| Name | pyiron-lammps JSON |
| Version |
0.2.13
JSON |
| download |
| home_page | None |
| Summary | Vector-oriented LAMMPS interface to rapidly iterate over series of atomistic structures or interatomic potentials. |
| upload_time | 2024-04-19 02:44:08 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | <3.13,>=3.9 |
| license | BSD 3-Clause License Copyright (c) 2023, pyiron All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
pyiron
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# pyiron_lammps
[](https://github.com/pyiron/pyiron_lammps/actions)
[](https://coveralls.io/github/pyiron/pyiron_lammps?branch=main)
## Disclaimer
The `pyiron_lammps` package is under development.
## Idea
* The `pyiron_lammps` package is designed to calculate concentration dependent material properties, like the elastic constants, energy-volume curves and phonons for interatomic potentials.
* It uses `mpi4py` for parallel execution, does not write any files to the file system and does not use any database. With this combination is it one order of magnitude faster than competing software packages for evaluating material properties for interatomic potentials.
* In contrast to all other `pyiron_*` packages, `pyiron_lammps` does not depent on `pyiron_base`. Overall the dependencies are designed to be minimal.
## Example
```python
import pyiron_lammps as pyr
# Generate SQS Structure
structure = pyr.generate_sqs_structure(
structure_template=pyr.get_ase_bulk("Al", cubic=True).repeat([3,3,3]),
element_lst=["Fe", "Ni", "Cr", "Co", "Cu"],
count_lst=[22, 22, 22, 21, 21]
)[0]
# Select Potential
potential = '2021--Deluigi-O-R--Fe-Ni-Cr-Co-Cu--LAMMPS--ipr1'
df_pot = pyr.get_potential_dataframe(
structure=structure,
resource_path="/Users/janssen/mambaforge/share/iprpy"
)
df_pot_selected = df_pot[df_pot.Name==potential].iloc[0]
# Optimize Structure
structure_opt = pyr.optimize_structure(
structure=structure,
potential_dataframe=df_pot_selected
)
# Calculate Elastic Constants
elastic_matrix = pyr.calculate_elastic_constants(
structure=structure_opt,
potential_dataframe=df_pot_selected,
num_of_point=5,
eps_range=0.005,
sqrt_eta=True,
fit_order=2
)
print(elastic_matrix)
```
## Features
* `generate_sqs_structure` - generate an SQS structure using `sqsgenerator`.
* `get_ase_bulk` - create an `ase.build.bulk` structure.
* `get_lammps_engine` - create an `LAMMPS` instance, these instances can then be shared between multiple serial calculation.
* `get_potential_dataframe` - load dataframe of suitable interatomic potentials for the selected atomistic structure from the NIST database.
* `optimize_structure` - optimize the `cell` and the `positions` of a given structure, while maintaining the cell shape.
* `calculate_elastic_constants` - calculate the elastic constants.
* `calculate_elastic_constants_with_minimization` - combine the structure optimization and the calculation of the elastic constants.
* `optimize_structure_parallel` - optimize a list of atomistic structures all with the same interatomic potential.
* `calculate_elastic_constants_parallel` - calculate the elastic constants for a list of atomistic structures.
* `calculate_elastic_constants_with_minimization_parallel` - combine the structure optimization and the calculation of the elastic constants for a list of atomistic structures.
## License and Acknowledgments
`pyiron_lammps` is licensed under the BSD license.
