Summary: vizualization of 3-D flow field



 Hello.
 Below is a summary of the responses I have received concerning visualization of
 3-D data, in particular, visualization of a 3-d flow field.  I have also
 included possible solutions to a recent problem sent to the CCL which
 corresponds to a related aspect of data analysis; viz., visualization of some
 sort of iso-surface (generalized contouring).
 I have attempted to make all listings below as anonymous as possible
 (plagarism).  For the most part, all programs shown below were compiled (or
 precompiled binaries used) on a SGI (SiliconGraphics,Inc.) R10000 running IRIX
 6.2 (except for the Fortner products).  I should note that there were many
 others I have tested as well; a list of those follow:
 		Plotmtv	- Great, almost as easy as xmgr!!!!!!
 		YetAnoextHuckMolorbprog - Nice for display of band structures,
 						etc.
 		graph3d -
 		robot -
 		scian -
 		tecate -
 		tipsy -
 		uncert -
 The last six are vacuous since either I do not remember the programs efficacy
 or there were compilation problems.
 Any questions, comments or concerns, please do not hesitate to send me an
 email.
 Iraj.
 P.S. I should note that Vu is a beautiful program that has aided us in our
 projects tremendously (sp).  Images created from this program can be found at
 http://www.cerca.umontreal.ca/vu/Welcome_eng.html.  Make
 sure you check out the
 gallery at http://www.cerca.umontreal.ca/vu/gallery/Welcome_eng.html.
 The
 people behind Vu are very gratious and the program is free for those in
 acadamia.
 Iraj Daizadeh
 Department of Chemistry
 University of California
 Davis, CA 95616
 email: daizadeh;at;indigo.ucdavis.edu
 Phone: 916.754.8695
 --------------------------------------------------------------------------------
 Below was the problem:
 Hello.
 Would anyone know an easy-to-learn program that allows for visualizing data
 from a file in 3-dimension Euclidean space something that looks like a fluid
 dynamics simulation?  I started to write such a piece of code using Tcl/Tk but
 speed is of the essence (as always).
 Thanks in advance.
 Iraj Daizadeh
 Department of Chemistry
 University of California
 Davis, CA 95616
 --------------------------------------------------------------------------------
 #1)
 I use FAST, developed here, and available for free (I think).  It does
 3D scalar and vector fields on a wide variety of grids, including, of
 course, uniform cartesian.
 For some examples of what it can do for molecules, see
 http://science.nas.nasa.gov/~creon/papers/mgms96/
 for availablitty of FAST, look at
 http://science.nas.nasa.gov/Software/FAST/
 #2)
 Check out software at
         http://www.fortner.com/
      I have never used their stuff, but it looks impressive (and they have
   been in business for a while). It is not free - but I think their main
   modules come as a package for less than $1,000.
 Fortner:
 http://www.fortner.com/docs/demos_all.html
 #3)
 Try pgplot.  It's not available in netlib but it's excellent and free.
 See   http://astro.caltech.edu/~tjp/pgplot/
 It may not do *exactly* what you need but I think it'll come close,
 probably a lot closer than other free tools.
 #4)
 Sorry about the delay, but hours are not always so extensible as I might wish!
 Yes! VU can create pictures of 3-d fields using streamlines and/or vectors.
 Yes!! VU can displayed atoms and links between them using spheres and
 cylinders colored according to the usual standards.
 And Yes!!! you can put all of this on screen at the same time!
 We have created a couple of new images in the VU gallery representing small
 molecules in which a cutting plane is used to probe and visualize a scalar
 field.  These are not big protein but rather small molecules, but the idea
 is the same.  I invited you to go check again the VU home page at
 http://www.cerca.umontreal.ca/vu/gallery/ to check these new
 additions.
 VU is developped mainly for use in Computational Fluid Dynamics (CFD), but
 it also usefull for other application domains.  It is being use extensively
 for chemistry applications here at Cerca and nearby universities, and also
 at the University of Hannover with AllChem (their web address is in VU
 HomePage).
 ** VU allows for 2-d and 3-d exploration of scalar fields as well as vector
 fields.  Furthermore, VU can also display geometric entities such as curves and
 surfaces.
 ** Scalar fields can be probed/represented using either :
   - iso-surfaces in 3-d space,
   - iso-lines on arbitrary cutting planes
   - iso-lines on surfaces of constant coordinate from a structured grid.
   - graphs, i.e. continuously shaded images representing the values of a
     scalar field on  cutting planes (or surfaces of constant coordinate from
     a structured grid).
 ** Vector fields can be probed/represented using either :
   - arrows (scalable)
   - streamlines in various number and location, all of which is specified
 interactivally.
   - dynamic particle tracing: non static images in which particle
     (represented as small spheres) are injected in various location to probe
     the vector fields.
 ** VU can extract information from these various fields and present them
 in a tabular form in a file or directly at the cursor location.
 ** VU uses `expressions' such as "sqrt(px*px+py*py+pz*pz)" to indicate
 color
 mapping, deformation or scaling factor for use in creating images (at least
 colorfull if not always meaningfull!).
