> p, "&"
del p
if (0):
show_fit(
two_thetas_obs, miller_indices, wavelength, refined.unit_cell())
print refined.unit_cell()
print
print libtbx.utils.format_cpu_times()
def rietveld_refine_structure(crystalstructure,
wavelength=wavelengths.characteristic("CU").as_angstrom(),
I_obs=None, Profile=None, ProfileFile=None):
"""This function tries to rietveld refine a structure using FullProf.
If I_obs is given neither a Profile or a ProfileFile may be specified.
'Profile' and 'ProfileFile' are also exclusive.
:param crystalstructure: the starting model for the refinement
:type crystalstructure: cctbx.xray.structure
:param wavelength: the x-ray wavelength for the given intensity data
:type wavelength: float
:param I_obs: observed Intensities
:type I_obs: cctbx.miller
:param Profile: a XRD profile given as a list/tuple of (2-theta, intensity)-tuples
:type Profile: list/tuple(tuple(2theta,I))
:param ProfileFile: path to a XRD profile as FullProf .prf file
:type ProfileFile: string
"""
# Check preconditions
if [I_obs, Profile, ProfileFile].count(None) != 2:
raise(ValueError("You may only pass one of I_obs, Profile and ProfileFile"))
# start work
from write_pcr import write_pcr
import tempfile
import shutil
import os
# write pcr file and execute FullProf
try:
f = tempfile.NamedTemporaryFile(suffix=".pcr", delete=False)
except IOError: raise
pcrfile = f.name
basepath = os.path.splitext(pcrfile)[0]
write_pcr(f, crystalstructure, jobtype=0,
wavelength=wavelength, I_obs=I_obs)
f.close()
try:
if ProfileFile is not None:
shutil.copyfile(ProfileFile, basepath+".dat")
elif Profile is not None:
# write out profile file for FullProf
# XXX: todo implement
pass
except IOError: raise
run_fullprof(pcrfile, verbose=0)
# XXX Todo: extract refined structure from resulting .pcr/.new
# XXX Todo: extract Rwp of refined structure from resulting .pcr/.new
return None, None
def to_diffraction_pattern(crystal_structure, wavelength='Cu'):
"""
Args:
wavelength = (Cr, Fe, Cu, Mo, Ag)
Return structure:
{'wavelength':wavelength, 'meta':['d_spacing', 'two_theta', 'amplitude', 'hkl'], 'data':[]}
Wavelengths from cctbx/eltbx/wavelengths.cpp
// BEGIN_COMPILED_IN_REFERENCE_DATA
{"CrA1", 2.28970}, {"CrA2", 2.29361}, {"Cr", 2.2909},
{"FeA1", 1.93604}, {"FeA2", 1.93998}, {"Fe", 1.9373},
{"CuA1", 1.54056}, {"CuA2", 1.54439}, {"Cu", 1.5418},
{"MoA1", 0.70930}, {"MoA2", 0.71359}, {"Mo", 0.7107},
{"AgA1", 0.55941}, {"AgA2", 0.56380}, {"Ag", 0.5608},
{"", 0}
// END_COMPILED_IN_REFERENCE_DATA
"""
