def test_del_state(self):
"Atom: delete state"
Fe57 = Atom( 'Fe', mass=57 )
Fe57.velocity = (0,0,1)
del Fe57.velocity
self._assertRaises( AttributeError, 'Fe57.velocity', locals())
return
def test_del_state(self):
"Atom: delete state"
Fe57 = Atom('Fe', mass=57)
Fe57.velocity = (0, 0, 1)
del Fe57.velocity
self._assertRaises(AttributeError, 'Fe57.velocity', locals())
return
def test_dsaworm(self):
'Structure: dsaw orm'
Fe57 = Atom('Fe', mass=57)
Al = Atom('Al')
atoms = [Fe57, Al]
lattice = Lattice(a=1, b=2, c=3, alpha=89, beta=91, gamma=92)
struct = Structure(atoms=atoms, lattice=lattice)
orm = self.orm
structrecord = orm(struct)
orm.save(struct)
struct_loaded = orm.load(Structure, structrecord.id)
props = ['sg', 'description']
for prop in props:
self.assertEqual(getattr(struct_loaded, prop),
getattr(struct, prop))
continue
props = ['a', 'b', 'c', 'alpha', 'beta', 'gamma']
for prop in props:
self.assertEqual(getattr(struct_loaded.lattice, prop),
getattr(struct.lattice, prop))
continue
self.assertEqual(len(struct_loaded), 2)
for atom in struct_loaded:
self.assertEqual(atom.__class__, Atom)
return
def supercell(S, mno):
"""Perform supercell expansion for a structure.
New lattice parameters are multiplied and fractional coordinates
divided by corresponding multiplier. New atoms are grouped with
their source in the original cell.
S -- an instance of Structure from matter.
mno -- sequence of 3 integers for cell multipliers along
the a, b and c axes.
Return a new expanded structure instance.
Raise TypeError when S is not Structure instance.
Raise ValueError for invalid mno argument.
"""
# check arguments
if len(mno) != 3:
emsg = "Argument mno must contain 3 numbers."
raise ValueError, emsg
elif min(mno) < 1:
emsg = "Multipliers must be greater or equal 1"
raise ValueError, emsg
if not isinstance(S, Structure):
emsg = "The first argument must be a Structure instance."
raise TypeError, emsg
# convert mno to a tuple of integers so it can be used as range limit.
mno = (int(mno[0]), int(mno[1]), int(mno[2]))
# create return instance
newS = Structure(S)
if mno == (1, 1, 1):
return newS
# back to business
ijklist = [(i,j,k)
for i in range(mno[0])
for j in range(mno[1])
for k in range(mno[2])]
# numpy.floor returns float array
mnofloats = numpy.array(mno, dtype=float)
# build a list of new atoms
newAtoms = []
for a in S:
for ijk in ijklist:
adup = Atom(a)
adup.xyz = (a.xyz + ijk)/mnofloats
newAtoms.append(adup)
# newS can own references in newAtoms, no need to make copies
newS.__setslice__(0, len(newS), newAtoms, copy=False)
# take care of lattice parameters
newS.lattice.setLatPar(
a=mno[0]*S.lattice.a,
b=mno[1]*S.lattice.b,
c=mno[2]*S.lattice.c )
return newS
def test_setable_state(self):
"Atom: setable state"
Fe57 = Atom('Fe', mass=57)
v = (0, 0, 1)
print '- Set velocity to %s ... ' % (v, ),
Fe57.velocity = v
print ' velocity = %s ' % (Fe57.velocity, )
print "- velocity's documentation: %s " % Atom.velocity.doc
return
def test_writeStr_xyz(self):
"""check string representation of normal xyz file"""
stru = self.stru
stru.description = "test of writeStr"
stru.lattice = Lattice(1.0, 2.0, 3.0, 90.0, 90.0, 90.0)
stru[:] = [Atom('H', [1., 1., 1.]), Atom('Cl', [3., 2., 1.])]
s1 = stru.writeStr(self.format)
s1 = re.sub('[ \t]+', ' ', s1)
s0 = "2\n%s\nH 1 2 3\nCl 3 4 3\n" % stru.description
self.assertEqual(s1, s0)
def test_write_xyz(self):
"""check writing of normal xyz file"""
stru = self.stru
stru.description = "test of writeStr"
stru.lattice = Lattice(1.0, 2.0, 3.0, 90.0, 90.0, 90.0)
stru[:] = [Atom('H', [1., 1., 1.]), Atom('Cl', [3., 2., 1.])]
