def hex_to_ortho(cell, tol=1e-5):
try:
assert np.isclose(cell.box.a, cell.box.b, rtol=tol)
assert not np.isclose(cell.box.a, cell.box.c, rtol=tol)
assert np.isclose(cell.box.alpha, 90.0, rtol=tol)
assert np.isclose(cell.box.beta, 90.0, rtol=tol)
assert np.isclose(cell.box.gamma, 120.0, rtol=tol) or np.isclose(cell.box.gamma, 60.0, rtol=tol)
except:
raise ValueError('Not a standard hexagonal box')
newcell = am.supersize(cell, 1, 2, 1)
newcell.normalize(style='lammps')
new_b = cell.box.b * 3.**0.5
newcell.box_set(origin=[0.0, 0.0, 0.0], scale=True)
newcell.box_set(a=cell.box.a, b=new_b, c=cell.box.c,
alpha=90.0, beta=90.0, gamma=90.0,
origin=cell.box.origin)
newcell.wrap()
return newcell
def hex_to_ortho(cell, tol=1e-5):
try:
assert np.isclose(cell.box.a, cell.box.b, rtol=tol)
assert not np.isclose(cell.box.a, cell.box.c, rtol=tol)
assert np.isclose(cell.box.alpha, 90.0, rtol=tol)
assert np.isclose(cell.box.beta, 90.0, rtol=tol)
assert np.isclose(cell.box.gamma, 120.0, rtol=tol) or np.isclose(cell.box.gamma, 60.0, rtol=tol)
except:
raise ValueError('Not a standard hexagonal box')
newcell = am.supersize(cell, 1, 2, 1)
newcell.normalize(style='lammps')
new_b = cell.box.b * 3.**0.5
newcell.box_set(origin=[0.0, 0.0, 0.0], scale=True)
newcell.box_set(a=cell.box.a, b=new_b, c=cell.box.c,
alpha=90.0, beta=90.0, gamma=90.0,
origin=cell.box.origin)
newcell.wrap()
return newcell
def trig_to_hex(cell, tol=1e-5):
try:
assert np.isclose(cell.box.a, cell.box.b, rtol=tol)
assert np.isclose(cell.box.a, cell.box.c, rtol=tol)
assert np.isclose(cell.box.alpha, cell.box.beta, rtol=tol)
assert np.isclose(cell.box.alpha, cell.box.beta, rtol=tol)
assert cell.box.alpha < 120.0
except:
raise ValueError('Not a standard trigonal box')
newcell = am.supersize(cell, 3, 1, 1)
newcell.box_set(avect = cell.box.bvect - cell.box.avect,
bvect = cell.box.avect - cell.box.cvect,
cvect = cell.box.avect + cell.box.bvect + cell.box.cvect,
origin= cell.box.origin)
newcell.wrap()
return newcell
def trig_to_hex(cell, tol=1e-5):
try:
assert np.isclose(cell.box.a, cell.box.b, rtol=tol)
assert np.isclose(cell.box.a, cell.box.c, rtol=tol)
assert np.isclose(cell.box.alpha, cell.box.beta, rtol=tol)
assert np.isclose(cell.box.alpha, cell.box.beta, rtol=tol)
assert cell.box.alpha < 120.0
except:
raise ValueError('Not a standard trigonal box')
newcell = am.supersize(cell, 3, 1, 1)
newcell.box_set(avect = cell.box.bvect - cell.box.avect,
bvect = cell.box.avect - cell.box.cvect,
cvect = cell.box.avect + cell.box.bvect + cell.box.cvect,
origin= cell.box.origin)
newcell.wrap()
return newcell
def supersize(self, a_size, b_size, c_size):
system = am.supersize(self, a_size, b_size, c_size)
self.__box = system.box
self.__atoms = system.atoms
self.__pbc = system.pbc
self.__prop = system.prop
def rotate_cubic(system, axes):
"""
Rotate a cubic system according to the specified crystallographic axes.
Returns an orthogonal system whose box lengths are:
a * sqrt(i^2+j^2+k^2)
where a is the original cubic box length, and ijk are the crystallographic
indicies for the specific direction.
"""
axes = np.asarray(axes)
#rotate system generically
system = am.rotate(system, axes)
#test for cubic
a = system.box.a
try:
assert np.isclose(a, system.box.b), str(a) + ' ' + str(system.box.b)
assert np.isclose(a, system.box.c), str(a) + ' ' + str(system.box.c)
assert np.isclose(90.0, system.box.alpha), str(system.box.alpha)
assert np.isclose(90.0, system.box.beta), str(system.box.beta)
assert np.isclose(90.0, system.box.gamma), str(system.box.gamma)
except:
raise ValueError('Cubic system not given')
#Test for integer axes values
try:
for ax_val in axes.flat:
assert np.isclose(ax_val, int(ax_val))
except:
raise ValueError('axes values must be integers')
#Get magnitudes of the axes
mag = np.linalg.norm(axes, axis=1)
#compute number of atoms for the new system
natoms = system.natoms*mag[0]*mag[1]*mag[2]
if np.isclose(int(round(natoms)), natoms):
natoms = int(round(natoms))
else:
raise ValueError('not an integer number of atoms associated with the axes.')
