def setUp(self):
if useStringConfig:
self.input = PWInput(config=stringConfig)
else:
self.input = PWInput(filename='pw.in')
#self.input.autoUpdate = False
self.input.parse()
def setUp(self):
if useStringConfig:
self.input = PWInput( config = stringConfig )
else:
self.input = PWInput( filename = 'pw.in' )
#self.input.autoUpdate = False
self.input.parse()
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, volPercRange):
"""
Performs volume expansion
volPercRange - list of percentage volume expansions relative to
equilibrium volume. Can be negative.
Equilibrium lattice parameters are provided through pwInput.eqv file \
(e.g. If pwInput = scf.in, then scf.in.eqv)
"""
# output container
output = {
"volume": [],
"energy": [],
"config": []
}
# name of file at eqilibrium is pwInput.eqv:
eqvFileName = self.pw.setting.get('pwInput') + '.eqv'
if not os.path.exists(eqvFileName):
raise Exception('Should provide PW input file at equilibrium')
os.system('cp ' + eqvFileName + ' ' + self.pw.setting.get('pwInput') )
self.pw.input.parse()
if self.pw.input.namelist('control').param('calculation') != "'relax'":
print self.pw.input.namelist('control').param('calculation')
raise Exception("""Should use "calculation = 'relax'" in "control" \
namelist""")
# initialize equilibrium lattice
pwInput0 = PWInput( filename = eqvFileName )
pwInput0.parse()
self.lattice0 = pwInput0.structure.lattice
output["config"].append( self.pw.input.toString() )
# obtain total energy at equilibrium:
self.pw.launch()
output["energy"] = self.pw.output.property('total energy')
output["volume"] = [0.0]
print volPercRange
for volPrcnt in volPercRange:
print "Optimizing volume at " + str(volPrcnt) + "% expansion"
cfg, e = self._volOpt(volPrcnt)
print cfg
print e
output["config"].append( cfg )
output["energy"].append( e )
output["volume"].append( volPrcnt )
print output
import pickle
pickle.dump( output, open(self.pickleName, 'wb') )
self._output = output
return self._output
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')
class TestStructureMethods(unittest.TestCase):
def setUp(self):
if useStringConfig:
self.input = PWInput(config=stringConfig)
else:
self.input = PWInput(filename='pw.in')
#self.input.autoUpdate = False
self.input.parse()
def test_read_pwoutput(self):
filename = os.path.join(testdata_dir, 'mgalb4_pw.out')
self.input.structure.read(filename, 'pwoutput')
#answer = """"Simple Hexagonal or Trigonal(P)" cell :\n 5.70000000 0.00000000 0.00000000\n-2.85000000 4.93634480 0.00000000\n 0.00000000 0.00000000 12.54000000\n\nAtomic positions in units of lattice parametr "a":\nAl 0.00000000 0.00000000 0.00000000 \nB 0.50000000 0.28867510 0.52052140 \nB 0.00000000 0.57735030 0.52052140 \nMg 0.00000000 0.00000000 1.11205140 \nB 0.50000000 0.28867510 1.70358160 \nB 0.00000000 0.57735030 1.70358160 \n\nAl 26.9825 al.ncpp\nB 11.0000 b.ncpp\nMg 24.3050 mg.ncpp\n"""
answer = """"Simple Hexagonal or Trigonal(P)" cell:
5.70000000 0.00000000 0.00000000
-2.85000000 4.93634480 0.00000000
0.00000000 0.00000000 12.54000000
Atomic positions in units of lattice parametr "a":
Al 0.00000000 0.00000000 0.00000000
B 0.50000000 0.28867510 0.52052140
B 0.00000000 0.57735030 0.52052140
Mg 0.00000000 0.00000000 1.11205140
B 0.50000000 0.28867510 1.70358160
B 0.00000000 0.57735030 1.70358160
Al 26.9825 al.ncpp
B 11.0000 b.ncpp
Mg 24.3050 mg.ncpp
"""
#print '*', str(self.input.structure), '*'
#print '*', str(self.input.structure), '*'
self.assertEqual(str(self.input.structure), answer)
filename = os.path.join(testdata_dir, 'fev3_pwgeom.out')
self.input.structure.read(filename, 'pwoutput')
# after geometry optimization:
answer = """"Face Centered Cubic" cell:
-5.50788176 0.00000000 5.50788176
0.00000000 5.50788176 5.50788176
-5.50788176 5.50788176 0.00000000
Atomic positions in units of lattice parametr "a":
V 0.00000000 0.00000000 0.00000000
V 0.50000000 0.00000000 0.00000000
V 0.25000000 0.25000000 0.25000000
Fe 0.75000000 0.25000000 0.25000000
V 50.9415 V.pbe-sp-van.UPF
Fe 55.8470 Fe.pbe-sp-van_ak.UPF
"""
answer_toString = """&CONTROL
calculation = 'scf',
restart_mode = 'from_scratch',
tstress = .true.,
tprnfor = .true.,
prefix = 'mgalb4',
pseudo_dir = '/home/user/pslib',
outdir = '/scratch/user',
/
&SYSTEM
ibrav = 2,
nbnd = 21,
nspin = 1,
occupations = 'smearing',
degauss = 0.025,
smearing = 'methfessel-paxton',
ecutwfc = 64.0,
ecutrho = 256.0,
celldm(1) = 11.0157635161,
celldm(2) = 1.0,
celldm(3) = 1.0,
celldm(4) = 0.0,
ntyp = 2,
nat = 4,
/
&ELECTRONS
conv_thr = 1.0d-10,
mixing_beta = 0.4,
/
ATOMIC_SPECIES
V 50.9415 V.pbe-sp-van.UPF
Fe 55.8470 Fe.pbe-sp-van_ak.UPF
ATOMIC_POSITIONS (alat)
V 0.00000000 0.00000000 0.00000000
V 0.50000000 0.00000000 0.00000000
V 0.25000000 0.25000000 0.25000000
Fe 0.75000000 0.25000000 0.25000000
K_POINTS (automatic)
32 32 16 0 0 0
"""
self.assertEqual(str(self.input.structure), answer)
