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updated Mobini example
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@j-zimmermann
j-zimmermann committed Feb 5, 2019
1 parent 95b7bca commit f107233
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382 changes: 124 additions & 258 deletions examples/Mobini2017/Mesh_twoWires.py
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3 changes: 2 additions & 1 deletion examples/Mobini2017/README.rst
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Expand Up @@ -17,6 +17,7 @@ The results will be stored in a directory named `results`.
Visualization
-------------

ParaView files to reproduce figured in our EMBC contribution can be generated by opening ParaView 5.5 and choosing the .pvsm respective file in the `load state` dialog.
ParaView files to reproduce figureis in our EMBC contribution can be generated by opening ParaView 5.5 and choosing the .pvsm respective file in the `load state` dialog.
Note that you have to choose the files again as ParaView stores absolute paths.
You can use the filename as such, but have to navigate to the `results` directory that will be created during a successful run.
The line plots have been generated by gnuplot scripts (.gnu). The plotted .tsv files were previously exported from ParaView.
Binary file modified examples/Mobini2017/geometryMobini_white.png
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11 changes: 8 additions & 3 deletions examples/Mobini2017/parameters_mobini2017.yml
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Expand Up @@ -17,14 +17,19 @@ degree:
2

geometry:
[r_el, r_well, h_well, h_el, dist_el]
[r_el, r_well, h_well, h_el, dist_el, level, l_el, ratio]

# based on https://www.tpp.ch/page/produkte/09_zellkultur_testplatte.php
# assumption: 80% filled
geometryvalues:
r_well : 0.0346
h_well : .01705
r_well : 0.01689
h_well : .01733
h_el : .001
r_el : 0.0005
dist_el : 0.022
level : 0.8
l_el : 0.05 # length of electrode
ratio : 0.44 # ratio of two parts of electrode => 0.44 means 22mm for the bottom and the rest for the upper part

