qe-analyzer 0.0.4

A small package for analyzing quantum espresso outputs

qe_analyzer convergenceTests.py [ecut, planewaves, energy, ecut**(3/2)]=extractECUTConvergenceInfo(file1) "head_ECUTcovergencePlot.png"=ECUTconvergenceTest(head, calcThresh=False, thresh=0.05) "TotEvsInequivK.png"=KconvergenceTest(fmt='*.out') kx, ky, kz, shiftx, khifty, shiftz, ecutwfc, energy, inequiv, time=extractKConvergenceInfo(file1) a, cba, totEnergy=importacLatticeParamEnergyFile(fname) mat, unA, unCbA, data=importAllLatParamFiles(fmt) "print(min data point a=, c/a=)"=plotCbAvsA(fmt, lim=0) copyPaste.py "updated file"=insertKptsFromXcrysden(kpfFile, updateFile) "output file and lines in console describing what is being replaced to allow for verification"=vcRelaxTransfer(inFileHead, outputF) electronBands.py [Ef, booleanHighestOccupied]=getEfSCF(scfFile) [k, energies]=importBands(file) [k, energies, xCoordinates, highSymmetryPoints]=buildBands(file2) plotBands(file, Ef=0, Kcoord=True, lbls=[], figsize=plt.rcParams.get('figure.figsize'), pad=1.08) phonons.py x, energy=importFreqGp(fname) pts, flfrq=generateXcoordMatdyn(matdynFile) plotPhononDispersion_cm(matdynF, figsize=plt.rcParams.get('figure.figsize'), pad=1.08 ,labels=[]) plotPhononDispersion_meV(matdynF, figsize=plt.rcParams.get('figure.figsize'), pad=1.08 ,labels=[])

convergenceTests.extractECUTConvergenceInfo(file1): """extracts ECUT convergence information from a given file, file1 outputs a list of [ECUT, # planewaves, energy, CPU time, and ECUT**(3/2)]

Parameters
----------
file1 : str
    DESCRIPTION. File to read in

Returns list containing
-------
ecutwfc : float
    DESCRIPTION. ECUT value 
planewaves : float
    DESCRIPTION. number of planewaves
energy : float
    DESCRIPTION. Total Energy
time: float
	DESCRIPTION. CPU time
ecutwfc**(3/2): float
	DESCRIPTION. ECUT value to the 2/3 power. Ecut**(2/3) should be proportional to the number of planewaves

"""

convergenceTests.ECUTconvergenceTest(head, calcThresh=False, thresh=0.05) """ Prints the filenames imported for an ECUT convergence test (series of files where ECUT is changing) assumes '${head}-${ECUT}.out' file naming, will ignore all other files in folder. Prints the filenames that it imports for this also saves the plot

Parameters
----------
head : str
    DESCRIPTION. The header to the filename. Assumes that your working directory contains files with 
	   '${head}-${ECUT}.out' formatting
calcThresh : boolean, optional
	DESCRIPTION. Do you want to pull out the ECUT associated with a convergence threshold?

thresh : float
	DESCRIPTION. The convergence threshold you would like
Returns
-------
None. A plot should show up and will be automatically saved to your working directory.
"""		

convergenceTests.extractKConvergenceInfo(file1) """ kx, ky, kz, shiftx, shifty, shiftx, ecutwfc, energy, inequiv,time =extractKConvergenceInfo('SrTiO3-260-0-16.out')

Parameters
----------
file1 : str
    DESCRIPTION. name of *.out file to extract information from

Returns
-------
kx : int
    DESCRIPTION.# k points in x direction
ky : int
    DESCRIPTION. # k points in y direction
kz : int
    DESCRIPTION. # k points in z direction
shiftx : int
    DESCRIPTION.0 or 1
shifty : int
    DESCRIPTION.0 or 1
shiftz : int
    DESCRIPTION.0 or 1
ecutwfc : float
    DESCRIPTION. cutoff energy
energy : float
    DESCRIPTION. total energy
inequiv : int
    DESCRIPTION. Number inequivalent k points
time : float
    DESCRIPTION. CPU time in minutes

"""

convergenceTests.KconvergenceTest(fmt='.out') """ plots energy vs # k point mesh in x, y, and z directions. If all equal, only does one plot KconvergenceTest('SrTiO3-260--*.out')

Parameters
----------
fmt : string, optional
    DESCRIPTION. The default is '*.out'. filename format for searching the working directory. This is like glob

Returns
-------
None.
"""

convergenceTests.importacLatticeParamEnergyFile(fname) '''

Parameters
----------
fname : TYPE
    DESCRIPTION.

