def test_xyz(self):
"Atom: xyz cartesian attribute"
from danse.ins.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 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_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 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 danse.ins.matter.expansion import supercell
al_333 = supercell(self.stru4, (3, 3, 3))
s1 = al_333.writeStr(self.format)
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 setUp(self):
self.lattice = Lattice()
self.places = 12
return
class TestLattice(unittest.TestCase):
"""test methods of Lattice class"""
def setUp(self):
self.lattice = Lattice()
self.places = 12
return
def assertListAlmostEqual(self, l1, l2, places=None):
"""wrapper for list comparison"""
if places is None: places = self.places
self.assertEqual(len(l1), len(l2))
for i in range(len(l1)):
self.assertAlmostEqual(l1[i], l2[i], places)
def test_setLatPar(self):
"""check calculation of standard unit cell vectors"""
from numpy import dot
from math import radians, sqrt, cos, sin
norm = lambda x : sqrt(sum([xi**2 for xi in x]))
cosd = lambda x : cos(radians(x))
sind = lambda x : sin(radians(x))
self.lattice.setLatPar(1.0, 2.0, 3.0, 80, 100, 120)
base = self.lattice.base
self.assertAlmostEqual(1.0, norm(base[0]), self.places)
self.assertAlmostEqual(2.0, norm(base[1]), self.places)
self.assertAlmostEqual(3.0, norm(base[2]), self.places)
self.assertAlmostEqual(cosd(80.0),
dot(base[1],base[2])/(2*3), self.places)
self.assertAlmostEqual(cosd(100.0),
dot(base[0],base[2])/(1*3), self.places)
self.assertAlmostEqual(cosd(120.0),
dot(base[0],base[1])/(1*2), self.places)
def test_setLatBase(self):
"""check calculation of unit cell rotation"""
import numpy
import numpy.linalg as numalg
base = numpy.array([[ 1.0, 1.0, 0.0],
[ 0.0, 1.0, 1.0],
[ 1.0, 0.0, 1.0]])
self.lattice.setLatBase(base)
self.assertAlmostEqual(self.lattice.a, numpy.sqrt(2.0), self.places)
self.assertAlmostEqual(self.lattice.b, numpy.sqrt(2.0), self.places)
self.assertAlmostEqual(self.lattice.c, numpy.sqrt(2.0), self.places)
self.assertAlmostEqual(self.lattice.alpha, 60.0, self.places)
self.assertAlmostEqual(self.lattice.beta, 60.0, self.places)
self.assertAlmostEqual(self.lattice.gamma, 60.0, self.places)
detR0 = numalg.det(self.lattice.baserot)
self.assertAlmostEqual(detR0, 1.0, self.places)
# try if rotation matrix works
self.assertEqual(numpy.all(base == self.lattice.base), True)
self.lattice.setLatPar(alpha=44, beta=66, gamma=88)
self.assertNotEqual(numpy.all(base == self.lattice.base), True)
self.lattice.setLatPar(alpha=60, beta=60, gamma=60)
self.assertListAlmostEqual(base[0], self.lattice.base[0])
self.assertListAlmostEqual(base[1], self.lattice.base[1])
self.assertListAlmostEqual(base[2], self.lattice.base[2])
# try base checking
self.assertRaises(LatticeError, self.lattice.setLatBase,
[[1, 0, 0], [1,0,0], [0,0,1]])
self.assertRaises(LatticeError, self.lattice.setLatBase,
[[1, 0, 0], [0,0,1], [0,1,0]])
return
def test_repr(self):
"""check string representation of this lattice"""
r = repr(self.lattice)
self.assertEqual(r, "Lattice()")
self.lattice.setLatPar(1, 2, 3, 10, 20, 30)
r = repr(self.lattice)
r0 = "Lattice(a=1, b=2, c=3, alpha=10, beta=20, gamma=30)"
self.assertEqual(r, r0)
base = [[ 1.0, 1.0, 0.0],
[ 0.0, 2.0, 2.0],
[ 3.0, 0.0, 3.0]]
self.lattice.setLatBase(base)
r = repr(self.lattice)
self.assertEqual(r, "Lattice(base=%r)" % self.lattice.base)
def test_monkhorst_pack(self):
self.lattice.setLatPar(3, 3, 3, 90, 90, 90)
grid = (2,2,2)
print self.lattice.getMonkhorstPackGrid(grid)
print self.lattice.getFracMonkhorstPackGrid(grid)
def parseLines(self, lines):
"""Parse list of lines in PDFfit format.
