EZAIMD

Command line tool that allows the user to easly run ab initio molecular dynamics (AIMD) interfacing with the Gaussian16. quantum chemical package.

Configuration

EZAIMD requires the use of a configuration file, which must be named config.yaml, in the root directory of a simulation. This configuration is used to generate input for the quantum chemical package Gaussian16. An example configuration is given bellow:

config.yaml:

---
mem: "140GB"
cpu: "0-47"
gpu: ~
checkpoint: "output.chk"
key_words: "#p WB97XD/Def2tzvpp SCF=XQC force"
title: "single point"
charge: 0
multiplicity: 1

NOTE: For a successful simulation, the force keyword is REQUIRED!

Setting Up A Simulation

A simulation requires two items, the configuration and a valid gaussian16 output file. Where a valid output file will contain molecular coordinates in standard orientation. If multiply coordinates are valid in an output file, the last set of coordinates will be used. EZAIMD will through an error when no atomic information can be read.

Once the requirements have been met, one can start a default settings simulation with the following command:

EZAIMD [Gaussian16 outputfile]

This will begin a simulation with:

Time step: 1fs

Number of steps: 10000

Options

A number of options are available to the user.

--freeze: freeze the requested atoms during the simulaiton.

Example

--freeze 1-10,90-100 will freeze atoms 1-10 and 90-100.

--time-step: alter the time step of the simulation, takes values in femtoseconds.

Example

--time-step 0.1 change the timestep form the defualt, 1fs, to 0.1fs.

--num-steps: alter the number of simulation steps. Requires interger values.

Example

--num-steps 50000 change the number of steps from the defualt, 10000, to 50000.

--restart: restart a simulation from save.json. Take no arguments.

Example

--restart will restart a simulaiton form the save.json file generated during the simulation.

Putting It All Together

As an example, to run a simulaiton with a time step of 0.5fs for 10000 steps, and hold atoms 1-4,6-10,12-25 fixed, the following command may be used:

EZAIMD [Gaussian16 output] --time-step 0.5 --freeze 1-4,6-10,12-25

If the above simulation fails to complete in the alloted time, one can restart this simulation as follows:

EZAIMD [Gaussian16 output] --restart