def __getitem__(self, i):
if not self.initialised:
if self is self.parent.hysteretic_connect:
self.calc_connect_hysteretic(self.parent)
else:
self.calc_connect(self.parent)
distance = farray(0.0)
diff = fzeros(3)
cosines = fzeros(3)
shift = fzeros(3, dtype=np.int32)
res = []
if not get_fortran_indexing():
i = i + 1 # convert to 1-based indexing
for n in frange(self.n_neighbours(i)):
j = self.neighbour(self.parent, i, n, distance, diff, cosines,
shift)
if not get_fortran_indexing():
j = j - 1
res.append(NeighbourInfo(j, distance, diff, cosines, shift))
if get_fortran_indexing():
res = farray(res) # to give 1-based indexing
return res
def select(self, mask=None, list=None, orig_index=True):
"""Return a new :class:`Atoms` containing a subset of the atoms in this Atoms object
One of either `mask` or `list` should be present. If `mask`
is given it should be a rank one array of length `self.n`. In
this case atoms corresponding to true values in `mask` will be
included in the result. If `list` is present it should be an
arry of list containing atom indices to include in the result.
If `orig_index` is True (default), the new object will contain
an ``orig_index`` property mapping the indices of the new atoms
back to the original larger Atoms object.
"""
if mask is not None:
mask = farray(mask)
out = self.__class__(n=mask.sum(),
lattice=self.lattice,
properties={},
params={})
_atoms.Atoms.select(out, self, mask=mask, orig_index=orig_index)
elif list is not None:
list = farray(list)
out = self.__class__(n=len(list), lattice=self.lattice)
_atoms.Atoms.select(out, self, list=list, orig_index=orig_index)
else:
raise ValueError('Either mask or list must be present.')
return out
def apply_cp2k_sort_order(at, rev_sort_index_filename='quip_rev_sort_index'):
"""Reorder atoms in `at` so that they match rev_sort_index read from file.
Returns sort_index and rev_sort_index arrays."""
fields = [int(x) for x in open(rev_sort_index_filename).read().split()]
rev_sort_index = farray(fields, dtype=np.int32)
rev_sort_index_copy = rev_sort_index.copy()
sort_index = farray(frange(at.n), dtype=np.int32)
insertion_sort(rev_sort_index_copy, sort_index)
at.add_property('rev_sort_index', rev_sort_index)
at.sort('rev_sort_index')
return sort_index, rev_sort_index
def add_thermostat(self,
type,
T,
gamma=None,
Q=None,
tau=None,
tau_cell=None,
p=None,
NHL_tau=None,
NHL_mu=None,
massive=None):
"""
Add a new thermostat to this Dynamics, and return its index.
By default, all thermostats apply to the whole system. The
'thermostat_region' property can be used to control which
thermostats affect which atoms. It should be set to the index
of the required thermostat for each atom.
:param type: string or integer giving thermostat type. The following types are supported::
``THERMOSTAT_NONE``, ``THERMOSTAT_LANGEVIN``, ``THERMOSTAT_NOSE_HOOVER``, ``THERMOSTAT_NOSE_HOOVER_LANGEVIN``,
``THERMOSTAT_LANGEVIN_NPT``, ``THERMOSTAT_LANGEVIN_PR``, ``THERMOSTAT_NPH_ANDERSEN``, ``THERMOSTAT_NPH_PR``,
``THERMOSTAT_LANGEVIN_OU``, ``THERMOSTAT_LANGEVIN_NPT_NB``.
:param T: target temperature for this thermostat, in K.
:param gamma: decay constant, in units of 1/fs
:param tau: time constant, in units of fs. tau == 1/gamma, and
only one of the two should be specified.
:param tau_cell: time constant for the cell degrees of freedom
(for variable cell thermostats only).
:param p: target pressure (for variable cell thermostats)
:param NHL_tau: time constant for Nose-Hoover-Langevein thermostats
:param NHL_mu: thermostat mass Nose-Hoover-Langevin thermostats
:param massive: set to True to enable massive Nose-Hoover-Langevin
"""
type = _thermostat_types.get(type, type)
new_index = self._ds.n_thermostat()
region_i = farray(0, dtype=np.int32)
self._ds.add_thermostat(type,
T,
gamma,
Q,
tau,
tau_cell,
p,
NHL_tau,
NHL_mu,
massive,
region_i=region_i)
assert (new_index == int(region_i))
return new_index
def find_mapping(at_in, vectors, lattice_constant, tol=1e-4):
"""
Find a mapping between pairs of atoms displaced by a given vector
(or by one of a number of given vectors).
