[RMCProfile-users] 来自"朱敏" <minzhu at mail.sim.ac.cn>的邮件

[Nicholas Funnell]

Dear Min Zhu,

I think the short bonds may simply be due to a combination of not allowing the refinement to run long enough and the use of potentials on a highly-disordered structure. I can see in your starting model that you have many bond distances shorter than 1 A, prior to refinement. It could be that RMCProfile just needs a bit longer to push all of these atoms apart. 

I can also see that you are using potentials - what this will do is search for the atom pairs declared by each '>STRETCH' instruction within +/- 10% (in your case) of the distance you would like the pair to be restrained to. This will happen at the start of the RMC refinement and a .bonds file will be generated, containing all the bonded pairs - these will remain 'bonded' throughout the refinement. Similarly no atoms will become 'bonded' over the course of refinement - the .bonds file is a permanent connectivity list. Given that lots of your atom-atom distances are unphysical, it could be the case that the potentials are causing the refinement to get stuck - unable to move the atoms as freely as they need to. 

You'll want to revisit your current potentials, as you have some that will be fighting against each other - for example your second and third entries, concerning the Sb-Te distances. Search distances of 2.91 +/- 10% and 2.85 +/- 10% will identify duplicate atom pairs because of the overlap in distance.  

I would suggest removing the potentials (and deleting any existing .bonds files) and using RMCProfile to push the atoms apart more first (run for longer), then perhaps using potentials much later in a subsequent refinement to tidy up the structure a bit? Alternatively, you could use 'dwbuild' to generate your random starting model, using stricter closest approach constraints when placing the atoms initially.

I should note I have little experience modelling glassy materials, and these can be very tricky to deal with. I think Helen is going to post a follow-up message to this with some tips for dealing with amorphous materials in general.

Best wishes,
Nick



On 9 Jun 2015, at 10:20, 朱敏 <minzhu at mail.sim.ac.cn> wrote:

>  Hello, everyone!
> 
>       I use the "Random" command to build a random structure (Ge2Sb2Te5, Te 3000 atoms, Sb 1200 atoms, Ge 1200 atoms, atomic number density  0.0315 A). But I find a problem: After RMC simulation, the obtained structure contain bonds smaller than 1 A. But minimum-distances were set to 2.90 (Te-Te),  2.85 (Te-Sb), 2.60 (Te-Ge), 2.60 (Sb-Sb), 2.65 (Sb-Ge), 2.45 (Ge-Ge) Angstrom. And many atoms are not bonding with other atoms, as shown below (Ge red, Sb green, Te blue). What's more, the partial F(Q)'s are also not right.  The wrong bonds, such as Ge-Ge bonds and Ge-Sb bonds, are too much. 
> Can anybody help me to find the reasons? All the starting file has been attached.
> 
>          Thank you very much.
> 
>           Kind regards, 
>           Min Zhu
> 
> 
> 
> 
> 
> <Ge2Sb2Te5.png><RMC Simulation.png><Partical F(Q).png><Ge2Sb2Te5.zip>_______________________________________________
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----------------------------------------------------------------------
Nicholas Funnell
Post-Doctoral Research Associate (Goodwin Group)
Inorganic Chemistry Laboratory
University of Oxford
Phone: 01865 272698