Skip to main content

Ab-Initio Molecular Dynamics Potential Development

Project description

All issues and contributions should be done on Gitlab. Github is used only as a mirror for visibility

DFTFIT

DFTFIT is a python code that used Ab Initio data from DFT calculations such as VASP, Quantum Espresso, and Siesta to develop molecular dynamic potentials. Our package differs from other similar codes in that we leverage LAMMPS as a calculator enabling a wide variety of potentials. The potentials include custom python functions and a wide variety or three-body interactions including the Tersoff, Stillinger-Weber, Gao-Weber, Vashishta, and COMB Potentials. All of which can be combined to have for example a Buckingham + Coulomb + ZBL potential. We also have an extensive set of multi-objective and single-objective optimizersthat can evaluate a potential for many properties including energy, forces, stress, lattice constants, elastic constants, bulk modulus, and shear modulus.

In general three things are required from the user.

  • Ab-Initio Training Data includes VASP, Siesta, and Quantum Espresso Calculations. Additionally the user may supply measured properties such as lattice constants, elastic constants, bulk modulus, and shear modulus.
  • configuration: specifies optimization algorithm and number of steps, sqlite database to store results, and MD calculator to use.
  • Potential among a rich set of two and three body potentials. Including a custom python function.
Latest Release latest release
Package Status status
License license
Build Status gitlab pipeline status
Documentation readthedocs documentation

Presentations:

Potentials

Any combination of the following potentials is a valid potential in DFTFIT.

Two-Body Potentials

  • custom python function
  • ZBL
  • Buckingham
  • Beck
  • coulombic interaction
  • Lennard Jones

Three-Body Potentials

  • Tersoff
  • Stillinger Weber
  • Gao Weber
  • Vashishta
  • COMB/COMB3

Measured Properties

  • energy
  • stress
  • forces
  • lattice constants (lengths)
  • elastic constants (voigt)
  • bulk modulus
  • shear modulus

Algorithm

We use generalized least squares method for finding the optimal parameters for a proposed potential. DFTFIT integrates with existing MD software as a potential calculator. Currently only LAMMPS is supported. This means the user has the freedom to use any of the potentials available in LAMMPS.

Our algorithm follows a highly cited publication that proposes a method for determining a new potential for Silicon using the force matching of DFT calcultions.

Optimization Equation

Parameters

  • n_c: number of system configurations
  • N number of atoms in each configuration
  • α, β: tensor with 3D dimensions [x, y, z]
  • cl: classical results from molecular dynamics potential
  • ai: ab initio results from dft simulation
  • w_f, w_s, w_e: weights to assign respectively for force, stress, energy
  • F, S, E: force, stress, and energy respectively.

Dependencies

Installation

For pypi installation. Note that installation of lammps-cython may fail and is required. You will need to install LAMMPS as documented here. You may have to do pip install numpy cython.

pip install dftfit

For conda installation

conda install -c costrouc -c matsci -c conda-forge dftfit

For docker installation

docker pull costrouc/dftfit

Documentation

The official documentation is hosted on readthedocs.org: https://dftfit.readthedocs.io/en/latest/

Running

DFTFIT provides a command line interface. Of course the package can be used as a standard python package.

Tutorial and Documentation

Contributing

All contributions, bug reports, bug fixes, documentation improvements, enhancements and ideas are welcome. These should be submitted at the Gitlab repository. Github is only used for visibility.

License

MIT

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

dftfit-0.4.11.tar.gz (41.3 kB view details)

Uploaded Source

Built Distribution

dftfit-0.4.11-py3-none-any.whl (52.3 kB view details)

Uploaded Python 3

File details

Details for the file dftfit-0.4.11.tar.gz.

File metadata

  • Download URL: dftfit-0.4.11.tar.gz
  • Upload date:
  • Size: 41.3 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.11.0 pkginfo/1.4.2 requests/2.19.1 setuptools/39.2.0 requests-toolbelt/0.8.0 tqdm/4.24.0 CPython/3.6.6

File hashes

Hashes for dftfit-0.4.11.tar.gz
Algorithm Hash digest
SHA256 c6e36a793f9f94746bb8a04fb8316404aeacfa918704de07b15e1b4b8b62242d
MD5 ded9ca032a13c98c922a7612a87ef5e4
BLAKE2b-256 4dbf8baeb44d7d318c27d8b4d89608d6f17921a6c4b979f00592cc8746a3ebbe

See more details on using hashes here.

File details

Details for the file dftfit-0.4.11-py3-none-any.whl.

File metadata

  • Download URL: dftfit-0.4.11-py3-none-any.whl
  • Upload date:
  • Size: 52.3 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/1.11.0 pkginfo/1.4.2 requests/2.19.1 setuptools/39.2.0 requests-toolbelt/0.8.0 tqdm/4.24.0 CPython/3.6.6

File hashes

Hashes for dftfit-0.4.11-py3-none-any.whl
Algorithm Hash digest
SHA256 eacd3e2936c2ae3d2b378433dd2d640b4e9e40d51c0c06ffdbba89173f3de759
MD5 6e072c88b839a48370a25d880b658076
BLAKE2b-256 67922a97ec459d9f1d5b5883f9a572f3e890d780bf1c057743c92fb54ee8c752

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page