def __init__(self, fname=None, taskName = 'total energy', tolerance = 1, nMaxSteps = 10):
"""taskName - currently can be 'total energy', 'single phonon',
or 'geometry'
tolerance - task convergence criteria in percents
nMaxSteps = maximum number of optimization steps for
the optimization routines"""
# Default values, see explanations below:
# convergerDic = {
# 'taskName': 'total energy',
# 'tolerance': '1',
# 'nMaxSteps': '10'
# }
QECalc.__init__(self,fname)
# value to converge with respect to k-points or energy cutoffs
# currently can be 'total energy', 'single phonon', or 'geometry':
# self.taskName = self.config.get('Converger', 'taskName')
# convergence criteria in percents:
# self.tolerance = self.config.getfloat('Converger','tolerance')
# maximum number of optimization steps:
# self.nMaxSteps = self.config.getint('Converger','nMaxSteps')
self.taskName = taskName
self.tolerance = tolerance
self.nMaxSteps = nMaxSteps
self.lookupTable = {
'total energy' : (self.pwscfLauncher, self.getTotalEnergy),
'single phonon': (self.singlePhononLauncher, self.getSinglePhonon),
'geometry' : (self.pwscfLauncher, self.getLatticeParameters)
# 'multiple phonon': (self.multiPhononLauncher, self.getMultiPhonon)
}
assert self.lookupTable.has_key(self.taskName), "Convergence \
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], ['d3', D3Task]]
self._populateTasks(filename, configString, sectionList, taskList)
#self.pw = PWTask(filename)
#self.ph = PHTask(filename)
#self.d3 = D3Task(filename)
self.pwph = PWPHMerger(self.pw,
self.ph,
cleanOutDir=self.pw.input.outDir())
self.taskList = [self.pwph, self.d3]
#Hack: make sure d3 task is serial (d3 does not seem to work in parallel)
for task in [self.pw, self.ph, self.d3]:
#task.setting.useTorque = 'False'
task.setSerial()
task.setting.serialPrefix = ''
def __init__(self, filename):
QECalc.__init__(self)
self.pw = PWTask(filename)
self.ph = PHTask(filename)
self.dynmat = DynmatTask(filename)
self.pwph = PWPHMerger(self.pw,self.ph, cleanOutDir = self.pw.input.outDir())
self.taskList = [self.pwph, self.dynmat]
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 __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 __init__(self, filename):
QECalc.__init__(self)
self.pw = PWTask(filename)
self.ph = PHTask(filename)
self.dynmat = DynmatTask(filename)
self.pwph = PWPHMerger(self.pw,
self.ph,
cleanOutDir=self.pw.input.outDir())
self.taskList = [self.pwph, self.dynmat]
def __init__(self, filename = None, configString = None, sectionList = None, taskList = None):
QECalc.__init__(self)
# tasks definition:
# specify taskName/taskConstructur pairs
self._taskSpec = [
['pw', PWTask]
]
self._populateTasks(filename, configString, sectionList, taskList)
def __init__(self, filename):
QECalc.__init__(self)
self._freqs = None
self._modes = None
self._qpts = None
self.pw = PWTask(filename)
self.ph = PHTask(filename)
self.q2r = Q2RTask(filename)
self.matdyn = MatdynTask(filename)
self.pwph = PWPHMerger(self.pw,self.ph, cleanOutDir = self.pw.input.outDir())
self.dispersion = PHDispersion(self.pw.input.structure, self.matdyn)
self.taskList = [self.pwph, self.q2r, self.matdyn]
def __init__(self, filename):
QECalc.__init__(self)
self._freqs = None
self._modes = None
self._qpts = None
self.pw = PWTask(filename)
self.ph = PHTask(filename)
self.q2r = Q2RTask(filename)
self.matdyn = MatdynTask(filename)
