def test_read_fdf():
dct = read_fdf(StringIO(sample_fdf))
# This is a "raw" parser, no type conversion is done.
ref = dict(potatoes=['5'],
coffee=['6.5'],
spam=[['1', '2.5', 'hello']])
assert dct == ref
def get_pseudo_wave_function(self, band=0, kpt=0, spin=None):
"""Return pseudo-wave-function array.
The method is limited to the gamma point, and is implemented
as a wrapper to denchar (a tool shipped with siesta);
denchar must be available in the command path.
When retrieving a p_w_f from a non-spin-polarized calculation,
spin must be None (default), and for spin-polarized
calculations, spin must be set to either 0 (up) or 1 (down).
As long as the necessary files are present and named
correctly, old p_w_fs can be read as long as the
calculator label is set. E.g.
>>> c = Siesta(label='name_of_old_calculation')
>>> pwf = c.get_pseudo_wave_function()
The broadcast and pad options are not implemented.
"""
# Not implemented: kpt=0, broadcast=True, pad=True
# kpoint must be Gamma
assert kpt == 0, (
"siesta.get_pseudo_wave_function is unfortunately limited " "to the gamma point only. kpt must be 0."
)
# In denchar, band numbering starts from 1
assert type(band) is int and band >= 0
band = band + 1
if spin is None:
spin_name = ""
elif spin == 0:
spin_name = ".UP"
elif spin == 1:
spin_name = ".DOWN"
label = self.label
# If <label>.WF<band>.cube already exist and is newer than <label>.fdf,
# just return it
fn_wf = label + (".WF%i%s.cube" % (band, spin_name))
fn_fdf = label + ".fdf"
if isfile(fn_wf) and isfile(fn_fdf) and (getmtime(fn_wf) > getmtime(fn_fdf)):
x, _ = read_cube_data(fn_wf)
return x
if not isfile(fn_fdf):
raise RuntimeError("Could not find the fdf-file. It is required as " "part of the input for denchar.")
fdf_mtime = getmtime(fn_fdf)
for suf in [".WFS", ".PLD", ".DM", ".DIM"]:
if not isfile(label + suf):
raise RuntimeError(
'Could not find file "%s%s" which is required '
"when extracting wave functions "
'(make sure the fdf options "WriteDenchar" is '
'True, and WaveFuncKpoints is [0.0 0.0 0.0]")' % (label, suf)
)
if not getmtime(label + suf) > fdf_mtime:
# This should be handled in a better way, e.g. by implementing
# a "calculation_required() and calculate()"
raise RuntimeError("The calculation is not up to date.")
# Simply read the old fdf-file and pick some meta info from there.
# However, strictly it's not always neccesary
fdf = read_fdf(fn_fdf)
if "latticeconstant" in fdf:
const = float(fdf["latticeconstant"][0])
unit = fdf["latticeconstant"][1]
else:
const = 1.0
unit = "Ang"
if "latticevectors" in fdf:
cell = np.array(fdf["latticevectors"], dtype="d")
else:
raise RuntimeError("Failed to find the lattice vectors in the fdf-file.")
if "spinpolarized" in fdf and fdf["spinpolarized"][0].lower() in ["yes", "true", ".true.", "T", ""]:
if spin is None:
raise RuntimeError("The calculation was spin polarized, pick either " "spin=0 or 1.")
else:
if not spin is None:
raise RuntimeError("The calculation was not spin polarized, " "spin argument must be None.")
denc_fdf = open(fn_fdf).readlines()
denc_fdf.append("Denchar.TypeOfRun 3D\n")
denc_fdf.append("Denchar.PlotWaveFunctions T\n")
for dim, dir in zip(cell.transpose(), ["X", "Y", "Z"]):
# Naive square box limits to denchar
denc_fdf.append("Denchar.Min%s %f %s\n" % (dir, const * dim.min(), unit))
denc_fdf.append("Denchar.Max%s %f %s\n" % (dir, const * dim.max(), unit))
# denchar rewinds stdin and fails if stdin is a pipe
denc_fdf_file = open(label + ".denchar.fdf", "w")
denc_fdf_file.write("".join(denc_fdf))
denc_fdf_file.close()
try:
from subprocess import Popen, PIPE
p = Popen(
"denchar", shell=True, stdin=open(label + ".denchar.fdf"), stdout=PIPE, stderr=PIPE, close_fds=True
)
exitcode = p.wait()
except ImportError:
raise RuntimeError("get_pseudo_wave_function implemented only with subprocess.")
if exitcode == 0:
if not isfile(fn_wf):
raise RuntimeError("Could not find the requested file (%s)" % fn_wf)
x, _ = read_cube_data(fn_wf)
return x
elif exitcode == 127:
raise RuntimeError("No denchar executable found. Make sure it is in the path.")
else:
import sys
print >> sys.stderr, "".join(p.stderr.readlines())
raise RuntimeError("Execution of denchar failed!")
def get_pseudo_wave_function(self, band=0, kpt=0, spin=None):
"""Return pseudo-wave-function array.
