def test_filter_apply(self):
input = QEInput(config=fixtures.textMain)
# Filter that adds parameters to input
fp = Filter("fPlus")
fp.setParam("control", "prefix", "'ni'")
fp.setParam("control", "pseudo_dir", "''")
fp.setParam("control", "outdir", "''")
fp.setCard({
"name": "occupations",
"lines": ("New line", )
}) # Add new card
fp.setNamelist({
"name": "cell",
"params": {
"hello": "world"
}
}) # Add new namelist
fp.setNamelist({"name": "phonon"})
fp.apply(input, "plus")
self.assertEqual(input.toString(), fixtures.assertPlus)
# Filter that removes parameters from input
fm = Filter("fMinus")
fm.setCard({"name": "atomic_species"})
fm.setNamelist({"name": "phonon"}) # Remove namelist
fm.setParam("cell",
"hello") # Remove parameter that makes namelist empty
fm.setParam("control", "prefix") # Remove parameter
fm.apply(input, "minus")
self.assertEqual(input.toString(), fixtures.assertMinus)
def save(self, filename=None):
if filename == None:
if self._setting != None:
self.filename = self._setting.get(self.type() + 'Input')
QEInput.save(self)
else:
QEInput.save(self, filename)
def save(self, filename=None):
if filename == None:
if self._setting != None:
self.filename = self._setting.get(self.type()+'Input')
QEInput.save(self)
else:
QEInput.save(self, filename)
def test_qeinput_namelist_exists(self):
input = QEInput(config=fixtures.textMain)
# If non-standard card is requested, it will not add it!
nl = input.namelist("SOME_NAMELIST")
self.assertFalse(input.namelistExists("some_namelist"))
nl = input.namelist("cell")
self.assertTrue(input.namelistExists("cell"))
def parse(self):
"""
Parses the configuration file and stores the values in qe dictionary
"""
if self._setting != None:
self.readFile(filename=self._setting.get(self.type() + 'Input'))
else:
QEInput.parse(self)
def readFile(self, filename):
"""
Reads and parses configuration input from file
filename: (str) -- File name
"""
QEInput.readFile(self, filename)
if self._setting != None:
self.filename = self._setting.get(self.type() + 'Input')
def parse(self):
"""
Parses the configuration file and stores the values in qe dictionary
"""
if self._setting != None:
self.readFile( filename = self._setting.get(self.type() + 'Input'))
else:
QEInput.parse(self)
def test_qeinput_card_exists(self):
input = QEInput(config=fixtures.textMain)
# If non-standard card is requested, it will not add it!
card = input.card("SOME_CARD")
self.assertFalse(input.cardExists("some_card"))
card = input.card("occupations")
self.assertTrue(input.cardExists("occupations"))
def readFile(self, filename):
"""
Reads and parses configuration input from file
filename: (str) -- File name
"""
QEInput.readFile(self, filename)
if self._setting != None:
self.filename = self._setting.get(self.type() + 'Input')
def test_qeinput_save(self):
fname = "temp.in"
input = QEInput(config=fixtures.textMain)
input.save(fname)
self.assertTrue(filecmp.cmp(fname, "ref.in"))
try:
os.remove(fname)
except OSError:
pass # Doesn't exist
def test_qeinput_save(self):
fname = "temp.in"
input = QEInput(config=fixtures.textMain)
input.save(fname)
self.assertTrue(filecmp.cmp(fname, "ref.in"))
try:
os.remove(fname)
except OSError:
pass # Doesn't exist
def toString(self, string = None):
if string != None:
qeConf = QEInput(config = string)
qeConf.parse()
else:
if self.qeConf != None:
qeConf = self.qeConf
else:
qeConf = QEInput(config = '')
self.updatePWInput(qeConf)
return qeConf.toString()
def test_qeinput_namelist(self):
input = QEInput()
nl = Namelist("control")
nl.set("title", "'Ni'")
input.addNamelist(nl)
nl2 = input.namelist("phonon")
self.assertEqual(input.toString(), fixtures.assertNewNamelist)
input.removeNamelist("control")
self.assertEqual(input.toString(), fixtures.assertNewNamelist2)
def test_qeinput_card(self):
input = QEInput()
c = Card("atomic_species")
c.setArg("temp")
c.addLine("Ni 26.98 Ni.pbe-nd-rrkjus.UPF")
input.addCard(c)
c2 = input.card("atomic_positions")
self.assertEqual(input.toString(), fixtures.assertNewCard)
input.removeCard("atomic_species")
self.assertEqual(input.toString(), fixtures.assertNewCard2)
def save(self, fname=None):
"""Writes/updates structure into PW config file,
if the file does not exist, new one will be created"""
if fname != None:
filename = fname
self.lattice.save(filename)
qeConf = QEInput(fname)
qeConf.parse()
else:
filename = self.filename
self.lattice.save(filename)
qeConf = self.qeConf
self.updatePWInput(qeConf)
qeConf.save(filename)
def __init__(self, filename=None, config=None, type = 'pw', setting = None,\
parse = True):
self._setting = setting
if isinstance(filename, Setting):
self._setting = filename
if self._setting != None:
fname = self._setting.get( type + 'Input')
else:
fname = filename
QEInput.__init__(self,fname, config, type = type, parse = parse)
if parse and (filename or config or setting ):
self.parse()
def __init__(self, filename=None, config=None, type = 'pw', setting = None,\
parse = True):
self._setting = setting
if isinstance(filename, Setting):
self._setting = filename
if self._setting != None:
fname = self._setting.get(type + 'Input')
else:
fname = filename
QEInput.__init__(self, fname, config, type=type, parse=parse)
if parse and (filename or config or setting):
self.parse()
def save(self, fname = None):
"""Will save the lattice either into its own file or into supplied with fname.
It will also create all relevant sections/cards"""
from os.path import exists
if fname != None:
filename = fname
if not exists(filename):
f = open(filename, 'w')
qeConf = QEInput(fname)
qeConf.parse()
else:
qeConf = self.qeConf
filename = qeConf.filename
self.updatePWInput(qeConf)
qeConf.save(filename)
def write(self, filename=None, format="pwinput"):
"""Save structure to file in the specified format
format -- structure formats
'pwinput' ( pw.x input, default), 'pwoutput' (pw.x output),
'bratoms', 'cif', 'discus', 'pdb', 'pdffit', 'rawxyz',
'xcfg', 'xyz'
No return value.
"""
if format == "pwinput":
self._qeInput.update(forceUpdate=True)
if filename == None:
filename = self._qeInput.filename
input = QEInput(config=self._qeInput.toString(), type='pw')
input.save(filename=filename)
else:
self.matter().write(filename=filename, format=format)
return
def write(self, filename = None, format = "pwinput"):
"""Save structure to file in the specified format
format -- structure formats
'pwinput' ( pw.x input, default), 'pwoutput' (pw.x output),
'bratoms', 'cif', 'discus', 'pdb', 'pdffit', 'rawxyz',
'xcfg', 'xyz'
No return value.
"""
if format == "pwinput":
self._qeInput.update( forceUpdate = True )
if filename == None:
filename = self._qeInput.filename
input = QEInput(config = self._qeInput.toString(), type='pw')
input.save( filename = filename)
else:
self.matter().write( filename = filename, format = format )
return
def test_qeinput_namelist(self):
input = QEInput()
nl = Namelist("control")
nl.set("title", "'Ni'")
input.addNamelist(nl)
nl2 = input.namelist("phonon")
self.assertEqual(input.toString(), fixtures.assertNewNamelist)
input.removeNamelist("control")
self.assertEqual(input.toString(), fixtures.assertNewNamelist2)
def test_qeinput_card(self):
input = QEInput()
c = Card("atomic_species")
c.setArg("temp")
c.addLine("Ni 26.98 Ni.pbe-nd-rrkjus.UPF")
input.addCard(c)
c2 = input.card("atomic_positions")
self.assertEqual(input.toString(), fixtures.assertNewCard)
input.removeCard("atomic_species")
self.assertEqual(input.toString(), fixtures.assertNewCard2)
def toString(self, string=None):
if string != None:
qeConf = QEInput(config=string)
qeConf.parse()
else:
if self.qeConf != None:
qeConf = self.qeConf
else:
qeConf = QEInput(config='')
self.updatePWInput(qeConf)
return qeConf.toString()
def test_filter_apply(self):
input = QEInput(config=fixtures.textMain)
# Filter that adds parameters to input
fp = Filter("fPlus")
fp.setParam("control", "prefix", "'ni'")
fp.setParam("control", "pseudo_dir", "''")
fp.setParam("control", "outdir", "''")
fp.setCard({"name": "occupations", "lines": ("New line",)}) # Add new card
fp.setNamelist({"name": "cell", "params": {"hello": "world"}}) # Add new namelist
fp.setNamelist({"name": "phonon"})
fp.apply(input, "plus")
self.assertEqual(input.toString(), fixtures.assertPlus)
# Filter that removes parameters from input
fm = Filter("fMinus")
fm.setCard({"name": "atomic_species"})
fm.setNamelist({"name": "phonon"}) # Remove namelist
fm.setParam("cell", "hello") # Remove parameter that makes namelist empty
fm.setParam("control", "prefix") # Remove parameter
fm.apply(input, "minus")
self.assertEqual(input.toString(), fixtures.assertMinus)
def test_qeinput_card_exists(self):
input = QEInput(config=fixtures.textMain)
