def testIDF():
settingString = """
[matdyn.x]
flvec = matdyn.modes
flfrq = matdyn.freq
fldos = matdyn.dos
"""
# No flfrc or matdynInput are needed for conversion to DOS
#flfrc = mgb2666.fc
#matdynInput = matdyn.in
# Initialize matdyn
matdyn = MatdynTask( configString = settingString)
#matdyn.syncSetting() # Why do I need this?
matdyn.output.parse()
axis, dos = matdyn.output.property('phonon dos')
# XXX Why nqGrid?
#nqGrid = [10,10,10]
#matdyn.input.qpoints.setAutomatic(nqGrid)
# save DOS in THz
idf.DOS.write(axis*TO_THZ, dos, filename = 'DOS.1', comment = '')
idfDOSData = idf.DOS.read('DOS.1')
print idfDOSData
def testIDF():
settingString = """
[matdyn.x]
flvec = matdyn.modes
flfrq = matdyn.freq
fldos = matdyn.dos
"""
# Initialize matdyn
matdyn = MatdynTask(configString=settingString)
matdyn.syncSetting()
matdyn.output.parse()
Pols, Freqs, qPoints = matdyn.output.property('multi phonon')
# convert to Hz**2 and save
idf.Omega2.write((Freqs * C * TWO_PI)**2, 'Omega2', '')
idf.Polarizations.write(Pols, 'Polarizations', 'Polarizations')
idfPolData = idf.Polarizations.read('Polarizations')
idfOmega2Data = idf.Omega2.read('Omega2')
pwInput = PWInput(filename="pw.in")
pwInput.parse()
# XXX
# - Why nqGrid?
# - Is there a way to get reciprocal lattice from matter?
nqGrid = [4, 4, 4]
#save lattice/grid information and make it angstrem compatible, multiply by 2pi:
genQgridinfo('Qgridinfo', nqGrid, \
pwInput.structure.lattice.matter().\
reciprocal().base*2.0*PI*A2B)
print idfPolData
print idfOmega2Data
import os
os.system('cat ./Qgridinfo')
def testIDF():
settingString = """
[matdyn.x]
flvec = matdyn.modes
flfrq = matdyn.freq
fldos = matdyn.dos
"""
# Initialize matdyn
matdyn = MatdynTask( configString = settingString)
matdyn.syncSetting()
matdyn.output.parse()
Pols, Freqs, qPoints = matdyn.output.property('multi phonon')
# convert to Hz**2 and save
idf.Omega2.write( (Freqs*C*TWO_PI)**2,'Omega2','')
idf.Polarizations.write(Pols, 'Polarizations','Polarizations')
idfPolData = idf.Polarizations.read('Polarizations')
idfOmega2Data = idf.Omega2.read('Omega2')
pwInput = PWInput(filename = "pw.in")
pwInput.parse()
# XXX
# - Why nqGrid?
# - Is there a way to get reciprocal lattice from matter?
nqGrid = [4,4,4]
#save lattice/grid information and make it angstrem compatible, multiply by 2pi:
genQgridinfo('Qgridinfo', nqGrid, \
pwInput.structure.lattice.matter().\
reciprocal().base*2.0*PI*A2B)
print idfPolData
print idfOmega2Data
import os
os.system('cat ./Qgridinfo')
