def tests():
# Currently assume some relative path stuff. This is apt to change once we
# make this into a module.
sys.path.insert(0, "..") # Make this the first thing since we want to override
from XYZ import XYZ # XYZ class
from reax_connection_table import Connection_Table
# Test files location:
structure_file = "tests/a10a_ph7.xyz"
connection_table_file = "tests/a10a_ph7.connect"
# Read in XYZ file. Store all the coordinates.
simulation_atoms = XYZ()
simulation_atoms.load(structure_file) # simulation_atoms.rows contains the data
print "Structure file loaded successfully: " + structure_file
# Read in connection table (ReaxFF fort.7 style, see ReaxFF manual for more info)
connection_table = Connection_Table()
connection_table.load(connection_table_file)
connection_table.next()
print "Connection table file loaded successfully: " + connection_table_file
molecule_helper = Molecule_Helper()
molecule_helper.simulation_atoms_class = simulation_atoms
molecule_helper.connection_table_class = connection_table
molecule_helper.bondorder_cutoff = 0.6
assert molecule_helper.atom_label_list_to_formula(["H", "O", "H"]) == "H2O"
# print molecule_helper.atom_label_list_to_formula(['H', 'O', 'H'])
assert molecule_helper.atom_label_list_to_formula(["H"]) == "H"
assert molecule_helper.atom_label_list_to_formula(["H", "H", "Ti", "O", "Ti", "P"]) == "H2OPTi2"
all_molecules = molecule_helper.get_all_molecules()
# We compare this to molfra.out file generated by ReaxFF with bond order
# cutoff of 0.6
assert molecule_helper.molecule_list_to_frequency_dict(all_molecules) == {
"HO20Ti10": 1,
"H2O81Ti40": 1,
"H3O41Ti20": 1,
"H2O": 149,
"O20Ti10": 6,
"HO": 1,
"H2O40Ti20": 1,
"HO21Ti10": 3,
}
print "All tests completed successfully!"
sys.exit(0)
def tests():
#Currently assume some relative path stuff. This is apt to change once we
#make this into a module.
sys.path.insert(0, "..") #Make this the first thing since we want to override
from XYZ import XYZ #XYZ class
from reax_connection_table import Connection_Table
#Test files location:
structure_file = 'tests/a10a_ph7.xyz'
connection_table_file = 'tests/a10a_ph7.connect'
#Read in XYZ file. Store all the coordinates.
simulation_atoms = XYZ()
simulation_atoms.load(structure_file) #simulation_atoms.rows contains the data
print 'Structure file loaded successfully: '+structure_file
#Read in connection table (ReaxFF fort.7 style, see ReaxFF manual for more info)
connection_table = Connection_Table()
connection_table.load(connection_table_file)
connection_table.next()
print 'Connection table file loaded successfully: '+connection_table_file
molecule_helper = Molecule_Helper()
molecule_helper.simulation_atoms_class = simulation_atoms
molecule_helper.connection_table_class = connection_table
molecule_helper.bondorder_cutoff = 0.6
assert molecule_helper.atom_label_list_to_formula(['H', 'O', 'H']) == 'H2O'
#print molecule_helper.atom_label_list_to_formula(['H', 'O', 'H'])
assert molecule_helper.atom_label_list_to_formula(['H']) == 'H'
assert molecule_helper.atom_label_list_to_formula(['H', 'H', 'Ti', 'O', 'Ti', 'P']) == 'H2OPTi2'
all_molecules = molecule_helper.get_all_molecules()
#We compare this to molfra.out file generated by ReaxFF with bond order
#cutoff of 0.6
assert molecule_helper.molecule_list_to_frequency_dict(all_molecules) == \
{'HO20Ti10': 1, 'H2O81Ti40': 1, 'H3O41Ti20': 1, 'H2O': 149, 'O20Ti10': 6, 'HO': 1, 'H2O40Ti20': 1, 'HO21Ti10': 3}
print 'All tests completed successfully!'
sys.exit(0)
