VMD-L Mailing List

From: maxim todoru (mtodoru_at_gmail.com)
Date: Fri Nov 12 2021 - 20:43:41 CST

I just recalculated and new files have been generated.
https://urldefense.com/v3/__https://www.mediafire.com/file/8o1w2irxgb1h3yj/diazomethane_elf.cube/file__;!!DZ3fjg!qBKA9DdEn1tcTV493dCeAhx3mqFeScNRzj23OfXU5WQnaKX2Dz0qY9OqlyXjjDT_yQ$
https://urldefense.com/v3/__https://www.mediafire.com/file/t3sn5mc49lbefy9/diazomethane_syn.cube/file__;!!DZ3fjg!qBKA9DdEn1tcTV493dCeAhx3mqFeScNRzj23OfXU5WQnaKX2Dz0qY9OqlyWEP-243A$

Le dim. 14 nov. 2021 à 09:44, Axel Kohlmeyer <akohlmey_at_gmail.com> a écrit :

> Ok. But those two files don't match, so you cannot easily create a
> visualization from them.
> The data and atom positions in the second file have a different position
> and orientation than in the first.
>
> ```
> Cube File
> ELF grid
> 5 -5.050000 -6.850000 -8.100000
> 102 0.100000 0.000000 0.000000
> 138 0.000000 0.100000 0.000000
> 156 0.000000 0.000000 0.100000
> 6 6.000000 0.000000 0.000000 -2.153297
> 7 7.000000 0.000000 0.000000 2.441117
> 7 7.000000 0.000000 0.000000 0.292850
> 1 1.000000 0.000000 1.798526 -3.108993
> 1 1.000000 0.000000 -1.798526 -3.108993
> ```
>
> and
>
> ```
> ELF grid
> 5 -7.500000 -6.800000 -5.000000
> 157 0.100000 0.000000 0.000000
> 137 0.000000 0.100000 0.000000
> 101 0.000000 0.000000 0.100000
> 7 7.000000 -0.287104 0.000179 0.000320
> 7 7.000000 -2.452843 -0.000085 -0.000291
> 6 6.000000 2.156895 -0.000060 0.000645
> 1 1.000000 3.118963 -1.800493 -0.002035
> 1 1.000000 3.119299 1.800194 -0.002035
> ```
>
> On Sun, Nov 14, 2021 at 2:10 AM anas forum <anasforum05_at_gmail.com> wrote:
>
>> Dear Axel,
>> the whole process of visualization is explained in the attached image
>> Visualization_Process.jpg.
>> https://urldefense.com/v3/__https://www.mediafire.com/file/tpj0gbhcj4te6c0/diazomethane_elf.cube/file__;!!DZ3fjg!qBKA9DdEn1tcTV493dCeAhx3mqFeScNRzj23OfXU5WQnaKX2Dz0qY9OqlyXoBmrUnw$
>> https://urldefense.com/v3/__https://www.mediafire.com/file/13h6ulencqwgzk8/diazomethane_syn.cube/file__;!!DZ3fjg!qBKA9DdEn1tcTV493dCeAhx3mqFeScNRzj23OfXU5WQnaKX2Dz0qY9OqlyUb9_rkCw$
>> About the color : red-cyan-green-purple
>>
>>
>> ᐧ
>>
>> Le dim. 14 nov. 2021 à 02:15, Axel Kohlmeyer <akohlmey_at_gmail.com> a
>> écrit :
>>
>>> I see no attachments in any of the e-mails in this thread.
>>> Also I would need a description of what volumetric data file you would
>>> want to use to represent the isosurface from and what other (volumetric)
>>> property/file you want to use for the coloring and more importantly, what
>>> the value (ranges) the different colors correspond to.
>>>
>>> On Sat, Nov 13, 2021 at 6:07 PM maxim todoru <mtodoru_at_gmail.com> wrote:
>>>
>>>> Dear Axel,
>>>> Evidently, you did not understand the example that i posted, and more
>>>> probably you never face an example like that before, but i will explain the
>>>> situation again : i want to color one isosurface contain four domains with
>>>> four different colors, every color in the isosurface mean something.
>>>> if you have some time, i suggest you to give it a try, i uploaded the
>>>> necessary files before. Prove me if i'm wrong, because i'm pretty sure you
>>>> won't succeed get the desired results (attached image diaz.png).
>>>>
>>>> Best regards,
>>>> Maxim
>>>>
>>>> Le samedi 13 novembre 2021, Axel Kohlmeyer <akohlmey_at_gmail.com> a
>>>> écrit :
>>>>
>>>>> maxim,
>>>>>
>>>>> it looks like you did not pay sufficient attention to the suggestions
>>>>> that you have been given. While you cannot do the kind of custom color
>>>>> scale you desire through the GUI, it can very well be done from the script
>>>>> interface and that ability has been with VMD for a *very* long time.
>>>>>
>>>>> You need to use the `colorinfo` and the `color` command for that. The
>>>>> script to create custom matlab inspired color maps should be used as an
>>>>> instructive example.
>>>>>
>>>>> VMD maintains a list of "named" colors (`colorinfo num` will tell you
>>>>> how many) and then you have "indexed" colors up to a maximum (see
>>>>> `colorinfo max`).
>>>>> you can change either type of color with the `color change <index>
>>>>> <red> <green> <blue>` command. Where you provide the RGB values for a given
>>>>> index in the color map, first to the named colors then to the colors used
>>>>> for the color scale.
>>>>>
>>>>> I strongly suggest you and your "Tcl experts" have a second look at
>>>>> that script and the VMD user's guide.
>>>>>
>>>>> Axel.
>>>>>
>>>>> --
>>>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!qBKA9DdEn1tcTV493dCeAhx3mqFeScNRzj23OfXU5WQnaKX2Dz0qY9OqlyVIG6jnSg$
>>>>> <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!uTTRumpI9Guiwy96fYz-0HF61X21qAdlrRuK1erxmYs_2qfqpo8iCXvG20BntjwcFg$>
>>>>> College of Science & Technology, Temple University, Philadelphia PA,
>>>>> USA
>>>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>>>
>>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!qBKA9DdEn1tcTV493dCeAhx3mqFeScNRzj23OfXU5WQnaKX2Dz0qY9OqlyVIG6jnSg$
>>> <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!uTTRumpI9Guiwy96fYz-0HF61X21qAdlrRuK1erxmYs_2qfqpo8iCXvG20BntjwcFg$>
>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>
>>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!qBKA9DdEn1tcTV493dCeAhx3mqFeScNRzj23OfXU5WQnaKX2Dz0qY9OqlyVIG6jnSg$
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>