"""
class FoundMapping:
pass
mapping = fzeros(at_in.n, dtype=np.int32)
at = at_in.copy()
# cutoff should be larger than all displacment vectors
vlen = [farray(vector).norm()*lattice_constant for vector in vectors]
at.set_cutoff(max(vlen)+0.5)
print 'cutoff = ', at.cutoff
at.calc_connect()
for i in at.indices:
try:
for neighb in at.neighbours[i]:
for vector in vectors:
if ((neighb.diff/lattice_constant - vector)**2).sum() < tol:
print i, neighb.j, vector
mapping[i] = neighb.j
raise FoundMapping
# corresponding atom is off the edge, so map atom onto itself
print i, 'not found!'
mapping[i] = i
except FoundMapping:
continue
return mapping
def get_bond_lengths(at):
"""Return a dictionary mapping tuples (Species1, Species2) to an farray of bond-lengths"""
at.calc_connect()
r_ij = farray(0.0)
res = {}
for i in frange(at.n):
for n in frange(at.n_neighbours(i)):
j = at.neighbour(i, n, distance=r_ij)
print i, j, at.z[i], at.z[j], r_ij
minij, maxij = min((i, j)), max((i, j))
key = (at.species[minij].stripstrings(),
at.species[maxij].stripstrings())
if not key in res: res[key] = []
res[key].append(r_ij.astype(float))
print res
return dict((k, farray(v)) for (k, v) in res.iteritems())
def _indices(self):
"""Return array of atoms indices
If global ``fortran_indexing`` is True, returns FortranArray containing
numbers 1..self.n. Otherwise, returns a standard numpuy array
containing numbers in range 0..(self.n-1)."""
if get_fortran_indexing():
return farray(list(frange(len(self))))
else:
return np.array(list(range(len(self))))
def __getattr__(self, name):
if self.netcdf_file is not None:
try:
return self.netcdf_file.__getattr__(name)
except AttributeError:
try:
a = self.netcdf_file.variables[name][:]
if get_fortran_indexing():
a = farray(a)
return a
except KeyError:
raise AttributeError('Attribute %s not found' % name)
else:
raise AttributeError('Attribute %s not found' % name)
def force_test(at, p, dx=1e-4):
"""
Compare analyric and numeric forces for the Potential `p` with Atoms `at`
Finite difference derivates are calculated by moving each atom by `dx`.
"""
analytic_f = fzeros((3, at.n))
p.calc(at, force=analytic_f)
num_f = fzeros((3, at.n))
ep, em = farray(0.0), farray(0.0)
for i in frange(at.n):
for j in (1, 2, 3):
ap = at.copy()
ap.pos[j, i] += dx
p.calc(ap, energy=ep)
print 'e+', j, i, ep
ap.pos[j, i] -= 2.0 * dx
p.calc(ap, energy=em)
print 'e-', j, i, em
num_f[j, i] = -(ep - em) / (2 * dx)
return analytic_f, num_f, analytic_f - num_f
def get_lattice_params(lattice):
"""
Wrapper around Fortran :func:`get_lattice_params_`
Returns parameters of `lattice` as 6-tuple (a,b,c,alpha,beta,gamma).
"""
a, b, c, alpha, beta, gamma = (farray(0.), farray(0.), farray(0.),
farray(0.), farray(0.), farray(0.))