# If non-standard card is requested, it will not add it!
card = input.card("SOME_CARD")
self.assertFalse(input.cardExists("some_card"))
card = input.card("occupations")
self.assertTrue(input.cardExists("occupations"))
def test_qeinput_namelist_exists(self):
input = QEInput(config=fixtures.textMain)
# If non-standard card is requested, it will not add it!
nl = input.namelist("SOME_NAMELIST")
self.assertFalse(input.namelistExists("some_namelist"))
nl = input.namelist("cell")
self.assertTrue(input.namelistExists("cell"))
def test_qeinput_filter(self):
input = QEInput(config=fixtures.textMain)
f = Filter("fPlus")
f.setParam("control", "calculation", "'md'")
f.setCard({"name": "occupations", "lines": ("New line", )})
input.applyFilter(f, "plus")
self.assertEqual(input.toString(), fixtures.assertInputFilterPlus)
f = Filter("fMinus")
f.setNamelist({"name": "control"})
f.setCard({"name": "k_points"})
input.applyFilter(f, "minus")
self.assertEqual(input.toString(), fixtures.assertInputFilterMinus)
def test_qeinput_filter(self):
input = QEInput(config=fixtures.textMain)
f = Filter("fPlus")
f.setParam("control", "calculation", "'md'")
f.setCard({"name": "occupations", "lines": ("New line",)})
input.applyFilter(f, "plus")
self.assertEqual(input.toString(), fixtures.assertInputFilterPlus)
f = Filter("fMinus")
f.setNamelist({"name":"control"})
f.setCard({"name": "k_points"})
input.applyFilter(f, "minus")
self.assertEqual(input.toString(), fixtures.assertInputFilterMinus)
def save(self, fname=None):
"""Writes/updates structure into PW config file,
if the file does not exist, new one will be created"""
if fname != None:
filename = fname
self.lattice.save(filename)
qeConf = QEInput(fname)
qeConf.parse()
else:
filename = self.filename
self.lattice.save(filename)
qeConf = self.qeConf
self.updatePWInput(qeConf)
qeConf.save(filename)
def save(self, fname=None):
"""Will save the lattice either into its own file or into supplied with fname.
It will also create all relevant sections/cards"""
from os.path import exists
if fname != None:
filename = fname
if not exists(filename):
f = open(filename, 'w')
qeConf = QEInput(fname)
qeConf.parse()
else:
qeConf = self.qeConf
filename = qeConf.filename
self.updatePWInput(qeConf)
qeConf.save(filename)
def test_qeinput_read(self):
input = QEInput()
input.readString(fixtures.textMain) # Load input from string
self.assertEqual(input.config, fixtures.textMain) # config is set
nl = input.namelist("control")
c = input.card("atomic_positions")
self.assertEqual(nl.get("calculation"), "'scf'")
self.assertEqual(c.line(0), "Ni 0.00 0.00 0.00")
input.readFile("matdyn.in")
self.assertEqual(input.filename, "matdyn.in") # filename is set
input.readFile("ni.scf.in") # Load input from file
nl = input.namelist("control")
c = input.card("atomic_positions")
self.assertEqual(nl.get("calculation"), "'scf'")
self.assertEqual(c.line(0), "Ni 0.00 0.00 0.00")
def test_qeinput_remove(self):
input = QEInput(config=fixtures.textMain)
input.removeCard("atomic_species") # Remove non-existing card
input.removeNamelist("control") # Remove non-existing namelist
def test_qeinput_read(self):
input = QEInput()
input.readString(fixtures.textMain) # Load input from string
self.assertEqual(input.config, fixtures.textMain) # config is set
nl = input.namelist("control")
c = input.card("atomic_positions")
self.assertEqual(nl.get("calculation"), "'scf'")
self.assertEqual(c.line(0), "Ni 0.00 0.00 0.00")
input.readFile("matdyn.in")
self.assertEqual(input.filename, "matdyn.in") # filename is set
input.readFile("ni.scf.in") # Load input from file
nl = input.namelist("control")
c = input.card("atomic_positions")
self.assertEqual(nl.get("calculation"), "'scf'")
self.assertEqual(c.line(0), "Ni 0.00 0.00 0.00")
def getLatticeParamsFromPWSCF(self, ibrav, fname):
qeConf = QEInput(fname)
qeConf.parse()
return self.parsePWInput(ibrav, qeConf)
def setLatticeFromPWSCF(self, fname):
self.qeConf = QEInput(fname)
self.qeConf.parse()
setLatticeFromPWInput(self, qeConf)
def test_qeinput_remove(self):
input = QEInput(config=fixtures.textMain)
input.removeCard("atomic_species") # Remove non-existing card
input.removeNamelist("control") # Remove non-existing namelist
def test_qeinput_attach(self):
"This unit test is useful for matdyn simulation type"
input = QEInput()
input.addAttach("176\n\
0.000000 0.000000 0.456392 0.000000")
self.assertEqual(input.toString(), fixtures.assertAttach)
def test_qeinput_type(self):
input = QEInput(type="ph")
self.assertEqual(input.type(), "ph")
base = self._base / self._a
self.setLattice(ibrav=self._ibrav, a=self._a, base=base)
else:
if self._ibrav == 0:
pass
else:
self._type = value
type = property(_get_type,
_set_type,
doc="""QE lattice type: 'celldm',
'traditional' or 'generic cubic', 'generic hexagonal'(implies ibrav = 0""")
if __name__ == '__main__':
pwInput = QEInput('scf.in', type='pw')
pwInput.parse()
qeLattice = QELattice(qeConf=pwInput)
print qeLattice.latticeParams()
# qeLattice = QELattice(fname = 'qwe.in')
# qeLattice.setLatticeFromPrimitiveVectors(12,qeLattice.lattice().base)
# print qeLattice.latticeParams()
# qeLattice.latticeType = 'generic hexagonal'
# qeLattice.bb = 12
qeLattice.a = 13.0
qeLattice.b = 24.0
qeLattice.c = 3.