# California Institute of Technology
# (C) 2010 All Rights Reserved
#
# File coded by: Nikolay Markovskiy
#
# See AUTHORS.txt for a list of people who contributed.
# See LICENSE.txt for license information.
#
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
from qecalc.qetask.matdyntask import MatdynTask
from qecalc.qetask.pwtask import PWTask
from qeutils.phdos import PhononDOS
if __name__ == "__main__":
matdyn = MatdynTask(configString="")
pw = PWTask(configString="")
pw.syncSetting()
dos = PhononDOS(matdynTask=matdyn, structure=pw.input.structure)
# grid has to be huge since a simple histogramming will be used
qgrid = [64, 64, 64]
# generate qpoints and launch matdyn task
dos.launch(nqpoints=qgrid, partialDOS=True)
# this line is required if matdyn.modes exisits from previoius run and
# dos.launch() is commented out
#dos.loadPhonons()
#dos.DOS()
from qecalc.qetask.matdyntask import MatdynTask
from qecalc.qetask.pwtask import PWTask
from qeutils import kmesh
from qeutils.bandstobxsf import bandstobxsf
matdyn = MatdynTask('config.ini')
pw = PWTask('config.ini')
pw.input.parse()
matdyn.input.parse()
qmesh = [17,17,17]
qpoints = kmesh.kMeshCart(qmesh,pw.input.structure.lattice.reciprocalBase())
matdyn.input.qpoints.set(qpoints)
matdyn.input.save()
matdyn.launch()
#matdyn.output.parse()
modes, freqs, qpts = matdyn.output.property('multi phonon')
bands = kmesh.packBands(qmesh, freqs)
phononEnergy = 720.0
bandstobxsf(phononEnergy, pw.input.structure.lattice.reciprocalBase(), bands,\
'phonons.bxsf')
from qecalc.qetask.pwtask import PWTask from qeutils import kmesh from qeutils.bandstobxsf import bandstobxsf configString = """ [pw.x] pwInput: scf.in pwOutput: scf.out [matdyn.x] matdynInput: matdyn.in matdynOutput: matdyn.out """ matdyn = MatdynTask(configString = configString) pw = PWTask(configString = configString) pw.input.parse() matdyn.input.parse() qmesh = [17,17,17] qpoints = kmesh.kMeshCart(qmesh,pw.input.structure.lattice.reciprocalBase()) matdyn.input.qpoints.set(qpoints) matdyn.input.save() matdyn.launch() #matdyn.syncSetting()
from qecalc.qetask.matdyntask import MatdynTask
from qecalc.qetask.pwtask import PWTask
from qeutils.phdispersion import PHDispersion
import numpy
configString = """
[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 )
def testIDF():
# matdyn setting:
settingString = """
[matdyn.x]
matdynInput = matdyn.in
flfrc = mgb2666.fc
"""
#*********************Initialize matdyn*****************************************
matdyn = MatdynTask( configString = settingString)
matdyn.syncSetting()
#*******************************************************************************
print 'generating "Phonons on the Grid"'
# scf.in with fields relevant to structure information
pwString = """
&SYSTEM
ibrav = 4
celldm(1) = 5.78552800736
celldm(3) = 1.13577682118
nat = 3
ntyp = 2
/
ATOMIC_SPECIES
Mg 24.305 mg_6.ncpp
B 11.0 B.pbe-n-van_ak.UPF
ATOMIC_POSITIONS ALAT
Mg 0. 0. 0.
B 0.5 0.28867513 0.56788841
B 0. 0.57735027 0.56788841
"""
nqGrid = [4,4,4]
#initialize structure:
pwInput = PWInput(config = pwString)
pwInput.parse()
qpoints = kmesh.kMeshCart(nqGrid,pwInput.structure.lattice.reciprocalBase())
#update qpoints and launch matdyn
matdyn.input.qpoints.set(qpoints)
matdyn.input.save()
matdyn.launch()
#matdyn.output.toString()
matdyn.output.parse()
Pols, Freqs, qPoints = matdyn.output.property('multi phonon')
# convert to Hz**2 and save
Omega2.write( (Freqs*C*TWO_PI)**2,'Omega2.idf','')
Polarizations.write(Pols, 'Polarizations.idf','Polarizations')
idfPolData = Polarizations.read('Polarizations.idf')
idfOmega2Data = Omega2.read('Omega2.idf')
#save lattice/grid information and make it angstrem compatible, multiply by 2pi:
