def fromString(self, data):
Structure.fromString(self, data)
# [MS-NLMP] page 27
# Payload data can be present in any order within the Payload field,
# with variable-length padding before or after the data
domain_offset = self['domain_offset']
domain_end = self['domain_len'] + domain_offset
self['domain_name'] = data[domain_offset:domain_end]
host_offset = self['host_offset']
host_end = self['host_len'] + host_offset
self['host_name'] = data[host_offset:host_end]
user_offset = self['user_offset']
user_end = self['user_len'] + user_offset
self['user_name'] = data[user_offset:user_end]
ntlm_offset = self['ntlm_offset']
ntlm_end = self['ntlm_len'] + ntlm_offset
self['ntlm'] = data[ntlm_offset:ntlm_end]
lanman_offset = self['lanman_offset']
lanman_end = self['lanman_len'] + lanman_offset
self['lanman'] = data[lanman_offset:lanman_end]
def conventional(self, symprec=1e-5):
"""
conventional structure
Arugments:
symprec (symmetry tolerance): distance tolerance in Cartesian coordinates to find crystal symmetry
"""
cell = self.structure.formatting('cell')
cell = (cell['lattice'], cell['positions'], cell['numbers'])
# method 1
lattice, scaled_positions, numbers = spglib.standardize_cell(
cell, symprec=symprec)
newcell = (lattice, scaled_positions, numbers)
# method 2
#newcell=spglib.standardize_cell(cell, symprec=symprec)
if newcell == None:
raise StructureFactoryError('The search is failed')
else:
poscar = self.__toPOSCAR(newcell)
self.structure.pop() # delete old object
self.structure = Structure().append(poscar)
return self.structure
def make_movie(self, filename, filepath=None):
if 'structures' in self:
from structure import Structure
if filepath == None:
filepath = os.path.join(self.abspath, filename)
else:
filepath = os.path.join(filepath, filename)
#end if
movie = ''
structures = self.structures
print structures
aA = convert(self.input.system['celldm(1)'], 'B', 'A')
cell = self.input.cell_parameters.vectors
for i in range(len(structures)):
s = structures[i]
struct = Structure(elem=s.atoms,
pos=s.positions,
axes=cell,
scale=aA,
units='A')
struct = struct.tile(2, 2, 2)
ss = struct.write_xyz()
movie += ss
open(filepath, 'w').write(movie)
def load_diffs():
date_2011 = datetime.datetime(year=2011, month=1, day=1)
date_2012 = datetime.datetime(year=2012, month=1, day=1)
diff_2012 = [
Diff(DiffType.ADD, position=4, add='u'),
Diff(DiffType.REMOVE, position=4, remove=1)
]
title_12_subsections = [
Structure(1, Representation.ROMAN, 'Part'),
Structure(3, Representation.ROMAN, 'Part')
]
title_12_subsections[0].subsections = [
Structure(1, Representation.UPPERCASE, 'Section'),
Structure(2, Representation.UPPERCASE, 'Section')
]
title_12 = Structure(12,
Representation.NUMERIC,
'Title',
dates=[date_2011, date_2012],
texts={
date_2011: 'Hello',
date_2012: 'Hellu'
},
diffs={
date_2011: [],
date_2012: diff_2012
},
subsections=title_12_subsections)
return {12: title_12}
def read_xsf(self, filepath, component=None):
component = self.process_component_name(component)
vlog('Reading density data from XSF file for component "{}"'.format(
component),
time=True)
if isinstance(filepath, XsfFile):
vlog('XSF file already loaded, reusing data.')
xsf = filepath
copy_values = True
else:
vlog('Loading data from file', n=1, time=True)
vlog('file location: {}'.format(filepath), n=2)
vlog('memory before: ', n=2, mem=True)
xsf = XsfFile(filepath)
vlog('load complete', n=2, time=True)
vlog('memory after: ', n=2, mem=True)
copy_values = False
#end if
# read structure
if not self.has_attribute('structure'):
vlog('Reading structure from XSF data', n=1, time=True)
s = Structure()
s.read_xsf(xsf)
self.set_attribute('structure', s)
#end if
# read grid
if not self.has_attribute('grid'):
vlog('Reading grid from XSF data', n=1, time=True)
g = read_grid(xsf)
self.set_attribute('grid', g)
self.set_attribute('distance_units', 'B')
#end if
# read values
xsf.remove_ghost()
d = xsf.get_density()
values = d.values_noghost.ravel()
if copy_values:
values = values.copy()
#end if
# create grid function for component
vlog('Constructing grid function from XSF data', n=1, time=True)
f = grid_function(
type='parallelotope',
grid=self.grid,
values=values,
copy=False,
)
self.set_attribute(component, f)
self.set_attribute('distance_units', 'A')
vlog('Read complete', n=1, time=True)
vlog('Current memory:', n=1, mem=True)
def __init__(self,structure=None,net_charge=0,net_spin=0,particles=None,**valency):
self.pseudized = False
if structure is None:
self.structure = Structure()
else:
self.structure = structure
#end if
if particles is None:
self.particles = Particles()
else:
self.particles = particles.copy()
#end if
self.folded_system = None
if self.structure.has_folded():
if self.structure.is_tiled():
vratio = structure.volume()/structure.folded_structure.volume()
ncells = int(round(vratio))
if abs(vratio-ncells)>1e-4:
self.error('volume of system does not divide evenly into folded system')
#end if
if net_charge%ncells!=0:
self.error('net charge of system does not divide evenly into folded system')
#end if
if isinstance(net_spin,str):
net_spin_fold = net_spin
elif net_spin%ncells!=0:
self.error('net_spin of system does not divide evenly into folded system')
else:
net_spin_fold = net_spin/ncells
#end if
net_charge_fold = net_charge/ncells
elif not self.structure.has_axes(): # folded molecule
# net charge/spin are not physically meaningful
# for a point group folded molecule
# set them to safe values; they will not be used later
net_charge_fold = 0
net_spin_fold = 'low'
else:
self.error('folded structure is not correctly integrated with full structure\nfolded physical system cannot be constructed')
#end if
self.folded_system = PhysicalSystem(
structure = structure.folded_structure,
net_charge = net_charge_fold,
net_spin = net_spin_fold,
particles = particles,
**valency
)
#end if
self.valency_in = obj(**valency)
self.net_charge_in = net_charge