 ** VU can also use transparency in any image, in order to be able able to `see'
 what is behind a cutting plane or an iso-surface.
 ** VU uses OpenGL and Motif (both fairly standard libraries) and works on
 UNIX workstations: IRIX, AIX, HP-UX, OSF1 and Linux.
 In a nutshell, VU can creates many and various images of 2-d and 3-d scalar
 and vector fields from a solution computed over a set of grid nodes.  The
 input file for VU specifies the mesh used and the computed solution fields.
 You may see and read about some examples in the VU Web pages.  However, if
 the fact that some of the web pages crucial for a full understanding of the
 capabilities of the program and of its input file might not be in english,
 you could forward a sample test case of your data to support_vu in order to
 establish its usuability in your case.  Even if the documentation has not
 been yet completely translated and made avalailable on the Web, VU is
 nonetheless available in four languages: french, english, german and spanish.
 #5)
 IBM visualization data explorer/IRIS explorer will do.
 A while ago, i downloaded the comparison of these visualization softwares.
 Now  I dont remember the  URL. But u can find them in my homepage.
 http://144.16.73.100/~parthi/home.html
 and CLICK "visualization". u can see the comparison of four
 visualization softwares.
 #6)
 One possibility for almost all visualization tasks is to write a
 simple program to transform the data to a VRML file and then use a
 VRML browser to visualize it. For more information about VRML, look at
 the VRML repository (http://www.sdsc.edu/vrml/). For an example of
 code that generates VRML, look at the VRML module on my Python page
 (http://www.yi.com/home/HinsenKonrad/python.html).
 #7)
 I'm glad you enjoyed the site.  I usually use Matlab or Mathematica to plot
 my vectors.  Unfortunately, both of these programs are commercial so you
 must buy them.  There may be shareware available on the internet to do the
 same thing.  Happy hunting.
 #8)
 I don't know what your constraints are: systems, time, money,
 expertise ...  but if I were in your position, I could knock out a
 visualization of "data from a file in 3-dimension Euclidean space
 something that looks like a fluid dynamics simulation" in 30-60
 minutes using AVS.  Have you any familiarity with it at all?  There
 were other packages (IBM's Data Explorer and SGI's IRIS Explorer)
 which did much the same thing and were all the rage 3-4 years ago.
 #9)
 Vis5D will suit your needs if your data are sampled on a rectangular
 3-D grid, and you have values for px, py and pz at each grid point.
 See Section 3.1 of the Vis5D README file for instructions about
 getting your data into Vis5D.  I recommend map projection 0 (generic)
 and vertical coordinate system 0 (generic), since your data are not
 related to Earth coordinat (latitude and longitude).  If you use
 the names 'U', 'V' and 'W' for px, py and pz then Vis5D will
 recognize these as the three components of a vector field.  If you
 don't, then you can use the 'UVW VARS' widget to tell Vis5D which
 fields are vector components.  In generic coordinates, vector
 components are in the units given for North, South, East, West,
 Top and Bottom bounds, per second.  If you have a time sequence of
 data (i.e., a changing vector field), Vis5D will trace motion trajectories
 for you.  You'll need to correctly assign dates and times to time steps
 to get realistic motions.  If you only have one time step, you can still
 look at motion trajectories by just repeating the same data over a sequence
 of times.  Good luck.
 #10)
 The purpose of this message is to give you a quick feeling for how the NCAR
 graphics package can be used to display graphs of your data from the Cray. The
 NCAR graphics package consists of libraries of C and Fortran callable subrou-
 tines for creating graphs and utilities for displaying them.
 #11)
 MSI's software developer's kit does exactly what you want. It includes
 an API set to visualize iso-surfaces, molecular structure, trajectories,
 normal modes, plots/graphs, etc. It also allows you in a few steps to put
 an interface together to any computational chemistry code.
 For general information about this toolkit visit:
 http://www.msi.com/support/sdk/
 for specific information on plotting iso-surfaces visit:
 http://www.msi.com/support/sdk/users/examples/iso/README.html
 #12)
 Dear CCLers, although I'm pretty sure this question has been already
 posed (and I beg your pardon for posing it again), I have to ask about a
 3D visualisation tool. I worked with SciAn, which is pretty good indeed,
 but the only existing version needs Z buffer and DGL. Looking on the net
 I found a software called vis5d, pretty good the same but tuned for
 metereological data and I found too time-expensive to adapt it to
 visualize orbitals, electronic density and so on. I'm using molden but I
 would like to find out soemthing more general (I'm trying to use ELF
 also, and this feature is not implemented in molden).
 The software I'm looking for should manage x,y,z,function_value in order
 to give isosurfaces of the function I'm trying to plot. Something not
 strictly platform-dependant would be very fine.
 Thank you for all the information you will provide.
 Iraj Daizadeh
 Department of Chemistry
 University of California
 Davis, CA  95616
 email:  daizadeh;at;indigo.ucdavis.edu
 Phone:  916.754.8695
 Fax:    916.752.8995