#d_min = 3
# f_calc is the intensity?
# Need to sanatize the Site labels !!
miller_indices = crystal_structure.build_miller_set(anomalous_flag=False, d_min=1, d_max=20)
wavelength_in_ang = wavelengths.characteristic(wavelength).as_angstrom()
unit_cell = crystal_structure.unit_cell()
pattern = []
f_calc = crystal_structure.structure_factors(d_min=1, algorithm="direct").f_calc()
for hkl, j in zip(f_calc.indices(), f_calc.data()):
two_theta = unit_cell.two_theta(hkl, wavelength_in_ang, deg=True)
d = unit_cell.d(hkl)
#print hkl, d, abs(j), two_theta
#xrds.append({"hkl":list(hkl), "amplitude":abs(j), "d-spacing":d, "two_theta":two_theta})
pattern.append([abs(j), list(hkl), two_theta, d])
#return xrds
'''
f_calc = crystal_structure.structure_factors(d_min=d_min).f_calc()
millers = crystal_structure.structure_factors(d_min=d_min).miller_set()
miller_indices = millers.indices()
wavelength = wavelengths.characteristic('CU').as_angstrom()
two_thetas = crystal_structure.unit_cell().two_theta(millers.indices(), wavelength, deg=True)
d_spacings = f_calc.d_spacings()
unit_cell = c.crystal_structure.unit_cell()
'''
d = {'wavelength':{'element':wavelength, 'in_angstroms': wavelength_in_ang}, 'meta':['amplitude', 'hkl', 'two_theta', 'd_spacing'], 'pattern':pattern}
return d
def write_pcr(s,
phases,
title="unnamed",
jobtype=0,
nprof=0,
nbckgd=0,
wavelength=wavelengths.characteristic("CU").as_angstrom(),
I_obs=None,
scale_down=1.0):
"""Write a pcr file to a file or IO buffer.
:param s: a buffer/file to write to
:type s: StringIO or filestream
:param phases: a list/tuple/set of structures or a single crystal structucture
:type phases: list(cctbx.xray_structure) or cctbx.xray_structure
:param title: a title to be used in the pcr file
:type title: string
:param jobtype: the jobtype to be used (0=xray refine, 2=xray powdersim)
:type jobtype: integer
:param nprof: the default peak profile to be used
:type nprof: integer
:param nbckgd: the type of background to be used
:type nbckgd: integer
:param wavelength: the wavelength to be used in Angstroms
:type wavelength: float
:param I_obs: observed intensities
:type I_obs: cctbx.miller
:param scale_down: factor to divide intensities by (to avoid overflows)
:type scale_down: float
"""
# handle case of being called with only one phase
if not isinstance(phases, (tuple, list, set)):
phases = (phases, )
# XXX Todo: handle case of given I_obs (= refine without a full profile)
pcrfile = _pcr_skelleton(phases=phases,
title=title,
jobtype=jobtype,
nprof=nprof,
nbckgd=nbckgd,
scale_down=scale_down)
if jobtype == 2:
pcrfile = _set_ref_flags(pcrfile)
else:
pcrfile = _set_ref_flags(pcrfile,
freeparams=["scale", "lattice", "profile"])
print(pcrfile, file=s)
def write_pcr(s,
phases,
title="unnamed",
jobtype=0,
nprof=0,
nbckgd=0,
wavelength=wavelengths.characteristic("CU").as_angstrom(),
I_obs=None,
scale_down=1.0):
"""Write a pcr file to a file or IO buffer.
:param s: a buffer/file to write to
:type s: StringIO or filestream
:param phases: a list/tuple/set of structures or a single crystal structucture
:type phases: list(cctbx.xray_structure) or cctbx.xray_structure
:param title: a title to be used in the pcr file
:type title: string
:param jobtype: the jobtype to be used (0=xray refine, 2=xray powdersim)
:type jobtype: integer
:param nprof: the default peak profile to be used
:type nprof: integer
:param nbckgd: the type of background to be used
:type nbckgd: integer
:param wavelength: the wavelength to be used in Angstroms
:type wavelength: float
:param I_obs: observed intensities
:type I_obs: cctbx.miller
:param scale_down: factor to divide intensities by (to avoid overflows)
:type scale_down: float