stru.write(self.tmpname, self.format)
f_s = open(self.tmpname).read()
f_s = re.sub('[ \t]+', ' ', f_s)
s_s = "2\n%s\nH 1 2 3\nCl 3 4 3\n" % stru.description
self.assertEqual(f_s, s_s)
def test_writeStr_xyz_Supercell(self):
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)
from matter.expansion import supercell
al_333 = supercell(self.stru4, (3, 3, 3))
s1 = al_333.writeStr(self.format)
def test_setable_state(self):
"Atom: setable state"
Fe57 = Atom( 'Fe', mass=57 )
v = (0,0,1)
# print '- Set velocity to %s ... ' % (v,),
Fe57.velocity = v
# print ' velocity = %s ' % (Fe57.velocity,)
self.assertEqual(Fe57.velocity, v)
# print "- velocity's documentation: %s " % Atom.velocity.doc
self.assert_(Atom.velocity.doc)
return
def test1(self):
'makeXYZfileContent'
from matter import Lattice, Atom, Structure
Al = Atom('Al', (0, 0, 0))
Fe = Atom('Fe', (0.5, 0.5, 0.5))
atoms = [Al, Fe]
lattice = Lattice(1, 1, 1, 90, 90, 90)
s = Structure(atoms, lattice)
content = struct_utils.makeXYZfileContent(s, latticeAsDescription=True)
self.assertEqual(len(content), 4)
self.assertEqual(int(content[0]), 2)
self.assertEqual(len(content[1].split(' ')), 9)
return
def test_xyz(self):
"Atom: xyz cartesian attribute"
from matter import Lattice
C = Atom( 'C', [0.1, 0.2, 0.3], lattice = Lattice(2,2,2,90,90,90))
self.assertEqual(list(C.xyz), [0.1, 0.2, 0.3])
self.assertEqual(list(C.xyz_cartn), [0.2, 0.4, 0.6])
return
def test_xyz(self):
"Atom: xyz cartesian attribute"
from matter import Lattice
C = Atom('C', [0.1, 0.2, 0.3], lattice=Lattice(2, 2, 2, 90, 90, 90))
print "fractional pos=%s" % C.xyz
print "cartesian pos=%s" % C.xyz_cartn
return
def makeUnitcell():
from matter import Atom, Structure, Lattice
atoms = [Atom('Ni')]
# positions = [(0,0,0)]
cellvectors = [ (3.57,0,0), (0,3.57,0), (0,0,3.57) ]
lattice = Lattice(base=cellvectors)
return Structure(lattice=lattice, atoms=atoms)
def test_writeStr_rawxyz(self):
"""check writing of normal xyz file"""
stru = self.stru
stru.description = "test of writeStr"
stru.lattice = Lattice(1.0, 2.0, 3.0, 90.0, 90.0, 90.0)
# plain version
stru[:] = [Atom('H', [1., 1., 1.])]
s1 = stru.writeStr(self.format)
s1 = re.sub('[ \t]+', ' ', s1)
s0 = "H 1 2 3\n"
def makeMatter():
from matter import Structure, Atom, Lattice
atoms = [Atom('Fe', xyz=(0, 0, 0)), Atom('Al', xyz=(0.5, 0.5, 0.5))]
lattice = Lattice(base=((1., 0, 0), (0, 1., 0), (0, 0, 1.)))
return Structure(atoms, lattice)
def test_str(self):
"Atom: __str__"
Fe57 = Atom( 'Fe', mass=57 )
Fe57.velocity = (0,0,1)
# print Fe57
return
def test_load_matter(self):
from matter import Structure, Atom, 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])
a = 2. * 5.663 / 1.889725989 # set a in angstrom
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(structure = struct, ibrav = 2, massList = massList, psList = psList)
self.input.structure.load(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 str(self.input.structure)
self.assertEqual(str(self.input.structure), answer1)
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])
a = 2. * 5.663 / 1.889725989 # set a in angstrom
struct2 = 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))
self.input.structure.load(structure=struct2,
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
"""
#print str(self.input.structure)
self.assertEqual(str(self.input.structure), answer2)
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
# USA
# read and view pickled structure object
from matter import Structure, Lattice, Atom
at1 = Atom('C', [0.333333333333333, 0.666666666666667, 0])
at2 = Atom('C', [0.666666666666667, 0.333333333333333, 0])
a = 2.4612
c = 6.7079
graphite = Structure([at1, at2], lattice=Lattice(a, a, c, 90, 90, 120))
print graphite
import pickle
output = open('graphite.pkl', 'wb')
pickle.dump(graphite, output)
output.close()
pkl_file = open('graphite.pkl', 'rb')
g2 = pickle.load(pkl_file)
print g2
def test_str(self):
"Atom: __str__"
Fe57 = Atom('Fe', mass=57)
Fe57.velocity = (0, 0, 1)
print Fe57
return
def test_natural_element(self):
"Atom: natural element ctor"
Fe = Atom('Fe')
print Fe
return
def test_del_ctorarg(self):
"Atom: delete ctor arg"
Fe57 = Atom('Fe', mass=57)
self._assertRaises(AttributeError, "del Fe57.Z", locals())
return
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 test_isotope_ctor(self):
"Atom: isotope ctor"
Fe57 = Atom('Fe', mass=57)
print "- Z=%s" % Fe57.Z
print "- mass=%s" % Fe57.mass
return
def test_undefined_state(self):
"Atom: undefined state"
Fe57 = Atom('Fe', mass=57)
self._assertRaises(AttributeError, "Fe57.velocity", locals())
return
def test_isotope_ctor(self):
"Atom: isotope ctor"
Fe57 = Atom( 'Fe', mass=57 )
self.assertEqual(Fe57.Z, 26)
self.assertEqual(Fe57.mass, 57)
return
