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January 21, 2020, 12:06 |
Postprocessing .vtk file OpenFOAM
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#1 |
New Member
Kaboka
Join Date: Dec 2019
Posts: 19
Rep Power: 6 |
Hello everyone,
I am simulating a sloshing case inside the 3D cylindirical tank. I used the following code in my control dict file and got the free surface points as a .vtk file. However I have these .vtk files for my every timesteps for all the points of free surface. What I want is to plot a graph of the deflection of the point which is at the leftmost corner for all time steps. Could anybody help me how to post process this point for every timestep and plot that graph in python or excel please ? or is there any other method to do it? Thank in advance HTML Code:
functions { freeSurface { type surfaces; functionObjectLibs ( "libsampling.so" ); outputControl outputTime; outputInterval 1; surfaceFormat vtk; fields ( alpha.water ); surfaces ( freeSurface { type isoSurfaceCell; isoField alpha.water; isoValue 0.5; interpolate false; regularise false; } ); interpolationScheme cell; } ); |
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January 22, 2020, 01:29 |
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#2 |
Senior Member
Join Date: Aug 2013
Posts: 407
Rep Power: 16 |
Hi,
You should be able to do this using the vtk library/package in python. I had to do something similar and my approach was to use python vtk library to read in and extract information from .vtk files Hope this helps. Cheers, Antimony |
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January 22, 2020, 10:11 |
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#3 |
New Member
Kaboka
Join Date: Dec 2019
Posts: 19
Rep Power: 6 |
Hi Antimony,
Thanks for the answer. I tried it with python but somehow it doesn't work. If it's possible could you share your python code with me? Thanks a lot in advance. I also put the python code below. HTML Code:
#!/usr/bin/python # elevationVsTime # Read VTK files with isosurface # Track one (x,z) coordinate in time import os import re from vtk import * from optparse import OptionParser from numpy import * print ("elevationVsTime v0.2") # Read command line arguments parser = OptionParser() parser.add_option("-f","--input-file",dest="coords",type="string",help="Filename containing coordinates",metavar="FILE",default="coords") (options, args) = parser.parse_args() print ("Reading coordinates from file \"",options.coords,"\"") f = loadtxt(options.coords) #- Search starting point x = f[:,0] y = x*0+0.7 z = f[:,1] points = len(x) print (points," points found") #- List input points for i in range(0, points-1): print ("Point ",i," (",x[i],",",z[i],")") # Import timedirectories # read the vtk directory and get all the time steps and return list basedir = "freeSurface/" timesteps=[] for root,dir,file in os.walk(basedir,True): p,time = os.path.split(root) if (bool(re.search("^[0-9.]",time))): timesteps.append(time) filename = file[0] basename = 'elevationVsTime' timesteps = sorted(timesteps) # This sorts alphabetically # "Progress-bar" necessity - Ntimes = len(timesteps) frac = round(Ntimes/10.0); counter = 0 #- Time-info - known bug here print ("Timerange: [",timesteps[0],",",timesteps[Ntimes-1],"]") ## Read for ts in timesteps: #- Counter info -- this info is approximate counter = counter+1 if ( counter%frac == 0 ): print (round(counter/frac)*10,"%") #- Read VTK file readfile = basedir + ts + "/" + filename reader = vtkPolyDataReader() reader.SetFileName(readfile) reader.Update() output = reader.GetOutput() #- For each timestep, find the closest coordinate on the 0/ plane for i in range(points): writefile = basename + str(i) file = open(writefile,'a+') #- Coordinate to find closest point xfind = [x[i], y[i], z[i]] #- Find point p = output.FindPoint(xfind) #- Coordinate of point xfound = output.GetPoint(p) y[i] = xfound[1] #- Write to file print >> file, ts, y[i] file.close() |
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March 24, 2020, 04:56 |
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#4 |
New Member
Kaboka
Join Date: Dec 2019
Posts: 19
Rep Power: 6 |
Could you help me with the programming, please?
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March 31, 2020, 23:18 |
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#5 |
Senior Member
Join Date: Aug 2013
Posts: 407
Rep Power: 16 |
Hi,
What is the issue that you are facing with the code? Can you explain in detail? Cheers, Antimony |
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April 1, 2020, 07:05 |
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#6 | ||
New Member
Kaboka
Join Date: Dec 2019
Posts: 19
Rep Power: 6 |
Quote:
I am getting this error. I think I have to define a coordinate system that is inside the coords.txt but I do not know what the code exactly wants from me. PHP Code:
Quote:
HTML Code:
https://openfoamwiki.net/index.php/Tip_Surface_elevation_in_time I would be appreciated if you help me. Thanks in advance |
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April 1, 2020, 09:11 |
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#7 |
Senior Member
Yan Zhang
Join Date: May 2014
Posts: 120
Rep Power: 12 |
Hello,
I am really interested in using python to plot with the vtk file input. Could you please offer an example?