self.assertEqual(self.input.toString(), answer_toString)
def test_read_pwinput(self):
filename = os.path.join(testdata_dir, 'al_pw.in')
self.input.structure.read(filename, 'pwinput')
answer = """"Face Centered Cubic" cell:
-3.85000000 0.00000000 3.85000000
0.00000000 3.85000000 3.85000000
-3.85000000 3.85000000 0.00000000
Atomic positions in units of lattice parametr "a":
Al 0.00000000 0.00000000 0.00000000
Al 26.9800 Al.pz-vbc.UPF
"""
answer_toString = """&CONTROL
calculation = 'scf',
restart_mode = 'from_scratch',
tstress = .true.,
tprnfor = .true.,
prefix = 'mgalb4',
pseudo_dir = '/home/user/pslib',
outdir = '/scratch/user',
/
&SYSTEM
ibrav = 2,
nbnd = 21,
nspin = 1,
occupations = 'smearing',
degauss = 0.025,
smearing = 'methfessel-paxton',
ecutwfc = 64.0,
ecutrho = 256.0,
celldm(1) = 7.7,
celldm(2) = 1.0,
celldm(3) = 1.0,
celldm(4) = 0.0,
ntyp = 1,
nat = 1,
/
&ELECTRONS
conv_thr = 1.0d-10,
mixing_beta = 0.4,
/
ATOMIC_SPECIES
Al 26.9800 Al.pz-vbc.UPF
ATOMIC_POSITIONS (alat)
Al 0.00000000 0.00000000 0.00000000
K_POINTS (automatic)
32 32 16 0 0 0
"""
self.assertEqual(str(self.input.structure), answer)
#print self.input.structure.toString()
self.assertEqual(self.input.structure.toString(), answer_toString)
def test_read_cif(self):
filename = os.path.join(testdata_dir, 'PbTe.cif')
self.input.structure.read(filename, 'cif')
answer = """"generic" cell:
12.20951961 0.00000000 0.00000000
0.00000000 12.20951961 0.00000000
0.00000000 0.00000000 12.20951961
Atomic positions in crystal coordinates:
Pb2+ 0.50000000 0.50000000 0.50000000
Pb2+ 0.50000000 0.00000000 0.00000000
Pb2+ 0.00000000 0.50000000 0.00000000
Pb2+ 0.00000000 0.00000000 0.50000000
Te 0.00000000 0.00000000 0.00000000
Te 0.00000000 0.50000000 0.50000000
Te 0.50000000 0.00000000 0.50000000
Te 0.50000000 0.50000000 0.00000000
Pb2+ 0.0000
Te 0.0000
"""
self.assertEqual(str(self.input.structure), answer)
#filename = os.path.join(testdata_dir, 'LiNbO3.cif')
#self.input.structure.read(filename, 'cif')
#self.input.structure.reduce()
#print self.input.toString()
def test_load_diffpy(self):
from diffpy.Structure.structure import Structure
from diffpy.Structure.atom import Atom
from diffpy.Structure.lattice import Lattice
at1 = Atom('V', [0., 0., 0.])
at2 = Atom('V', [0.5, 0., 0.])
at3 = Atom('V', [0., 0.5, 0.])
at4 = Atom('V', [0., 0., 0.5])
at5 = Atom('V', [0.5, 0.5, 0.])
at6 = Atom('V', [0., 0.5, 0.5])
at7 = Atom('V', [0.5, 0., 0.5])
at8 = Atom('V', [0.5, 0.5, 0.5])
at9 = Atom('V', [0.25, 0.25, 0.25])
at10 = Atom('Fe', [0.75, 0.25, 0.25])
at11 = Atom('V', [0.75, 0.75, 0.25])
at12 = Atom('Fe', [0.25, 0.75, 0.25])
at13 = Atom('Fe', [0.25, 0.25, 0.75])
at14 = Atom('V', [0.75, 0.25, 0.75])
at15 = Atom('Fe', [0.75, 0.75, 0.75])
at16 = Atom('V', [0.25, 0.75, 0.75])
# set a in angstrom
a = 2. * 5.663 / 1.889725989
struct = Structure( [ at1, at2, at3, at4, at5, at6, at7, at8, at9, \
at10, at11, at12, at13, at14, at15, at16], \
lattice = Lattice(a, a, a, 90, 90, 90) )
#print struct
massList = [50.9415, 55.847]
psList = ['V.pbe-n-van.UPF', 'Fe.pbe-nd-rrkjus.UPF']
self.input.structure.load(source = 'diffpy', structure = struct, \
ibrav = 2, massList = massList, psList = psList)
answer1 = """"Face Centered Cubic" cell:
-5.66300000 0.00000000 5.66300000
0.00000000 5.66300000 5.66300000
-5.66300000 5.66300000 0.00000000
Atomic positions in units of lattice parametr "a":
V 0.00000000 0.00000000 0.00000000
V 0.50000000 0.00000000 0.00000000
V 0.25000000 0.25000000 0.25000000
Fe 0.75000000 0.25000000 0.25000000
V 50.9415 V.pbe-n-van.UPF
Fe 55.8470 Fe.pbe-nd-rrkjus.UPF
"""
#print self.input.toString()
self.assertEqual(str(self.input.structure), answer1)
self.input.structure.load(source = 'diffpy', structure = struct, \
massList = massList, psList = psList)
answer2 = """"generic" cell:
11.32600000 0.00000000 0.00000000
0.00000000 11.32600000 0.00000000
0.00000000 0.00000000 11.32600000
Atomic positions in units of lattice parametr "a":
V 0.00000000 0.00000000 0.00000000
V 2.99673076 0.00000000 0.00000000
V 0.00000000 2.99673076 0.00000000
V 0.00000000 0.00000000 2.99673076
V 2.99673076 2.99673076 0.00000000
V 0.00000000 2.99673076 2.99673076
V 2.99673076 0.00000000 2.99673076
V 2.99673076 2.99673076 2.99673076
V 1.49836538 1.49836538 1.49836538
Fe 4.49509614 1.49836538 1.49836538
V 4.49509614 4.49509614 1.49836538
Fe 1.49836538 4.49509614 1.49836538
Fe 1.49836538 1.49836538 4.49509614
V 4.49509614 1.49836538 4.49509614
Fe 4.49509614 4.49509614 4.49509614
V 1.49836538 4.49509614 4.49509614
V 50.9415 V.pbe-n-van.UPF
Fe 55.8470 Fe.pbe-nd-rrkjus.UPF
"""
self.assertEqual(str(self.input.structure), answer2)
def test_load_matter(self):
try:
from matter import Structure, Atom, Lattice
except ImportError:
return
at1 = Atom('V', [0., 0., 0.])
at2 = Atom('V', [0.5, 0., 0.])
at3 = Atom('V', [0., 0.5, 0.])
at4 = Atom('V', [0., 0., 0.5])
at5 = Atom('V', [0.5, 0.5, 0.])
