def testATKScript2(self):
""" Test that we can generate an ATK script from the configuration. """
# Setup a valid KMCUnitCell.
cell_vectors = [[ 5.640000e+00, 0.330000e+00, 0.120000e+00],
[ 0.110000e+00, 5.460000e+00, 0.100000e+00],
[ 0.500000e+00, 0.430000e+00, 5.410000e+00]]
basis_points = [[ 0.200000e+00, 0.300000e+00, 0.400000e+00],
[ 5.200000e-01, 5.400000e-01, 5.010000e-01]]
unit_cell = KMCUnitCell(
cell_vectors=cell_vectors,
basis_points=basis_points)
# Setup the lattice and types.
lattice = KMCLattice(
unit_cell=unit_cell,
repetitions=(4,4,4),
periodic=(True, True, True))
types = ['Ce3','O','Empty','O','Ce','O','Empty','O','Empty',
'O','Ce','O','Empty','Vacancy','Ce','O','Ce','O','Empty',
'O','Ce','O','Empty','O','Empty','O','Ce','O','Empty',
'O','Ce','O','Empty','O','Ce','O','Empty','O','Ce',
'O','Ce3','O','Empty','O','Ce','O','Empty','O','Empty',
'O','Ce','O','Empty','O','Ce','O','Ce','O','Empty',
'O','Ce','O','Empty','O','Ce','O','Empty','O','Ce',
'O','Empty','O','Empty','O','Ce','O','Empty','O','Ce',
'O','Ce','O','Empty','O','Ce','O','Empty','O','Empty',
'O','Ce','O','Empty','O','Ce','O','Empty','O','Ce',
'O','Empty','O','Ce','O','Ce','O','Empty','O','Ce',
'O','Empty','O','Empty','O','Ce','O','Empty','O','Ce',
'O','Ce','O','Empty','O','Ce','O','Empty','O']
possible_types = ['Ce3','Empty','O','Ce','Vacancy']
# Setup the configuration.
configuration = KMCConfiguration(
lattice=lattice,
types=types,
possible_types=possible_types)
# Determine a mapping between our types and valid ATK types.
# Types not present in the mapping are ignored in the ATK script.
type_map = {
"Ce3" : "Vanadium",
"Ce" : "Cerium",
"O" : "Oxygen",
}
# Get the ATK script.
atk_script = configuration._atkScript(type_map)
# Check that it looks as we expect.
ref_script = """# ----------------------------------------------------------
# ATK 12.8.2 BulkConfiguration script generated from KMCLib
# configuration version 1.0.
# ----------------------------------------------------------
# Specify the lattice parameters.
vector_a = [ 22.56000000, 1.32000000, 0.48000000]*Angstrom
vector_b = [ 0.44000000, 21.84000000, 0.40000000]*Angstrom
vector_c = [ 2.00000000, 1.72000000, 21.64000000]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)
# Define the elements.
elements = [Vanadium, Oxygen, Oxygen, Cerium, Oxygen, Oxygen,
Oxygen, Cerium, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Vanadium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen]
# Define the coordinates.
coordinates = [[ 5.00000000e-02, 7.50000000e-02, 1.00000000e-01],
[ 1.30000000e-01, 1.35000000e-01, 1.25250000e-01],
[ 1.30000000e-01, 1.35000000e-01, 3.75250000e-01],
[ 5.00000000e-02, 7.50000000e-02, 6.00000000e-01],
[ 1.30000000e-01, 1.35000000e-01, 6.25250000e-01],
[ 1.30000000e-01, 1.35000000e-01, 8.75250000e-01],
[ 1.30000000e-01, 3.85000000e-01, 1.25250000e-01],
[ 5.00000000e-02, 3.25000000e-01, 3.50000000e-01],
[ 1.30000000e-01, 3.85000000e-01, 3.75250000e-01],
[ 5.00000000e-02, 3.25000000e-01, 8.50000000e-01],
[ 1.30000000e-01, 3.85000000e-01, 8.75250000e-01],
