kim-property - KIM-PROPERTY utility module.
Project description
KIM-PROPERTY utility module
The objective is to make it as easy as possible to convert a script (for example a LAMMPS script) that computes a KIM property to a KIM Test.
This utility module has 5 modes:
1- Create
Take as input the property instance ID and property definition name and
create initial property instance data structure. It checks and indicates
whether the property definition exists in OpenKIM.
2- Destroy
Delete a previously created property instance ID.
3- Modify
Incrementally build the property instance by receiving keys with
associated arguments. It can "append" and add to a key's existing array
argument.
4- Remove
Remove a key.
5- Dump
Take as input the generated instance and a filename, validate each
instance against the property definition and either issues an error or
writes the instance out to file in edn format. Final validation should
make sure all keys/arguments are legal and all required keys are
provided.
To get started, you'll need to install the kim-property
package. Please refer
to the installation instructions.
Create
Creating property instances::
>>> kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
'[{"property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal" "instance-id" 1}]'
>>> property_inst = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
>>> kim_property_create(2, 'atomic-mass', property_inst)
'[{"property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal" "instance-id" 1} {"property-id" "tag:brunnels@noreply.openkim.org,2016-05-11:property/atomic-mass" "instance-id" 2}]'
>>> property_inst = kim_property_create(2, 'atomic-mass', property_inst)
>>> property_inst_obj = kim_edn.loads(property_inst)
>>> print(kim_edn.dumps(property_inst_obj, indent=4))
[
{
"property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal"
"instance-id" 1
}
{
"property-id" "tag:brunnels@noreply.openkim.org,2016-05-11:property/atomic-mass"
"instance-id" 2
}
]
>>> kim_property_create(1, 'cohesive-energy-relation-cubic-crystal', property_disclaimer="This is an example disclaimer.")
'[{"property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal" "instance-id" 1 "disclaimer" "This is an example disclaimer."}]'
>>> property_inst = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
>>> kim_property_create(2, 'atomic-mass', property_inst, "This is an example disclaimer for atomic-mass.")
'[{"property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal" "instance-id" 1} {"property-id" "tag:brunnels@noreply.openkim.org,2016-05-11:property/atomic-mass" "instance-id" 2 "disclaimer" "This is an example disclaimer for atomic-mass."}]'
A property instance is stored in a subset of the KIM-EDN format as described in
KIM Property Instances.
Each property instance must contain the property-id
and instance-id
.
kim-property
utility module can create a new property instance, using a KIM
property ID. A KIM property ID is an identifier of a KIM Property Definition,
which can be,
(1) a property short name,
(2) the full unique ID of the property (including the contributor and date),
(3) a file name corresponding to a local property definition file.
Examples of each of these cases are shown below:
>>> kim_property_create(1, 'atomic-mass')
>>> kim_property_create(2, 'cohesive-energy-relation-cubic-crystal')
>>> kim_property_create(1, 'tag:brunnels@noreply.openkim.org,2016-05-11:property/atomic-mass')
>>> kim_property_create(2, 'tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal')
>>> kim_property_create(1, 'new-property.edn')
>>> kim_property_create(2, '/home/mary/marys-kim-properties/dissociation-energy.edn')
In the last example, "new-property.edn" and "/home/mary/marys-kim-properties/dissociation-energy.edn" are the names of files that contain user-defined (local) property definitions.
Destroy
Destroying property instances::
>>> property_inst_obj = '[{"property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal" "instance-id" 1}]'
>>> kim_property_destroy(property_inst_obj, 1)
'[]'
>>> property_inst_obj = '[{"property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal" "instance-id" 1} {"property-id" "tag:brunnels@noreply.openkim.org,2016-05-11:property/atomic-mass" "instance-id" 2}]'
>>> kim_property_destroy(property_inst_obj, 2)
'[{"property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal" "instance-id" 1}]'
Modify
Modifying (setting) property instances.
Once a kim_property_create
has been given to instantiate a property
instance, maps associated with the property's keys can be edited using the
kim_property_modify.
In using this command, the special keyword "key" should be given, followed
by the property key name and the key-value pair in the map associated with
the key that is to be set.
For example, the cohesive-energy-relation-cubic-crystal
property definition
consists of property keys named "short-name", "species", ...