self.pwph = PWPHMerger(self.pw,self.ph, cleanOutDir = self.pw.input.outDir())
self.dispersion = PHDispersion(self.pw.input.structure.lattice, self.matdyn)
self.dos = PhononDOS(self.matdyn)
self.taskList = [self.pwph, self.q2r, self.matdyn]
def __init__(self, fname, indexRange, prcntVolume, modePrefix):
"""indexRange is for files' indexing. prcntVolume - coresponding volume
expansions"""
self.qecalc = QECalc(fname)
self.__modePrefix = modePrefix
self.__indexRange = indexRange
self.__prcntVolume = prcntVolume
if len(indexRange) != len(prcntVolume):
raise Exception(
"QuasiHarmonic dimensions: indexRange != prcntVolume")
self.loadPhonons()
self.__polyOrder = 1
self.fitMatdyn()
def __init__(self, filename):
QECalc.__init__(self)
self.pw = PWTask(filename)
self.ph = PHTask(filename)
self.d3 = D3Task(filename)
self.pwph = PWPHMerger(self.pw,
self.ph,
cleanOutDir=self.pw.input.outDir())
self.taskList = [self.pwph, self.d3]
#Hack: make sure d3 task is serial (d3 does not seem to work in parallel)
for task in [self.pw, self.ph, self.d3]:
task.setting.useTorque = 'False'
task.setting.paraPrefix = ''
task.setting.paraPostfix = ''
def hexVolOpt(a0, c0_a0, volumeExpansion):
'''provide initial(equilibrium) lattice parameters a0, c0/a0, and \
desired volume expansion in percents at which one should run \
the optimization '''
qe = QECalc('config.ini')
if qe.structure.lattice.ibrav != 4:
raise Exception("The lattice must be hexagonal")
# Initial(equilibrium) volume:
c0 = a0 * c0_a0
volume = a0 * a0 * c0
volume = volume + volume * volumeExpansion / 100.
# initial assumption: all latice parameters expand equally in percents
cExpansion = (1. + volumeExpansion / 100.)**(1. / 3.)
c = c0 * cExpansion
prcntC = 0.2 # percent of c we want to bracket around it for minima search(does not have to warantee the minima is inside)s
brentOut = brent(getHexEnergy, (volume, qe),
(c - c * prcntC / 100, c + c * prcntC / 100),
tol=1.e-5,
full_output=1)
print brentOut
c = brentOut[0]
energy = brentOut[1]
a = np.sqrt(volume / c)
return a, c / a, energy
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],
['dynmat', DynmatTask]
]
self._populateTasks(filename, configString, sectionList, taskList)
#self.pw = PWTask(filename)
#self.ph = PHTask(filename)
#self.dynmat = DynmatTask(filename)
self.pwph = PWPHMerger(self.pw,self.ph, cleanOutDir = True)
self.taskList = [self.pwph, self.dynmat]
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],
['dynmat', DynmatTask]]
self._populateTasks(filename, configString, sectionList, taskList)
#self.pw = PWTask(filename)
#self.ph = PHTask(filename)
#self.dynmat = DynmatTask(filename)
self.pwph = PWPHMerger(self.pw, self.ph, cleanOutDir=True)
self.taskList = [self.pwph, self.dynmat]
def __init__(self, fname, indexRange, prcntVolume, modePrefix):
"""indexRange is for files' indexing. prcntVolume - coresponding volume
expansions"""
self.qecalc = QECalc(fname)
self.__modePrefix = modePrefix
self.__indexRange = indexRange
self.__prcntVolume = prcntVolume
if len(indexRange) != len(prcntVolume):
raise Exception("QuasiHarmonic dimensions: indexRange != prcntVolume")
self.loadPhonons()
self.__polyOrder = 1
self.fitMatdyn()
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],
['d3', D3Task]
]
self._populateTasks(filename, configString, sectionList, taskList)
#self.pw = PWTask(filename)
#self.ph = PHTask(filename)
#self.d3 = D3Task(filename)
self.pwph = PWPHMerger(self.pw,self.ph, cleanOutDir = True)
