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 doc2diffpy(doc):
""" Convert doc into diffpy Structure object. """
from numpy import asarray
from diffpy.Structure.atom import Atom
from diffpy.Structure.lattice import Lattice
from diffpy.Structure.structure import Structure
lattice = Lattice(a=doc['lattice_abc'][0][0],
b=doc['lattice_abc'][0][1],
c=doc['lattice_abc'][0][2],
alpha=doc['lattice_abc'][1][0],
beta=doc['lattice_abc'][1][1],
gamma=doc['lattice_abc'][1][2])
atoms = []
for ind, atom in enumerate(doc['atom_types']):
# encode atype as utf-8 or you will waste hours of your life
atoms.append(
Atom(atype=atom.encode('utf-8'),
xyz=asarray(doc['positions_frac'][ind])))
title = None
for sources in doc['source']:
if sources.endswith('.res') or sources.endswith('.castep'):
title = sources.split('/')[-1].split('.')[0].encode('utf-8')
return Structure(atoms, lattice, title=title)
def __init__(self, ibrav = 1,a = 1. ,b = 1.,c = 1.,
cBC = 0.,cAC = 0. ,cAB = 0., base = None, lattice = None ):
self.formatString = '%# .8f %# .8f %# .8f'
self._qeInput = None
#self._qeInput = None
self._type = 'celldm'
# diffpyStructure container class, used for lattice operations
self.__primitiveLattice = Lattice()
# Lattice vectors in bohr or angstrom:
self._base = None
# initialize the lattice if there is enough information
if ibrav > 0 and base != None:
self.setLatticeFromQEVectors(ibrav, base)
else:
self.setLattice(ibrav ,a ,b , c, cBC ,cAC ,cAB, base)
# copy constructor:
if isinstance(ibrav, QELattice) or lattice != None:
if lattice.ibrav > 0:
self.setLattice( ibrav = lattice.ibrav, a = lattice.a, \
b = lattice.b, c = lattice.c,
cBC = lattice.cBC, cAC = lattice.cAC,\
cAB = lattice.cAB)
else:
self.setLattice( ibrav = lattice.ibrav, a = lattice.a, \
base = lattice.base )
# copy input:
from pwinput import PWInput
self._qeInput = PWInput()
self._qeInput.readString( lattice._qeInput.toString() )
def __init__(self, ibrav = 1,a = 1. ,b = 1.,c = 1.,
cBC = 0.,cAC = 0. ,cAB = 0., fname = None, base = None ):
# Lattice.__init__(self)
self.filename = fname
self._type = 'celldm'
self.qeConf = None # should be none if nothing to parse
self._primitiveLattice = Lattice()
self._standardLattice = Lattice()
self._base = None
self._a0 = None
if self.filename != None:
self.setLatticeFromPWSCF(self.filename)
else:
if ibrav > 0 and base != None:
self.setLatticeFromQEVectors(ibrav, base)
else:
self.setLattice(ibrav ,a ,b , c, cBC ,cAC ,cAB, base)
def _matter_diffpy(self, structure):
"""
converts matter Structure object to diffpy.Structure
returns diffpy.Structure object
"""
l = structure.lattice
lat = Lattice( a=l.a, b=l.b, c=l.c, alpha=l.alpha, \
beta=l.beta, gamma=l.gamma)
stru = Structure(lattice=lat)
for a in structure:
stru.addNewAtom(atype = a.symbol, xyz = a.xyz, name = a.symbol, \
anisotropy=a.anisotropy, U=a.U, Uisoequiv=a.Uisoequiv, \
lattice=lat)
return stru
def __init__(self,
atoms=[],
lattice=None,
title=None,
filename=None,
format=None):
"""define group of atoms in a specified lattice.
atoms -- list of Atom instances to be included in this Structure.
When atoms argument is an existing Structure instance,
the new Structure is its copy.
lattice -- instance of Lattice defining coordinate systems, property.
title -- string description of the structure
filename -- optional, name of a file to load the structure from.
Overrides atoms argument when specified.
format -- optional structure format of the loaded filename. By default
all structure formats are tried one by one. Ignored when
filename has not been specified.
Structure(stru) create a copy of Structure instance stru.