qeLattice.ibrav = 4
print qeLattice.b, qeLattice.c,
print qeLattice.latticeParams()
qeLattice.saveLatticeToPWSCF('./scf_2.in')
def __init__(self, filename=None, config=None):
QEInput.__init__(self,filename, config, type='d3')
self.qpoints = D3Qpoints(self)
else:
filename = self.filename
self.lattice.save(filename)
qeConf = self.qeConf
#qeConf.parse()
self.updatePWInput(qeConf)
qeConf.save(filename)
def diffpy(self):
return self.structure
# def placeInLattice(self, new_lattice):
# def getLattice(self):
# return self.structure.lattice
if __name__ == '__main__':
pwInput = QEInput('scf.in', type='pw')
#pwInput.parse()
myStruct = QEStructure(qeConf=pwInput)
#myStruct.lattice.ibrav = 4
#print myStruct.lattice.a
#print myStruct.lattice.c
#myStruct.lattice.a = 43
#pwInput.save()
#myStruct.saveStructureToPWSCF('scf_2.in')
#print myStruct.structure
myStruct.parseOutput('geom.out')
print myStruct.toString()
def __init__(self, filename=None, config=None):
QEInput.__init__(self,filename, config, type='matdyn')
self.qpoints = MatdynQpoints(self)
def __init__(self, filename=None, config=None):
QEInput.__init__(self,filename, config, type='pw')
self.structure = QEStructure(self)
self.kpoints = PWKpoints(self)
class QELattice(object):
"""Class QELattice for working with crystal lattices in QE notation
Uses diffpy.Lattice class for storage
Following parameters are dynamically linked to other properties
(E.g. lattice vectors):
ibrav - lattice type
if ibrav = 0, only 'a' prameter is relevant
a, b, c, cBC, cAC ,cAB - lattice parameters
type - lattice type to save into PWSCF cfg file ('celldm');
'traditional' - using a,b,c,cosAC, cosAB, cosBC;
'generic cubic', 'generic hexagonal' - assume exiasting
section 'CELL_PARAMETERS', 'generic' types also
assume/set ibrav = 0
setLattice() will set everything at once
"""
def __init__(self, ibrav = 1,a = 1. ,b = 1.,c = 1.,
cBC = 0.,cAC = 0. ,cAB = 0., qeConf = None, base = None ):
# Lattice.__init__(self)
self.formatString = '%# .8f %# .8f %# .8f'
self.qeConf = qeConf
self._type = 'celldm'
self._primitiveLattice = Lattice()
self._standardLattice = Lattice()
self._base = None
self._a0 = None
if self.qeConf != None:
self.setLatticeFromPWInput(self.qeConf)
else:
if ibrav > 0 and base != None:
self.setLatticeFromQEVectors(ibrav, base)
else:
self.setLattice(ibrav ,a ,b , c, cBC ,cAC ,cAB, base)
def setLatticeFromQEVectors(self, ibrav, vectors):
""" Will extract conventional lattice parameters from primitive vectors.
'vectors' - is a list with primitive vectors (in QE notation),
including lattice parameters. For example from PWSCF output"""
from numpy import dot
# default values:
a = b = c = 1.0
cBC = cAC = cAB = 0.0
v = numpy.array(vectors, dtype = float)
if ibrav == 0:
raise NotImplementedError
# sc simple cubic:
if ibrav == 1:
a = v[0,0]
if ibrav == 2:
a = b = c = sqrt( 2.0*dot(v[0,:],v[0,:]) )
if ibrav == 3:
a = b = c = 2.0*sqrt( dot(v[0,:],v[0,:])/3.0)
if ibrav == 4:
a = b = sqrt( dot(v[0,:],v[0,:]))
c = sqrt( dot(v[2,:],v[2,:]))
cAB = cosd(120.0)
if ibrav == 5:
a = b = c = sqrt( dot(v[0,:],v[0,:]))
cBC = cAC = cAB = dot(v[0,:],v[2,:])/a**2
if ibrav == 6:
a = b = sqrt( dot(v[0,:],v[0,:]))
c = sqrt( dot(v[2,:],v[2,:]))
if ibrav == 7:
a = b = v[1,0] - v[2,0]
c = v[1,2] + v[2,2]
if ibrav == 8:
a = v[0,0]
b = v[1,1]
c = v[2,2]
if ibrav == 9:
a = v[0,0] - v[1,0]
b = v[0,1] + v[1,1]
c = v[2,2]
if ibrav == 10:
a = v[2,0] - v[0,0] - v[1,0]
b = v[2,1] - v[0,1] + v[1,1]
c = v[0,2] - v[1,2] + v[2,2]
if ibrav == 11:
a = v[0,0] - v[1,0]
b = v[1,1] - v[2,1]
c = v[0,2] - v[2,2]
if ibrav == 12:
a = v[0,0]
b = sqrt( dot(v[1,:],v[1,:]))
cAB = v[1,0]/b
c = v[2,2]
if ibrav == 13:
a = v[0,0] + v[2,0]
b = sqrt( dot(v[1,:],v[1,:]))
c = v[2,2] - v[0,2]
cAB = v[1,0]/b
if ibrav == 14:
a = v[0,0]
b = sqrt( dot(v[1,:],v[1,:]))
cAB = v[1,0]/b
c = sqrt( dot(v[2,:],v[2,:]))
cAC = v[2,0]/c
cBC = v[2,1]*sqrt(1.0 - cAB**2)/c + cAC*cAB
self.setLattice(ibrav, a, b, c, cBC, cAC, cAB)
def setLatticeFromPWInput(self, qeConf = None):
if qeConf == None:
qeConf = self.qeConf
else:
self.qeConf = qeConf
if qeConf == None:
raise NotImplementedError("writeLatticeToPWSCF: qeConf was not properly initialized")
if 'ibrav' in self.qeConf.namelists['system'].params:
ibrav = int(self.qeConf.namelist('system').param('ibrav'))
if ibrav >= 0:
a, b, c, cBC, cAC, cAB, base = self.parsePWInput(ibrav, qeConf)
else:
raise NotImplementedError("ibrav should be integer >= 0")
else:
raise NotImplementedError("config file should have ibrav defined")
self.setLattice(ibrav, a, b, c, cBC, cAC, cAB, base)
def setLatticeFromPWSCF(self, fname):
self.qeConf = QEInput(fname)
self.qeConf.parse()
setLatticeFromPWInput(self, qeConf)
def setLattice(self, ibrav, a = None, b = None, c = None,
cBC = None, cAC = None, cAB = None, base = None):
""" 'base', numpy array of lattice vectors, and 'a' will only be used
if ibrav == 0. Otherwise, ibrav + lattice parameters will be used"""
from math import acos
# if [ibrav, a,b,c,cBC,cAC,cAB, base] == 8*[None]:
# return None
if ibrav == None:
raise NonImplementedError('ibrav should be specified')
self._ibrav = ibrav
self._a0 = a
if self._ibrav == 0:
# print 'Found "generic" cell:'
if base == None:
raise NonImplementedError('base must be specified')
if a == None: a = 1.0
qeBase = numpy.array(base, dtype = float)*a
# print qeBase
self._a = 1.0
self._primitiveLattice.setLatBase(qeBase)
self._standardLattice.setLatBase(qeBase)
else:
# Make sure all lattice parameters are mutually consistent
# according to ibrav. base array is not used:
if ibrav < 4 or ibrav == 5:
if a is not None:
self._a = self._b = self._c = a
else:
if b is not None:
self._a = self._b = self._c = b
else:
if c is not None:
self._a = self._b = self._c = c
else:
self._b = self._c = self._a
if ibrav < 4:
self._cBC = self._cAC = self._cAB = 0.0
if ibrav == 4 or ibrav == 6 or ibrav == 7:
if a is not None:
self._a = self._b = a
else:
if b is not None:
self._a = self._b = b
else:
self._b = self._a
if c is not None:
self._c = c
if ibrav == 4:
self._cAB = cosd(120.0)
self._cBC = self._cAC = 0.0
if ibrav == 5:
if cBC is not None:
self._cBC = self._cAC = self._cAB = cBC
else:
if cAC is not None:
self._cBC = self._cAC = self._cAB = cAC
else:
if cAB is not None:
self._cBC = self._cAC = self._cAB = cAB
else:
self._cAC = self._cAB = self._cBC
if ibrav == 6 or ibrav == 7:
self._cBC = self._cAC = self._cAB = 0.0
if ibrav > 7 and ibrav <= 14:
if a is not None:
self._a = a
if b is not None:
self._b = b
if c is not None:
self._c = c
if ibrav > 7 and ibrav < 12:
self._cBC = self._cAC = self._cAB = 0.0
if ibrav == 12 or ibrav == 13:
if cAB is not None:
self._cAB = cAB
else:
if cBC is not None or cAC is not None:
raise Exception("Should specify cos(AB) only for" + \
" ibrav = 12 or ibrav = 13" )
self._cBC = self._cAC = 0.0
if ibrav == 14:
if cBC is not None:
self._cBC = cBC
if cAC is not None:
self._cAC = cAC
if cAB is not None:
self._cAB = cAB
qeBaseTuple = self._getQEBaseFromParCos(self._ibrav, self._a, self._b,
self._c, self._cBC, self._cAC, self._cAB)
qeBase = numpy.array(qeBaseTuple[1], dtype = float)*qeBaseTuple[0]
self._primitiveLattice.setLatBase(qeBase)
alpha = degrees(acos(self._cBC))
beta = degrees(acos(self._cAC))
gamma = degrees(acos(self._cAB))
self._standardLattice.setLatPar(self._a,self._b,self._c,alpha,beta,gamma)
self._base = qeBase
def toString(self):
st = ''
if self._ibrav == 0:
st = st + '"generic" cell:\n'
else:
qeBaseTuple = self._getQEBaseFromParCos(self._ibrav, self._a, self._b,
self._c, self._cBC, self._cAC, self._cAB)
qeBase = numpy.array(qeBaseTuple[1], dtype = float)*qeBaseTuple[0]
st = st + '"' + qeBaseTuple[2] + '" cell:\n'
for i in range(3):
v = self._primitiveLattice.base[i,:]
st = st + self.formatString%(v[0], v[1], v[2])
st = st + '\n'
return st
def latticeParams(self):
return [self._a, self._b,self._c, self._cBC, self._cAC, self._cAB]
def diffpy(self):
'''Returns diffpy.Lattice object. Do not use it for reading QE
(standard cell) lattice parameters. Use latticeParams, or a, b, c , ...
