Topics

1

General Questions and Answers / Optimize Geometry

« on: August 14, 2016, 12:13 »

Hello, I am doing a very basic geometry optimization, but I can't seem to get results. The output nc looks exactly like the input configuration.

I repeated the molecule and applied a conventional cell transform. Then, I added a calculator and a Optimize Geometry block. I set the Calculator to DFT, with  Morck-packhorst grid, Kpt Sampling 6x2x2, Energy cutoff 100 Ry, Exchange correlation LDA.
I set for the Optimize Geometry Force less than 0.001 ev/A, Stress less than 0.001 ev/A cubed. I unticked Constrain Cell.

Any suggestions would be appreciated, thanks. Attached are the files

2

General Questions and Answers / Calcite and Water

« on: June 13, 2016, 12:04 »

Hello,
    Sorry to post a new thread, but I think the older thread was locked. I am trying to find the adsorption energy for calcite and water with some substitutions. I firstly want to optimize the water with calcite surface. I have tried to hold the water rigid and calcite fixed, and vice versa, and tried to hold them both rigid but nothing is happening.  If you can take a look at the attached, I'd appreciate it. Thanks!

3

General Questions and Answers / Liquids

« on: May 24, 2016, 03:53 »

Hello, I would like to replicate the results of http://pubs.acs.org/doi/abs/10.1021/jp411151u
They used Quantum Espresso and some other pieces of sofware to find the adsorption energy of calcite in proximity to water, and the the free energy of solvation for Mg 2+ and SO4 2- substituted in calcite in proximity to water.
I would like to know if ATK can do these calculations?

To find the energy of adsorption, I want to find a reasonable example of an initial configuration of water molecules close to a calcite surface. Classical molecular dynamics should give me such a configuration of lowest energy.  How do I build water and how do I run MD for the water near the calcite?

Can ATK then calculate:
 Total energy of calcite with n adsorbed water molecules
Total energy of calcite in vacuum
Number of adsorbed water molecules
Total energy of isolated water molecule


To find the free energy of adsorption, how do I build Mg 2+ and SO4 2-  and how do I substitute one Ca2+ ion with an Mg2+ ion? And how do I substitute one CO3- ion with an SO42- ion? And then can ATK calculate the energies?

Thank you very much

4

General Questions and Answers / Embedding in Amorphous Structures

« on: March 2, 2016, 18:50 »

Hello,
     I was able to follow the tutorial on generating amorphous structures from cristobalite. I would like now to embed some particles into the material, particularly Ag, and vary the concentration of those particles. If anyone has any suggestions, I would really appreciate it.
Thanks!