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 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 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.
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}]'
>>> str = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
>>> kim_property_create(2, 'atomic-mass', str)
'[{"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}]'
>>> str = kim_property_create(2, 'atomic-mass', str)
>>> obj = kim_edn.loads(str)
>>> print(kim_edn.dumps(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
}
]
Destroy
Destroying property instances::
>>> obj = '[{"property-id" "tag:staff@noreply.openkim.org,2014-04-15:property/cohesive-energy-relation-cubic-crystal" "instance-id" 1}]'
>>> kim_property_destroy(obj, 1)
'[]'
>>> 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(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::
>>> str = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
>>> str = kim_property_modify(str, 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")
>>> obj = kim_edn.loads(str)
>>> print(kim_edn.dumps(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
}
}
]
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.
>>> str = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
>>> str = kim_property_modify(str, 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")
>>> obj = kim_edn.loads(str)
>>> print(kim_edn.dumps(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
}
}
]
>>> str = kim_property_modify(str, 1,
"key", "basis-atom-coordinates",
"source-value", "2", "1:2", "0.5", "0.5")
>>> obj = kim_edn.loads(str)
>>> print(kim_edn.dumps(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
]
]
}
}
]
>>> str = kim_property_modify(str, 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")
>>> obj = kim_edn.loads(str)
>>> print(kim_edn.dumps(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
]
]
}
}
]
>>> str = kim_property_modify(str, 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")
>>> obj = kim_edn.loads(str)
>>> print(kim_edn.dumps(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
}
}
]
Remove
Removing (a) key(s) from a property instance::
>>> str = kim_property_create(1, 'cohesive-energy-relation-cubic-crystal')
>>> str = kim_property_modify(str, 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")
>>> str = kim_property_remove(str, 1, "key", "a", "source-unit")
>>> str = kim_property_remove(str, 1, "key", "cohesive-potential-energy", "key", "basis-atom-coordinates")
>>> obj = kim_edn.loads(str)
>>> print(kim_edn.dumps(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
}
}
]
Installing kim_property
Requirements
You need Python 3.6 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
pip3instead ofpip.
pip3 install kim_property
- Depending on your configuration, you may have to run
piplike this:
python3 -m pip install kim_property
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
Once the conda-forge channel has been enabled, kim_property can be installed
with:
conda install kim_property
It is possible to list all of the versions of kim_property available on your
platform with:
conda search kim_property --channel conda-forge
Copyright
Copyright (c) 2020, Regents of the University of Minnesota.
All Rights Reserved
Contributing
Contributors:
Yaser Afshar
Release history Release notifications | RSS feed
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Source Distribution
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