instead'''
return self._primitiveLattice
def parsePWInput(self, ibrav, qeConf = None):
if qeConf == None:
qeConf = self.qeConf
if qeConf == None:
raise NotImplementedError("writeLatticeToPWSCF: qeConf was not properly initialized")
cBC = 0.0
cAC = 0.0
cAB = 0.0
if 'celldm(1)' in qeConf.namelists['system'].params:
self._type = 'celldm' # celldm(i), i=1,6
a = float(qeConf.namelist('system').param('celldm(1)'))
if ibrav == 0:
# lattice is set in the units of celldm(1)
# need to parse CELL_PARAMETERS
cellParLines = qeConf.card('cell_parameters').lines()
print cellParLines
cellParType = qeConf.card('cell_parameters').arg()
if cellParType == 'cubic' or cellParType == None:
self._type = 'generic cubic'
else:
if cellParType == 'hexagonal':
self._type = 'generic hexagonal'
# convert card into list
base = []
for line in cellParLines:
if '!' not in line:
words = line.split()
base.append([float(w) for w in words])
return a, None, None, None, None, None, numpy.array(base)
if ibrav > 0 and ibrav < 4:
return a, a, a, cBC, cAC, cAB, None
if ibrav == 4:
cAB = cosd(120.0)
if ibrav == 4 or ibrav == 6 or ibrav == 7:
c_a = float(qeConf.namelist('system').param('celldm(3)'))
return a, a, c_a*a, cBC, cAC, cAB, None
if ibrav == 5:
cAB = float(qeConf.namelist('system').param('celldm(4)'))
return a, a, a, cAB, cAB, cAB, None
if ibrav > 7 and ibrav < 12:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
return a, b_a*a, c_a*a, cBC, cAC, cAB, None
if ibrav == 12 or ibrav == 13:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
cAB = float(qeConf.namelist('system').param('celldm(4)'))
return a, b_a*a, c_a*a, cBC, cAC, cAB, None
if ibrav == 14:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
cBC = float(qeConf.namelist('system').param('celldm(4)'))
cAC = float(qeConf.namelist('system').param('celldm(5)'))
cAB = float(qeConf.namelist('system').param('celldm(6)'))
return a, b_a*a, c_a*a, cBC, cAC, cAB, None
else:
if ibrav == 0:
print "Should specify celldm(1) if use 'generic' lattice"
raise NotImplementedError
a = float(qeConf.namelist('system').param('A'))
self._type = 'traditional' # A, B, C, cosAB, cosAC, cosBC
if ibrav > 0 and ibrav < 4:
return a, a, a, cBC, cAC, cAB, None
if ibrav == 4:
cAB = cosd(120.0)
if ibrav == 4 or ibrav == 6 or ibrav == 7:
c = float(qeConf.namelist('system').param('C'))
return a, a, c, cBC, cAC, cAB, None
if ibrav == 5:
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, a, a, cAB, cAB, cAB, None
if ibrav > 7 and ibrav < 12:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
return a, b, c, cBC, cAC, cAB, None
if ibrav == 12 or ibrav == 13:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, b, c, cBC, cAC, cAB, None
if ibrav == 14:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
cBC = float(qeConf.namelist('system').param('cosBC'))
cAC = float(qeConf.namelist('system').param('cosAC'))
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, b, c, cBC, cAC, cAB, None
def getLatticeParamsFromPWSCF(self, ibrav, fname):
qeConf = QEInput(fname)
qeConf.parse()
return self.parsePWInput(ibrav, qeConf)
def updatePWInput(self, qeConf = None):
if qeConf == None:
qeConf = self.qeConf
if qeConf == None:
raise NotImplementedError("writeLatticeToPWSCF: qeConf was not properly initialized")
if 'system' not in qeConf.namelists:
qeConf.createNamelist('system')
# clear geometry from qeConf:
qeConf.namelist('system').remove('a')
qeConf.namelist('system').remove('b')
qeConf.namelist('system').remove('c')
qeConf.namelist('system').remove('cosab')
qeConf.namelist('system').remove('cosbc')
qeConf.namelist('system').remove('cosac')
qeConf.namelist('system').remove('celldm(1)')
qeConf.namelist('system').remove('celldm(2)')
qeConf.namelist('system').remove('celldm(3)')
qeConf.namelist('system').remove('celldm(4)')
qeConf.namelist('system').remove('celldm(5)')
qeConf.namelist('system').remove('celldm(6)')
if 'cell_parameters' in qeConf.cards:
qeConf.removeCard('cell_parameters')
if self._type == 'celldm':
qeConf.namelist('system').add('ibrav', self._ibrav)
qeConf.namelist('system').add('celldm(1)', self._a)
qeConf.namelist('system').add('celldm(2)', self._b/self._a)
qeConf.namelist('system').add('celldm(3)', self._c/self._a)
if self._ibrav < 14:
qeConf.namelist('system').add('celldm(4)', self._cAB)
else:
qeConf.namelist('system').add('celldm(4)', self._cBC)
qeConf.namelist('system').add('celldm(5)', self._cAC)
qeConf.namelist('system').add('celldm(6)', self._cAB)
else:
if self._type == 'traditional':
qeConf.namelist('system').add('ibrav', self._ibrav)
qeConf.namelist('system').add('A', self._a)
qeConf.namelist('system').add('B', self._b)
qeConf.namelist('system').add('C', self._c)
qeConf.namelist('system').add('cosAB', self._cAB)
qeConf.namelist('system').add('cosAC', self._cAC)
qeConf.namelist('system').add('cosBC', self._cBC)
else:
if 'generic' in self._type:
qeConf.namelist('system').add('celldm(1)', 1.0)
self._ibrav = 0
qeConf.namelist('system').add('ibrav', self._ibrav)
if self._type == 'generic hexagonal':
cardArg = 'hexagonal'
if self._type == 'generic cubic' or self._type == None:
cardArg = 'cubic'
qeConf.createCard('cell_parameters')
qeConf.card('cell_parameters').setArgument(cardArg)
qeConf.card('cell_parameters').removeLines()
for i in range(3):
v = self._primitiveLattice.base[i,:]
qeConf.card('cell_parameters').addLine(\
self.formatString%(v[0], v[1], v[2]))
def save(self, fname = None):
"""Will save the lattice either into its own file or into supplied with fname.
