def setUp(self):
# at1 = Atom('C', [0.333333333333333, 0.666666666666667, 0])
# at2 = Atom('C', [0.666666666666667, 0.333333333333333, 0])
at1 = Atom('C', [0, 0, 0])
at2 = Atom('C', [1, 1, 1])
self.stru = Structure([at1, at2],
lattice=Lattice(1, 1, 1, 90, 90, 120))
ciffile = os.path.join(testdata_dir, 'PbTe.cif')
self.stru2 = Structure()
self.stru2.read(ciffile)
ciffile = os.path.join(testdata_dir, 'graphite.cif')
self.stru3 = Structure()
self.stru3.read(ciffile)
at1 = Atom('Al', [0.0, 0.0, 0.0])
at2 = Atom('Al', [0.0, 0.5, 0.5])
at3 = Atom('Al', [0.5, 0.0, 0.5])
at4 = Atom('Al', [0.5, 0.5, 0.0])
self.stru4 = Structure([at1, at2, at3, at4],
lattice=Lattice(4.05, 4.05, 4.05, 90, 90, 90),
sgid=225)
self.places = 12
def __init__(self, ibrav = 1,a = 1. ,b = 1.,c = 1.,
cBC = 0.,cAC = 0. ,cAB = 0., base = None, lattice = None, qeInput = None ):
self.formatString = '%# .8f %# .8f %# .8f'
self._qeInput = qeInput
#self._qeInput = None
self._type = 'celldm'
# Lattice 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 test_NaI(self):
"""check supercell expansion for Al.
"""
at1 = Atom('Na', [0.0, 0.0, 0.0])
at2 = Atom('Na', [0.0, 0.5, 0.5])
at3 = Atom('Na', [0.5, 0.0, 0.5])
at4 = Atom('Na', [0.5, 0.5, 0.0])
at5 = Atom('I', [0.5, 0.5, 0.5])
at6 = Atom('I', [0.0, 0.0, 0.5])
at7 = Atom('I', [0.0, 0.5, 0.0])
at8 = Atom('I', [0.5, 0.0, 0.0])
naI = Structure( [ at1, at2, at3, at4, at5, at6, at7, at8],
lattice = Lattice(6.482, 6.482, 6.482, 90, 90, 90),
sgid = 225 )
lines = []
for sym,pos in zip(naI.symbols, naI.xyz_cartn):
lines.append( sym+' %f %f %f' % tuple(pos) )
lines.append('\n')
naI_sup = supercell(naI, (2,2,2))
for sym,pos in zip(naI_sup.symbols, naI_sup.xyz_cartn):
lines.append(sym+' %f %f %f' % tuple(pos))
expected = open('expected-test_NaI-TestSuperCell').readlines()
self.assertEqual(len(lines), len(expected))
for l1, l2 in zip(lines, expected):
self.assertEqual(l1.strip(), l2.strip())
return
def setUp(self):
# at1 = Atom('C', [0.333333333333333, 0.666666666666667, 0])
# at2 = Atom('C', [0.666666666666667, 0.333333333333333, 0])
at1 = Atom('C', [0, 0, 0])
at2 = Atom('C', [1, 1, 1])
self.stru = Structure([at1, at2],
lattice=Lattice(1, 1, 1, 90, 90, 120))
self.places = 12
def testGetChemicalFormula(self):
at1 = Atom('C', [0.333333333333333, 0.666666666666667, 0])
at2 = Atom('C', [0.666666666666667, 0.333333333333333, 0])
#at3 = Atom('H', [0, 0, 0])
stru = Structure([at1, at2],
lattice=Lattice(3.8, 3.8, 5.6, 90, 90, 120))
print 'formula: ', stru.getChemicalFormula()
return
def test_placeInLattice(self):
"""check Structure.placeInLattice() -- conversion of coordinates
"""
stru = self.stru
new_lattice = Lattice(.5, .5, .5, 90, 90, 60)
stru.placeInLattice(new_lattice)
a0 = stru[0]
self.assertListAlmostEqual(a0.xyz, 3*[0.0])
a1 = stru[1]
self.assertListAlmostEqual(a1.xyz, [2.0, 0.0, 2.0])
def testChemicalFormulaPositionsSymbols(self):
at1 = Atom('C', [0.333333333333333, 0.666666666666667, 0])
at2 = Atom('C', [0.666666666666667, 0.333333333333333, 0])
#at3 = Atom('H', [0, 0, 0])
stru = Structure( [ at1, at2], lattice=Lattice(3.8, 3.8, 5.6, 90, 90, 120) )
assert stru.getChemicalFormula()=='C_2'
#self.assertListAlmostEqual(stru.xyz, [[0.33333333333333298, 0.66666666666666696, 0.0], [0.66666666666666696, 0.33333333333333298, 0.0]])
#self.assertListAlmostEqual(stru.xyz_cartn,[[1.0969655114602876, 1.9000000000000017, 0.0], [2.1939310229205784, -2.0020877317117325e-15, 0.0]])
#self.assertListAlmostEqual(stru.symbols, ['C', 'C'])
#print "here's the lattice", stru.lattice.base
return
def test1(self):
'Structure: property "primitive_unitcell"'
lattice = Lattice(a=2, b=2, c=2, alpha=90, beta=90, gamma=90)
atoms = [
Atom('Ni', (0, 0, 0)),
Atom('Ni', (0, 0.5, 0.5)),
Atom('Ni', (0.5, 0, 0.5)),
Atom('Ni', (0.5, 0.5, 0)),
]
struct = Structure(lattice=lattice, atoms=atoms, sgid=225)
print struct.primitive_unitcell
return
def test_al_supercell(self):
"""check supercell expansion for Al.
