def setUp(self):
"""do MOF full cell"""
#first replace the deuterium with a hydrogen molecule: 0.741/6.8354 = 0.108406238
# so each H atom is located 0.054203119 above and below the deuterium center
self.cifParser = CifParser('MOF74_neutron_4K_a-2H.cif')
class MofParse_TestCase(unittest.TestCase):
def setUp(self):
"""do MOF full cell"""
#first replace the deuterium with a hydrogen molecule: 0.741/6.8354 = 0.108406238
# so each H atom is located 0.054203119 above and below the deuterium center
self.cifParser=CifParser('MOF74_neutron_4K_a-2H.cif')
def testCoords(self):
coords = self.cifParser.cifToAtomAndCoordinateList()
#print coords
#print len(coords)
#assert coords==[['C', '0.00000', '0.00000', '0.00000'],
# ['C', '0.33333', '0.66667', '0.00000']]
def testAllCoords(self):
coords=self.cifParser.generateAllCoordinates()
cell=self.cifParser.getUnitCellAsVectors()
#this is risky because of round off error problems
print coords
print len(coords)
print cell
sc = Supercell(coords, cell)#, 1, 1, 1)#, coordType='cartesian')
sc.i.m=1
sc.i.n=1
sc.i.l=2
sc.create()
sc.writeSupCellXYZFile('MOF74_neutron_4K_a-2H-112.xyz')
class MofParse_TestCase(unittest.TestCase):
def setUp(self):
"""do MOF full cell"""
#first replace the deuterium with a hydrogen molecule: 0.741/6.8354 = 0.108406238
# so each H atom is located 0.054203119 above and below the deuterium center
self.cifParser = CifParser('MOF74_neutron_4K_a-2H.cif')
def testCoords(self):
coords = self.cifParser.cifToAtomAndCoordinateList()
#print coords
#print len(coords)
#assert coords==[['C', '0.00000', '0.00000', '0.00000'],
# ['C', '0.33333', '0.66667', '0.00000']]
def testAllCoords(self):
coords = self.cifParser.generateAllCoordinates()
cell = self.cifParser.getUnitCellAsVectors()
#this is risky because of round off error problems
print coords
print len(coords)
print cell
sc = Supercell(coords, cell) #, 1, 1, 1)#, coordType='cartesian')
sc.i.m = 1
sc.i.n = 1
sc.i.l = 2
sc.create()
sc.writeSupCellXYZFile('MOF74_neutron_4K_a-2H-112.xyz')
def setUp(self):
"""do MOF full cell"""
#first replace the deuterium with a hydrogen molecule: 0.741/6.8354 = 0.108406238
# so each H atom is located 0.054203119 above and below the deuterium center
self.cifParser=CifParser('MOF74_neutron_4K_a-2H.cif')
class Li2B12H12Parse_TestCase(unittest.TestCase):
def setUp(self):
"""do Li2B12H12 full cell"""
self.cifParser = CifParser(os.getcwd() + os.sep + 'li2b12h12.cif')
def testCoords(self):
coords = self.cifParser.cifToAtomAndCoordinateList()
#print coords
#print len(coords)
def testAllCoords(self):
coords = self.cifParser.generateAllCoordinates()
cell = self.cifParser.getUnitCellAsVectors()
print 'li2b12h12'
pprintCoords(coords)
print len(coords)
print cell
sc = Supercell(coords, cell, 1, 1, 1)
sc.writeSupCellXYZFile(os.getcwd() + os.sep + 'li2b12h12.xyz')
class Li2B12H12Parse_TestCase(unittest.TestCase):
def setUp(self):
"""do Li2B12H12 full cell"""
self.cifParser=CifParser(os.getcwd()+os.sep+'li2b12h12.cif')
def testCoords(self):
coords = self.cifParser.cifToAtomAndCoordinateList()
#print coords
#print len(coords)
def testAllCoords(self):
coords = self.cifParser.generateAllCoordinates()
cell = self.cifParser.getUnitCellAsVectors()
print 'li2b12h12'
pprintCoords(coords)
print len(coords)
print cell
sc = Supercell(coords, cell, 1, 1, 1)
sc.writeSupCellXYZFile(os.getcwd()+os.sep+'li2b12h12.xyz')
