def test_check_instance_optional_key_marked_required_are_present(self):
"""Test the inctances optional presence of the keys marked as required."""
import kim_edn
# property instance is not a dict
pi = ["property-id"]
pd = kim_edn.load(
join("tests", "fixtures",
"cohesive-energy-relation-cubic-crystal.edn"))
self.assertRaises(
self.KIMPropertyError, self.kim_property.
check_instance_optional_key_marked_required_are_present, pi, pd)
# property definition is not a dict
pi = {
"property-id":
"tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal",
"instance-id": 1
}
pd = ["property-id"]
self.assertRaises(
self.KIMPropertyError, self.kim_property.
check_instance_optional_key_marked_required_are_present, pi, pd)
pi = {
"property-id":
"tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal",
"instance-id": 1
}
pd = kim_edn.load(
join("tests", "fixtures",
"cohesive-energy-relation-cubic-crystal.edn"))
self.assertRaises(
self.KIMPropertyError, self.kim_property.
check_instance_optional_key_marked_required_are_present, pi, pd)
def test_dump(self):
"""Test the dump functionality."""
# Create the property instance with the property name
str_obj = self.kim_property.kim_property_create(
1, 'cohesive-energy-relation-cubic-crystal')
str_obj = self.kim_property.kim_property_modify(
str_obj, 1,
"key", "short-name",
"source-value", "1", "fcc",
"key", "species",
"source-value", "1:4", "Al", "Al", "Al", "Al",
"key", "a",
"source-value", "1:5", "3.9149", "4.0000", "4.032", "4.0817", "4.1602",
"source-unit", "angstrom", "digits", "5",
"key", "basis-atom-coordinates",
"source-value", "2", "1:2", "0.5", "0.5",
"key", "basis-atom-coordinates",
"source-value", "3", "1:3", "0.5", "0.0", "0.5",
"key", "basis-atom-coordinates",
"source-value", "4", "2:3", "0.5", "0.5",
"key", "cohesive-potential-energy",
"source-value", "1:5", "3.324", "3.3576", "3.3600", "3.3550", "3.3260",
"source-std-uncert-value", "1:5", "0.002", "0.0001", "0.00001", "0.0012", "0.00015",
"source-unit", "eV",
"digits", "5")
kim_obj = kim_edn.load(str_obj)[0]
out_str = kim_edn.dumps(kim_obj, indent=0) + '\n'
sio = StringIO()
# Fail when there is no property instance to dump it.
for str_obj1 in [None, 'None', '', '[]']:
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_dump,
str_obj1, sio)
self.kim_property.kim_property_dump(str_obj, sio, indent=0)
self.assertTrue(sio.getvalue() == out_str)
# Fail to create a file to dump the property
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_modify,
str_obj, "output/results.edn")
str_obj = self.kim_property.kim_property_create(
2, 'atomic-mass', str_obj)
str_obj = self.kim_property.kim_property_modify(
str_obj, 2,
"key", "species", "source-value", "Al",
"key", "mass", "source-value", 26.98, "source-unit", "grams/mole")
self.kim_property.kim_property_dump(str_obj, sio, indent=0)
def test_property_from_string(self):
"""Check the property definition from a KIM-EDN string."""
# Property definition edn file
edn_file = join("tests", "fixtures", "atomic-mass.edn")
self.assertTrue(isfile(edn_file))
pd = kim_edn.load(edn_file)
fp = kim_edn.dumps(pd)
# Complete check on the property definition
self.kim_property.check_property_definition(fp)
def main():
"""Validate and pretty-print KIM-EDN tool main file."""
prog = 'python -m kim_edn.tool'
description = ('A simple command line interface for KIM-EDN module '
'to validate and pretty-print kim-EDN objects.')
parser = argparse.ArgumentParser(prog=prog, description=description)
parser.add_argument(
'infile',
nargs='?',
type=argparse.FileType(encoding="utf-8"),
help='a KIM-EDN file to be validated or pretty-printed',
default=sys.stdin)
parser.add_argument('outfile',
nargs='?',
type=argparse.FileType('w', encoding="utf-8"),
help='write the output of infile to outfile',
default=sys.stdout)
parser.add_argument(
'--sort-keys',
action='store_true',
default=False,
help='sort the output of dictionaries alphabetically by key')
parser.add_argument('--edn-lines',
action='store_true',
default=False,
help='parse input using the kim_edn lines format')
options = parser.parse_args()
with options.infile as infile, options.outfile as outfile:
try:
if options.edn_lines:
objs = (kim_edn.loads(line) for line in infile)
else:
objs = (kim_edn.load(infile), )
for obj in objs:
kim_edn.dump(obj,
outfile,
sort_keys=options.sort_keys,
indent=4)
outfile.write('\n')
except ValueError as e:
raise SystemExit(e)
def test_create_sorted(self):
"""Test create functionality and sorting based on instance-id."""
str1 = self.kim_property.kim_property_create(2, 'atomic-mass')
str1 = self.kim_property.kim_property_modify(str1, 2, "key", "species", "source-value", "Ar",
"key", "mass", "source-value", 39.948, "source-unit", "grams/mole")
str1 = self.kim_property.kim_property_create(
5, "cohesive-energy-lattice-invariant-shear-unrelaxed-path-cubic-crystal", str1)
str1 = self.kim_property.kim_property_create(
1, 'cohesive-energy-relation-cubic-crystal', str1)
kim_obj = kim_edn.load(str1)
self.assertTrue(kim_obj[0]["instance-id"] == 1)
self.assertTrue(kim_obj[1]["instance-id"] == 2)
self.assertTrue(kim_obj[2]["instance-id"] == 5)
def check_property_definition(fp, _m=KEY_FORMAT.match):
r"""Check the KIM property definition format.