The method is limited to the gamma point, and is implemented
as a wrapper to denchar (a tool shipped with siesta);
denchar must be available in the command path.
When retrieving a p_w_f from a non-spin-polarized calculation,
spin must be None (default), and for spin-polarized
calculations, spin must be set to either 0 (up) or 1 (down).
As long as the necessary files are present and named
correctly, old p_w_fs can be read as long as the
calculator label is set. E.g.
>>> c = Siesta(label='name_of_old_calculation')
>>> pwf = c.get_pseudo_wave_function()
The broadcast and pad options are not implemented.
"""
# Not implemented: kpt=0, broadcast=True, pad=True
# kpoint must be Gamma
assert kpt == 0, \
"siesta.get_pseudo_wave_function is unfortunately limited " \
"to the gamma point only. kpt must be 0."
# In denchar, band numbering starts from 1
assert type(band) is int and band >= 0
band = band + 1
if spin is None:
spin_name = ""
elif spin == 0:
spin_name = ".UP"
elif spin == 1:
spin_name = ".DOWN"
label = self.label
# If <label>.WF<band>.cube already exist and is newer than <label>.fdf,
# just return it
fn_wf = label + ('.WF%i%s.cube' % (band, spin_name))
fn_fdf = label + '.fdf'
if isfile(fn_wf) and isfile(fn_fdf) and (getmtime(fn_wf) >
getmtime(fn_fdf)):
x, _ = read_cube_data(fn_wf)
return x
if not isfile(fn_fdf):
raise RuntimeError(
'Could not find the fdf-file. It is required as '
'part of the input for denchar.')
fdf_mtime = getmtime(fn_fdf)
for suf in ['.WFS', '.PLD', '.DM', '.DIM']:
if not isfile(label + suf):
raise RuntimeError(
'Could not find file "%s%s" which is required '
'when extracting wave functions '
'(make sure the fdf options "WriteDenchar" is '
'True, and WaveFuncKpoints is [0.0 0.0 0.0]")' %
(label, suf))
if not getmtime(label + suf) > fdf_mtime:
# This should be handled in a better way, e.g. by implementing
# a "calculation_required() and calculate()"
raise RuntimeError('The calculation is not up to date.')
# Simply read the old fdf-file and pick some meta info from there.
# However, strictly it's not always neccesary
fdf = read_fdf(fn_fdf)
if 'latticeconstant' in fdf:
const = float(fdf['latticeconstant'][0])
unit = fdf['latticeconstant'][1]
else:
const = 1.0
unit = 'Ang'
if 'latticevectors' in fdf:
cell = np.array(fdf['latticevectors'], dtype='d')
else:
raise RuntimeError(
'Failed to find the lattice vectors in the fdf-file.')
if 'spinpolarized' in fdf and \
fdf['spinpolarized'][0].lower() in ['yes', 'true', '.true.', 'T', '']:
if spin is None:
raise RuntimeError(
'The calculation was spin polarized, pick either '
'spin=0 or 1.')
else:
if not spin is None:
raise RuntimeError('The calculation was not spin polarized, '
'spin argument must be None.')
denc_fdf = open(fn_fdf).readlines()
denc_fdf.append('Denchar.TypeOfRun 3D\n')
denc_fdf.append('Denchar.PlotWaveFunctions T\n')
for dim, dir in zip(cell.transpose(), ['X', 'Y', 'Z']):
# Naive square box limits to denchar
denc_fdf.append('Denchar.Min%s %f %s\n' %
(dir, const * dim.min(), unit))
denc_fdf.append('Denchar.Max%s %f %s\n' %
(dir, const * dim.max(), unit))
# denchar rewinds stdin and fails if stdin is a pipe
denc_fdf_file = open(label + '.denchar.fdf', 'w')
denc_fdf_file.write(''.join(denc_fdf))
denc_fdf_file.close()
p = Popen('denchar',
shell=True,
stdin=open(label + '.denchar.fdf'),
stdout=PIPE,
stderr=PIPE,
close_fds=True)
exitcode = p.wait()
if exitcode == 0:
if not isfile(fn_wf):
raise RuntimeError('Could not find the requested file (%s)' %
fn_wf)
x, _ = read_cube_data(fn_wf)
return x
elif exitcode == 127:
raise RuntimeError(
'No denchar executable found. Make sure it is in the path.')
else:
import sys
print >> sys.stderr, ''.join(p.stderr.readlines())
raise RuntimeError('Execution of denchar failed!')