def __call__(self, *args):
if os.path.exists(self.fn):
print 'Reading configuration from checkpoint file %s...' % self.fn
a = io.read(self.fn)
else:
a = self.func(*args)
io.write(self.fn, a)
return a
def __call__(self, *args):
if os.path.exists(self.fn):
print 'Reading configuration from checkpoint file %s...' % self.fn
a = io.read(self.fn)
else:
a = self.func(*args)
io.write(self.fn, a)
return a
def voropp_for_non_orthorhombic_cells(_a, q='%v', voropp_path=VOROPP_PATH,
fast=False, dump=None):
"""
Run voro++ on current configuration and return selected quantities.
Parameter *q* can be a list of voro++ output quantities.
Run 'voro++ -hc' to see options. Will take care of Lees-Edwards boundary
conditions by embedding a sheared cell in its periodic images and then
throwing away the border (will hence be slower).
"""
# Make a copy because we will modify the Atoms object
a = _a.copy()
nat = len(a)
# Wrap into cell
a.set_scaled_positions(a.get_scaled_positions()%1.0)
# shear_dx should go into the cell
if 'shear_dx' in a.info:
lx, ly, lz = a.get_cell().diagonal()
cx, cy, cz = a.get_cell()
assert abs(cz[0]) < 1e-12
assert abs(cz[1]) < 1e-12
shear_dx = a.info['shear_dx']
cz[0] = shear_dx[0]
cz[1] = shear_dx[1]
a.set_cell([cx, cy, cz], scale_atoms=False)
a.set_scaled_positions(a.get_scaled_positions()%1.0)
cx, cy, cz = a.get_cell()
if fast:
# Make 2 copies of the box in each direction. Could fail!
a *= ( 2, 2, 2 )
# Translate such that the box with the lowest indices sits in the middle
a.translate(cx/2+cy/2+cz/2)
else:
# Make 3 copies of the box in each direction
a *= ( 3, 3, 3 )
# Translate such that the box with the lowest indices sits in the middle
a.translate(cx+cy+cz)
# Wrap back to box
a.set_scaled_positions(a.get_scaled_positions()%1.0)
# Get enclosing box
lower, upper = get_enclosing_orthorhombic_box(a.get_cell())
elx, ely, elz = upper-lower
# Shift and set cell such that the general system is enclosed in the
# orthorhombic box
a.translate(-lower)
a.set_cell([elx,ely,elz], scale_atoms=False)
# Dump snapshot for debugging purposes
if dump:
write(dump, a)
# Do Voronoi analysis
x, y, z = a.get_positions().T
f = open('tmp.voronoi', 'w')
for jn, ( jx, jy, jz ) in enumerate(zip(x, y, z)):
print >> f, jn, jx, jy, jz
f.close()
if isinstance(q, str) or isinstance(q, unicode):
c = '%s' % format(q)
else:
c = reduce(lambda x,y: '{0} {1}'.format(x,y), map(lambda x: '%'+x, q))
os.system('{0} -o -p -c "%i {1}" 0 {2} 0 {3} 0 {4} tmp.voronoi' \
.format(voropp_path, c, elx, ely, elz))
r = np.loadtxt('tmp.voronoi.vol', unpack=True)
os.remove('tmp.voronoi')
os.remove('tmp.voronoi.vol')
# Sort particles according to their ids
r = r[:,np.array(r[0,:], dtype=int)]
# Use only the lowest indices (i.e. the box in the middle)
if r.shape[0] == 2:
return r[1,:nat]
else:
return r[1:,:nat]
io.read_cyc(a, opt.cellfn)
if opt.center is not None:
if opt.center:
a.center()
if opt.acf is not None:
attach_charges(a, opt.acf)
if convlen is not None:
a.set_cell(a.get_cell() * convlen, scale_atoms=True)
if opt.wrap_to_cell:
a.set_scaled_positions(a.get_scaled_positions())
if opt.clear_velocities:
a.set_momenta(None)
if opt.supercell is not None:
supercell = map(int, opt.supercell.split(','))
a *= supercell
d = {}
if opt.specorder is not None:
d['specorder'] = opt.specorder.split(',')
if opt.format is not None:
d['format'] = opt.format
io.write(outfn, a, **d)
def voropp_for_non_orthorhombic_cells(_a,
q='%v',
voropp_path=VOROPP_PATH,
fast=False,
dump=None):
"""
Run voro++ on current configuration and return selected quantities.
