Questions relating to graphing and displaying numerical data

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1
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1answer
39 views

Matlab: Creating a matrix that represents a colored, sinusoidally-modulated grating

I would like to draw a texture (in Matlab - Psychtoolbox) which is composed of a sinusoidally-modulated isoluminant (magenta & cyan) grating. I do have the RGB matrices of the two phases (for ...
0
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0answers
22 views

GNU Software to construct crystal superlattices

I am looking for software recommendations. I want to know if there is any GNU visualization software that is capable of of joining two periodic crystals. For example, I want to be able to join a slab ...
11
votes
1answer
189 views

Visualization of quadtree & octree grids

So-called quadtree and octree grids are quite attractive for applications requiring adaptive mesh refinement. They are for example used in Gerris and Paramesh. Is anyone aware of a good file format ...
3
votes
2answers
537 views

CFD visualization workflow: Visit vs Paraview vs Tecplot and others

For those familiar with more of these tools than I am, what are the pros and cons of the various tools available? Right now I exclusively use Tecplot for CFD visualization, but it leaves a lot to be ...
0
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0answers
16 views

How would you draw arbitrarily oriented sphere with each hemisphere of a different color?

I refer to spheres like these: http://www.pa.msu.edu/cmp/csc/simulferrofl.html Actually, I could do it with OpenGL, but not with Java3D. I wonder it is easier to build them with Java3D, Paraview, ...
1
vote
1answer
42 views

What are the computational solutions for periodic visualization of simulation?

I like to set my scientific simulation programs to generate a picture after a certain number of iterations, such that I can follow what is happening and maybe cancel the simulation before the ...
9
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3answers
360 views

Second order tensor field visualization software

Is there an overview available over tensor visualization software? My personal preference is: A software which is free, well documented, and offers visualization techniques for different physical ...
1
vote
0answers
155 views

best package choice for visualizing agent based model simulations in python

This is a visualization/programming design problem. I am working on building a geospatial agent based model, meaning that there are multiple agents interacting within some particular spatial container....
0
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0answers
55 views

Visualization of Discontinuous Galerkin solution

Is there any simple way to visualise the solution of discontinous galerkin for poisson problem in matlab when monomials are used as basis function. ? Thanks alot.
2
votes
2answers
72 views

What's the role of visualization?

I'm just starting at scientific computing and I'm seeing that results can be generated merely by plotting the variables. Of course more variables lead to more axes/dimensions so e.g. a three variable ...
2
votes
1answer
144 views

Creating a 3D spatial density map from simulation results

I want so visualize the spatial density for my simulation. The result of my simulation is a (time-dependent) system of large number (~100k) of moving particles in a confined space. Each particle has ...
3
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0answers
193 views

C60 orbital calculation

I am currently trying to reproduce the results published by Hands et al.1 using MATLAB. They calculated the bases of the C60 wave functions of HOMO, LUMO and LUMO+1. I did the following: I ...
0
votes
1answer
192 views

Paraview: Multiple csv files to time series

I have multiple CSV files with point-coordinates and, possibly, multiple data values attached to them, i.e., the rows look like x y z data1 data2 ... Is there ...
3
votes
2answers
195 views

Should a colorbar have constant values throughout a simulation?

The default option for matplotlib's pcolormesh (also true for VisIt and I think also true for Matlab) is to allow the maximum and minimum of a colorbar vary. Which ...
2
votes
0answers
16 views

Is there a library which allows for converting 4D implicit surfaces to simplexes?

I have a 4D surface in the form of the spin quadric. I would like to display this surface onto the screen. One of the method which I would like to use to present surface onto the screen is projection. ...
0
votes
0answers
232 views

3D animation of a vector field (ParaView)

I am trying to create an animation of a 3d vector field in ParaView. All my data is in three matrices (201 x 201 x 201) corresponding to vectors components in x,y,z directions. And it's calculated in ...
1
vote
2answers
63 views

Help on writing sofware: general guidelines, in particular separation of computation and visualization

Although I already did some work in the intersection of theory and simulation I'm still very new to this field and I need some guidance. If anybody can give some recommendations for introductory ...
0
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2answers
283 views

How-to: Epic visualizations of 3D fractals?

