VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Mar 19 2011 - 17:53:16 CDT

On Sat, Mar 19, 2011 at 6:15 PM, Xiaogang Wang <xgwang.dalian_at_gmail.com> wrote:
>
> On Sat, 19 Mar 2011, Axel Kohlmeyer wrote:
>
>> On Sat, Mar 19, 2011 at 2:23 AM, Xiaogang Wang <xgwang.dalian_at_gmail.com>
>> wrote:
>>>
>>> Hello,
>>>
>>> My volumetric data is not on a grid. Can VMD read it
>>> and plot isosurface by interpolating between my data ?
>>
>> no.
>>
> Thanks for your answer. It is disappointing. Gnuplot can do this sort of
> thing for contour plots (3D).  Its recent version seems to be able to read
> "non-grid" volumetric data. But its 4D plot is rather weak compared to VMD.

VMD is a program to display molecules not gridded data.
gnuplot is a program to display such data.
if you need something that looks better, there are a
lot of alternatives. OpenDX comes to mind, ParaView,
VistIT, Gsharp, or Matlab, just to name a few

if you absolutely want to use VMD, then you have to write
a small program/script that places your data on a regular grid.
in principle, you can even do that with Tcl, i.e. VMD
and instead of writing out a grid file, you can assign the data
directly. see e.g.:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/readcube/
which has an (now obsolete) reader for cube files.

axel.

>
> Xiaogang
>
>
>>> The data set is not structureless, though. It is mapped from
>>> a 3D grid.  An example data set has the following 8 points,
>>> mapped from an original 2x2x2 grid.
>>
>>>
>>> x1  y1  z1  f(x1,y1,z1)
>>> x2  y2  z2  f(x2,y2,z2)
>>> x3  y3  z3  f(x3,y3,z3)
>>> x4  y4  z4  f(x4,y4,z4)
>>> x5  y5  z5  f(x5,y5,z5)
>>> x6  y6  z6  f(x6,y6,z6)
>>> x7  y7  z7  f(x7,y7,z7)
>>> x8  y8  z8  f(x8,y8,z8)
>>>
>>>
>>> Thanks.
>>> Xiaogang Wang
>>>
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer
>> akohlmey_at_gmail.com  http://goo.gl/1wk0
>>
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.