"""
at1 = Atom('Al', [0.0, 0.0, 0.0])
at2 = Atom('Al', [0.0, 0.5, 0.5])
at3 = Atom('Al', [0.5, 0.0, 0.5])
at4 = Atom('Al', [0.5, 0.5, 0.0])
self.stru4 = Structure( [ at1, at2, at3, at4],
lattice=Lattice(4.05, 4.05, 4.05, 90, 90, 90),
sgid = 225 )
al_sup = supercell(self.stru4, (3,3,3))
#print al_sup
return
def test2a(self):
'Structure: methood "symConsistent"'
lattice = Lattice(a=2, b=2, c=2, alpha=90, beta=90, gamma=90)
atoms = [
Atom('Ni', (0, 0, 0)),
Atom('Ni', (0, 0.5, 0.5)),
Atom('Ni', (0.5, 0, 0.5)),
Atom('Ni', (0.5, 0.5, 0)),
]
struct = Structure(lattice=lattice, atoms=atoms, sgid=225)
verdict, pos, op = struct.symConsistent()
self.assert_(verdict)
return
def __restoreFromInventory__(self, inventory):
atoms = []
from matter.Atom import Atom
from matter.Lattice import Lattice
for symbol, pos in zip(inventory.atom_symbols, inventory.atom_positions):
atoms.append(Atom(symbol, pos))
self.__init__(
atoms=atoms,
lattice=Lattice(base=inventory.lattice_base),
sgid=inventory.spacegroup_num,
description=inventory.short_description,
)
#self.primitive_unitcell = inventory.primitive_unitcell
return
def test1(self):
'Structure: property "primitive_unitcell"'
lattice = Lattice(a=2, b=2, c=2, alpha=90, beta=90, gamma=90)
atoms = [
Atom('Ni', (0, 0, 0)),
Atom('Ni', (0, 0.5, 0.5)),
Atom('Ni', (0.5, 0, 0.5)),
Atom('Ni', (0.5, 0.5, 0)),
]
struct = Structure(lattice=lattice, atoms=atoms, sgid=225)
pcell = struct.primitive_unitcell
self.assert_(pcell)
self.assertArrayEqual(pcell.base,
[[-1., 0., 1.], [0., 1., 1.], [-1., 1., 0.]])
return
def test3(self):
'Structure: "primitive_unitcell"'
lattice = Lattice(a=2, b=2, c=2, alpha=90, beta=90, gamma=90)
atoms = [
Atom('Fe', (0, 0, 0)),
Atom('Pd', (0, 0.5, 0.5)),
Atom('Pd', (0.5, 0, 0.5)),
Atom('Pd', (0.5, 0.5, 0)),
]
struct = Structure(lattice=lattice, atoms=atoms, sgid=221)
verdict, pos, op = struct.symConsistent()
print verdict, pos, op
self.assert_(verdict)
self.assertEqual(len(struct.primitive_unitcell.atoms), 4)
return
def test_naI_supercell(self):
"""check supercell expansion for Al.
