def __init__(self,
filename=None,
configString=None,
sectionList=None,
taskList=None):
QECalc.__init__(self)
# tasks definition:
# specify taskName/taskConstructur pairs
self._taskSpec = [['pw', PWTask], ['ph', PHTask], ['q2r', Q2RTask],
['matdyn', MatdynTask]]
# Merging map sets tasks to be merged. Last two columns identify name
# of default task (its input and output objects will be directly
#accessible) and last column is the name of merged task object (e.g.'pwph')
#is not implemented yet !!!!
self._mergingMap = [
['pw', 'ph', 'pw', 'pwph'],
]
self._populateTasks(filename, configString, sectionList, taskList)
self.pwph = PWPHMerger(self.pw, self.ph, cleanOutDir=True)
self.taskList = [self.pwph, self.q2r, self.matdyn]
self._dispersion = PHDispersion(self.pw.input.structure.lattice,
self.matdyn)
self.dos = PhononDOS(self.matdyn)
def gammaDispersion(self, *pathNPoints):
#self.pw.input.parse()
#self.matdyn.input.parse()
self.dispersion = PHDispersion( self.pw.input.structure.lattice, self.matdyn)
if self.freqs.fitter.type != 'polynom':
raise Exception('This method is only relevant for polynomial fit')
self.dispersion = PHDispersion( self.pw.input.structure.lattice, self.matdyn)
self.dispersion.setPath(*pathNPoints)
self.dispersion.setValues(-self.freqs.coeff()[:,:,-1])
self.dispersion.save('gamma_disp')
self.dispersion.plot()
def gammaDispersion(self, *pathNPoints):
#self.pw.input.parse()
#self.matdyn.input.parse()
self.dispersion = PHDispersion(self.pw.input.structure.lattice,
self.matdyn)
if self.freqs.fitter.type != 'polynom':
raise Exception('This method is only relevant for polynomial fit')
self.dispersion = PHDispersion(self.pw.input.structure.lattice,
self.matdyn)
self.dispersion.setPath(*pathNPoints)
self.dispersion.setValues(-self.freqs.coeff()[:, :, -1])
self.dispersion.save('gamma_disp')
self.dispersion.plot()
def __init__(self, filename = None, configString = None, sectionList = None, taskList = None):
QECalc.__init__(self)
# tasks definition:
# specify taskName/taskConstructur pairs
self._taskSpec = [
['pw', PWTask],
['ph', PHTask],
['q2r', Q2RTask],
['matdyn', MatdynTask]
]
# Merging map sets tasks to be merged. Last two columns identify name
# of default task (its input and output objects will be directly
#accessible) and last column is the name of merged task object (e.g.'pwph')
#is not implemented yet !!!!
self._mergingMap = [ ['pw', 'ph', 'pw','pwph'],
]
self._populateTasks(filename, configString, sectionList, taskList)
self.pwph = PWPHMerger(self.pw,self.ph, cleanOutDir = True)
self.taskList = [self.pwph, self.q2r, self.matdyn]
self._dispersion = PHDispersion(self.pw.input.structure.lattice, self.matdyn)
self.dos = PhononDOS(self.matdyn)
class VoluPhon():
def __init__(self, prcntVolume, filename = None ):
"""
This class requires a set of "n_matdyn.modes" files
corresponding to different volume expansions
prcntVolume - array with
"""
self.pw = PWTask(filename = filename)
self.matdyn = MatdynTask(filename = filename)
self.__prcntVolume = prcntVolume
def setA(self, values, fitter):
self.a = volufit.ValueFit(self.__prcntVolume, values, fitter)
def setC(self, values, fitter):
self.c = volufit.ValueFit(self.__prcntVolume, values, fitter)
def setEnergy(self, values, fitter):
self.energy = volufit.ValueFit(self.__prcntVolume, values, fitter)
def setPhonons(self, indexRange, fitter):
"""Will read freqs from x_matdyn.modes files and fit the freqs"""
matdynModesName = self.matdyn.setting.get('flvec')
self.matdyn.setting.set('flvec', str(indexRange[0]) + '_' + matdynModesName)
self.matdyn.output.parse()
Pol, Omega, qPoints = self.matdyn.output.property('multi phonon')
volOmega = numpy.zeros(shape=(len(indexRange), numpy.shape(Omega)[0], \
numpy.shape(Omega)[1] ) )
volOmega[0] = Omega
for i in range(1,len(indexRange)):
self.matdyn.setting.set('flvec', str(indexRange[i]) + '_' + matdynModesName)
