Automated Forcefield Optimization Extension 0.10.2
Auto-FOX is a library for analyzing potential energy surfaces (PESs) and using the resulting PES descriptors for constructing forcefield parameters. Further details are provided in the documentation.
Currently implemented
This package is a work in progress; the following functionalities are currently implemented:
The MultiMolecule class, a class designed for handling and processing potential energy surfaces. (1)
A multi-XYZ reader. (2)
A radial and angular distribution generator (RDF & ADF). (3)
A root mean squared displacement generator (RMSD). (4)
A root mean squared fluctuation generator (RMSF). (5)
Tools for describing shell structures in, e.g., nanocrystals or dissolved solutes. (6)
A Monte Carlo forcefield parameter optimizer. (7)
Using Auto-FOX
An input file with some basic examples is provided in the FOX.examples directory.
An example MD trajectory of a CdSe quantum dot is included in the FOX.data directory.
The absolute path + filename of aforementioned trajectory can be retrieved as following:
>>> from FOX import example_xyzFurther examples and more detailed descriptions are available in the documentation.
Installation
Anaconda environments
While not a strictly required, it stronly recomended to use the virtual environments of Anaconda.
Anaconda comes with a built-in installer; more detailed installation instructions are available for a wide range of OSs.
See the Anaconda documentation.
Anaconda environments can be created, enabled and disabled by, respectively, typing:
Create environment: conda create -n FOX -c conda-forge python pip
Enable environment: conda activate FOX
Disable environment: conda deactivate
Installing Auto-FOX
If using Conda, enable the environment: conda activate FOX
Install Auto-FOX with PyPi: pip install auto-FOX --upgrade
Congratulations, Auto-FOX is now installed and ready for use!
Optional dependencies
The plotting of data produced by Auto-FOX requires Matplotlib. Matplotlib is distributed by both PyPi and Anaconda:
Anaconda: conda install --name FOX -y -c conda-forge matplotlib
PyPi: pip install matplotlib
Construction of the angular distribution function in parallel requires DASK.
Anaconda: conda install -name FOX -y -c conda-forge dask
RDKit is required for a number of .psf-related recipes.
Anaconda: conda install -name FOX -y -c conda-forge rdkit
PyPi: pip install rdkit
Release files for Auto-FOX 0.10.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| Auto-FOX-0.10.2.tar.gz | 23.1 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| Auto_FOX-0.10.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 47.3 MB
Release files / Auto-FOX-0.10.2.tar.gz
| Download URL | Auto-FOX-0.10.2.tar.gz |
|---|---|
| Size | 23.1 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
6765ce8fc44006c945874d9d685876c385c078b80c89df653c8bca7ccb242471
|
|
BLAKE2b-256 checksum How to use checksums |
80a7ad2ab6a6d47def844f80fa33d2ce795b593be678d2ffdf6a646a330d2915
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.9.13
|
Release files / Auto_FOX-0.10.2-py3-none-any.whl
| Download URL | Auto_FOX-0.10.2-py3-none-any.whl |
|---|---|
| Size | 24.1 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
49c8793fca75dae68e2b9e3b13d1a60849c967e50feddd0efa83291c3e326c26
|
|
BLAKE2b-256 checksum How to use checksums |
587bd6e948dccec4b4af666e2257e96bad8debca4e43027286b84402fb292cb3
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.9.13
|