self.taskList = [self.pwph, self.d3]
#Hack: make sure d3 task is serial (d3 does not seem to work in parallel)
for task in [self.pw, self.ph, self.d3]:
#task.setting.useTorque = 'False'
task.setSerial()
def __init__(self,
fname=None,
taskName='total energy',
tolerance=1,
nMaxSteps=10):
"""taskName - currently can be 'total energy', 'single phonon',
or 'geometry'
tolerance - task convergence criteria in percents
nMaxSteps = maximum number of optimization steps for
the optimization routines"""
# Default values, see explanations below:
# convergerDic = {
# 'taskName': 'total energy',
# 'tolerance': '1',
# 'nMaxSteps': '10'
# }
QECalc.__init__(self, fname)
# value to converge with respect to k-points or energy cutoffs
# currently can be 'total energy', 'single phonon', or 'geometry':
# self.taskName = self.config.get('Converger', 'taskName')
# convergence criteria in percents:
# self.tolerance = self.config.getfloat('Converger','tolerance')
# maximum number of optimization steps:
# self.nMaxSteps = self.config.getint('Converger','nMaxSteps')
self.taskName = taskName
self.tolerance = tolerance
self.nMaxSteps = nMaxSteps
self.lookupTable = {
'total energy': (self.pwscfLauncher, self.getTotalEnergy),
'single phonon': (self.singlePhononLauncher, self.getSinglePhonon),
'geometry': (self.pwscfLauncher, self.getLatticeParameters)
# 'multiple phonon': (self.multiPhononLauncher, self.getMultiPhonon)
}
assert self.lookupTable.has_key(self.taskName), "Convergence \
class QuasiHarmonic():
def __init__(self, fname, indexRange, prcntVolume, modePrefix):
"""indexRange is for files' indexing. prcntVolume - coresponding volume
expansions"""
self.qecalc = QECalc(fname)
self.__modePrefix = modePrefix
self.__indexRange = indexRange
self.__prcntVolume = prcntVolume
if len(indexRange) != len(prcntVolume):
raise Exception(
"QuasiHarmonic dimensions: indexRange != prcntVolume")
self.loadPhonons()
self.__polyOrder = 1
self.fitMatdyn()
def fitFunc(self, p, x):
return p[0] * x
#+ p[1] * x * x
#+ p[2] * x * x * x + p[3] * x * x * x * x
def fitOmega(self, prcntOmega):
# fitfunc = lambda p, x: p[0] * x + p[1] * x * x
errFunc = lambda p, x, y: (y - self.fitFunc(p, x))
# initial parameters:
pinit = [prcntOmega[1] / self.__prcntVolume[1]]
# pinit = [1,0]
v, success = leastsq(errFunc,
pinit,
args=(self.__prcntVolume, prcntOmega))
if success < 1 or success > 4:
print success
print prcntOmega
print v
# assert success != 1, "fitOmega: Fitting was not successful"
return v
def getQuasiFreqs(prcntVol):
"""Returns array of freqs, corresponding to the provided volume expansion"""
nPoints = shape(self.__coeffOmega)[0]
nModes = shape(self.__coeffOmega)[1]
fittedFreqs = zeros(shape=(nPoints, nModes))
for i in range(nPoints):
for j in range(nModes):
p = self.__coeffOmega[i, j]
fittedFreqs[i, j] = p[0] * prcntVol
return (fittedFreqs + 1.0) * self.__omega0
def getFittedFreqs(prcntVol):
nPoints = shape(self.__coeffOmega)[0]
nModes = shape(self.__coeffOmega)[1]
fittedFreqs = zeros(shape=(nPoints, nModes))
for i in range(nPoints):
for j in range(nModes):
p = self.__coeffOmega[i, j]
fittedFreqs[i, j] = fitFunc(p, prcntVol)
return (fittedFreqs + 1.0) * self.__omega0
def loadPhonons(self):
fname = self.__modePrefix + str(self.__indexRange[0]) + '.modes'
Pol, Omega, qPoints = self.qecalc.getMultiPhonon(fname)
self.__volOmega = zeros(shape=(len(self.__indexRange), shape(Omega)[0],
