| Name | structuretoolkit JSON |
| Version |
0.0.22
JSON |
| download |
| home_page | None |
| Summary | build, analyse and visualise atomistic structures for materials science |
| upload_time | 2024-04-08 16:35:47 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | BSD 3-Clause License Copyright (c) 2018, Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department 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.
|
# structuretoolkit
[](https://github.com/pyiron/structuretoolkit/actions/workflows/unittests.yml)
[](https://coveralls.io/github/pyiron/structuretoolkit?branch=main)
Originally developed as part of the `pyiron_atomistics` module the `structuretoolkit` was release as standalone library
for analysing, building and visualising atomistic structures. Internally it uses the `ase.atoms.Atoms` class to
represent atomistic structures in python. The `structuretoolkit` is integrated inside `pyiron_atomistics`.
## Disclaimer
The `structuretoolkit` is currently under development.
## Example
```python
import structuretoolkit as stk
from ase.build import bulk
structure = bulk("Al", cubic=True)
stk.analyse.get_adaptive_cna_descriptors(structure)
stk.plot3d(structure)
```
## Features
### Analysis
* `stk.analyse.get_neighbors()`
* `stk.analyse.get_neighborhood()`
* `stk.analyse.get_equivalent_atoms()`
* `stk.analyse.get_steinhardt_parameters()`
* `stk.analyse.get_centro_symmetry_descriptors()`
* `stk.analyse.get_diamond_structure_descriptors()`
* `stk.analyse.get_adaptive_cna_descriptors()`
* `stk.analyse.get_voronoi_volumes()`
* `stk.analyse.find_solids()`
* `stk.analyse.get_mean_positions()`
* `stk.analyse.get_average_of_unique_labels()`
* `stk.analyse.get_interstitials()`
* `stk.analyse.get_layers()`
* `stk.analyse.get_voronoi_vertices()`
* `stk.analyse.get_voronoi_neighbors()`
* `stk.analyse.get_delaunay_neighbors()`
* `stk.analyse.get_cluster_positions()`
* `stk.analyse.get_strain()`
### Build
* `stk.build.get_grainboundary_info()`
* `stk.build.grainboundary()`
* `stk.build.high_index_surface()`
* `stk.build.get_high_index_surface_info()`
* `stk.build.sqs_structures()`
* `stk.build.pyxtal()`
* `stk.build.B2()`
* `stk.build.C14()`
* `stk.build.C15()`
* `stk.build.C36()`
* `stk.build.D03()`
### Visualize
* `stk.visualize.plot3d()`
### Common
* `stk.common.ase_to_pymatgen()`
* `stk.common.pymatgen_to_ase()`
* `stk.common.pymatgen_read_from_file()`
* `stk.common.ase_to_pyscal()`
* `stk.common.apply_strain()`
* `stk.common.center_coordinates_in_unit_cell()`
* `stk.common.get_extended_positions()`
* `stk.common.get_vertical_length()`
* `stk.common.get_wrapped_coordinates()`
* `stk.common.select_index()`
Raw data
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"description": "# structuretoolkit \n\n[](https://github.com/pyiron/structuretoolkit/actions/workflows/unittests.yml)\n[](https://coveralls.io/github/pyiron/structuretoolkit?branch=main)\n\nOriginally developed as part of the `pyiron_atomistics` module the `structuretoolkit` was release as standalone library\nfor analysing, building and visualising atomistic structures. Internally it uses the `ase.atoms.Atoms` class to \nrepresent atomistic structures in python. The `structuretoolkit` is integrated inside `pyiron_atomistics`.\n\n## Disclaimer \nThe `structuretoolkit` is currently under development. \n\n## Example\n\n```python\nimport structuretoolkit as stk\nfrom ase.build import bulk\n\nstructure = bulk(\"Al\", cubic=True)\nstk.analyse.get_adaptive_cna_descriptors(structure)\nstk.plot3d(structure)\n```\n\n## Features \n### Analysis\n* `stk.analyse.get_neighbors()`\n* `stk.analyse.get_neighborhood()`\n* `stk.analyse.get_equivalent_atoms()`\n* `stk.analyse.get_steinhardt_parameters()`\n* `stk.analyse.get_centro_symmetry_descriptors()` \n* `stk.analyse.get_diamond_structure_descriptors()` \n* `stk.analyse.get_adaptive_cna_descriptors()` \n* `stk.analyse.get_voronoi_volumes()` \n* `stk.analyse.find_solids()`\n* `stk.analyse.get_mean_positions()`\n* `stk.analyse.get_average_of_unique_labels()`\n* `stk.analyse.get_interstitials()`\n* `stk.analyse.get_layers()`\n* `stk.analyse.get_voronoi_vertices()`\n* `stk.analyse.get_voronoi_neighbors()`\n* `stk.analyse.get_delaunay_neighbors()`\n* `stk.analyse.get_cluster_positions()`\n* `stk.analyse.get_strain()`\n\n### Build\n* `stk.build.get_grainboundary_info()`\n* `stk.build.grainboundary()`\n* `stk.build.high_index_surface()`\n* `stk.build.get_high_index_surface_info()`\n* `stk.build.sqs_structures()`\n* `stk.build.pyxtal()`\n* `stk.build.B2()`\n* `stk.build.C14()`\n* `stk.build.C15()`\n* `stk.build.C36()`\n* `stk.build.D03()`\n\n### Visualize \n* `stk.visualize.plot3d()`\n\n### Common \n* `stk.common.ase_to_pymatgen()`\n* `stk.common.pymatgen_to_ase()`\n* `stk.common.pymatgen_read_from_file()`\n* `stk.common.ase_to_pyscal()`\n* `stk.common.apply_strain()`\n* `stk.common.center_coordinates_in_unit_cell()`\n* `stk.common.get_extended_positions()`\n* `stk.common.get_vertical_length()`\n* `stk.common.get_wrapped_coordinates()`\n* `stk.common.select_index()`\n",
"bugtrack_url": null,
"license": "BSD 3-Clause License Copyright (c) 2018, Max-Planck-Institut f\u00fcr Eisenforschung GmbH - Computational Materials Design (CM) Department 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. ",
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