Check the KIM property definition format from a deserialized ``fp``.
Arguments:
fp (a ``.read()``-supporting file-like object,
or a name string to a file containing a KIM-EDN document
or a string
or a KIM-EDN object) to a property definition Python object.
"""
# property definition
if isinstance(fp, dict):
pd = fp
# Other format should be loaded by kim_edn
else:
pd = kim_edn.load(fp)
if isinstance(pd, dict):
try:
check_required_keys_present(pd, rk=required_keys)
check_property_id_format(pd["property-id"])
check_property_title_format(pd["property-title"])
# Check optional fields.
for k in pd:
if k not in required_keys:
check_property_optional_key_map(k, pd[k], _m=_m)
except KIMPropertyError:
msg = '{} \n'.format(fp)
msg += str(KIMPropertyError)
raise KIMPropertyError(msg)
else:
msg = 'input to the function :\n'
msg += '{}\n'.format(fp)
msg += 'is not a correct KIM-EDN type.'
raise KIMPropertyError(msg)
def test_unpickle_kim_properties(self):
"""Test unpickling the KIM properties."""
# Fails when can't load pickle from unicode string
self.assertRaises(self.KIMPropertyError,
unpickle_kim_properties,
'kim_properties.pickle')
# Property definition edn file
edn_file1 = join("tests", "fixtures", "atomic-mass.edn")
self.assertTrue(isfile(edn_file1))
edn_file2 = join("tests", "fixtures",
"cohesive-energy-relation-cubic-crystal.edn")
self.assertTrue(isfile(edn_file2))
properties = {"tag:[email protected],2016-05-11:property/atomic-mass": kim_edn.load(edn_file1),
"tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal": kim_edn.load(edn_file2)}
bio = BytesIO()
pickle_kim_properties(properties, bio)
# Test the unpickle utility
_properties, _name_to_id, _id_to_name = unpickle_kim_properties(
bio.getvalue())
name_to_id = {"atomic-mass": "tag:[email protected],2016-05-11:property/atomic-mass",
"cohesive-energy-relation-cubic-crystal": "tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal"}
id_to_name = {"tag:[email protected],2016-05-11:property/atomic-mass": "atomic-mass",
"tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal": "cohesive-energy-relation-cubic-crystal"}
self.assertTrue(_properties == properties)
self.assertTrue(_name_to_id == name_to_id)
self.assertTrue(_id_to_name == id_to_name)
bio1 = BytesIO()
# Fails when neither can open nor load the input
self.assertRaises(self.KIMPropertyError,
unpickle_kim_properties,
bio1.getvalue())
def test_pickle_kim_properties(self):
"""Test pickling the KIM properties."""
# Property definition edn file
edn_file1 = join("tests", "fixtures", "atomic-mass.edn")
self.assertTrue(isfile(edn_file1))
edn_file2 = join("tests", "fixtures",
"cohesive-energy-relation-cubic-crystal.edn")
self.assertTrue(isfile(edn_file2))
properties = {"tag:[email protected],2016-05-11:property/atomic-mass": kim_edn.load(edn_file1),
"tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal": kim_edn.load(edn_file2)}
name_to_id = {"atomic-mass": "tag:[email protected],2016-05-11:property/atomic-mass",
"cohesive-energy-relation-cubic-crystal": "tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal"}
id_to_name = {"tag:[email protected],2016-05-11:property/atomic-mass": "atomic-mass",
"tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal": "cohesive-energy-relation-cubic-crystal"}
bio = BytesIO()
pickle_kim_properties(properties, bio)
_properties, _name_to_id, _id_to_name = pickle.loads(bio.getvalue())
self.assertTrue(_properties == properties)
self.assertTrue(_name_to_id == name_to_id)
self.assertTrue(_id_to_name == id_to_name)
sio = StringIO()
self.assertRaises(self.KIMPropertyError, pickle_kim_properties,
properties, sio)
def check_property_instances(fi, fp=None, fp_path=None, _m=KEY_FORMAT.match):
r"""Check the KIM property instances format.
Check the KIM property instances format from a deserialized ``fi``.
Property Instances are either Predictions or items of Reference Data and
must conform to the specification in the associated Property Definition.
A Property Instance is stored in a subset of the EDN format. Multiple
Property Instances in a file may optionally be contained within an array
represented by a start bracket \(\[\) at the beginning, and an end
bracket \(\]\) at the end of the file:
Arguments:
fi (a ``.read()``-supporting file-like object,
or a name string to a file containing a KIM-EDN document
or a string
or a KIM-EDN object) to a property instance Python object.
fp (a ``.read()``-supporting file-like object,
or a name string to a file containing a KIM-EDN document
or a string) to a property definition Python object.
(default: None)
fp_path should be an absolute path (or a valid relative path)
to the KIM property definition folder. (default: None)
or
a KIM properties object containing all the available properties
"""
# Check whether the property definition is provided?
if fp is None:
# Check whether the path is provided to the property files?
if fp_path is None:
msg = 'either the absolute path to the KIM properties '
msg += 'or a KIM property definition should be provided.'
raise KIMPropertyError(msg)
if isinstance(fp_path, str):
# Check whether the provided path is an absolute path?
if not isabs(fp_path):
# Loosen the check for the relative path which exists
if isdir(fp_path):
fp_path = abspath(fp_path)
else:
msg = 'the path KIM properties should be an '
msg += 'absolute path name.'
raise KIMPropertyError(msg)
elif not isinstance(fp_path, dict):
msg = 'wrong KIM properties object.'
raise KIMPropertyError(msg)
# Property definition file is provided
elif fp_path is not None:
msg = 'only the absolute path to the KIM properties '
msg += 'or a KIM property file should be provided (not both).'
