Electronic Structure Group

General interests of the group are understanding the electronic structure of materials using density functional theory. Current interests include charge transfer excitations in donor acceptor complexes (organic photovolatics), linear and non linear polarizabilities of molecules.

Dr. Perla Balbuena visits us!

Dr. Perla Balbuena from Texas A&M in College Station, visited the physics department Friday April 4, she gave a talk in the physics department seminar.
Her talk was titled: "Modeling solid-electrolytes in intefacial reactions relevant to Li-ion batteries".

Plotting wave functions using Jmol

In order to plot the Wavefunction files that NRLMOL genertates, you must do the following steps:

Using the NRLMOL repository

In order to obtain a copy of NRLMOL from the repository you must follow this instructions:

How to mount a remote filesystem

As stated earlier this applies to Linux users, if you use Windows, you can log into quantum adn follow this tutorial from there.

sshfs will mount a remote file system to a directory on your local machine, this wall you don't need to log in to that machine and you local machine "sees" you remote files as local.

Tags:

How to setup passwordless ssh

This article will explain a way to connect to remote machines without a password.

Note to Windows users: Since this applies to Linux machines you will have to log in with putty to quantum, and set up the passowordless ssh to remote machines from there. This may seem impractical, but it's actually a required step for sshfs (to be covered in the next article).

Using the Stampede cluster

In order to submit jobs in the Stampede cluster at the Texas Advanced Computer Center, you must compile the code there.
In the Makefile:
Make sure that you use the mpif90 compiler.
Uncomment the TACC section in the linking options.
There's no need to load the mkl and/or scalapack module (like in the Lonestar cluster), here they are loaded automatically.
Submitting Jobs
This cluster uses the SLURM batch system, the commands are a little different.
Here is a sample job script from the TACC website:

Sparcity of Hamiltonian and overlap matrices

We are currently running tests to implement Scalapack, and are jotting down the percentage of zeros in the test system (a zero is considered whe its < 1e-8), the test system is Sc3N@C80-Phtalocyanine.
For the Hamiltonian matrix: out of 11117970 upper triangular elements, 5009259 correspond to zeros (45%)
For the overlap matrix 5384683 are zeros (48%)

How to run a job with less processors than a full node in Hopper

The Hopper system at NERSC has 24 processors per node, usually we just submit jobs using full node usage for example:

#PBS -q regular
#PBS -l mppwidth=256
#PBS -l walltime=24:00:00
#PBS -N 256_job
#PBS -e $PBS_JOBID.err
#PBS -o $PBS_JOBID.out
#PBS -V
cd $PBS_O_WORKDIR
echo "Changing to workdir $PBS_O_WORKDIR"
echo "listing workdir contents"
ls -ltr
aprun -n 256 ./cluster > log.txt

More basis testing

Here is a more complete set of basis testing using different basis sets.

Note: Whenever there is a zero in the NRLMOL results, it means that the basis for that atom was not available at the time.

Click here.

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