VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Nov 14 2021 - 02:44:41 CST
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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!qoe0xN9m6AHUiBB7WavvI6WAgGY0bv4xs2KQw8iYMUqeQ4vhKn5KCWzB1oLbb6CFFw$
> https://urldefense.com/v3/__https://www.mediafire.com/file/13h6ulencqwgzk8/diazomethane_syn.cube/file__;!!DZ3fjg!qoe0xN9m6AHUiBB7WavvI6WAgGY0bv4xs2KQw8iYMUqeQ4vhKn5KCWzB1oJ-dqBvSg$
> 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!qoe0xN9m6AHUiBB7WavvI6WAgGY0bv4xs2KQw8iYMUqeQ4vhKn5KCWzB1oJJyqtY2A$
>>>> <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!uTTRumpI9Guiwy96fYz-0HF61X21qAdlrRuK1erxmYs_2qfqpo8iCXvG20BntjwcFg$>
>>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>>
>>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!qoe0xN9m6AHUiBB7WavvI6WAgGY0bv4xs2KQw8iYMUqeQ4vhKn5KCWzB1oJJyqtY2A$
>> <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!uTTRumpI9Guiwy96fYz-0HF61X21qAdlrRuK1erxmYs_2qfqpo8iCXvG20BntjwcFg$>
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!qoe0xN9m6AHUiBB7WavvI6WAgGY0bv4xs2KQw8iYMUqeQ4vhKn5KCWzB1oJJyqtY2A$ College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
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