raise KIMPropertyError(msg)
# Property instance
if isinstance(fi, (list, dict)):
pi = fi
else:
pi = kim_edn.load(fi)
if isinstance(pi, dict):
check_required_keys_present(pi, rk=required_keys)
check_property_id_format(pi["property-id"])
if fp is None:
if isinstance(fp_path, dict):
if pi["property-id"] in fp_path:
fp = fp_path[pi["property-id"]]
else:
msg = 'the requested property ID = \n"'
msg += pi["property-id"]
msg += '"\ndoes not exist in the input KIM properties.'
raise KIMPropertyError(msg)
else:
_path, _, _, _property_name = get_property_id_path(
pi["property-id"])
if isfile(join(fp_path, _path)):
fp = join(fp_path, _path)
elif isfile(join(fp_path, _property_name + ".edn")):
fp = join(fp_path, _property_name + ".edn")
else:
msg = 'unable to find a KIM property definition at {\n"'
msg += join(fp_path, _path)
msg += '",\nnor at\n"'
msg += join(fp_path, _property_name + ".edn")
msg += '"}'
raise KIMPropertyError(msg)
del _path
del _property_name
if isinstance(fp, dict):
# It is already in the KIM-EDN format
pd = fp
else:
# property definition
pd = kim_edn.load(fp)
# We have to check if required keys are there
check_required_keys_present(pd, rk=def_required_keys)
if pd["property-id"] != pi["property-id"]:
msg = 'wrong property definition is provided.\n'
msg += 'Property id :\n'
msg += '{}\n'.format(pd["property-id"])
msg += 'read from the property definition file is different '
msg += 'from the property id :\n'
msg += '{}\n'.format(pi["property-id"])
msg += 'read from the property instance file.'
raise KIMPropertyError(msg)
check_instance_id_format(pi["instance-id"])
# Check optional fields.
for k in pi:
if k not in required_keys:
if k in pd:
check_instance_optional_key_map(k, pi[k], pd[k], _m=_m)
else:
check_instance_optional_key_map(k, pi[k], _m=_m)
# Check optional variables marked required are present in the instance.
check_instance_optional_key_marked_required_are_present(pi, pd)
elif isinstance(pi, list):
instance_id = []
for pi_ in pi:
check_required_keys_present(pi_, rk=required_keys)
check_property_id_format(pi_["property-id"])
if fp is None:
if isinstance(fp_path, dict):
if pi_["property-id"] in fp_path:
pd = fp_path[pi_["property-id"]]
else:
msg = 'the requested property ID = \n"'
msg += pi_["property-id"]
msg += '"\ndoes not exist in the input KIM '
msg += 'properties.'
raise KIMPropertyError(msg)
else:
_path, _, _, _property_name = get_property_id_path(
pi_["property-id"])
if isfile(join(fp_path, _path)):
fp = join(fp_path, _path)
elif isfile(join(fp_path, _property_name + ".edn")):
fp = join(fp_path, _property_name + ".edn")
else:
msg = 'unable to find a KIM property definition '
msg += 'at {\n"'
msg += join(fp_path, _path)
msg += '",\nnor at\n"'
msg += join(fp_path, _property_name + ".edn")
msg += '"}'
raise KIMPropertyError(msg)
# property definition
pd = kim_edn.load(fp)
# Set fp back to None for the next property in the loop
fp = None
else:
if isinstance(fp, dict):
# It is already in the KIM-EDN format
pd = fp
else:
# property definition
pd = kim_edn.load(fp)
# We have to check if required keys are there
check_required_keys_present(pd, rk=def_required_keys)
if pd["property-id"] != pi_["property-id"]:
msg = 'wrong property definition is provided.\n'
msg += 'Property id :\n'
msg += '{}\n'.format(pd["property-id"])
msg += 'read from the property definition file is different '
msg += 'from the property id :\n'
msg += '{}\n'.format(pi_["property-id"])
msg += 'read from the property instance file.'
raise KIMPropertyError(msg)
check_instance_id_format(pi_["instance-id"])
if pi_["instance-id"] in instance_id:
msg = 'the "instance-id’s" cannot repeat.'
raise KIMPropertyError(msg)
instance_id.append(pi_["instance-id"])
# Check optional fields.
for k in pi_:
if k not in required_keys:
if k in pd:
check_instance_optional_key_map(k,
pi_[k],
pd[k],
_m=_m)
else:
check_instance_optional_key_map(k, pi_[k], _m=_m)
# Check optional variables marked required
# are present in the instance.
check_instance_optional_key_marked_required_are_present(pi_, pd)
else:
msg = 'input to the function does not have a correct KIM-EDN format.'
raise KIMPropertyError(msg)
def test_remove(self):
"""Test the remove functionality."""
# Create the property instance with the property name
str_obj = self.kim_property.kim_property_create(
1, 'cohesive-energy-relation-cubic-crystal')
str_obj = self.kim_property.kim_property_modify(
str_obj, 1,
"key", "short-name",
"source-value", "1", "fcc",
"key", "species",
"source-value", "1:4", "Al", "Al", "Al", "Al",
"key", "a",
"source-value", "1:5", "3.9149", "4.0000", "4.032", "4.0817", "4.1602",
"source-unit", "angstrom", "digits", "5",
"key", "basis-atom-coordinates",
"source-value", "2", "1:2", "0.5", "0.5",
"key", "basis-atom-coordinates",
"source-value", "3", "1:3", "0.5", "0.0", "0.5",
"key", "basis-atom-coordinates",
"source-value", "4", "2:3", "0.5", "0.5",
"key", "cohesive-potential-energy",
"source-value", "1:5", "3.324", "3.3576", "3.3600", "3.3550", "3.3260",
"source-std-uncert-value", "1:5", "0.002", "0.0001", "0.00001", "0.0012", "0.00015",
"source-unit", "eV",
"digits", "5")
kim_obj = kim_edn.load(str_obj)[0]
self.assertTrue("a" in kim_obj)
self.assertTrue("source-value" in kim_obj["a"])
self.assertTrue("cohesive-potential-energy" in kim_obj)
self.assertTrue("basis-atom-coordinates" in kim_obj)
# Fail when there is no property instance to remove the content.
for str_obj1 in [None, 'None', '', '[]']:
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_remove,
str_obj1, 1, "key", "a")
