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  1. #1

    Atomic Blender - Cluster

    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:

    Cluster_02.png

    Cluster_05.png

    Cluster_09_ensemble_perspectives.png



    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
    Last edited by Blendphys; 02-Jun-12 at 08:41.



  2. #2



  3. #3
    Member Meta-Androcto's Avatar
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    hi, just having a play with this now, cool stuff



  4. #4
    Originally Posted by Meta-Androcto View Post
    hi, just having a play with this now, cool stuff
    Thanks Meta-Androcto



  5. #5
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    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 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



  6. #6
    Originally Posted by matali View Post
    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 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
    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
    Yes, true. But this is a start ... . PS: Don't forget us, the physicists ... .



  7. #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...



  8. #8
    Originally Posted by Uncle Entity View Post
    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...
    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.
    Last edited by Blendphys; 29-May-12 at 13:34.



  9. #9
    Member Scrible's Avatar
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    FYI, AtomicBlender was mentioned in a reputable german computer magazine called c't.
    c't 2012 Heft 12 page 49

    Congrats!



  10. #10
    Originally Posted by Scrible View Post
    FYI, AtomicBlender was mentioned in a reputable german computer magazine called c't.
    c't 2012 Heft 12 page 49
    Congrats!
    Thanks Scrible. Is it an announcement? And: is it in the print version (I need to pay for the article)?



  11. #11
    Member Scrible's Avatar
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    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 ...if you want I could drop them an eMail; they might correct that in a following issue.

    Maybe not so reputable.



  12. #12
    Originally Posted by Scrible View Post
    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.
    Ah, nice.
    Though I just noticed that they made a mistake, confusing the export of .PDB files with .PDF ...if you want I could drop them an eMail; they might correct that in a following issue.
    Maybe not so reputable.
    PDF? Okay, just send them an email ... thanks.



  13. #13

    New cluster shape

    Dear all.

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

    Icosahedron_v01.png
    Last edited by Blendphys; 09-Jun-12 at 09:17.



  14. #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:
    ncontent.jpeg
    Last edited by Blendphys; 25-Jul-12 at 15:27.



  15. #15
    Member PKHG's Avatar
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    Hi Blendphys,
    meta-adrocto told me you are busy with 'atoms' and ' molecules' ... and I saw it working in 2.64 very nice.

    Some one else did some stuff too it is Jonathan Ng with and to 2.64 upgraded version (by me) to be found in
    http://blenderartists.org/forum/show...98#post2226398

    there are nice ideas too ... riggifying things especially ;-)

    Maybe you have a look too?

    Greets
    Peter



  16. #16
    Originally Posted by PKHG View Post
    Hi Blendphys,
    meta-adrocto told me you are busy with 'atoms' and ' molecules' ... and I saw it working in 2.64 very nice.
    Some one else did some stuff too it is Jonathan Ng with and to 2.64 upgraded version (by me) to be found in
    http://blenderartists.org/forum/show...98#post2226398
    there are nice ideas too ... riggifying things especially ;-)
    Maybe you have a look too?
    Greets
    Peter
    Hey Peter,

    thanks for the link. This 'VSEPR Tool' is very nice indeed! In fact, it is a modeler for constructing molecules and other structures inside the Blender 3D scene.
    Are you the main developer right now? - The reason why I'm asking is that we could enlarge the whole 'Atomic Blender' palette, in which the 'VSEPR Tool' could be part of the project. For instance, we could call it 'Atomic Blender - Vsperr' or 'Atomic Blender - Modeller'. What do you think?

    It would be nice to build some science stuff under the name 'Atomic Blender' ... .

    Cheers,

    Blendphys.



  17. #17
    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



  18. #18
    Hi Nanochemist.

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

    Originally Posted by Nanochemist View Post
    I am a new Blender User (trying to write a thesis in chemistry). I ve found atomic cluster amazing ...
    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.
    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.



  19. #19
    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.



  20. #20
    Originally Posted by chloesdad View Post
    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.
    Am i missing something simple? Do I need to bring mesh objects into the scene first, etc? (Tried with mesh spheres, didn't work.)
    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.
    Last edited by Blendphys; 09-Jun-13 at 13:17.



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