Numerical simulation of condensed matter or fluid systems, can be done at
several length scales.
We discuss three and provide examples of public domain
codes for electronic and atomic scale systems as well as a brief discussion of
fluid modeling. The two codes to be presented in detail are QUANTUMESPRESSO
for electronic properties and LAMMPS for molecular dynamics. Both are
installed on TAMNUN. Especially for the electronic scale there are many
alternatives, but these have been selected due to their public domain nature
and to the availability of good tutorial and example material as well as
local expertise and serendipity in obtaining help. Not to mention the codes
successful and staightforward implementation on distributed MPI machines
such as TAMNUN. For more information on TAMNUN, you can look at my links
from earlier in the course.
The following is a guide to general procedure for simulation with large public or private codes at any scale for TAMNUN users.
If possible look at the list of codes on TAMNUN
(or the computer you will use) which on TAMNUN can be found on the web
from within the firewall at:
Check out the literature for simulations of the same or similar materials.
Just like you compare a simple simulation with an analytic solution in some
limit it is good to compare your results from a published simulation of a
similar case. See which codes they used.
If you do not find overlap at this stage, you can either seek advice,
officially from the HPC consultant, unofficially I will help students
who have taken Computational physics in the future.
Select one or more of the codes on TAMNUN, codes, or if nothing
and you find a public domain code send a polite request to HPC@technion.ac.il
with the link to the download page. If its a public domain code that requires
registration register and send your user/password with the request, or
download and place in a folder on tx/aluf/t2 with full address. The systems people can lift things if you give the full path and its more efficient
than emailing enormous files.
If the code costs or has a limited license, check that it is suitable before
buying it. If someone else at the Technion has bought it, be in touch to get
but do not expect them to let you use code they bought, although I, for example,
will let people try out VASP for which I paid several thousand dollars but insist they pay for their own copy if its useful.
Once you have the code look for a source of demos/samples to run.
These can be used to check the installation if it is a new one, and
to teach you if its an old one.
There are many Computational Physics projects that include instructions
for codes -
and some of you will be adding to this collection. Not all are perfectly clear,
but the really bad ones (and there were not many) have not been listed.
Many codes do not include graphics. There are instructions in many ofthe projects mentioned in the links below to output electronic density
or atomistic configurations
in AViz, but other graphics is used for graphs of functions, e.g. gnuplot.
A few code use commercial
graphics provided by the students' research group, but I try to avoid this so everyone can use the webpages later on.
Let us start with a quick revision of condensed matter theory, and links
to some great earlier projects.