An instance of this property could be created like so::
>>> property_inst = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
>>> property_inst = kim_property_modify(property_inst, 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")
>>> property_inst_obj = kim_edn.loads(property_inst)
>>> print(kim_edn.dumps(property_inst_obj, indent=4))
[
{
"property-id" "tag:staff@noreply.openkim.org,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
}
}
]
>>> property_inst = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
>>> property_inst = kim_property_modify(property_inst, 1,
"disclaimer", "This is an example disclaimer.",
"key", "short-name",
"source-value", "1", "fcc")
>>> property_inst_obj = kim_edn.loads(property_inst)
>>> print(kim_edn.dumps(property_inst_obj, indent=4))
[
{
"property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal"
"instance-id" 1
"disclaimer" "This is an example disclaimer."
"short-name" {
"source-value" [
"fcc"
]
}
}
]
For cases where there are multiple keys or a key receives an array of values
computed one at a time, the kim_property_modify
can be called multiple
times and append values to a given key.
>>> property_inst = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
>>> property_inst = kim_property_modify(property_inst, 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")
>>> property_inst_obj = kim_edn.loads(property_inst)
>>> print(kim_edn.dumps(property_inst_obj, indent=4))
[
{
"property-id" "tag:staff@noreply.openkim.org,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
}
}
]
>>> property_inst = kim_property_modify(property_inst, 1,
"key", "basis-atom-coordinates",
"source-value", "2", "1:2", "0.5", "0.5")
>>> property_inst_obj = kim_edn.loads(property_inst)
>>> print(kim_edn.dumps(property_inst_obj, indent=4))
[
{
"property-id" "tag:staff@noreply.openkim.org,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
]
]
}
}
]
>>> property_inst = kim_property_modify(property_inst, 1,
"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")
>>> property_inst_obj = kim_edn.loads(property_inst)
>>> print(kim_edn.dumps(property_inst_obj, indent=4))
[
{
"property-id" "tag:staff@noreply.openkim.org,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
]
]
}
}
]
>>> property_inst = kim_property_modify(property_inst, 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")
>>> property_inst_obj = kim_edn.loads(property_inst)
>>> print(kim_edn.dumps(property_inst_obj, indent=4))
[
{
"property-id" "tag:staff@noreply.openkim.org,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
}
}
]
Note:
Variables which are introduced with a specified extent of either an empty
vector []
or [1]
, are scalars.
Calling a kim_property_modify
will update the scalars and vector values
which are already set.
For example:
>>> property_inst = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
>>> property_inst = kim_property_modify(property_inst, 1,
"key", "space-group",
"source-value", "Immm")
>>> property_inst_obj = kim_edn.loads(property_inst)
>>> print(kim_edn.dumps(property_inst_obj, indent=4))
[
{
"property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal"
"instance-id" 1
"space-group" {
"source-value" "Immm"
}
}
]
Calling the kim_property_modify
again set the scalar variable with a new
value.
>>> property_inst = kim_property_modify(property_inst, 1,
"key", "space-group",
"source-value", "P6_3/mmc")
>>> property_inst_obj = kim_edn.loads(property_inst)
>>> print(kim_edn.dumps(property_inst_obj, indent=4))
[
{
"property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal"
"instance-id" 1
"space-group" {
"source-value" "P6_3/mmc"
}
}
]
Note:
If the source-value key is a scalar, the values of the uncertainty and digits
keys must be scalars. Thus, calling the kim_property_modify
with a non-scalar
key where the source-value key is a scalar fails.
Note:
If the source-value key's value is an array (EDN vector), the values of the uncertainty and digits keys must be either arrays of the same extent, or scalars in which case they are taken to apply equally to all values in the source-value array. The keys associated with uncertainty and precision conform to the ISO Guide to the Expression of Uncertainty in Measurement and the ThermoML standard notation.
The keys associated with uncertainty and precision of the KIM Property Instances are:
- source-std-uncert-value
- source-expand-uncert-value
- coverage-factor
- source-asym-std-uncert-neg
- source-asym-std-uncert-pos
- source-asym-expand-uncert-neg
- source-asym-expand-uncert-pos
- uncert-lev-of-confid
- digits
In below example, the a
-key source-value key's value is an array, which means
the value of the digits
-key must be either an array of the same extent, or a
scalar.