I have seen videos like this before in the past of things like "3D Mandlebulbs" and similar fractal sets, but can anyone tell me what sorts of programs are actually used create these visualizations? ...
1
vote
1answer
109 views

Visualizing the difference of two sets of VTK files

I have two sets of 300 VTK files and I want to get a graph comparing the average difference of the two sets. All files have a structured grid containing a scalar value named phi. At the end, I need a ...
0
votes
1answer
55 views

Rendering Huge Data with Renderman Interface Bytestream

I have tones of geometrical objects (spheres, meshes) I want to render: One way would be to first write a .rib file which could be certainly done and then push that file to a renderman compliant ...
7
votes
2answers
712 views

How can one produce a proper streamline plot?

I recently had trouble producing a proper streamline plot in Mathematica, and apparently the problem is a good bit harder than I appreciated. I would like to know if there exist general algorithms to ...
1
vote
1answer
276 views

VTK File: How do I save data on a cell face?

I am writing a program that creates a vtk file with a Rectilinear Grid. I am able to save data to each one of the cells using CELL_DATA, but now, I need to save data to each one of the cell faces (x6)....
1
vote
0answers
166 views

Printing a plot in Octave-3.8.1 breaks LaTeX labels [closed]

Since upgrading to Octave 3.8 I have been unable to export plots with LaTeX labels. When the figure is displayed the labels render fine but when I try to export the figure using the ...
2
votes
2answers
2k views

Visualising Maxwell's equations using MATLAB

I asked this question to help me understand what is going on in one of Maxwell's equations. I am happy with following through the maths on paper now, but would like to use MATLAB to take it one step ...
4
votes
2answers
1k views

Using numpy arrays in Paraview programmable filter

How can I access a field in Paraview's programmable filter as a numpy array? I want to: Import an existing field as a numpy array Create a similar array for output Register it as a new field for ...
2
votes
2answers
610 views

visualization of 3D probability flow

I have a master equation for $P(N_A^+,N_B^+,N_C^+,t)$, with $N_A^+,N_B^+,N_C^+$ all discrete. The numerical integration is done by this Matlab program using Euler's method. Despite the crude Euler's ...
6
votes
2answers
309 views

Simulating advection over a network of 1D pipes

I am trying to create a simulation to help visualize how different chemical components flow through a network of pipes with associated valves, pumps, and chemical inputs. In this simulation, the pipes ...
0
votes
1answer
73 views

Plotting 3d dimensional histogarm in a spatial grid

Is there any tool to plot 3d dimensional histogram in a spatial grid? Preferably are there any filters or operators in Paraview or Visit for this?
6
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3answers
3k views

Visualizing finite element solutions in MATLAB

On my triangular mesh, I have the $(x,y,z)$ coordinates of each vertex of each triangle. For higher order elements, I refine each element a few times so I have more points to work with. If I just need ...
8
votes
4answers
4k views

How do I calculate the numerical difference between two fields stored in two different VTK files with the same structure?

Suppose I have two VTK files, both in structured grid format. The structured grids are the same (they have the same list of points, in the same order), and there is a field, call it "Phi", in each VTK ...
1
vote
2answers
411 views

Converting VTK point dataset of scalar values to a smooth surface

Does Paraview or Visit have any filters to draw a smooth surface for a set of points?
0
votes
1answer
193 views

quiver3 gives non-conformant arguments?