[ 5.00000000e-02, 5.75000000e-01, 1.00000000e-01],
[ 1.30000000e-01, 6.35000000e-01, 1.25250000e-01],
[ 1.30000000e-01, 6.35000000e-01, 3.75250000e-01],
[ 5.00000000e-02, 5.75000000e-01, 6.00000000e-01],
[ 1.30000000e-01, 6.35000000e-01, 6.25250000e-01],
[ 1.30000000e-01, 6.35000000e-01, 8.75250000e-01],
[ 1.30000000e-01, 8.85000000e-01, 1.25250000e-01],
[ 5.00000000e-02, 8.25000000e-01, 3.50000000e-01],
[ 1.30000000e-01, 8.85000000e-01, 3.75250000e-01],
[ 1.30000000e-01, 8.85000000e-01, 6.25250000e-01],
[ 5.00000000e-02, 8.25000000e-01, 8.50000000e-01],
[ 1.30000000e-01, 8.85000000e-01, 8.75250000e-01],
[ 3.80000000e-01, 1.35000000e-01, 1.25250000e-01],
[ 3.00000000e-01, 7.50000000e-02, 3.50000000e-01],
[ 3.80000000e-01, 1.35000000e-01, 3.75250000e-01],
[ 3.80000000e-01, 1.35000000e-01, 6.25250000e-01],
[ 3.00000000e-01, 7.50000000e-02, 8.50000000e-01],
[ 3.80000000e-01, 1.35000000e-01, 8.75250000e-01],
[ 3.00000000e-01, 3.25000000e-01, 1.00000000e-01],
[ 3.80000000e-01, 3.85000000e-01, 1.25250000e-01],
[ 3.80000000e-01, 3.85000000e-01, 3.75250000e-01],
[ 3.00000000e-01, 3.25000000e-01, 6.00000000e-01],
[ 3.80000000e-01, 3.85000000e-01, 6.25250000e-01],
[ 3.80000000e-01, 3.85000000e-01, 8.75250000e-01],
[ 3.80000000e-01, 6.35000000e-01, 1.25250000e-01],
[ 3.00000000e-01, 5.75000000e-01, 3.50000000e-01],
[ 3.80000000e-01, 6.35000000e-01, 3.75250000e-01],
[ 3.80000000e-01, 6.35000000e-01, 6.25250000e-01],
[ 3.00000000e-01, 5.75000000e-01, 8.50000000e-01],
[ 3.80000000e-01, 6.35000000e-01, 8.75250000e-01],
[ 3.00000000e-01, 8.25000000e-01, 1.00000000e-01],
[ 3.80000000e-01, 8.85000000e-01, 1.25250000e-01],
[ 3.80000000e-01, 8.85000000e-01, 3.75250000e-01],
[ 3.00000000e-01, 8.25000000e-01, 6.00000000e-01],
[ 3.80000000e-01, 8.85000000e-01, 6.25250000e-01],
[ 3.80000000e-01, 8.85000000e-01, 8.75250000e-01],
[ 5.50000000e-01, 7.50000000e-02, 1.00000000e-01],
[ 6.30000000e-01, 1.35000000e-01, 1.25250000e-01],
[ 6.30000000e-01, 1.35000000e-01, 3.75250000e-01],
[ 5.50000000e-01, 7.50000000e-02, 6.00000000e-01],
[ 6.30000000e-01, 1.35000000e-01, 6.25250000e-01],
[ 6.30000000e-01, 1.35000000e-01, 8.75250000e-01],
[ 6.30000000e-01, 3.85000000e-01, 1.25250000e-01],
[ 5.50000000e-01, 3.25000000e-01, 3.50000000e-01],
[ 6.30000000e-01, 3.85000000e-01, 3.75250000e-01],
[ 6.30000000e-01, 3.85000000e-01, 6.25250000e-01],
[ 5.50000000e-01, 3.25000000e-01, 8.50000000e-01],
[ 6.30000000e-01, 3.85000000e-01, 8.75250000e-01],
[ 5.50000000e-01, 5.75000000e-01, 1.00000000e-01],
[ 6.30000000e-01, 6.35000000e-01, 1.25250000e-01],
[ 6.30000000e-01, 6.35000000e-01, 3.75250000e-01],
[ 5.50000000e-01, 5.75000000e-01, 6.00000000e-01],
[ 6.30000000e-01, 6.35000000e-01, 6.25250000e-01],
[ 6.30000000e-01, 6.35000000e-01, 8.75250000e-01],
[ 6.30000000e-01, 8.85000000e-01, 1.25250000e-01],
[ 5.50000000e-01, 8.25000000e-01, 3.50000000e-01],
[ 6.30000000e-01, 8.85000000e-01, 3.75250000e-01],
[ 6.30000000e-01, 8.85000000e-01, 6.25250000e-01],
[ 5.50000000e-01, 8.25000000e-01, 8.50000000e-01],