_atoms.get_lattice_params(lattice, a, b, c, alpha, beta, gamma)
return tuple(float(x) for x in (a, b, c, alpha, beta, gamma))
def unpack_reftraj_output_str_to_results(data):
lines = data.strip().split('\n')
nstep = int(lines[0])
natoms = int(lines[1])
energy = float(lines[2])
force = farray(np.loadtxt(lines[3:-1])).T
v6 = [float(v) for v in lines[-1].split()]
virial = fzeros((3, 3))
virial[1, 1], virial[2, 2], virial[3,
3], virial[1,
2], virial[2,
3], virial[1,
3] = v6
virial[2, 1] = virial[1, 2]
virial[3, 2] = virial[2, 3]
virial[3, 1] = virial[1, 3]
return (nstep, natoms, energy, force, virial)
def find_atoms_within_cutoff(atoms, cutoff, d=0):
tmp_atoms = Atoms(atoms, fortran_indexing=False)
tmp_atoms.calc_connect()
over = []
rij = farray(0.0)
for i in frange(len(tmp_atoms)):
for n in frange(tmp_atoms.n_neighbours(i)):
j = tmp_atoms.neighbour(i, n, distance=rij)
# print j
if rij < cutoff and i > j:
if d == 0:
over.append(j - 1)
else:
over.append(i - 1)
# for i in range(len(atoms)): #python method, may be slower than fortran index?
# indices, offsets = tmp_atoms.neighbours.get_neighbors(i)
# for j, offset in zip(indices, offsets):
# diff=tmp_atoms.get_distance(i,j)
# if diff < cutoff and i > j : #i>j is important for returning only one atom id
# over.append(j)
return over
def orthorhombic_slab(at,
tol=1e-5,
min_nrep=1,
max_nrep=5,
graphics=False,
rot=None,
periodicity=None,
vacuum=None,
shift=None,
verbose=True):
"""Try to construct an orthorhombic cell equivalent to the
primitive cell `at`, using supercells up to at most `max_nrep`
repeats. Symmetry must be exact within a tolerance of `tol`. If
`rot` is not None, we first transform `at` by the rotation
matrix `rot`. The optional argument `periodicity` can be used to
fix the periodicity one or more directions. It should be a three
component vector with value zero in the unconstrained
directions. The vector `vacuum` can be used to add vacuum in one
or more directions. `shift` is a three component vector which
can be used to shift the positions in the final cell. """
def atoms_near_plane(at, n, d, tol=1e-5):
"""Return a list of atoms within a distance `tol` of the plane defined by np.dot(n, at.pos) == d"""
pd = np.dot(n, at.pos) - d
return (abs(pd) < tol).nonzero()[0]
def sort_by_distance(at, ref_atom, dir, candidates):
"""Return a copy of `candidates` sorted by perpendicular distance from `ref_atom` in direction `dir`"""
distances_candidates = zip(
[at.pos[dir, i] - at.pos[dir, ref_atom] for i in candidates],
candidates)
distances_candidates.sort()
return [p for (d, p) in distances_candidates]
def orthorhombic_box(at):
"""Return a copy of `at` in an orthorhombic box surrounded by vacuum"""
at = at.copy()
at.map_into_cell()
at.set_lattice(
[[2.0 * (at.pos[1, :].max() - at.pos[1, :].min()), 0.0, 0.0],
[0.0, 2.0 * (at.pos[2, :].max() - at.pos[2, :].min()), 0.0],
[0.0, 0.0, 2.0 * (at.pos[3, :].max() - at.pos[3, :].min())]],
scale_positions=False)
at.map_into_cell()
return at
def discard_outliers(at, indices, dirs, keep_fraction=0.5):
"""Return a copy of `indices` with the atoms with fractional coordinates along directions in `dirs`
outside +/-`keep_fraction`/2 excluded. Lattice used is close fitting, `at.lattice`/2."""
g = np.linalg.inv(at.lattice / 2)
t = np.dot(g, at.pos[:, indices])
return indices[np.logical_and(
t[dirs, :] >= -keep_fraction / 2.0,
t[dirs, :] < keep_fraction / 2.0).all(axis=1)]
def check_candidate_plane(at,
ref_plane,
cand_plane,
dirs,
verbose=False,
label=''):
"""Check whether in-plane displacements of atoms listed in `ref_plane` match those of `cand_plane` in directions given by `dirs`"""
