WatAnalysis

Introduction

This is a package for (parallel) analysis of water structures/dynamics at metal/water interfaces. Some codes here are developed based on MDAnalysis or pmda package.

Installation

This package (in particular the hydrogen bond functionality) requires a custom version of MDAnalysis to select specific interfacial regions. Install it before installing WatAnalysis:

git clone https://github.com/ChiahsinChu/mdanalysis.git -b devel-relprop
cd mdanalysis
pip install --upgrade package/
cd ..

To install WatAnalysis, clone the repository and run the following commands in the repository root:

git clone https://github.com/ChiahsinChu/WatAnalysis.git
cd WatAnalysis
pip install .

User Guide

1. waterstructure: water structure analysis

2. waterdynamics: water dynamics analysis

   This module is built on the basis of MDAnalysis.analysis.waterdynamics.

3. temp: instantaneous temperature of selected atoms

Workflow mode

Supported functions

• density profile: DensityAnalysis
• dipole angular distribution: AngularDistribution
• hydrogen bond: HydrogenBondAnalysis
• correlation function:
  • survivial probability: SurvivalProbability
  • flux correlation function: FluxCorrelationFunction
  • water reorientation: WaterReorientation

Developer Guide