[ 6.30000000e-01, 8.85000000e-01, 8.75250000e-01],
[ 8.80000000e-01, 1.35000000e-01, 1.25250000e-01],
[ 8.00000000e-01, 7.50000000e-02, 3.50000000e-01],
[ 8.80000000e-01, 1.35000000e-01, 3.75250000e-01],
[ 8.80000000e-01, 1.35000000e-01, 6.25250000e-01],
[ 8.00000000e-01, 7.50000000e-02, 8.50000000e-01],
[ 8.80000000e-01, 1.35000000e-01, 8.75250000e-01],
[ 8.00000000e-01, 3.25000000e-01, 1.00000000e-01],
[ 8.80000000e-01, 3.85000000e-01, 1.25250000e-01],
[ 8.80000000e-01, 3.85000000e-01, 3.75250000e-01],
[ 8.00000000e-01, 3.25000000e-01, 6.00000000e-01],
[ 8.80000000e-01, 3.85000000e-01, 6.25250000e-01],
[ 8.80000000e-01, 3.85000000e-01, 8.75250000e-01],
[ 8.80000000e-01, 6.35000000e-01, 1.25250000e-01],
[ 8.00000000e-01, 5.75000000e-01, 3.50000000e-01],
[ 8.80000000e-01, 6.35000000e-01, 3.75250000e-01],
[ 8.80000000e-01, 6.35000000e-01, 6.25250000e-01],
[ 8.00000000e-01, 5.75000000e-01, 8.50000000e-01],
[ 8.80000000e-01, 6.35000000e-01, 8.75250000e-01],
[ 8.00000000e-01, 8.25000000e-01, 1.00000000e-01],
[ 8.80000000e-01, 8.85000000e-01, 1.25250000e-01],
[ 8.80000000e-01, 8.85000000e-01, 3.75250000e-01],
[ 8.00000000e-01, 8.25000000e-01, 6.00000000e-01],
[ 8.80000000e-01, 8.85000000e-01, 6.25250000e-01],
[ 8.80000000e-01, 8.85000000e-01, 8.75250000e-01]]
# Setup the configuration.
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=coordinates )
# ----------------------------------------------------------
"""
self.assertEqual(atk_script, ref_script)
def testATKScript2(self):
""" Test that we can generate an ATK script from the configuration. """
# Setup a valid KMCUnitCell.
cell_vectors = [[5.640000e+00, 0.330000e+00, 0.120000e+00],
[0.110000e+00, 5.460000e+00, 0.100000e+00],
[0.500000e+00, 0.430000e+00, 5.410000e+00]]
basis_points = [[0.200000e+00, 0.300000e+00, 0.400000e+00],
[5.200000e-01, 5.400000e-01, 5.010000e-01]]
unit_cell = KMCUnitCell(cell_vectors=cell_vectors,
basis_points=basis_points)
# Setup the lattice and types.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(4, 4, 4),
periodic=(True, True, True))
types = [
'Ce3', 'O', 'Empty', 'O', 'Ce', 'O', 'Empty', 'O', 'Empty', 'O',
'Ce', 'O', 'Empty', 'Vacancy', 'Ce', 'O', 'Ce', 'O', 'Empty', 'O',
'Ce', 'O', 'Empty', 'O', 'Empty', 'O', 'Ce', 'O', 'Empty', 'O',
'Ce', 'O', 'Empty', 'O', 'Ce', 'O', 'Empty', 'O', 'Ce', 'O', 'Ce3',
'O', 'Empty', 'O', 'Ce', 'O', 'Empty', 'O', 'Empty', 'O', 'Ce',
'O', 'Empty', 'O', 'Ce', 'O', 'Ce', 'O', 'Empty', 'O', 'Ce', 'O',
'Empty', 'O', 'Ce', 'O', 'Empty', 'O', 'Ce', 'O', 'Empty', 'O',
'Empty', 'O', 'Ce', 'O', 'Empty', 'O', 'Ce', 'O', 'Ce', 'O',
'Empty', 'O', 'Ce', 'O', 'Empty', 'O', 'Empty', 'O', 'Ce', 'O',
'Empty', 'O', 'Ce', 'O', 'Empty', 'O', 'Ce', 'O', 'Empty', 'O',
'Ce', 'O', 'Ce', 'O', 'Empty', 'O', 'Ce', 'O', 'Empty', 'O',
'Empty', 'O', 'Ce', 'O', 'Empty', 'O', 'Ce', 'O', 'Ce', 'O',
'Empty', 'O', 'Ce', 'O', 'Empty', 'O'
]
possible_types = ['Ce3', 'Empty', 'O', 'Ce', 'Vacancy']
# Setup the configuration.
configuration = KMCConfiguration(lattice=lattice,
types=types,
possible_types=possible_types)
