Construction Zone

Modules for generating nanoscale+ atomic scenes, primarily using pymatgen as generators with S/TEM image simulation in mind.

Full documentation can be found here: https://construction-zone.readthedocs.io/.

If you use Construction Zone in your own work, we kindly ask that you cite the following: Rangel DaCosta, Luis, & Scott, Mary. (2021). Construction Zone (v2021.08.04). Zenodo. https://doi.org/10.5281/zenodo.5161161

Installation

Construction Zone can be easily installed with pip:

pip install czone

We strongly recommend utilizing an environment manager such as Anaconda, and installing Construction Zone into your environment of choice.

To install Construction Zone into a clean environment with Anaconda, you could do the following:

conda create -n environment_name python=3.7
conda activate environment_name
pip install czone

In this example, we manually set the target Python version to v3.7. Construction Zone has been tested only for Python 3.7 and above; earlier versions may work but are not supported.

Stable versions of Construction Zone will be passed onto PyPi. To use the current, development version of Construction Zone, you can set up the Python package in development mode. Again, we recommend doing so with an environment manager.

An example development installation could be achieved by the following:

conda create -n environment_name python=3.7
conda activate environment_name
git clone https://github.com/lerandc/construction_zone.git 
cd construction_zone
python setup.py --develop

Development mode installations import Python packages directly from the source every time. You could freely edit the source code yourself, or just use the installation to pull fresh code from the development branch by running git pull in the repository directory.

Manual Coverage Summaray (LRD, 2 Feb. 2024):

We have begun writing unit tests for Construction Zone. A partial coverage summary can be found below. For more a more detailed coverage summary, and information about testing priorities and a testing road map, please look towards the `tests' folder. Once unit tests for the core modules have been completed, CZ will be updated on relevant installatio channels. Minor to major refactoring can be expected in certain areas, but we will aim to have miminal breaking API changes, where possible.

(x = total, + = partial (direct), - = partial (indirect), blank = none)

[ ] Generator \ | [ ] Amorphous Algorithms \ | [ ] Generator Core

[x] Molecule

[ ] Prefab \ | [ ] Prefab Core \ | [ ] Wulff

[ ] Scene

[ ] Surface \ | [ ] Adsorbate \ | [ ] Alpha shapes

[-] Transform \ | [ ] Post \ | [ ] Strain \ | [-] Transform Core

[ ] Util \ | [ ] Measure \ | [ ] Misc.

[ ] Viz

[+] Volume \ | [+] Algebraic \ | [ ] Volume Core \ | [ ] Voxel

Acknowledgment

We acknowledge support for the development of Construction Zone from the Toyota Research Institute. This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Advanced Scientific Computing Research, Department of Energy Computational Science Graduate Fellowship under Award Number DE-SC0021110.

This software was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.