self.net_spin_in = net_spin
self.update_particles(clear=False)
self.check_folded_system()
def __init__(self, data=None, alignment=0):
self.__ctx_items = []
Structure.__init__(self, data, alignment)
if data is None:
self['Pad'] = ''
self['ctx_items'] = ''
self['sec_trailer'] = ''
self['auth_data'] = ''
def __init__(self, data = None, alignment = 0):
self.__ctx_items = []
Structure.__init__(self,data,alignment)
if data is None:
self['Pad'] = ''
self['ctx_items'] = ''
self['sec_trailer'] = ''
self['auth_data'] = ''
def fromString(self, data):
Structure.fromString(self,data)
# Parse the ctx_items
data = self['ctx_items']
for i in range(self['ctx_num']):
item = CtxItemResult(data)
self.__ctx_items.append(item)
data = data[len(item):]
def _get_fk_data(self, table_name, fk, fk_value):
reltable = Structure.get_fk_referenced_table(table_name, fk)
reltable_pk = Structure.get_primary_key(reltable)
if not self._cache.relation_exists(table_name, reltable):
sql = SQLBuilder(reltable)
sql.add_where_literal(Column(reltable, reltable_pk).in_(self._cache.get_all_keys(table_name, fk)))
data = Query().execute_and_fetch(**sql.build_select())
self._cache.save_relation(table_name, reltable, data)
return Row(self._cache.get_relation_row(reltable, reltable_pk, fk_value), reltable, self)
def __init__(self, data = None, alignment = 0):
Structure.__init__(self, data, alignment)
if data is None:
self['max_tfrag'] = 4280
self['max_rfrag'] = 4280
self['assoc_group'] = 0
self['ctx_num'] = 1
self['ctx_items'] = ''
self.__ctx_items = []
def getBooStructure(self):
natoms=sum(self.atoms)
strcVecs=Structure(self.elements,self.atoms,self.positions,self.lattice).getStructure()
keys=strcVecs.keys()
booStructure={}
for key in keys:
vecs=strcVecs[key]
boos=np.array([])
for vec in vecs:
boos=np.append(boos,Boo(vec).getBoo())
booStructure[key]=boos
return booStructure
def __init__(self,
structure=None,
net_charge=0,
net_spin=0,
particles=None,
**valency):
self.pseudized = False
if structure is None:
self.structure = Structure()
else:
self.structure = structure
#end if
if particles is None:
self.particles = Particles()
else:
self.particles = particles.copy()
#end if
self.folded_system = None
if self.structure.folded_structure != None:
vratio = structure.volume() / structure.folded_structure.volume()
ncells = int(round(vratio))
if abs(vratio - ncells) > 1e-4:
self.error(
'volume of system does not divide evenly into folded system'
)
#end if
if net_charge % ncells != 0:
self.error(
'net charge of system does not divide evenly into folded system'
)
#end if
if net_spin % ncells != 0:
self.error(
'net_spin of system does not divide evenly into folded system'
)
#end if
self.folded_system = PhysicalSystem(
structure=structure.folded_structure,
net_charge=net_charge / ncells,
net_spin=net_spin / ncells,
particles=particles,
**valency)
#end if
self.valency_in = obj(**valency)
self.net_charge_in = net_charge
self.net_spin_in = net_spin
self.update_particles(clear=False)
self.check_folded_system()
def load_us_code(src):
## Invariant: for the meta-structure, order = title #.
file_ = open(src, 'r')
file_.close()
mar1 = datetime.date(2018, 3, 1)
structure = Structure('Title', '18', 18,
subsections=[Structure('Section', '2', 2,
dates=[mar1],
texts={mar1:''},
diffs={mar1:[]})])
structure = Structure('US Code', '0', 0, subsections=[structure])
return structure
def __init__(self, url):
'''Construct a new Firebase reference from a full Firebase URL.'''
self.connection = Connection(url, self)
self.base_url = url
self.structure = Structure(self)
self.subscriptions = {}
self.history = []
self.connection.daemon = True
self.connection.start()
self._keep_alive()
atexit.register(self.close)
DataRef.__init__(self, self, '')
def __init__(self, data = None, alignment = 0):
Structure.__init__(self,data, alignment)
if data is None:
self['ver_major'] = 5
self['ver_minor'] = 0
self['flags'] = MSRPC_FIRSTFRAG | MSRPC_LASTFRAG
self['type'] = MSRPC_REQUEST
self.__frag_len_set = 0
self['auth_len'] = 0
self['pduData'] = ''
self['auth_data'] = ''
self['sec_trailer'] = ''
self['pad'] = ''
def get_result(self, result_name, sim):
result = obj()
input = self.input
if result_name == 'structure':
# get structure from CONTCAR
ccfile = os.path.join(self.locdir, self.identifier + '.CONTCAR')
if not os.path.exists(ccfile):
self.error(
'CONTCAR file does not exist for relax simulation at ' +
self.locdir)
#end if
contcar = Poscar(ccfile)
structure = Structure()
if contcar.elem is not None:
structure.read_poscar(ccfile)
else:
elem, elem_count = self.system.structure.order_by_species()
structure.read_poscar(ccfile, elem=elem)
#end if
if input.poscar.dynamic is not None:
structure.freeze(input.poscar.dynamic, negate=True)
#end if
result.structure = structure
else:
self.error('ability to get result ' + result_name +
' has not been implemented')
#end if
return result
def __init__(self):
Structure.__init__(self)
self['flags'] = (
NTLMSSP_NEGOTIATE_128 | NTLMSSP_NEGOTIATE_KEY_EXCH |
# NTLMSSP_LM_KEY |
NTLMSSP_NEGOTIATE_NTLM | NTLMSSP_NEGOTIATE_UNICODE |
# NTLMSSP_ALWAYS_SIGN |
NTLMSSP_NEGOTIATE_SIGN | NTLMSSP_NEGOTIATE_SEAL |
# NTLMSSP_TARGET |
0)
self['host_name'] = ''
self['domain_name'] = ''
self['os_version'] = ''
self._workstation = ''
def __init__(self, version, revision, pageSize=8192, data=None):
if (version < 0x620) or (version == 0x620 and revision < 0x0b):
# For sure the old format
self.structure = self.structure_2003_SP0 + self.common
elif version == 0x620 and revision < 0x11:
# Exchange 2003 SP1 and Windows Vista and later
self.structure = self.structure_0x620_0x0b + self.common
else:
# Windows 7 and later
self.structure = self.structure_win7 + self.common
if pageSize > 8192:
self.structure += self.extended_win7
Structure.__init__(self, data)
def supercell(self, dim):
"""
create supercell
Arguments:
dim: size of supercell. i.e. [2,2,2]
Return:
object of supercell structure.