Because Structure is inherited from a list it can use list expansions,
for example:
oxygen_atoms = [ for a in stru if a.element == "O" ]
oxygen_stru = Structure(oxygen_atoms, lattice=stru.lattice)
"""
# if filename is specified load it and return
if filename is not None:
if any((atoms, lattice, title)):
emsg = "Cannot use filename and atoms arguments together."
raise ValueError(emsg)
readkwargs = (format is not None) and {'format': format} or {}
self.read(filename, **readkwargs)
return
# copy initialization, must be first to allow lattice, title override
if isinstance(atoms, Structure):
Structure.__copy__(atoms, self)
# assign arguments:
if title is not None:
self.title = title
if lattice is not None:
self.lattice = lattice
elif self.lattice is None:
self.lattice = Lattice()
# insert atoms unless already done by __copy__
if not len(self) and len(atoms):
self.extend(atoms)
return
def test_xyz_cartn(self):
"""check Atom.xyz_cartn property
"""
hexagonal = Lattice(1, 1, 1, 90, 90, 120)
a0 = Atom('C', [0, 0, 0], lattice=hexagonal)
a1 = Atom('C', [1, 1, 1], lattice=hexagonal)
self.assertTrue(all(a0.xyz_cartn == 0))
rc1 = numpy.array([0.75**0.5, 0.5, 1])
self.assertTrue(numpy.allclose(rc1, a1.xyz_cartn))
a1.xyz_cartn[2] = 0
self.assertTrue(numpy.allclose([1, 1, 0], a1.xyz))
a1.xyz_cartn[:2] = 0
self.assertTrue(all(a1.xyz == 0))
a3 = Atom('C', [1, 2, 3])
self.assertTrue(numpy.array_equal(a3.xyz, a3.xyz_cartn))
a3.xyz_cartn = 1.3
self.assertTrue(all(1.3 == a3.xyz_cartn))
self.assertTrue(all(1.3 == a3.xyz))
return
def __copy__(self, target=None):
'''Create a deep copy of this instance.
target -- optional target instance for copying, useful for
copying a derived class. Defaults to new instance
of the same type as self.
Return a duplicate instance of this object.
'''
if target is None:
target = Structure()
elif target is self:
return target
# copy attributes as appropriate:
target.title = self.title
target.lattice = Lattice(self.lattice)
target.pdffit = copy.deepcopy(self.pdffit)
# copy all atoms to the target
target[:] = self
return target
def _setReducedStructureFromDiffpyStructure(self,
structure,
ibrav,
massList=[],
psList=[]):
"""
structure - diffpy.Structure object
ibrav - Lattice index
psList - list of strings with potential names
diffpyStructure object will be modified with reduced atomic positions
"""
import copy
diffpyLattice = copy.deepcopy(structure.lattice)
a = diffpyLattice.a
b = diffpyLattice.b
c = diffpyLattice.c
cAB = cosd(diffpyLattice.gamma)
cBC = cosd(diffpyLattice.alpha)
cAC = cosd(diffpyLattice.beta)
qeLattice = QELattice(ibrav = ibrav, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
qeLattice._qeInput = self._qeInput
self.lattice = qeLattice
# make a deep copy:
reducedStructure = Structure(atoms=structure)
reducedStructure.placeInLattice(Lattice(base=qeLattice.diffpy().base))
# collect atoms that are at equivalent position to some previous atom
duplicates = set([
a1 for i0, a0 in enumerate(reducedStructure)
for a1 in reducedStructure[i0 + 1:]
if self._element(a0) == self._element(a1)
and equalPositions(a0.xyz, a1.xyz, eps=1e-4)
])
