BLaSA - Bond Lattice Sampling and Analytical Approximation

©️ TD Swinburne 2020 MIT License swinburne@cinam.univ-mrs.fr

Execution and analysis of bond lattice dynamics. When using this code, please cite

Anharmonic free energy of lattice vibrations in fcc crystals from a mean field bond
Accepted for publication in PRB Rapid Communications, August 2020 Thomas D Swinburne, Jan Janssen, Mira Todorova, Gideon Simpson, Petr Plechac, Mitchell Luskin and Jörg Neugebauer

Setting the parameters

• All parameters are in input.json. Default parameters are those used in the above publication.

• Energy units are electron volts, length units are Angstrom.

• dump_folder : output data will be stored in run/dump_folder, which will be created if required

• workers_per_value : number of workers assigned to each parameter value. Must factorize total number of cores

• md -> bins : number of histogram bins

• md -> n : supercell has n^3 unit cells

• md -> therm, steps : number of timesteps to thermalize and sample

• potential -> D0, a0, AL : Morse potential V(r) = D0 * exp(-AL*(r-a0))

• potential -> r_min, r_max : limits for histogram

• am_array: list of strains to sample. am=0.01 is 1% tensile strain

• t_array: list of temperatures

• RT_array : list of transverse strength ratios to sample.

• JointHist : 0/1. Turns on recording of joint histograms to investigate bond-bond correlations. Returns three bins*bins arrays.

Cloud hosted analysis notebooks

• This repository is hosted online using binder -
• Due to the CPU hour restrictions of this service we do not recommend generating high quality reference data online, only running the analysis notebooks

Automated data generation and analysis with Snakemake (recommended)

• Requires a working conda package manager
• Install Snakemake workflow manager

conda install -c bioconda -c conda-forge snakemake

• Run calculations with

snakemake --use-conda --cores 10

where --cores is the total number of CPUs. This must be an integer multiple of workers_per_value

Manual data generation and analysis

• Instructions can be found here