def test_class_unit():
assert np.allclose(units.convert('J', 'J', 'J'), 1)
assert approx(units.convert('kg', 'g')) == 1.e3
assert approx(units.convert('eV', 'J')) == 1.60217733e-19
assert approx(units.convert('J', 'eV')) == 1/1.60217733e-19
assert approx(units.convert('J^2', 'eV**2')) == (1/1.60217733e-19) ** 2
assert approx(units.convert('J/2', 'eV/2')) == (1/1.60217733e-19)
assert approx(units.convert('J', 'eV/2')) == (1/1.60217733e-19) * 2
assert approx(units.convert('J2', '2eV')) == (1/1.60217733e-19)
assert approx(units.convert('J2', 'eV')) == (1/1.60217733e-19) * 2
assert approx(units.convert('J/m', 'eV/Ang')) == unit_convert('J', 'eV') / unit_convert('m', 'Ang')
units('J**eV', 'eV**eV')
units('J/m', 'eV/m')
def _read_supercell(self):
""" Deferred routine """
f, l = self.step_to('unit_cell_cart', case=False)
if not f:
raise ValueError(
"The unit-cell vectors could not be found in the seed-file.")
l = self.readline()
lines = []
while not l.startswith('end'):
lines.append(l)
l = self.readline()
# Check whether the first element is a specification of the units
pos_unit = lines[0].split()
if len(pos_unit) > 2:
unit = 1.
else:
unit = unit_convert(pos_unit[0].capitalize(), 'Ang')
# Remove the line with the unit...
lines.pop(0)
# Create the cell
cell = np.empty([3, 3], np.float64)
for i in [0, 1, 2]:
cell[i, :] = [float(x) for x in lines[i].split()]
return SuperCell(cell * unit)
def _read_geometry(self, sc, *args, **kwargs):
""" Defered routine """
is_frac = True
f, _ = self.step_to('atoms_frac', case=False)
if not f:
is_frac = False
self.fh.seek(0)
f, _ = self.step_to('atoms_cart', case=False)
if not f:
raise ValueError("The geometry coordinates (atoms_frac/cart) could not be found in the seed-file.")
# Read the next line to determine the units
unit = self.readline()
unit = unit_convert(unit.strip().capitalize(), 'Ang')
s = []
xyz = []
l = self.readline()
while not 'end' in l:
# Get the species and
l = l.split()
s.append(l[0])
xyz.append(list(map(float, l[1:4])))
l = self.readline()
# Convert
xyz = np.array(xyz, np.float64) * unit
if is_frac:
xyz = np.dot(sc.cell.T, xyz.T).T
return Geometry(xyz, atom=s, sc=sc)
def test_unit_convert():
assert approx(unit_convert('kg', 'g')) == 1.e3
assert approx(unit_convert('eV', 'J')) == 1.60217733e-19
assert approx(unit_convert('J', 'eV')) == 1/1.60217733e-19
assert approx(unit_convert('J', 'eV', opts={'^': 2})) == (1/1.60217733e-19) ** 2
assert approx(unit_convert('J', 'eV', opts={'/': 2})) == (1/1.60217733e-19) / 2
assert approx(unit_convert('J', 'eV', opts={'*': 2})) == (1/1.60217733e-19) * 2
from __future__ import division, print_function
# Import sile objects
from .sile import SileScaleUp
from ..sile import *
# Import the geometry object
import sisl._array as _a
from sisl import Geometry, Atom, SuperCell
from sisl.unit import unit_convert
import numpy as np
__all__ = ['refSileScaleUp', 'restartSileScaleUp']
Bohr2Ang = unit_convert('Bohr', 'Ang')
Ang2Bohr = unit_convert('Ang', 'Bohr')
class refSileScaleUp(SileScaleUp):
""" REF file object for ScaleUp """
@Sile_fh_open
def read_supercell(self):
""" Reads a supercell from the Sile """
# 1st line is number of supercells
nsc = _a.fromiteri(map(int, self.readline().split()[:3]))
self.readline() # natoms, nspecies
self.readline() # species
cell = _a.fromiterd(map(float, self.readline().split()[:9]))
# Typically ScaleUp uses very large unit-cells
# so supercells will typically be restricted to [3, 3, 3]
"""
Sile object for reading/writing ascii files from BigDFT
"""
from .sile import SileBigDFT
from ..sile import *
from sisl._internal import set_module
from sisl import Geometry, Atom, SuperCell
from sisl.unit import unit_convert
import numpy as np
__all__ = ['asciiSileBigDFT']
Bohr2Ang = unit_convert('Bohr', 'Ang')
@set_module("sisl.io.bigdft")
class asciiSileBigDFT(SileBigDFT):
""" ASCII file object for BigDFT """
def _setup(self, *args, **kwargs):
""" Initialize for `asciiSileBigDFT` """
self._comment = ['#', '!']
@sile_fh_open()
def read_geometry(self):
""" Reads a supercell from the Sile """
# 1st line is arbitrary
self.readline(True)
def test_unit_convert_f2():
with pytest.raises(ValueError):
unit_convert('eV', 'kg')
def test_unit_convert_f1():
with pytest.raises(ValueError):
unit_convert('eV', 'megaerg')
def test_unit_convert_f2():
unit_convert('eV', 'kg')
def test_unit_convert_f1():
unit_convert('eV', 'megaerg')
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
import numpy as np
# Import sile objects
from sisl.io.sile import *
from sisl._internal import set_module
from sisl import Geometry, Atom, SuperCell, Grid, SislError
from sisl.unit import unit_convert
__all__ = ['cubeSile']
Ang2Bohr = unit_convert('Ang', 'Bohr')
@set_module("sisl.io")
class cubeSile(Sile):
""" CUBE file object """
@sile_fh_open()
def write_supercell(self,
sc,
fmt='15.10e',
size=None,
origin=None,
*args,
**kwargs):
""" Writes `SuperCell` object attached to this grid
Parameters