It will also create all relevant sections/cards"""
from os.path import exists
if fname != None:
filename = fname
if not exists(filename):
f = open(filename, 'w')
qeConf = QEInput(fname)
qeConf.parse()
else:
qeConf = self.qeConf
filename = qeConf.filename
self.updatePWInput(qeConf)
qeConf.save(filename)
def recipCartesian(self, kPoint):
"""Conversts vector on fractional coordinates in reciprocal space into
a vector in cartesian coordinates"""
recip_base = self.diffpy().reciprocal().base*self._a
return numpy.dot( kPoint, recip_base)
def reciprocalBase(self):
return self.diffpy().reciprocal().base*self._a
def _getQEBaseFromParCos( self, ibrav = 1, a = 1., b = 1., c = 1.,
cBC = 0.,cAC = 0. ,cAB = 0.):
c_a = float(c)/a
# description dictionary of QE base vectors:
QEBase = {
# sc simple cubic:
1 : (a, [[1, 0, 0],
[0, 1, 0],
[0, 0, 1]],
'Simple Cubic'),
# fcc face centered cubic:
2 : (a/2., [[-1, 0, 1],
[0, 1, 1],
[-1, 1, 0]],
'Face Centered Cubic'),
# bcc body entered cubic:
3 : (a/2., [[1, 1, 1],
[-1, 1, 1],
[-1, -1, 1]],
'Body Centered Cubic'),
# simple hexagonal and trigonal(p):
4 : (a, [[1, 0, 0],
[-0.5, sqrt(3.0)/2.0, 0.],
[0, 0, c_a]],
'Simple Hexagonal or Trigonal(P)'),
# trigonal(r):
5 : (a, [[sqrt((1.-cAB)/2.),-sqrt((1.-cAB)/6.), sqrt((1.+2.*cAB)/3.)],
[0, 2.*sqrt((1.-cAB)/6.), sqrt((1.+2.*cAB)/3.)],
[-sqrt((1.-cAB)/2.), -sqrt((1.-cAB)/6.), sqrt((1.+2.*cAB)/3.)]],
'Trigonal(R)'),
# simple tetragonal (p):
6 : (a, [[1, 0, 0],
[0, 1, 0.],
[0, 0, c_a]],
'Simple Tetragonal(P)'),
# body centered tetragonal (i):
7 : (a/2., [[1, -1, c_a],
[1, 1, c_a],
[-1, -1, c_a]],
'Body Centered Tetragonal (I)'),
# simple orthorhombic (p):
8 : (1.0, [[a, 0., 0.],
[0., b, 0.],
[0., 0., c]],
'Simple Orthorhombic (P)'),
# bco base centered orthorhombic:
9: (1.0, [[a/2., b/2., 0.],
[-a/2., b/2., 0.],
[0., 0., c]],
'Base Centered Orthorhombic'),
# face centered orthorhombic:
10: (1.0, [[a/2., 0., c/2.],
[a/2., b/2., 0.],
[0., b/2., c/2.]],
'Face Centered Orthorhombic' ),
# body centered orthorhombic:
11: (1.0, [[a/2., b/2., c/2.],
[-a/2., b/2., c/2.],
[-a/2., -b/2., c/2.]],
'Body Centered Orthorhombic'),
# monoclinic (p):
12: (1.0, [[a, 0, 0],
[b*cAB, b*sqrt(1.0 - cAB**2), 0],
[0, 0, c]],
'Monoclinic (P)'),
# base centered monoclinic:
13: (1.0, [[a/2., 0, -c/2.],
[b*cAB, b*sqrt(1.0 - cAB**2), 0],
[a/2., 0, c/2.]],
'Base Centered Monoclinic'),
# triclinic:
14: (1.0, [[a, 0, 0],
[b*cAB, b*sqrt(1.0 - cAB**2), 0],
[c*cAC, c*( cBC-cAC*cAB )/sqrt(1.-cAB**2), c*sqrt( 1. +
2.*cBC*cAC*cAB - cBC**2 - cAC**2 - cAB**2)/sqrt(1.-cAB**2)]],
'Triclinic')
}
return QEBase[ibrav]
####################################################################
# property handlers
####################################################################
# lattice parameters
def _get_a0(self):
if self._a0 != None:
return self._a0
else:
return self._a
a0 = property(_get_a0, doc ="old lattice parameter a0")
def _get_a(self):
return self._a
def _set_a(self, value):
self._a = value
self.setLattice(ibrav = self._ibrav, a = self._a)
a = property(_get_a, _set_a, doc ="lattice parameter a")
def _get_b(self):
return self._b
def _set_b(self, value):
self._b = value
self.setLattice(ibrav = self._ibrav, b = self._b)
b = property(_get_b, _set_b, doc ="""lattice parameter b""")
def _get_c(self):
return self._c
def _set_c(self, value):
self._c = value
self.setLattice(ibrav = self._ibrav, c = self._c)
c = property(_get_c, _set_c, doc ="""lattice parameter c""")
def _get_cBC(self):
return self._cBC
def _set_cBC(self, value):
self._cBC = value
self.setLattice(ibrav = self._ibrav, cBC = self._cBC)
cBC = property(_get_cBC, _set_cBC, doc ="""lattice parameter cBC""")
def _get_cAC(self):
return self._cAC
def _set_cAC(self, value):
self._cAC = value
self.setLattice(ibrav = self._ibrav, cAC = self._cAC)
cAC = property(_get_cAC, _set_cAC, doc ="""lattice parameter cAC""")
def _get_cAB(self):
return self._cAB
def _set_cAB(self, value):
self._cAB = value
self.setLattice(ibrav = self._ibrav, cAB = self._cAB)
cAB = property(_get_cAB, _set_cAB, doc ="""lattice parameter cAB""")
def _get_ibrav(self):
return self._ibrav
def _set_ibrav(self, value):
if value < 0: value = 0
ibravOld = self._ibrav
self._ibrav = value
if value == 0:
base = self._base/self._a
if ibravOld != 4:
self._type = 'generic cubic'
else:
self._type = 'generic hexagonal'
self.setLattice(ibrav = self._ibrav, a = self._a, base = base)
else:
if 'generic' in self._type:
self._type = 'celldm'
self.setLatticeFromQEVectors(self._ibrav, self.diffpy().base)
# self.setLattice(self._ibrav)
ibrav = property(_get_ibrav, _set_ibrav, doc ="""Lattice symmetry parameter
ibrav""")
def _get_type(self):
return self._type
def _set_type(self, value):
if 'generic' in value:
self._type = value
self._ibrav = 0
base = self._base/self._a
self.setLattice(ibrav = self._ibrav, a = self._a, base = base)
else:
if self._ibrav == 0:
pass
else:
self._type = value
type = property(_get_type, _set_type, doc ="""QE lattice type: 'celldm',
'traditional' or 'generic cubic', 'generic hexagonal'(implies ibrav = 0""")
def setLatticeFromPWSCF(self, fname):
self.qeConf = QEInput(fname)
self.qeConf.parse()
setLatticeFromPWInput(self, qeConf)
def test_qeinput_parse(self):
input = QEInput(config=fixtures.textMain, parse=False)
self.assertEqual(input.toString(), "")
input = QEInput(config=fixtures.textMain, parse=True)
self.assertEqual(input.namelistExists("control"), True)
class QELattice(object):
"""Class QELattice for working with crystal lattices in QE notation
Uses diffpy.Lattice class for storage
Following parameters are dynamically linked to other properties
(E.g. lattice vectors):
ibrav - lattice type
if ibrav = 0, only 'a' prameter is relevant
a, b, c, cBC, cAC ,cAB - lattice parameters
type - lattice type to save into PWSCF cfg file ('celldm');
'traditional' - using a,b,c,cosAC, cosAB, cosBC;
'generic cubic', 'generic hexagonal' - assume exiasting
section 'CELL_PARAMETERS', 'generic' types also
assume/set ibrav = 0
setLattice() will set everything at once
"""
def __init__(self,
ibrav=1,
a=1.,
b=1.,
c=1.,
cBC=0.,
cAC=0.,
cAB=0.,
qeConf=None,
base=None):
# Lattice.__init__(self)
self.formatString = '%# .8f %# .8f %# .8f'
self.qeConf = qeConf
self._type = 'celldm'
self._primitiveLattice = Lattice()
self._standardLattice = Lattice()
self._base = None
self._a0 = None
if self.qeConf != None:
self.setLatticeFromPWInput(self.qeConf)
else:
if ibrav > 0 and base != None:
self.setLatticeFromQEVectors(ibrav, base)
else:
self.setLattice(ibrav, a, b, c, cBC, cAC, cAB, base)
# def _setDefaults(self):
# self.formatString = '%# .8f %# .8f %# .8f'
# self._type = 'celldm'
# self._primitiveLattice = Lattice()
# self._standardLattice = Lattice()
# self._base = None
# self._a0 = None
# self.setLattice(1. ,a ,b , c, cBC ,cAC ,cAB, base)
def setLatticeFromQEVectors(self, ibrav, vectors):
""" Will extract conventional lattice parameters from primitive vectors.
