def get_cuds_collection(include_parent=True):
"""Returns Collection holding the CUDS metadata.
If `include_parent` is true, the generated CUDS element entities
will also include attributes of their parent.
Note, this requires softpy.
"""
import softpy
with open(os.path.join(thisdir, 'metadata', 'cuba.yml')) as f:
cuba = yaml.load(f.read())
with open(os.path.join(thisdir, 'metadata', 'simphony_metadata.yml')) as f:
cuds = yaml.load(f.read())
entities, relations = generate_cuds_entities(cuds,
cuba,
include_parent=include_parent)
uuid = softpy.uuid_from_entity('CUDS', '1.0', 'http://emmc.info/meta')
c = softpy.Collection(uuid=uuid)
c.name = 'CUDS'
c.version = cuds['VERSION']
for jsondict in entities:
entity = softpy.entity(jsondict)
c.add(entity.name, entity)
for relation in relations:
c.add_relation(*relation)
# Save all metadata in a database
s = StringIO() if sys.version_info.major >= 3 else BytesIO()
json.dump(entities, s)
s.seek(0)
softpy.register_metadb(softpy.JSONMetaDB(s))
s.close()
return c
},
{
"name": "masses",
"type": "double",
"unit": "u",
"dims": [
"N"
],
"description": "Mass of each atom"
}
]
}
"""
# 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)
import sys
import re
import math
import warnings
import json
import ast
from vasp_outcar import CONTCAR, OUTCAR
thisdir = os.path.abspath(os.path.dirname(__file__))
entitydir = os.path.join(thisdir, '../entities')
try:
import softpy
HAVE_SOFT = True
BaseDFTData = softpy.entity(
open(os.path.join(entitydir, 'eu.nanosim.vasp.dftdata.json')))
except ImportError:
warnings.warn('SOFT is not available')
HAVE_SOFT = False
BaseDFTData = object
if sys.version_info.major >= 3:
basestring = str
class VASP_DATA(object):
"""
Read data from OUTCAR-files.
The root directory with subdirectories must be set up in as specific
manner, for info see manual.
The CONTCAR and OUTCAR file must be in the corresponding directories.
import sys
import re
import math
import warnings
import json
import ast
from vasp_outcar import CONTCAR, OUTCAR
thisdir = os.path.abspath(os.path.dirname(__file__))
entitydir = os.path.join(thisdir, '../entities')
try:
import softpy
HAVE_SOFT = True
BaseDFTData = softpy.entity(
open(os.path.join(entitydir, 'eu.nanosim.vasp.dftdata.json')))
except ImportError:
warnings.warn('SOFT is not available')
HAVE_SOFT = False
BaseDFTData = object
if sys.version_info.major >= 3:
basestring = str
class VASP_DATA(object):
"""
Read data from OUTCAR-files.
The root directory with subdirectories must be set up in as specific
manner, for info see manual.
The CONTCAR and OUTCAR file must be in the corresponding directories.
thisdir = os.path.dirname(__file__)
coll = softpy.Collection()
assert coll.get_num_entities() == 0
assert coll.get_num_relations() == 0
coll.name = 'foo'
assert coll.name == 'foo'
coll.version = '1.0'
assert coll.version == '1.0'
with open(os.path.join(thisdir, 'person.json')) as f:
Person = softpy.entity(f)
jack = Person(name='Jack', age=42, skills=[])
alda = Person(name='Alda', age=39, skills=['foo'])
fred = Person(name='Fred', age=12, skills=['bar'])
coll.add('Jack', jack)
coll.add('Alda', alda)
coll.add('Fred', fred)
assert coll.get_num_entities() == 3
coll.add_relation('Jack', 'loves', 'Alda')
coll.add_relation('Jack', 'loves', 'Fred')
coll.add_relation('Jack', 'husband_of', 'Alda')
coll.add_relation('Jack', 'father_of', 'Fred')
assert coll.find_relations('Jack', 'loves') == {'Fred', 'Alda'}
#!/usr/bin/env python # -*- coding: utf-8 -*- from __future__ import print_function import os import softpy thisdir = os.path.dirname(__file__) Person = softpy.entity(open(os.path.join(thisdir, "person.json"))) jack = Person() coll = softpy.Collection() assert len(coll) == 0 coll["jack"] = jack # assert len(coll) == 1
jsondb = softpy.JSONMetaDB('metadb.json')
jsondb.clear()
assert jsondb.has('Person', '0.2.4', 'http://sintef.no/meta/soft') is False
jsondb.insert(open('person.json'))
assert jsondb.has('Person', '0.2.4', 'http://sintef.no/meta/soft') is True
types = jsondb.types()
assert types[0] == ('Person', '0.2.4', 'http://sintef.no/meta/soft')
softpy.register_metadb(jsondb)
meta = softpy.Metadata(name='Person',
version='0.2.4',
namespace='http://sintef.no/meta/soft')
Person = softpy.entity(name='Person',
version='0.2.4',
namespace='http://sintef.no/meta/soft')
jack = Person(name='Jack', age=42, skills=['foo', 'bar'])
assert jack.soft_metadata == meta
jsondb.close()
try:
import pymongo
except ImportError:
import warnings
warnings.warn('pymongo not installed - skipping mongodb test...')
