https://github.com/andrewtarzia/spindry

Low-cost host-guest conformer generation
https://github.com/andrewtarzia/spindry

high-throughput host-guest materials-informatics monte-carlo porous-materials simulation

Last synced: about 2 months ago
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Low-cost host-guest conformer generation

• Host: GitHub
• URL: https://github.com/andrewtarzia/spindry
• Owner: andrewtarzia
• License: mit
• Created: 2021-03-31T10:24:57.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2024-02-29T12:29:32.000Z (10 months ago)
• Last Synced: 2024-10-12T11:47:19.604Z (2 months ago)
• Topics: high-throughput, host-guest, materials-informatics, monte-carlo, porous-materials, simulation
• Language: Python
• Homepage: https://spindry.readthedocs.io/en/latest/
• Size: 798 KB
• Stars: 3
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: readme.rst
  • License: LICENSE

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README

        
SpinDry

=======

:author: Andrew Tarzia

A Monte Carlo-based host-guest conformer generator using cheap and unphysical

potentials.

Please submit an issue with any questions or bugs!

``SpinDry`` uses the Monte-Carlo/molecule interface provided by my other code

``MCHammer`` (https://github.com/andrewtarzia/MCHammer)

Installation

------------

Install using pip:

.. code-block:: bash

  pip install spindry

Algorithm

---------

SpinDry implements a simple Metropolis Monte-Carlo algorithm to translate and

rotate the guest molecules.

All atom positions/bond lengths within the host and guest are kept rigid and

do not contribute to the potential energy.

The algorithm uses, by default, a simple Lennard-Jones nonbonded potential to

define the potential energy surface such that steric clashes are avoided. Atom

radii are taken from STREUSSEL ().

Custom potential functions can also be defined now -- see

``examples/custom_potential_function.py``.

The default MC algorithm is as follows:

For ``step`` in *N* steps:

    1. Define a translation of the guest by a random unit-vector and a random

    [-1, 1) step along the that vector.

    2. Define a rotation of the guest by a random [-1, 1) * ``rotation_step_size``

    angle and a random unit axis.

    3. Compute system potential ``U_nb``:

        ``U_nb`` is the nonbonded potential, defined by the Lennard-Jones

        potential:

            ``U_nb = sum_i,j (epsilon_nb * ((sigma / r_ij)^12 - (sigma / r_ij)^6))``,

            where ``epsilon_nb`` defines the strength of the potential,

            ``sigma`` defines the position where the potential becomes

            repulsive and ``r_ij`` is the pairwise distance between atoms

            ``i`` and ``j``.

    4. Accept or reject move:

        Accept if ``U_i`` < ``U_(i-1)`` or ``exp(-beta(U_i - U_(i-1))`` >

        ``R``, where ``R`` is a random number [0, 1) and ``beta`` is the

        inverse Boltzmann temperature.

        Reject otherwise.

    5. If ``num_conformers`` is met, quit.

Examples

--------

The workflow for a porous organic cage built using *stk*

() is shown in ``examples/`` for a single guest

and multiple guests.

The Spinner class yields a ``SupraMolecule`` conformer. Only conformers that

pass the MC conditions are yielded. The examples in ``examples`` show how to

access the structures of these conformers as ``.xyz`` files or `stk` molecules.

Contributors and Acknowledgements

---------------------------------

I developed this code as a post doc in the Jelfs research group at Imperial

College London (,

).

This code was reviewed and edited by: Lukas Turcani

()

License

-------

This project is licensed under the MIT license.