at6 = Atom('V', [0., 0.5, 0.5])
at7 = Atom('V', [0.5, 0., 0.5])
at8 = Atom('V', [0.5, 0.5, 0.5])
at9 = Atom('V', [0.25, 0.25, 0.25])
at10 = Atom('Fe', [0.75, 0.25, 0.25])
at11 = Atom('V', [0.75, 0.75, 0.25])
at12 = Atom('Fe', [0.25, 0.75, 0.25])
at13 = Atom('Fe', [0.25, 0.25, 0.75])
at14 = Atom('V', [0.75, 0.25, 0.75])
at15 = Atom('Fe', [0.75, 0.75, 0.75])
at16 = Atom('V', [0.25, 0.75, 0.75])
# set a in angstrom
a = 2. * 5.663 / 1.889725989
struct = Structure( [ at1, at2, at3, at4, at5, at6, at7, at8, at9, \
at10, at11, at12, at13, at14, at15, at16], \
lattice = Lattice(a, a, a, 90, 90, 90) )
#print struct
massList = [50.9415, 55.847]
psList = ['V.pbe-n-van.UPF', 'Fe.pbe-nd-rrkjus.UPF']
self.input.structure.load(source = 'matter', structure = struct, \
ibrav = 2, massList = massList, psList = psList)
answer1 = """"Face Centered Cubic" cell:
-5.66300000 0.00000000 5.66300000
0.00000000 5.66300000 5.66300000
-5.66300000 5.66300000 0.00000000
Atomic positions in units of lattice parametr "a":
V 0.00000000 0.00000000 0.00000000
V 0.50000000 0.00000000 0.00000000
V 0.25000000 0.25000000 0.25000000
Fe 0.75000000 0.25000000 0.25000000
V 50.9415 V.pbe-n-van.UPF
Fe 55.8470 Fe.pbe-nd-rrkjus.UPF
"""
self.assertEqual(str(self.input.structure), answer1)
self.input.structure.load(source = 'matter', structure = struct, \
massList = massList, psList = psList)
answer2 = """"generic" cell:
11.32600000 0.00000000 0.00000000
0.00000000 11.32600000 0.00000000
0.00000000 0.00000000 11.32600000
Atomic positions in units of lattice parametr "a":
V 0.00000000 0.00000000 0.00000000
V 2.99673076 0.00000000 0.00000000
V 0.00000000 2.99673076 0.00000000
V 0.00000000 0.00000000 2.99673076
V 2.99673076 2.99673076 0.00000000
V 0.00000000 2.99673076 2.99673076
V 2.99673076 0.00000000 2.99673076
V 2.99673076 2.99673076 2.99673076
V 1.49836538 1.49836538 1.49836538
Fe 4.49509614 1.49836538 1.49836538
V 4.49509614 4.49509614 1.49836538
Fe 1.49836538 4.49509614 1.49836538
Fe 1.49836538 1.49836538 4.49509614
V 4.49509614 1.49836538 4.49509614
Fe 4.49509614 4.49509614 4.49509614
V 1.49836538 4.49509614 4.49509614
V 50.9415 V.pbe-n-van.UPF
Fe 55.8470 Fe.pbe-nd-rrkjus.UPF
"""
self.assertEqual(str(self.input.structure), answer2)
def test_list(self):
answer = """Al 0.000000 0.000000 0.000000 26.982500 al_1.ncpp
B 0.666667 0.333333 0.234036 11.000000 B.pbe-n-van_ak.UPF
B 0.333333 0.666667 0.234036 11.000000 B.pbe-n-van_ak.UPF
Mg 0.000000 0.000000 0.499998 24.305000 mg.ncpp
B 0.666667 0.333333 0.765961 11.000000 B.pbe-n-van_ak.UPF
B 0.333333 0.666667 0.765961 11.000000 B.pbe-n-van_ak.UPF
"""
s = ''
for a in self.input.structure:
s = s + str(a) + '\n'
self.assertEqual(s, answer)
def test_diffpy(self):
answer = """lattice=Lattice(base=array([[ 5.7889 , 0. , 0. ],
[ -2.89445 , 5.01333446, 0. ],
[ 0. , 0. , 12.87515038]]))
Al 0.000000 0.000000 0.000000 1.0000
B 0.666667 0.333333 0.234036 1.0000
B 0.333333 0.666667 0.234036 1.0000
Mg 0.000000 0.000000 0.499998 1.0000
B 0.666667 0.333333 0.765961 1.0000
B 0.333333 0.666667 0.765961 1.0000"""
self.assertEqual(str(self.input.structure.diffpy()), answer)
def test_readStr(self):
al_pw_str = """&CONTROL
calculation = 'scf',
restart_mode = 'from_scratch',
pseudo_dir = '/home/user/pslib',
outdir = 'temp/',
prefix = 'al',
tprnfor = .true.,
tstress = .true.,
/
&SYSTEM
ibrav = 2,
ecutwfc = 17.5,
occupations = 'smearing',
smearing = 'marzari-vanderbilt',
degauss = 0.05,
celldm(1) = 7.7,
celldm(2) = 1.0,
celldm(3) = 1.0,
celldm(4) = 0.0,
ntyp = 1,
nat = 1,
/
&ELECTRONS
diagonalization = 'david',
mixing_beta = 0.7,
/
ATOMIC_SPECIES
Al 26.9800 Al.pz-vbc.UPF
ATOMIC_POSITIONS (alat)
Al 0.00000000 0.00000000 0.00000000
K_POINTS
3
0.0625000 0.0625000 0.0625000 1.00
0.0625000 0.0625000 0.1875000 3.00
0.0625000 0.0625000 0.3125000 3.00"""
answer = """"Face Centered Cubic" cell:
-3.85000000 0.00000000 3.85000000
0.00000000 3.85000000 3.85000000
-3.85000000 3.85000000 0.00000000
Atomic positions in units of lattice parametr "a":
Al 0.00000000 0.00000000 0.00000000
Al 26.9800 Al.pz-vbc.UPF
"""
self.input.structure.readStr(al_pw_str)
self.assertEqual(str(self.input.structure), answer)
def test_fileInit(self):
from qecalc.qetask.qeparser.qestructure import QEStructure
filename = os.path.join(testdata_dir, 'al_pw.in')
stru = QEStructure(filename=filename)
answer = """"Face Centered Cubic" cell:
-3.85000000 0.00000000 3.85000000
0.00000000 3.85000000 3.85000000
-3.85000000 3.85000000 0.00000000
Atomic positions in units of lattice parametr "a":
Al 0.00000000 0.00000000 0.00000000
Al 26.9800 Al.pz-vbc.UPF
"""
self.assertEqual(str(stru), answer)
stru = QEStructure()
filename = os.path.join(testdata_dir, 'PbTe.cif')
