def freq(strchg, numAtomsUC, gulpName, tempName):
"""
Executes a gulp program with the string changes neccesary
and returns the frequencies.
ntpy.gulp.freq(strchg, numAtomsUC, gulpName, tempName)
Parameters
----------
strchg : dict of type str
A dictionary holding key:value pairs. Each key
is original string to be replaced and each value
is the new string to be subsituted.
numAtomsUC : int
The number of atoms in the unit cell.
gulpName : str
A string containing the original file name. If
the file is not included in the pathway then it
can be the absolute or relative pathway to the
file.
tempName : str
A string containing the new file name. If the
file is not included in the pathway then it can
be the absolute or relative pathway to the file.
"""
# String change the template file
st.sed(strchg, gulpName, tempName)
# Execute the new gulp file
os.system('gulp <'+ tempName+ ' > output.gulp')
# os.system('gulp '+ tempName+ ' output.gulp')
# Extract the frequencies
freq = np.zeros( (3 * numAtomsUC), dtype=float)
freq = np.loadtxt(tempName+ '.freq', comments='--')
freq[:] = freq[:] * 2.0 * np.pi * ct.value('c') * ct.value('tocenti') * lj.value('tau')
# Remove the .freq file
os.system('rm '+ tempName+ '.freq')
return freq
def vel(strchg,
numAtomsUC,
gulpName,
tempName,
kpt,
latConst,
deltaKpt=1e-3,
gulpExe='gulp'):
"""
Executes a gulp program with the string changes neccesary
and returns the velocities.
ntpy.gulp.vel(strchg, numAtomsUC, gulpName, tempName, deltaKpt=1e-3, gulpExe='gulp')
Parameters
----------
strchg : dict of type str
A dictionary holding key:value pairs. Each key
is original string to be replaced and each value
is the new string to be subsituted.
numAtomsUC : int
The number of atoms in the unit cell.
gulpName : str
A string containing the original file name. If
the file is not included in the pathway then it
can be the absolute or relative pathway to the
file.
tempName : str
A string containing the new file name. If the
file is not included in the pathway then it can
be the absolute or relative pathway to the file.
kpt : array of type float
A numpy array of size 3 that has the three
dimension k-point to be used.
latConst : float
A float of the lattice constant in angstroms.
deltaKpt : float, optional
A float that determines what difference to use
for the difference theorem. Defaults to 10e-5.
gulpExe : str, optional
A string of the gulp executable. Defaults to
"gulp".
Returns
----------
vel : numpy array of type float
Returns the velocity for the kpt in a array of
shape (3 * numAtomsUC, 3)
"""
def _kptstrchg(strchg, kpt):
strchg['KPT'] = '{:.10f} {:.10f} {:.10f}'.format(
kpt[0], kpt[1], kpt[2])
return strchg
vel = np.zeros((3 * numAtomsUC, 3), dtype=float)
# Convert to m/s
velConv = ((1.0 / ct.value('centi')) *
ct.value('c')) / (1.0 / (latConst * ct.value('ang')))
# For all three directions
for idim in range(3):
if kpt[idim] == 0.5: # kpt at right boundary
freqVal = freq(strchg,
numAtomsUC,
gulpName,
tempName,
gulpExe=gulpExe)
# Change kpt
kpt[idim] = kpt[idim] - deltaKpt
strchg = _kptstrchg(strchg, kpt)
freqValMdk = freq(strchg,
numAtomsUC,
gulpName,
tempName,
gulpExe=gulpExe)
vel[:, idim] = ((freqVal - freqValMdk) / deltaKpt) * velConv
# Reset kpt
kpt[idim] = kpt[idim] + deltaKpt
strchg = _kptstrchg(strchg, kpt)
elif kpt[idim] == -0.5: # kpt at left boundary
freqVal = freq(strchg,
numAtomsUC,
gulpName,
tempName,
gulpExe=gulpExe)
# Change kpt
kpt[idim] = kpt[idim] + deltaKpt
strchg = _kptstrchg(strchg, kpt)
freqValPdk = freq(strchg,
numAtomsUC,
gulpName,
tempName,
gulpExe=gulpExe)
vel[:, idim] = ((freqValPdk - freqVal) / deltaKpt) * velConv
# Reset kpt
kpt[idim] = kpt[idim] - deltaKpt
strchg = _kptstrchg(strchg, kpt)
elif kpt[idim] == 0.0: # kpt at gamma point
freqVal = freq(strchg,
numAtomsUC,
gulpName,
tempName,
gulpExe=gulpExe)
# Change kpt
kpt[idim] = kpt[idim] + deltaKpt
strchg = _kptstrchg(strchg, kpt)
freqValPdk = freq(strchg,
numAtomsUC,
gulpName,
tempName,
gulpExe=gulpExe)
vel[:, idim] = ((freqValPdk - freqVal) / deltaKpt) * velConv
# Reset kpt
kpt[idim] = kpt[idim] - deltaKpt
strchg = _kptstrchg(strchg, kpt)
else:
freqVal = freq(strchg,
numAtomsUC,
gulpName,
tempName,
gulpExe=gulpExe)
# Change kpt
kpt[idim] = kpt[idim] + deltaKpt
strchg = _kptstrchg(strchg, kpt)
freqValPdk = freq(strchg,
numAtomsUC,
gulpName,
tempName,
gulpExe=gulpExe)
kpt[idim] = kpt[idim] - (2.0 * deltaKpt)
strchg = _kptstrchg(strchg, kpt)
freqValMdk = freq(strchg,
numAtomsUC,
gulpName,
tempName,
gulpExe=gulpExe)
vel[:, idim] = ((freqValPdk - freqValMdk) /
(2.0 * deltaKpt)) * velConv
# Reset kpt
kpt[idim] = kpt[idim] + deltaKpt
strchg = _kptstrchg(strchg, kpt)
return vel
def vel(strchg, numAtomsUC, gulpName, tempName, kpt, latConst, deltaKpt=1e-3, gulpExe='gulp'):
"""
Executes a gulp program with the string changes neccesary
and returns the velocities.