materials:
[Air, Medium]
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27 changes: 27 additions & 0 deletions examples/Mobini2017/paraview/field_along_z.tsv
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@@ -0,0 +1,27 @@
"f_101:0" "f_101:1" "f_101:2" "vtkValidPointMask" "arc_length" "Points:0" "Points:1" "Points:2"
0.0067493 32.874 -0.011658 1 0 9.5181e-07 5.9828e-06 0
0.0028702 32.817 0.030013 1 0.0005456 9.5181e-07 5.9828e-06 0.0005456
-0.0064539 32.76 0.034366 1 0.0010912 9.5181e-07 5.9828e-06 0.0010912
-0.013082 32.57 -0.054212 1 0.0016368 9.5181e-07 5.9828e-06 0.0016368
-0.0076559 32.316 -0.051239 1 0.0021824 9.5181e-07 5.9828e-06 0.0021824
0.00012727 32.03 -0.0030524 1 0.002728 9.5181e-07 5.9828e-06 0.002728
-0.0028232 31.638 -0.0092059 1 0.0032736 9.5181e-07 5.9828e-06 0.0032736
-0.0035284 31.244 -0.0069511 1 0.0038192 9.5181e-07 5.9828e-06 0.0038192
-0.0023616 30.814 -0.0064292 1 0.0043648 9.5181e-07 5.9828e-06 0.0043648
-0.0014295 30.383 -0.0061741 1 0.0049104 9.5181e-07 5.9828e-06 0.0049104
-0.0017296 29.907 -0.005032 1 0.005456 9.5181e-07 5.9828e-06 0.005456
-0.0062166 29.441 -0.0037425 1 0.0060016 9.5181e-07 5.9828e-06 0.0060016
-0.00088495 28.986 -0.0044792 1 0.0065472 9.5181e-07 5.9828e-06 0.0065472
0.0015679 28.536 -0.01066 1 0.0070928 9.5181e-07 5.9828e-06 0.0070928
-0.0026346 28.086 -0.0031965 1 0.0076384 9.5181e-07 5.9828e-06 0.0076384
-0.0051085 27.662 -0.0029609 1 0.008184 9.5181e-07 5.9828e-06 0.008184
-0.0067098 27.268 -0.0023357 1 0.0087296 9.5181e-07 5.9828e-06 0.0087296
-0.0064558 26.936 0.009218 1 0.0092752 9.5181e-07 5.9828e-06 0.0092752
-0.0016056 26.603 -0.0018756 1 0.0098208 9.5181e-07 5.9828e-06 0.0098208
-0.001635 26.344 -0.005492 1 0.010366 9.5181e-07 5.9828e-06 0.010366
-0.005187 26.071 0.010265 1 0.010912 9.5181e-07 5.9828e-06 0.010912
-0.0035871 25.857 -0.023019 1 0.011458 9.5181e-07 5.9828e-06 0.011458
-0.0018272 25.64 -0.087747 1 0.012003 9.5181e-07 5.9828e-06 0.012003
-0.0039466 25.581 -0.077043 1 0.012549 9.5181e-07 5.9828e-06 0.012549
-0.0068863 25.556 -0.050388 1 0.013094 9.5181e-07 5.9828e-06 0.013094
-0.0047272 25.477 -0.022677 1 0.01364 9.5181e-07 5.9828e-06 0.01364
42 changes: 42 additions & 0 deletions examples/Mobini2017/paraview/field_between_electrodes.tsv
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@@ -0,0 +1,42 @@
"f_60:0" "f_60:1" "f_60:2" "vtkValidPointMask" "arc_length" "Points:0" "Points:1" "Points:2"
0.0013359 179.17 0.68306 1 0 0.0075 -0.011 0.001
2.3956 97.348 18.134 1 0.00055 0.0075 -0.01045 0.001
3.8086 75.372 17.028 1 0.0011 0.0075 -0.0099 0.001
4.7255 64.038 13.753 1 0.00165 0.0075 -0.00935 0.001
5.2612 56.452 10.597 1 0.0022 0.0075 -0.0088 0.001
5.4673 50.711 8.1774 1 0.00275 0.0075 -0.00825 0.001
5.4852 46.167 6.3965 1 0.0033 0.0075 -0.0077 0.001
5.3176 42.533 5.0415 1 0.00385 0.0075 -0.00715 0.001
5.0577 39.627 3.933 1 0.0044 0.0075 -0.0066 0.001
4.7499 37.306 3.1208 1 0.00495 0.0075 -0.00605 0.001
4.3828 35.39 2.522 1 0.0055 0.0075 -0.0055 0.001
3.9626 33.758 2.0344 1 0.00605 0.0075 -0.00495 0.001
3.5371 32.499 1.6539 1 0.0066 0.0075 -0.0044 0.001
3.108 31.494 1.2946 1 0.00715 0.0075 -0.00385 0.001
2.6649 30.669 1.0784 1 0.0077 0.0075 -0.0033 0.001
2.2339 29.938 0.80338 1 0.00825 0.0075 -0.00275 0.001
1.8003 29.485 0.61123 1 0.0088 0.0075 -0.0022 0.001
1.3437 29.012 0.47194 1 0.00935 0.0075 -0.00165 0.001
0.87782 28.791 0.29362 1 0.0099 0.0075 -0.0011 0.001
0.44899 28.61 0.13737 1 0.01045 0.0075 -0.00055 0.001
-0.0067369 28.592 -0.010266 1 0.011 0.0075 0 0.001
-0.44286 28.616 -0.12861 1 0.01155 0.0075 0.00055 0.001
-0.88761 28.838 -0.30995 1 0.0121 0.0075 0.0011 0.001
-1.3435 29.08 -0.48618 1 0.01265 0.0075 0.00165 0.001
-1.771 29.464 -0.63323 1 0.0132 0.0075 0.0022 0.001
-2.2187 30.028 -0.8564 1 0.01375 0.0075 0.00275 0.001
-2.6672 30.617 -1.0445 1 0.0143 0.0075 0.0033 0.001
-3.1155 31.394 -1.3204 1 0.01485 0.0075 0.00385 0.001
-3.5502 32.485 -1.6287 1 0.0154 0.0075 0.0044 0.001
-3.9576 33.792 -1.9927 1 0.01595 0.0075 0.00495 0.001
-4.3717 35.394 -2.5329 1 0.0165 0.0075 0.0055 0.001
-4.7201 37.317 -3.0806 1 0.01705 0.0075 0.00605 0.001
-5.0534 39.698 -4.0386 1 0.0176 0.0075 0.0066 0.001
-5.3105 42.552 -4.8915 1 0.01815 0.0075 0.00715 0.001
-5.4726 46.171 -6.3488 1 0.0187 0.0075 0.0077 0.001
-5.4765 50.686 -8.1626 1 0.01925 0.0075 0.00825 0.001
-5.2464 56.462 -10.608 1 0.0198 0.0075 0.0088 0.001
-4.7266 64.137 -13.728 1 0.02035 0.0075 0.00935 0.001
-3.801 75.359 -17.045 1 0.0209 0.0075 0.0099 0.001
-2.3772 97.109 -18.441 1 0.02145 0.0075 0.01045 0.001
0.1436 177.34 -1.1076 1 0.022 0.0075 0.011 0.001
6 changes: 3 additions & 3 deletions examples/Mobini2017/paraview/field_tupaj.py
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Expand Up @@ -12,8 +12,8 @@ def Tupaj_func(V, a, d, x):
a = 0.0005
# spacing between electrodes
d = 0.022
xmin = -0.01
xmax = 0.01
xmin = -0.01025
xmax = 0.01025

xvalues = np.linspace(xmin, xmax, 50)
result = np.empty(len(xvalues))
Expand All @@ -30,4 +30,4 @@ def Tupaj_func(V, a, d, x):
# plot and output
plt.plot(xvalues, result)
plt.show()
np.savetxt('field_tupaj.txt', np.transpose([xvalues, result]), delimiter=',', header='position, field')
np.savetxt('field_tupaj.txt', np.transpose([xvalues, result]), delimiter='\t', header='position\tAnalytical')
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