"""
# step:
# 1. move atom
# 2. change the lattice vector
# 3. call formatting
# 4. pop old
# 5. append new
# check dim
if (sum(1 for x in dim if x <= 0) >= 1) or (sum(
1 for x in dim if not isinstance(x, int)) >= 1):
raise StructureFactoryError('invalid dim')
atom_set = self.structure.atoms.all()
for i in xrange(0, dim[0]): # x
for j in xrange(0, dim[1]): # y
for k in xrange(0, dim[2]): # z
for atom in atom_set:
Atom.objects.create(structure=self.structure,
element=atom.element,
x=(atom.x + i) / dim[0],
y=(atom.y + j) / dim[1],
z=(atom.z + k) / dim[2])
# delete old atoms
for atom in atom_set:
atom.delete()
lattice = self.structure.lattice
for i in xrange(0, lattice.shape[0]):
lattice[i] = lattice[i] * dim[i]
self.structure.lattice = lattice
self.structure.save()
#poscar=self.structure.formatting(isConstraint=constrained)
poscar = self.structure.formatting(isConstraint=False)
self.structure.pop() # delete old object
self.structure = Structure().append(poscar)
return self.structure
def select(self, *args):
if args:
map(lambda arg: self._check_is_instance(arg, 'Column'), args)
args = list(args)
args.append(Column(self._table_name, Structure.get_primary_key(self._table_name)))
self._sql.add_select_args(args)
return self._table_selected_instance()
def update(self, event):
new = False
if 'structures' in event:
# print('structure update')
for id_, value in event['structures'].iteritems():
# print('%s -- %s' % (id_, value))
if id_ in self._structures:
self._structures[id_].update(value)
else:
new = True
self._structures.update(
{id_: Structure(id_, data=value, nestapi=self)})
if 'devices' in event:
# print(event)
for cat, device in event['devices'].iteritems():
for k, v in device.iteritems():
k = bytes(k)
if k in self._devices:
self._devices[k].update(v)
else:
new = True
self._devices.update({k: get_device(cat)(
k, data=v, nestapi=self)})
if new:
self.upnp_devices = self._structures.values() +\
self._devices.values()
if self.parent:
self.parent.update()
def sizeof(form):
try:
from data import structures
except:
from .data import structures
try:
from structure import Structure
except:
from .structure import Structure
if isinstance(form, str):
form = getattr(structures, form)
h = Structure(form)
return h.sizeof()
def read_atom_structure(path,
atoms_prim,
atom_basis,
defect_atom_index=None,
axis=None,
center=None):
""" read atomic structure of super lattice
Returns
Args
"""
if center is None:
center = np.array([0, 0, 0])
# axis = axis or 2
# span = [1, 1, 0]
# span[axis] = 0
tol = 0.11
struct = Structure.read_contcar(path, 'POSCAR')
dist_mat_vec = struct.frac_dist_mat(span=[1, 1, 0], offset=center)
if defect_atom_index is not None:
# we deal with only one element!
# First element! O.N.L.Y.!
# TODO(Sunghyun Kim): treat n elements.
indice = range(struct.get_n_elements()[0])
for ind in defect_atom_index:
indice.remove(ind)
indice = np.array(indice)
dist_mat_vec = dist_mat_vec[indice, :, :]
dist_mat_vec = dist_mat_vec[:, indice, :]
n_Si = len(indice)
else:
n_Si = struct.get_n_elements()[0]
dist_mat_vec = dist_mat_vec[:n_Si, :n_Si]
atoms_prim_new = []
for i in atoms_prim:
atoms_prim_new.append(i - np.sum(np.array(defect_atom_index) < i))
atoms_prim = atoms_prim_new
atom_basis_new = []
for i in atom_basis:
atom_basis_new.append(i - np.sum(np.array(defect_atom_index) < i))
atom_basis = atom_basis_new
lat_mat_sc = struct.lattice.get_matrix()
lat_mat_prim = get_lat_mat_prim(lat_mat_sc, dist_mat_vec, atoms_prim)
lat_mat_prim = np.dot(lat_mat_prim, lat_mat_sc)
overlap = get_overlap(dist_mat_vec, atom_basis, lat_mat_sc, lat_mat_prim,
tol)
proj_coord = get_proj_coord(dist_mat_vec, lat_mat_sc, lat_mat_prim)
lat_mat_sc_refine = get_lat_mat_sc_refine(lat_mat_sc, lat_mat_prim)
layer_ind = get_layer_index(struct, proj_coord, overlap, indice,
lat_mat_prim, axis, atom_basis)
return lat_mat_sc, lat_mat_prim, lat_mat_sc_refine, proj_coord, dist_mat_vec, overlap, indice, layer_ind
def getBooStructure(self):
bondsDics = Structure(self.lattice, self.positions, self.elements,
self.atoms).getStructure()
keys = bondsDics.keys()
#the keys are the atoms.