'vectors' - is a list with primitive vectors (in QE notation),
including lattice parameters. For example from PWSCF output"""
from numpy import dot
# default values:
a = b = c = 1.0
cBC = cAC = cAB = 0.0
v = numpy.array(vectors, dtype=float)
if ibrav == 0:
raise NotImplementedError
# sc simple cubic:
if ibrav == 1:
a = v[0, 0]
if ibrav == 2:
a = b = c = sqrt(2.0 * dot(v[0, :], v[0, :]))
if ibrav == 3:
a = b = c = 2.0 * sqrt(dot(v[0, :], v[0, :]) / 3.0)
if ibrav == 4:
a = b = sqrt(dot(v[0, :], v[0, :]))
c = sqrt(dot(v[2, :], v[2, :]))
cAB = cosd(120.0)
if ibrav == 5:
a = b = c = sqrt(dot(v[0, :], v[0, :]))
cBC = cAC = cAB = dot(v[0, :], v[2, :]) / a**2
if ibrav == 6:
a = b = sqrt(dot(v[0, :], v[0, :]))
c = sqrt(dot(v[2, :], v[2, :]))
if ibrav == 7:
a = b = v[1, 0] - v[2, 0]
c = v[1, 2] + v[2, 2]
if ibrav == 8:
a = v[0, 0]
b = v[1, 1]
c = v[2, 2]
if ibrav == 9:
a = v[0, 0] - v[1, 0]
b = v[0, 1] + v[1, 1]
c = v[2, 2]
if ibrav == 10:
a = v[2, 0] - v[0, 0] - v[1, 0]
b = v[2, 1] - v[0, 1] + v[1, 1]
c = v[0, 2] - v[1, 2] + v[2, 2]
if ibrav == 11:
a = v[0, 0] - v[1, 0]
b = v[1, 1] - v[2, 1]
c = v[0, 2] - v[2, 2]
if ibrav == 12:
a = v[0, 0]
b = sqrt(dot(v[1, :], v[1, :]))
cAB = v[1, 0] / b
c = v[2, 2]
if ibrav == 13:
a = v[0, 0] + v[2, 0]
b = sqrt(dot(v[1, :], v[1, :]))
c = v[2, 2] - v[0, 2]
cAB = v[1, 0] / b
if ibrav == 14:
a = v[0, 0]
b = sqrt(dot(v[1, :], v[1, :]))
cAB = v[1, 0] / b
c = sqrt(dot(v[2, :], v[2, :]))
cAC = v[2, 0] / c
cBC = v[2, 1] * sqrt(1.0 - cAB**2) / c + cAC * cAB
self.setLattice(ibrav, a, b, c, cBC, cAC, cAB)
def setLatticeFromPWInput(self, qeConf=None):
if qeConf == None:
qeConf = self.qeConf
else:
self.qeConf = qeConf
if qeConf == None:
raise NotImplementedError(
"writeLatticeToPWSCF: qeConf was not properly initialized")
#self.setLattice(ibrav = 1,a = 1,b = 1,c = 1, cBC = 0,cAC = 0 ,cAB = 0)
#if 'system' not in self.qeConf.namelists:
# if 'cell_parameters' not in self.qeConf.cards:
# return
# else:
#jr self.ibrav = 0
if 'ibrav' in self.qeConf.namelists['system'].params:
ibrav = int(self.qeConf.namelist('system').param('ibrav'))
if ibrav >= 0:
a, b, c, cBC, cAC, cAB, base = self.parsePWInput(ibrav, qeConf)
else:
raise NotImplementedError("ibrav should be integer >= 0")
else:
raise NotImplementedError("config file should have ibrav defined")
self.setLattice(ibrav, a, b, c, cBC, cAC, cAB, base)
def setLatticeFromPWSCF(self, fname):
self.qeConf = QEInput(fname)
self.qeConf.parse()
setLatticeFromPWInput(self, qeConf)
def setLattice(self,
ibrav,
a=None,
b=None,
c=None,
cBC=None,
cAC=None,
cAB=None,
base=None):
""" 'base', numpy array of lattice vectors, and 'a' will only be used
if ibrav == 0. Otherwise, ibrav + lattice parameters will be used"""
from math import acos
# if [ibrav, a,b,c,cBC,cAC,cAB, base] == 8*[None]:
# return None
if ibrav == None:
raise NonImplementedError('ibrav should be specified')
self._ibrav = ibrav
self._a0 = a
if self._ibrav == 0:
# print 'Found "generic" cell:'
if base == None:
raise NonImplementedError('base must be specified')
if a == None: a = 1.0
qeBase = numpy.array(base, dtype=float) * a
# print qeBase
self._a = 1.0
if 'generic' not in self._type:
self._type = 'generic cubic'
self._primitiveLattice.setLatBase(qeBase)
self._standardLattice.setLatBase(qeBase)
else:
# Make sure all lattice parameters are mutually consistent
# according to ibrav. base array is not used:
if ibrav < 4 or ibrav == 5:
if a is not None:
self._a = self._b = self._c = a
else:
if b is not None:
self._a = self._b = self._c = b
else:
if c is not None:
self._a = self._b = self._c = c
else:
self._b = self._c = self._a
if ibrav < 4:
self._cBC = self._cAC = self._cAB = 0.0
if ibrav == 4 or ibrav == 6 or ibrav == 7:
if a is not None:
self._a = self._b = a
else:
if b is not None:
self._a = self._b = b
else:
self._b = self._a
if c is not None:
self._c = c
if ibrav == 4:
self._cAB = cosd(120.0)
self._cBC = self._cAC = 0.0
if ibrav == 5:
if cBC is not None:
self._cBC = self._cAC = self._cAB = cBC
else:
if cAC is not None:
self._cBC = self._cAC = self._cAB = cAC
else:
if cAB is not None:
self._cBC = self._cAC = self._cAB = cAB
else:
self._cAC = self._cAB = self._cBC
if ibrav == 6 or ibrav == 7:
self._cBC = self._cAC = self._cAB = 0.0
if ibrav > 7 and ibrav <= 14:
if a is not None:
self._a = a
if b is not None:
self._b = b
if c is not None:
self._c = c
if ibrav > 7 and ibrav < 12:
self._cBC = self._cAC = self._cAB = 0.0
if ibrav == 12 or ibrav == 13:
if cAB is not None:
self._cAB = cAB
else:
if cBC is not None or cAC is not None:
raise Exception("Should specify cos(AB) only for" + \
" ibrav = 12 or ibrav = 13" )
self._cBC = self._cAC = 0.0
if ibrav == 14:
if cBC is not None:
self._cBC = cBC
if cAC is not None:
self._cAC = cAC
if cAB is not None:
self._cAB = cAB
qeBaseTuple = self._getQEBaseFromParCos(self._ibrav, self._a,
self._b, self._c,
self._cBC, self._cAC,
self._cAB)
qeBase = numpy.array(qeBaseTuple[1], dtype=float) * qeBaseTuple[0]
self._primitiveLattice.setLatBase(qeBase)
alpha = degrees(acos(self._cBC))
beta = degrees(acos(self._cAC))
gamma = degrees(acos(self._cAB))
self._standardLattice.setLatPar(self._a, self._b, self._c, alpha,
beta, gamma)
self._base = qeBase
# def toString(self):
# st = ''
# if self._ibrav == 0:
# st = st + '"generic" cell:\n'
# else:
# qeBaseTuple = self._getQEBaseFromParCos(self._ibrav, self._a, self._b,
# self._c, self._cBC, self._cAC, self._cAB)
# qeBase = numpy.array(qeBaseTuple[1], dtype = float)*qeBaseTuple[0]
# st = st + '"' + qeBaseTuple[2] + '" cell:\n'
# for i in range(3):
# v = self._primitiveLattice.base[i,:]
# st = st + self.formatString%(v[0], v[1], v[2])
# st = st + '\n'
# return st
def toString(self, string=None):
if string != None:
qeConf = QEInput(config=string)
qeConf.parse()
else:
if self.qeConf != None:
qeConf = self.qeConf
else:
qeConf = QEInput(config='')
self.updatePWInput(qeConf)
return qeConf.toString()
def latticeParams(self):
return [self._a, self._b, self._c, self._cBC, self._cAC, self._cAB]
def diffpy(self):
'''Returns diffpy.Lattice object. Do not use it for reading QE
(standard cell) lattice parameters. Use latticeParams, or a, b, c , ...
