def A(name, index, type = None):
from matter.Atom import Atom
#hack--sometimes 'name' contains element and sometimes 'type'
if len(name)<3:
return Atom(name)
if len(type)<3:
return Atom(type)
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 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 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 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 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 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 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 __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 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 getAtomsInOneUnitCell(matter):
"get atoms in one unit cell, including atoms in the faces"
from matter.Atom import Atom
from matter.SymmetryUtilities import expandPosition
# list of atoms to return
ret = []
# cache['H'] are a list of positions that are already
# include in result atom list
cache = {}
#
sg = matter.sg
for atom in matter:
symbol = atom.symbol
# all equivalent but unique positions for this atom
positions, pops, pmult = expandPosition(sg, atom.xyz)
# get the cache for this type of atom
cache1 = cache.get(symbol)
if cache1 is None:
cache1 = cache[symbol] = []
# loop over all positions
for position in positions:
position = tuple(position)
if position in cache1:
continue
# add new position to cache, and the new atom to the result list
# cache1.append(position)
# ret.append(Atom(symbol, position))
# also see if the position is at boundary, if so, add all
# boundary atoms
positions_at_boundary = getPositionsAtBoundary(position)
for pos in positions_at_boundary:
cache1.append(pos)
ret.append(Atom(symbol, pos))
continue
continue
continue
return ret
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()