# Which pair of planes has more atoms, reference or candidate?
if len(ref_plane) < len(cand_plane):
smaller = ref_plane
larger = cand_plane
else:
smaller = cand_plane
larger = ref_plane
matches = {}
for j in smaller:
for k in larger:
if at.z[k] == at.z[j] and abs(at.pos[dirs, k] -
at.pos[dirs, j]).max() < tol:
matches[j] = k
break
if verbose:
print ' ', label, len(matches), '/', len(smaller), 'matches'
return len(matches) == len(smaller)
if rot is not None:
at = transform(at, rot)
xyz = fidentity(3)
nrep = min_nrep - 1
max_dist = fzeros(3)
if periodicity is not None:
periodicity = farray(periodicity)
periodicity = dict(
zip((periodicity != 0).nonzero()[0],
periodicity[periodicity != 0]))
else:
periodicity = {}
if verbose:
for (dir, p) in periodicity.iteritems():
print 'Periodicity in direction %d fixed at %f' % (dir, p)
if graphics:
import atomeye
viewer = atomeye.AtomEyeViewer()
while sorted(periodicity.keys()) != [1, 2, 3]:
nrep += 1
if nrep > max_nrep:
raise ValueError('Maximum size of supercell (%d) exceeded' %
max_nrep)
if verbose:
print '\n\nSupercell %d' % nrep
sup = supercell(at, nrep, nrep, nrep)
box = orthorhombic_box(sup)
box.pos[:] = box.pos - np.tile(box.pos.mean(axis=2), [box.n, 1]).T
for dir in set([1, 2, 3]) - set(periodicity.keys()):
if verbose:
print ' Direction %d' % dir
other_dirs = list(set([1, 2, 3]) - set([dir]))
pos_index = zip(box.pos[dir, :], frange(box.n))
pos_index.sort()
# Find a pair of planes
while pos_index:
ref_pos1, ref_atom1 = pos_index.pop(0)
# Find atom to define second plane
while pos_index:
ref_pos2, ref_atom2 = pos_index.pop(0)
if abs(ref_pos2 - ref_pos1) > tol: break
else:
continue
ref_plane1 = atoms_near_plane(box, xyz[:, dir],
box.pos[dir, ref_atom1], tol)
ref_plane2 = atoms_near_plane(box, xyz[:, dir],
box.pos[dir, ref_atom2], tol)
# Only keep reference atoms in the centre of the cell
ref_plane1 = discard_outliers(box, ref_plane1, other_dirs)
ref_plane2 = discard_outliers(box, ref_plane2, other_dirs)
if len(ref_plane1) > 2 and len(ref_plane2) > 2:
# Now we've got two planes, both with more than two atoms in them
break
else:
# Used up all atoms without finding two planes
if verbose:
print ' No valid reference planes found.\n'
continue
if verbose:
print ' Reference plane #1 through atom %d ' % ref_atom1
print ' Reference plane #2 through atom %d at distance %r\n' % (
ref_atom2, ref_pos2 - ref_pos1)
if graphics:
highlight = fzeros(box.n)
highlight[ref_plane1] = 1
highlight[ref_plane2] = 2
box.add_property('highlight', highlight, overwrite=True)
viewer.show(box, 'highlight')
viewer.wait()
raw_input('continue')
candidates = [
i for i in frange(box.n)
if box.pos[dir,
i] > box.pos[dir, ref_atom2] + max_dist[dir] + tol
]
candidates = sort_by_distance(box, ref_atom1, dir, candidates)
while candidates:
cand1 = candidates.pop(0)
max_dist[dir] = box.pos[dir, cand1] - box.pos[dir, ref_atom1]
if verbose:
print ' Trying plane through atom %d distance %r' % (
cand1, max_dist[dir])
cand_plane1 = atoms_near_plane(box, xyz[:, dir],
box.pos[dir, cand1], tol)
for cand2 in sort_by_distance(
box, ref_atom1, dir,
set(candidates) - set(cand_plane1)):
if abs((box.pos[dir, cand2] - box.pos[dir, cand1]) -
(box.pos[dir, ref_atom2] -
box.pos[dir, ref_atom1])) < tol:
if verbose:
print ' Found pair to plane, passing through atom %d distance %r ' % (
cand2,
box.pos[dir, cand2] - box.pos[dir, ref_atom1])
break
else:
if verbose:
print ' Cannot find second candidate plane.\n'
candidates = sort_by_distance(
box, ref_atom1, dir,
set(candidates) - set(cand_plane1))
continue
if graphics:
highlight[cand_plane1] = 3
box.highlight[:] = highlight
viewer.show(box, 'highlight')
