def main(args):
function = get_function(args.function)
distances = np.linspace(args.range[0], args.range[1], args.ndata)
with connect(args.dbname) as db:
for d in distances:
pos_dict = {
"units":
"angstroem",
"boundary_conditions":
"free",
"positions": [
{
args.element: [0, 0, 0]
},
{
args.element: [d, 0, 0]
},
],
}
posinp = Posinp.from_dict(pos_dict)
atoms = posinp_to_ase_atoms(posinp)
energy = function.value(d)
forces = np.array([
[-1.0 * function.first_derivative(-d), 0, 0],
[-1.0 * function.first_derivative(d), 0, 0],
])
db.write(atoms, data={"energy": energy, "forces": forces})
def generate_graphene_cell(xsize, zsize):
base_cell = np.array([2.4674318, 0, 4.2737150])
positions = []
reduced_pos = np.array([[0, 0, 0], [0, 0, 1.0 / 3], [0.5, 0, 0.5],
[0.5, 0, 5.0 / 6]])
for i in range(xsize):
for j in range(zsize):
p = (np.array([i, 0, j]) + reduced_pos) * base_cell
for pi in p:
positions.append({"C": pi})
pos_dict = {
"units": "angstroem",
"cell": base_cell * np.array([xsize, 0, zsize]),
"positions": positions,
}
pos = Posinp.from_dict(pos_dict)
return pos