# Filter out duplicate atoms. Use slice assignment so that
# reducedStructure is not replaced with a list.
reducedStructure[:] = [
a for a in reducedStructure if not a in duplicates
]
atomNames = []
for a in reducedStructure:
if self._element(a) not in atomNames:
atomNames.append(self._element(a))
atomicSpecies = {}
for i, elem in enumerate(atomNames):
if len(massList) - 1 < i:
mass = 0
else:
mass = massList[i]
if len(psList) - 1 < i:
ps = ''
else:
ps = psList[i]
atomicSpecies[elem] = (mass, ps)
self[:] = []
# convert to bohr units
self.lattice.setLattice(ibrav, self.lattice.a*1.889725989, \
self.lattice.b*1.889725989,
self.lattice.c*1.889725989)
for atom in reducedStructure:
elem = self._element(atom)
self.addNewAtom(atype = elem, xyz = atom.xyz, \
mass = atomicSpecies[elem][0], \
potential = atomicSpecies[elem][1],\
lattice = self.lattice, optConstraint = [])
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)
#!/usr/bin/env python
import math
import numpy
# To change this template, choose Tools | Templates
# and open the template in the editor.
from diffpy.Structure.structure import Structure
from diffpy.Structure.lattice import Lattice
myAtoms = ['Mg', 'B', 'B']
myLattice = Lattice()
theta = -30. * math.pi / 180.
rotMatrix = [[math.cos(theta), -math.sin(theta), 0],
[math.sin(theta), math.cos(theta), 0], [0, 0, 1]]
#myLattice.setLatPar(1., 1, 1.,gamma=120.0)#,baserot = rotMatrix)
print myLattice.base
a = 5.2
c = 6.3
base = [[1, 0, 0], [-1. / 2., math.sqrt(3.) / 2., 0.], [0, 0, c / a]]
myLattice.setLatBase(base)
print myLattice.base
print "baserot:"
print myLattice.baserot
myLattice.setLatPar(5.2, 5.2, 6.3, gamma=120.0, baserot=myLattice.baserot)
print myLattice.base
#myLattice.setLatBase(numpy.array(base)*a)
#print myLattice
#print myLattice.abcABG()
def setReducedStructureFromDiffpyStructure(self, structure, ibrav, massList = [], psList = []):
"""
structure - diffpy.Structure object
ibrav - Lattice index
psList - list of strings with pseudopotential names
diffpyStructure object will be modified with reduced atomic positions
"""
#self.atomicSpecies = OrderedDict()
#self.optConstraints = []
#self.atomicPositionsType = 'crystal'
diffpyLattice = structure.lattice
a = diffpyLattice.a
b = diffpyLattice.b
c = diffpyLattice.c
cAB = cosd(diffpyLattice.gamma)
cBC = cosd(diffpyLattice.alpha)
cAC = cosd(diffpyLattice.beta)
qeLattice = QELattice(ibrav = ibrav, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
self.lattice = qeLattice
# make a deep copy (does not wok now)
#reducedStructure = Structure(diffpyStructure)
reducedStructure = structure
reducedStructure.placeInLattice(Lattice(base=qeLattice.diffpy().base))
# collect atoms that are at equivalent position to some previous atom
duplicates = set([a1
for i0, a0 in enumerate(reducedStructure) for a1 in reducedStructure[i0+1:]
if self._element(a0) == self._element(a1) and equalPositions(a0.xyz, a1.xyz, eps=1e-4)])
# Filter out duplicate atoms. Use slice assignment so that
# reducedStructure is not replaced with a list.
reducedStructure[:] = [a for a in reducedStructure if not a in duplicates]
self.structure = reducedStructure
atomNames = []
for a in reducedStructure:
if self._element(a) not in atomNames:
atomNames.append(self._element(a))
#print atomNames
#print len(massList)
for i, elem in enumerate(atomNames):
if len(massList) - 1 < i:
mass = 0
else:
mass = massList[i]
if len(psList) - 1 < i:
ps = ''
else:
ps = psList[i]
#print mass, ps
# atomDict[a] =
# for i, atom in enumerate(reducedStructure):
# elem = self._element(atom)
# if len(massList) - 1 < i:
# mass = 0
# else:
# mass = massList[i]
# if len(psList) - 1 < i:
# ps = ''
# else:
# ps = psList[i]
self.atomicSpecies[elem] = AtomicSpecies(elem, mass, ps)
for atom in reducedStructure:
self.optConstraints.append([])
# convert to bohr units
self.lattice.setLattice(ibrav, self.lattice.a*1.889725989, \
self.lattice.b*1.889725989,
self.lattice.c*1.889725989)
self.nat = len(reducedStructure)
self.ntyp = len(self.atomicSpecies)
