def setUp(self):
self.symbols = ['Mg','O']
self.param_names = ['chrg_Mg', 'chrg_O',
'MgMg_A', 'MgMg_rho', 'MgMg_C',
'OO_A', 'OO_rho', 'OO_C',
'MgO_A', 'MgO_rho', 'MgO_C']
self.pot = potential.Buckingham(symbols = self.symbols)
def test_to_string_w_param_dict(self):
param_dict = {}
param_dict['chrg_Mg'] = +2.0
param_dict['chrg_O'] = -2.0
param_dict['MgMg_A'] = 0.0
param_dict['MgMg_rho'] = 0.5
param_dict['MgMg_C'] = 0.0
param_dict['MgO_A'] = 821.6
param_dict['MgO_rho'] = 0.3242
param_dict['MgO_C'] = 0.0
param_dict['OO_A'] = 2274.00
param_dict['OO_rho'] = 0.1490
param_dict['OO_C'] = 27.88
pot_orig = potential.Buckingham(symbols = symbols)
print(pot_orig.to_string(param_dict))
def setUp(self):
self.symbols = ['Mg','O']
self.param_names = ['chrg_Mg', 'chrg_O',
'MgMg_A', 'MgMg_rho', 'MgMg_C',
'OO_A', 'OO_rho', 'OO_C',
'MgO_A', 'MgO_rho', 'MgO_C']
self.param_dict = {}
self.param_dict['chrg_Mg'] = +2.0
self.param_dict['chrg_O'] = -2.0
self.param_dict['MgMg_A'] = 0.0
self.param_dict['MgMg_rho'] = 0.5
self.param_dict['MgMg_C'] = 0.0
self.param_dict['MgO_A'] = 821.6
self.param_dict['MgO_rho'] = 0.3242
self.param_dict['MgO_C'] = 0.0
self.param_dict['OO_A'] = 2274.00
self.param_dict['OO_rho'] = 0.1490
self.param_dict['OO_C'] = 27.88
self.pot_orig = potential.Buckingham(symbols = self.symbols)
def setUp(self):
symbols = ['Mg', 'O']
fname = 'potential.mod'
param_dict = {}
param_dict['chrg_Mg'] = +2.0
param_dict['chrg_O'] = -2.0
param_dict['MgMg_A'] = 0.0
param_dict['MgMg_rho'] = 0.5
param_dict['MgMg_C'] = 0.0
param_dict['MgO_A'] = 821.6
param_dict['MgO_rho'] = 0.3242
param_dict['MgO_C'] = 0.0
param_dict['OO_A'] = 2274.00
param_dict['OO_rho'] = 0.1490
param_dict['OO_C'] = 27.88
self.buck = potential.Buckingham(symbols=symbols)
self.buck.param = param_dict.copy()
self.task = lammps_task.LammpsMinimizeStructure(fname, self.buck)
gulp_input_filename = 'gulp.in'
#task = GulpPhononCalculation(task_name,task_directory)
#### TEST POTENTIAL POTENTIAL ####
#print('----- test that buckingham potential provides the right format -----')
#task.potential = potential.Buckingham(['Mg','O'])
#task.param_dict = copy.deepcopy(param_dict)
#print(task.potential.gulp_potential_section_to_string(param_dict))
#### TEST IF WE CAN CAN WRITE THE INPUT FILE ####
#gulp_input_filename = os.path.join(task.task_directory,'gulp.in')
#poscar_input_filename = os.path.join('rsrc','MgO_NaCl_prim.vasp')
#task.write_gulp_input_file(\
# filename=gulp_input_filename,
# poscar=vasp_input_filename)
#### TEST IF WE CAN RUN THE BUCKINGHAM POTENTIAL ####
#task.structure_filename = os.path.join('rsrc','MgO_NaCl_prim.vasp')
#task.run()
task = GulpPhononCalculation(task_name, task_directory)
task.potential = potential.Buckingham(['Mg', 'O'])
task.param_dict = copy.deepcopy(param_dict)
task.structure_file = os.path.join(\
task.task_directory,
vasp_input_filename)
task.write_gulp_input_file(\
filename=os.path.join(task.task_directory,gulp_input_filename),
poscar=vasp_input_filename)
task.run()
import pypospack.task.lammps as tsk_lammps
import pypospack.potential as potential
if __name__ == '__main__':
task_name = 'task_name'
task_directory = 'task_name'
task = tsk_lammps.LammpsSimulation(\
task_name = task_name,
task_directory = task_directory)
print('task.status:{}'.format(task.status))
pot = potential.Buckingham(['Mg', 'O'])
task.potential = pot
print('write_lammps_input_file():{}'.format(
task.lammps_input_file_to_string()))
def test_attr_param_dict(self):
for p in self.param_names:
self.assertEqual(
self.pot_clone.param[p],
self.pot_orig.param[p])
if __name__ == '__main__':
# unittest.main()
symbols = ['Mg','O']
param_names = ['chrg_Mg', 'chrg_O',
'MgMg_A', 'MgMg_rho', 'MgMg_C',
'OO_A', 'OO_rho', 'OO_C',
'MgO_A', 'MgO_rho', 'MgO_C']
param_dict = {}
param_dict['chrg_Mg'] = +2.0
param_dict['chrg_O'] = -2.0
param_dict['MgMg_A'] = 0.0
param_dict['MgMg_rho'] = 0.5
param_dict['MgMg_C'] = 0.0
param_dict['MgO_A'] = 821.6
param_dict['MgO_rho'] = 0.3242
param_dict['MgO_C'] = 0.0
param_dict['OO_A'] = 2274.00
param_dict['OO_rho'] = 0.1490
param_dict['OO_C'] = 27.88
pot_orig = potential.Buckingham(symbols = symbols)
print(pot_orig.to_string(param_dict))