booStructure = {}
for key in keys:
vecs = bondsDics[key]
boos = []
for vec in vecs:
boos.append(Boo(vec).getBoo())
booStructure[key] = np.array(boos)
return booStructure
def groFrameIterator(stream):
"""Read a GRO file stream frame by frame"""
if type(stream) == str:
if stream.endswith(".gz"):
stream = gzip.open(stream)
else:
stream = open(stream)
# For efficiency, we need to know the precision
precision = None
while True:
try:
title = stream.next()
except StopIteration:
break
natoms = stream.next().strip()
if not natoms:
break
natoms = int(natoms)
if not precision:
a = stream.next()
prec = len(a.split(".")[-2]) + 1
atoms = [groAtom(a, precision)]
atoms.extend(
[groAtom(stream.next(), precision) for i in range(natoms - 1)])
else:
atoms = [groAtom(stream.next(), precision) for i in range(natoms)]
box = groBoxRead(stream.next())
yield Structure(title=title, atoms=atoms, box=box)
def fromString(self, data):
Structure.fromString(self, data)
domain_offset = self['domain_offset']
domain_end = self['domain_len'] + domain_offset
self['domain_name'] = data[domain_offset:domain_end]
host_offset = self['host_offset']
host_end = self['host_len'] + host_offset
self['host_name'] = data[host_offset:host_end]
hasOsInfo = self['flags'] & NTLMSSP_NEGOTIATE_VERSION
if len(data) >= 36 and hasOsInfo:
self['os_version'] = data[32:40]
else:
self['os_version'] = ''
def _get_rel_data_restricted(self, sql):
attr, pk = self._restricted_table_attr, self._get_pk()
relation_fk = Structure.get_foreign_key_for_table(attr, self._table_name)
sql.add_where_condition(relation_fk, self.data[pk])
data = Query().execute_and_fetch(**sql.build_select())
from resultset import ResultSet
return ResultSet(data, attr)
def _get_rel_data_restricted(self, sql):
saved = self._restricted_table_call
table_name, relation, pk, pk_value = saved['table_name'], saved['relation'], saved['pk'], saved['pk_value']
relation_fk = Structure.get_foreign_key_for_table(relation, table_name)
if not self._cache.relation_exists(table_name, relation):
if sql._select_args:
sql.add_select_arg(Column(relation, relation_fk))
if sql._limit:
union_sql = []
union_parameters = []
union_dict = {}
for id in self._cache.get_all_keys(table_name, pk):
limiting_sql = copy.deepcopy(sql)
limiting_sql.add_where_literal(Column(relation, relation_fk) == id)
union_dict = limiting_sql.build_select()
union_sql.append('(%s)' % union_dict['sql'])
union_parameters.extend(union_dict['parameters'])
union_dict['sql'], union_dict['parameters'] = ' UNION '.join(union_sql), union_parameters
data = Query().execute_and_fetch(**union_dict)
self._cache.save_relation(table_name, relation, data)
else:
sql.add_where_literal(Column(relation, relation_fk).in_(self._cache.get_all_keys(table_name, pk)))
data = Query().execute_and_fetch(**sql.build_select())
self._cache.save_relation(table_name, relation, data)
return ResultSet(self._cache.get_relation_set(relation, relation_fk, pk_value), relation, self._cache)
def domain_defect(complex, strand_num, domain_num, structure):
""" Calculates the defect of the binding of the given domain in
the complex against the domain's expected binding given in the
specified target structure. If the domain is not completely bound
or unbound, the results are not very meaningful.
The defect is calculated as a fraction of the domain's length."""
from structure import Structure
strandlist = [lst[:] for lst in structure.to_strandlist()]
strands = structure.strands
domain_start = sum(
[d.length for d in strands[strand_num].domains[:domain_num]])
domain_end = domain_start + strands[strand_num].domains[domain_num].length
n = 0
for strand_n, strand_struct in enumerate(strandlist):
for i, bound in enumerate(strand_struct):
is_domain = (strand_n == strand_num
and domain_start <= i < domain_end)
is_bound_to_domain = (bound != None and bound != '?'
and bound[0] == strand_num
and domain_start <= bound[1] < domain_end)
if not is_domain and not is_bound_to_domain:
strandlist[strand_n][i] = '?'
else:
n += 1
new_struct = Structure(structure=strandlist, strands=structure.strands)
return defect(complex, new_struct) / float(n)
def _get_pk(self):
pk = Structure.get_primary_key(self._table_name)
if self.data.get(pk) is not None:
return pk
else:
raise PyPgException(
'Incorectly formated naming for primary key. Please provide manager.Naming instance or set strict mode on.'
)
def _get_rel_data_restricted(self, sql):
attr, pk = self._restricted_table_attr, self._get_pk()
relation_fk = Structure.get_foreign_key_for_table(
attr, self._table_name)
sql.add_where_condition(relation_fk, self.data[pk])
data = Query().execute_and_fetch(**sql.build_select())
from resultset import ResultSet
return ResultSet(data, attr)
def select(self, *args):
if args:
map(lambda arg: self._check_is_instance(arg, 'Column'), args)
args = list(args)
args.append(
Column(self._table_name,
Structure.get_primary_key(self._table_name)))
self._sql.add_select_args(args)
return self._table_selected_instance()
def make_movie(self,filename,filepath=None):
if 'structures' in self:
from structure import Structure
if filepath==None:
filepath = os.path.join(self.abspath,filename)
else:
filepath = os.path.join(filepath,filename)
#end if
movie = ''
structures = self.structures
aA = convert(self.input.system['celldm(1)'],'B','A')
cell = self.input.cell_parameters.vectors
for i in range(len(structures)):
s = structures[i]
struct = Structure(elem=s.atoms,pos=s.positions,axes=cell,scale=aA,units='A')
struct=struct.tile(2,2,2)
ss=struct.write_xyz()
movie += ss
open(filepath,'w').write(movie)
def __init__(self, url):
"""Construct a new Firebase reference from a full Firebase URL."""
self.connection = Connection(url, self)
self.base_url = url
self.structure = Structure(self)
self.subscriptions = {}
self.history = []
self.connection.daemon = True
self.connection.start()
atexit.register(self.close)
DataRef.__init__(self, self, "")
def __init__(self, url, ssl_options=None):
'''Construct a new Firebase reference from a full Firebase URL.'''
