ramanishsingh / analysis_viscosity

Calcuate viscosity from HOOMD log files.

analysis_viscosity

This package calcuates viscosity from HOOMD log files. The main analysis code is taken from PyLat (https://github.com/MaginnGroup/PyLAT).

How to use this package

Run the parameters_main.py to calculate viscosty for the log files stored in ../simulation/{$i} folder (the relative path can be changed). Please check unit conversion in viscio.py (lines 100-115) and timestep (llog['timestep']). Default units are L:nm, E: kJ/mol, and Mass: au.

Quantities that should be logged

• Temperature
• All components of pressure
• lx, ly, and lz
• Timestep

Relevant papers

• https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b00066
• https://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00351
• https://pubs.acs.org/doi/pdf/10.1021/jp062885s