self.matdyn.output.parse()
Pol, Omega, qPoints = self.matdyn.output.property('multi phonon')
volOmega[i] = Omega
self.matdyn.setting.set('flvec', matdynModesName)
self.freqs = volufit.FreqFit(self.__prcntVolume, volOmega,fitter)
def gammaDispersion(self, *pathNPoints):
#self.pw.input.parse()
#self.matdyn.input.parse()
self.dispersion = PHDispersion( self.pw.input.structure.lattice, self.matdyn)
if self.freqs.fitter.type != 'polynom':
raise Exception('This method is only relevant for polynomial fit')
self.dispersion = PHDispersion( self.pw.input.structure.lattice, self.matdyn)
self.dispersion.setPath(*pathNPoints)
self.dispersion.setValues(-self.freqs.coeff()[:,:,-1])
self.dispersion.save('gamma_disp')
self.dispersion.plot()
def prcntVolume (self):
return self.__prcntVolume
class VoluPhon():
def __init__(self, prcntVolume, filename=None):
"""
This class requires a set of "n_matdyn.modes" files
corresponding to different volume expansions
prcntVolume - array with
"""
self.pw = PWTask(filename=filename)
self.matdyn = MatdynTask(filename=filename)
self.__prcntVolume = prcntVolume
def setA(self, values, fitter):
self.a = volufit.ValueFit(self.__prcntVolume, values, fitter)
def setC(self, values, fitter):
self.c = volufit.ValueFit(self.__prcntVolume, values, fitter)
def setEnergy(self, values, fitter):
self.energy = volufit.ValueFit(self.__prcntVolume, values, fitter)
def setPhonons(self, indexRange, fitter):
"""Will read freqs from x_matdyn.modes files and fit the freqs"""
matdynModesName = self.matdyn.setting.get('flvec')
self.matdyn.setting.set('flvec',
str(indexRange[0]) + '_' + matdynModesName)
self.matdyn.output.parse()
Pol, Omega, qPoints = self.matdyn.output.property('multi phonon')
volOmega = numpy.zeros(shape=(len(indexRange), numpy.shape(Omega)[0], \
numpy.shape(Omega)[1] ) )
volOmega[0] = Omega
for i in range(1, len(indexRange)):
self.matdyn.setting.set('flvec',
str(indexRange[i]) + '_' + matdynModesName)
self.matdyn.output.parse()
Pol, Omega, qPoints = self.matdyn.output.property('multi phonon')
volOmega[i] = Omega
self.matdyn.setting.set('flvec', matdynModesName)
self.freqs = volufit.FreqFit(self.__prcntVolume, volOmega, fitter)
def gammaDispersion(self, *pathNPoints):
#self.pw.input.parse()
#self.matdyn.input.parse()
self.dispersion = PHDispersion(self.pw.input.structure.lattice,
self.matdyn)
if self.freqs.fitter.type != 'polynom':
raise Exception('This method is only relevant for polynomial fit')
self.dispersion = PHDispersion(self.pw.input.structure.lattice,
self.matdyn)
self.dispersion.setPath(*pathNPoints)
self.dispersion.setValues(-self.freqs.coeff()[:, :, -1])
self.dispersion.save('gamma_disp')
self.dispersion.plot()
def prcntVolume(self):
return self.__prcntVolume
class MultiPhononCalc(QECalc):
""" Calc for multi phonon calculations:
Task list:
pw -- PWTask
ph -- PHTask
q2r -- Q2RTask
matdyn -- MatdynTask
pwph -- PWPHMerger - task merger used for submission of pw.x and ph.x
commands in a single command string
taskList = [pwph, q2r, matdyn]
Example:
>>> mphonCalc = MultiPhononCalc('config.ini')
>>> mphon.launch()
>>> print mphon.pw.output.property('total energy')
>>> print mphon.matdyn.output.listParsers()
>>> print mphon.matdyn.output.property('phonon dos')
>>> polVecs, freqs, qpoints = mphon.lookupProperty('multi phonon')
"""
def __init__(self, filename = None, configString = None, sectionList = None, taskList = None):
QECalc.__init__(self)
# tasks definition:
# specify taskName/taskConstructur pairs
self._taskSpec = [
['pw', PWTask],
['ph', PHTask],
['q2r', Q2RTask],
['matdyn', MatdynTask]
]
# Merging map sets tasks to be merged. Last two columns identify name
# of default task (its input and output objects will be directly
#accessible) and last column is the name of merged task object (e.g.'pwph')
#is not implemented yet !!!!