self.connection = Connection(url, self, ssl_options=ssl_options)
self.base_url = url
self.structure = Structure(self)
self.subscriptions = {}
self.history = []
self.connection.daemon = True
self.connection.start()
self._keep_alive()
atexit.register(self.close)
DataRef.__init__(self, self, '')
def __getattr__(self, attr):
self._check_deleted()
if Structure.is_foreign_key(self._table_name, attr):
if self._result_set:
return self._result_set._get_fk_data(self._table_name, attr, self.data[attr])
else:
reltable = Structure.get_fk_referenced_table(self._table_name, attr)
reltable_pk = Structure.get_primary_key(reltable)
sql = SQLBuilder(reltable)
sql.add_where_condition(reltable_pk, self.data[attr])
data = Query().execute_and_fetch(**sql.build_select())
return Row(data[0], reltable)
else:
self._check_relation_exists(attr)
pk = self._get_pk()
if self._result_set:
return self._result_set._get_rel_data(self._table_name, attr, pk, self.data[pk])
else:
self._restricted_table_attr = attr
from restricted import RestrictedTableSelect
return RestrictedTableSelect(attr, SQLBuilder(attr), self)
def __init__(self,structure=None,net_charge=0,net_spin=0,particles=None,**valency):
self.pseudized = False
if structure is None:
self.structure = Structure()
else:
self.structure = structure
#end if
if particles is None:
self.particles = Particles()
else:
self.particles = particles.copy()
#end if
self.folded_system = None
if self.structure.folded_structure!=None:
vratio = structure.volume()/structure.folded_structure.volume()
ncells = int(round(vratio))
if abs(vratio-ncells)>1e-4:
self.error('volume of system does not divide evenly into folded system')
#end if
if net_charge%ncells!=0:
self.error('net charge of system does not divide evenly into folded system')
#end if
if net_spin%ncells!=0:
self.error('net_spin of system does not divide evenly into folded system')
#end if
self.folded_system = PhysicalSystem(
structure = structure.folded_structure,
net_charge = net_charge/ncells,
net_spin = net_spin/ncells,
particles = particles,
**valency
)
#end if
self.valency_in = obj(**valency)
self.net_charge_in = net_charge
self.net_spin_in = net_spin
self.update_particles(clear=False)
self.check_folded_system()
def __init__(self,structure=None,net_charge=0,net_spin=0,particles=None,**valency):
self.structure = structure
self.particles = particles
if structure==None:
self.structure = Structure()
#end if
if particles==None:
self.particles = Particles()
#end if
self.folded_system = None
if self.structure.folded_structure!=None:
self.folded_system = PhysicalSystem(
structure = structure.folded_structure,
net_charge = net_charge,
net_spin = net_spin,
particles = particles,
**valency
)
#end if
#add ions
pc = dict()
elem = list(self.structure.elem)
for ion in set(elem):
pc[ion] = elem.count(ion)
#end for
self.add_particles(**pc)
#pseudize
if len(valency)>0:
self.pseudize(**valency)
#end if
#add electrons
self.generate_electrons(net_charge,net_spin)
self.check_folded_system()
def get_result(self, result_name, sim):
result = obj()
input = self.input
if result_name == "structure":
# OUTCAR structure is not as precise as CONTCAR structure
# pa = self.load_analyzer_image()
# elem = input.poscar.elem
# elem_count = input.poscar.elem_count
# atoms = []
# for i in range(len(elem)):
# atoms += elem_count[i]*[elem[i]]
##end for
# structure = Structure(
# units = 'A',
# axes = pa.lattice_vectors.copy(),
# elem = atoms,
# pos = pa.position.copy()
# )
# get structure from CONTCAR
ccfile = os.path.join(self.locdir, self.identifier + ".CONTCAR")
if not os.path.exists(ccfile):
self.error("CONTCAR file does not exist for relax simulation at " + self.locdir)
# end if
contcar = Poscar(ccfile)
structure = Structure()
if contcar.elem != None:
structure.read_poscar(ccfile)
else:
elem, elem_count = self.system.structure.order_by_species()
structure.read_poscar(ccfile, elem=elem)
# end if
if input.poscar.dynamic != None:
structure.freeze(input.poscar.dynamic, negate=True)
# end if
result.structure = structure
else:
self.error("ability to get result " + result_name + " has not been implemented")
# end if
return result
def join(self, table, on=None):
self._check_is_instance(table, 'Table')
if on:
self._check_is_instance(on, 'Literal')
self._validate_on(table, on)
else:
Structure.tables_related(self._table_name, table._table_name)
try:
fk = Structure.get_foreign_key_for_table(self._table_name, table._table_name)
except PyPgException:
fk = Structure.get_foreign_key_for_table(table._table_name, self._table_name)
on = Column(table._table_name, fk) == \
Column(self._table_name, Structure.get_primary_key(self._table_name))
else:
on = Column(self._table_name, fk) == \
Column(table._table_name, Structure.get_primary_key(table._table_name))
self._sql.add_join(table._table_name, on)
return self._table_select_instance()
class RootDataRef(DataRef):
'''A reference to a root of a Firbase.'''
def __init__(self, url, ssl_options=None):
'''Construct a new Firebase reference from a full Firebase URL.'''
self.connection = Connection(url, self, ssl_options=ssl_options)
self.base_url = url
self.structure = Structure(self)
self.subscriptions = {}
self.history = []
self.connection.daemon = True
self.connection.start()
self._keep_alive()
atexit.register(self.close)
DataRef.__init__(self, self, '')
def _process(self, message):
'''Process a single incoming message'''
# This whole thing needs to be rewritten to use all the new information about the protocol
debug(message)
# If message type is data
if message['t'] == 'd':
data = message['d']
# If r is in data and set to 1 then it's probably a response
# to something we sent like a sub request or an auth token
if 'r' in data:
historical_entry = self.history[data['r']-1]
request = historical_entry['message']
callbacks = historical_entry['callbacks']
error = data['b']['s']
if error != 'ok':
if error == 'permission_denied':
path = request['d']['b']['p']
print 'FIREBASE WARNING: on() or once() for %s failed: %s' % (path, error)
elif error == 'expired_token' or error == 'invalid_token':
print 'FIREBASE WARNING: auth() failed: %s' % (error)
else:
path = request['d']['b']['p']
print 'FIREBASE WARNING: unknown for %s failed: %s' % (path, error)
onCancel = callbacks.get('onCancel', None)
if not onCancel is None:
onCancel(error)
onComplete = callbacks.get('onComplete', None)
if not onComplete is None:
onComplete(error if error != 'ok' else None)
# If t is in data then it's the response to the initial connection, maybe
elif 't' in data:
pass
# If a is in data, it's a new data blob for a node, maybe
elif 'a' in data:
if data['a'] == 'c':
# This type of message is created when we lose permission to read
# and it requires some extra effort to implement as we call onCancel
# for all effected callbacks, which are any anscestors of the path
pass
else:
b_data = data['b']
path = b_data['p']
path_data = b_data['d']
self._store(path, path_data)
# If message type is... control?
if message['t'] == 'c':
pass
def _store(self, path, path_data):
'''Store a single path worth of data into the strucutre.'''
