Atomic Blender - Cluster


(Blendphys) #1

Hi all. Here is my 3rd “Atomic Blender” addon. It’s name is: Atomic Blender - Cluster

The addon is already in the in contrib section (Preferences: Testing => Add Mesh). It should be in release 2.63.7 (r47085).

This addon creates a cluster, which is composed of atoms (balls) that are arranged in an ordered crystal lattice. The addon can be used to visualize some clusters from mathematics and physics. Pyramid and octahedron shaped but also spherical clusters can be chosen. There is also the possibility to load parabolic shaped clusters. The latter have been introduced to model e.g. atomic force microscopy (AFM) tips.

Here are some examples:




Note that the clusters are obtained by cutting a specific bulk lattice (e.g., bcc, hcp, etc.)!

Wiki

Tracker

What do you think? Comments?

Blendphys.

PS: I probably used this material: Gold


(Blendphys) #2

Hmm, no comments ? :eek:


(Meta-Androcto) #3

hi, just having a play with this now, cool stuff :slight_smile:


(Blendphys) #4

Thanks Meta-Androcto :cool:


(matali) #5

Hi,
What you do looks really great, but finding a purpose for most of the artist/architect here is not that easy. Starting to build a new community of chemistry researcher on blenderartist will take time :wink: But why not.
Maybe speak of your add-on on some chemistry forums to make them start use blender ?
Just my 2 cents, maybe we can use your add-on for art actually.
Cheers


(Blendphys) #6

I’ve already recognized that all Atomic Blender addons are somewhat restricted for Blender artists. However, there is some demand from scientists indeed, which I can best see via the log files of my private pages and from some comments of my colleagues.

Starting to build a new community of chemistry researcher on blenderartist will take time :wink:

Yes, true. But this is a start … . PS: Don’t forget us, the physicists … .


(Uncle Entity) #7

Those skin examples look, shall we say, blocky.

It can’t be too hard to distribute them evenly on the surface of a sphere – y’all physicists should be able to come up with an algorithm for that in like two seconds I would imagine…


(Blendphys) #8

Uncle Entity, as described in the Wiki, the clusters are produced from a cut, which depends on the cluster shape and which is applied to an atomic bulk lattice. If you use a sphere the size is given by its diameter. Under all these conditions you cannot do it differently. BTW: "to distribute them evenly on the surface means basically “destroying the lattice”.

However, I see what you mean: You want to have evenly distributed balls on a big sphere such that there are no ‘holes’ anymore.
On the other side: I find these clusters with ‘holes’ so fascinating since they allow precisely studying (visualizing) the different facets (e.g. (111), (001), (110)) of especially these spherical clusters.

The aim presenting the spheres above is to demonstrate the skin effect. You can certainly choose a skin value, which permits a closed shell cluster. You need to try out different values, mostly skin = 0.15 (small clusters) or 0.05 (large ones) is sufficiently small for having only 1 or 2 atomic skin layered clusters.


(Scrible) #9

FYI, AtomicBlender was mentioned in a reputable german computer magazine called c’t.
c’t 2012 Heft 12 page 49

Congrats!


(Blendphys) #10

Thanks Scrible. Is it an announcement? And: is it in the print version (I need to pay for the article)?


(Scrible) #11

Yes, it’s a printed version.
It’s just a short message about Blender 2.63 in general, mainly referencing the ability to use n-gons now. At the end they mention that many add-ons are available, such as Atomic Blender.

Though I just noticed that they made a mistake, confusing the export of .PDB files with .PDF :frowning: …if you want I could drop them an eMail; they might correct that in a following issue.

Maybe not so reputable. :o


(Blendphys) #12

Ah, nice.

Though I just noticed that they made a mistake, confusing the export of .PDB files with .PDF :frowning: …if you want I could drop them an eMail; they might correct that in a following issue.
Maybe not so reputable. :o

PDF? Okay, just send them an email … thanks.


(Blendphys) #13

Dear all.

Thanks to a Fortran code of one of my colleagues I could include icosahedron shaped clusters. Here are some clusters:



(Blendphys) #14

Dear all.

I just used the Atomic Blender ad-dons to create a Cover Inside Picture for our article in Advanced Materials. It nicely demonstrates that Blender is VERY useful to create artwork in Science:


(Nanochemist) #15

Hi Blendphys,

I am a new Blender User (trying to write a thesis in chemistry). I ve found atomic cluster amazing but as I am working on ternary nanocrystals, I was wondering if it was possible to have a cluster with different atoms size and colors (and how to achieve it ? as it seems that the cluster is only one object were I cannot seperate object)

Thanks


(Blendphys) #16

Hi Nanochemist.

I’m sorry for my late reply but I’m quite busy at the moment.

Thanks for your positive comments.

… but as I am working on ternary nanocrystals, I was wondering if it was possible to have a cluster with different atoms size and colors …

So far, one can only use one type of atom. If there are more than one type of atom, the number of possible configurations goes almost to infinity for large clusters. This is why it doesn’t make sense to introduce more than one type of atom. If there are several atom types, it depends on the user how these different atoms shall be positioned in a cluster. However …

… (and how to achieve it ? …

… in principle, one can create two clusters of same shape, structure and size (number of atoms), which differ in the atom type (e.g., Pt and Pd). Then, one deletes the atoms in one cluster, which are represented in the other one, and vice-versa. After this, one superimposes both structures. - All this asks for some manual (hard) hand work. :yes:
In fact, one has to …

… as it seems that the cluster is only one object were I cannot seperate object)

… work in the ‘Edit Mode’ and delete the specific vertices. Since you don’t know this I would highly suggest to learn something about:

  1. key words: Object Mode, Edit Mode, Blender
  2. key words: Dupliverts, Blender

    The latter key words can be used to find some video tutorials in YouTube. The videos you can find there greatly explain everything in detail. Note that with the vertices, you can change the position of the atoms. If you want to have atoms with a different size, color, etc. separate them. This can be done with the button ‘Separate’ in the Atomic Blender Utilities panel.

As you might know, details about the Atomic Blender addons can be found on the Wiki pages:

Cluster
PDB
XYZ
Panel

If you have further questions, please, don’t hesitate to ask here. I try to respond asap.

Greetings, Blendphys.


(chloesdad) #17

Hi
I’ve tried installing add_mesh_clusters.zip twice following instructions on the Wiki. Installed ,zip file, activated addon, rebooted Blender. It does not show up in Toolbar panel.

Mac osx, Blender 2.67b r57123m.

Am i missing something simple? Do I need to bring mesh objects into the scene first, etc? (Tried with mesh spheres, didn’t work.)

Thanks in advance for help.


(Blendphys) #18

Chloesdad,

the addon does not show up in the Toolbar panel after the installation! What you have to do is to activate it via

Menu -> Add -> Mesh -> Atom cluster

and then the addon (a panel) appears. From there, you create your clusters … . Did you choose ‘Save as default’ in the options during the installation? If not, it doesn’t work when you close Blender and re-start it.

EDIT: I modified the Wiki page and explicitly mention now that one has to activate the panel via the menu.


(chloesdad) #19

Thank you Blendphys. All is well, works wonderfully. Thanks for your time.