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QuantumWise

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What is QuantumWise?

QuantumWise is a commercial software package for atomic-scale modeling of nanostructures, fully supported and delivered in an easy-to-use interface along with Python input scripting, tailored from state-of-the-art methods. The package contains a graphical user interface so-called Virtual NanoLab (VNL) and Atomistix ToolKit (ATK) which is a general-purpose atomic-scale modeling platform that combines a wide range of methods and models to investigate nanostructured materials.

Some features of the software are:

  • Graphical user interface: Virtual NanoLab (VNL) to build geometries and set up calculations
  • Geometry optimization
  • Electronic structure and transport problems
  • Compute electrical, optical, mechanical properties of nanostructures and materials
  • Study Phonons and thermal properties
  • Noncollinear magnetism, spintronics
  • Surface Science, complex interfaces
  • Perform molecular dynamics calculations
  • Investigate classical empirical potentials
  • VNL supports creating inputs for VASP, LAMMPS, ABINIT, QuantumEspresso and, read their output and analize
  • ...

To know more about its features, please visit the page Feature List.

Basic Usage

QuantumWise environment can be set with the following module command:

module load quantumwise

VNL GUI can be opened as:

vnl &

A small job can be run as serial by using python based interpreter atkpython as:

atkpython input.py

However, we strongly recommend to use batch script to run jobs on compute nodes. There one can submit jobs on both single and multiple nodes.

Submitting a job to SGE

A parallel job can be submitted on multiple nodes with script as:

#!/bin/csh

#$ -M netid@nd.edu       # Email address for job notification
#$ -m abe                # Send mail when job begins, ends and aborts
#$ -pe mpi-12 24         # Specify parallel environment and legal core size
#$ -q long               # Specify queue
#$ -N job_name           # Specify job name

module load mpich
module load quantumwise

echo "Job Started at:"
date

mpiexec -n $NSLOTS atkpython input.py

echo "Job Ended at:"
date

Notes on parallel runs:

  • Current ATK build is compatible with MPICH-based MPI runtime, e.g. MPICH or MVAPICH2 (but not OpenMPI).
  • Using multi-threading and MPI parallelization simultaneously, can have a negative impact on the parallel speedup. So, the multi-threading in the Intel MKL library can be controlled by setting up the following OpenMP enviroment:
export OMP_NUM_THREADS=2 (for example)
export OMP_DYNAMIC=FALSE

A serial job can be submitted on a single node with the script as:

#!/bin/csh

#$ -M netid@nd.edu       # Email address for job notification
#$ -m abe                # Send mail when job begins, ends and aborts
#$ -pe smp 1             # Specify parallel environment and legal core size
#$ -q long               # Specify queue
#$ -N job_name           # Specify job name

module load quantumwise

echo "Job Started at:"
date

atkpython input.py 

echo "Job Ended at:"
date

Tutorials

For beginners, a few examples, including job-scripts and instructions of how to run them, are available at /opt/crc/q/quantumwise/Tutorials. Please copy these files to your AFS space and run them following the instructions given in "README" file.

More tutorials can be found at QuantumWise official site VNL/ATK-tutorial.

License Information

  • Currently Prof. Suman Datta's research group purchased 3 masters and 32 slaves licenses for ATK.
  • Basic VNL GUI is not limited to license restrictions.

Further Information

QuantumWise User's Documentation

See the official website: QuantumWise