shape(Omega)[1]))
self.__volPol = zeros(shape=(len(self.__indexRange), shape(Pol)[0],
shape(Pol)[1], shape(Pol)[2],
shape(Pol)[3]))
self.__volPol[0] = Pol
self.__volOmega[0] = Omega
for i in range(1, len(indexRange)):
fname = self.__modePrefix + str(self.__indexRange[i]) + '.modes'
Pol, Omega, qPoints = self.qecalc.getMultiPhonon(fname)
self.__volPol[i] = Pol
self.__volOmega[i] = Omega
# return volPol, volOmega, qPoints
def fitMatdyn(self):
# volPol, volOmega, qPoints = loadPhonons(indexRange, prefix)
# prcntVol = array(indexRange)/1000.0
# percent change in Omegas relative to equilibrium
self.__volPrcntOmega = zeros(shape(self.__volOmega))
# introduce Omega0 to get rid of 0s in denominator
Omega0 = copy(self.__volOmega[0])
self.__omega0 = Omega0
for i in range(shape(Omega0)[0]):
for j in range(shape(Omega0)[1]):
if Omega0[i, j] == 0.:
Omega0[i, j] = 1
for i in range(len(self.__indexRange)):
self.__volPrcntOmega[i] = (self.__volOmega[i] -
self.__volOmega[0]) / Omega0
self.__coeffOmega = zeros(shape=(shape(Omega0)[0], shape(Omega0)[1],
self.__polyOrder))
nonlinearity = 0
for i in range(shape(Omega0)[0]):
for j in range(shape(Omega0)[1]):
self.__coeffOmega[i,
j] = self.fitOmega(self.__volPrcntOmega[:, i,
j])
if self.__polyOrder > 1:
nonlinearity = nonlinearity + abs(self.__coeffOmega[i,
j][1])
# print volPrcntOmega[:,1000,3]
# print fitOmega(prcntVol, volPrcntOmega[:,1000,3])
# plot(volPrcntOmega[:,1000,3])
# show()
# return prcntVol, coeffOmega, volOmega, nonlinearity
def gammaDispersion(self, *pathNPoints):
self.qecalc.dispersion.setPath(*pathNPoints)
self.qecalc.dispersion.setValues(-self.__coeffOmega[:, :, 0])
self.qecalc.dispersion.plot()
class QuasiHarmonic():
def __init__(self, fname, indexRange, prcntVolume, modePrefix):
"""indexRange is for files' indexing. prcntVolume - coresponding volume
expansions"""
self.qecalc = QECalc(fname)
self.__modePrefix = modePrefix
self.__indexRange = indexRange
self.__prcntVolume = prcntVolume
if len(indexRange) != len(prcntVolume):
raise Exception("QuasiHarmonic dimensions: indexRange != prcntVolume")
self.loadPhonons()
self.__polyOrder = 1
self.fitMatdyn()
def fitFunc(self, p, x):
return p[0] * x
#+ p[1] * x * x
#+ p[2] * x * x * x + p[3] * x * x * x * x
def fitOmega(self, prcntOmega):
# fitfunc = lambda p, x: p[0] * x + p[1] * x * x
errFunc = lambda p, x, y: (y - self.fitFunc(p, x))
# initial parameters:
pinit = [prcntOmega[1]/self.__prcntVolume[1]]
# pinit = [1,0]
v, success = leastsq(errFunc, pinit, args=(self.__prcntVolume, prcntOmega))
if success < 1 or success > 4:
print success
print prcntOmega
print v
# assert success != 1, "fitOmega: Fitting was not successful"
return v
def getQuasiFreqs(prcntVol):
"""Returns array of freqs, corresponding to the provided volume expansion"""
nPoints = shape(self.__coeffOmega)[0]
nModes = shape(self.__coeffOmega)[1]
fittedFreqs = zeros(shape = (nPoints, nModes) )
for i in range( nPoints ):
for j in range( nModes ):
p = self.__coeffOmega[i,j]
fittedFreqs[i,j] = p[0]*prcntVol
return (fittedFreqs+1.0)*self.__omega0
def getFittedFreqs(prcntVol):
nPoints = shape(self.__coeffOmega)[0]
nModes = shape(self.__coeffOmega)[1]
fittedFreqs = zeros(shape = (nPoints, nModes) )
for i in range( nPoints ):
for j in range( nModes ):
p = self.__coeffOmega[i,j]
fittedFreqs[i,j] = fitFunc(p, prcntVol)
return (fittedFreqs+1.0)*self.__omega0
def loadPhonons(self):