stru.read(filename=filename, format='cif')
answer = """&SYSTEM
ibrav = 0,
celldm(1) = 1.889725989,
ntyp = 2,
nat = 8,
/
ATOMIC_SPECIES
Pb2+ 0.0000
Te 0.0000
ATOMIC_POSITIONS (crystal)
Pb2+ 0.50000000 0.50000000 0.50000000
Pb2+ 0.50000000 0.00000000 0.00000000
Pb2+ 0.00000000 0.50000000 0.00000000
Pb2+ 0.00000000 0.00000000 0.50000000
Te 0.00000000 0.00000000 0.00000000
Te 0.00000000 0.50000000 0.50000000
Te 0.50000000 0.00000000 0.50000000
Te 0.50000000 0.50000000 0.00000000
CELL_PARAMETERS (cubic)
6.46100000 0.00000000 0.00000000
0.00000000 6.46100000 0.00000000
0.00000000 0.00000000 6.46100000
"""
#print stru.toString( stringConfig )
self.assertEqual(stru.toString(stringConfig), answer)
def test_writeStr(self):
answer = """CRYST1 5.789 5.789 12.875 90.00 90.00 120.00
ATOM 1 Al 1 0.000 0.000 0.000 1.00 0.00 Al
ATOM 2 B 1 2.894 1.671 3.013 1.00 0.00 B
ATOM 3 B 1 -0.000 3.342 3.013 1.00 0.00 B
ATOM 4 Mg 1 0.000 0.000 6.438 1.00 0.00 Mg
ATOM 5 B 1 2.894 1.671 9.862 1.00 0.00 B
ATOM 6 B 1 -0.000 3.342 9.862 1.00 0.00 B
TER 7 1
END
"""
self.assertEqual(self.input.structure.writeStr(format='pdb'), answer)
def test_constructor(self):
from qecalc.qetask.qeparser.qelattice import QELattice
from qecalc.qetask.qeparser.qestructure import QEStructure
from qecalc.qetask.qeparser.qeatom import QEAtom
filename = os.path.join(testdata_dir, 'fev3_pwgeom.out')
self.input.structure.read(filename, 'pwoutput')
vmass = 50.94150
vpot = 'V_potential'
femass = 55.84700
fepot = 'Fe_potential'
at1 = QEAtom('V', [0., 0., 0.], vmass, vpot)
at2 = QEAtom('V', [0.5, 0., 0.], vmass, vpot)
at3 = QEAtom('V', [0., 0.5, 0.], vmass, vpot)
at4 = QEAtom('V', [0., 0., 0.5], vmass, vpot)
at5 = QEAtom('V', [0.5, 0.5, 0.], vmass, vpot)
at6 = QEAtom('V', [0., 0.5, 0.5], vmass, vpot)
at7 = QEAtom('V', [0.5, 0., 0.5], vmass, vpot)
at8 = QEAtom('V', [0.5, 0.5, 0.5], vmass, vpot)
at9 = QEAtom('V', [0.25, 0.25, 0.25], vmass, vpot)
at10 = QEAtom('Fe', [0.75, 0.25, 0.25], femass, fepot)
at11 = QEAtom('V', [0.75, 0.75, 0.25], vmass, vpot)
at12 = QEAtom('Fe', [0.25, 0.75, 0.25], femass, fepot)
at13 = QEAtom('Fe', [0.25, 0.25, 0.75], femass, fepot)
at14 = QEAtom('V', [0.75, 0.25, 0.75], vmass, vpot)
at15 = QEAtom('Fe', [0.75, 0.75, 0.75], femass, fepot)
at16 = QEAtom('V', [0.25, 0.75, 0.75], vmass, vpot)
lattice = QELattice(lattice=self.input.structure.lattice)
#print lattice
new_struct = QEStructure( [ at1, at2, at3, at4, at5, at6, at7, at8, at9, \
at10, at11, at12, at13, at14, at15, at16], \
lattice = lattice )
answer = """"Face Centered Cubic" cell:
-5.50788176 0.00000000 5.50788176
0.00000000 5.50788176 5.50788176
-5.50788176 5.50788176 0.00000000
Atomic positions in crystal coordinates:
V 0.00000000 0.00000000 0.00000000
V 0.50000000 0.00000000 0.00000000
V 0.00000000 0.50000000 0.00000000
V 0.00000000 0.00000000 0.50000000
V 0.50000000 0.50000000 0.00000000
V 0.00000000 0.50000000 0.50000000
V 0.50000000 0.00000000 0.50000000
V 0.50000000 0.50000000 0.50000000
V 0.25000000 0.25000000 0.25000000
Fe 0.75000000 0.25000000 0.25000000
V 0.75000000 0.75000000 0.25000000
Fe 0.25000000 0.75000000 0.25000000
Fe 0.25000000 0.25000000 0.75000000
V 0.75000000 0.25000000 0.75000000
Fe 0.75000000 0.75000000 0.75000000
V 0.25000000 0.75000000 0.75000000
V 50.9415 V_potential
Fe 55.8470 Fe_potential
"""
self.assertEqual(str(new_struct), answer)
new_struct = QEStructure(self.input.structure)
# Check if the constructor messes _qeInput
self.input.structure.lattice.a = 10
new_struct.lattice.a = 12
s1 = self.input.structure.toString()
s2 = new_struct.toString()
self.assertNotEqual(s1, s2)
def test_reduce(self):
filename = os.path.join(testdata_dir, 'PbTe.cif')
self.input.structure.read(filename, 'cif')
self.input.structure.reduce(ibrav=2)
answer = """"Face Centered Cubic" cell:
-6.10475981 0.00000000 6.10475981
0.00000000 6.10475981 6.10475981
-6.10475981 6.10475981 0.00000000
Atomic positions in crystal coordinates:
Pb2+ -0.50000000 1.50000000 -0.50000000
Te 0.00000000 0.00000000 0.00000000
Pb2+ 0.0000
Te 0.0000
"""
self.assertEqual(str(self.input.structure), answer)
class TestStructureMethods(unittest.TestCase):
def setUp(self):
if useStringConfig:
self.input = PWInput( config = stringConfig )
else:
self.input = PWInput( filename = 'pw.in' )
#self.input.autoUpdate = False
self.input.parse()
def test_read_pwoutput(self):
filename = os.path.join(testdata_dir, 'mgalb4_pw.out')
self.input.structure.read(filename, 'pwoutput')
