Coverage for /builds/kinetik161/ase/ase/io/cube.py: 89.32%
103 statements
« prev ^ index » next coverage.py v7.2.7, created at 2023-12-10 11:04 +0000
1"""
2IO support for the Gaussian cube format.
4See the format specifications on:
5http://local.wasp.uwa.edu.au/~pbourke/dataformats/cube/
6"""
8import time
10import numpy as np
12from ase.atoms import Atoms
13from ase.io import read
14from ase.units import Bohr
16ATOMS = 'atoms'
17CASTEP = 'castep'
18DATA = 'data'
21def write_cube(file_obj, atoms, data=None, origin=None, comment=None):
22 """Function to write a cube file.
24 file_obj: str or file object
25 File to which output is written.
26 atoms: Atoms
27 The Atoms object specifying the atomic configuration.
28 data : 3-dim numpy array, optional (default = None)
29 Array containing volumetric data as e.g. electronic density
30 origin : 3-tuple
31 Origin of the volumetric data (units: Angstrom)
32 comment : str, optional (default = None)
33 Comment for the first line of the cube file.
34 """
36 if data is None:
37 data = np.ones((2, 2, 2))
38 data = np.asarray(data)
40 if data.dtype == complex:
41 data = np.abs(data)
43 if comment is None:
44 comment = "Cube file from ASE, written on " + time.strftime("%c")
45 else:
46 comment = comment.strip()
47 file_obj.write(comment)
49 file_obj.write("\nOUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z\n")
51 if origin is None:
52 origin = np.zeros(3)
53 else:
54 origin = np.asarray(origin) / Bohr
56 file_obj.write(
57 "{:5}{:12.6f}{:12.6f}{:12.6f}\n".format(
58 len(atoms), *origin))
60 for i in range(3):
61 n = data.shape[i]
62 d = atoms.cell[i] / n / Bohr
63 file_obj.write("{:5}{:12.6f}{:12.6f}{:12.6f}\n".format(n, *d))
65 positions = atoms.positions / Bohr
66 numbers = atoms.numbers
67 for Z, (x, y, z) in zip(numbers, positions):
68 file_obj.write(
69 "{:5}{:12.6f}{:12.6f}{:12.6f}{:12.6f}\n".format(
70 Z, 0.0, x, y, z)
71 )
73 data.tofile(file_obj, sep="\n", format="%e")
76def read_cube(file_obj, read_data=True, program=None, verbose=False):
77 """Read atoms and data from CUBE file.
79 file_obj : str or file
80 Location to the cube file.
81 read_data : boolean
82 If set true, the actual cube file content, i.e. an array
83 containing the electronic density (or something else )on a grid
84 and the dimensions of the corresponding voxels are read.
85 program: str
86 Use program='castep' to follow the PBC convention that first and
87 last voxel along a direction are mirror images, thus the last
88 voxel is to be removed. If program=None, the routine will try
89 to catch castep files from the comment lines.
90 verbose : bool
91 Print some more information to stdout.
93 Returns a dict with the following keys:
95 * 'atoms': Atoms object
96 * 'data' : (Nx, Ny, Nz) ndarray
97 * 'origin': (3,) ndarray, specifying the cube_data origin.
98 * 'spacing': (3, 3) ndarray, representing voxel size
99 """
101 readline = file_obj.readline
102 line = readline() # the first comment line
103 line = readline() # the second comment line
105 # The second comment line *CAN* contain information on the axes
106 # But this is by far not the case for all programs
107 axes = []
108 if "OUTER LOOP" in line.upper():
109 axes = ["XYZ".index(s[0]) for s in line.upper().split()[2::3]]
110 if not axes:
111 axes = [0, 1, 2]
113 # castep2cube files have a specific comment in the second line ...
114 if "castep2cube" in line:
115 program = CASTEP
116 if verbose:
117 print("read_cube identified program: castep")
119 # Third line contains actual system information:
120 line = readline().split()
121 num_atoms = int(line[0])
123 # num_atoms can be negative.
124 # Negative num_atoms indicates we have extra data to parse after
125 # the coordinate information.
126 has_labels = num_atoms < 0
127 num_atoms = abs(num_atoms)
129 # There is an optional last field on this line which indicates
130 # the number of values at each point. It is typically 1 (the default)
131 # in which case it can be omitted, but it may also be > 1,
132 # for example if there are multiple orbitals stored in the same cube.
133 num_val = int(line[4]) if len(line) == 5 else 1
135 # Origin around which the volumetric data is centered
136 # (at least in FHI aims):
137 origin = np.array([float(x) * Bohr for x in line[1:4:]])
139 cell = np.empty((3, 3))
140 shape = []
141 spacing = np.empty((3, 3))
143 # The upcoming three lines contain the cell information
144 for i in range(3):
145 n, x, y, z = (float(s) for s in readline().split())
146 shape.append(int(n))
148 # different PBC treatment in castep, basically the last voxel row is
149 # identical to the first one
150 if program == CASTEP:
151 n -= 1
152 cell[i] = n * Bohr * np.array([x, y, z])
153 spacing[i] = np.array([x, y, z]) * Bohr
154 pbc = [(v != 0).any() for v in cell]
156 numbers = np.empty(num_atoms, int)
157 positions = np.empty((num_atoms, 3))
158 for i in range(num_atoms):
159 line = readline().split()
160 numbers[i] = int(line[0])
161 positions[i] = [float(s) for s in line[2:]]
163 positions *= Bohr
165 atoms = Atoms(numbers=numbers, positions=positions, cell=cell, pbc=pbc)
167 # CASTEP will always have PBC, although the cube format does not
168 # contain this kind of information
169 if program == CASTEP:
170 atoms.pbc = True
172 dct = {ATOMS: atoms}
173 labels = []
175 # If we originally had a negative num_atoms, parse the extra fields now.
176 # The first field of the first line tells us how many other fields there
177 # are to parse, but we have to guess how many rows this information is
178 # split over.
179 if has_labels:
180 # Can't think of a more elegant way of doing this...
181 fields = readline().split()
182 nfields = int(fields[0])
183 labels.extend(fields[1:])
185 while len(labels) < nfields:
186 fields = readline().split()
187 labels.extend(fields)
189 labels = [int(x) for x in labels]
191 if read_data:
192 # Cube files can contain more than one density,
193 # so we need to be a little bit careful about where one ends
194 # and the next begins.
195 raw_volume = [float(s) for s in file_obj.read().split()]
196 # Split each value at each point into a separate list.
197 raw_volumes = [np.array(raw_volume[offset::num_val])
198 for offset in range(0, num_val)]
200 datas = []
202 # Adjust each volume in turn.
203 for data in raw_volumes:
204 data = data.reshape(shape)
205 if axes != [0, 1, 2]:
206 data = data.transpose(axes).copy()
208 if program == CASTEP:
209 # Due to the PBC applied in castep2cube, the last entry
210 # along each dimension equals the very first one.
211 data = data[:-1, :-1, :-1]
213 datas.append(data)
215 datas = np.array(datas)
217 dct[DATA] = datas[0]
218 dct["origin"] = origin
219 dct["spacing"] = spacing
220 dct["labels"] = labels
221 dct["datas"] = datas
223 return dct
226def read_cube_data(filename):
227 """Wrapper function to read not only the atoms information from a cube file
228 but also the contained volumetric data.
229 """
230 dct = read(filename, format="cube", read_data=True, full_output=True)
231 return dct[DATA], dct[ATOMS]