lbasurto's blog

Installing libnxc

This covers how to install Libnxc, a library that contains Machine Learned functionals to be used in DFT codes developed by Marivi Fernandez and Sebastian Dick, available in github

In order to use the library, the libtorch library from Pytorch is needed, it can be obtained here

Neuralxc installation

In order to install neuralxc, a python virtual environment must be used. This ensures compatibility with the application and the versions of the python binary and other dependent applications (scikit-learn,pytorch,ase, etc). The virtual environment must be installed with python version 3.6 from the /usr/bin folder.
The command to create the virtual environment is:
virtualenv -p=/usr/bin/python3.6 virtual_env_name
where virtual_env_name is the name given to the virtual environment (a directory is created with that name).

Creating multiplots with Gnuplot

To create a multiplot using Gnuplot try this sample script, you can modify it to fit your needs.

Show output in browser

Do you want to see the output of NRLMOL in a browser when running calculations on a local machine?

Follow the instructions listed here.

Sparse representation

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
Non Zero=1906717

We need a script for that

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.

Sparsity 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 when its < 1e-8), the test system is Sc3N@C80-Phtalocyanine.
For the Hamiltonian matrix: out of 11,117,970 upper triangular elements, 5,009,259 correspond to zeros (45%)
For the overlap matrix 5,384,683 are zeros (48%)

Basis testing

We have conducted a test of running NRLMOL with different basis sets to comapre against Gaussian for a series of atoms, differences wher found, here are the energies using basis STO-3G.
We looked at Vanadium to account for the difference.
We tried refining the mesh, it did not work.
We compared the two basis sets used (the were the same).
So the difference in the calculation lies elsewhere.

Density Functional Theory video

I found this Youtube video on DFT.

Check it out:


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