viewer.wait()
cand_plane2 = atoms_near_plane(box, xyz[:, dir],
box.pos[dir, cand2], tol)
if graphics:
highlight[cand_plane2] = 4
box.highlight[:] = highlight
viewer.show(box, 'highlight')
viewer.wait()
highlight[cand_plane1] = 0
highlight[cand_plane2] = 0
# Remove cand_plane1 from list of candidates
candidates = sort_by_distance(
box, ref_atom1, dir,
set(candidates) - set(cand_plane1))
# Check ref_plane1 against cand_plane1 and ref_plane2 against cand_plane2 in directions
# listed in other_dirs
match1 = check_candidate_plane(box, ref_plane1, cand_plane1,
other_dirs, verbose,
'Plane #1:')
match2 = check_candidate_plane(box, ref_plane2, cand_plane2,
other_dirs, verbose,
'Plane #2:')
if match1 and match2:
periodicity[dir] = box.pos[dir, cand1] - box.pos[dir,
ref_atom1]
if verbose:
print '\n Periodicity in direction %d is %f\n' % (
dir, box.pos[dir, cand1] - box.pos[dir, ref_atom1])
if graphics:
highlight[cand_plane1] = 3
highlight[cand_plane2] = 3
box.highlight[:] = highlight
viewer.show(box, 'highlight')
viewer.wait()
raw_input('continue...')
break
if graphics:
raw_input('continue...')
else:
# Failed to find match for direction dir
continue
# Finally, construct new cell by selecting atoms within first unit cell
lattice = farray(np.diag([periodicity[1], periodicity[2], periodicity[3]]))
g = np.linalg.inv(lattice)
nrepx, nrepy, nrepz = fit_box_in_cell(periodicity[1], periodicity[2],
periodicity[3], at.lattice)
sup = supercell(at, nrepx, nrepy, nrepz)
sup.map_into_cell()
# small shift to avoid coincidental cell alignments
delta = np.tile([0.01, 0.02, 0.03], [sup.n, 1]).T
if shift is not None and vacuum is not None:
delta = delta + np.tile(shift, [sup.n, 1]).T
t = np.dot(g, sup.pos) + delta
orthorhombic = sup.select(np.logical_and(t >= -0.5, t < 0.5).all(axis=1))
if vacuum:
lattice = farray(np.diag(lattice.diagonal() + vacuum))
if shift is not None and vacuum is None:
if verbose:
print 'Shifting positions by %s' % np.dot(lattice, shift)
orthorhombic.pos += np.tile(np.dot(lattice, shift),
[orthorhombic.n, 1]).T
orthorhombic.set_lattice(lattice, scale_positions=False)
orthorhombic.map_into_cell()
return orthorhombic
def CP2KDirectoryReader(run_dir,
at_ref=None,
proj='quip',
calc_qm_charges=None,
calc_virial=False,
out_i=None,
qm_vacuum=6.0,
run_suffix='_extended',
format=None):
if at_ref is None:
filepot_xyz = os.path.join(run_dir, 'filepot.xyz')
if not os.path.exists(filepot_xyz):
# try looking up one level
filepot_xyz = os.path.join(run_dir, '../filepot.xyz')
if os.path.exists(filepot_xyz):
at_ref = Atoms(filepot_xyz)
else:
at_ref = Atoms(os.path.join(run_dir, 'cp2k_output.out'),
format='cp2k_output')
at = at_ref.copy()
cp2k_output_filename, cp2k_output = read_text_file(
os.path.join(run_dir, 'cp2k_output.out'))
cp2k_params = CP2KInputHeader(
os.path.join(run_dir, 'cp2k_input.inp.header'))
at.params.update(cp2k_params)
run_type = cp2k_run_type(cp2k_output=cp2k_output,
cp2k_input_header=cp2k_params)
try:
cluster_mark = getattr(at, 'cluster_mark' + run_suffix)
qm_list_a = ((cluster_mark != HYBRID_NO_MARK).nonzero()[0]).astype(
np.int32)
except AttributeError:
qm_list_a = fzeros(0, dtype=np.int32)
if calc_qm_charges is None:
calc_qm_charges = ''
try:
cur_qmmm_qm_abc = [
float(cp2k_params['QMMM_ABC_X']),
float(cp2k_params['QMMM_ABC_Y']),
float(cp2k_params['QMMM_ABC_Z'])
]
except KeyError:
if 'QM_cell' + run_suffix in at.params:
cur_qmmm_qm_abc = at.params['QM_cell' + run_suffix]
else:
cur_qmmm_qm_abc = qmmm_qm_abc(at, qm_list_a, qm_vacuum)
quip_cp2k_at = Atoms(os.path.join(run_dir, 'quip_cp2k.xyz'))
rev_sort_index_file = os.path.join(run_dir, '../quip_rev_sort_index')
