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 kim_property_destroy(property_instances, instance_id):
"""Destroy a kim property instance.
Delete a previously created property instance.
For example::
>>> obj = '[{"property-id" "tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal" "instance-id" 1}]'
>>> kim_property_destroy(obj, 1)
'[]'
>>> obj = '[{"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}]'
>>> kim_property_destroy(obj, 2)
'[{"property-id" "tag:[email protected],2014-04-15:property/cohesive-energy-relation-cubic-crystal" "instance-id" 1}]'
Arguments:
property_instances {string} -- A string containing the serialized
KIM-EDN formatted property instances.
instance_id {int} -- A positive integer identifying the property
instance.
Returns:
string -- serialized KIM-EDN formatted property instances.
"""
if not isinstance(instance_id, int):
msg = 'the "instance_id" is not an `int`.'
raise KIMPropertyError(msg)
if property_instances is None or \
property_instances in ('None', '', '[]'):
return '[]'
# 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"]:
property_id = a_property_instance["property-id"]
unset_property_id(property_id)
kim_property_instances.remove(a_property_instance)
# Return the serialize KIM property instances
return kim_edn.dumps(kim_property_instances)
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 kim_property_remove(property_instances, instance_id, *argv):
"""Remove or delete a key from the property instance.
Arguments:
property_instances {string} -- A string containing the serialized
KIM-EDN formatted property instances.
instance_id {int} -- A positive integer identifying the property
instance.
Returns:
string -- serialized KIM-EDN formatted property instances.
"""
if property_instances is None or property_instances in ('None', '', '[]'):
msg = 'there is no property instance to remove the content.'
raise KIMPropertyError(msg)
if not isinstance(instance_id, int):
msg = 'the "instance_id" is not an `int`.'
raise KIMPropertyError(msg)
# Deserialize the KIM property instances.
kim_property_instances = kim_edn.loads(property_instances)
a_property_instance = None
for p in kim_property_instances:
if p["instance-id"] == instance_id:
a_property_instance = p
break
if a_property_instance is None:
msg = 'the requested instance id :\n{}\n'.format(instance_id)
msg += 'doesn\'t match any of the property instances ids.'
raise KIMPropertyError(msg)
# Number of arguments
n_arguments = len(argv)
# key keyword
k_keyword = False
# new keyword
new_keyword = None
new_keyword_map = {}
i = 0
while i < n_arguments:
try:
arg = argv[i]
except IndexError:
msg = 'unexpected index exception happened.'
raise KIMPropertyError(msg)
if arg == 'key':
k_keyword = True
i += 1
continue
if k_keyword:
k_keyword = False
# new keyword
new_keyword = arg
if new_keyword not in a_property_instance:
msg = 'the key {} '.format(new_keyword)
msg += 'doesn\'t exist in the property instance.'
raise KIMPropertyError(msg)
# Remove the whole key if it is requested
if i + 1 < n_arguments:
try:
arg = argv[i + 1]
except IndexError:
msg = 'unexpected index exception happened.'
raise KIMPropertyError(msg)
if arg == 'key':
del a_property_instance[new_keyword]
i += 1
continue
# There is no more argument delete a key and stop
else:
del a_property_instance[new_keyword]
break
new_keyword_map = a_property_instance[new_keyword]
i += 1
continue
if arg in new_keyword_map:
del new_keyword_map[arg]
i += 1
continue
return kim_edn.dumps(kim_property_instances)
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)