[CIG-SHORT] Matlab HDF5 file, Use Coordinates and Topology to build the domain

[Brad Aagaard]

Teng,

It sounds like you are looking for something more suitable for 
visualization than Matlab. ParaView is a good alternative. It is easy to 
select various visualization options (wireframe, surface, lines, points, 
etc). It has scripting capabilities via Python; the PyLith v2.2.1 manual 
and new examples/3d/subduction examples suite demonstrate how to use 
Python scripts with ParaView.

Regards,
Brad


On 10/17/2017 11:09 PM, Li, Teng wrote:
> Hi Brad,
> 
> Thanks for your reply.
> 
> And I tried to use Matlab patch function to make a 2d color plot of the whole domain. The input includes x coordinate, y coordinate, and topology. However, due to the huge amount of cell numbers, the color is always black if I don't zoom in too much. Furthermore, in order to edit edge color, I must have all points data of each cell, not the cell data in h5 file. So I wonder whether there are other ways that we can make a 2d color plot based on the coordinates, topology and cell value data?
> 
> Thanks!
> 
> Best,
> Teng
> Teng Li
> 
> Master Candidate in Structures
> 
> Department of Civil and Environmental Engineering
> 
> University of Illinois at Urbana-Champaign
> 
> 205 North Mathews Ave, Urbana, IL. 61801
> 
> Phone:(217)8196210, Email: tengli2 at illinois.edu
> 
> 
> 
> ________________________________________
> From: CIG-SHORT [cig-short-bounces at geodynamics.org] on behalf of Brad Aagaard [baagaard at usgs.gov]
> Sent: Tuesday, October 17, 2017 3:35 PM
> To: cig-short at geodynamics.org
> Subject: Re: [CIG-SHORT] Matlab HDF5 file, Use Coordinates and Topology to build the domain
> 
> The topology (how the vertices are connected into cells) and geometry
> (where the vertices are) of the mesh in the HDF5 files are defined by:
> 
> geometry/vertices (coordinates of the vertices)
> topology/cells (index of vertices in each cell)
> 
> You will see that a mesh with 2-D triangular cells has 3 vertices per
> cell and each vertex has 2 coordinates (x and y). Likewise, a mesh with
> 2-D quadrilateral cells has 4 vertices per cell.
> 
> So for a 2-D triangular cell with index I, the coordinates of the
> vertices are:
> 
> vertices[cells[I,0],:]
> vertices[cells[I,1],:]
> vertices[cells[I,2],:]
> 
> Regards,
> Brad
> 
> 
> On 10/17/2017 01:29 PM, Li, Teng wrote:
>> Hi list,
>>
>> I have a question about showing the model stress in the post processing
>> step. I first output stress.vtk files and visualize them in Paraview.
>> However, I am not good at using paraview python to post process the
>> stress data. So I save the vtk files as csv files. Because the time step
>> is 118, so I have 118 csv files. So I need to load each in Matlab and
>> process them one by one.
>>
>> I think a smarter way is to output the stress.h5 file. And I read the
>> stress.h5 file and find the following components:
>> stress: stress_x, stress_y, stress_z. (2d problem). Coordinates: one row
>> for x coordinate, and another for y coordinate. And Topology: each
>> column has four numbers, I think it shows which four nodes form a cell.
>>
>> However, I find that the number of columns in Coordinates and Topology
>> are different. So that should mean the coordinates are not for the
>> cells. I plan to use pcolor to show the stress. So I need to first build
>> the mesh according to the node coordinates and topology. And then I can
>> use 3d color plot to show the stress distribution.
>>
>> Although I can see the model directly in Trelis and Paraview. However, I
>> need to build the domain in Matlab to the Coordinates and Topology. And
>> then plot the stress of each cell. Can you help me to build the domain
>> according to the Coordinates and Topology?
>>
>> Best,
>> Teng
>>
>>
>> Teng Li
>>
>> Master Candidate in Structures
>>
>> Department of Civil and Environmental Engineering
>>
>> University of Illinois at Urbana-Champaign
>>
>> 205 North Mathews Ave, Urbana, IL. 61801
>>
>> Phone:(217)8196210, Email: tengli2 at illinois.edu
>>
>>
>>
> 
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