#answer = """"Simple Hexagonal or Trigonal(P)" cell :\n 5.70000000 0.00000000 0.00000000\n-2.85000000 4.93634480 0.00000000\n 0.00000000 0.00000000 12.54000000\n\nAtomic positions in units of lattice parametr "a":\nAl 0.00000000 0.00000000 0.00000000 \nB 0.50000000 0.28867510 0.52052140 \nB 0.00000000 0.57735030 0.52052140 \nMg 0.00000000 0.00000000 1.11205140 \nB 0.50000000 0.28867510 1.70358160 \nB 0.00000000 0.57735030 1.70358160 \n\nAl 26.9825 al.ncpp\nB 11.0000 b.ncpp\nMg 24.3050 mg.ncpp\n"""
answer = """"Simple Hexagonal or Trigonal(P)" cell:
5.70000000 0.00000000 0.00000000
-2.85000000 4.93634480 0.00000000
0.00000000 0.00000000 12.54000000
Atomic positions in units of lattice parametr "a":
Al 0.00000000 0.00000000 0.00000000
B 0.50000000 0.28867510 0.52052140
B 0.00000000 0.57735030 0.52052140
Mg 0.00000000 0.00000000 1.11205140
B 0.50000000 0.28867510 1.70358160
B 0.00000000 0.57735030 1.70358160
Al 26.9825 al.ncpp
B 11.0000 b.ncpp
Mg 24.3050 mg.ncpp
"""
#print '*', str(self.input.structure), '*'
#print '*', str(self.input.structure), '*'
self.assertEqual(str(self.input.structure), answer)
filename = os.path.join(testdata_dir, 'fev3_pwgeom.out')
self.input.structure.read(filename, 'pwoutput')
# after geometry optimization:
answer = """"Face Centered Cubic" cell:
-5.50788176 0.00000000 5.50788176
0.00000000 5.50788176 5.50788176
-5.50788176 5.50788176 0.00000000
Atomic positions in units of lattice parametr "a":
V 0.00000000 0.00000000 0.00000000
V 0.50000000 0.00000000 0.00000000
V 0.25000000 0.25000000 0.25000000
Fe 0.75000000 0.25000000 0.25000000
V 50.9415 V.pbe-sp-van.UPF
Fe 55.8470 Fe.pbe-sp-van_ak.UPF
"""
answer_toString="""&CONTROL
calculation = 'scf',
restart_mode = 'from_scratch',
tstress = .true.,
tprnfor = .true.,
prefix = 'mgalb4',
pseudo_dir = '/home/user/pslib',
outdir = '/scratch/user',
/
&SYSTEM
ibrav = 2,
nbnd = 21,
nspin = 1,
occupations = 'smearing',
degauss = 0.025,
smearing = 'methfessel-paxton',
ecutwfc = 64.0,
ecutrho = 256.0,
celldm(1) = 11.0157635161,
celldm(2) = 1.0,
celldm(3) = 1.0,
celldm(4) = 0.0,
ntyp = 2,
nat = 4,
/
&ELECTRONS
conv_thr = 1.0d-10,
mixing_beta = 0.4,
/
ATOMIC_SPECIES
V 50.9415 V.pbe-sp-van.UPF
Fe 55.8470 Fe.pbe-sp-van_ak.UPF
ATOMIC_POSITIONS (alat)
V 0.00000000 0.00000000 0.00000000
V 0.50000000 0.00000000 0.00000000
V 0.25000000 0.25000000 0.25000000
Fe 0.75000000 0.25000000 0.25000000
K_POINTS (automatic)
32 32 16 0 0 0
"""
self.assertEqual(str(self.input.structure), answer)
self.assertEqual(self.input.toString(), answer_toString)
def test_read_pwinput(self):
filename = os.path.join(testdata_dir, 'al_pw.in')
self.input.structure.read(filename, 'pwinput')
answer = """"Face Centered Cubic" cell:
-3.85000000 0.00000000 3.85000000
0.00000000 3.85000000 3.85000000
-3.85000000 3.85000000 0.00000000
Atomic positions in units of lattice parametr "a":
Al 0.00000000 0.00000000 0.00000000
Al 26.9800 Al.pz-vbc.UPF
"""
answer_toString = """&CONTROL
calculation = 'scf',
restart_mode = 'from_scratch',
tstress = .true.,
tprnfor = .true.,
prefix = 'mgalb4',
pseudo_dir = '/home/user/pslib',
outdir = '/scratch/user',
/
&SYSTEM
ibrav = 2,
nbnd = 21,
nspin = 1,
occupations = 'smearing',
degauss = 0.025,
smearing = 'methfessel-paxton',
ecutwfc = 64.0,
ecutrho = 256.0,
celldm(1) = 7.7,
celldm(2) = 1.0,
celldm(3) = 1.0,
celldm(4) = 0.0,
ntyp = 1,
nat = 1,
/
&ELECTRONS
conv_thr = 1.0d-10,
mixing_beta = 0.4,
/
ATOMIC_SPECIES
Al 26.9800 Al.pz-vbc.UPF
ATOMIC_POSITIONS (alat)
Al 0.00000000 0.00000000 0.00000000
K_POINTS (automatic)
32 32 16 0 0 0
"""
self.assertEqual(str(self.input.structure), answer)
#print self.input.structure.toString()
self.assertEqual(self.input.structure.toString(), answer_toString)
def test_read_cif(self):
filename = os.path.join(testdata_dir, 'PbTe.cif')
self.input.structure.read(filename, 'cif')
answer = """"generic" cell:
12.20951961 0.00000000 0.00000000
0.00000000 12.20951961 0.00000000
0.00000000 0.00000000 12.20951961
Atomic positions in crystal coordinates:
Pb2+ 0.50000000 0.50000000 0.50000000
Pb2+ 0.50000000 0.00000000 0.00000000
Pb2+ 0.00000000 0.50000000 0.00000000
Pb2+ 0.00000000 0.00000000 0.50000000
Te 0.00000000 0.00000000 0.00000000
Te 0.00000000 0.50000000 0.50000000
Te 0.50000000 0.00000000 0.50000000
Te 0.50000000 0.50000000 0.00000000
Pb2+ 0.0000
Te 0.0000
"""
self.assertEqual(str(self.input.structure), answer)
#filename = os.path.join(testdata_dir, 'LiNbO3.cif')
#self.input.structure.read(filename, 'cif')
#self.input.structure.reduce()
#print self.input.toString()
def test_load_diffpy(self):
from diffpy.Structure.structure import Structure
from diffpy.Structure.atom import Atom
from diffpy.Structure.lattice import Lattice
at1 = Atom('V', [0., 0., 0.])
at2 = Atom('V', [0.5, 0., 0.])
at3 = Atom('V', [0., 0.5, 0.])
at4 = Atom('V', [0., 0., 0.5])
at5 = Atom('V', [0.5, 0.5, 0.])