# Fails when the "instance_id" is not an `int`.
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_remove,
str_obj, 1.0, "key", "a")
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_remove,
str_obj, "1", "key", "a")
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_remove,
str_obj, [1], "key", "a")
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_remove,
str_obj, {1}, "key", "a")
# Fails when the requested instance id doesn\'t match any
# of the property instances ids.
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_remove,
str_obj, 10, "key", "a")
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_remove,
str_obj, 2, "key", "a")
# Fails when the key doesn\'t exist in the property instance.
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_remove,
str_obj, 1, "key", "new_item")
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_remove,
str_obj, 1, "key", "aa")
# Removing the whole key
str_obj1 = self.kim_property.kim_property_remove(
str_obj, 1, "key", "a")
kim_obj1 = kim_edn.load(str_obj1)[0]
self.assertFalse("a" in kim_obj1)
del str_obj1
del kim_obj1
# Removing the internal key from the key-map pairs for key
str_obj2 = self.kim_property.kim_property_remove(
str_obj, 1, "key", "a", "source-value")
kim_obj2 = kim_edn.load(str_obj2)[0]
self.assertTrue("a" in kim_obj2)
self.assertFalse("source-value" in kim_obj2["a"])
del str_obj2
del kim_obj2
# Removing multiple keys
str_obj3 = self.kim_property.kim_property_remove(
str_obj, 1, "key", "cohesive-potential-energy", "key", "basis-atom-coordinates")
kim_obj3 = kim_edn.load(str_obj3)[0]
self.assertFalse("cohesive-potential-energy" in kim_obj3)
self.assertFalse("basis-atom-coordinates" in kim_obj3)
str_obj3 = self.kim_property.kim_property_remove(
str_obj3, 1, "key", "a", "source-unit")
kim_obj3 = kim_edn.load(str_obj3)[0]
self.assertTrue("a" in kim_obj3)
self.assertTrue("source-value" in kim_obj3["a"])
self.assertFalse("source-unit" in kim_obj3["a"])
# Test for scalar values
str_obj4 = self.kim_property.kim_property_modify(
str_obj3, 1,
"key", "space-group",
"source-value", "Immm")
str_obj4 = self.kim_property.kim_property_modify(
str_obj4, 1,
"key", "space-group",
"source-value", "Fm-3m")
kim_obj4 = kim_edn.load(str_obj4)[0]
self.assertTrue(kim_obj4["space-group"]["source-value"] == "Fm-3m")
str_obj4 = self.kim_property.kim_property_remove(
str_obj4, 1, "key", "space-group", "source-value")
kim_obj4 = kim_edn.load(str_obj4)[0]
self.assertFalse("source-value" in kim_obj4["space-group"])
str_obj4 = self.kim_property.kim_property_modify(
str_obj4, 1,
"key", "space-group",
"source-value", "Fm-3m")
kim_obj4 = kim_edn.load(str_obj4)[0]
self.assertTrue(kim_obj4["space-group"]["source-value"] == "Fm-3m")
def test_modify(self):
"""Test the modify functionality."""
# Fails when the input is none or not created
for str_obj in [None, '', 'None', '[]']:
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_modify, str_obj, 1)
# Fails when there is a different instance id
str_obj = '[{"property-id" "tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal" "instance-id" 1}]'
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_modify, str_obj, 2)
# Fails when not having the instance id
str_obj = '[{"property-id" "tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal"}]'
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_modify, str_obj, 1)
# Fails when not having the property id
str_obj = '[{"instance-id" 1}]'
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_modify, str_obj, 1)
# Create the property instance with the property name
str_obj = self.kim_property.kim_property_create(
1, 'cohesive-energy-relation-cubic-crystal')
# Fails when the instance id is not an integer
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_modify, str_obj, 1.0)
str_obj = self.kim_property.kim_property_modify(
str_obj, 1,
"key", "short-name",
"source-value", "1", "fcc",
"key", "species",
"source-value", "1:4", "Al", "Al", "Al", "Al",
"key", "a",
"source-value", "1:5", "3.9149", "4.0000", "4.032", "4.0817", "4.1602",
"source-unit", "angstrom", "digits", "5",
"key", "basis-atom-coordinates",
"source-value", "2", "1:2", "0.5", "0.5",
"key", "basis-atom-coordinates",
"source-value", "3", "1:3", "0.5", "0.0", "0.5",
"key", "basis-atom-coordinates",
"source-value", "4", "2:3", "0.5", "0.5",
"key", "cohesive-potential-energy",
"source-value", "1:5", "3.324", "3.3576", "3.3600", "3.3550", "3.3260",
"source-std-uncert-value", "1:5", "0.002", "0.0001", "0.00001", "0.0012", "0.00015",
"source-unit", "eV",
"digits", "5")
kim_obj = kim_edn.load(str_obj)[0]
