Questions tagged [visualization]

Questions relating to graphing and displaying numerical data

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6
votes
2answers
537 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 ...
1
vote
1answer
87 views

How to interpret Turing Machine illustrations on p79 of Stephen Wolfram's “A New Kind of Science” book?

I am reading Stephen Wolfram's "A New Kind of Science". At present, I cannot understand how the cellular automata illustrations on p79 are created. In the patterns, the active cell, representing the ...
6
votes
3answers
6k 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 ...
3
votes
1answer
229 views

Is there an Implementation of the Hilbert curve from $[0,1]$ to $[0,1]^n$, where $n$ is large? ($n=10,000$, say)

I would like to map each point in $[0,1]$ to $[0,1]^n$ with a Hilbert curve, where $n=10,000$. That is $$ f: [0,1] \to [0,1]^n, $$ is the $n$-dimensional Hilbert curve. I found the library of Cortesi,...
0
votes
1answer
283 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
573 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
767 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 The current options are outdated (for instance, Jmol uses Java).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 ...
3
votes
1answer
107 views

Equal Area Sampling on Curved Surface:

I have a quantity $\beta(\mathbf{x}) \in \mathbb{R}$ that I wish to compute on a curved, smooth surface defined by $\{\mathbf{x}: \Gamma(\mathbf{x})=0\} \subset \mathbb{R}^{3}$. (This surface is ...
0
votes
3answers
244 views

CAD like visualisation of 3D vector data?

It looks like MATLAB and Mathematica is often used for post-processing and data visualization of 3D vector data. Now consider you are simulating 3D objects and get out gradient fields etc., is there ...
3
votes
2answers
544 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 ...
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
3answers
280 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.
3
votes
1answer
90 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 ...
5
votes
1answer
7k 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
1answer
713 views

How to do local FFT on huge 3D vector data cell mesh and visualize it spatially?

Simulation type: I'm running a simulation with the OOMMF micromagnetics package http://math.nist.gov/oommf/ where are magnet is represented by a mesh of 3 million cells, it gets excited by a ...
0
votes
1answer
92 views

mapping data with a spike to a heat map

I have the following dataset that I need to display on the heat map: [30, 15, 66, 7, 9999, 78, 42, 132] So if I map the values to the color scale using a linear function I only see the spike while ...
3
votes
0answers
2k 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,...
6
votes
1answer
729 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 ...
4
votes
3answers
154 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 ...
5
votes
1answer
1k views

Drawing isocontour data of 3d discrete volume with mayavi2

I'm trying to visualize the propagation of heat in a discrete sphere surface. The sphere is hollow, only the voxels of the boundary have value. Visualization in matlab using isosurface shows correct ...
3
votes
1answer
235 views

Looking for parMetis visualizer?

Is there any visualizer for parMetis (mpmetis), which can visualize FEM mesh grids after partitioning?
10
votes
3answers
351 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 ...
4
votes
0answers
106 views

Existing software/scripts for spiral graphs?

I am looking for existing software or scripts to generate spiral graphs from cyclical (time) data, as presented by Webber and Muller. The graphs shown in the paper look like a great means of ...
12
votes
2answers
831 views

How can one mathematically describe the “cartoon” type of representation of proteins?

Proteins are typically represented in a cartoon form, with β sheets as arrows and α helices as coils: I'm wondering, is there somewhere a reference that describes the construction of this ...
12
votes
4answers
1k views

Making a Molecular editor/visualizer: Object oriented programming, data structures, and molecules

I am new to programming and I am trying to solve my first big problem and write my first big program. I have looked for open source examples of code to learn from, but so far have only found code in ...
7
votes
1answer
398 views

Generalized least squares gradient of a vector field

For computing the gradient of a scalar field, one can use the weighted least squares method as described in the paper Revisiting the Least-squares Procedure for Gradient Reconstruction on Unstructured ...
6
votes
2answers
427 views

Tools for computing an electric field based on location of charges?

I have the positions of a large number of charges (the strengths are known, but are also variables). Are there any tools that will allow me to visualize the electric field induced by these charges (or ...
1
vote
1answer
219 views

Error message when trying to get PETSc to draw to an X terminal by passing -mat_view_draw

I've made a matrix, and now I want to draw it on the screen to make a basic check of correctness. The documentation for MatAssemblyEnd() states that I can pass an ...
4
votes
2answers
4k views

Can gnuplot's PNG terminal use superscripts and subscipts?

I know that gnuplot's epslatex terminal can display superscipts and subscripts in titles and label axes. Is this also possible when using gnuplot's ...
6
votes
4answers
5k views

Tools for visualizing large 3D volumes

I have a sequence of 2D images (png files) encoding the partitioning (segmentation) of a large biological 3D volume. In these files, each pixel has a color, representing the 3D object the pixel ...
9
votes
1answer
311 views

Given values on a mesh, what algorithm can I use to construct efficiently level set contours?

I have a mesh, faces $F$, edges $E$, and vertices $V$, and I have a list of predefined level set contours. What algorithm can I use to construct contours in the most efficient manner? A plot of the ...
5
votes
5answers
2k views

How do I create an animation from a 2D model or dataset?

I found the following thread in the physics stackexchange where I saw the video called output attached to the main post. The video can be found here. How would I go about creating such an animation?
4
votes
2answers
327 views

Tools/solutions for visualization of molecular simulation trajectories?

I have so far been using VMD to create visualizations of molecular trajectories. However, I find myself not entirely satisfied with the quality of the resulting animations—when you want to do snapshot-...
2
votes
1answer
173 views

How can I set different axes for different plots in gnuplot?

I want to plot a few sets of data points on the same x-axis that have different units. How can I set different axes for each incompatible quantity?

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