at6 = Atom('V', [0., 0.5, 0.5])
at7 = Atom('V', [0.5, 0., 0.5])
at8 = Atom('V', [0.5, 0.5, 0.5])
at9 = Atom('V', [0.25, 0.25, 0.25])
at10 = Atom('Fe', [0.75, 0.25, 0.25])
at11 = Atom('V', [0.75, 0.75, 0.25])
at12 = Atom('Fe', [0.25, 0.75, 0.25])
at13 = Atom('Fe', [0.25, 0.25, 0.75])
at14 = Atom('V', [0.75, 0.25, 0.75])
at15 = Atom('Fe', [0.75, 0.75, 0.75])
at16 = Atom('V', [0.25, 0.75, 0.75])
# set a in angstrom
a = 2.*5.663/1.889725989
struct = Structure( [ at1, at2, at3, at4, at5, at6, at7, at8, at9, \
at10, at11, at12, at13, at14, at15, at16], \
lattice = Lattice(a, a, a, 90, 90, 90) )
#print struct
massList = [50.9415, 55.847]
psList = ['V.pbe-n-van.UPF', 'Fe.pbe-nd-rrkjus.UPF']
self.input.structure.load(source = 'diffpy', structure = struct, \
ibrav = 2, massList = massList, psList = psList)
answer1 = """"Face Centered Cubic" cell:
-5.66300000 0.00000000 5.66300000
0.00000000 5.66300000 5.66300000
-5.66300000 5.66300000 0.00000000
Atomic positions in units of lattice parametr "a":
V 0.00000000 0.00000000 0.00000000
V 0.50000000 0.00000000 0.00000000
V 0.25000000 0.25000000 0.25000000
Fe 0.75000000 0.25000000 0.25000000
V 50.9415 V.pbe-n-van.UPF
Fe 55.8470 Fe.pbe-nd-rrkjus.UPF
"""
#print self.input.toString()
self.assertEqual(str(self.input.structure), answer1)
self.input.structure.load(source = 'diffpy', structure = struct, \
massList = massList, psList = psList)
answer2 = """"generic" cell:
11.32600000 0.00000000 0.00000000
0.00000000 11.32600000 0.00000000
0.00000000 0.00000000 11.32600000
Atomic positions in units of lattice parametr "a":
V 0.00000000 0.00000000 0.00000000
V 2.99673076 0.00000000 0.00000000
V 0.00000000 2.99673076 0.00000000
V 0.00000000 0.00000000 2.99673076
V 2.99673076 2.99673076 0.00000000
V 0.00000000 2.99673076 2.99673076
V 2.99673076 0.00000000 2.99673076
V 2.99673076 2.99673076 2.99673076
V 1.49836538 1.49836538 1.49836538
Fe 4.49509614 1.49836538 1.49836538
V 4.49509614 4.49509614 1.49836538
Fe 1.49836538 4.49509614 1.49836538
Fe 1.49836538 1.49836538 4.49509614
V 4.49509614 1.49836538 4.49509614
Fe 4.49509614 4.49509614 4.49509614
V 1.49836538 4.49509614 4.49509614
V 50.9415 V.pbe-n-van.UPF
Fe 55.8470 Fe.pbe-nd-rrkjus.UPF
"""
self.assertEqual(str(self.input.structure), answer2)
def test_load_matter(self):
try:
from matter import Structure, Atom, Lattice
except ImportError:
return
at1 = Atom('V', [0., 0., 0.])
at2 = Atom('V', [0.5, 0., 0.])
at3 = Atom('V', [0., 0.5, 0.])
at4 = Atom('V', [0., 0., 0.5])
at5 = Atom('V', [0.5, 0.5, 0.])
at6 = Atom('V', [0., 0.5, 0.5])
at7 = Atom('V', [0.5, 0., 0.5])
at8 = Atom('V', [0.5, 0.5, 0.5])
at9 = Atom('V', [0.25, 0.25, 0.25])
at10 = Atom('Fe', [0.75, 0.25, 0.25])
at11 = Atom('V', [0.75, 0.75, 0.25])
at12 = Atom('Fe', [0.25, 0.75, 0.25])
at13 = Atom('Fe', [0.25, 0.25, 0.75])
at14 = Atom('V', [0.75, 0.25, 0.75])
at15 = Atom('Fe', [0.75, 0.75, 0.75])
at16 = Atom('V', [0.25, 0.75, 0.75])
# set a in angstrom
a = 2.*5.663/1.889725989
struct = Structure( [ at1, at2, at3, at4, at5, at6, at7, at8, at9, \
at10, at11, at12, at13, at14, at15, at16], \
lattice = Lattice(a, a, a, 90, 90, 90) )
#print struct
massList = [50.9415, 55.847]
psList = ['V.pbe-n-van.UPF', 'Fe.pbe-nd-rrkjus.UPF']
self.input.structure.load(source = 'matter', structure = struct, \
ibrav = 2, massList = massList, psList = psList)
answer1 = """"Face Centered Cubic" cell:
-5.66300000 0.00000000 5.66300000
0.00000000 5.66300000 5.66300000
-5.66300000 5.66300000 0.00000000
Atomic positions in units of lattice parametr "a":
V 0.00000000 0.00000000 0.00000000
V 0.50000000 0.00000000 0.00000000
V 0.25000000 0.25000000 0.25000000
Fe 0.75000000 0.25000000 0.25000000
V 50.9415 V.pbe-n-van.UPF
Fe 55.8470 Fe.pbe-nd-rrkjus.UPF
"""
self.assertEqual(str(self.input.structure), answer1)
self.input.structure.load(source = 'matter', structure = struct, \
massList = massList, psList = psList)
answer2 = """"generic" cell:
11.32600000 0.00000000 0.00000000
0.00000000 11.32600000 0.00000000
0.00000000 0.00000000 11.32600000
Atomic positions in units of lattice parametr "a":
V 0.00000000 0.00000000 0.00000000
V 2.99673076 0.00000000 0.00000000
V 0.00000000 2.99673076 0.00000000
V 0.00000000 0.00000000 2.99673076
V 2.99673076 2.99673076 0.00000000
V 0.00000000 2.99673076 2.99673076
V 2.99673076 0.00000000 2.99673076
V 2.99673076 2.99673076 2.99673076
V 1.49836538 1.49836538 1.49836538
Fe 4.49509614 1.49836538 1.49836538
V 4.49509614 4.49509614 1.49836538
Fe 1.49836538 4.49509614 1.49836538
Fe 1.49836538 1.49836538 4.49509614
V 4.49509614 1.49836538 4.49509614
Fe 4.49509614 4.49509614 4.49509614
V 1.49836538 4.49509614 4.49509614
V 50.9415 V.pbe-n-van.UPF
Fe 55.8470 Fe.pbe-nd-rrkjus.UPF
"""
self.assertEqual(str(self.input.structure), answer2)
def test_list(self):
