Simulation Tools

Simulation Tools#

Atomistic simulation environment (ASE)#

ASE is a Python based simulation environment that can be used to manage/create/control your simulations on multiple standard simulation softwares. We are going to cover some use cases of ASE. We will use it through the interactive Python environment.

Create an ASE environment on Adroit using conda

Execute the following commands

#Load the anaconda module
module load anaconda3/2024.2

#Create a conda environment ASE
conda create --name ase python=3.8 ase pandas matplotlib --channel conda-forge

#To check the environment execute the following
conda activate ase

#You should see a small **(ase)** text at the start of your command line

conda install ase-notebook --channel conda-forge

LAMMPS#

Typical input files required (The names can be changed)#

  • in.lammps: Input file. This file has all the parameters controlling the simulations (e.g. Thermostat, Barostate, Ensemble)

  • geom.xyz: (optional) Geometry file. This file describes the coordinates of your simulation system. Alternatively, you can also define your system geometry in the input file.

  • potential file: (optional) A file defining the MD potential that you are using.

LAMMPS example script#

Installing LAMMPS

#!bin/bash

VERSION=17Apr2024
wget https://github.com/lammps/lammps/archive/refs/tags/patch_${VERSION}.tar.gz
tar zvxf patch_${VERSION}.tar.gz
cd lammps-patch_${VERSION}
mkdir build && cd build

# include the modules below in your Slurm scipt
module purge
module load intel/19.1.1.217 intel-mpi/intel/2019.7

Making with cmake#

Adriot

cmake3 \
-D CMAKE_INSTALL_PREFIX=$HOME/.local \
-D LAMMPS_MACHINE=adroit \ 
-D CMAKE_BUILD_TYPE=Release \
-D CMAKE_CXX_COMPILER=icpc \
-D CMAKE_CXX_FLAGS_RELEASE="-Ofast -xHost -DNDEBUG" \
-D CMAKE_Fortran_COMPILER=/opt/intel/compilers_and_libraries_2020.1.217/linux/bin/intel64/ifort \
-D BUILD_OMP=yes \
-D BUILD_MPI=yes \
-D PKG_KSPACE=yes -D FFT=MKL -D FFT_SINGLE=no \
-D PKG_OPENMP=yes \
-D PKG_MOLECULE=yes \
-D PKG_RIGID=yes \
-D PKG_REAXFF=yes\
-D ENABLE_TESTING=yes ../cmake

Della

cmake3 \
-D CMAKE_INSTALL_PREFIX=$HOME/.local \
-D LAMMPS_MACHINE=della \
-D CMAKE_BUILD_TYPE=Release \
-D CMAKE_CXX_COMPILER=icpc \
-D CMAKE_CXX_FLAGS_RELEASE="-Ofast -xHost -DNDEBUG" \
-D CMAKE_Fortran_COMPILER=/opt/intel/compilers_and_libraries_2020.1.217/linux/bin/intel64/ifort \
-D BUILD_OMP=yes \
-D BUILD_MPI=yes \
-D PKG_KSPACE=yes -D FFT=MKL -D FFT_SINGLE=no \
-D PKG_OPENMP=yes \
-D PKG_MOLECULE=yes \
-D PKG_RIGID=yes \
-D PKG_REAXFF=yes\
-D ENABLE_TESTING=yes ../cmake

Finish with compiling the executable for lammps

make -j 10
#make test
make install

Once this has been compiled, execute ls and you will find a file named lmps_adriot or lmps_della in the same directory.

Move that file into a folder in which you store your executables. Normally, I would recommend storing it in /home/<NET-ID>/.local/bin, since it is already in $PATH.

However, we will try to use a LAMMPS executable that has been already compiled that can be found on canvas.

Use the following job submission script to submit a LAMMPS job

#!/bin/bash
#SBATCH --job-name=lj-melt       # create a short name for your job
#SBATCH --nodes=1                # node count
#SBATCH --ntasks=4               # total number of tasks across all nodes
#SBATCH --cpus-per-task=1        # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --mem-per-cpu=1G         # memory per cpu-core (4G is default)
#SBATCH --time=00:05:00          # total run time limit (HH:MM:SS)
#SBATCH --mail-type=begin        # send email when job begins
#SBATCH --mail-type=end          # send email when job ends
#SBATCH --mail-user=<YourNetID>@princeton.edu

module purge
module load intel/19.1.1.217 intel-mpi/intel/2019.7
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

# Argument as such: srun [executable location] [mode (-in)] [input file (.melt, .lammps)]
# Change the executable location to where you store your compiled lammps file.
srun /home/al9001/.local/bin/lmp_adroit -in in.melt

The input file can be copied from below

units           lj
atom_style      atomic

lattice         fcc 0.8442
region          box block 0 30 0 30 0 30
create_box      1 box
create_atoms    1 box
mass            1 1.0

velocity        all create 1.0 87287

pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0 2.5

neighbor        0.3 bin
neigh_modify    every 20 delay 0 check no

fix             1 all nve
fix             2 all langevin 1.0 1.0 1.0 48279

timestep        0.005

thermo          5000
run             10000

OVITO#

OVITO is an easy to use visualization software that can also be used to convert different geometry file formats. You can download and install the free version locally on your computer for visualization.

PACKMOL#

PACKMOL is a tool to generate initial MD configurations for molecules. Please download it using the link with wget in your home folder (/home/Princeton_ID/).

Steps to find download link:

  1. Click on given link

  2. Click on “[LATEST RELEASE]”. This will bring you to a page on Github.

  3. Over the hyperlink with the text .tar.gz, right click and select copy link.

I will download the most recent version of packmol with this command with the url from the steps above.

wget https://github.com/m3g/packmol/archive/refs/tags/v20.14.4+docs1.tar.gz

The download file should be renamed into “packmol.tar.gz”

Unzip this file using the following command

tar -xf packmol.tar.gz

Change the directory to Packmol and compile it using the command

make

This would produce a file called packmol, you can then move this into your ~/.local/bin folder.

Also download the examples.zip file from the website and upload it to your home folder (or, use wget). Unzip it using the following command

unzip examples.zip

Change the directory to examples folder and execute following command to generate an example geometry.

# Remember that it is "<" not ">". If you use ">" in your command, your input file will be wiped clean and you will have to re-enter your inputs.
/location_to_packmol/packmol < mixture.inp

VASP#

Some basics#

Files used to run VASP calculations

  • INCAR: This file describes the input parameters required for different calculations (For example: A molecule will have different parameters than a crystal)

  • KPOINTS: Description of reciprocal space

  • POSCAR: Define the geometry of your system

  • POTCAR: Concatenated pseudopotentials for elements of your system

Running VASP on Adroit/Della#

We will try to use a VASP executable that has been already compiled because VASP requires a license.

Use the following job submission script to submit a VASP job

#!/bin/bash
#SBATCH --job-name=vasp          # create a short name for your job
#SBATCH --nodes=1                # node count
#SBATCH --ntasks-per-node=8      # total number of tasks per node
#SBATCH --cpus-per-task=2        # cpu-cores per task (>1 if multi-threaded tasks)
#SBATCH --mem-per-cpu=4G         # memory per cpu-core (4G is default)
#SBATCH --time=00:01:00          # total run time limit (HH:MM:SS)
#SBATCH --mail-type=begin        # send email when job begins
#SBATCH --mail-type=end          # send email when job ends
#SBATCH --mail-user=<YourNetID>@princeton.edu

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
export PATH=$PATH:/home/al9001/software/vasp.6.2.1/bin/

module purge
module load intel/2021.1.2 intel-mpi/intel/2021.1.1

srun vasp_std
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