"""
# handle case of being called with only one phase
if not isinstance(phases, (tuple, list, set)):
phases = (phases, )
# XXX Todo: handle case of given I_obs (= refine without a full profile)
pcrfile = _pcr_skelleton(phases=phases,
title=title,
jobtype=jobtype,
nprof=nprof,
nbckgd=nbckgd,
scale_down=scale_down)
if jobtype == 2:
pcrfile = _set_ref_flags(pcrfile)
else:
pcrfile = _set_ref_flags(pcrfile, freeparams=["scale","lattice","profile"])
print(pcrfile, file=s)
def run():
two_thetas_obs = flex.double()
miller_indices = flex.miller_index()
for line in two_theta_and_index_list:
fields = line.split()
assert len(fields) == 4
two_thetas_obs.append(float(fields[0]))
miller_indices.append([int(s) for s in fields[1:]])
wavelength = wavelengths.characteristic("CU").as_angstrom()
unit_cell_start = uctbx.unit_cell((10, 10, 10, 90, 90, 90))
show_fit(two_thetas_obs, miller_indices, wavelength, unit_cell_start)
refined = refinery(two_thetas_obs, miller_indices, wavelength,
unit_cell_start)
print()
show_fit(two_thetas_obs, miller_indices, wavelength, refined.unit_cell())
print(refined.unit_cell())
print()
print(libtbx.utils.format_cpu_times())
def run(args):
if (len(args) == 0) or ("--help" in args):
raise Usage("""
eltbx.show_fp_fdp.py --elements=S,CL --wavelength=1.54
eltbx.show_fp_fdp.py --elements=S,CL --source=CuA1""")
parser = option_parser()
parser.add_option('--elements')
parser.add_option('--xray_source')
parser.add_option('--wavelength')
options, args = parser.parse_args(args)
if (options.xray_source is not None):
print("Source: %s" % options.xray_source)
elif (options.wavelength is not None):
print("Wavelength: %g Angstrom" % float(options.wavelength))
print()
for element in options.elements.split(','):
print("Element: %s" % element)
fdp = []
for table_name, table in (('Henke et al.', henke.table),
('Sasaki et al.', sasaki.table)):
inelastic_scattering = table(element)
if (options.xray_source):
fp_fdp = inelastic_scattering.at_angstrom(
wavelengths.characteristic(
options.xray_source).as_angstrom())
elif (options.wavelength):
fp_fdp = inelastic_scattering.at_angstrom(
float(options.wavelength))
else:
raise Sorry(
"Either --xray_source=... or --wavelength=... required")
print(" %-14s: f'=%-9.6g, f''=%-9.6f" %
(table_name, fp_fdp.fp(), fp_fdp.fdp()))
fdp.append(fp_fdp.fdp())
print(" diff f''=%.2f %%" % ((fdp[1] - fdp[0]) /
(fdp[1] + fdp[0]) * 100))
def run():
two_thetas_obs = flex.double()
miller_indices = flex.miller_index()
for line in two_theta_and_index_list:
fields = line.split()
assert len(fields) == 4
two_thetas_obs.append(float(fields[0]))
miller_indices.append([int(s) for s in fields[1:]])
wavelength = wavelengths.characteristic("CU").as_angstrom()
unit_cell_start = uctbx.unit_cell((10,10,10,90,90,90))
show_fit(
two_thetas_obs, miller_indices, wavelength, unit_cell_start)
refined = refinery(
two_thetas_obs, miller_indices, wavelength, unit_cell_start)
print
show_fit(
two_thetas_obs, miller_indices, wavelength, refined.unit_cell())
print refined.unit_cell()
print
print libtbx.utils.format_cpu_times()
def generator(xray_structure,
data_are_intensities=True,
title=None,
wavelength=None,
temperature=None,
full_matrix_least_squares_cycles=None,
conjugate_gradient_least_squares_cycles=None,
overall_scale_factor=None,
weighting_scheme_params=None,
sort_scatterers=True,
unit_cell_dims=None,
unit_cell_esds=None):
space_group = xray_structure.space_group()
assert not space_group.is_centric() or space_group.is_origin_centric(),\
centric_implies_centrosymmetric_error_msg
assert [
full_matrix_least_squares_cycles,
conjugate_gradient_least_squares_cycles
].count(None) in (0, 1)
if title is None:
title = '????'