Parameter *q* can be a list of voro++ output quantities.
Run 'voro++ -hc' to see options. Will take care of Lees-Edwards boundary
conditions by embedding a sheared cell in its periodic images and then
throwing away the border (will hence be slower).
"""
# Make a copy because we will modify the Atoms object
a = _a.copy()
nat = len(a)
# Wrap into cell
a.set_scaled_positions(a.get_scaled_positions() % 1.0)
# shear_dx should go into the cell
if 'shear_dx' in a.info:
lx, ly, lz = a.get_cell().diagonal()
cx, cy, cz = a.get_cell()
assert abs(cz[0]) < 1e-12
assert abs(cz[1]) < 1e-12
shear_dx = a.info['shear_dx']
cz[0] = shear_dx[0]
cz[1] = shear_dx[1]
a.set_cell([cx, cy, cz], scale_atoms=False)
a.set_scaled_positions(a.get_scaled_positions() % 1.0)
cx, cy, cz = a.get_cell()
if fast:
# Make 2 copies of the box in each direction. Could fail!
a *= (2, 2, 2)
# Translate such that the box with the lowest indices sits in the middle
a.translate(cx / 2 + cy / 2 + cz / 2)
else:
# Make 3 copies of the box in each direction
a *= (3, 3, 3)
# Translate such that the box with the lowest indices sits in the middle
a.translate(cx + cy + cz)
# Wrap back to box
a.set_scaled_positions(a.get_scaled_positions() % 1.0)
# Get enclosing box
lower, upper = get_enclosing_orthorhombic_box(a.get_cell())
elx, ely, elz = upper - lower
# Shift and set cell such that the general system is enclosed in the
# orthorhombic box
a.translate(-lower)
a.set_cell([elx, ely, elz], scale_atoms=False)
# Dump snapshot for debugging purposes
if dump:
write(dump, a)
# Do Voronoi analysis
x, y, z = a.get_positions().T
f = open('tmp.voronoi', 'w')
for jn, (jx, jy, jz) in enumerate(zip(x, y, z)):
print >> f, jn, jx, jy, jz
f.close()
if isinstance(q, str) or isinstance(q, unicode):
c = '%s' % format(q)
else:
c = reduce(lambda x, y: '{0} {1}'.format(x, y),
map(lambda x: '%' + x, q))
os.system('{0} -o -p -c "%i {1}" 0 {2} 0 {3} 0 {4} tmp.voronoi' \
.format(voropp_path, c, elx, ely, elz))
r = np.loadtxt('tmp.voronoi.vol', unpack=True)
os.remove('tmp.voronoi')
os.remove('tmp.voronoi.vol')
# Sort particles according to their ids
r = r[:, np.array(r[0, :], dtype=int)]
# Use only the lowest indices (i.e. the box in the middle)
if r.shape[0] == 2:
return r[1, :nat]
else:
return r[1:, :nat]
io.read_cyc(a, opt.cellfn)
if opt.center is not None:
if opt.center:
a.center()
if opt.acf is not None:
attach_charges(a, opt.acf)
if convlen is not None:
a.set_cell(a.get_cell()*convlen, scale_atoms=True)
if opt.wrap_to_cell:
a.set_scaled_positions(a.get_scaled_positions())
if opt.clear_velocities:
a.set_momenta(None)
if opt.supercell is not None:
supercell = map(int, opt.supercell.split(','))
a *= supercell
d = { }
if opt.specorder is not None:
d['specorder'] = opt.specorder.split(',')
if opt.format is not None:
d['format'] = opt.format
io.write(outfn, a, **d)