Return Structure object or raise StructureFormatError.
"""
p_nl = 0
rlist = []
try:
self.stru = PDFFitStructure()
stru = self.stru
cell_line_read = False
stop = len(lines)
while stop > 0 and lines[stop - 1].strip() == "":
stop -= 1
ilines = iter(lines[:stop])
# read header of PDFFit file
for l in ilines:
p_nl += 1
words = l.split()
if len(words) == 0 or words[0][0] == '#':
continue
elif words[0] == 'title':
stru.description = l.lstrip()[5:].strip()
elif words[0] == 'scale':
stru.pdffit['scale'] = float(words[1])
elif words[0] == 'sharp':
l1 = l.replace(',', ' ')
sharp_pars = [float(w) for w in l1.split()[1:]]
if len(sharp_pars) < 4:
stru.pdffit['delta2'] = sharp_pars[0]
stru.pdffit['sratio'] = sharp_pars[1]
stru.pdffit['rcut'] = sharp_pars[2]
else:
stru.pdffit['delta2'] = sharp_pars[0]
stru.pdffit['delta1'] = sharp_pars[1]
stru.pdffit['sratio'] = sharp_pars[2]
stru.pdffit['rcut'] = sharp_pars[3]
elif words[0] == 'spcgr':
key = 'spcgr'
start = l.find(key) + len(key)
value = l[start:].strip()
stru.pdffit['spcgr'] = value
elif words[0] == 'shape':
self._parse_shape(l)
elif words[0] == 'cell':
cell_line_read = True
l1 = l.replace(',', ' ')
latpars = [float(w) for w in l1.split()[1:7]]
stru.lattice = Lattice(*latpars)
elif words[0] == 'dcell':
l1 = l.replace(',', ' ')
stru.pdffit['dcell'] = [float(w) for w in l1.split()[1:7]]
elif words[0] == 'ncell':
l1 = l.replace(',', ' ')
stru.pdffit['ncell'] = [int(w) for w in l1.split()[1:5]]
elif words[0] == 'format':
if words[1] != 'pdffit':
emsg = "%d: file is not in PDFfit format" % p_nl
raise StructureFormatError(emsg)
elif words[0] == 'atoms' and cell_line_read:
break
else:
self.ignored_lines.append(l)
# Header reading finished, check if required lines were present.
if not cell_line_read:
emsg = "%d: file is not in PDFfit format" % p_nl
raise StructureFormatError(emsg)
# Load data from atom entries.
p_natoms = reduce(lambda x, y: x * y, stru.pdffit['ncell'])
# we are now inside data block
for l in ilines:
p_nl += 1
wl1 = l.split()
element = wl1[0][0].upper() + wl1[0][1:].lower()
xyz = [float(w) for w in wl1[1:4]]
occ = float(wl1[4])
stru.addNewAtom(element, xyz=xyz, occupancy=occ)
a = stru.getLastAtom()
p_nl += 1
wl2 = ilines.next().split()
a.sigxyz = [float(w) for w in wl2[0:3]]
a.sigo = float(wl2[3])
p_nl += 1
wl3 = ilines.next().split()
p_nl += 1
wl4 = ilines.next().split()
p_nl += 1
wl5 = ilines.next().split()
p_nl += 1
wl6 = ilines.next().split()
a.sigU = numpy.zeros((3, 3), dtype=float)
a.U11 = float(wl3[0])
a.U22 = float(wl3[1])
a.U33 = float(wl3[2])
a.sigU[0, 0] = float(wl4[0])
a.sigU[1, 1] = float(wl4[1])
a.sigU[2, 2] = float(wl4[2])
a.U12 = float(wl5[0])
a.U13 = float(wl5[1])
a.U23 = float(wl5[2])
a.sigU[0, 1] = a.sigU[1, 0] = float(wl6[0])
a.sigU[0, 2] = a.sigU[2, 0] = float(wl6[1])
a.sigU[1, 2] = a.sigU[2, 1] = float(wl6[2])
if len(stru) != p_natoms:
emsg = "expected %d atoms, read %d" % (p_natoms, len(stru))
raise StructureFormatError(emsg)
if stru.pdffit['ncell'][:3] != [1, 1, 1]:
superlatpars = [
latpars[i] * stru.pdffit['ncell'][i] for i in range(3)
] + latpars[3:]
superlattice = Lattice(*superlatpars)
stru.placeInLattice(superlattice)
stru.pdffit['ncell'] = [1, 1, 1, p_natoms]
except (ValueError, IndexError):
emsg = "%d: file is not in PDFfit format" % p_nl