if wavelength is None:
wavelength = wavelengths.characteristic('Mo').as_angstrom()
sgi = xray_structure.space_group_info()
uc = xray_structure.unit_cell()
yield 'TITL %s in %s\n' % (title, sgi.type().lookup_symbol())
if unit_cell_dims is None:
unit_cell_dims = uc.parameters()
yield 'CELL %.5f %s\n' % (wavelength,
' '.join(('%.4f ', ) * 3 +
('%.3f', ) * 3) % unit_cell_dims)
if unit_cell_esds:
yield 'ZERR %i %f %f %f %f %f %f\n' % (
(sgi.group().order_z(), ) + unit_cell_esds)
else:
yield 'ZERR %i 0. 0. 0. 0. 0. 0.\n' % sgi.group().order_z()
latt = 1 + 'PIRFABC'.find(sgi.group().conventional_centring_type_symbol())
if not space_group.is_origin_centric(): latt = -latt
yield 'LATT %i\n' % latt
for i in xrange(space_group.n_smx()):
rt_mx = space_group(0, 0, i)
if rt_mx.is_unit_mx(): continue
yield 'SYMM %s\n' % rt_mx
yield '\n'
uc_content = xray_structure.unit_cell_content()
for e in uc_content:
uc_content[e] = "%.1f" % uc_content[e]
sfac = []
unit = []
prior = ('C', 'H')
for e in prior:
if e in uc_content:
sfac.append(e)
unit.append(uc_content[e])
dsu = [(tiny_pse.table(e).atomic_number(), e) for e in uc_content]
dsu.sort()
sorted = [item[-1] for item in dsu]
for e in sorted:
if (e not in prior):
sfac.append(e)
unit.append(uc_content[e])
yield 'SFAC %s\n' % ' '.join(sfac)
for e in sfac:
yield 'DISP %s 0 0 0\n' % e
yield 'UNIT %s\n' % ' '.join(unit)
sf_idx = dict([(e, i + 1) for i, e in enumerate(sfac)])
yield '\n'
if temperature:
yield 'TEMP %.0f\n' % temperature
if full_matrix_least_squares_cycles:
yield 'L.S. %i\n' % full_matrix_least_squares_cycles
if conjugate_gradient_least_squares_cycles:
yield 'CGLS %i\n' % conjugate_gradient_least_squares_cycles
yield '\n'
if weighting_scheme_params is not None:
if (isinstance(weighting_scheme_params, str)):
yield 'WGHT %s\n' % weighting_scheme_params
else:
a, b = weighting_scheme_params
if b is None:
yield 'WGHT %.6f\n' % a
else:
yield 'WGHT %.6f %.6f\n' % (a, b)
if overall_scale_factor is not None:
yield 'FVAR %.8f\n' % overall_scale_factor
fmt_tmpl = ('%-4s', '%2i') + ('%11.6f', ) * 3 + ('%11.5f', )
fmt_iso = ' '.join(fmt_tmpl + ('%10.5f', ))
fmt_aniso = ' '.join(fmt_tmpl + ('%.5f', ) * 2 + ('=\n ', ) +
('%.5f', ) * 4)
if sort_scatterers:
dsu = [(tiny_pse.table(sc.scattering_type).atomic_number(), sc)
for sc in xray_structure.scatterers()]
dsu.sort(reverse=True)
scatterers = flex.xray_scatterer([item[-1] for item in dsu])
else:
scatterers = xray_structure.scatterers()
atomname_set = set()
for sc in scatterers:
assert sc.fp == 0 # not implemented
assert sc.fdp == 0 # not implemented
assert sc.flags.use_u_iso() ^ sc.flags.use_u_aniso(),\
both_iso_and_aniso_in_use_error_msg
atomname = sc.label.strip()
assert len(atomname) != 0
assert len(atomname) <= 4
if (atomname in atomname_set):
raise RuntimeError('Duplicate atom name: "%s"' % atomname)
atomname_set.add(atomname)
params = (atomname, sf_idx[sc.scattering_type]) + sc.site
occ = sc.weight()
if not sc.flags.grad_occupancy(): occ += 10
params += (occ, )
if sc.flags.use_u_iso():
yield fmt_iso % (params + (sc.u_iso, )) + "\n"
else:
u11, u22, u33, u12, u13, u23 = adptbx.u_star_as_u_cif(
uc, sc.u_star)
yield fmt_aniso % (params + (u11, u22, u33, u23, u13, u12)) + "\n"
if data_are_intensities: hklf = 4
else: hklf = 3
yield 'HKLF %i\n' % hklf
def _pcr_skelleton(phases,
title="unnamed",
jobtype=0,
nprof=0,
nbckgd=0,
wavelength=wavelengths.characteristic("CU").as_angstrom(),
scale_down=1.0):
"""Create a pcr skelleton with placeholder strings for different refinement
options.