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https://openfoam.top |
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May 21, 2020, 09:45 |
Possible Code solution?
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#8 | ||
Senior Member
Carlos Rubio Abujas
Join Date: Jan 2018
Location: Spain
Posts: 127
Rep Power: 9 |
Hi kaboka,
Quote:
Code:
elevationVsTime --input-file coordinate_file It assumes that the points are in (X,Z) format, probably because that was the special need of the author. The code use these points to check against the different surfaces what are the closest ones. Then the y coordinate is saved into a file. Quote:
is it possible to simplify the problem to getting the high of the highest point? I've wrote a simple code for doing so, maybe you can tweak it for your specific purposes. You may have to change the data on the beginning for your case. In the core you have a np.array of the points in the surface, so you can do whatever manipulation you may consider necessary. Code:
#!/usr/bin/python3 import os, sys, re import vtk import matplotlib.pyplot as plt import numpy as np ### - DATA - ### BASEDIR = '../postProcessing/freeSurface' output_file = 'results.out' print('- - - - - Searching VTK surfaces - - - - -') # Ensure that the folder exists if not os.path.exists(BASEDIR): print('ERROR: No folder "{}" found'.format(BASEDIR)) sys.exit(1) # Read all the vtk files. Ensure that they're read in chronological order. vtk_files = [ os.path.join(root, datafile) for root, folders, files in os.walk(BASEDIR) for datafile in files if datafile.lower().endswith('vtk') ] readTimeInstant = lambda x: float(re.findall('\d+\.?\d*[eE]?[-+]?\d*', x)[0]) vtk_files.sort(key=readTimeInstant) print('{} vtk files have been found'.format(len(vtk_files))) print() print('- - - - - Loading VTK surfaces - - - - -') # Variables to be extracted all_points = [] time = [] zmax_list = [] zmax_list2 = [] for i, filename in enumerate(vtk_files): print('Loading files... ', end='') print('{}/{}'.format(i+1, len(vtk_files))) # Read the file reader = vtk.vtkPolyDataReader() reader.SetFileName(filename) reader.Update() data = reader.GetOutput() # - Here is where the magic happens - # # Read the file: time.append(readTimeInstant(filename)) # Point-By-Point analysis [slower] surface_points = np.array( [data.GetPoint(i) for i in range(data.GetNumberOfPoints())] ) ## Extract the maximum index xind, yind, zind = 0, 1, 2 # <-- Use whatever index is down for your case zmax_list.append( surface_points.max(axis=0)[zind] ) # Evaluate only bounds [faster] bbox = data.GetBounds() xmin, xmax, ymin, ymax, zmin, zmax = bbox zmax_list2.append(zmax) print() print('- - - - - Writting Results - - - - -') with open(output_file, 'w') as f: f.write('Time[s]:\tZ Max[m]:\n') for t,z in zip(time, zmax_list): f.write('{} \t{}\n'.format(t, z)) print('results have been saved into "{}"' \ .format(os.path.abspath(output_file))) print() # -- Both graphs shall be equal -- print('- - - - - Plotting Results - - - - -') plt.plot(time, zmax_list, label='zmax_list') plt.plot(time, zmax_list2, label='zmax_list2') plt.xlabel('Time [s]:') plt.ylabel('Height [m]:') plt.grid() plt.legend() plt.show() print() print('DONE!') Hopes it helps! |
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June 16, 2020, 10:31 |
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#9 |
New Member
Kaboka
Join Date: Dec 2019
Posts: 19
Rep Power: 6 |
Hello Carlos,
Thanks a lot, that was super explained. I will work on it. Bests |
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May 22, 2024, 14:44 |
VTK for alpha=0.5
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#10 |
New Member
Mustafa
Join Date: Sep 2020
Posts: 3
Rep Power: 6 |
for OpenFOAM-v2012+
Code:
freeSurface { type surfaces; libs (sampling); interpolationScheme cell; writeControl runTime; writeInterval 0.1; surfaceFormat vtk; fields ( alpha.water ); surfaces ( freeSurface { type isoSurfaceCell; isoField alpha.gas; isoValue 0.5; interpolate true; regularise false; } ); } |
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freesurface, vtk |
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