Returns
-------
a : float
    DESCRIPTION. lattice constant a in Bohr
cba : float
    DESCRIPTION.c/a ratio
totEnergy : float
    DESCRIPTION. total energy in Ry

'''	

convergenceTests.importAllLatParamFiles(fmt) """ import all lattice parameter files. Use this for debugging any issues with plotCbAvsA. This is used in plotCbAvsA. Prints the filenames of all files imported to allow you to check that things import properly Parameters ---------- fmt : str DESCRIPTION. Format used by glob to describe the files involved in the lattice parameter data

Returns
-------
mat : numpy array of floats
    DESCRIPTION. Array of total energies
unA : 1-d sorted numpy array
    DESCRIPTION. Array of unique values in the a-lattice parameter
unCbA : 1-d sorted numpy array
    DESCRIPTION. Array of unique values in c/a
data : numpy array
    DESCRIPTION. raw data extracted from files, useful for debugging

"""

convergenceTests.plotCbAvsA(fmt, lim=0): """ Plots C/A vs A when A is in Bohr fmt='graphite__.out'
plotCbAvsA(fmt)
Parameters ---------- fmt : str DESCRIPTION. Format used by glob to describe the files involved in the lattice parameter data lim : float, optional DESCRIPTION. The default is -45.599. Describes the energy threshold above which all become one color.

Returns
-------
None.

"""

copyPaste.insertKptsFromXcrysden(kpfFile, updateFile): """ Generates a new *.in file entitled updateFile(minus.in)_update.in by incorporating the k-points listed in kpfFile (real form of k-point coordinates)

Parameters
----------
kpfFile : str
    DESCRIPTION. Filename, including extension, of the XCRYSDEN *.kpf file 
    containing the points you want to add
updateFile : TYPE
    DESCRIPTION. Filename, including extension, of the *.in file that you 
    want to update/replace k-points of. This should leave other blocks alone.

Returns
-------
None.

"""

copyPaste.vcRelaxTransfer(inFileHead, outputF): ''' Applies the new lattice parameters and atom sites obtained from a vc-relax calculation to a new *.in file example: vcRelaxTransfer('Si-vcRelax', 'Si-vcRelax2.in') Caution: Not fully tested.

Parameters
----------
inFileHead : str
    DESCRIPTION. Head of pw.x input and output files used for vc-relax calculation ([HEAD].in and [HEAD].out). No extension included
outputF : str
    DESCRIPTION. Name of the new pw.x input file that you want to create. MUST INCLUDE *.in EXTENSION!

Returns
-------
None.

'''

electronBands.getEfSCF(scfFile): """ Extracts Fermi level from SCF file

Parameters
----------
scfFile : str
    DESCRIPTION. Filename (or path to file and filename)

Returns
-------
list
    DESCRIPTION. [Ef, highest occupied], The first element is the Fermi level. 
    The second element is a boolean describing whether the file said it was 
      the highest occupied orbital (True) or truly the Fermi level (False) 

"""

electronBands.importBands(file): """ import bands structure in a mannner ready for plotting Parameters ---------- file : str DESCRIPTION. band.x output file $[prefix]_bandx.out file generated by running bands.x Kcoord : boolean, optional

Returns
-------
k : array of float64
    DESCRIPTION. x-coordinates associated with k-points to use for plot. This is a 1-d array (vector)
Energies : array of float64
    DESCRIPTION. array such that each column represents a band
x2 : list
    DESCRIPTION. x-coordinates associated with special k points
hsp : list
    DESCRIPTION. Each element in the list is a set of coordinates [kx, ky, kz] 
    describing the high-symmetry points. 
"""	

electronBands.buildBands(file2): """Extracts energy vs k for plotting into 1D array k and numpy array; also extracts special points for plotting

Parameters
----------
file2 : str
    DESCRIPTION. band.x output file $[prefix]_bandx.out file generated by running bands.x
Kcoord : boolean, optional

Returns
-------
k : array of float64
    DESCRIPTION. x-coordinates associated with k-points to use for plot. This is a 1-d array (vector)
Energies : array of float64
    DESCRIPTION. array such that each column represents a band
x2 : list
    DESCRIPTION. x-coordinates associated with special k points
hsp : list
    DESCRIPTION. Each element in the list is a set of coordinates [kx, ky, kz] 
    describing the high-symmetry points. 