class LiBH4HexParse_TestCase(unittest.TestCase):
def setUp(self):
"""do LiBH4 full cell"""
#self.cifParser=CifParser(home+'/liBH4/hexagonal.cif')
self.cifParser = CifParser(os.getcwd() + os.sep + 'hexagonal.cif')
def testCoords(self):
coords = self.cifParser.cifToAtomAndCoordinateList()
#print coords
#print len(coords)
def testAllCoords(self):
coords = self.cifParser.generateAllCoordinates()
cell = self.cifParser.getUnitCellAsVectors()
print 'hexagonal'
pprintCoords(coords)
print len(coords)
print cell
sc = Supercell(coords, cell, 1, 1, 1)
sc.writeSupCellXYZFile(os.getcwd() + os.sep + 'hexagonal.xyz')
class LiBH4HexParse_TestCase(unittest.TestCase):
def setUp(self):
"""do LiBH4 full cell"""
#self.cifParser=CifParser(home+'/liBH4/hexagonal.cif')
self.cifParser=CifParser(os.getcwd()+os.sep+'hexagonal.cif')
def testCoords(self):
coords = self.cifParser.cifToAtomAndCoordinateList()
#print coords
#print len(coords)
def testAllCoords(self):
coords = self.cifParser.generateAllCoordinates()
cell = self.cifParser.getUnitCellAsVectors()
print 'hexagonal'
pprintCoords(coords)
print len(coords)
print cell
sc = Supercell(coords, cell, 1, 1, 1)
sc.writeSupCellXYZFile(os.getcwd()+os.sep+'hexagonal.xyz')
class LiBH4OrthoParse_TestCase(unittest.TestCase):
def setUp(self):
"""do LiBH4 full cell"""
self.cifParser = CifParser(os.getcwd() + os.sep + 'orthorhombic.cif')
def testCoords(self):
coords = self.cifParser.cifToAtomAndCoordinateList()
print "cif coords:"
pprintCoords(coords)
def testAllCoords(self):
coords = self.cifParser.generateAllCoordinates()
cell = self.cifParser.getUnitCellAsVectors()
#this is risky because of round off error problems
print "all coords:"
pprintCoords(coords)
print len(coords)
print cell
sc = Supercell(coords, cell, 1, 1, 1) #, coordType='cartesian')
sc.writeSupCellXYZFile(os.getcwd() + os.sep + 'orthorhombic.xyz')
class NaAlH4_TestCase(unittest.TestCase):
def setUp(self):
"""do NaAlH4 full cell"""
self.cifParser=CifParser(os.getcwd()+os.sep+'naalh4.cif')
def testCoords(self):
coords = self.cifParser.cifToAtomAndCoordinateList()
print "cif coords:"
pprintCoords(coords)
def testAllCoords(self):
coords=self.cifParser.generateAllCoordinates()
cell=self.cifParser.getUnitCellAsVectors()
#this is risky because of round off error problems
print "all coords:"
pprintCoords(coords)
print len(coords)
print cell
sc = Supercell(coords, cell, 1, 1, 1)#, coordType='cartesian')
sc.writeSupCellXYZFile(os.getcwd()+os.sep+'naalh4.xyz')
def setUp(self):
"""do LiBH4 full cell"""
self.cifParser=CifParser(os.getcwd()+os.sep+'orthorhombic.cif')
def setUp(self):
"""do NaAlH4 full cell"""
self.cifParser=CifParser(os.getcwd()+os.sep+'naalh4.cif')
def setUp(self):
"""do Li2B12H12 full cell"""
self.cifParser=CifParser(os.getcwd()+os.sep+'li2b12h12.cif')
def setUp(self):
"""do LiBH4 full cell"""
#self.cifParser=CifParser(home+'/liBH4/hexagonal.cif')
self.cifParser=CifParser(os.getcwd()+os.sep+'hexagonal.cif')
def setUp(self):
"""do Li2B12H12 full cell"""
self.cifParser = CifParser(os.getcwd() + os.sep + 'li2b12h12.cif')
def setUp(self):
"""do LiBH4 full cell"""
#self.cifParser=CifParser(home+'/liBH4/hexagonal.cif')
self.cifParser = CifParser(os.getcwd() + os.sep + 'hexagonal.cif')
def setUp(self):
"""do LiBH4 full cell"""
self.cifParser = CifParser(os.getcwd() + os.sep + 'orthorhombic.cif')