Property_Instance = '{"property-id" "tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal" "instance-id" 1 "short-name" {"source-value" ["fcc"]} "species" {"source-value" ["Al" "Al" "Al" "Al"]} "a" {"source-value" [3.9149 4.0 4.032 4.0817 4.1602] "source-unit" "angstrom" "digits" 5} "basis-atom-coordinates" {"source-value" [[0.0 0.0 0.0] [0.5 0.5 0.0] [0.5 0.0 0.5] [0.0 0.5 0.5]]} "cohesive-potential-energy" {"source-value" [3.324 3.3576 3.36 3.355 3.326] "source-std-uncert-value" [0.002 0.0001 1e-05 0.0012 0.00015] "source-unit" "eV" "digits" 5}}'
self.assertTrue(Property_Instance == kim_edn.dumps(kim_obj))
# Create the property instance with the property name
str_obj = self.kim_property.kim_property_create(
1, 'cohesive-energy-relation-cubic-crystal')
str_obj = self.kim_property.kim_property_modify(
str_obj, 1,
"key", "short-name",
"source-value", "1", "fcc",
"key", "species",
"source-value", "1:4", "Al", "Al", "Al", "Al")
str_obj = self.kim_property.kim_property_modify(
str_obj, 1,
"key", "a",
"source-value", "1:5", "3.9149", "4.0000", "4.032", "4.0817", "4.1602")
str_obj = self.kim_property.kim_property_modify(
str_obj, 1,
"key", "a",
"source-unit", "angstrom", "digits", "5")
str_obj = self.kim_property.kim_property_modify(
str_obj, 1,
"key", "basis-atom-coordinates",
"source-value", "4", "2:3", "0.5", "0.5",
"key", "basis-atom-coordinates",
"source-value", "3", "3", "0.5",
"key", "basis-atom-coordinates",
"source-value", "2", "1:2", "0.5", "0.5")
str_obj = self.kim_property.kim_property_modify(
str_obj, 1,
"key", "basis-atom-coordinates",
"source-value", "3", "1", "0.5")
str_obj = self.kim_property.kim_property_modify(
str_obj, 1,
"key", "cohesive-potential-energy",
"source-value", "1:5", "3.324", "3.3576", "3.3600", "3.3550", "3.3260",
"source-std-uncert-value", "1:5", "0.002", "0.0001", "0.00001", "0.0012", "0.00015",
"source-unit", "eV",
"digits", "5")
kim_obj = kim_edn.load(str_obj)[0]
self.assertTrue(Property_Instance == kim_edn.dumps(kim_obj))
# Test for scalar values
str_obj = self.kim_property.kim_property_modify(
str_obj, 1,
"key", "space-group",
"source-value", "Immm")
kim_obj = kim_edn.load(str_obj)[0]
self.assertTrue(kim_obj["space-group"]["source-value"] == "Immm")
str_obj = self.kim_property.kim_property_modify(
str_obj, 1,
"key", "space-group",
"source-value", "Fm-3m")
kim_obj = kim_edn.load(str_obj)[0]
self.assertTrue(kim_obj["space-group"]["source-value"] == "Fm-3m")
# Fails when new keyword is not in the property definition
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_modify,
str_obj, 1,
"key", "a", "source-value", 2.5)
# Fails when not in the standard key-value pairs
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_modify,
str_obj, 1,
"key", "basis-atom-coordinates", "source-unknown", 2.5)
# Fails when not enough input
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_modify,
str_obj, 1,
"key", "basis-atom-coordinates", "source-value", 3)
msg = 'there is not enough input arguments '
msg += 'to use.\nProcessing the {"basis-atom-coordinates"}:'
msg += '{"source-value"} input arguments failed.\nThe second '
msg += 'index is missing from the input arguments.'
self.assertRaisesRegex(self.KIMPropertyError, msg,
self.kim_property.kim_property_modify,
str_obj, 1,
"key", "basis-atom-coordinates", "source-value", 3)
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_modify,
str_obj, 1,
"key", "basis-atom-coordinates", "source-value", 3, 3)
msg = 'there is not enough input arguments '
msg += 'to use.\nProcessing the {"basis-atom-coordinates"}:'
msg += '{"source-value"} input arguments failed.\n'
msg += 'At least we need one further input.'
self.assertRaisesRegex(self.KIMPropertyError, msg,
self.kim_property.kim_property_modify,
str_obj, 1,
"key", "basis-atom-coordinates", "source-value", 3, 3)
self.assertRaises(self.KIMPropertyError,
self.kim_property.kim_property_modify,
str_obj, 1,
"key", "basis-atom-coordinates", "source-value", 3, 4)
msg = 'this dimension has a fixed length = 3, while, '
msg += 'wrong index = 4 is requested.\nProcessing the '
msg += '{"basis-atom-coordinates"}:{"source-value"} input arguments,'
msg += ' wrong index at the second dimension is requested.'
self.assertRaisesRegex(self.KIMPropertyError, msg,
self.kim_property.kim_property_modify,
str_obj, 1,
"key", "basis-atom-coordinates", "source-value", 3, 4)
def pickle_kim_properties(properties=None,
fp=join(kim_properties_path,
'kim_properties.pickle'),
protocol=0):
"""Serialize KIM properties.
Keyword Arguments:
properties {dict} -- KIM properties dictionary indexed by properties
full IDs. (default: {None})
fp {string, or a ``.write()``-supporting bytes-like object} -- fp is a
file name string to open it or a ``.write()``-supporting
bytes-like object.
protocol {int} -- protocol which can be used for pickling.