Does anyone know why I'm seeing these errors? I'm not giving it a matrix. ...
3
votes
4answers
331 views

Finding a molecular dynamics visualization library for C

I asked this question over at stackoverflow, and got blasted for it. I am currently working with legacy MD code written in C that my university uses, and haven't moved to a more modern library like ...
2
votes
0answers
501 views

Optimizing display of millions of triangles per second

I am working on a web-based molecular visualization program for a research project (e.g., one that can display XYZ and PDB files). The current options are outdated (for instance, Jmol uses Java). My ...
6
votes
3answers
4k views

Python scripting in Paraview

I've been using the basic visualization features of Paraview. Now, I want to go further by writing python macros to handle some specific tasks. My question for the advanced users: Are there any ...
4
votes
2answers
503 views

VTK file format to image file

Is there a way to convert vtk file without visualizing into a image file such as png in the bash terminal itself? I have found that for the vtk files that I visualize to take longer time than its ...
0
votes
1answer
250 views

Setting background image with respect to a point in Paraview

How to set image with respect to a point in Paraview? I have a vtk file within a rectangular domain starting with the lower left point -1842,10000, I want to set a background image whose lower left ...
3
votes
2answers
244 views

VTK: Subset of Points with same color

I have a set of points, among which a subset needs to have the same color in vtk file format. For ex. all agents with table value 0.0, 0.0, 0.0, 0.0 will have same color. Here is my vtk ...
5
votes
3answers
193 views

Quick data visualization

What is the quickest and simplest way to graph or visualize numerical data that is output as text files? Transferring to Matlab is slow, Excel is clunky, things like automatic scaling are essential.
2
votes
2answers
1k views

Best VTK visualizing software?

I have a large VTK file with rectangular data, it seems Paraview cannot handle the size of the file, so it crashes and Visit navigation is extremely slow? Can anyone point me to good open source ...
5
votes
2answers
137 views

Which visualisation software for a layered graph?

I have produced a CSV file in the following format: ...
2
votes
1answer
61 views

Best file format for bond connectivity?

I need to generate an output file from my molecular data that can be loaded into VMD to visualize the bond connectivity. I'm not sure what the best choice is. I know the PDB format has a HETATOM ...
4
votes
2answers
355 views

High quality molecular renderings

I would like to use a high-quality renderer (physically based path-tracing or MLT) to generate some images of molecular systems I have. Right now I'm just using some of the simple renderers in VMD, ...
5
votes
1answer
4k views

How to generate sloped streamslice plot of magnetic field in Matlab

I am currently working on my bachelor thesis, where I am calculating trajectory of electrons and ions in Hall Effect Ion Thruster. However, to be sure what I am calculating, I need to know how does ...
3
votes
0answers
995 views

Create 2D plot from two data sets in ParaView

I'm currently running a CFD simulation for an internal flow and need to compare my computed results to experimental data. The experimental data is saved as a comma separated file with columns for x,y,...
5
votes
1answer
411 views

how to visualize lattice with periodic, helical, etc. boundary conditions?

I am trying to write a special hexagonal lattice generator, with several kinds of boundary conditions, such as helical BC, periodic BC, and I find it hard to verify whether it works correctly. I tried ...
2
votes
4answers
1k views

Magnetic field visualization on Mac OS X?

Does somebody know about any tool for simulation and visualization of magnetic fields either of permanent magnets or solenoids, that can be used on Mac OS X? Maybe there is some software for Linux, ...
4
votes
3answers
142 views

Offline (visualisation) rendering in scientific computing

I need to simulate the movement of a large number of agents. The processes that govern the agents' movement are complex and so the entire process requires parallelisation. The output from this ...
22
votes
6answers
4k views

Visualizing very large link graphs

I am looking for a tool to visualize very large directional link graphs. I currently have ~2million nodes with ~10million edges. I have tried a few different things, but most take hours to even do ...
10
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3answers
262 views

Ways of visualizing event data in search of performance issues

I'm trying to optimize an MPI application with a highly asynchronous communication pattern. Each rank has a list of things to compute, and sends messages as necessary if the inputs or outputs reside ...