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, 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()
# 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
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):
