June 2014

We need a script for that

lbasurto's picture
Submitted by lbasurto on Thu, 06/05/2014 - 13:30

We need to write python or perl script that will generate a CLUSTER file for fragment analysis.

Building on what we already have, we could use the memebership files that we already use for DOS calculations in donor-acceptor systems.

These membership files are tied to the XMOL.DAT file for the complete structure. So, we can use them to create a CLUSTER file that will list the atoms according to the memebership files.

Any volunteers? I will offer you a glass of water if you do it.

Sparse representation

lbasurto's picture
Submitted by lbasurto on Thu, 06/12/2014 - 13:00

We have analyzed three big systems for sparse representation, the biggest one is the triad surrounded by water molecules that Carlos is working on:
It contains 666 atoms, the hamiltonian and overlapr matrices are 7792 X 7792 stored as an array of 30361528 elements. Of these only 800842 are non zero for the hamiltonian matrix and 930451 for the overlap matrix. The condition for sparse representation using the Yale format is satisfied.
The other system is just the triad
Atoms=207
N=6157
N_tot=18957403
HAM
Non Zero=1906717
OVL

Visit from Ulises

admin's picture
Submitted by admin on Sat, 06/21/2014 - 14:32

Our own remote reseach associate professor Dr. Jose Uilses Reveles is currently visiting us from Richmond VA.

In the photo is also included our summer project colaborator, CPS PhD student Henry Moncada.

Pictured from left to right
Henry, Dr. Zope, Shusil, Fatemeh, Dr. Baruah, Luis and Ulises