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():
from fromage.utils.atom import Atom
from fromage.utils.mol import Mol
mol_a = Mol([Atom("C", 1)])
mol_b = Mol([Atom("C", 2)])
mol_c = Mol([Atom("C", 3)])
mol_d = Mol([Atom("C", 4)])
lis = [mol_a, mol_b, mol_c, mol_d]
print(all_dimers(lis))
def test_fit_to_pot(benz_pot_cub, benz_clust_char):
print(benz_pot_cub.grid)
sample_point = Atom("", 0, 0, 0)
sample_point.es = 0.17671
print(benz_clust_char.es_pot([0, 0, 0]))
fixed_atoms = benz_clust_char.select(0)
var_atoms = Mol([i for i in benz_clust_char if i not in fixed_atoms])
fi.fit_points(var_atoms, fixed_atoms, Mol([sample_point]))
out_clust = var_atoms + fixed_atoms
print(out_clust.es_pot([0, 0, 0]))
return
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_qe(in_name):
"""
Read the final positions of a QE calculation.
Parameters
----------
in_name : str
Name of the file to read
Returns
-------
atoms : list of Atom objects
Last set of atoms in the file
"""
with open(in_name) as file_qe:
content = file_qe.readlines()
last_pos = 0
for line in content[::-1]:
if "ATOMIC_POSITIONS" in line.split():
last_pos = content[::-1].index(line)
break
atoms = []
for line in content[-last_pos:]:
if line == "End final coordinates\n":
break
elem, xPos, yPos, zPos = line.split()
atom_2_add = Atom(elem, xPos, yPos, zPos, 0)
atoms.append(atom_2_add)
return atoms
def read_gauss(in_name):
"""
Read atoms in a Gaussian input file.
The format is quite strict, better modify this function before using it.
Parameters
----------
in_name : str
Name of the file to read
Returns
-------
atoms : list of Atom objects
Last set of atoms in the file
"""
with open(in_name) as file_gauss:
content = file_gauss.readlines()
for line in content:
if line != "\n":
if line.split()[0].isdigit():
last_pos = content.index(line)
break
atoms = []
for line in content[last_pos + 1:]:
if line == "\n" or not line:
break
elem, xPos, yPos, zPos = line.split()
atom_2_add = Atom(elem, xPos, yPos, zPos, 0)
atoms.append(atom_2_add)
return atoms
def read_g_pos(in_name):
"""
Read positions from a Gaussian log file.
Parameters
----------
in_name : str
Name of the file to read
Returns
-------
atoms : list of Atom objects
Atomic positions at the beginning of the file for a single point .log
"""
with open(in_name) as gauss_file:
content = gauss_file.readlines()
# Input orientation
for i, line in enumerate(content):
if 'Input orientation:' in line:
ori_line = i
break
atoms = []
for line in content[ori_line + 5:]:
if not line.strip()[0].isdigit(): # if line not number
break
line_bits = [float(i) for i in line.split()]
symbol = per.num_to_elem(line_bits[1])
atom_to_add = Atom(symbol, line_bits[3], line_bits[4], line_bits[5], 0)
atoms.append(atom_to_add)
return atoms
def read_vasp(in_name):
"""
Read VASP POSCAR-like file.
The real use of this function is to handle one file which contains both
coordinates and vectors. The actual VASP program is not used anywhere else.
Make sure the "lattice constant" scaling is set to 1.0, "selective dynamics"
is not enabled and the file is in Cartesian coordinates.