(default: {0})
"""
# List of KIM properties to be pickled
kim_properties_list = []
if properties is None:
# KIM property files.
kim_property_files = []
# KIM property files path. An absolute path (or a valid relative path)
# to the KIM property files folder.
kim_property_files_path = join(dirname(abspath(__file__)), pardir,
"external", "openkim-properties",
"properties")
if isdir(abspath(kim_property_files_path)):
kim_property_files_path = abspath(kim_property_files_path)
else:
msg = 'property files can not be found!'
raise KIMPropertyError(msg)
# KIM property names.
kim_property_names = [
"atomic-mass",
"bulk-modulus-isothermal-cubic-crystal-npt",
"bulk-modulus-isothermal-hexagonal-crystal-npt",
"cohesive-energy-lattice-invariant-shear-path-cubic-crystal",
"cohesive-energy-lattice-invariant-shear-unrelaxed-path-cubic-crystal",
"cohesive-energy-relation-cubic-crystal",
"cohesive-energy-shear-stress-path-cubic-crystal",
"cohesive-free-energy-cubic-crystal",
"cohesive-free-energy-hexagonal-crystal",
"cohesive-potential-energy-2d-hexagonal-crystal",
"cohesive-potential-energy-cubic-crystal",
"cohesive-potential-energy-hexagonal-crystal",
"configuration-cluster-fixed",
"configuration-cluster-relaxed",
"configuration-nonorthogonal-periodic-3d-cell-fixed-particles-fixed",
"configuration-nonorthogonal-periodic-3d-cell-fixed-particles-relaxed",
"configuration-nonorthogonal-periodic-3d-cell-relaxed-particles-fixed",
"configuration-nonorthogonal-periodic-3d-cell-relaxed-particles-relaxed",
"configuration-periodic-2d-cell-fixed-particles-fixed",
"dislocation-core-energy-cubic-crystal-npt",
"elastic-constants-first-strain-gradient-isothermal-cubic-crystal-npt",
"elastic-constants-first-strain-gradient-isothermal-monoatomic-hexagonal-crystal-npt",
"elastic-constants-isothermal-cubic-crystal-npt",
"enthalpy-of-mixing-curve-substitutional-binary-cubic-crystal-npt",
"enthalpy-of-mixing-curve-substitutional-binary-cubic-crystal-nvt",
"extrinsic-stacking-fault-relaxed-energy-fcc-crystal-npt",
"gamma-surface-relaxed-fcc-crystal-npt",
"grain-boundary-symmetric-tilt-energy-ideal-cubic-crystal",
"grain-boundary-symmetric-tilt-energy-relaxed-cubic-crystal",
"grain-boundary-symmetric-tilt-energy-relaxed-relation-cubic-crystal",
"intrinsic-stacking-fault-relaxed-energy-fcc-crystal-npt",
"linear-thermal-expansion-coefficient-cubic-crystal-npt",
"melting-temperature-constant-pressure-cubic-crystal",
"monovacancy-formation-energy-monoatomic-cubic-diamond",
"monovacancy-neutral-formation-free-energy-crystal-npt",
"monovacancy-neutral-migration-energy-crystal-npt",
"monovacancy-neutral-relaxation-volume-crystal-npt",
"monovacancy-neutral-relaxed-formation-potential-energy-crystal-npt",
"monovacancy-neutral-unrelaxed-formation-potential-energy-crystal-npt",
"phonon-dispersion-dos-cubic-crystal-npt",
"phonon-dispersion-relation-cubic-crystal-npt",
"shear-stress-path-cubic-crystal",
"stacking-fault-relaxed-energy-curve-fcc-crystal-npt",
"structure-2d-hexagonal-crystal-npt",
"structure-cubic-crystal-npt",
"structure-hexagonal-crystal-npt",
"structure-monoclinic-crystal-npt",
"structure-orthorhombic-crystal-npt",
"structure-rhombohedral-crystal-npt",
"structure-tetragonal-crystal-npt",
"structure-triclinic-crystal-npt",
"surface-energy-broken-bond-fit-cubic-bravais-crystal-npt",
"surface-energy-cubic-crystal-npt",
"surface-energy-ideal-cubic-crystal",
"unstable-stacking-fault-relaxed-energy-fcc-crystal-npt",
"unstable-twinning-fault-relaxed-energy-fcc-crystal-npt",
"verification-check",
]
# KIM property full IDs.
kim_property_ids = [
"tag:[email protected],2016-05-11:property/atomic-mass",
"tag:[email protected],2014-04-15:property/bulk-modulus-isothermal-cubic-crystal-npt",
"tag:[email protected],2014-04-15:property/bulk-modulus-isothermal-hexagonal-crystal-npt",
"tag:[email protected],2015-05-26:property/cohesive-energy-lattice-invariant-shear-path-cubic-crystal",
"tag:[email protected],2015-05-26:property/cohesive-energy-lattice-invariant-shear-unrelaxed-path-cubic-crystal",
"tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal",
"tag:[email protected],2015-05-26:property/cohesive-energy-shear-stress-path-cubic-crystal",
"tag:[email protected],2014-04-15:property/cohesive-free-energy-cubic-crystal",
"tag:[email protected],2014-04-15:property/cohesive-free-energy-hexagonal-crystal",
"tag:[email protected],2015-05-26:property/cohesive-potential-energy-2d-hexagonal-crystal",
"tag:[email protected],2014-04-15:property/cohesive-potential-energy-cubic-crystal",
"tag:[email protected],2014-04-15:property/cohesive-potential-energy-hexagonal-crystal",
"tag:[email protected],2014-04-15:property/configuration-cluster-fixed",
"tag:[email protected],2014-04-15:property/configuration-cluster-relaxed",
"tag:[email protected],2014-04-15:property/configuration-nonorthogonal-periodic-3d-cell-fixed-particles-fixed",
"tag:[email protected],2014-04-15:property/configuration-nonorthogonal-periodic-3d-cell-fixed-particles-relaxed",
"tag:[email protected],2014-04-15:property/configuration-nonorthogonal-periodic-3d-cell-relaxed-particles-fixed",
"tag:[email protected],2014-04-15:property/configuration-nonorthogonal-periodic-3d-cell-relaxed-particles-relaxed",
"tag:[email protected],2015-10-12:property/configuration-periodic-2d-cell-fixed-particles-fixed",
"tag:[email protected],2021-02-24:property/dislocation-core-energy-cubic-crystal-npt",
