Messages

1

General Questions and Answers / Re: Optimize Geometry

« on: August 15, 2016, 23:06 »

Thanks a lot, Petr. I tried to fix that, and now I did get a trajectory with initial and final positions, but the positions are still exactly the same. What would you recommend? I am sure there is some silly error that I am not seeing. The files are attached

2

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

3

General Questions and Answers / Re: Calcite and Water

« on: June 15, 2016, 12:09 »

Thanks a lot! That's a big help.

4

General Questions and Answers / Re: Calcite and Water

« on: June 14, 2016, 12:30 »

Thanks a lot. I have a cif for calcite, and I cleaved it along 104.  I set the top vacuum at 10 A, the thickness at 15, and bottom vacuum 0. I selected some atoms in the center, held them fixed, and optimized the geometry. I did not get any NC file as an output, and when I opened the py in the Builder, it looked the same as before optimized.

If you could take a look at the attached, I'd appreciate it.

5

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!

6

General Questions and Answers / Re: Liquids

« on: June 2, 2016, 19:04 »

Thanks, I tried first rigid water with fixed calcite, and then I tried fixed water with fixed calcite. After running OptimizeGeometry, both ways are giving me the same thing in the Viewer--- which is that the program hasn't moved the water or calcite at all. It looks the same as when I dropped the water into the calcite window in the Builder. What could be wrong? Thanks

7

General Questions and Answers / Re: Liquids

« on: June 1, 2016, 09:21 »

Thanks,  I am trying to follow steps similar to http://docs.quantumwise.com/tutorials/geometry_optimization.html
However, I don't want the water to actually bond to the calcite surface but just to be close. How can I prevent the geometry optimization from bonding them?

8

General Questions and Answers / Re: Liquids

« on: May 30, 2016, 12:50 »

Thanks a lot, Jess. So now I have water and calcite 104 in my Builder stash. How would I now run the MD of water close to a calcite surface? Do I choose Interface?
Thanks

9

General Questions and Answers / Re: Liquids

« on: May 29, 2016, 11:38 »

Hello,
I'm trying to construct water as described in the tutorial you linked, but I am having trouble. I open the Editor, paste in the code, and then send to the Job Manager. It runs, but nothing but the log file and py file appear in the lab floor; where would the output appear such as mentioned in the query example? How can I add a water molecule to an interaction with another molecule?

10

General Questions and Answers / Re: Liquids

« on: May 25, 2016, 06:48 »

Thanks, that helps a lot!

11

General Questions and Answers / Re: Liquids

« on: May 24, 2016, 16:23 »

Thanks for your reply.
How do we construct the water? Do we simply add hydrogen and oxygen into the Builder-- how would we prevent it bonding with the other atoms?

12

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

13

General Questions and Answers / Re: Embedding in Amorphous Structures

« on: March 3, 2016, 10:44 »

Thanks a lot!

14

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!