Parameters
----------
in_name : str
Name of the file to read
Returns
-------
M : 3x3 matrix
Lattice vectors
atoms : list of Atom types
Atoms in the file
"""
with open(in_name) as vasp_file:
vasp_content = vasp_file.readlines()
# lattice vectors
vec1 = vasp_content[2].split()
vec2 = vasp_content[3].split()
vec3 = vasp_content[4].split()
# matrix from vectors
M = np.zeros((3, 3))
M[0] = vec1
M[1] = vec2
M[2] = vec3
# reads names of elements and amounts
species = vasp_content[5].split()
amounts_str = vasp_content[6].split()
amounts = map(int, amounts_str)
# make Atom objects from file
atoms = []
for element in species:
# position of the first and last atom of one kind
# in the vasp file
firstAt = 8 + sum(amounts[:species.index(element)])
lastAt = 8 + sum(amounts[:species.index(element) + 1])
for line in vasp_content:
if vasp_content.index(line) in range(firstAt, lastAt):
xAtom, yAtom, zAtom = map(float, line.split())
atoms.append(Atom(element, xAtom, yAtom, zAtom))
return M, atoms
def test_fit_benz_clust(benz_clust_char):
sample_point = Atom("", 0, 0, 0)
sample_point2 = Atom("", 0.1, 0, 0)
sample_point.es = 0
sample_point2.es = 0
fi.fit_points(benz_clust_char, None, Mol([sample_point, sample_point2]))
return
def test_fit_benz_clust_shell(benz_clust_char):
sample_point = Atom("", 0, 0, 0)
sample_point2 = Atom("", 0.1, 0, 0)
sample_point.es = 0
sample_point2.es = 0
fixed_atoms = benz_clust_char.select(0)
var_atoms = Mol([i for i in benz_clust_char if i not in fixed_atoms])
fi.fit_points(var_atoms, fixed_atoms, Mol([sample_point, sample_point2]))
return
def test_same_atoms_as():
mol_a_lis = [Atom("C", 1., 0., 0.), Atom("H", 1., 1., 1.)]
mol_b_lis = [Atom("H", 1., 1., 1.), Atom("C", 1., 0., 0.)]
mol_c_lis = [Atom("C", 1., 0., 0.), Atom("C", 1., 1., 1.)]
mol_a = Mol(mol_a_lis)
mol_b = Mol(mol_b_lis)
mol_c = Mol(mol_c_lis)
assert mol_a.same_atoms_as(mol_b) == True
assert mol_a.same_atoms_as(mol_c) == False
def read_xyz(in_name):
"""
Read a .xyz file.
Works for files containing several configurations e.g. a relaxation
trajectory.
Parameters
----------
in_name : str
Name of the file to read
Returns
-------
atom_step = list of lists of Atom objects
Each element of the list represents a configuration of atoms
"""
with open(in_name) as xyz_file:
xyz_content = xyz_file.readlines()
# main list where each element is a relaxation step
atom_step = []
for i, line in enumerate(xyz_content):
# if the line is the amount of atoms in the system
if line.strip():
if line.split()[0].isdigit():
# list of atom objects inside on relaxation step
atoms = []
# from 2 lines after the amount of atoms to the last atom line
# for the relaxation step
for line_in_step in xyz_content[i + 2:i + int(line) + 2]:
elemAtom = line_in_step.split()[0]
xAtom, yAtom, zAtom = map(float, line_in_step.split()[1:])
atoms.append(Atom(elemAtom, xAtom, yAtom, zAtom))
atom_step.append(atoms)
xyz_file.close()
return atom_step
def array2atom(template, pos):
"""
Turn an array of the form x1, y1, z1, x2, y2, z2 etc. into a list of Atom
objects
Parameters
----------
template : list of Atom objects
A list of the same length of the desired one used to determine the
elements of the atoms
pos : list of floats
List of coordinates of the form x1, y1, z1, x2, y2, z2 etc.
Returns
-------
out_atoms : list of Atom objects
Resulting atoms
"""
sliced_pos = [pos[i:i + 3] for i in range(0, len(pos), 3)]
out_atoms = []
for atom in zip(template, sliced_pos):
new_atom = Atom(atom[0].elem, atom[1][0], atom[1][1], atom[1][2], 0)
out_atoms.append(new_atom)
return out_atoms
def o_at():
"""Return am O Atom object at x = 0.8"""
out_at = Atom("O", 0.8, 0.0, 0.0)
return out_at
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]))
def c_o():
c_at = Atom("C", 0.0, 0.0, 0.0)
o_at = Atom("O", 1.0, 0.0, 0.0)
out_mol = Mol([c_at, o_at])
return out_mol
def c_o():
"""CO Mol object"""
c_at = Atom("C", 0.0, 0.0, 0.0)
o_at = Atom("O", 1.0, 0.0, 0.0)
out_mol = Mol([c_at, o_at])
return out_mol
def newat():
"""Atom object C at origin"""
return Atom("C", 0.0, 0.0, 0.0)
def c_at():
"""Return a C Atom object at origin"""
out_at = Atom("C", 0.0, 0.0, 0.0)
return out_at
def o_at_outside():
"""Return am O Atom object outside of the 111 cell"""
out_at = Atom("O", 2.1, -0.3, 1.4)
return out_at