def load_cells():
"""Load the two test supercells."""
p1 = os.path.join(testdir(), "POSCAR")
c1 = aread(p1, format="vasp")
p2 = os.path.join(testdir(), "POSCAR2")
c2 = aread(p2, format="vasp")
return (c1, c2)
def load_cells():
"""Load the two test supercells."""
p1 = os.path.join(testdir(), "POSCAR")
c1 = aread(p1, format="vasp")
p2 = os.path.join(testdir(), "POSCAR2")
c2 = aread(p2, format="vasp")
return (c1, c2)
def read_initial_positions(args):
# Initial cif files
print("Give data directory path:")
DATAPATH = input()
print("Give directories with datafiles:")
data_flist = [folder for folder in input().split(',')]
init_dict = {}
print("Creating dictionary to keep initial positions...")
for folder in data_flist:
folder_path = DATAPATH + '/' + folder
for path in Path(folder_path).rglob('*.cif'): # every structure
struct_dict = {}
atoms = aread(path)
positions = atoms.get_positions()
count_ions = 0
for ion in atoms.get_chemical_symbols():
struct_dict[ion + str(count_ions)] = tuple(
list(positions[count_ions, :]))
count_ions += 1
init_dict[(path.name, folder)] = struct_dict
# print("File "+path.name+" is done.")
print("Dumped " + str(len(init_dict.keys())) + " structures\' initial \
positions into " + args.test_dir + "/temp.p")
import pickle
pickle.dump(init_dict, open(args.test_dir + "/temp.p", "wb"))
def setUp(self):
# The test POSCAR file is in the same directory.
path = os.path.join(testdir(), "POSCAR")
self.cell = aread(path, format="vasp")
def energy_function_wrapper(r, N, *args):
assert r.shape == (3 * N, )
pos = r.reshape(15, 3)
Cpot = pot.Coulomb()
Cpot.set_parameters(*args[1:6])
Bpot = pot.Buckingham()
Bpot.set_parameters(*args[6:])
energy = buckingham_coulomb(pos, Cpot, Bpot, N, *args[0])
print(energy)
if __name__ == '__main__':
atoms = aread("../../Data/random/RandomStart_Sr3Ti3O9/1.cif")
r = np.array(flatten(atoms.positions))
vects = np.array(atoms.get_cell())
volume = abs(np.linalg.det(vects))
N = len(atoms.get_positions())
accuracy = 0.00001 # Demanded accuracy of terms
alpha = N**(1 / 6) * pi**(1 / 2) / volume**(1 / 3)
real_cut = (-np.log(accuracy))**(1 / 2) / alpha
recip_cut = 2 * alpha * (-np.log(accuracy))**(1 / 2)
energy_function_wrapper(r, len(atoms.positions), alpha, real_cut,\
recip_cut, atoms.get_chemical_symbols(),\
charge_dict)
# res = minimize(funct, atoms.positions, method='BFGS', \
# options={'gtol': 1e-3, 'disp': True})
def setUp(self):
# The test POSCAR file is in the same directory.
path = os.path.join(testdir(), "POSCAR")
self.cell = aread(path, format="vasp")
