- Ryther Anderson
- Yamil Colón
- Diego Gómez-Gualdrón
Our Topologically Based Crystal Constructor (ToBaCCo) was developed to rapidly produce molecular representations of porous crystals as crystallographic information (.cif) files, which can then be used for molecular simulation or for materials characterization.
ToBaCCo has been tested for Python 2.7 and Python 3.7. We recommend building a Python 2.7/3.7 environment using Anaconda. You will need the following packages:
- numpy
- networkx
- scipy
To set up a Python X.7 environment first install Anaconda. After installing Anaconda, run:
conda create --name my_tobacco python=X.7
where my_tobacco is the name of the environment (which can be changed to whatever you like) and X is 2 or 3. ToBaCCo will probably work with Python 3.Y, but has only been tested for 3.7 and 3.8. Next, load your new environment:
conda activate my_tobacco
(this command changes for Windows, see https://docs.anaconda.com/anaconda/user-guide/tasks/switch-environment/) Finally, install the above packages, thus:
conda install numpy
conda install networkx
conda install scipy
Once these are installed, you can clone or download the repository and start running ToBaCCo. Please note that only certain versions of these packages have been tested. Specifically, for Python 2.7 the tested versions are numpy=1.14.2, networkx=2.2, and scipy=1.1.0. For Python 3.7 the tested versions are numpy=1.19.1 and numpy=1.15.4, networkx=2.2 and networkx=2.5, and scipy=1.1.0, scipy=1.3.1, and scipy=1.5.2.
Execute the tobacco.py file to run ToBaCCo:
python tobacco.py
For more details on ToBaCCo inputs, outputs, and configuration see the ToBaCCo_manual.pdf included with the repository.
GNU General Public License (can be viewed in the LICENSE file included in this repository)