but
mapping:rbf-thin-plate-splinesis maybe not the best choice if your fluid (interface) mesh is large. Better use compact basis functions. Read more here: https://precice.org/configuration-mapping.html#radial-basis-function-mapping
Hello, @uekerman Benjamin, if we choose compact basis functions such as rbf-compact-tps-c2 as you recommend, is PETSc required to be installed?
@AymenAmiral1997 that's a difficult question to answer. I will rephrase your question to "which structure solver should I use for FSI with preCICE". Assuming that you are not already familiar with one of the two (which would be the natural option):
- FEniCS is a framework in which you have to (and can) define your own solver. You can use some of our tutorials as starting points. Similarly for deal.II (which we have more experience with for FSI).
- CalculiX is a ready-to-use solver for structure FEM simulations. It is a bit old, but well-tested by its community. It has a bit of cryptic configuration format and post-processing tools, though.
At the bottom of this page you can see that we get similar results with both.
At the end of the day, I would suggest to use deal.II or FEniCS if you are willing to edit/write some code and you want to know exactly what is going on, or use CalculiX if you want a larger palette of options already implemented.
Hello. I used to precice 1.6.1 for FSI simulation. Simulations completed with no error. Now I want to use precice 2.3.0 for same simulations. I installed and tested tutorials there are no error. I use nearest-neighbor mapping for my case and there is error "Mapping distance not available due to empty partition." and fluid stuck. I tried rbf-thin-plate-splines mapping this error does not occur but fluid still stuck. Full error text;
---[precice] Mapping distance not available due to empty partition.
---[precice] Mapping distance not available due to empty partition.
[Harun:00195] Process received signal
[Harun:00195] Signal: Floating point exception (8)
[Harun:00195] Signal code: Integer divide-by-zero (1)
[Harun:00195] Failing at address: 0x7fb4a460ceb1
[Harun:00195] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x143c0)[0x7fb4a3e7e3c0]
[Harun:00195] [ 1] /home/harun/preCICE/precice-2.3.0/lib/libprecice.so.2(_ZN7precice9partition17ReceivedPartition22createOwnerInformationEv+0xca1)[0x7fb4a460ceb1]
[Harun:00195] [ 2] /home/harun/preCICE/precice-2.3.0/lib/libprecice.so.2(_ZN7precice9partition17ReceivedPartition7computeEv+0x3ff)[0x7fb4a460d97f]
[Harun:00195] [ 3] /home/harun/preCICE/precice-2.3.0/lib/libprecice.so.2(_ZN7precice4impl19SolverInterfaceImpl17computePartitionsEv+0x1df)[0x7fb4a462cf8f]
[Harun:00195] [ 4] /home/harun/preCICE/precice-2.3.0/lib/libprecice.so.2(_ZN7precice4impl19SolverInterfaceImpl10initializeEv+0x502)[0x7fb4a463e6e2]
[Harun:00195] [ 5] SU2_CFD(+0x7176c0)[0x55ba40ad76c0]
[Harun:00195] [ 6] SU2_CFD(+0x52e704)[0x55ba408ee704]
[Harun:00195] [ 7] SU2_CFD(+0x179894)[0x55ba40539894]
[Harun:00195] [ 8] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7fb4a3c9c0b3]
How can I fix this issue? Can someone help me? Thanks.
gather-scatter with preCICE v2.3.0, have a look at the XML configuration documentation on our website. There you will find various configuration options and also the relevant tags in each of them.
I am trying to run SU2 with Calculix on a large cluster. I launch both applications using a shell script., which is in turn controlled by a python script. The python script essentially takes all the necessary files and rearranges them into "Fluid" and "Solid" sub directories and then calls "execute.sh" to launch both applications. For smaller cases, this workflow works. However, for a large case, precice gets stuck at the following stage:
---[precice] Setting up preliminary slaves communication to coupling partner/s
---[precice] Receive global mesh Calculix_Mesh
---[precice] Prepare partition for mesh SU2_Mesh0
---[precice] Broadcast mesh Calculix_Mesh
---[precice] Filter mesh Calculix_Mesh by bounding box on slaves
---[precice] Mapping distance min:4.2294e-10 max:3.29171 avg: -nan var: -nan cnt: 928
---[precice] Mapping distance min:4.2294e-10 max:3.29171 avg: -nan var: -nan cnt: 928
Hi, I have a problem with the RBF interpolation in the fenics-x adapter. When I run my simulation I get the following warning:
WARNING:py.warnings:/usr/local/lib/python3.8/dist-packages/scipy/interpolate/rbf.py:257: LinAlgWarning: Ill-conditioned matrix (rcond=5.53004e-22): result may not be accurate.
self.nodes = linalg.solve(self.A, self.di)I found out that the interpolated values in my coupling_expression differ by 10°C from those in precice.read_data() and the simulation diverges. Do you have any idea how I could debug that?
When I set the values from precice.read_data() manually on my coupling expression the simulation works well.
The interpolation problem might not be well-defined if you map along an axis-symmetric surface. This means, preCICE tries to compute, for example, a 3D interpolant out of 2D information. If so, preCICE throws an error RBF linear system has not converged or Interpolation matrix C is not invertible. In this case, you can restrict the interpolation problem by ignoring certain coordinates, e.g. x-dead="true" to ignore the x coordinate.
I found out the following: It's better with the Rbf (max error of 15%) compared to segregated_interpolant_2d (max error of 19%). I used the following code
from scipy.interpolate import Rbf
from scipy.linalg import lstsq
import numpy as np
coords_x = np.loadtxt("interpolation_coords_x.txt")
coords_y = np.loadtxt("interpolation_coords_y.txt")
data = np.loadtxt("interpolation_data.txt")
def segregated_interpolant_2d(coords_x, coords_y, data):
...
rbf_interp = Rbf(coords_x, coords_y, data)
print(max(abs((rbf_interp(coords_x, coords_y) - data)/data)))
seg_interp = segregated_interpolant_2d(coords_x, coords_y, data)
print(max(abs((seg_interp (coords_x, coords_y) - data)/data)))with coords, data exported from the simulation.
Both errors look too large to me. Rbfs are interpolating, so I would expect a much lower error. Here just an example with artificial data:
from scipy.interpolate import Rbf
import numpy as np
x = np.random.rand(100)
y = np.random.rand(100)
d = np.random.rand(100)
rbf = Rbf(x,y,d)
print(np.max(abs((rbf(x,y) - d)/d)))If your data fluctuating a lot, the error might become large, though. I can simulate this effect with my toy example, by artificially scaling some values:
from scipy.interpolate import Rbf
import numpy as np
x = np.random.rand(100)
y = np.random.rand(100)
d = np.random.rand(100)
d[::2] *= 1000000
rbf = Rbf(x,y,d)
print(np.max(abs((rbf(x,y) - d)/d)))Because this starts to look complicated and I don't really see a clear solution: Can we move to discourse? https://precice.discourse.group/
Then you could also share your data and I can take a look at it.
rbf = Rbf(coords[0,:], coords[1,:], data, function='thin-plate')and did not get any error. Without the added basis function I was able to recreate the problem.
Checkout the blog post for a full overview.
Binding releases will follow soon.