answer = """Al 0.000000 0.000000 0.000000 26.982500 al_1.ncpp
B 0.666667 0.333333 0.234036 11.000000 B.pbe-n-van_ak.UPF
B 0.333333 0.666667 0.234036 11.000000 B.pbe-n-van_ak.UPF
Mg 0.000000 0.000000 0.499998 24.305000 mg.ncpp
B 0.666667 0.333333 0.765961 11.000000 B.pbe-n-van_ak.UPF
B 0.333333 0.666667 0.765961 11.000000 B.pbe-n-van_ak.UPF
"""
s = ''
for a in self.input.structure:
s = s + str(a) + '\n'
self.assertEqual(s, answer)
def test_diffpy(self):
answer = """lattice=Lattice(base=array([[ 5.7889 , 0. , 0. ],
[ -2.89445 , 5.01333446, 0. ],
[ 0. , 0. , 12.87515038]]))
Al 0.000000 0.000000 0.000000 1.0000
B 0.666667 0.333333 0.234036 1.0000
B 0.333333 0.666667 0.234036 1.0000
Mg 0.000000 0.000000 0.499998 1.0000
B 0.666667 0.333333 0.765961 1.0000
B 0.333333 0.666667 0.765961 1.0000"""
self.assertEqual(str(self.input.structure.diffpy()), answer)
def test_readStr(self):
al_pw_str = """&CONTROL
calculation = 'scf',
restart_mode = 'from_scratch',
pseudo_dir = '/home/user/pslib',
outdir = 'temp/',
prefix = 'al',
tprnfor = .true.,
tstress = .true.,
/
&SYSTEM
ibrav = 2,
ecutwfc = 17.5,
occupations = 'smearing',
smearing = 'marzari-vanderbilt',
degauss = 0.05,
celldm(1) = 7.7,
celldm(2) = 1.0,
celldm(3) = 1.0,
celldm(4) = 0.0,
ntyp = 1,
nat = 1,
/
&ELECTRONS
diagonalization = 'david',
mixing_beta = 0.7,
/
ATOMIC_SPECIES
Al 26.9800 Al.pz-vbc.UPF
ATOMIC_POSITIONS (alat)
Al 0.00000000 0.00000000 0.00000000
K_POINTS
3
0.0625000 0.0625000 0.0625000 1.00
0.0625000 0.0625000 0.1875000 3.00
0.0625000 0.0625000 0.3125000 3.00"""
answer = """"Face Centered Cubic" cell:
-3.85000000 0.00000000 3.85000000
0.00000000 3.85000000 3.85000000
-3.85000000 3.85000000 0.00000000
Atomic positions in units of lattice parametr "a":
Al 0.00000000 0.00000000 0.00000000
Al 26.9800 Al.pz-vbc.UPF
"""
self.input.structure.readStr(al_pw_str)
self.assertEqual(str(self.input.structure), answer)
def test_fileInit(self):
from qecalc.qetask.qeparser.qestructure import QEStructure
filename = os.path.join(testdata_dir, 'al_pw.in')
stru = QEStructure(filename = filename)
answer = """"Face Centered Cubic" cell:
-3.85000000 0.00000000 3.85000000
0.00000000 3.85000000 3.85000000
-3.85000000 3.85000000 0.00000000
Atomic positions in units of lattice parametr "a":
Al 0.00000000 0.00000000 0.00000000
Al 26.9800 Al.pz-vbc.UPF
"""
self.assertEqual(str(stru), answer)
stru = QEStructure()
filename = os.path.join(testdata_dir, 'PbTe.cif')
stru.read(filename = filename, format = 'cif')
answer ="""&SYSTEM
ibrav = 0,
celldm(1) = 1.889725989,
ntyp = 2,
nat = 8,
/
ATOMIC_SPECIES
Pb2+ 0.0000
Te 0.0000
ATOMIC_POSITIONS (crystal)
Pb2+ 0.50000000 0.50000000 0.50000000
Pb2+ 0.50000000 0.00000000 0.00000000
Pb2+ 0.00000000 0.50000000 0.00000000
Pb2+ 0.00000000 0.00000000 0.50000000
Te 0.00000000 0.00000000 0.00000000
Te 0.00000000 0.50000000 0.50000000
Te 0.50000000 0.00000000 0.50000000
Te 0.50000000 0.50000000 0.00000000
CELL_PARAMETERS (cubic)
6.46100000 0.00000000 0.00000000
0.00000000 6.46100000 0.00000000
0.00000000 0.00000000 6.46100000
"""
#print stru.toString( stringConfig )
self.assertEqual(stru.toString( stringConfig ), answer )
def test_writeStr(self):
answer = """CRYST1 5.789 5.789 12.875 90.00 90.00 120.00
ATOM 1 Al 1 0.000 0.000 0.000 1.00 0.00 Al
ATOM 2 B 1 2.894 1.671 3.013 1.00 0.00 B
ATOM 3 B 1 -0.000 3.342 3.013 1.00 0.00 B
ATOM 4 Mg 1 0.000 0.000 6.438 1.00 0.00 Mg
ATOM 5 B 1 2.894 1.671 9.862 1.00 0.00 B
ATOM 6 B 1 -0.000 3.342 9.862 1.00 0.00 B
TER 7 1
END
"""
self.assertEqual(self.input.structure.writeStr(format = 'pdb'), answer)
def test_constructor(self):
from qecalc.qetask.qeparser.qelattice import QELattice
from qecalc.qetask.qeparser.qestructure import QEStructure
from qecalc.qetask.qeparser.qeatom import QEAtom
filename = os.path.join(testdata_dir, 'fev3_pwgeom.out')
self.input.structure.read(filename, 'pwoutput')
vmass = 50.94150
vpot = 'V_potential'
femass = 55.84700
fepot = 'Fe_potential'
at1 = QEAtom('V', [0., 0., 0.], vmass, vpot)
at2 = QEAtom('V', [0.5, 0., 0.], vmass, vpot)
at3 = QEAtom('V', [0., 0.5, 0.], vmass, vpot)
at4 = QEAtom('V', [0., 0., 0.5], vmass, vpot)
at5 = QEAtom('V', [0.5, 0.5, 0.], vmass, vpot)
at6 = QEAtom('V', [0., 0.5, 0.5], vmass, vpot)
at7 = QEAtom('V', [0.5, 0., 0.5], vmass, vpot)
at8 = QEAtom('V', [0.5, 0.5, 0.5], vmass, vpot)
at9 = QEAtom('V', [0.25, 0.25, 0.25], vmass, vpot)
at10 = QEAtom('Fe', [0.75, 0.25, 0.25], femass, fepot)
at11 = QEAtom('V', [0.75, 0.75, 0.25], vmass, vpot)
at12 = QEAtom('Fe', [0.25, 0.75, 0.25], femass, fepot)
at13 = QEAtom('Fe', [0.25, 0.25, 0.75], femass, fepot)
at14 = QEAtom('V', [0.75, 0.25, 0.75], vmass, vpot)
at15 = QEAtom('Fe', [0.75, 0.75, 0.75], femass, fepot)
at16 = QEAtom('V', [0.25, 0.75, 0.75], vmass, vpot)