# Determine a mapping between our types and valid ATK types.
# Types not present in the mapping are ignored in the ATK script.
type_map = {
"Ce3": "Vanadium",
"Ce": "Cerium",
"O": "Oxygen",
}
# Get the ATK script.
atk_script = configuration._atkScript(type_map)
# Check that it looks as we expect.
ref_script = """# ----------------------------------------------------------
# ATK 12.8.2 BulkConfiguration script generated from KMCLib
# configuration version 1.0.
# ----------------------------------------------------------
# Specify the lattice parameters.
vector_a = [ 22.56000000, 1.32000000, 0.48000000]*Angstrom
vector_b = [ 0.44000000, 21.84000000, 0.40000000]*Angstrom
vector_c = [ 2.00000000, 1.72000000, 21.64000000]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)
# Define the elements.
elements = [Vanadium, Oxygen, Oxygen, Cerium, Oxygen, Oxygen,
Oxygen, Cerium, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Vanadium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen, Oxygen,
Cerium, Oxygen, Oxygen, Cerium, Oxygen, Cerium,
Oxygen, Oxygen, Cerium, Oxygen, Oxygen]
# Define the coordinates.
coordinates = [[ 5.00000000e-02, 7.50000000e-02, 1.00000000e-01],
[ 1.30000000e-01, 1.35000000e-01, 1.25250000e-01],
[ 1.30000000e-01, 1.35000000e-01, 3.75250000e-01],
[ 5.00000000e-02, 7.50000000e-02, 6.00000000e-01],
[ 1.30000000e-01, 1.35000000e-01, 6.25250000e-01],
[ 1.30000000e-01, 1.35000000e-01, 8.75250000e-01],
[ 1.30000000e-01, 3.85000000e-01, 1.25250000e-01],
[ 5.00000000e-02, 3.25000000e-01, 3.50000000e-01],
[ 1.30000000e-01, 3.85000000e-01, 3.75250000e-01],
[ 5.00000000e-02, 3.25000000e-01, 8.50000000e-01],
[ 1.30000000e-01, 3.85000000e-01, 8.75250000e-01],
[ 5.00000000e-02, 5.75000000e-01, 1.00000000e-01],
[ 1.30000000e-01, 6.35000000e-01, 1.25250000e-01],
[ 1.30000000e-01, 6.35000000e-01, 3.75250000e-01],
[ 5.00000000e-02, 5.75000000e-01, 6.00000000e-01],
[ 1.30000000e-01, 6.35000000e-01, 6.25250000e-01],
[ 1.30000000e-01, 6.35000000e-01, 8.75250000e-01],
[ 1.30000000e-01, 8.85000000e-01, 1.25250000e-01],
[ 5.00000000e-02, 8.25000000e-01, 3.50000000e-01],
[ 1.30000000e-01, 8.85000000e-01, 3.75250000e-01],
[ 1.30000000e-01, 8.85000000e-01, 6.25250000e-01],
[ 5.00000000e-02, 8.25000000e-01, 8.50000000e-01],
[ 1.30000000e-01, 8.85000000e-01, 8.75250000e-01],
[ 3.80000000e-01, 1.35000000e-01, 1.25250000e-01],
[ 3.00000000e-01, 7.50000000e-02, 3.50000000e-01],
[ 3.80000000e-01, 1.35000000e-01, 3.75250000e-01],
[ 3.80000000e-01, 1.35000000e-01, 6.25250000e-01],
[ 3.00000000e-01, 7.50000000e-02, 8.50000000e-01],
[ 3.80000000e-01, 1.35000000e-01, 8.75250000e-01],
[ 3.00000000e-01, 3.25000000e-01, 1.00000000e-01],
[ 3.80000000e-01, 3.85000000e-01, 1.25250000e-01],
[ 3.80000000e-01, 3.85000000e-01, 3.75250000e-01],
[ 3.00000000e-01, 3.25000000e-01, 6.00000000e-01],
[ 3.80000000e-01, 3.85000000e-01, 6.25250000e-01],
[ 3.80000000e-01, 3.85000000e-01, 8.75250000e-01],
[ 3.80000000e-01, 6.35000000e-01, 1.25250000e-01],