genQgridinfo('Qgridinfo.idf', nqGrid, \
pwInput.structure.lattice.matter().\
reciprocal().base*2.0*3.14159265*1.889725989)
print idfPolData
print idfOmega2Data
#*******************************************************************************
print 'generating "Phonon DOS"'
nqGrid = [10,10,10]
matdyn.input.qpoints.setAutomatic(nqGrid)
matdyn.input.save()
matdyn.launch()
matdyn.output.parse()
axis, dos = matdyn.output.property('phonon dos')
# save DOS in THz
DOS.write(axis*0.0299792458, dos, filename = 'DOS', comment = '')
idfDOSData = DOS.read('DOS')
print idfDOSData
#import numpy
#import numpy.linalg as numalg
#print 2 * 3.14159265 * numalg.inv(numpy.transpose(pwInput.structure.lattice.matter().base/1.889725989))
#*********************Cleaning**************************************************
import os
os.system('cat ./Qgridinfo.idf')
from qecalc.qetask.matdyntask import MatdynTask
from qecalc.qetask.pwtask import PWTask
from qeutils.phdispersion import PHDispersion
import numpy
configString = """
[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 )
from qecalc.qetask.matdyntask import MatdynTask
matdyn = MatdynTask('config.ini')
matdyn.output.parse()
Pol, Omegas, qPoints = matdyn.output.property('multi phonon')
print Pol
print Omegas
#setting.matdynModes = 'blahblah.modes'
#matdyn.output.parse()
#mphonOut, Omegas, qPoints = matdyn.output.property('multi phonon', withUnits = True)
def testIDF():
# matdyn setting:
settingString = """
[matdyn.x]
matdynInput = matdyn.in
flfrc = mgb2666.fc
"""
#*********************Initialize matdyn*****************************************
matdyn = MatdynTask(configString=settingString)
matdyn.syncSetting()
#*******************************************************************************
print 'generating "Phonons on the Grid"'
# scf.in with fields relevant to structure information
pwString = """
&SYSTEM
ibrav = 4
celldm(1) = 5.78552800736
celldm(3) = 1.13577682118
nat = 3
ntyp = 2
/
ATOMIC_SPECIES
Mg 24.305 mg_6.ncpp
B 11.0 B.pbe-n-van_ak.UPF
ATOMIC_POSITIONS ALAT
Mg 0. 0. 0.
B 0.5 0.28867513 0.56788841
B 0. 0.57735027 0.56788841
"""
nqGrid = [4, 4, 4]
#initialize structure:
pwInput = PWInput(config=pwString)
pwInput.parse()
qpoints = kmesh.kMeshCart(nqGrid,
pwInput.structure.lattice.reciprocalBase())
#update qpoints and launch matdyn
matdyn.input.qpoints.set(qpoints)
matdyn.input.save()
matdyn.launch()
#matdyn.output.toString()
matdyn.output.parse()
Pols, Freqs, qPoints = matdyn.output.property('multi phonon')
# convert to Hz**2 and save
Omega2.write((Freqs * C * TWO_PI)**2, 'Omega2.idf', '')
Polarizations.write(Pols, 'Polarizations.idf', 'Polarizations')
idfPolData = Polarizations.read('Polarizations.idf')
idfOmega2Data = Omega2.read('Omega2.idf')
#save lattice/grid information and make it angstrem compatible, multiply by 2pi:
genQgridinfo('Qgridinfo.idf', nqGrid, \
pwInput.structure.lattice.matter().\
reciprocal().base*2.0*3.14159265*1.889725989)
print idfPolData
print idfOmega2Data
#*******************************************************************************
print 'generating "Phonon DOS"'
nqGrid = [10, 10, 10]
matdyn.input.qpoints.setAutomatic(nqGrid)
matdyn.input.save()
matdyn.launch()
matdyn.output.parse()
axis, dos = matdyn.output.property('phonon dos')
# save DOS in THz
DOS.write(axis * 0.0299792458, dos, filename='DOS', comment='')
idfDOSData = DOS.read('DOS')
print idfDOSData
#import numpy
#import numpy.linalg as numalg
#print 2 * 3.14159265 * numalg.inv(numpy.transpose(pwInput.structure.lattice.matter().base/1.889725989))
#*********************Cleaning**************************************************
import os
os.system('cat ./Qgridinfo.idf')