"""
at1 = Atom('Na', [0.0, 0.0, 0.0])
at2 = Atom('Na', [0.0, 0.5, 0.5])
at3 = Atom('Na', [0.5, 0.0, 0.5])
at4 = Atom('Na', [0.5, 0.5, 0.0])
at5 = Atom('I', [0.5, 0.5, 0.5])
at6 = Atom('I', [0.0, 0.0, 0.5])
at7 = Atom('I', [0.0, 0.5, 0.0])
at8 = Atom('I', [0.5, 0.0, 0.0])
naI = Structure([at1, at2, at3, at4, at5, at6, at7, at8],
lattice=Lattice(6.482, 6.482, 6.482, 90, 90, 90),
sgid=225)
for sym, pos in zip(naI.symbols, naI.xyz_cartn):
print sym + ' %f %f %f' % tuple(pos)
print
naI_sup = supercell(naI, (2, 2, 2))
for sym, pos in zip(naI_sup.symbols, naI_sup.xyz_cartn):
print sym + ' %f %f %f' % tuple(pos)
def OrthorhombicPeriodicUniverse(vecLengths):
from matter.Lattice import Lattice
return Lattice(base=[[vecLengths[0],0,0], [0,vecLengths[1],0],
[0,0,vecLengths[2]]])
from dsaw.db import connect db = connect(db='postgres:///test') db.autocommit(True) from dsaw.model.visitors.OrmManager import OrmManager orm = OrmManager(db) from matter.Lattice import Lattice l1 = Lattice() l1.id = 'l1' orm.save(l1) orm.destroyAllTables()
def _setReducedStructureFromMatterStructure(self,
structure,
ibrav,
massList=[],
psList=[]):
"""
structure - matter.Structure object
ibrav - Lattice index
psList - list of strings with potential names
matterStructure object will be modified with reduced atomic positions
"""
import copy
matterLattice = copy.deepcopy(structure.lattice)
# there is a big problem with what Nikolay is doing because he is initializing QELattice with abcalbega which
# leaves room for errors in how the basis vectors are chosen compared to the old lattice
a = matterLattice.a
b = matterLattice.b
c = matterLattice.c
cAB = cosd(matterLattice.gamma)
cBC = cosd(matterLattice.alpha)
cAC = cosd(matterLattice.beta)
qeLattice = QELattice(ibrav = ibrav, a = a, b = b, c = c, cBC = cBC, \
cAC = cAC, cAB = cAB)
#what he should do is initialize the vectors of QELattice with the vectors of matterLattice
#
qeLattice._qeInput = self._qeInput
self.lattice = qeLattice
# make a deep copy:
reducedStructure = Structure(atoms=structure)
reducedStructure.placeInLattice(Lattice(base=qeLattice.matter().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 a0.symbol == a1.symbol
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 a.symbol not in atomNames:
atomNames.append(a.symbol)
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:
self.addNewAtom(atype = atom.symbol, xyz = atom.xyz, \
mass = atomicSpecies[atom.symbol][0], \
potential = atomicSpecies[atom.symbol][1],\
lattice = self.lattice, optConstraint = [])
from dsaw.db import connect
db = connect(db='postgres:///test', echo=True)
db.autocommit(True)
from dsaw.model.visitors.OrmManager import OrmManager
orm = OrmManager(db)
from matter.Atom import Atom
from matter.Lattice import Lattice
from matter.orm.BigStructure import Structure
at1 = Atom('C', [0.333333333333333, 0.666666666666667, 0])
at2 = Atom('C', [0.666666666666667, 0.333333333333333, 0])
hexag = Lattice(2.456, 2.456, 6.696, 90, 90, 120)
graphite = Structure([at1, at2], lattice=hexag, sgid=194)
graphite.id = 'graphite'
print graphite
#lattice=Lattice(a=2.456, b=2.456, c=6.696, alpha=90, beta=90, gamma=120)
#C 0.333333 0.666667 0.000000 1.0000
#C 0.666667 0.333333 0.000000 1.0000
from matter.expansion import supercell
graphite_sheet = supercell(graphite, (10, 10, 1))
graphite_sheet.id = 'sheet'
print graphite_sheet.getChemicalFormula()
#C200
orm.save(graphite_sheet)
#orm.destroyAllTables()
def ParallelepipedicPeriodicUniverse(vecs):
from matter.Lattice import Lattice
return Lattice(base=vecs)
from properties import *
import numpy
from matter.Lattice import Lattice
cartesian_lattice = Lattice()
class AtomPropertyCurator(type):
"""meta class for Atom class to collect all properties and set up
some class constants.
It establishes:
- Atom class's docstring
- a list of names of properties
- the list of setable attributes, "_setable", (to be used in method __setattr__ of Atom class).
NOTE: Brandon doesn't like this third one...user-scripters should be able to set whatever
they want...why limit them? Alex read this note :)
"""
def __init__(AtomClass, name, bases, dict):
from matter import METACLASS_CTOR_NEEDS_TYPE
if METACLASS_CTOR_NEEDS_TYPE:
type.__init__(AtomClass, name, bases, dict)
else:
type.__init__(name, bases, dict)
isotopeNumberProperties, inferredProperties, states = AtomPropertyCurator.collectProperties( AtomClass )
properties = isotopeNumberProperties + inferredProperties + states
AtomClass.propertyNames = [ p.name for p in properties ]
propStr = '\n'.join(
[ " %s: %s" % (p.name, p.doc) for p in properties ] )
#global doc