def write_outputdata(self, uri, driver='txt', options=None):
"""Writes VASP data to `uri` using `driver`
Valid drivers are all drivers supported by SOFT in addition to "txt".
Additional options to the driver can be provided via `options`.
The "txt" driver is decoupled from SOFT and uses `uri` as the
output base name. If `options` is "short", less details are written.
"""
if driver == 'txt':
if options is None:
self.write_outputdata_txt(uri)
elif options == 'short':
self.write_outputdata_txt_short(uri)
else:
raise ValueError(
'Only option supported by the txt driver is "short", '
'got %r' % (options, ))
else:
with softpy.Storage(driver, uri, options) as s:
s.save(self)
# Create new Structure entity based on the metadata
Structure = softpy.entity(metadata)
# Create a empty Structure instance
s = Structure()
s.structure = 'water'
s.symbols = ['H', 'H', 'O']
s.spacegroup = 1
s.total_energy = 446.32
s.masses = np.array([1., 1., 16.])
s.soft_internal_check_dimension_sizes()
# Write the structure to file
with softpy.Storage('hdf5', 'softpy-test-factory.h5') as storage:
storage.save(s)
# Create new Structure instance initiated from file
s2 = Structure(uuid=s.soft_get_id(), driver='hdf5',
uri='softpy-test-factory.h5')
# Check that the entities are equals
for name in 'id', 'meta_name', 'meta_version', 'meta_namespace':
f = getattr(softpy, 'get_' + name)
assert f(s) == f(s2)
assert s.soft_get_property_names() == s2.soft_get_property_names()
# Test to add another collection to coll
subcoll = softpy.Collection()
anna = Person(name='Anna', age=78, skills=['piano'])
subcoll.add('Anna', anna)
coll.add('relatives', subcoll)
# Test to add metadata to coll
coll.add('Person', Person)
# Save the collection to hdf5
# Note that we must set append=yes to also store the instances. This will
# cause trouble with existing names the second time we run the test, so
# we remove the h5 file first.
if os.path.exists('softpy-test-collection.h5'):
os.remove('softpy-test-collection.h5')
with softpy.Storage('hdf5', 'softpy-test-collection.h5', 'append=yes') as s:
coll.save(s)
# Create a metadata database with all metadata defined in json files
# in the current directory - needed in order to instanciate entities
# and metadata read from the stored hdf5 file
#softpy.register_metadb(softpy.JSONDirMetaDB(thisdir))
softpy.register_jsondir(thisdir)
# Create a new collection, loaded from hdf5
coll2 = softpy.Collection(uuid=coll.uuid, driver='hdf5',
uri='softpy-test-collection.h5')
assert coll2.uuid == coll.uuid
with open(os.path.join(thisdir, 'metadata', 'simphony_metadata.yml')) as f:
cuds = yaml.load(f.read())
# Crate CUDS entities and relations
entities, relations = generate_cuds_entities(cuds, cuba)
# Write CUDS entities and relations
write_cuds_entities(os.path.join(thisdir, 'metadata', 'cuds_entities'))
import softpy
# Create a collection with all CUDS entities and relations
c = get_cuds_collection()
with softpy.Storage(
driver='hdf5',
uri='softcuds.h5',
#options='append=yes',
) as s:
c.save(s)
# Create a collection of CUDS instances
ci = get_cuds_instance_collection(
cuds_collection=c,
name='CRYSTAL_STRUCTURE',
dimensions={'CRYSTAL_STRUCTURE.ATOM_SITES.ATOM_SITE': [2]},
initial_values={})
print('labels:\n', ci.get_labels())
crystal_structure = ci.get_instance('CRYSTAL_STRUCTURE')
#with softpy.Storage(driver='hdf5',
assert softpy.entity_get_meta_name(e) == 'MyStructure'
assert softpy.entity_get_meta_version(e) == '0.1.1'
assert softpy.entity_get_meta_namespace(e) == 'http://sintef.no/meta/soft'
assert softpy.entity_get_dimensions(e) == ['I', 'J']
assert softpy.entity_get_dimension_size(e, 'I') == 3
assert softpy.entity_get_dimension_size(e, 'J') == 4
assert softpy.entity_get_id(e) == e.id
assert e.name == 'MyStructure'
assert e.version == '0.1.1'
assert e.namespace == 'http://sintef.no/meta/soft'
assert e.dimensions == ['I', 'J']
assert e.dimension_sizes == [3, 4]
s = softpy.Storage('hdf5', 'softpy-test-entity.h5')
s.save(e)
s.load(e)
d = e.user_data
assert d.name == 'NaCl'
assert d.spgr == 225
assert d.latt == 5.64
assert np.allclose(
d.posi, np.array([(0.0, 0.0, 0.0), (0.5, 0.5, 0.5)]).flatten())
del e
class Person(object):
def __init__(self, name='', age=0.0, distances=(), uuid=None):
def _unwrap(s, constants=None, functions=()):
"""Returns unwrapped object from its string representation `s`."""
try:
return softpy.arithmetic_eval(s, constants, functions)
except softpy.ArithmeticError:
try:
return ast.literal_eval(s)
except ValueError:
warnings.warn('converted to string: %r' % s)
return s
a = 4.6
c = 2.95
rutile = crystal(['Ti', 'O'],
basis=[(0, 0, 0), (0.3, 0.3, 0.0)],
spacegroup=136,
cellpar=[a, a, c, 90, 90, 90])
rutile.set_constraint(ase.constraints.FixAtoms(indices=(1, 3)))
r = SoftAtoms(rutile)
s = softpy.Storage(driver='hdf5', uri='atoms.h5')
s.save(r)
s.close()
rr = SoftAtoms(driver='hdf5', uri='atoms.h5', uuid=r.soft_get_id())
rr.write('rutile.cif')
import softpy
Initial = softpy.entity(open('initial.json'))
i = Initial(dimension_sizes=[50,50])
i.dt = 2.0e-3
i.startt = 0.0
i.endt = 2.0
i.nu = 1.0e-2
i.sample_interval = 1.0
s = softpy.Storage(driver='hdf5', uri='init.h5')
s.save(i)
s.close()
print(softpy.get_id(i));