self._mergingMap = [ ['pw', 'ph', 'pw','pwph'],
]
self._populateTasks(filename, configString, sectionList, taskList)
self.pwph = PWPHMerger(self.pw,self.ph, cleanOutDir = True)
self.taskList = [self.pwph, self.q2r, self.matdyn]
self._dispersion = PHDispersion(self.pw.input.structure.lattice, self.matdyn)
self.dos = PhononDOS(self.matdyn)
def _get_dispersion(self):
self._dispersion.matdynTask = self.matdyn
self._dispersion.setLattice(self.pw.input.structure.lattice)
return self._dispersion
dispersion = property(_get_dispersion, doc ="dispersion object")
def syncInputs(self):
for task in self.taskList:
task.input.parse()
# remove amass from phonon input
for param in self.ph.input.namelist('input').params:
if 'amass(' in param:
self.ph.input.namelist('input').remove(param)
# initialize amass based on PW input
for i, atom in enumerate(self.pw.input.structure.atomicSpecies):
amass = 'amass(' + str(i+1) + ')'
self.ph.input.namelist('input').add(amass,atom.mass)
#sync outdir based on PW input
self.ph.input.namelist('input').add('outdir', \
self.pw.input.namelist('control').param('outdir'))
class MultiPhononCalc(QECalc):
""" Calc for multi phonon calculations:
Task list:
pw -- PWTask
ph -- PHTask
q2r -- Q2RTask
matdyn -- MatdynTask
pwph -- PWPHMerger - task merger used for submission of pw.x and ph.x
commands in a single command string
taskList = [pwph, q2r, matdyn]
Example:
>>> mphonCalc = MultiPhononCalc('config.ini')
>>> mphon.launch()
>>> print mphon.pw.output.property('total energy')
>>> print mphon.matdyn.output.listParsers()
>>> print mphon.matdyn.output.property('phonon dos')
>>> polVecs, freqs, qpoints = mphon.lookupProperty('multi phonon')
"""
def __init__(self,
filename=None,
configString=None,
sectionList=None,
taskList=None):
QECalc.__init__(self)
# tasks definition:
# specify taskName/taskConstructur pairs
self._taskSpec = [['pw', PWTask], ['ph', PHTask], ['q2r', Q2RTask],
['matdyn', MatdynTask]]
# Merging map sets tasks to be merged. Last two columns identify name
# of default task (its input and output objects will be directly
#accessible) and last column is the name of merged task object (e.g.'pwph')
#is not implemented yet !!!!
self._mergingMap = [
['pw', 'ph', 'pw', 'pwph'],
]
self._populateTasks(filename, configString, sectionList, taskList)
self.pwph = PWPHMerger(self.pw, self.ph, cleanOutDir=True)
self.taskList = [self.pwph, self.q2r, self.matdyn]
self._dispersion = PHDispersion(self.pw.input.structure.lattice,
self.matdyn)
self.dos = PhononDOS(self.matdyn)
def _get_dispersion(self):
self._dispersion.matdynTask = self.matdyn
self._dispersion.setLattice(self.pw.input.structure.lattice)
return self._dispersion
dispersion = property(_get_dispersion, doc="dispersion object")
def syncInputs(self):
for task in self.taskList:
task.input.parse()
# remove amass from phonon input
for param in self.ph.input.namelist('input').params:
if 'amass(' in param:
self.ph.input.namelist('input').remove(param)
# initialize amass based on PW input
for i, atom in enumerate(self.pw.input.structure.atomicSpecies):
amass = 'amass(' + str(i + 1) + ')'
self.ph.input.namelist('input').add(amass, atom.mass)
#sync outdir based on PW input
self.ph.input.namelist('input').add('outdir', \
self.pw.input.namelist('control').param('outdir'))
# input/output files relevant to multiple phonon calculation
matdynInput: matdyn.in
matdynOutput: matdyn.out
flfrc: mgb2666.fc
"""
if __name__ == "__main__":
matdyn = MatdynTask(configString = configString)
pw = PWTask(configString = configString)
pw.input.parse()
matdyn.input.parse()
matdyn.syncSetting()
phDisp = PHDispersion(pw.input.structure.lattice, matdyn)
#phDisp.launch('M', 'Gamma', 'A', 'L', 200, 200, 200)
nP = 100
phDisp.launch('Gamma', 'K', 'M', 'Gamma', 'A','H', 'L', 'A', nP, nP, nP, nP , nP , nP, nP)
#phDisp.launch('Gamma', 'H', nP)
#phDisp.launch('Gamma', 'K', 'M', 'Gamma', nP , nP, nP)
#phDisp.launch( 'Gamma', 'K', nP )
# phDisp.solveIndex((0,0,0), [-0.1,0.2,0.4])
# matdyn.output.parse()
#
# Pol, Omegas, qPoints = matdyn.output.property('multi phonon')
# Pol2 = Pol.reshape(Pol.shape[0], Pol.shape[1], Pol.shape[2]*Pol.shape[3])
# print Pol2
[matdyn.x]
# input/output files relevant to multiple phonon calculation
matdynInput: matdyn.in
matdynOutput: matdyn.out
flfrc: mgb2666.fc
"""
if __name__ == "__main__":
matdyn = MatdynTask(configString=configString)
pw = PWTask(configString=configString)
pw.input.parse()
matdyn.input.parse()
matdyn.syncSetting()
phDisp = PHDispersion(pw.input.structure.lattice, matdyn)
#phDisp.launch('M', 'Gamma', 'A', 'L', 200, 200, 200)
nP = 100
phDisp.launch('Gamma', 'K', 'M', 'Gamma', 'A', 'H', 'L', 'A', nP, nP, nP,
nP, nP, nP, nP)
#phDisp.launch('Gamma', 'H', nP)
#phDisp.launch('Gamma', 'K', 'M', 'Gamma', nP , nP, nP)
#phDisp.launch( 'Gamma', 'K', nP )
# phDisp.solveIndex((0,0,0), [-0.1,0.2,0.4])
# matdyn.output.parse()
#
# Pol, Omegas, qPoints = matdyn.output.property('multi phonon')
# Pol2 = Pol.reshape(Pol.shape[0], Pol.shape[1], Pol.shape[2]*Pol.shape[3])