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.
QuantumWise environment can be set with the following module command:
module load quantumwise
VNL GUI can be opened as:
A small job can be run as serial by using python based interpreter atkpython as:
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 email@example.com # 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 firstname.lastname@example.org # 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
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.
- 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.
See the official website: QuantumWise