"tag:[email protected],2016-05-24:property/elastic-constants-first-strain-gradient-isothermal-cubic-crystal-npt",
"tag:[email protected],2016-05-24:property/elastic-constants-first-strain-gradient-isothermal-monoatomic-hexagonal-crystal-npt",
"tag:[email protected],2014-05-21:property/elastic-constants-isothermal-cubic-crystal-npt",
"tag:[email protected],2017-07-31:property/enthalpy-of-mixing-curve-substitutional-binary-cubic-crystal-npt",
"tag:[email protected],2017-07-31:property/enthalpy-of-mixing-curve-substitutional-binary-cubic-crystal-nvt",
"tag:[email protected],2015-05-26:property/extrinsic-stacking-fault-relaxed-energy-fcc-crystal-npt",
"tag:[email protected],2015-05-26:property/gamma-surface-relaxed-fcc-crystal-npt",
"tag:[email protected],2016-01-23:property/grain-boundary-symmetric-tilt-energy-ideal-cubic-crystal",
"tag:[email protected],2016-01-23:property/grain-boundary-symmetric-tilt-energy-relaxed-cubic-crystal",
"tag:[email protected],2016-02-18:property/grain-boundary-symmetric-tilt-energy-relaxed-relation-cubic-crystal",
"tag:[email protected],2015-05-26:property/intrinsic-stacking-fault-relaxed-energy-fcc-crystal-npt",
"tag:[email protected],2015-07-30:property/linear-thermal-expansion-coefficient-cubic-crystal-npt",
"tag:[email protected],2014-08-21:property/melting-temperature-constant-pressure-cubic-crystal",
"tag:[email protected],2014-04-15:property/monovacancy-formation-energy-monoatomic-cubic-diamond",
"tag:[email protected],2015-07-28:property/monovacancy-neutral-formation-free-energy-crystal-npt",
"tag:[email protected],2015-09-16:property/monovacancy-neutral-migration-energy-crystal-npt",
"tag:[email protected],2015-07-28:property/monovacancy-neutral-relaxation-volume-crystal-npt",
"tag:[email protected],2015-07-28:property/monovacancy-neutral-relaxed-formation-potential-energy-crystal-npt",
"tag:[email protected],2015-07-28:property/monovacancy-neutral-unrelaxed-formation-potential-energy-crystal-npt",
"tag:[email protected],2014-05-21:property/phonon-dispersion-dos-cubic-crystal-npt",
"tag:[email protected],2014-05-21:property/phonon-dispersion-relation-cubic-crystal-npt",
"tag:[email protected],2015-05-26:property/shear-stress-path-cubic-crystal",
"tag:[email protected],2015-05-26:property/stacking-fault-relaxed-energy-curve-fcc-crystal-npt",
"tag:[email protected],2015-05-26:property/structure-2d-hexagonal-crystal-npt",
"tag:[email protected],2014-04-15:property/structure-cubic-crystal-npt",
"tag:[email protected],2014-04-15:property/structure-hexagonal-crystal-npt",
"tag:[email protected],2014-04-15:property/structure-monoclinic-crystal-npt",
"tag:[email protected],2014-04-15:property/structure-orthorhombic-crystal-npt",
"tag:[email protected],2014-04-15:property/structure-rhombohedral-crystal-npt",
"tag:[email protected],2014-04-15:property/structure-tetragonal-crystal-npt",
"tag:[email protected],2014-04-15:property/structure-triclinic-crystal-npt",
"tag:[email protected],2014-05-21:property/surface-energy-broken-bond-fit-cubic-bravais-crystal-npt",
"tag:[email protected],2014-05-21:property/surface-energy-cubic-crystal-npt",
"tag:[email protected],2014-05-21:property/surface-energy-ideal-cubic-crystal",
"tag:[email protected],2015-05-26:property/unstable-stacking-fault-relaxed-energy-fcc-crystal-npt",
"tag:[email protected],2015-05-26:property/unstable-twinning-fault-relaxed-energy-fcc-crystal-npt",
"tag:[email protected],2017-02-01:property/verification-check",
]
for _id in kim_property_ids:
_path, _, _, _ = get_property_id_path(_id)
kim_property_files.append(join(kim_property_files_path, _path))
if not isfile(kim_property_files[-1]):
msg = 'the property file =\n"'
msg += kim_property_files[-1]
msg += '"\ncan not be found!'
raise KIMPropertyError(msg)
del kim_property_files_path
# KIM properties dictionary indexed by properties full IDs.
kim_properties = {
k: kim_edn.load(v)
for k, v in zip(kim_property_ids, kim_property_files)
}
# KIM properties name to full ID dictionary.
property_name_to_property_id = \
dict(zip(kim_property_names, kim_property_ids))
# KIM properties full ID to name dictionary.
property_id_to_property_name = \
dict(zip(kim_property_ids, kim_property_names))
del kim_property_names
del kim_property_ids
kim_properties_list = [
kim_properties,
property_name_to_property_id,
property_id_to_property_name,
]
else:
if not isinstance(properties, dict):
msg = 'wrong input, "properties" is not a `dict`.'
raise KIMPropertyError(msg)
if len(properties) == 0:
msg = 'wrong input, "properties" is empty.'
raise KIMPropertyError(msg)
property_ids = list(properties.keys())
property_names = []
for _id in property_ids:
_, _, _, _name = get_property_id_path(_id)
property_names.append(_name)
# KIM properties name to full ID dictionary.
name_to_property_id = dict(zip(property_names, property_ids))
# KIM properties full ID to name dictionary.
id_to_property_name = dict(zip(property_ids, property_names))
del property_names
del property_ids
kim_properties_list = [
properties,
name_to_property_id,
id_to_property_name,
]
if isinstance(fp, str):
# See if this is a file name
with open(fp, 'wb') as f:
# Pickle the kim_properties
pickle.dump(kim_properties_list, f, protocol=protocol)
else:
try:
pickle.dump(kim_properties_list, fp, protocol=protocol)
except:
msg = 'wrong input. ("fp" should refer to a bytes-like object.)'
raise KIMPropertyError(msg)
def kim_property_create(instance_id, property_name, property_instances=None):
"""Create a new kim property instance.