fields = [int(x) for x in open(rev_sort_index_file).read().split()]
rev_sort_index = farray(fields, dtype=np.int32)
#verbosity_push(PRINT_SILENT)
cp2k_energy, cp2k_force = read_output(quip_cp2k_at, qm_list_a,
cur_qmmm_qm_abc, run_dir, proj,
calc_qm_charges, calc_virial, True,
3, at.n, out_i)
#verbosity_pop()
qm_list = None
if os.path.exists(os.path.join(run_dir, 'cp2k_input.qmmm_qm_kind')):
qm_kind_grep_cmd = "grep MM_INDEX %s/cp2k_input.qmmm_qm_kind | awk '{print $2}'" % run_dir
qm_list = [int(i) for i in os.popen(qm_kind_grep_cmd).read().split()]
if qm_list is not None:
if run_type == 'QMMM':
reordering_index = getattr(at, 'reordering_index', None)
at.add_property('qm', False, overwrite=True)
if reordering_index is not None:
qm_list = reordering_index[qm_list]
at.qm[qm_list] = True
elif run_type == 'QS':
at.add_property('qm_orig_index', 0, overwrite=True)
for i, qm_at in fenumerate(qm_list):
at.qm_orig_index[i] = sort_index[qm_at]
at.add_property('force', cp2k_force, overwrite=True)
at.params['energy'] = cp2k_energy
yield at
def CP2KOutputReader(fh,
module=None,
type_map=None,
kind_map=None,
format=None):
# mapping from run type to (default module index, list of available module)
run_types = {
'QS': ['QUICKSTEP'],
'QMMM': ['FIST', 'QM/MM', 'QUICKSTEP'],
'MM': ['FIST']
}
filename, lines = read_text_file(fh)
run_type = cp2k_run_type(cp2k_output=lines)
if type_map is None:
type_map = {}
if kind_map is None:
kind_map = {}
try:
available_modules = run_types[run_type]
except KeyError:
raise ValueError('Unknown CP2K run type %s' % run_type)
if module is None:
module = available_modules[0]
try:
cell_index = available_modules.index(module)
except ValueError:
raise ValueError("Don't know how to read module %s from file %s" %
(module, filename))
cell_lines = [
i for i, line in enumerate(lines) if line.startswith(" CELL| Vector a")
]
if cell_lines == []:
raise ValueError("Cannot find cell in file %s" % filename)
try:
cell_line = cell_lines[cell_index]
except IndexError:
raise ValueError(
"Cannot find cell with index %d in file %s for module %s" %
(cell_index, filename, module))
lattice = fzeros((3, 3))
for i in [0, 1, 2]:
lattice[:,
i + 1] = [float(c) for c in lines[cell_line + i].split()[4:7]]
try:
start_line = lines.index(
" MODULE %s: ATOMIC COORDINATES IN angstrom\n" % module)
except ValueError:
raise ValueError(
"Cannot find atomic positions for module %s in file %s" %
(module, filename))
kinds = []
species = []
Zs = []
pos = []
masses = []
Zeffs = []
types = []
qeffs = []
for line in lines[start_line + 4:]:
if line.strip() == '':
break
if module == 'FIST':
atom, kind, typ, x, y, z, qeff, mass = line.split()
types.append(typ)
Z = type_map.get(typ, 0)
kind = int(kind)
if Z == 0:
Z = kind_map.get(kind, 0)
Zs.append(Z)
qeffs.append(float(qeff))
else:
atom, kind, sp, Z, x, y, z, Zeff, mass = line.split()
species.append(sp)
Zs.append(int(Z))
Zeffs.append(float(Zeff))
kinds.append(int(kind))
pos.append([float(x), float(y), float(z)])
masses.append(float(mass))
at = Atoms(n=len(kinds), lattice=lattice)
at.pos[...] = farray(pos).T
at.set_atoms(Zs)
at.add_property('mass', farray(masses) * MASSCONVERT)
at.add_property('kind', kinds)
if module == 'FIST':
at.add_property('type', ' ' * TABLE_STRING_LENGTH)
at.add_property('qm', False)
at.qm[:] = (at.type.stripstrings()
== '_QM_') | (at.type.stripstrings() == '_LNK')
at.type[...] = s2a(types, TABLE_STRING_LENGTH)
at.add_property('qeff', qeffs)
else:
at.species[...] = s2a(species, TABLE_STRING_LENGTH)
at.add_property('zeff', Zeffs)
yield at
def crack_make_seed_curved_front(slab, params):
"""Given a slab, introduce a 3D curved crack front."""