#create a new box with scaled lattice parameters
box = am.Box(a=a*mag[0], b=a*mag[1], c=a*mag[2], origin=system.box.origin)
#supersize the rotated box
m = int(ceil(max(mag)))
system = am.supersize(system, (-m, m), (-m, m), (-m, m))
#filter atoms for only those in the new box
data = system.atoms.data
#round x-positions near xlo, xhi and only keep data for atoms where xlo <= x < xhi
data[np.where(np.isclose(data.T[1], box.xlo, atol=1e-8, rtol=0)), 1] = box.xlo
data = data[data.T[1] >= box.xlo]
data[np.where(np.isclose(data.T[1], box.xhi, atol=1e-8, rtol=0)), 1] = box.xhi
data = data[data.T[1] < box.xhi]
#round y-positions near ylo, yhi and only keep data for atoms where ylo <= y < yhi
data[np.where(np.isclose(data.T[2], box.ylo, atol=1e-8, rtol=0)), 2] = box.ylo
data = data[data.T[2] >= box.ylo]
data[np.where(np.isclose(data.T[2], box.yhi, atol=1e-8, rtol=0)), 2] = box.yhi
data = data[data.T[2] < box.yhi]
#round z-positions near zlo, zhi and only keep data for atoms where zlo <= z < zhi
data[np.where(np.isclose(data.T[3], box.zlo, atol=1e-8, rtol=0)), 3] = box.zlo
data = data[data.T[3] >= box.zlo]
data[np.where(np.isclose(data.T[3], box.zhi, atol=1e-8, rtol=0)), 3] = box.zhi
data = data[data.T[3] < box.zhi]
#deepcopy the data array to guarantee that it is new and separate
data = deepcopy(data)
#rebuild views
start = 0
view = OrderedDict()
for k in system.atoms.view:
vshape = (len(data), ) + system.atoms.view[k].shape[1:]
view[k] = data[:, start : start + system.atoms.view[k][0].size]
view[k].shape = vshape
start = start + system.atoms.view[k][0].size
#create atoms from natoms, data, view and dtype
atoms = am.Atoms(data=data, view=view, prop_dtype=system.atoms.dtype)
assert natoms == atoms.natoms, 'natom mismatch after rotation!'
#return new system
return am.System(box=box, atoms=atoms)
def rotate_cubic(system, axes):
"""
Rotate a cubic system according to the specified crystallographic axes.
Returns an orthogonal system whose box lengths are:
a * sqrt(i^2+j^2+k^2)
where a is the original cubic box length, and ijk are the crystallographic
indicies for the specific direction.
"""
axes = np.asarray(axes)
#rotate system generically
system = am.rotate(system, axes)
#test for cubic
a = system.box.a
try:
assert np.isclose(a, system.box.b), str(a) + ' ' + str(system.box.b)
assert np.isclose(a, system.box.c), str(a) + ' ' + str(system.box.c)
assert np.isclose(90.0, system.box.alpha), str(system.box.alpha)
assert np.isclose(90.0, system.box.beta), str(system.box.beta)
assert np.isclose(90.0, system.box.gamma), str(system.box.gamma)
except:
raise ValueError('Cubic system not given')
#Test for integer axes values
try:
for ax_val in axes.flat:
assert np.isclose(ax_val, int(ax_val))
except:
raise ValueError('axes values must be integers')
#Get magnitudes of the axes
mag = np.linalg.norm(axes, axis=1)
#compute number of atoms for the new system
natoms = system.natoms * mag[0] * mag[1] * mag[2]
if np.isclose(int(round(natoms)), natoms):
natoms = int(round(natoms))
else:
raise ValueError(
'not an integer number of atoms associated with the axes.')
#create a new box with scaled lattice parameters
box = am.Box(a=a * mag[0],
b=a * mag[1],
c=a * mag[2],
origin=system.box.origin)
#supersize the rotated box
m = int(ceil(max(mag)))
system = am.supersize(system, (-m, m), (-m, m), (-m, m))
#filter atoms for only those in the new box
data = system.atoms.data
#round x-positions near xlo, xhi and only keep data for atoms where xlo <= x < xhi
data[np.where(np.isclose(data.T[1], box.xlo, atol=1e-8, rtol=0)),
1] = box.xlo
data = data[data.T[1] >= box.xlo]
data[np.where(np.isclose(data.T[1], box.xhi, atol=1e-8, rtol=0)),
1] = box.xhi
data = data[data.T[1] < box.xhi]
#round y-positions near ylo, yhi and only keep data for atoms where ylo <= y < yhi
data[np.where(np.isclose(data.T[2], box.ylo, atol=1e-8, rtol=0)),
2] = box.ylo
data = data[data.T[2] >= box.ylo]
data[np.where(np.isclose(data.T[2], box.yhi, atol=1e-8, rtol=0)),
2] = box.yhi
data = data[data.T[2] < box.yhi]
#round z-positions near zlo, zhi and only keep data for atoms where zlo <= z < zhi
data[np.where(np.isclose(data.T[3], box.zlo, atol=1e-8, rtol=0)),
3] = box.zlo
data = data[data.T[3] >= box.zlo]
data[np.where(np.isclose(data.T[3], box.zhi, atol=1e-8, rtol=0)),
3] = box.zhi
data = data[data.T[3] < box.zhi]
#deepcopy the data array to guarantee that it is new and separate
data = deepcopy(data)
#rebuild views
start = 0
view = OrderedDict()
for k in system.atoms.view:
vshape = (len(data), ) + system.atoms.view[k].shape[1:]
view[k] = data[:, start:start + system.atoms.view[k][0].size]
view[k].shape = vshape
start = start + system.atoms.view[k][0].size
#create atoms from natoms, data, view and dtype
atoms = am.Atoms(data=data, view=view, prop_dtype=system.atoms.dtype)
assert natoms == atoms.natoms, 'natom mismatch after rotation!'
#return new system
return am.System(box=box, atoms=atoms)