def get_random_cell(a, nvec):
if nvec == 0:
return Cell(None)
while True:
if a <= 0:
raise ValueError('The first argument must be strictly positive.')
rvecs = np.random.uniform(0, a, (nvec,3))
cell = Cell(rvecs)
if cell.volume > a**nvec*0.1:
return cell
def _load_vasp_header(f):
'''Load the cell and atoms from a VASP file
File specification provided here:
http://cms.mpi.univie.ac.at/vasp/guide/node59.html
**Arguments:**
f
An open file object
**Returns:** ``title``, ``cell``, ``numbers``, ``coordinates``
'''
# read the title
title = f.next().strip()
# read the universal scaling factor
scaling = float(f.next().strip())
# read cell parameters in angstrom, without the universal scaling factor.
# each row is one cell vector
rvecs = []
for i in xrange(3):
rvecs.append([float(w) for w in f.next().split()])
rvecs = np.array(rvecs)*angstrom*scaling
# Convert to cell object
cell = Cell(rvecs)
# note that in older VASP version the following line might be absent
vasp_numbers = [periodic[w].number for w in f.next().split()]
vasp_counts = [int(w) for w in f.next().split()]
numbers = []
for n, c in zip(vasp_numbers, vasp_counts):
numbers.extend([n]*c)
numbers = np.array(numbers)
line = f.next()
# the 7th line can optionally indicate selective dynamics
if line[0].lower() in ['s']:
line = f.next()
# parse direct/cartesian switch
cartesian = line[0].lower() in ['c', 'k']
# read the coordinates
coordinates = []
for line in f:
# check if all coordinates are read
if (len(line.strip()) == 0) or (len(coordinates) == numbers.shape[0]):
break
coordinates.append([float(w) for w in line.split()[:3]])
if cartesian:
coordinates = np.array(coordinates)*angstrom*scaling
else:
coordinates = np.dot(np.array(coordinates), rvecs)
return title, cell, numbers, coordinates
def _read_cube_header(f):
# Read the title
title = f.readline().strip()
# skip the second line
f.readline()
def read_grid_line(line):
"""Read a grid line from the cube file"""
words = line.split()
return (int(words[0]),
np.array([float(words[1]),
float(words[2]),
float(words[3])], float)
# all coordinates in a cube file are in atomic units
)
# number of atoms and origin of the grid
natom, origin = read_grid_line(f.readline())
# numer of grid points in A direction and step vector A, and so on
shape0, axis0 = read_grid_line(f.readline())
shape1, axis1 = read_grid_line(f.readline())
shape2, axis2 = read_grid_line(f.readline())
shape = np.array([shape0, shape1, shape2], int)
axes = np.array([axis0, axis1, axis2])
cell = Cell(axes * shape.reshape(-1, 1))
ugrid = UniformGrid(origin, axes, shape, np.ones(3, int))
def read_coordinate_line(line):
"""Read an atom number and coordinate from the cube file"""
words = line.split()
return (int(words[0]), float(words[1]),
np.array([float(words[2]),
float(words[3]),
float(words[4])], float)
# all coordinates in a cube file are in atomic units
)
numbers = np.zeros(natom, int)
pseudo_numbers = np.zeros(natom, float)
coordinates = np.zeros((natom, 3), float)
for i in xrange(natom):
numbers[i], pseudo_numbers[i], coordinates[i] = read_coordinate_line(
f.readline())
# If the pseudo_number field is zero, we assume that no effective core
# potentials were used.
if pseudo_numbers[i] == 0.0:
pseudo_numbers[i] = numbers[i]
return title, coordinates, numbers, cell, ugrid, pseudo_numbers
def _load_vasp_header(f, nskip):
'''Load the cell and atoms from a VASP file
**Arguments:**
f
An open file object
nskip
The number of lines to skip after the line with elements
**Returns:** ``title``, ``cell``, ``numbers``, ``coordinates``
'''
# reat the title
title = f.next().strip()
f.next()
# read cell parameters in angstrom. each row is one cell vector
rvecs = []
for i in xrange(3):
rvecs.append([float(w) for w in f.next().split()])
rvecs = np.array(rvecs) * angstrom
# Convert to cell object
cell = Cell(rvecs)
vasp_numbers = [periodic[w].number for w in f.next().split()]
vasp_counts = [int(w) for w in f.next().split()]
numbers = []
for n, c in zip(vasp_numbers, vasp_counts):
numbers.extend([n] * c)
numbers = np.array(numbers)
# skip some lines
for i in xrange(nskip):
f.next()
assert f.next().startswith('Direct')
# read the fractional coordinates and convert to Cartesian
coordinates = []
for line in f:
if len(line.strip()) == 0:
break
coordinates.append([float(w) for w in line.split()[:3]])
coordinates = np.dot(np.array(coordinates), rvecs)
return title, cell, numbers, coordinates
def eval_spline(self, cubic_spline, center, output, cell=None):
'''Evaluate a spherically symmetric function
**Arguments:**
cubic_spline
A cubic spline with the radial dependence
center
The center of the spherically symmetric function
output
The output array
**Optional arguments:**
cell
A unit cell when periodic boundary conditions are used.
'''
if cell is None:
cell = Cell(None)
eval_spline_grid(cubic_spline, center, output, self.points, cell)
def eval_decomposition(self, cubic_splines, center, output, cell=None):
'''Evaluate a spherical decomposition
**Arguments:**
cubic_splines
A list cubic splines, where each item is a radial function
that is associated with a corresponding real spherical harmonic.
center
The center of the spherically symmetric function
output
The output array
**Optional arguments:**
cell
A unit cell when periodic boundary conditions are used.
'''
if cell is None:
cell = Cell(None)
eval_decomposition_grid(cubic_splines, center, output, self.points, cell)
def eval_spline(self, cubic_spline, center, output, cell=None):
if cell is None:
cell = Cell(None)
eval_spline_grid(cubic_spline, center, output, self.points, cell)