(for internal use)
:param phases: a list/tuple/set of structures
:type phases: list(cctbx.xray_structure)
:param title: a title to be used in the pcr file
:type title: string
:param jobtype: the jobtype to be used
:type jobtype: integer
:param nprof: the default peak profile to be used
:type nprof: integer
:param nbckgd: the type of background to be used
:type nbckgd: integer
:param wavelength: the wavelength to be used in Angstroms
:type wavelength: float
:param scale_down: factor to divide intensities by (to avoid overflows)
:type scale_down: float
:returns: the pcr skelleton as a string
:rtype: string
"""
nphase = len(phases)
ret = "COMM " + title + "\n"
ret += """\
!Job Npr Nph Nba Nex Nsc Nor Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut
{0} {1} {2} {3} 0 0 0 {dum} 0 0 0 0 0 0 0 0 0 0 1
""".format(jobtype,nprof,nphase,nbckgd,dum=1 if jobtype == 2 else 0)
ret += """\
!
!Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 Syo Prf Ins Rpa Sym Hkl Fou Sho Ana
2 0 1 1 1 0 0 0 1 1 {filetype} 0 1 4 2 0 0
!
! lambda1 Lambda2 Ratio Bkpos Wdt Cthm muR AsyLim Rpolarz ->Patt# 1
{xlambda} {xlambda} 1.0000 60.000 5.0000 0.0000 0.0000 50.00 0.0000
!
!NCY Eps R_at R_an R_pr R_gl Thmin Step Thmax PSD Sent0
20 0.01 1.00 1.00 1.00 1.00 10.0000 0.100000 100.0000 0.000 0.000
!
!
#__npar__# !Number of refined parameters
""".format(filetype="0", xlambda=wavelength)
ret += """\
!
! Zero Code SyCos Code SySin Code Lambda Code MORE ->Patt# 1
0.00000 0.0 0.00000 0.0 0.00000 0.0 0.000000 0.00 0
! Background coefficients/codes for Pattern# 1 (Polynomial of 6th degree)
0.000 0.000 0.000 0.000 0.000 0.000
0.00 0.00 0.00 0.00 0.00 0.00
"""
for i in range(nphase):
ret += _make_phase_block(phases[i], number=i+1, name="", scale_down=scale_down)
return ret
def simulate_powder_pattern(crystalstructure,
wavelength=wavelengths.characteristic("CU").as_angstrom(),
filename="",
keep_results=False,
scale_down=1.0):
"""
Get integrated intensities and a a simulated XRD profile calculated with
FullProf (has to be installed and callable via "fp2k").