If you use pyiron in your scientific work, [please consider citing](http://www.sciencedirect.com/science/article/pii/S0927025618304786):
```
@article{pyiron-paper,
title = {pyiron: An integrated development environment for computational materials science},
journal = {Computational Materials Science},
volume = {163},
pages = {24 - 36},
year = {2019},
issn = {0927-0256},
doi = {https://doi.org/10.1016/j.commatsci.2018.07.043},
url = {http://www.sciencedirect.com/science/article/pii/S0927025618304786},
author = {Jan Janssen and Sudarsan Surendralal and Yury Lysogorskiy and Mira Todorova and Tilmann Hickel and Ralf Drautz and Jörg Neugebauer},
keywords = {Modelling workflow, Integrated development environment, Complex simulation protocols},
}
```
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"description": "# pyiron_lammps\n\n[](https://github.com/pyiron/pyiron_lammps/actions)\n[](https://coveralls.io/github/pyiron/pyiron_lammps?branch=main)\n\n## Disclaimer\nThe `pyiron_lammps` package is under development. \n\n## Idea\n* The `pyiron_lammps` package is designed to calculate concentration dependent material properties, like the elastic constants, energy-volume curves and phonons for interatomic potentials. \n* It uses `mpi4py` for parallel execution, does not write any files to the file system and does not use any database. With this combination is it one order of magnitude faster than competing software packages for evaluating material properties for interatomic potentials. \n* In contrast to all other `pyiron_*` packages, `pyiron_lammps` does not depent on `pyiron_base`. Overall the dependencies are designed to be minimal. \n\n## Example\n```python\nimport pyiron_lammps as pyr\n\n# Generate SQS Structure\nstructure = pyr.generate_sqs_structure(\n structure_template=pyr.get_ase_bulk(\"Al\", cubic=True).repeat([3,3,3]), \n element_lst=[\"Fe\", \"Ni\", \"Cr\", \"Co\", \"Cu\"], \n count_lst=[22, 22, 22, 21, 21]\n)[0]\n\n# Select Potential\npotential = '2021--Deluigi-O-R--Fe-Ni-Cr-Co-Cu--LAMMPS--ipr1'\ndf_pot = pyr.get_potential_dataframe(\n structure=structure, \n resource_path=\"/Users/janssen/mambaforge/share/iprpy\"\n)\ndf_pot_selected = df_pot[df_pot.Name==potential].iloc[0]\n\n# Optimize Structure\nstructure_opt = pyr.optimize_structure(\n structure=structure, \n potential_dataframe=df_pot_selected\n)\n\n# Calculate Elastic Constants\nelastic_matrix = pyr.calculate_elastic_constants(\n structure=structure_opt, \n potential_dataframe=df_pot_selected, \n num_of_point=5, \n eps_range=0.005, \n sqrt_eta=True, \n fit_order=2\n)\nprint(elastic_matrix)\n```\n\n## Features\n* `generate_sqs_structure` - generate an SQS structure using `sqsgenerator`.\n* `get_ase_bulk` - create an `ase.build.bulk` structure.\n* `get_lammps_engine` - create an `LAMMPS` instance, these instances can then be shared between multiple serial calculation.\n* `get_potential_dataframe` - load dataframe of suitable interatomic potentials for the selected atomistic structure from the NIST database.\n* `optimize_structure` - optimize the `cell` and the `positions` of a given structure, while maintaining the cell shape.\n* `calculate_elastic_constants` - calculate the elastic constants.\n* `calculate_elastic_constants_with_minimization` - combine the structure optimization and the calculation of the elastic constants.\n* `optimize_structure_parallel` - optimize a list of atomistic structures all with the same interatomic potential. \n* `calculate_elastic_constants_parallel` - calculate the elastic constants for a list of atomistic structures. \n* `calculate_elastic_constants_with_minimization_parallel` - combine the structure optimization and the calculation of the elastic constants for a list of atomistic structures. \n\n## License and Acknowledgments\n`pyiron_lammps` is licensed under the BSD license.\n\nIf you use pyiron in your scientific work, [please consider citing](http://www.sciencedirect.com/science/article/pii/S0927025618304786):\n\n```\n@article{pyiron-paper,\n title = {pyiron: An integrated development environment for computational materials science},\n journal = {Computational Materials Science},\n volume = {163},\n pages = {24 - 36},\n year = {2019},\n issn = {0927-0256},\n doi = {https://doi.org/10.1016/j.commatsci.2018.07.043},\n url = {http://www.sciencedirect.com/science/article/pii/S0927025618304786},\n author = {Jan Janssen and Sudarsan Surendralal and Yury Lysogorskiy and Mira Todorova and Tilmann Hickel and Ralf Drautz and J\u00f6rg Neugebauer},\n keywords = {Modelling workflow, Integrated development environment, Complex simulation protocols},\n}\n```\n",
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