fname = self.__modePrefix + str(self.__indexRange[0]) + '.modes'
Pol, Omega, qPoints = self.qecalc.getMultiPhonon(fname)
self.__volOmega = zeros(shape=(len(self.__indexRange), shape(Omega)[0], shape(Omega)[1] ) )
self.__volPol = zeros(shape=(len(self.__indexRange), shape(Pol)[0], shape(Pol)[1], shape(Pol)[2], shape(Pol)[3] ) )
self.__volPol[0] = Pol
self.__volOmega[0] = Omega
for i in range(1,len(indexRange)):
fname = self.__modePrefix + str(self.__indexRange[i]) + '.modes'
Pol, Omega, qPoints = self.qecalc.getMultiPhonon(fname)
self.__volPol[i] = Pol
self.__volOmega[i] = Omega
# return volPol, volOmega, qPoints
def fitMatdyn(self):
# volPol, volOmega, qPoints = loadPhonons(indexRange, prefix)
# prcntVol = array(indexRange)/1000.0
# percent change in Omegas relative to equilibrium
self.__volPrcntOmega = zeros(shape(self.__volOmega))
# introduce Omega0 to get rid of 0s in denominator
Omega0 = copy(self.__volOmega[0])
self.__omega0 = Omega0
for i in range(shape(Omega0)[0]):
for j in range(shape(Omega0)[1]):
if Omega0[i,j] == 0.:
Omega0[i, j] = 1
for i in range(len(self.__indexRange)):
self.__volPrcntOmega[i] = (self.__volOmega[i] - self.__volOmega[0])/Omega0
self.__coeffOmega = zeros( shape = ( shape(Omega0)[0], shape(Omega0)[1], self.__polyOrder) )
nonlinearity = 0
for i in range( shape(Omega0)[0] ):
for j in range( shape(Omega0)[1] ):
self.__coeffOmega[i,j] = self.fitOmega(self.__volPrcntOmega[:,i,j])
if self.__polyOrder > 1:
nonlinearity = nonlinearity + abs(self.__coeffOmega[i,j][1])
# print volPrcntOmega[:,1000,3]
# print fitOmega(prcntVol, volPrcntOmega[:,1000,3])
# plot(volPrcntOmega[:,1000,3])
# show()
# return prcntVol, coeffOmega, volOmega, nonlinearity
def gammaDispersion(self, *pathNPoints):
self.qecalc.dispersion.setPath(*pathNPoints)
self.qecalc.dispersion.setValues(-self.__coeffOmega[:,:,0])
self.qecalc.dispersion.plot()
def __init__(self, fname):
QECalc.__init__(self, fname)
def __init__(self, fname):
QECalc.__init__(self, fname)
self.__freqs = None
self.__modes = None
self.__qpts = None
prcntC = 0.2 # percent of c we want to bracket around it for minima search(does not have to warantee the minima is inside)s
brentOut = brent(getHexEnergy, (volume, qe), (c-c*prcntC/100, c+c*prcntC/100), tol = 1.e-7, full_output = 1)
print brentOut
c = brentOut[0]
energy = brentOut[1]
a = np.sqrt(volume/c)
return a, c/a, energy
if __name__ == '__main__':
# volPercRange = scipy.linspace(0.1, 3.0, 29)
volPercRange = scipy.linspace(0.2, 2.4 , 12)
# !!!!!! Make sure you have correct starting scf.in at equilibrium
qe = QECalc('config.ini')
a0 = qe.structure.lattice.a
c0 = qe.structure.lattice.c
apar = [a0]
c_apar = [c0/a0]
# obtain total energy at equilibrium:
qe.pwscfLauncher()
energy = qe.getTotalEnergy()
print volPercRange
for volPrcnt in volPercRange:
print "Optimizing volume at " + str(volPrcnt) + "% expansion"
a, c_a, e = hexVolOpt(a0, c0/a0, volPrcnt)
print e, a, c_a
apar.append(a)
c_apar.append(c_a)
energy.append(e)
def __init__(self, fname):
QECalc.__init__(self, fname)
self.__freqs = None
self.__modes = None
self.__qpts = None
def __init__(self, filename):
QECalc.__init__(self)
self.pw = PWTask(filename)
self.taskList = [self.pw]
brentOut = brent(getHexEnergy, (volume, qe),
(c - c * prcntC / 100, c + c * prcntC / 100),
tol=1.e-7,
full_output=1)
print brentOut
c = brentOut[0]
energy = brentOut[1]
a = np.sqrt(volume / c)
return a, c / a, energy