orig_width = slab.params['OrigWidth']
orig_height = slab.params['OrigHeight']
orig_depth = slab.params['OrigDepth']
crack_length = params.crack_seed_length/orig_width
crack_curvature = params.crack_curvature
crack_depth = 1.0
if params.crack_g > 0.:
epsilon_max = crack_g_to_strain(params.crack_g,
slab.YoungsModulus,
slab.PoissonRatio_yx,
orig_height)
else:
epsilon_max = params.crack_strain
# ... then shift so coordinates are in ranges x=[0..a], y=[0..b], z=[0..c]
slab.pos += np.tile(np.array([orig_width, orig_height, orig_depth])[:,np.newaxis]/2., slab.n)
xlin = 0.5*crack_length*orig_width
crack_center = farray([crack_length*orig_width, 0.5*orig_height, 0.])
epsilon_min = 0.
epsilon_local = 0.
dy = 0.
a = crack_curvature
x1 = crack_length*orig_width
x2 = x1 + crack_depth
z1 = 0.
z2 = orig_depth
slope = (x2-x1)/(z2-z1)
dymax = 0.5*epsilon_max*orig_height
z = slab.pos[3,:]
crack_x_center = crack_curvature*(z*z - z1*z1) + (slope-crack_curvature*(z2+z1))*(z-z1) + crack_center[1]
##slab.add_property('xc', crack_x_center, overwrite=True)
dymin = abs(slab.pos[2,:]-crack_center[2])*epsilon_max
dy = dymin
dy[slab.pos[1,:] < xlin] = dymax
mask = (slab.pos[1,:] > xlin) & (slab.pos[1,:] <= crack_x_center)
##slab.add_property('mask', mask, overwrite=True)
dy[mask] = (dymax - dymin[mask])/(xlin - crack_x_center[mask])*abs(slab.pos[1,mask] - xlin) + dymax
dy *= np.sign(slab.pos[2,:] - crack_center[2])
##slab.add_property('dy', dy, overwrite=True)
slab.pos[2,:] += dy
# Centre slab in cell
slab.pos += np.tile((np.array([params.crack_vacuum_size/2.]*3) +
np.diag(slab.lattice)/2.)[:,np.newaxis], slab.n)
slab.map_into_cell()
slab.params['CrackPosx'] = crack_center[1] + params.crack_vacuum_size/2.
slab.params['CrackPosy'] = crack_center[2] + params.crack_vacuum_size/2.
opt.range = slice(opt.range, opt.range + 1, +1)
else:
opt.range = slice(opt.range, opt.range - 1, -1)
for infile in infiles:
basename = os.path.basename(os.path.splitext(infile)[0])
configs = AtomsReader(infile,
start=opt.range.start,
stop=opt.range.stop,
step=opt.range.step)
for frame, q0 in enumerate(configs):
print 'Read %d atoms from file %s frame %d' % (q0.n, infile, frame)
diameter = farray(0, dtype=np.int32)
ring_sizes = range(1, opt.max_ring_size + 1)
if opt.supercell is None:
q = q0
else:
print 'Forming %d x %d x %d supercell' % tuple(opt.supercell)
q = supercell(q0, opt.supercell[0], opt.supercell[1],
opt.supercell[2])
q.map_into_cell()
q.set_cutoff(opt.si_o_cutoff)
q.calc_connect()
if opt.tetra:
print 'Converting topology from Si-O-Si to Si-Si'