if not path or path[0] != "/":
path = "/%s" % path
self.structure.store(path, path_data)
def _send(self, message, callbacks=None):
'''Send a single message to Firebase.'''
historical_entry = {
'message': message,
'callbacks': {} if callbacks is None else callbacks
}
self.history.append(historical_entry)
message['d']['r'] = len(self.history)
self.connection.send(message)
def _subscribe(self, path, query, callbacks=None):
'''Subscribe to updates regarding a path'''
isSubscribed = self._is_subscribed(path, query)
# A subscription (listen) request takes two main arguments, p (path) and q (query).
if not isSubscribed:
message = {"t":"d", "d":{"r":0, "a":"l", "b":{"p":path}}}
if not query is None:
message['d']['b']['q'] = query
self._send(message, callbacks)
self.subscriptions[path] = query
return True
else:
# Should probably trigger callbacks['onComplete'] here
return False
def _keep_alive(self):
'''Send a keep-alive packet to Firebase'''
def send():
self._send({"t":"d", "d":{"r":0}})
Timer(60.0, send).start()
Timer(60.0, send).start()
def _bind(self, path, event, callback):
'''Bind a single callback to an event on a path'''
event_key = '.event-'+event
structure_path = self.structure.get(path, {})
self.structure[path] = structure_path
events = structure_path.get(event_key, [])
events.append(callback)
self.structure[path][event_key] = events
def _is_subscribed(self, path, query):
'''Return True if already subscribed to this path or an ancestor.'''
return any([s.split('/')==path.split('/')[:len(s.split('/'))] for s in self.subscriptions.keys()])
def __init__(self, basename):
Structure.__init__(self, basename)
self.flaps = []
def return_system(self):
ibrav = self.system.ibrav
if ibrav!=0:
self.error('ability to handle non-zero ibrav not yet implemented')
#end if
scale,axes,kaxes = self.get_common_vars('scale','axes','kaxes')
elem = list(self.atomic_positions.atoms)
ap = self.atomic_positions.copy()
ap.change_specifier('bohr',self)
pos = ap.positions
kp = self.k_points.copy()
kp.change_specifier('tpiba',self)
kpoints = kp.kpoints*(2*pi)/scale
center = axes.sum(0)/2
structure = Structure(
axes = axes,
elem = elem,
scale = scale,
pos = pos,
center = center,
kpoints = kpoints,
units = 'B',
rescale = False
)
structure.zero_corner()
structure.recenter()
ion_charge = 0
valency = dict()
atoms = list(self.atomic_positions.atoms)
for atom in self.atomic_species.atoms:
pseudo_file = self.atomic_species.pseudopotentials[atom]
if self.pseudopotentials!=None and pseudo_file in self.pseudopotentials:
pseudopot = self.pseudopotentials[pseudo_file]
element = pseudopot.element
valence = int(pseudopot.Z)
ion_charge += atoms.count(atom)*valence
valency[atom] = valence
else:
self.error('file '+pseudo_file+' was not listed in Pseudopotentials object\n please specify pseudopotentials with the settings function',trace=False)
#end if
#end for
if 'nelup' in self.system:
nup = self.system.nelup
ndn = self.system.neldw
net_charge = ion_charge - nup - ndn
net_spin = nup - ndn
elif 'tot_magnetization' in self.system:
net_spin = self.system.tot_magnetization
if 'nelec' in self.system:
net_charge = ion_charge - self.system.nelec
else:
net_charge = 0
#end if
else:
net_spin = 0
if 'nelec' in self.system:
net_charge = ion_charge - self.system.nelec
else:
net_charge = 0
#end if
#end if
system = PhysicalSystem(structure,net_charge,net_spin,**valency)
return system
def getData(self):
addr = self['SourceIP'].split('.')
addr = [int(x) for x in addr]
addr = (((addr[0] << 8) + addr[1] << 8) + addr[2] << 8) + addr[3]
self['_SourceIP'] = addr
return Structure.getData(self)
def __init__(self, result, reason, tsUUID, tsVer):
Structure.__init__(self)
self['Result'] = result
self['Reason'] = reason
self['TransferSyntaxUUID'] = tsUUID.bytes_le
self['TransferSyntaxVer'] = tsVer
def _check_relation_exists(self, relation):
Structure.table_exists(relation)
Structure.tables_related(relation, self._table_name)
class PhysicalSystem(Matter):
def __init__(self,structure=None,net_charge=0,net_spin=0,particles=None,**valency):
self.pseudized = False
if structure is None:
self.structure = Structure()
else:
self.structure = structure
#end if
if particles is None:
self.particles = Particles()
else:
self.particles = particles.copy()
#end if
self.folded_system = None
if self.structure.folded_structure!=None:
vratio = structure.volume()/structure.folded_structure.volume()
ncells = int(round(vratio))
if abs(vratio-ncells)>1e-4:
self.error('volume of system does not divide evenly into folded system')
#end if
if net_charge%ncells!=0:
self.error('net charge of system does not divide evenly into folded system')
#end if
if net_spin%ncells!=0:
self.error('net_spin of system does not divide evenly into folded system')
#end if
self.folded_system = PhysicalSystem(
structure = structure.folded_structure,
net_charge = net_charge/ncells,
net_spin = net_spin/ncells,
particles = particles,
**valency
)
#end if
self.valency_in = obj(**valency)
self.net_charge_in = net_charge
self.net_spin_in = net_spin
self.update_particles(clear=False)
self.check_folded_system()
#end def __init__
def update_particles(self,clear=True):
#add ions
pc = dict()
elem = list(self.structure.elem)
for ion in set(elem):
pc[ion] = elem.count(ion)
#end for
missing = set(pc.keys())-set(self.particles.keys())
if len(missing)>0 or len(elem)==0:
if clear:
self.particles.clear()
#end if
self.add_particles(**pc)
#pseudize
if len(self.valency_in)>0:
self.pseudize(**self.valency_in)
#end if
#add electrons
self.generate_electrons(self.net_charge_in,self.net_spin_in)
#end if
#end def update_particles
def update(self):
self.net_charge = self.structure.background_charge
self.net_spin = 0
for p in self.particles:
self.net_charge += p.count*p.charge
self.net_spin += p.count*p.spin
#end for
self.net_charge = int(round(float(self.net_charge)))
self.net_spin = int(round(float(self.net_spin)))
#end def update
def add_particles(self,**particle_counts):
pc = self.particle_collection # all known particles
plist = []
for name,count in particle_counts.iteritems():
particle = pc.get_particle(name)