-
The value of the
digits
-key is a scalar:>>> property_inst = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal') >>> property_inst = kim_property_modify(property_inst, 1, "key", "a", "source-value", "1:5", "3.9149", "4.0000", "4.032", "4.0817", "4.1602", "source-unit", "angstrom", "digits", "5") >>> property_inst_obj = kim_edn.loads(property_inst) >>> print(kim_edn.dumps(property_inst_obj, indent=4)) [ { "property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal" "instance-id" 1 "a" { "source-value" [ 3.9149 4.0 4.032 4.0817 4.1602 ] "source-unit" "angstrom" "digits" 5 } } ]
-
The value of the
digits
-key is an array of the same extent:>>> property_inst = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal') >>> property_inst = kim_property_modify(property_inst, 1, "key", "a", "source-value", "1:5", "3.9149", "4.0000", "4.032", "4.0817", "4.1602", "source-unit", "angstrom", "digits", "1:5", "5", "5", "5", "5", "5") >>> property_inst_obj = kim_edn.loads(property_inst) >>> print(kim_edn.dumps(property_inst_obj, indent=4)) [ { "property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal" "instance-id" 1 "a" { "source-value" [ 3.9149 4.0 4.032 4.0817 4.1602 ] "source-unit" "angstrom" "digits" [ 5 5 5 5 5 ] } } ]
Remove
Removing (a) key(s) from a property instance::
>>> property_inst = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
>>> property_inst = kim_property_modify(property_inst, 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")
>>> property_inst = kim_property_remove(property_inst, 1, "key", "a", "source-unit")
>>> property_inst = kim_property_remove(property_inst, 1, "key", "cohesive-potential-energy", "key", "basis-atom-coordinates")
>>> property_inst_obj = kim_edn.loads(property_inst)
>>> print(kim_edn.dumps(property_inst_obj, indent=4))
[
{
"property-id" "tag:staff@noreply.openkim.org,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
]
"digits" 5
}
}
]
Dump
First, it validates the generated instances against the property definition.
Then serializes it to a KIM-EDN
formatted stream and dumps it to a fp
(a .write()
-supporting file-like
object or a name string to open a file).
The validation makes sure all keys/arguments are legal and all required keys are provided.
>>> property_inst = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
>>> property_inst = kim_property_modify(property_inst, 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_property_dump(property_inst, "results.edn")
or
>>> property_inst = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
>>> property_inst = kim_property_modify(property_inst, 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")
>>> property_inst_obj = kim_edn.loads(property_inst)
>>> kim_property_dump(property_inst_obj, "results.edn")
or
>>> property_inst = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
>>> property_inst = kim_property_modify(property_inst, 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")
>>> with open("results.edn", 'w') as fp:
kim_property_dump(property_inst, fp)
An example with two property instances,
>>> property_inst = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
>>> property_inst = kim_property_modify(property_inst, 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")
>>> property_inst = kim_property_create(2, 'atomic-mass', property_inst)
>>> property_inst = kim_property_modify(property_inst, 2,
"key", "mass",
"source-value", "1.434e-19", "source-unit", "si",
"key", "species",
"source-value", "Al")
>>> kim_property_dump(property_inst, "results.edn")
Installing kim-property
Requirements
You need Python 3.8 or later to run kim-property
. You can have multiple
Python versions (2.x and 3.x) installed on the same system without problems.
To install Python 3 for different Linux flavors, macOS and Windows, packages
are available at
https://www.python.org/getit/
Using pip
pip is the most popular tool for installing Python packages, and the one included with modern versions of Python.
kim-property
can be installed with pip
:
pip install kim-property
Note:
Depending on your Python installation, you may need to use pip3
instead of
pip
.
pip3 install kim-property
Depending on your configuration, you may have to run pip
like this:
python3 -m pip install kim-property
Using pip (GIT Support)
pip
currently supports cloning over git
pip install git+https://github.com/openkim/kim-property.git
For more information and examples, see the pip install reference.
Using conda
conda is the package management tool for Anaconda Python installations.
Installing kim-property
from the conda-forge
channel can be achieved
by adding conda-forge
to your channels with:
conda config --add channels conda-forge
conda config --set channel_priority strict
Once the conda-forge
channel has been enabled, kim-property
can be
installed with conda
:
conda install kim-property
or with mamba
:
mamba install kim-property
It is possible to list all of the versions of kim-property
available on
your platform with conda
:
conda search kim-property --channel conda-forge
or with mamba
:
mamba search kim-property --channel conda-forge
Alternatively, mamba repoquery
may provide more information:
# Search all versions available on your platform:
mamba repoquery search kim-property --channel conda-forge
# List packages depending on `kim-property`:
mamba repoquery whoneeds kim-property --channel conda-forge
# List dependencies of `kim-property`:
mamba repoquery depends kim-property --channel conda-forge
Copyright
Copyright (c) 2020-2024, Regents of the University of Minnesota.
All Rights Reserved
Contributing
Contributors:
Yaser Afshar
Project details
Release history Release notifications | RSS feed
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