def eig(strchg, numAtomsUC, gulpName, tempName, kpt):
"""
Executes a gulp program with the string changes neccesary
and returns the eigenvectors.
ntpy.gulp.eig(strchg, numAtomsUC, gulpName, tempName, kpt)
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.
kpt : array of type float
A numpy array of size 3 that has the three
dimension k-point to be used.
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')
# Grep out eigenvectors
st.grep(' 1 x', 3 * numAtomsUC, 'output.gulp', 'eigvec_grep.dat')
xyzDict = dict({ 'x' : ''})
st.sed(xyzDict, 'eigvec_grep.dat', 'eigvec2.dat')
os.system('rm eigvec_grep.dat')
xyzDict = dict({ 'y' : ''})
st.sed(xyzDict, 'eigvec2.dat', 'eigvec3.dat')
os.system('rm eigvec2.dat')
xyzDict = dict({ 'z' : ''})
st.sed(xyzDict, 'eigvec3.dat', 'eigvec4.dat')
os.system('rm eigvec3.dat')
# Read in eigvecs
if kpt[0] == 0.0 and kpt[1] == 0.0 and kpt[2] == 0.0:
# If Gamma Point gulp only prints the real values
dummy = np.loadtxt('eigvec4.dat', usecols=(1,2,3,4,5,6), comments='--')
dummy = np.reshape(dummy, (3 * numAtomsUC, -1))
eig = np.zeros( (3 * numAtomsUC, 3 * numAtomsUC), dtype=complex)
for i in range(3 * numAtomsUC):
eig[i,:] = dummy[i,:]
else:
eig = np.loadtxt('eigvec4.dat', usecols=(1,2,3,4,5,6), comments='--').view(complex)
eig = np.reshape(eig, (3 * numAtomsUC, -1))
os.system('rm eigvec4.dat')
return eig
def freq(strchg, numAtomsUC, gulpName, tempName, gulpExe='gulp'):
"""
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.
gulpExe : str, optional
A string of the gulp executable. Defaults to
"gulp".
Returns
----------
freq : numpy array of type float
A array returning the frequencies of the k-point.
The array is of shape (3 * numAtomsUC)
"""
# String change the template file
st.sed(strchg, gulpName, tempName)
# Execute the new gulp file
system(gulpExe + ' <' + tempName + ' > output.gulp')
# system('gulp '+ tempName+ ' output.gulp')
# Extract the frequencies
freq = np.zeros((3 * numAtomsUC), dtype=float)
freq = np.loadtxt(tempName + '.freq', comments='--')
# Remove the .freq file
system('rm ' + tempName + '.freq')
return freq
def freq(strchg, numAtomsUC, gulpName, tempName, gulpExe='gulp'):
"""
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.
gulpExe : str, optional
A string of the gulp executable. Defaults to
"gulp".
Returns
----------
freq : numpy array of type float
A array returning the frequencies of the k-point.
The array is of shape (3 * numAtomsUC)
"""
# String change the template file
st.sed(strchg, gulpName, tempName)
# Execute the new gulp file
system(gulpExe+ ' <'+ tempName+ ' > output.gulp')
# system('gulp '+ tempName+ ' output.gulp')
# Extract the frequencies
freq = np.zeros( (3 * numAtomsUC), dtype=float)
freq = np.loadtxt(tempName+ '.freq', comments='--')
# Remove the .freq file
system('rm '+ tempName+ '.freq')
return freq
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 eig(strchg, numAtomsUC, gulpName, tempName, kpt, gulpExe='gulp'):
"""
Executes a gulp program with the string changes neccesary
and returns the eigenvectors.
ntpy.gulp.eig(strchg, numAtomsUC, gulpName, tempName, kpt)
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.
gulpExe : str, optional
A string of the gulp executable. Defaults to
"gulp".