if particle is None:
self.error('particle {0} is unknown'.format(name))
else:
particle = particle.copy()
#end if
particle.set_count(count)
plist.append(particle)
#end for
self.particles.add_particles(plist)
self.update()
#end def add_particles
def generate_electrons(self,net_charge=0,net_spin=0):
nelectrons = -net_charge + self.net_charge
if net_spin=='low':
net_spin = nelectrons%2
#end if
nup = float(nelectrons + net_spin - self.net_spin)/2
ndown = float(nelectrons - net_spin + self.net_spin)/2
if abs(nup-int(nup))>1e-3:
self.error('requested spin state {0} incompatible with {1} electrons'.format(net_spin,nelectrons))
#end if
nup = int(nup)
ndown = int(ndown)
self.add_particles(up_electron=nup,down_electron=ndown)
#end def generate_electrons
def pseudize(self,**valency):
errors = False
for ion,valence_charge in valency.iteritems():
if ion in self.particles:
ionp = self.particles[ion]
if isinstance(ionp,Ion):
self.particles[ion] = ionp.pseudize(valence_charge)
self.pseudized = True
else:
self.error(ion+' cannot be pseudized',exit=False)
#end if
else:
self.error(ion+' is not in the physical system',exit=False)
errors = True
#end if
#end for
if errors:
self.error('system cannot be generated')
#end if
self.valency = obj(**valency)
self.update()
#end def pseudize
def check_folded_system(self):
sys_folded = self.folded_system!=None
struct_folded = self.structure.folded_structure!=None
if sys_folded!=struct_folded:
self.error('folding of physical system and structure is not consistent\n system folded: {0}\n structure folded: {1}'.format(sys_folded,struct_folded))
#end if
if sys_folded and id(self.structure.folded_structure)!=id(self.folded_system.structure):
self.error('structure of folded system and folded structure are distinct\n this is not allowed and may be a developer error')
#end if
#end def check_folded_system
def change_units(self,units):
self.structure.change_units(units,folded=False)
if self.folded_system!=None:
self.folded_system.change_units(units)
#end if
#end def change_units
def group_atoms(self):
self.structure.group_atoms(folded=False)
if self.folded_system!=None:
self.folded_system.group_atoms()
#end if
#end def group_atoms
def rename(self,folded=True,**name_pairs):
self.particles.rename(**name_pairs)
self.structure.rename(folded=False,**name_pairs)
if self.pseudized:
for old,new in name_pairs.iteritems():
if old in self.valency:
if new not in self.valency:
self.valency[new] = self.valency[old]
#end if
del self.valency[old]
#end if
#end for
self.valency_in = self.valency
#end if
if self.folded_system!=None and folded:
self.folded_system.rename(folded=folded,**name_pairs)
#end if
#end def rename
def copy(self):
cp = DevBase.copy(self)
if self.folded_system!=None and self.structure.folded_structure!=None:
del cp.folded_system.structure
cp.folded_system.structure = cp.structure.folded_structure
#end if
return cp
#end def copy
def load(self,filepath):
DevBase.load(self,filepath)
if self.folded_system!=None and self.structure.folded_structure!=None:
del self.folded_system.structure
self.folded_system.structure = self.structure.folded_structure
#end if
#end def load
def tile(self,*td,**kwargs):
extensive = True
net_spin = None
if 'extensive' in kwargs:
extensive = kwargs['extensive']
#end if
if 'net_spin' in kwargs:
net_spin = kwargs['net_spin']
#end if
supercell = self.structure.tile(*td)
supercell.remove_folded()
if extensive:
ncells = int(round(supercell.volume()/self.structure.volume()))
net_charge = ncells*self.net_charge
if net_spin is None:
net_spin = ncells*self.net_spin
#end if
else:
net_charge = self.net_charge
if net_spin is None:
net_spin = self.net_spin
#end if
#end if
system = self.copy()
supersystem = PhysicalSystem(
structure = supercell,
net_charge = net_charge,
net_spin = net_spin,
**self.valency
)
supersystem.folded_system = system
supersystem.structure.set_folded(system.structure)
return supersystem
#end def tile
def remove_folded_system(self):
self.folded_system = None
self.structure.remove_folded_structure()
#end def remove_folded_system
def remove_folded(self):
self.remove_folded_system()
#end def remove_folded
def get_primitive(self):
if self.folded_system is None:
fs = self
else:
fs = self.folded_system
while fs.folded_system!=None:
fs = fs.folded_system
#end while
#end if
return fs
#end def get_primitive
def folded_representation(self,arg0,arg1=None):
self.error('folded_representation needs a developers attention to make it equivalent with tile')
if isinstance(arg0,PhysicalSystem):
folded_system = arg0
elif isinstance(arg0,str):
shape = arg0
tiling = arg1
if tiling is None:
tiling = (1,1,1)
#end if
if not 'generation_info' in self:
self.error('system was not formed with generate_physical_system, cannot form folded representation')
#end if
structure,element,scale,units,net_charge,net_spin,particles,valency = \
self.generation_info.tuple('structure','element','scale','units', \
'net_charge','net_spin','particles','valency')
folded_system = generate_physical_system(
structure = structure,
shape = shape,
element = element,
tiling = tiling,
scale = scale,
units = units,
net_charge = net_charge,
net_spin = net_spin,
particles = particles,
**valency
)
else:
self.error('unrecognized inputs in folded_representation')
#end if
tilematrix,kmap = self.structure.fold(folded_system.structure,'tilematrix','kmap')
self.set(
folded_system = folded_system,
tilematrix = tilematrix,
kmap = kmap
)
return folded_system
#end def folded_representation
def large_Zeff_elem(self,Zmin):
elem = []
for atom,Zeff in self.valency.iteritems():
if Zeff>Zmin:
elem.append(atom)
#end if
#end for
return elem
#end def large_Zeff_elem
def ae_pp_species(self):
species = set(self.structure.elem)
if self.pseudized:
pp_species = set(self.valency.keys())
ae_species = species-pp_species
else:
pp_species = set()
ae_species = species
#end if
return ae_species,pp_species
def __init__(self, data = None, alignment = 0):
Structure.__init__(self,data,alignment)
if data is None:
self['SupportedVersions'] = ''
def test_structure(N,lt):
'''
N:
The size of the lattice.
lt:
The lattice type.