It takes as input the property instance ID and property definition name
and creates initial property instance data structure. If the
"property_instances" obj is already exist it adds the newly created
property instance to the obj and fails if it already exist there.
For example::
>>> kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
'[{"property-id" "tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal" "instance-id" 1}]'
>>> str = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
Creating and addition of a second property instance::
>>> kim_property_create(2, 'atomic-mass', str)
'[{"property-id" "tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal" "instance-id" 1} {"property-id" "tag:[email protected],2016-05-11:property/atomic-mass" "instance-id" 2}]'
>>> str = kim_property_create(2, 'atomic-mass', str)
>>> obj = kim_edn.loads(str)
>>> print(kim_edn.dumps(obj, indent=4))
[
{
"property-id" "tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal"
"instance-id" 1
}
{
"property-id" "tag:[email protected],2016-05-11:property/atomic-mass"
"instance-id" 2
}
]
Arguments:
instance_id {int} -- A positive integer identifying the property
instance.
property_name {string} --
- A string containing the property name or
- unique ID of the property, or
- a path-like object giving the pathname (absolute or relative to
the current working directory) of the file to be opened
property_instances {string} -- A string containing the serialized
KIM-EDN formatted property instances. (default: {None})
Returns:
string -- serialized KIM-EDN formatted property instances.
"""
global KIM_PROPERTIES
global PROPERTY_NAME_TO_PROPERTY_ID
global PROPERTY_ID_TO_PROPERTY_NAME
global NEW_PROPERTY_IDS
if not isinstance(instance_id, int):
msg = 'the "instance_id" is not an `int`.'
raise KIMPropertyError(msg)
# Check instance id format to prevent mistakes as early as possible
check_instance_id_format(instance_id)
if not isinstance(property_name, str):
msg = 'the "property_name" is not an `str`.'
raise KIMPropertyError(msg)
if property_instances is None:
kim_property_instances = []
else:
# Deserialize the KIM property instances.
kim_property_instances = kim_edn.loads(property_instances)
for a_property_instance in kim_property_instances:
if instance_id == a_property_instance["instance-id"]:
msg = 'the "instance-id"’s cannot repeat. '
msg += 'In the case where there are multiple property '
msg += 'instances, the instance-id’s cannot repeat.'
raise KIMPropertyError(msg)
# KIM property names.
kim_property_names = list(PROPERTY_NAME_TO_PROPERTY_ID.keys())
# KIM property full IDs.
kim_property_ids = list(PROPERTY_ID_TO_PROPERTY_NAME.keys())
new_property_instance = {}
# If the property_name is a path-like object to a file to be opened
if isfile(property_name):
# Load the property definition from a file
pd = kim_edn.load(property_name)
# Check the correctness of th eproperty definition
check_property_definition(pd)
# Get the property ID
_property_id = pd["property-id"]
# Check to make sure that this property does not exist in OpenKIM
if _property_id in KIM_PROPERTIES:
msg = 'the input property_name file contains a property ID:\n'
msg += '"{}"\nwhich already '.format(_property_id)
msg += 'exists in the KIM Property Definition list.\n'
msg += 'Use the KIM Property Definition or update the ID in the'
msg += 'property_name file.\n'
msg += 'See the KIM Property Definitions at '
msg += 'https://openkim.org/properties for more detailed '
msg += 'information.'
raise KIMPropertyError(msg)
# Add the new property definition to KIM_PROPERTIES
KIM_PROPERTIES[_property_id] = pd
# Get the property name
_, _, _, _property_name = get_property_id_path(_property_id)
PROPERTY_NAME_TO_PROPERTY_ID[_property_name] = _property_id
PROPERTY_ID_TO_PROPERTY_NAME[_property_id] = _property_name
kim_property_names.append(_property_name)
kim_property_ids.append(_property_id)
# Keep the record of a newly added properties
if NEW_PROPERTY_IDS is None:
NEW_PROPERTY_IDS = []
NEW_PROPERTY_IDS.append(_property_id)
# Set the new instance property ID
new_property_instance["property-id"] = _property_id
else:
if property_name in kim_property_names:
new_property_instance["property-id"] = \
PROPERTY_NAME_TO_PROPERTY_ID[property_name]
elif property_name in kim_property_ids:
new_property_instance["property-id"] = property_name
else:
msg = 'the requested "property_name" :\n'
msg += '"{}"\n'.format(property_name)
msg += 'is not a valid KIM property name nor '
msg += 'a path-like object to a file.\n'
msg += 'See the KIM Property Definitions at '
msg += 'https://openkim.org/properties for more detailed '
msg += 'information.'
raise KIMPropertyError(msg)
new_property_instance["instance-id"] = instance_id
# Add the newly created property instance to the collection
kim_property_instances.append(new_property_instance)
# If there are multiple keys sort them based on instance-id
if len(kim_property_instances) > 1:
kim_property_instances = sorted(kim_property_instances,
key=lambda i: i["instance-id"])
# Return the serialize KIM property instances
return kim_edn.dumps(kim_property_instances)