Returns
----------
eig : numpy array of type complex
A eigenvector array where columns correspond to
modes and rows correspond to atoms in the unit
cell, where each unit cell atom is split into
x, y, z. Shape of array is (3 * numAtomsUC,
3 * numAtomsUC)
"""
numModes = 3 * numAtomsUC
# String change the template file
st.sed(strchg, gulpName, tempName)
# Execute the new gulp file
system(gulpExe + ' <' + tempName + ' > output.gulp')
# Grep out eigenvectors
st.grep(' 1 x', 3 * numAtomsUC, 'output.gulp', 'eigvec_grep.dat')
xyzDict = dict({'x': ''})
st.sed(xyzDict, 'eigvec_grep.dat', 'eigvec2.dat')
system('rm eigvec_grep.dat')
xyzDict = dict({'y': ''})
st.sed(xyzDict, 'eigvec2.dat', 'eigvec3.dat')
system('rm eigvec2.dat')
xyzDict = dict({'z': ''})
st.sed(xyzDict, 'eigvec3.dat', 'eigvec4.dat')
system('rm eigvec3.dat')
# Read in eigvecs
if kpt[0] == 0.0 and kpt[1] == 0.0 and kpt[2] == 0.0:
# If Gamma Point gulp only prints the real values
dummy = np.loadtxt('eigvec4.dat',
usecols=(1, 2, 3, 4, 5, 6),
comments='--')
eig = np.zeros((numModes, numModes), dtype=complex)
for iSlice in range(0, numModes, 3 * 2):
eig[:,iSlice:iSlice+(3*2)] = dummy[iSlice*numAtomsUC/2:iSlice*numAtomsUC/2 \
+(numModes),:]
else:
dummy = np.loadtxt('eigvec4.dat',
usecols=(1, 2, 3, 4, 5, 6),
comments='--').view(complex)
eig = np.zeros((numModes, numModes), dtype=complex)
for iSlice in range(0, numModes, 3):
eig[:,iSlice:iSlice+3] = dummy[iSlice*numAtomsUC:iSlice*numAtomsUC \
+numModes,:]
system('rm eigvec4.dat')
return eig
def eig(strchg, numAtomsUC, gulpName, tempName, kpt, gulpExe='gulp'):
"""
Executes a gulp program with the string changes neccesary
and returns the eigenvectors.
ntpy.gulp.eig(strchg, numAtomsUC, gulpName, tempName, kpt)
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.
gulpExe : str, optional
A string of the gulp executable. Defaults to
"gulp".
Returns
----------
eig : numpy array of type complex
A eigenvector array where columns correspond to
modes and rows correspond to atoms in the unit
cell, where each unit cell atom is split into
x, y, z. Shape of array is (3 * numAtomsUC,
3 * numAtomsUC)
"""
numModes = 3 * numAtomsUC
# String change the template file
st.sed(strchg, gulpName, tempName)
# Execute the new gulp file
system(gulpExe+ ' <'+ tempName+ ' > output.gulp')
# Grep out eigenvectors
st.grep(' 1 x', 3 * numAtomsUC, 'output.gulp', 'eigvec_grep.dat')
xyzDict = dict({ 'x' : ''})
st.sed(xyzDict, 'eigvec_grep.dat', 'eigvec2.dat')
system('rm eigvec_grep.dat')
xyzDict = dict({ 'y' : ''})
st.sed(xyzDict, 'eigvec2.dat', 'eigvec3.dat')
system('rm eigvec2.dat')
xyzDict = dict({ 'z' : ''})
st.sed(xyzDict, 'eigvec3.dat', 'eigvec4.dat')
system('rm eigvec3.dat')
# Read in eigvecs
if kpt[0] == 0.0 and kpt[1] == 0.0 and kpt[2] == 0.0:
# If Gamma Point gulp only prints the real values
dummy = np.loadtxt('eigvec4.dat', usecols=(1,2,3,4,5,6), comments='--')
eig = np.zeros( (numModes, numModes), dtype=complex)
for iSlice in range(0,numModes,3*2):
eig[:,iSlice:iSlice+(3*2)] = dummy[iSlice*numAtomsUC/2:iSlice*numAtomsUC/2 \
+(numModes),:]
else:
dummy = np.loadtxt('eigvec4.dat', usecols=(1,2,3,4,5,6), comments='--').view(complex)
eig = np.zeros( (numModes, numModes), dtype=complex)
for iSlice in range(0,numModes,3):
eig[:,iSlice:iSlice+3] = dummy[iSlice*numAtomsUC:iSlice*numAtomsUC \
+numModes,:]
system('rm eigvec4.dat')
return eig