"""

electronBands.plotBands(file, Ef=0, Kcoord=True, lbls=[], figsize=plt.rcParams.get('figure.figsize'), pad=1.08): """ Return a plot of the data from file. plotBands(file) plotBands(file, getEfSCF('si_scf.out')[0], False, ['L', r'$\Gamma$', 'X']) plotBands(file, 0, False, ['L', r'$\Gamma$', 'X'])

Parameters
----------
file : str
    DESCRIPTION. band.x output file $[prefix]_bandx.out file generated by running bands.x
Ef : float, optional
    DESCRIPTION. Fermi level. Can be extracted using 
Kcoord : boolean, optional
    DESCRIPTION. The default is True. For the k-axis, use the special point coordinates (kx, ky, kz) for labels. 
    If false, requires lbls to include a list of labels of the appropriate length eg:['L', r'$\Gamma$', X]
lbls : list
    DESCRIPTION. The default is []. List of length number of high-symmetry points, optional only if Kcoord=True. 
figsize: (float, float), optional
    DESCRIPTION. The default is plt.rcParams.get('figure.figsize'). Figure width and height in inches
pad: float, optional
    DESCRIPTION. The default is 1.08. Padding around figure for tight_layout
Returns
-------
None.

"""

phonons.importFreqGp(fname) """ imports data from *.freq.gp file

Parameters
----------
fname : str
    DESCRIPTION.file name to be imported

Returns
-------
x: 1-d numpy array
    DESCRIPTION. k point x-value for plotting (2pi/a)
energy: 2-d numpy array
    DESCRIPTION. each column is a different band.

phonons.generateXcoordMatdyn(matdynFile) """ generates X-labels (special K-points) from matdyn file assumes q_in_band_form=True

Parameters
----------
matdynFile : TYPE
    DESCRIPTION.

Returns
-------
pts : 2-d numpy array
    DESCRIPTION. special points such that column 0 is kx, column 1 is ky, column 2 is kz, column 3 is the x-coordinate for the E-vs-k plot
flfrq : str
    DESCRIPTION. filename from matdyn file for where to expect the phonon data for processing (*.freq.gp file)

"""

phonons.plotPhononDispersion_cm(matdynF, figsize=plt.rcParams.get('figure.figsize'), pad=1.08 ,labels=[]): """ Plots phonon dispersion assuming q_in_band_form for special points

plotPhononDispersion_cm('diamond_matdyn.in')
plotPhononDispersion_cm('diamond_matdyn.in', labels=['L', r'$\Gamma$', 'X'])

Parameters
----------
matdynF : str
    DESCRIPTION. Filename of the matdyne input file that you used to generate the *.freq.gp file
figsize : tuple, optional
    DESCRIPTION. The default is plt.rcParams.get('figure.figsize'). See matplotlib.pyplot.plot for details
pad : float, optional
    DESCRIPTION. The default is 1.08. padding around the figure in plt.tight_layout()
labels : list of strings, optional
    DESCRIPTION. The default is []. Labels to use for the special points. 
    If the length of this is not equal to the number of special points listed in matdynF, these labels will not be used.
    assumes q_in_band_form

Returns
-------
None.

"""

phonons.plotPhononDispersion_meV(matdynF, figsize=plt.rcParams.get('figure.figsize'), pad=1.08 ,labels=[]) """ Plots phonon dispersion assuming q_in_band_form for special points

plotPhononDispersion_meV('diamond_matdyn.in')
plotPhononDispersion_meV('diamond_matdyn.in', labels=['L', r'$\Gamma$', 'X'])


Parameters
----------
matdynF : str
    DESCRIPTION. Filename of the matdyne input file that you used to generate the *.freq.gp file
figsize : tuple, optional
    DESCRIPTION. The default is plt.rcParams.get('figure.figsize'). See matplotlib.pyplot.plot for details
pad : float, optional
    DESCRIPTION. The default is 1.08. padding around the figure in plt.tight_layout()
labels : list of strings, optional
    DESCRIPTION. The default is []. Labels to use for the special points. 
    If the length of this is not equal to the number of special points listed in matdynF, these labels will not be used.
    assumes q_in_band_form

Returns
-------
None.

"""