if __name__ == '__main__':
# volPercRange = scipy.linspace(0.1, 3.0, 29)
volPercRange = scipy.linspace(0.2, 2.4, 12)
# !!!!!! Make sure you have correct starting scf.in at equilibrium
qe = QECalc('config.ini')
a0 = qe.structure.lattice.a
c0 = qe.structure.lattice.c
apar = [a0]
c_apar = [c0 / a0]
# obtain total energy at equilibrium:
qe.pwscfLauncher()
energy = qe.getTotalEnergy()
print volPercRange
for volPrcnt in volPercRange:
print "Optimizing volume at " + str(volPrcnt) + "% expansion"
a, c_a, e = hexVolOpt(a0, c0 / a0, volPrcnt)
print e, a, c_a
apar.append(a)
c_apar.append(c_a)
energy.append(e)
v) + self.fitPhononEnergy.fittedValue(v)
def minimizeTotalFreeEnergy(self, minVol, maxVol):
import scipy.optimize
brentOut=scipy.optimize.brent(self.totalFreeEnergy,(),
(minVol, maxVol),\
tol = 1.e-5, full_output = 1)
# print '\n\nBrentOut:'
# print brentOut
optPrcntVolume = brentOut[0]
optFreeEnergy = brentOut[1]
return optPrcntVolume
if __name__ == "__main__":
qecalc = QECalc("config.ini")
voluPhon = VoluPhon("config.ini", prcntVol)
voluPhon.setA(a_range[indexRange], 'polynom', 1, True)
c_range = a_range * c_a_range
voluPhon.setC(c_range[indexRange], 'polynom', 1, True)
# Generate phonon doses from different fc files
for i in indexRange:
os.system('cp ' + str(i) + '_' + fc_name + ' ' + fc_name)
qecalc.matdynLauncher()
os.system('cp ' + matdynfldos + ' ' + str(i) + '_' + matdynfldos)
#plot free energies:
for temperature in temperatures:
lines = ''
phonon = []
for i, v in zip(indexRange, prcntVol):
def __init__(self, filename):
QECalc.__init__(self)
self.pw = PWTask(filename)
self.taskList = [self.pw]
# for a, c in zip(aRange, cRange):
# varnameValue(task.pwscfInput, 'celldm(1)', a)
# varnameValue(task.pwscfInput, 'celldm(2)', a)
# varnameValue(task.pwscfInput, 'celldm(3)', c/a)
# task.getLauncher()
# energies.append(task.getEstimator())
# file = open('energies'+strvolumeExpansion)+'.txt','w')
# for a,c, e in zip(aRange, cRange, energies):
# print a, c, e
if __name__ == '__main__':
# volPercRange = scipy.linspace(0.1, 3.0, 29)
volPercRange = scipy.linspace(0.2, 1.2, 6)
qe = QECalc('config.ini')
a0 = qe.structure.lattice.a
c0 = qe.structure.lattice.c
apar = []
c_apar = []
print volPercRange
for volPrcnt in volPercRange:
print "Optimizing volume at " + str(volPrcnt) + "% expansion"
a, c_a, vol = hexVolOpt(a0, c0 / a0, volPrcnt)
print vol, a, c_a
apar.append(a)
c_apar.append(c_a)
print "a:"
print apar
print "c/a:"
print c_apar
def __init__(self, fname):
QECalc.__init__(self,fname)
def minimizeTotalFreeEnergy(self,minVol, maxVol):
import scipy.optimize
brentOut=scipy.optimize.brent(self.totalFreeEnergy,(),
(minVol, maxVol),\
tol = 1.e-5, full_output = 1)
# print '\n\nBrentOut:'
# print brentOut
optPrcntVolume = brentOut[0]
optFreeEnergy = brentOut[1]
return optPrcntVolume
if __name__ == "__main__":
qecalc = QECalc("config.ini")
voluPhon = VoluPhon("config.ini", prcntVol)
voluPhon.setA(a_range[indexRange], 'polynom', 1, True)
c_range = a_range*c_a_range
voluPhon.setC(c_range[indexRange], 'polynom', 1, True)
# Generate phonon doses from different fc files
# for i in indexRange:
# os.system('cp ' + str(i) + '_' + fc_name + ' ' + fc_name)
# qecalc.matdynLauncher()
# os.system('cp ' + matdynfldos + ' ' + str(i) + '_' + matdynfldos )
#plot free energies:
for temperature in temperatures:
lines = ''
phonon = []
for i,v in zip(indexRange, prcntVol):