IonSolvR: Ion Solvation Repository

Downloading Individual IonSolvR records using wget

Instead of accessing individual trajectories from the Database page you can also use wget at the (linux) command line:

wget https://ionsolvr.newcastle.edu.au/[SOLVENT]/[SOLUTE]/[NSOLVENT]/[SOLVENT][SOLUTE][NSOLVENT].zip

For example, to look at a chloride ion in a solvent of 64 water molecules:

wget https://ionsolvr.newcastle.edu.au/water/Cl/64/waterCl64.zip

Downloading the whole (or sub) repository directly

The following wget script may be downloaded to loop over the entire repository or a subset of the repository.

It currently has three modes of use:

1. A test function to ensure downloads are working correctly:

./IonSolvRwget.sh test

will download a small trajectory that has 1 water molecule "in" 4 water molecules.

2. A generic three parameter function where you state the desired solvent, solute and number of solvent molecules. This takes the form:

./IonSolvRwget.sh [SOLVENT] [SOLUTE] [NSOLVENT]

As an example to download chloride in 64 water molecules you can use the following line:

./IonSolvRwget.sh water Cl 64

3. An all function that will download the entire repository. (Warning! Currently IonSolvR is > 1.5TB). To use this function, use the command:

./IonSolvRwget.sh all

4. A validation function that will download the timestep and coupling strength parameter validation data (~150GB). To use this function, use the command:

./IonSolvRwget.sh validation

5.To download a "Lite" version of a particular record (either the final geometry or final 1 ps of the molecular dynamics simulation)

wget https://ionsolvr.newcastle.edu.au/[SOLVENT]/[SOLUTE]/[NSOLVENT]/FINAL_run/md_opt.xyz

Or for just the final geometry

wget https://ionsolvr.newcastle.edu.au/[SOLVENT]/[SOLUTE]/[NSOLVENT]/FINAL_run/md_opt.gen

Analysing trajectory equilibration with velocity_checker.py

The following velocity_checker.py script may be downloaded to check the equilibration time of any specific trajectory.

It's usage is as follows:

velocity_checker.py [-h] [--verbose] [--savefig] [--saveas SAVEAS] [--histmax HISTMAX] [--histbins HISTBINS] [--traj_range TRAJ_RANGE] traj_file out_file

where the traj_file is a .xyz file containing element, x coordinates, y coordinates, z coordinates, x velocites, y velocites, z velocites information and the out_file contains the energy and temperature information over time. TRAJ_RANGE is the number of frames to include in this analysis (i.e. ps * 100). HISTBINS and HISTMAX are used for calculating the RMSD's.

For queries (or recommendations) please contact ionsolvr@newcastle.edu.au