exc_type, exc_value, exc_traceback = sys.exc_info()
raise StructureFormatError, emsg, exc_traceback
return stru
def setUp(self):
self.lattice = Lattice()
self.places = 12
return
class TestLattice(unittest.TestCase):
"""test methods of Lattice class"""
def setUp(self):
self.lattice = Lattice()
self.places = 12
return
def assertListAlmostEqual(self, l1, l2, places=None):
"""wrapper for list comparison"""
if places is None: places = self.places
self.assertEqual(len(l1), len(l2))
for i in range(len(l1)):
self.assertAlmostEqual(l1[i], l2[i], places)
def test_setLatPar(self):
"""check calculation of standard unit cell vectors"""
from numpy import dot
from math import radians, sqrt, cos, sin
norm = lambda x: sqrt(sum([xi**2 for xi in x]))
cosd = lambda x: cos(radians(x))
sind = lambda x: sin(radians(x))
self.lattice.setLatPar(1.0, 2.0, 3.0, 80, 100, 120)
base = self.lattice.base
self.assertAlmostEqual(1.0, norm(base[0]), self.places)
self.assertAlmostEqual(2.0, norm(base[1]), self.places)
self.assertAlmostEqual(3.0, norm(base[2]), self.places)
self.assertAlmostEqual(cosd(80.0),
dot(base[1], base[2]) / (2 * 3), self.places)
self.assertAlmostEqual(cosd(100.0),
dot(base[0], base[2]) / (1 * 3), self.places)
self.assertAlmostEqual(cosd(120.0),
dot(base[0], base[1]) / (1 * 2), self.places)
def test_setLatBase(self):
"""check calculation of unit cell rotation"""
import numpy
import numpy.linalg as numalg
base = numpy.array([[1.0, 1.0, 0.0], [0.0, 1.0, 1.0], [1.0, 0.0, 1.0]])
self.lattice.setLatBase(base)
self.assertAlmostEqual(self.lattice.a, numpy.sqrt(2.0), self.places)
self.assertAlmostEqual(self.lattice.b, numpy.sqrt(2.0), self.places)
self.assertAlmostEqual(self.lattice.c, numpy.sqrt(2.0), self.places)
self.assertAlmostEqual(self.lattice.alpha, 60.0, self.places)
self.assertAlmostEqual(self.lattice.beta, 60.0, self.places)
self.assertAlmostEqual(self.lattice.gamma, 60.0, self.places)
detR0 = numalg.det(self.lattice.baserot)
self.assertAlmostEqual(detR0, 1.0, self.places)
# try if rotation matrix works
self.assertEqual(numpy.all(base == self.lattice.base), True)
self.lattice.setLatPar(alpha=44, beta=66, gamma=88)
self.assertNotEqual(numpy.all(base == self.lattice.base), True)
self.lattice.setLatPar(alpha=60, beta=60, gamma=60)
self.assertListAlmostEqual(base[0], self.lattice.base[0])
self.assertListAlmostEqual(base[1], self.lattice.base[1])
self.assertListAlmostEqual(base[2], self.lattice.base[2])
# try base checking
self.assertRaises(LatticeError, self.lattice.setLatBase,
[[1, 0, 0], [1, 0, 0], [0, 0, 1]])
self.assertRaises(LatticeError, self.lattice.setLatBase,
[[1, 0, 0], [0, 0, 1], [0, 1, 0]])
return
def test_repr(self):
"""check string representation of this lattice"""
r = repr(self.lattice)
self.assertEqual(r, "Lattice()")
self.lattice.setLatPar(1, 2, 3, 10, 20, 30)
r = repr(self.lattice)
r0 = "Lattice(a=1, b=2, c=3, alpha=10, beta=20, gamma=30)"
self.assertEqual(r, r0)
base = [[1.0, 1.0, 0.0], [0.0, 2.0, 2.0], [3.0, 0.0, 3.0]]
self.lattice.setLatBase(base)
r = repr(self.lattice)
self.assertEqual(r, "Lattice(base=%r)" % self.lattice.base)
def test_monkhorst_pack(self):
self.lattice.setLatPar(3, 3, 3, 90, 90, 90)
grid = (2, 2, 2)
print self.lattice.getMonkhorstPackGrid(grid)
print self.lattice.getFracMonkhorstPackGrid(grid)