:param crystalstructure: a crystal structure to calculate the intensities for
:type crystalstructure: cctbx.xray.structure
:param wavelength: x-ray wavelength in angstroms
:type wavelength: float
:param filename: a filepath to save the in- and output of FullProf to
:type filename: string
:param keep_results: keep the (temporary) files from FullProf for a later \
manual inspection
:type keep_results: boolean
:param scale_down: factor to divide intensities by (to avoid overflows)
:type scale_down: float
:returns: calculated integral intensities, calculated profile
:rtype: cctbx.miller, list(tuple(float,int))
XXX Todo: implement extraction of calculated profile
"""
from write_pcr import write_pcr
from iotbx.reflection_file_reader import any_reflection_file
import tempfile
import os
# write pcr file and execute FullProf
try:
if filename == "":
f = tempfile.NamedTemporaryFile(suffix=".pcr", delete=False)
else:
f = open(filename, "w")
except IOError: raise
pcrfile = f.name
basepath = os.path.splitext(pcrfile)[0]
write_pcr(f, crystalstructure, jobtype=2,
wavelength=wavelength, scale_down=scale_down)
f.close()
if scale_down > 10000: raise
run_fullprof(pcrfile, verbose=0)
# fix hkl file for hkl reader
hklfile = basepath + ".fou"
f = open(hklfile, "r")
lines = f.readlines()[1:]
f.close()
hklfile = basepath + ".hkl"
if keep_results == True:
os.rename(hklfile, basepath + ".hkldata") # backup old hkl file
f = open(hklfile, "w")
f.writelines(lines)
f.close()
# extract intensities
f_calc = None
try:
rf = any_reflection_file(file_name=hklfile)
f_calc = rf.as_miller_arrays(
crystal_symmetry=crystalstructure.crystal_symmetry(),
assume_shelx_observation_type_is="intensities")[0]
except KeyboardInterrupt: raise
except Exception:
# an overflow occured
return simulate_powder_pattern(crystalstructure, wavelength=wavelength,
filename=filename, keep_results=keep_results,
scale_down=scale_down*10.0)
profile = None
# clean up
if keep_results == False:
for ext in [".pcr", ".sym", ".fou", ".ins", ".prf", ".sim", ".sum", ".out",
".hkl", ".hkldata", "1.fst", "1.sub"]:
try:
os.unlink(basepath + ext)
except KeyboardInterrupt: raise
except Exception: pass
return f_calc, profile
def simulate_powder_pattern(
crystalstructure,
wavelength=wavelengths.characteristic("CU").as_angstrom(),
filename="",
keep_results=False,
scale_down=1.0):
"""
Get integrated intensities and a a simulated XRD profile calculated with
FullProf (has to be installed and callable via "fp2k").
:param crystalstructure: a crystal structure to calculate the intensities for
:type crystalstructure: cctbx.xray.structure
:param wavelength: x-ray wavelength in angstroms
:type wavelength: float
:param filename: a filepath to save the in- and output of FullProf to
:type filename: string
:param keep_results: keep the (temporary) files from FullProf for a later \
manual inspection
:type keep_results: boolean
:param scale_down: factor to divide intensities by (to avoid overflows)
:type scale_down: float
:returns: calculated integral intensities, calculated profile
:rtype: cctbx.miller, list(tuple(float,int))
XXX Todo: implement extraction of calculated profile
"""
from iotbx.write_pcr import write_pcr
from iotbx.reflection_file_reader import any_reflection_file
import tempfile
import os
# write pcr file and execute FullProf
try:
if filename == "":
f = tempfile.NamedTemporaryFile(suffix=".pcr", delete=False)
else:
f = open(filename, "w")
except IOError:
raise
pcrfile = f.name
basepath = os.path.splitext(pcrfile)[0]
write_pcr(f,
crystalstructure,
jobtype=2,
wavelength=wavelength,
scale_down=scale_down)
f.close()
if scale_down > 10000: raise
run_fullprof(pcrfile, verbose=0)
# fix hkl file for hkl reader
hklfile = basepath + ".fou"
f = open(hklfile, "r")
lines = f.readlines()[1:]
f.close()
hklfile = basepath + ".hkl"
if keep_results == True:
os.rename(hklfile, basepath + ".hkldata") # backup old hkl file
f = open(hklfile, "w")
f.writelines(lines)
f.close()
# extract intensities
f_calc = None
try:
rf = any_reflection_file(file_name=hklfile)
f_calc = rf.as_miller_arrays(
crystal_symmetry=crystalstructure.crystal_symmetry(),
assume_shelx_observation_type_is="intensities")[0]
except KeyboardInterrupt:
raise
except Exception:
# an overflow occured
return simulate_powder_pattern(crystalstructure,
wavelength=wavelength,
filename=filename,
keep_results=keep_results,
scale_down=scale_down * 10.0)
profile = None
# clean up
if keep_results == False:
for ext in [
".pcr", ".sym", ".fou", ".ins", ".prf", ".sim", ".sum", ".out",
".hkl", ".hkldata", "1.fst", "1.sub"
]:
try:
os.unlink(basepath + ext)
except KeyboardInterrupt:
raise
except Exception:
pass
return f_calc, profile
def _pcr_skelleton(phases,
title="unnamed",
jobtype=0,
nprof=0,
nbckgd=0,
wavelength=wavelengths.characteristic("CU").as_angstrom(),
scale_down=1.0):
"""Create a pcr skelleton with placeholder strings for different refinement
options.
