def read_points(in_name):
"""
Read point charges from an in-house Ewald.c output.
The modified version of Ewald.c is needed. The extension is .pts-cry
Parameters
----------
in_name : str
Name of the file to read
Returns
-------
points : Mol object
Point charges in the file. They have element "point"
"""
with open(in_name) as pts_file:
pts_content = pts_file.readlines()
# store point charges here
points = Mol([])
for line in pts_content:
xIn, yIn, zIn, qIn = map(float, line.split())
point = Atom("point", xIn, yIn, zIn, qIn)
points.append(point)
return points
def read_cube(in_file):
"""
Read a cube file and return a Mol and a CubeGrid object
Parameters
----------
in_file : str
Input file name
Returns
-------
out_mol : Mol object
The atoms in the cube file
out_cub : CubeGrid object
The grid in the cube file where all distances are in Angstrom
"""
vectors = np.zeros((3, 3))
xyz_nums = [0, 0, 0]
values = []
out_mol = Mol([])
ind = 0
natoms = 0
with open(in_file) as lines:
for line in lines:
if ind == 2:
natoms = int(line.split()[0])
origin = np.array([float(i)
for i in line.split()[1:]]) / pt.bohrconv
if ind == 3:
xyz_nums[0] = int(line.split()[0])
vectors[0] = np.array([float(i) for i in line.split()[1:]
]) / pt.bohrconv
if ind == 4:
xyz_nums[1] = int(line.split()[0])
vectors[1] = np.array([float(i) for i in line.split()[1:]
]) / pt.bohrconv
if ind == 5:
xyz_nums[2] = int(line.split()[0])
vectors[2] = np.array([float(i) for i in line.split()[1:]
]) / pt.bohrconv
out_cub = CubeGrid(vectors, xyz_nums[0], xyz_nums[1],
xyz_nums[2], origin)
out_cub.set_grid_coord()
if 6 <= ind < (6 + natoms):
line_s = line.split()
new_atom = Atom()
new_atom.elem = per.num_to_elem(int(line_s[0]))
new_atom.set_pos([float(i) / pt.bohrconv for i in line_s[2:]])
out_mol.append(new_atom)
if ind >= (6 + natoms):
values.extend([float(i) for i in line.split()])
ind += 1
values_arr = np.array(values)
out_cub.grid[:, 3] = values_arr
return out_cub, out_mol
def test_sample(benz_pot_cub, benz_cell):
pts = fi.shell_region(benz_pot_cub.grid, benz_cell, 0.2, 0.7)
out_mol = Mol([])
for point in pts:
out_mol.append(Atom("point", point[0], point[1], point[2]))
