Questions relating to graphing and displaying numerical data

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2
votes
1answer
39 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
166 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
127 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
58 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
votes
3answers
769 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 ...
4
votes
4answers
645 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
73 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
92 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
148 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 ...
1
vote
0answers
118 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 ...
5
votes
3answers
708 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 ...
2
votes
1answer
119 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
0answers
35 views

How to cut a solid (mesh) using VISIT?

I'm quite new using Visit and I would like to visualize a cut (sectional view) of a solid (mesh). Using the "slicing" option I can define a plane and get the surface of the cut, but I would like to ...
0
votes
1answer
82 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
106 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
142 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
368 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
109 views

Which visualisation software for a layered graph?

I have produced a CSV file in the following format: position number, list of positions it links to, second list of positions it links to,....., sixth list of positions it links to. All the items are ...
2
votes
1answer
42 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
125 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
2k 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
381 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 ...
5
votes
1answer
164 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
2answers
458 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
133 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 ...
20
votes
4answers
2k 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
votes
3answers
209 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 ...
6
votes
1answer
527 views

Visualizing discontinuous Galerkin/finite element data

I would like to visualize simulation results, obtained using the discontinuous Galerkin (DG) approach, within ParaView. Similarly to finite volume methods, the problem domain is divided into ...
4
votes
0answers
88 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 ...
11
votes
3answers
880 views

Algorithms for (adaptive?) function plotting

I am looking for algorithms to draw standard 2d-graphs for functions that may or may not have singularities. The purpose is to write a "Mini-CAS", so I have no a priori knowledge of the types of ...
9
votes
4answers
488 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 ...
5
votes
1answer
405 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 ...
4
votes
1answer
4k views

How do I plot a transparent cylinder in matlab?

I know that I can use the following commands to create an opaque cylinder in matlab: N=100; [X,Y,Z]=cylinder(R,N); surf(X,Y,Z); I want to plot an arrow inside ...
10
votes
2answers
380 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 ...
4
votes
2answers
144 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 ...
4
votes
5answers
592 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?