'''
lts=construct_lattice(N=N,lattice_shape=lt)
tgroup=TranslationGroup(Rs=lts.a*lts.N[:,newaxis],per=(True,False))
lt=Structure(lts.sites)
#test for bonds
lt.usegroup(tgroup)
lt.initbonds(K=17)
#finding neighbors
print 'find nearest neighbor %s'%lt.b1s.N
print 'find second nearest neighbor %s'%lt.b2s.N
print 'find third nearest neighbor %s'%lt.b3s.N
isite=array([1]*lt.vdim)
#find a site at specific position.
print 'finding - %s'%isite,lt.findsite(isite)
i=0
if lts.dimension==2:
j=lts.l2index((0,N[1]-1,0))
print 'measureing distance between site %s and %s -> %s'%(i,j,lt.measure(i,j))
j=lts.l2index((N[0]-1,0,0))
print 'measureing distance between site %s and %s -> %s'%(i,j,lt.measure(i,j))
else:
j=lt.nsite-1
print 'measureing distance between site %s and %s -> %s'%(i,j,lt.measure(i,))
ion()
lt.show_bonds()
lt.show_sites()
pdb.set_trace()
cla()
#test for save and load functionality.
lt.save_bonds()
lt2=Structure(lts.sites)
lt2.load_bonds()
lt2.show_bonds()
lt2.show_sites()
axis('equal')
pdb.set_trace()
def _get_pk(self):
pk= Structure.get_primary_key(self._table_name)
if self.data.get(pk) is not None:
return pk
else:
raise PyPgException('Incorectly formated naming for primary key. Please provide manager.Naming instance or set strict mode on.')
def getData(self):
self['ctx_num'] = len(self.__ctx_items)
for i in self.__ctx_items:
self['ctx_items'] += i.getData()
return Structure.getData(self)
def __getattr__(self, name):
Structure.table_exists(name)
return Table(name)
class RootDataRef(DataRef):
"""A reference to a root of a Firbase."""
def __init__(self, url):
"""Construct a new Firebase reference from a full Firebase URL."""
self.connection = Connection(url, self)
self.base_url = url
self.structure = Structure(self)
self.subscriptions = {}
self.history = []
self.connection.daemon = True
self.connection.start()
atexit.register(self.close)
DataRef.__init__(self, self, "")
def _process(self, message):
"""Process a single incoming message"""
# This whole thing needs to be rewritten to use all the new information about the protocol
debug(message)
# If message type is data
if message["t"] == "d":
data = message["d"]
# If r is in data and set to 1 then it's probably a response
# to something we sent like a sub request or an auth token
if "r" in data:
historical_entry = self.history[data["r"] - 1]
request = historical_entry["message"]
callbacks = historical_entry["callbacks"]
error = data["b"]["s"]
if error != "ok":
if error == "permission_denied":
path = request["d"]["b"]["p"]
print "FIREBASE WARNING: on() or once() for %s failed: %s" % (path, error)
elif error == "expired_token" or error == "invalid_token":
print "FIREBASE WARNING: auth() failed: %s" % (error)
else:
path = request["d"]["b"]["p"]
print "FIREBASE WARNING: unknown for %s failed: %s" % (path, error)
onCancel = callbacks.get("onCancel", None)
if not onCancel is None:
onCancel(error)
onComplete = callbacks.get("onComplete", None)
if not onComplete is None:
onComplete(error if error != "ok" else None)
# If t is in data then it's the response to the initial connection, maybe
elif "t" in data:
pass
# If a is in data, it's a new data blob for a node, maybe
elif "a" in data:
if data["a"] == "c":
# This type of message is created when we lose permission to read
# and it requires some extra effort to implement as we call onCancel
# for all effected callbacks, which are any anscestors of the path
pass
else:
b_data = data["b"]
path = b_data["p"]
path_data = b_data["d"]
self._store(path, path_data)
# If message type is... control?
if message["t"] == "c":
pass
def _store(self, path, path_data):
"""Store a single path worth of data into the strucutre."""
if not path or path[0] != "/":
path = "/%s" % path
self.structure.store(path, path_data)
def _send(self, message, callbacks=None):
"""Send a single message to Firebase."""
historical_entry = {"message": message, "callbacks": {} if callbacks is None else callbacks}
self.history.append(historical_entry)
message["d"]["r"] = len(self.history)
self.connection.send(message)
def _subscribe(self, path, query, callbacks=None):
"""Subscribe to updates regarding a path"""
isSubscribed = self._is_subscribed(path, query)
# A subscription (listen) request takes two main arguments, p (path) and q (query).
if not isSubscribed:
message = {"t": "d", "d": {"r": 0, "a": "l", "b": {"p": path}}}
if not query is None:
message["d"]["b"]["q"] = query
self._send(message, callbacks)
self.subscriptions[path] = query
return True
else:
# Should probably trigger callbacks['onComplete'] here
return False
def _bind(self, path, event, callback):
"""Bind a single callback to an event on a path"""
event_key = ".event-" + event
structure_path = self.structure.get(path, {})
self.structure[path] = structure_path
events = structure_path.get(event_key, [])
events.append(callback)
self.structure[path][event_key] = events
def _is_subscribed(self, path, query):
"""Return True if already subscribed to this path or an ancestor."""
return any([s.split("/") == path.split("/")[: len(s.split("/"))] for s in self.subscriptions.keys()])
def __dir__(self):
attrs = ['create_mview', 'drop_view', 'set_debug', 'set_log', 'set_strict', 'set_naming', 'set_logger']
return Structure.get_all_tables() + attrs