else:
mongodb = softpy.MongoMetaDB('mongodb://localhost:27017/', 'metadb_test',
'metadata')
mongodb.clear()
assert mongodb.has('Person', '0.2.4',
import warnings
import pickle
import ast
import base64
import numpy as np
import ase
import ase.constraints
from ase.calculators.emt import EMT
from ase.lattice.spacegroup import Spacegroup, crystal
from ase.visualize import view
import softpy
import dill
BaseSoftAtoms = softpy.entity(open('atoms.json'))
class SoftAtoms(BaseSoftAtoms, ase.Atoms):
"""An ase.Atoms subclass behaving as a SOFT entity.
Takes the same arguments as ase.Atoms with the following additions:
symbols - same meaning as in Atoms, except that it also can be an
existing Atoms object
uuid - optional, id of instance to load from driver
driver - optional, driver to use for loading data: "json", "hdf5", "mongo"
uri - optional, from where to load data
options - optional, additional options passed to the driver
"""
def __new__(cls, symbols=None, uuid=None, driver=None, uri=None,
thisdir = os.path.dirname(__file__)
coll = softpy.Collection()
assert coll.get_num_entities() == 0
assert coll.get_num_relations() == 0
coll.name = 'foo'
assert coll.name == 'foo'
coll.version = '1.0'
assert coll.version == '1.0'
Person = softpy.entity(open(os.path.join(thisdir, 'person.json')))
jack = Person(name='Jack', age=42, skills=[])
alda = Person(name='Alda', age=39, skills=['foo'])
fred = Person(name='Fred', age=12, skills=['bar'])
coll.register_entity('Jack', jack)
coll.register_entity('Alda', alda)
coll.register_entity('Fred', fred)
assert coll.get_num_entities() == 3
coll.add_relation('Jack', 'loves', 'Alda')
coll.add_relation('Jack', 'loves', 'Fred')
coll.add_relation('Jack', 'husband_of', 'Alda')
coll.add_relation('Jack', 'father_of', 'Fred')
assert coll.find_relations('Jack', 'loves') == {'Fred', 'Alda'}
assert coll.find_relations('Alda', '^loves') == {'Jack'}
},
{
"name": "masses",
"type": "double",
"unit": "u",
"dims": [
"N"
],
"description": "Mass of each atom"
}
]
}
"""
# 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)
import warnings
import pickle
import ast
import base64
import numpy as np
import ase
import ase.constraints
from ase.calculators.emt import EMT
from ase.lattice.spacegroup import Spacegroup, crystal
from ase.visualize import view
import softpy
import dill
BaseSoftAtoms = softpy.entity(open('atoms.json'))
class SoftAtoms(BaseSoftAtoms, ase.Atoms):
"""An ase.Atoms subclass behaving as a SOFT entity.
Takes the same arguments as ase.Atoms with the following additions:
symbols - same meaning as in Atoms, except that it also can be an
existing Atoms object
uuid - optional, id of instance to load from driver
driver - optional, driver to use for loading data: "json", "hdf5", "mongo"
uri - optional, from where to load data
options - optional, additional options passed to the driver
"""
def __new__(cls,
thisdir = os.path.dirname(__file__)
# Load SOFT metadata database
softpy.register_metadb(softpy.JSONDirMetaDB(os.path.join(thisdir, 'metadata')))
# Load CUDS metadata database (created by softcuds.py)
softpy.register_metadb(
softpy.JSONDirMetaDB(
os.path.join(thisdir, 'metadata', 'cuds_entities', '1.0')))
# Read cif data
cf = ReadCif('VO2_rutile.cif')
rut = cf['VO2_rut_ini']
# Create a Python class representation of cifdata-0.1
CifData = softpy.entity('cifdata', '0.1', 'http://emmc.info/meta')
# Create uninitialised CifData instance
cifdata = CifData()
# Initialise the instance from the cif file
cifkeys = [k.lower() for k in rut.keys()] # newer versions of PyCifRW
# changed all keys to lower-case
for name in cifdata.soft_get_property_names():
tag = '_' + name.lower()
if tag in cifkeys:
value = rut[tag]
elif name == 'atom_site_type_symbol':
value = [
re.match('[A-Z][a-z]{0,2}', l).group()
for l in rut['_atom_site_label']
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));