lattice = QELattice(lattice = self.input.structure.lattice)
#print lattice
new_struct = QEStructure( [ at1, at2, at3, at4, at5, at6, at7, at8, at9, \
at10, at11, at12, at13, at14, at15, at16], \
lattice = lattice )
answer = """"Face Centered Cubic" cell:
-5.50788176 0.00000000 5.50788176
0.00000000 5.50788176 5.50788176
-5.50788176 5.50788176 0.00000000
Atomic positions in crystal coordinates:
V 0.00000000 0.00000000 0.00000000
V 0.50000000 0.00000000 0.00000000
V 0.00000000 0.50000000 0.00000000
V 0.00000000 0.00000000 0.50000000
V 0.50000000 0.50000000 0.00000000
V 0.00000000 0.50000000 0.50000000
V 0.50000000 0.00000000 0.50000000
V 0.50000000 0.50000000 0.50000000
V 0.25000000 0.25000000 0.25000000
Fe 0.75000000 0.25000000 0.25000000
V 0.75000000 0.75000000 0.25000000
Fe 0.25000000 0.75000000 0.25000000
Fe 0.25000000 0.25000000 0.75000000
V 0.75000000 0.25000000 0.75000000
Fe 0.75000000 0.75000000 0.75000000
V 0.25000000 0.75000000 0.75000000
V 50.9415 V_potential
Fe 55.8470 Fe_potential
"""
self.assertEqual(str(new_struct), answer)
new_struct = QEStructure(self.input.structure)
# Check if the constructor messes _qeInput
self.input.structure.lattice.a = 10
new_struct.lattice.a = 12
s1 = self.input.structure.toString()
s2 = new_struct.toString()
self.assertNotEqual(s1, s2)
def test_reduce(self):
filename = os.path.join(testdata_dir, 'PbTe.cif')
self.input.structure.read(filename, 'cif')
self.input.structure.reduce(ibrav = 2)
answer = """"Face Centered Cubic" cell:
-6.10475981 0.00000000 6.10475981
0.00000000 6.10475981 6.10475981
-6.10475981 6.10475981 0.00000000
Atomic positions in crystal coordinates:
Pb2+ -0.50000000 1.50000000 -0.50000000
Te 0.00000000 0.00000000 0.00000000
Pb2+ 0.0000
Te 0.0000
"""
self.assertEqual(str(self.input.structure), answer)
def testMatter():
pwInput = PWInput(config=testSCFString)
struct = matter.Structure()
struct.read('data/graphite.cif', format='cif')
#struct.read('data/PbTe.cif', format='cif')
#struct.read('data/Ni.stru', format='pdffit')
#struct.read('data/CdSe-wurtzite.stru', format='pdffit')
print struct
print struct.lattice.base
#struct = Structure(filename='data/Ni.stru')
#struct = Structure(filename='data/graphite.cif')
#struct = Structure(filename='data/PbTe.cif')
#struct = Structure(filename='data/CdSe-wurtzite.stru')
#struct = Structure(pbte)
# does not work well in matter:
#s = pbte.writeStr(format='cif')
at1 = Atom('V', [0., 0., 0.])
at2 = Atom('V', [0.5, 0., 0.])
at3 = Atom('V', [0., 0.5, 0.])
at4 = Atom('V', [0., 0., 0.5])
at5 = Atom('V', [0.5, 0.5, 0.])
at6 = Atom('V', [0., 0.5, 0.5])
at7 = Atom('V', [0.5, 0., 0.5])
at8 = Atom('V', [0.5, 0.5, 0.5])
at9 = Atom('V', [0.25, 0.25, 0.25])
at10 = Atom('Fe', [0.75, 0.25, 0.25])
at11 = Atom('V', [0.75, 0.75, 0.25])
at12 = Atom('Fe', [0.25, 0.75, 0.25])
at13 = Atom('Fe', [0.25, 0.25, 0.75])
at14 = Atom('V', [0.75, 0.25, 0.75])
at15 = Atom('Fe', [0.75, 0.75, 0.75])
at16 = Atom('V', [0.25, 0.75, 0.75])
struct2 = Structure([
at1, at2, at3, at4, at5, at6, at7, at8, at9, at10, at11, at12, at13,
at14, at15, at16
],
lattice=Lattice(2, 2, 2, 90, 90, 90))
#print struct
massList = [50., 55.]
psList = ['ps1', 'ps2']
#massList = [1, 2, 3, 4, 5, 6,1, 2, 3, 4, 5, 6]
#psList = ['ps1', 'ps2', 'ps2', 'ps3', 'ps4','ps1', 'ps2', 'ps2', 'ps3', 'ps4']
# pwInput.structure.load(ibrav = 0, structure = struct, \
# massList = massList, psList = psList)
#pwInput.structure.load(structure = struct )
#print pwInput.structure.atomLabels()
pwInput.structure.load(structure = struct, ibrav = 2, \
massList = massList, psList = psList)
# pwInput.structure.setStructureFromDiffpyStructure(struct, \
# massList = massList,\
# psList = psList)
# pwInput.structure.setReducedStructureFromDiffpyStructure(struct, ibrav = 2, \
# massList = massList,\
# psList = psList)
# this will update string s:
#s = ''
#s = pwInput.structure.toString(string = s)
#pwInput.removeNamelist('system')
#pwInput.removeCard('atomic_species')
#pwInput.removeCard('atomic_positions')
#pwInput.removeCard('cell_parameters')
#pwInput.structure.parseInput()
s = pwInput.structure.toString()
#pwInput.structure.atomicPositionsType = 'alat'
#s = pwInput.structure.toString()
#pwInput.structure.save('scf.in')
print s
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 parseStr(self, s):
"""Create Structure instance from a string."""
input = PWInput()
input.readString(s)
return self.__genStructure(input)
def parse(self, filename):
"""Create Structure instance from a file."""
self.filename = filename
input = PWInput(filename=filename)
return self.__genStructure(input)
def parseStr(self, s):
"""Create Structure instance from a string."""
input = PWInput()
input.readString(s)
return self.__genStructure(input)
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')