[ 3.00000000e-01, 5.75000000e-01, 3.50000000e-01],
[ 3.80000000e-01, 6.35000000e-01, 3.75250000e-01],
[ 3.80000000e-01, 6.35000000e-01, 6.25250000e-01],
[ 3.00000000e-01, 5.75000000e-01, 8.50000000e-01],
[ 3.80000000e-01, 6.35000000e-01, 8.75250000e-01],
[ 3.00000000e-01, 8.25000000e-01, 1.00000000e-01],
[ 3.80000000e-01, 8.85000000e-01, 1.25250000e-01],
[ 3.80000000e-01, 8.85000000e-01, 3.75250000e-01],
[ 3.00000000e-01, 8.25000000e-01, 6.00000000e-01],
[ 3.80000000e-01, 8.85000000e-01, 6.25250000e-01],
[ 3.80000000e-01, 8.85000000e-01, 8.75250000e-01],
[ 5.50000000e-01, 7.50000000e-02, 1.00000000e-01],
[ 6.30000000e-01, 1.35000000e-01, 1.25250000e-01],
[ 6.30000000e-01, 1.35000000e-01, 3.75250000e-01],
[ 5.50000000e-01, 7.50000000e-02, 6.00000000e-01],
[ 6.30000000e-01, 1.35000000e-01, 6.25250000e-01],
[ 6.30000000e-01, 1.35000000e-01, 8.75250000e-01],
[ 6.30000000e-01, 3.85000000e-01, 1.25250000e-01],
[ 5.50000000e-01, 3.25000000e-01, 3.50000000e-01],
[ 6.30000000e-01, 3.85000000e-01, 3.75250000e-01],
[ 6.30000000e-01, 3.85000000e-01, 6.25250000e-01],
[ 5.50000000e-01, 3.25000000e-01, 8.50000000e-01],
[ 6.30000000e-01, 3.85000000e-01, 8.75250000e-01],
[ 5.50000000e-01, 5.75000000e-01, 1.00000000e-01],
[ 6.30000000e-01, 6.35000000e-01, 1.25250000e-01],
[ 6.30000000e-01, 6.35000000e-01, 3.75250000e-01],
[ 5.50000000e-01, 5.75000000e-01, 6.00000000e-01],
[ 6.30000000e-01, 6.35000000e-01, 6.25250000e-01],
[ 6.30000000e-01, 6.35000000e-01, 8.75250000e-01],
[ 6.30000000e-01, 8.85000000e-01, 1.25250000e-01],
[ 5.50000000e-01, 8.25000000e-01, 3.50000000e-01],
[ 6.30000000e-01, 8.85000000e-01, 3.75250000e-01],
[ 6.30000000e-01, 8.85000000e-01, 6.25250000e-01],
[ 5.50000000e-01, 8.25000000e-01, 8.50000000e-01],
[ 6.30000000e-01, 8.85000000e-01, 8.75250000e-01],
[ 8.80000000e-01, 1.35000000e-01, 1.25250000e-01],
[ 8.00000000e-01, 7.50000000e-02, 3.50000000e-01],
[ 8.80000000e-01, 1.35000000e-01, 3.75250000e-01],
[ 8.80000000e-01, 1.35000000e-01, 6.25250000e-01],
[ 8.00000000e-01, 7.50000000e-02, 8.50000000e-01],
[ 8.80000000e-01, 1.35000000e-01, 8.75250000e-01],
[ 8.00000000e-01, 3.25000000e-01, 1.00000000e-01],
[ 8.80000000e-01, 3.85000000e-01, 1.25250000e-01],
[ 8.80000000e-01, 3.85000000e-01, 3.75250000e-01],
[ 8.00000000e-01, 3.25000000e-01, 6.00000000e-01],
[ 8.80000000e-01, 3.85000000e-01, 6.25250000e-01],
[ 8.80000000e-01, 3.85000000e-01, 8.75250000e-01],
[ 8.80000000e-01, 6.35000000e-01, 1.25250000e-01],
[ 8.00000000e-01, 5.75000000e-01, 3.50000000e-01],
[ 8.80000000e-01, 6.35000000e-01, 3.75250000e-01],
[ 8.80000000e-01, 6.35000000e-01, 6.25250000e-01],
[ 8.00000000e-01, 5.75000000e-01, 8.50000000e-01],
[ 8.80000000e-01, 6.35000000e-01, 8.75250000e-01],
[ 8.00000000e-01, 8.25000000e-01, 1.00000000e-01],
[ 8.80000000e-01, 8.85000000e-01, 1.25250000e-01],
[ 8.80000000e-01, 8.85000000e-01, 3.75250000e-01],
[ 8.00000000e-01, 8.25000000e-01, 6.00000000e-01],
[ 8.80000000e-01, 8.85000000e-01, 6.25250000e-01],
[ 8.80000000e-01, 8.85000000e-01, 8.75250000e-01]]
