def test_kpoints(self):
pw = self.task['pw']
pw.setting.set('pwInput', 'data/al_pw.in')
pw.input.parse()
from qeutils import kmesh
qmesh = [2,2,2]
qpoints = kmesh.kMeshCart(qmesh,pw.input.structure.lattice.reciprocalBase())
pw.input.kpoints.set(qpoints)
self.assertEqual( (8, 3), pw.input.kpoints.coords.shape)
def testMatdyn():
#matdyn = MatdynTask( configString = "")
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
"""
matdynString = """
&INPUT
asr = 'crystal',
flfrc = '/home/dexity/espresso/qejobs/643E2QQI/default.fc',
dos = .true.,
nk1 = 4,
nk2 = 4,
nk3 = 4,
amass(1) = 26.98,
/
"""
# Initialize structure (PW input):
pwInput = PWInput(config=pwString)
pwInput.parse()
# Initialize MATDYN input
matdynInput = MatdynInput(config=matdynString)
matdynInput.parse()
print matdynInput.toString()
# Pass matdyn input to matdyn task
#matdyn.input = matdynInput
nl = matdynInput.namelist("input")
# Populate grid
nqGrid = [int(nl.param("nk1")), int(nl.param("nk2")), int(nl.param("nk3"))]
qpoints = kmesh.kMeshCart(nqGrid,
pwInput.structure.lattice.reciprocalBase())
# Generate grid point
#matdyn.input.qpoints.set(qpoints) # Generate Q-mesh
matdynInput.qpoints.set(qpoints)
open("matdyn.2.in", "w").write(matdynInput.toString())
def testMatdyn():
#matdyn = MatdynTask( configString = "")
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
"""
matdynString = """
&INPUT
asr = 'crystal',
flfrc = '/home/dexity/espresso/qejobs/643E2QQI/default.fc',
dos = .true.,
nk1 = 4,
nk2 = 4,
nk3 = 4,
amass(1) = 26.98,
/
"""
# Initialize structure (PW input):
pwInput = PWInput(config = pwString)
pwInput.parse()
# Initialize MATDYN input
matdynInput = MatdynInput(config = matdynString)
matdynInput.parse()
print matdynInput.toString()
# Pass matdyn input to matdyn task
#matdyn.input = matdynInput
nl = matdynInput.namelist("input")
# Populate grid
nqGrid = [int(nl.param("nk1")), int(nl.param("nk2")), int(nl.param("nk3"))]
qpoints = kmesh.kMeshCart(nqGrid, pwInput.structure.lattice.reciprocalBase())
# Generate grid point
#matdyn.input.qpoints.set(qpoints) # Generate Q-mesh
matdynInput.qpoints.set(qpoints)
open("matdyn.2.in", "w").write(matdynInput.toString())
def launch(self, nqpoints, partialDOS=False):
"""
launches matdyn task with a grid provided through list 'nqpoints'
"""
if partialDOS == False:
self.matdynTask.qpoints.setAutomatic(nqpoints)
self.matdynTask.input.save()
self.matdynTask.launch()
self.loadPhonons()
self.axis, self.dos = self.matdynTask.output.property("phonon dos")
else:
if self.structure == None:
raise ("PartialDOS: structure was not set")
qpoints = kmesh.kMeshCart(nqpoints, self.structure.lattice.reciprocalBase())
# update qpoints and launch matdyn
self.matdynTask.syncSetting()
self.matdynTask.input.qpoints.set(qpoints)
self.matdynTask.input.save()
self.matdynTask.launch()
self.loadPhonons()
def launch(self, nqpoints, partialDOS=False):
"""
launches matdyn task with a grid provided through list 'nqpoints'
"""
if partialDOS == False:
self.matdynTask.qpoints.setAutomatic(nqpoints)
self.matdynTask.input.save()
self.matdynTask.launch()
self.loadPhonons()
self.axis, self.dos = self.matdynTask.output.property('phonon dos')
else:
if self.structure == None:
raise ('PartialDOS: structure was not set')
qpoints = kmesh.kMeshCart(nqpoints, \
self.structure.lattice.reciprocalBase())
#update qpoints and launch matdyn
self.matdynTask.syncSetting()
self.matdynTask.input.qpoints.set(qpoints)
self.matdynTask.input.save()
self.matdynTask.launch()
self.loadPhonons()
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')
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')
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')
