imce 1.0.0

A simple framework for molecular Monte Carlo sampling with uncertainty quantification

imce

Small Python based code for ab initio molecular simulations (using Monte Carlo) using modified sampling criteria (derived from computed spectra uncertainty in the molecular structure). See the following publication for further details: [DOI here]

Installation and Requirements:

Install XTB and STD2 as the required backends (see their respective manuals). On a M2 Macbook, STD2 is compiled with the following flags:

LDFLAGS="-L/opt/homebrew/opt/openblas/lib" CPPFLAGS="-I/opt/homebrew/opt/openblas/include" FC=gfortran-14 CC=gcc-14 meson setup _build -Dla_backend=openblas --wipe

The package can be installed locally with

pip install .

or (with additional packages for development)

pip install '.[dev]'

Usage:

The framework can be accessed as a Python module:

#!/usr/bin/env python3

import imce
from imce.utility import xyz_to_if, if_to_xyz

xtb = imce.xtb_std2_itrf(['ENERGY', 'UVVIS'])  

settings = imce.settings(seed = 0, windows = [[1.5, 8.0]], itrf = xtb, unit = 'eV', convolution_factor = 0.25)

mol = xyz_to_if('dfhbi.xyz')

simbox = imce.simbox(settings, '_uq_02_short.hdf5', mol)
simbox.init() 

sim = imce.uqmc(simbox, steps = 250, delta = 0.01875, sc = 0.2, method = 'UVVIS').run()

Then script is the run on the TU BS ThC cluster using the following command:

tcsub -q s -a generic imce_jobfile.py

Contributing:

Contributions require signature of the commit, acknowledging the following statement:

Developer Certificate of Origin
Version 1.1

Copyright (C) 2004, 2006 The Linux Foundation and its contributors.

Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.


Developer's Certificate of Origin 1.1

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