(for internal use)
:param phases: a list/tuple/set of structures
:type phases: list(cctbx.xray_structure)
:param title: a title to be used in the pcr file
:type title: string
:param jobtype: the jobtype to be used
:type jobtype: integer
:param nprof: the default peak profile to be used
:type nprof: integer
:param nbckgd: the type of background to be used
:type nbckgd: integer
:param wavelength: the wavelength to be used in Angstroms
:type wavelength: float
:param scale_down: factor to divide intensities by (to avoid overflows)
:type scale_down: float
:returns: the pcr skelleton as a string
:rtype: string
"""
nphase = len(phases)
ret = "COMM " + title + "\n"
ret += """\
!Job Npr Nph Nba Nex Nsc Nor Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut
{0} {1} {2} {3} 0 0 0 {dum} 0 0 0 0 0 0 0 0 0 0 1
""".format(jobtype,nprof,nphase,nbckgd,dum=1 if jobtype == 2 else 0)
ret += """\
!
!Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 Syo Prf Ins Rpa Sym Hkl Fou Sho Ana
2 0 1 1 1 0 0 0 1 1 {filetype} 0 1 4 2 0 0
!
! lambda1 Lambda2 Ratio Bkpos Wdt Cthm muR AsyLim Rpolarz ->Patt# 1
{xlambda} {xlambda} 1.0000 60.000 5.0000 0.0000 0.0000 50.00 0.0000
!
!NCY Eps R_at R_an R_pr R_gl Thmin Step Thmax PSD Sent0
20 0.01 1.00 1.00 1.00 1.00 10.0000 0.100000 100.0000 0.000 0.000
!
!
#__npar__# !Number of refined parameters
""".format(filetype="0", xlambda=wavelength)
ret += """\
!
! Zero Code SyCos Code SySin Code Lambda Code MORE ->Patt# 1
0.00000 0.0 0.00000 0.0 0.00000 0.0 0.000000 0.00 0
! Background coefficients/codes for Pattern# 1 (Polynomial of 6th degree)
0.000 0.000 0.000 0.000 0.000 0.000
0.00 0.00 0.00 0.00 0.00 0.00
"""
for i in range(nphase):
ret += _make_phase_block(phases[i], number=i+1, name="", scale_down=scale_down)
return ret
def generator(xray_structure,
data_are_intensities=True,
title=None,
wavelength=None,
temperature=None,
full_matrix_least_squares_cycles=None,
conjugate_gradient_least_squares_cycles=None,
overall_scale_factor=None,
weighting_scheme_params=None,
sort_scatterers=True,
unit_cell_dims=None,
unit_cell_esds=None
):
space_group = xray_structure.space_group()
assert not space_group.is_centric() or space_group.is_origin_centric(),\
centric_implies_centrosymmetric_error_msg
assert [full_matrix_least_squares_cycles,
conjugate_gradient_least_squares_cycles].count(None) in (0, 1)
if title is None:
title = '????'