instead'''
return self._primitiveLattice
def parsePWInput(self, ibrav, qeConf=None):
if qeConf == None:
qeConf = self.qeConf
if qeConf == None:
raise NotImplementedError(
"writeLatticeToPWSCF: qeConf was not properly initialized")
cBC = 0.0
cAC = 0.0
cAB = 0.0
# reset Lattice:
#self.setLattice(1. ,1 , 1, cBC ,cAC ,cAB)
if 'celldm(1)' in qeConf.namelists['system'].params:
self._type = 'celldm' # celldm(i), i=1,6
a = float(qeConf.namelist('system').param('celldm(1)'))
if ibrav == 0:
# lattice is set in the units of celldm(1)
# need to parse CELL_PARAMETERS
#if 'cell_parameters' not in qeConf.cards:
# return #qeConf.createCard('cell_parameters')
cellParLines = qeConf.card('cell_parameters').lines()
#print cellParLines
cellParType = qeConf.card('cell_parameters').arg()
if cellParType == 'cubic' or cellParType == None:
self._type = 'generic cubic'
else:
if cellParType == 'hexagonal':
self._type = 'generic hexagonal'
# convert card into list
base = []
for line in cellParLines:
if '!' not in line:
words = line.split()
base.append([float(w) for w in words])
return a, None, None, None, None, None, numpy.array(base)
if ibrav > 0 and ibrav < 4:
return a, a, a, cBC, cAC, cAB, None
if ibrav == 4:
cAB = cosd(120.0)
if ibrav == 4 or ibrav == 6 or ibrav == 7:
c_a = float(qeConf.namelist('system').param('celldm(3)'))
return a, a, c_a * a, cBC, cAC, cAB, None
if ibrav == 5:
cAB = float(qeConf.namelist('system').param('celldm(4)'))
return a, a, a, cAB, cAB, cAB, None
if ibrav > 7 and ibrav < 12:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
return a, b_a * a, c_a * a, cBC, cAC, cAB, None
if ibrav == 12 or ibrav == 13:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
cAB = float(qeConf.namelist('system').param('celldm(4)'))
return a, b_a * a, c_a * a, cBC, cAC, cAB, None
if ibrav == 14:
b_a = float(qeConf.namelist('system').param('celldm(2)'))
c_a = float(qeConf.namelist('system').param('celldm(3)'))
cBC = float(qeConf.namelist('system').param('celldm(4)'))
cAC = float(qeConf.namelist('system').param('celldm(5)'))
cAB = float(qeConf.namelist('system').param('celldm(6)'))
return a, b_a * a, c_a * a, cBC, cAC, cAB, None
else:
if ibrav == 0:
print "Should specify celldm(1) if use 'generic' lattice"
raise NotImplementedError
a = float(qeConf.namelist('system').param('A'))
self._type = 'traditional' # A, B, C, cosAB, cosAC, cosBC
if ibrav > 0 and ibrav < 4:
return a, a, a, cBC, cAC, cAB, None
if ibrav == 4:
cAB = cosd(120.0)
if ibrav == 4 or ibrav == 6 or ibrav == 7:
c = float(qeConf.namelist('system').param('C'))
return a, a, c, cBC, cAC, cAB, None
if ibrav == 5:
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, a, a, cAB, cAB, cAB, None
if ibrav > 7 and ibrav < 12:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
return a, b, c, cBC, cAC, cAB, None
if ibrav == 12 or ibrav == 13:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, b, c, cBC, cAC, cAB, None
if ibrav == 14:
b = float(qeConf.namelist('system').param('B'))
c = float(qeConf.namelist('system').param('C'))
cBC = float(qeConf.namelist('system').param('cosBC'))
cAC = float(qeConf.namelist('system').param('cosAC'))
cAB = float(qeConf.namelist('system').param('cosAB'))
return a, b, c, cBC, cAC, cAB, None
def getLatticeParamsFromPWSCF(self, ibrav, fname):
qeConf = QEInput(fname)
qeConf.parse()
return self.parsePWInput(ibrav, qeConf)
def updatePWInput(self, qeConf=None):
if qeConf == None:
qeConf = self.qeConf
if qeConf == None:
raise NotImplementedError(
"writeLatticeToPWSCF: qeConf was not properly initialized")
if 'system' not in qeConf.namelists:
qeConf.createNamelist('system')
# clear geometry from qeConf:
qeConf.namelist('system').remove('a')
qeConf.namelist('system').remove('b')
qeConf.namelist('system').remove('c')
qeConf.namelist('system').remove('cosab')
qeConf.namelist('system').remove('cosbc')
qeConf.namelist('system').remove('cosac')
qeConf.namelist('system').remove('celldm(1)')
qeConf.namelist('system').remove('celldm(2)')
qeConf.namelist('system').remove('celldm(3)')
qeConf.namelist('system').remove('celldm(4)')
qeConf.namelist('system').remove('celldm(5)')
qeConf.namelist('system').remove('celldm(6)')
if 'cell_parameters' in qeConf.cards:
qeConf.removeCard('cell_parameters')
if self._type == 'celldm':
qeConf.namelist('system').add('ibrav', self._ibrav)
qeConf.namelist('system').add('celldm(1)', self._a)
qeConf.namelist('system').add('celldm(2)', self._b / self._a)
qeConf.namelist('system').add('celldm(3)', self._c / self._a)
if self._ibrav < 14:
qeConf.namelist('system').add('celldm(4)', self._cAB)
else:
qeConf.namelist('system').add('celldm(4)', self._cBC)
qeConf.namelist('system').add('celldm(5)', self._cAC)
qeConf.namelist('system').add('celldm(6)', self._cAB)
else:
if self._type == 'traditional':
qeConf.namelist('system').add('ibrav', self._ibrav)
qeConf.namelist('system').add('A', self._a)
qeConf.namelist('system').add('B', self._b)
qeConf.namelist('system').add('C', self._c)
qeConf.namelist('system').add('cosAB', self._cAB)
qeConf.namelist('system').add('cosAC', self._cAC)
qeConf.namelist('system').add('cosBC', self._cBC)
else:
if 'generic' in self._type:
qeConf.namelist('system').add('celldm(1)', 1.0)
self._ibrav = 0
qeConf.namelist('system').add('ibrav', self._ibrav)
if self._type == 'generic hexagonal':
cardArg = 'hexagonal'
if self._type == 'generic cubic' or self._type == None:
cardArg = 'cubic'
qeConf.createCard('cell_parameters')
qeConf.card('cell_parameters').setArg(cardArg)
qeConf.card('cell_parameters').removeLines()
for i in range(3):
v = self._primitiveLattice.base[i, :]
qeConf.card('cell_parameters').addLine(\
self.formatString%(v[0], v[1], v[2]))
def save(self, fname=None):
"""Will save the lattice either into its own file or into supplied with fname.
It will also create all relevant sections/cards"""
from os.path import exists
filename = fname
if fname != None:
if not exists(filename):
f = open(filename, 'w')
qeConf = QEInput(fname)
qeConf.parse()
else:
qeConf = self.qeConf
filename = qeConf.filename
self.updatePWInput(qeConf)
qeConf.save(filename)
def recipCartesian(self, kPoint):
"""Conversts vector on fractional coordinates in reciprocal space into
a vector in cartesian coordinates"""
recip_base = self.diffpy().reciprocal().base * self._a
return numpy.dot(kPoint, recip_base)
def reciprocalBase(self):
"""
Get reciprocal lattice vectors in units of 2*pi/a
"""
return self.diffpy().reciprocal().base * self._a
def _getQEBaseFromParCos(self,
ibrav=1,
a=1.,
b=1.,
c=1.,
cBC=0.,
cAC=0.,
cAB=0.):
c_a = float(c) / a
# description dictionary of QE base vectors:
QEBase = {
# sc simple cubic:
1: (a, [[1, 0, 0], [0, 1, 0], [0, 0, 1]], 'Simple Cubic'),
# fcc face centered cubic:
2: (a / 2., [[-1, 0, 1], [0, 1, 1], [-1, 1,
0]], 'Face Centered Cubic'),
# bcc body entered cubic:
3: (a / 2., [[1, 1, 1], [-1, 1, 1], [-1, -1,
1]], 'Body Centered Cubic'),
# simple hexagonal and trigonal(p):
4: (a, [[1, 0, 0], [-0.5, sqrt(3.0) / 2.0, 0.],
[0, 0, c_a]], 'Simple Hexagonal or Trigonal(P)'),
# trigonal(r):
5: (a, [[
sqrt((1. - cAB) / 2.), -sqrt((1. - cAB) / 6.),
sqrt((1. + 2. * cAB) / 3.)