ntpy.gulp.vel(strchg, numAtomsUC, gulpName, tempName, deltaKpt=1e-3, gulpExe='gulp')
Parameters
----------
strchg : dict of type str
A dictionary holding key:value pairs. Each key
is original string to be replaced and each value
is the new string to be subsituted.
numAtomsUC : int
The number of atoms in the unit cell.
gulpName : str
A string containing the original file name. If
the file is not included in the pathway then it
can be the absolute or relative pathway to the
file.
tempName : str
A string containing the new file name. If the
file is not included in the pathway then it can
be the absolute or relative pathway to the file.
kpt : array of type float
A numpy array of size 3 that has the three
dimension k-point to be used.
latConst : float
A float of the lattice constant in angstroms.
deltaKpt : float, optional
A float that determines what difference to use
for the difference theorem. Defaults to 10e-5.
gulpExe : str, optional
A string of the gulp executable. Defaults to
"gulp".
Returns
----------
vel : numpy array of type float
Returns the velocity for the kpt in a array of
shape (3 * numAtomsUC, 3)
"""
def _kptstrchg(strchg, kpt):
strchg['KPT'] = '{:.10f} {:.10f} {:.10f}'.format(kpt[0], kpt[1], kpt[2])
return strchg
vel = np.zeros( (3 * numAtomsUC, 3), dtype=float)
# Convert to m/s
velConv = ((1.0 / ct.value('centi')) * ct.value('c')) / (1.0 / (latConst * ct.value('ang')))
# For all three directions
for idim in range(3):
if kpt[idim] == 0.5: # kpt at right boundary
freqVal = freq(strchg, numAtomsUC, gulpName, tempName, gulpExe=gulpExe)
# Change kpt
kpt[idim] = kpt[idim] - deltaKpt
strchg = _kptstrchg(strchg, kpt)
freqValMdk = freq(strchg, numAtomsUC, gulpName, tempName, gulpExe=gulpExe)
vel[:, idim] = ((freqVal - freqValMdk) / deltaKpt) * velConv
# Reset kpt
kpt[idim] = kpt[idim] + deltaKpt
strchg = _kptstrchg(strchg, kpt)
elif kpt[idim] == -0.5: # kpt at left boundary
freqVal = freq(strchg, numAtomsUC, gulpName, tempName, gulpExe=gulpExe)
# Change kpt
kpt[idim] = kpt[idim] + deltaKpt
strchg = _kptstrchg(strchg, kpt)
freqValPdk = freq(strchg, numAtomsUC, gulpName, tempName, gulpExe=gulpExe)
vel[:, idim] = ((freqValPdk - freqVal) / deltaKpt) * velConv
# Reset kpt
kpt[idim] = kpt[idim] - deltaKpt
strchg = _kptstrchg(strchg, kpt)
elif kpt[idim] == 0.0: # kpt at gamma point
freqVal = freq(strchg, numAtomsUC, gulpName, tempName, gulpExe=gulpExe)
# Change kpt
kpt[idim] = kpt[idim] + deltaKpt
strchg = _kptstrchg(strchg, kpt)
freqValPdk = freq(strchg, numAtomsUC, gulpName, tempName, gulpExe=gulpExe)
vel[:, idim] = ((freqValPdk - freqVal) / deltaKpt) * velConv
# Reset kpt
kpt[idim] = kpt[idim] - deltaKpt
strchg = _kptstrchg(strchg, kpt)
else:
freqVal = freq(strchg, numAtomsUC, gulpName, tempName, gulpExe=gulpExe)
# Change kpt
kpt[idim] = kpt[idim] + deltaKpt
strchg = _kptstrchg(strchg, kpt)
freqValPdk = freq(strchg, numAtomsUC, gulpName, tempName, gulpExe=gulpExe)
kpt[idim] = kpt[idim] - (2.0 * deltaKpt)
strchg = _kptstrchg(strchg, kpt)
freqValMdk = freq(strchg, numAtomsUC, gulpName, tempName, gulpExe=gulpExe)
vel[:, idim] = ((freqValPdk - freqValMdk) / (2.0 * deltaKpt)) * velConv
# Reset kpt
kpt[idim] = kpt[idim] + deltaKpt
strchg = _kptstrchg(strchg, kpt)
return vel