# Setup the configuration.
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=coordinates )
# ----------------------------------------------------------
"""
self.assertEqual(atk_script, ref_script)
def testATKScript1(self):
""" Test that we can generate an ATK script from the configuration. """
# Setup a valid KMCUnitCell.
unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.8,0.0,0.0],
[0.0,3.2,0.0],
[0.0,0.5,3.0]]),
basis_points=[[0.0, 0.0, 0.0],
[0.0, 0.5, 0.5],
[0.5,0.75,0.75]])
# Setup the lattice and types.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(1,1,1),
periodic=(False,False,False))
types = ['B','A','C']
possible_types = ['C', "A", "B", "D"]
# Setup the configuration.
config = KMCConfiguration(lattice=lattice,
types=types,
possible_types=possible_types)
# Determine a mapping between our types and valid ATK types.
# Types not present in the mapping are ignored in the ATK script.
types_mapping = { 'A' : 'Copper',
'C' : 'Iron',
'D' : 'Vanadium',
}
# Get the ATK script.
atk_script = config._atkScript(types_mapping)
# Check that it looks as we expect.
ref_script = """# ----------------------------------------------------------
# ATK 12.8.2 BulkConfiguration script generated from KMCLib
# configuration version 1.0.
# ----------------------------------------------------------
# Specify the lattice parameters.
vector_a = [ 2.80000000, 0.00000000, 0.00000000]*Angstrom
vector_b = [ 0.00000000, 3.20000000, 0.00000000]*Angstrom
vector_c = [ 0.00000000, 0.50000000, 3.00000000]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)
# Define the elements.
elements = [Copper, Iron]
# Define the coordinates.
coordinates = [[ 0.00000000e+00, 5.00000000e-01, 5.00000000e-01],
[ 5.00000000e-01, 7.50000000e-01, 7.50000000e-01]]
# Setup the configuration.
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=coordinates )
# ----------------------------------------------------------
"""
self.assertEqual(atk_script, ref_script)
def testATKScript1(self):
""" Test that we can generate an ATK script from the configuration. """
# Setup a valid KMCUnitCell.
unit_cell = KMCUnitCell(cell_vectors=numpy.array([[2.8, 0.0, 0.0],
[0.0, 3.2, 0.0],
[0.0, 0.5, 3.0]]),
basis_points=[[0.0, 0.0, 0.0], [0.0, 0.5, 0.5],
[0.5, 0.75, 0.75]])
# Setup the lattice and types.
lattice = KMCLattice(unit_cell=unit_cell,
repetitions=(1, 1, 1),
periodic=(False, False, False))
types = ['B', 'A', 'C']
possible_types = ['C', "A", "B", "D"]
# Setup the configuration.
config = KMCConfiguration(lattice=lattice,
types=types,
possible_types=possible_types)
# Determine a mapping between our types and valid ATK types.
# Types not present in the mapping are ignored in the ATK script.
types_mapping = {
'A': 'Copper',
'C': 'Iron',
'D': 'Vanadium',
}
# Get the ATK script.
atk_script = config._atkScript(types_mapping)
# Check that it looks as we expect.
ref_script = """# ----------------------------------------------------------
# ATK 12.8.2 BulkConfiguration script generated from KMCLib
# configuration version 1.0.
# ----------------------------------------------------------
# Specify the lattice parameters.
vector_a = [ 2.80000000, 0.00000000, 0.00000000]*Angstrom
vector_b = [ 0.00000000, 3.20000000, 0.00000000]*Angstrom
vector_c = [ 0.00000000, 0.50000000, 3.00000000]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)
# Define the elements.
elements = [Copper, Iron]
# Define the coordinates.
coordinates = [[ 0.00000000e+00, 5.00000000e-01, 5.00000000e-01],
[ 5.00000000e-01, 7.50000000e-01, 7.50000000e-01]]
# Setup the configuration.
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=coordinates )
# ----------------------------------------------------------
"""
self.assertEqual(atk_script, ref_script)