if wavelength is None:
wavelength = wavelengths.characteristic('Mo').as_angstrom()
sgi = xray_structure.space_group_info()
uc = xray_structure.unit_cell()
yield 'TITL %s in %s\n' % (title, sgi.type().lookup_symbol())
if unit_cell_dims is None:
unit_cell_dims = uc.parameters()
yield 'CELL %.5f %s\n' % (
wavelength,
' '.join(('%.4f ',)*3 + ('%.3f',)*3) % unit_cell_dims)
if unit_cell_esds:
yield 'ZERR %i %f %f %f %f %f %f\n' % ((sgi.group().order_z(),) + unit_cell_esds)
else:
yield 'ZERR %i 0. 0. 0. 0. 0. 0.\n' % sgi.group().order_z()
latt = 1 + 'PIRFABC'.find(sgi.group().conventional_centring_type_symbol())
if not space_group.is_origin_centric(): latt = -latt
yield 'LATT %i\n' % latt
for i in xrange(space_group.n_smx()):
rt_mx = space_group(0, 0, i)
if rt_mx.is_unit_mx(): continue
yield 'SYMM %s\n' % rt_mx
yield '\n'
uc_content = xray_structure.unit_cell_content()
for e in uc_content:
uc_content[e] = "%.1f" % uc_content[e]
sfac = []
unit = []
prior = ('C', 'H')
for e in prior:
if e in uc_content:
sfac.append(e)
unit.append(uc_content[e])
dsu = [ (tiny_pse.table(e).atomic_number(), e) for e in uc_content ]
dsu.sort()
sorted = [ item[-1] for item in dsu ]
for e in sorted:
if (e not in prior):
sfac.append(e)
unit.append(uc_content[e])
yield 'SFAC %s\n' % ' '.join(sfac)
for e in sfac:
yield 'DISP %s 0 0 0\n' % e
yield 'UNIT %s\n' % ' '.join(unit)
sf_idx = dict([ (e, i + 1) for i, e in enumerate(sfac) ])
yield '\n'
if temperature:
yield 'TEMP %.0f\n' % temperature
if full_matrix_least_squares_cycles:
yield 'L.S. %i\n' % full_matrix_least_squares_cycles
if conjugate_gradient_least_squares_cycles:
yield 'CGLS %i\n' % conjugate_gradient_least_squares_cycles
yield '\n'
if weighting_scheme_params is not None:
if (isinstance(weighting_scheme_params, str)):
yield 'WGHT %s\n' % weighting_scheme_params
else:
a, b = weighting_scheme_params
if b is None:
yield 'WGHT %.6f\n' % a
else:
yield 'WGHT %.6f %.6f\n' % (a, b)
if overall_scale_factor is not None:
yield 'FVAR %.8f\n' % overall_scale_factor
fmt_tmpl = ('%-4s', '%2i') + ('%11.6f',)*3 + ('%11.5f',)
fmt_iso = ' '.join(fmt_tmpl + ('%10.5f',))
fmt_aniso = ' '.join(fmt_tmpl + ('%.5f',)*2 + ('=\n ',) + ('%.5f',)*4)
if sort_scatterers:
dsu = [ (tiny_pse.table(sc.scattering_type).atomic_number(), sc)
for sc in xray_structure.scatterers() ]
dsu.sort(reverse=True)
scatterers = flex.xray_scatterer([ item[-1] for item in dsu ])
else:
scatterers = xray_structure.scatterers()
atomname_set = set()
for sc in scatterers:
assert sc.fp == 0 # not implemented
assert sc.fdp == 0 # not implemented
assert sc.flags.use_u_iso() ^ sc.flags.use_u_aniso(),\
both_iso_and_aniso_in_use_error_msg
atomname = sc.label.strip()
assert len(atomname) != 0
assert len(atomname) <= 4
if (atomname in atomname_set):
raise RuntimeError('Duplicate atom name: "%s"' % atomname)
atomname_set.add(atomname)
params = (atomname, sf_idx[sc.scattering_type]) + sc.site
occ = sc.weight()
if not sc.flags.grad_occupancy(): occ += 10
params += (occ, )
if sc.flags.use_u_iso():
yield fmt_iso % (params + (sc.u_iso,)) + "\n"
else:
u11, u22, u33, u12, u13, u23 = adptbx.u_star_as_u_cif(uc, sc.u_star)
yield fmt_aniso % (params + (u11, u22, u33, u23, u13, u12)) + "\n"
if data_are_intensities: hklf = 4
else: hklf = 3
yield 'HKLF %i\n' % hklf