], [0, 2. * sqrt((1. - cAB) / 6.),
sqrt((1. + 2. * cAB) / 3.)],
[
-sqrt((1. - cAB) / 2.), -sqrt((1. - cAB) / 6.),
sqrt((1. + 2. * cAB) / 3.)
]], 'Trigonal(R)'),
# simple tetragonal (p):
6: (a, [[1, 0, 0], [0, 1, 0.], [0, 0,
c_a]], 'Simple Tetragonal(P)'),
# body centered tetragonal (i):
7: (a / 2., [[1, -1, c_a], [1, 1, c_a],
[-1, -1, c_a]], 'Body Centered Tetragonal (I)'),
# simple orthorhombic (p):
8: (1.0, [[a, 0., 0.], [0., b, 0.],
[0., 0., c]], 'Simple Orthorhombic (P)'),
# bco base centered orthorhombic:
9: (1.0, [[a / 2., b / 2., 0.], [-a / 2., b / 2., 0.],
[0., 0., c]], 'Base Centered Orthorhombic'),
# face centered orthorhombic:
10: (1.0, [[a / 2., 0., c / 2.], [a / 2., b / 2., 0.],
[0., b / 2., c / 2.]], 'Face Centered Orthorhombic'),
# body centered orthorhombic:
11: (1.0, [[a / 2., b / 2., c / 2.], [-a / 2., b / 2., c / 2.],
[-a / 2., -b / 2.,
c / 2.]], 'Body Centered Orthorhombic'),
# monoclinic (p):
12: (1.0, [[a, 0, 0], [b * cAB, b * sqrt(1.0 - cAB**2), 0],
[0, 0, c]], 'Monoclinic (P)'),
# base centered monoclinic:
13: (1.0, [[a / 2., 0, -c / 2.],
[b * cAB, b * sqrt(1.0 - cAB**2), 0],
[a / 2., 0, c / 2.]], 'Base Centered Monoclinic'),
# triclinic:
14:
(1.0,
[[a, 0, 0], [b * cAB, b * sqrt(1.0 - cAB**2), 0],
[
c * cAC,
c * (cBC - cAC * cAB) / sqrt(1. - cAB**2), c *
sqrt(1. + 2. * cBC * cAC * cAB - cBC**2 - cAC**2 - cAB**2) /
sqrt(1. - cAB**2)
]], 'Triclinic')
}
return QEBase[ibrav]
####################################################################
# property handlers
####################################################################
# lattice parameters
def _get_a0(self):
if self._a0 != None:
return self._a0
else:
return self._a
a0 = property(_get_a0, doc="old lattice parameter a0")
def _get_a(self):
return self._a
def _set_a(self, value):
self._a = value
self.setLattice(ibrav=self._ibrav, a=self._a)
a = property(_get_a, _set_a, doc="lattice parameter a")
def _get_b(self):
return self._b
def _set_b(self, value):
self._b = value
self.setLattice(ibrav=self._ibrav, b=self._b)
b = property(_get_b, _set_b, doc="""lattice parameter b""")
def _get_c(self):
return self._c
def _set_c(self, value):
self._c = value
self.setLattice(ibrav=self._ibrav, c=self._c)
c = property(_get_c, _set_c, doc="""lattice parameter c""")
def _get_cBC(self):
return self._cBC
def _set_cBC(self, value):
self._cBC = value
self.setLattice(ibrav=self._ibrav, cBC=self._cBC)
cBC = property(_get_cBC, _set_cBC, doc="""lattice parameter cBC""")
def _get_cAC(self):
return self._cAC
def _set_cAC(self, value):
self._cAC = value
self.setLattice(ibrav=self._ibrav, cAC=self._cAC)
cAC = property(_get_cAC, _set_cAC, doc="""lattice parameter cAC""")
def _get_cAB(self):
return self._cAB
def _set_cAB(self, value):
self._cAB = value
self.setLattice(ibrav=self._ibrav, cAB=self._cAB)
cAB = property(_get_cAB, _set_cAB, doc="""lattice parameter cAB""")
def _get_ibrav(self):
return self._ibrav
def _set_ibrav(self, value):
if value < 0: value = 0
ibravOld = self._ibrav
self._ibrav = value
if value == 0:
base = self._base / self._a
if ibravOld != 4:
self._type = 'generic cubic'
else:
self._type = 'generic hexagonal'
self.setLattice(ibrav=self._ibrav, a=self._a, base=base)
else:
if 'generic' in self._type:
self._type = 'celldm'
self.setLatticeFromQEVectors(self._ibrav, self.diffpy().base)
# self.setLattice(self._ibrav)
ibrav = property(_get_ibrav,
_set_ibrav,
doc="""Lattice symmetry parameter
ibrav""")
def _get_type(self):
return self._type
def _set_type(self, value):
if 'generic' in value:
self._type = value
self._ibrav = 0
base = self._base / self._a
self.setLattice(ibrav=self._ibrav, a=self._a, base=base)
else:
if self._ibrav == 0:
pass
else:
self._type = value
type = property(_get_type,
_set_type,
doc="""QE lattice type: 'celldm',
'traditional' or 'generic cubic', 'generic hexagonal'(implies ibrav = 0""")
def test_qeinput_type(self):
input = QEInput(type="ph")
self.assertEqual(input.type(), "ph")
self._type = value
self._ibrav = 0
base = self._base/self._a
self.setLattice(ibrav = self._ibrav, a = self._a, base = base)
else:
if self._ibrav == 0:
pass
else:
self._type = value
type = property(_get_type, _set_type, doc ="""QE lattice type: 'celldm',
'traditional' or 'generic cubic', 'generic hexagonal'(implies ibrav = 0""")
if __name__ == '__main__':
pwInput = QEInput('scf.in', type = 'pw')
pwInput.parse()
qeLattice = QELattice(qeConf = pwInput)
print qeLattice.latticeParams()
# qeLattice = QELattice(fname = 'qwe.in')
# qeLattice.setLatticeFromPrimitiveVectors(12,qeLattice.lattice().base)
# print qeLattice.latticeParams()
# qeLattice.latticeType = 'generic hexagonal'
# qeLattice.bb = 12
qeLattice.a = 13.0
qeLattice.b = 24.0
qeLattice.c = 3.
qeLattice.ibrav = 4
print qeLattice.b, qeLattice.c,
print qeLattice.latticeParams()
qeLattice.saveLatticeToPWSCF('./scf_2.in')
def test_qeinput_attach(self):
"This unit test is useful for matdyn simulation type"
input = QEInput()
input.addAttach("176\n\
0.000000 0.000000 0.456392 0.000000")
self.assertEqual(input.toString(), fixtures.assertAttach)
def getLatticeParamsFromPWSCF(self, ibrav, fname):
qeConf = QEInput(fname)
qeConf.parse()
return self.parsePWInput(ibrav, qeConf)
def __init__(self, filename=None, config=None):
QEInput.__init__(self,filename, config, type='ph')
self.qpoints = PHQpoints(self)
def __init__(self, filename=None, config=None):
QEInput.__init__(self, filename, config, type='matdyn')
self.qpoints = MatdynQpoints(self)
def __init__(self, filename=None, config=None):
QEInput.__init__(self, filename, config, type='pw')
self.structure = QEStructure(self)
self.kpoints = PWKpoints(self)
def test_qeinput_parse(self):
input = QEInput(config=fixtures.textMain, parse=False)
self.assertEqual(input.toString(), "")
input = QEInput(config=fixtures.textMain, parse=True)
self.assertEqual(input.namelistExists("control"), True)
