[Openmd-users] Soham: OpenMD question on simulating gradient (with interdiffusion) coreshell NPs

[Dan Gezelter]

Soham,

That's an interesting problem.  I don't think we can create a gradient-composition NP using the builder programs without some modification, but there might be a (not very pretty) hack that would get you what you want.  If you create a sequence of increasing-radius particles, each with varying compositions, you could then use our md-solvator script.   md-solvator was intended to put particles or proteins in boxes of solvent by carving out solvent molecules that were within a fixed radius of any solute atom.   If you have a 100% Au particle of radius 5 treated as a solute, and a 90% Au particle as radius 10 treated as a solvent, then md-solvator might be able to combine the two in the way that you want.  If you repeat the process with larger "shells" you might be able to create a composition gradient.   Like I said, this isn't pretty, and I haven't tested it, but it just might do the job.

Let me know how it goes!

 --Dan Gezelter

> On Nov 3, 2014, at 9:49 AM, Soham Banerjee <sbanerjee23 at gmail.com> wrote:
> 
> Hello Dr. Gezelter, 
> 
> My name is Soham, a graduate student working for Simon Billinge at Columbia. I'd like to start by saying that I am very new to using OpenMD (and MD in general) but I've really enjoyed it using so far. The installation, documentation and website are fantastic, and even in the early stages I've had much more luck creating discrete nanoparticle models compared to RMC, DISCUS, and other more primitive brute force methods I've tried. Thank you for your efforts in developing this open MD platform. 
> 
> Without taking up too much of your time, I'd like to ask for some advice on generating some bimetallic (AgAuNPs) structural models with openMD. 
> 
> 1) I've used mostly nanoparticleBuilder now, but it seems that will take either a molFraction or shellRadius argument, but not both (which is exactly what I want to do!) We have PDFs, Pair Distribution Functions (real space transforms of high resolution scattering data, but you knew this) of alloyed AgAuNPs that have varying concentrations of each species. We predict (from TEM-EDX line scans) that the NPs have a 'gradient core-shell structure.' That is, for example at r=0 there is 100% Au, r=5: 90% Au and so on (or something along these lines). Is it possible to simulate this gradient structure with nanoparticleBuilder, or maybe I should try something else (zconstraints?). I've tried a few different things, such as making many layers of each component, but I keep running into the problem of not being able to adjust the mol fraction of each 'shell' as I move out from the center of the NP. I've refined some PDFs from the openMD simulated structures, but as anticipated, the pure coreshell or completely random alloying aren't fitting the bill when I refine this against the experimental PDFs.
> 
> I guess I only had one question, albeit a long one, for now! But, I feel the chances are solid that this is a simple task, I'm just not tackling it properly. You/your group has most certainly done this structural modeling with more interesting constraints (ie. http://www3.nd.edu/~gezelter/Research/images/cross_section_array_small.jpg, or your spontaneous alloying paper figure 5 with interdiffusion dependence). 
> 
> Thank you kindly for your time, I've really been enjoying the program over the last few days. Exporting the .xyz structural models allows me to render some pretty images, and coming from a world of .cif single unit cell structure files, visualizing a discrete NP in it's full glory has been awesome (and helpful). I think the PDF community could really benefit from an easy to use MD platform like this. Thanks again, and I hope you or perhaps some of your group members will bear with me if/when more questions come up (I already have some on the backburner about simulating internal/inhomogeneous strain in the NP). Apologies for the long e-mail!
> 
> Best,
> Soham
> -- 
> Soham Banerjee: Graduate MS-PhD Candidate
> Columbia University: APAM-MSE
> 500 West 120th Street
> New York, NY 10027
> Tel: 856-701-5361
> E-Mail: [sb3519 at columbia.edu]
>            [sbanerjee23 at gmail.com]



***********************************************
  J. Daniel Gezelter
  Associate Professor of Chemistry
  Department of Chemistry and Biochemistry
  251 Nieuwland Science Hall
  University of Notre Dame
  Notre Dame, IN 46556-5670

  phone:  +1 (574) 631-7595
  fax:    +1 (574) 631-6652
  e-mail: gezelter at nd.edu
  web:    http://www.nd.edu/~gezelter
************************************************