Update master (v202104.1.1)

Author: MakisH

elastic-tube-1d/README.md

@@ -25,6 +25,8 @@ The following parameters have been chosen:
 - Fluid density: $$ \rho = 1 $$
 - Young modulus: E = 10000
 
+Additionally the solvers use the parameters `N = 100` (number of cells), `tau = 0.01` (dimensionless timestep size), `kappa = 100` (dimensionless structural stiffness) by default. These values can be modified directly in each solver.
+
 ## Available solvers
 
 Both fluid and solid participant are supported in:
@@ -70,8 +72,6 @@ cd solid-cpp
 ./run.sh
 ```
 
-The solvers use the parameters `N = 100`, `tau = 0.01`, `kappa = 100` by default and can be modified in the solver.
-
 ### Python
 
 Open two separate terminals and start each participant by calling the respective run script. Only serial run is possible:
@@ -88,25 +88,21 @@ cd solid-python
 ./run.sh
 ```
 
-Parameters such as `N` can be modified directly at the `FluidSolver.py` and at the `SolidSolver.py`. The parameters must be consistent between the different solvers and participants.
-
-**Optional:** Visualization and video output of the fluid participant can be triggered via the options `--enable-plot` and `--write-video` of `FluidSolver.py`. To generate .vtk files during execution, you need to add the flag `--write-vtk`.
-
-![Elastic tube animation](images/tutorials-elastic-tube-1d-animation.gif)
+**Optional:** A run-time plot visualization can be trigged by passing `--enable-plot` in `run.sh` of `FluidSolver.py`. Additionally a video of the run-time plot visualization can be generated by additionally passing `--write-video`
 
 {% include warning.html content= "The C++ and Python solvers lead to different results. Please consider the Python results as the correct ones and refer to this [open issue](https://github.com/precice/tutorials/issues/195) for more insight. Contributions are particularly welcome here." %}
 
 ## Post-processing
 
+![Elastic tube animation](images/tutorials-elastic-tube-1d-animation.gif)
+
 The results from each simulation are stored in each `fluid-<participant>/output/` folder. You can visualize these VTK files using the provided `plot-diameter.sh` script
 
 ```bash
 ./plot-diameter.sh
 ```
 
-which will try to visualize the results from both fluid cases, if available.
-
-This script calls the more flexible `plot-vtk.py` Python script, which you can use as
+which will try to visualize the results from both fluid cases, if available. This script calls the more flexible `plot-vtk.py` Python script, which you can use as
 
 ```bash
 python3 plot-vtk.py <quantity> <case>/output/<prefix>

elastic-tube-1d/fluid-cpp/src/FluidSolver.cpp

@@ -72,11 +72,9 @@ int main(int argc, char **argv)
 
   interface.setMeshVertices(meshID, chunkLength, grid.data(), vertexIDs.data());
 
-  std::cout << "Initialize preCICE..." << std::endl;
-  interface.initialize();
-
   double t  = 0.0;
-  double dt = 0.01;
+  std::cout << "Initialize preCICE..." << std::endl;
+  double dt = interface.initialize();
 
   if (interface.isActionRequired(actionWriteInitialData())) {
     interface.writeBlockScalarData(pressureID, chunkLength, vertexIDs.data(), pressure.data());
@@ -102,7 +100,6 @@ int main(int argc, char **argv)
     if (interface.isActionRequired(actionWriteIterationCheckpoint())) {
       interface.markActionFulfilled(actionWriteIterationCheckpoint());
     }
-
 
     if (interface.isReadDataAvailable()) {
       interface.readBlockScalarData(crossSectionLengthID, chunkLength, vertexIDs.data(), crossSectionLength.data());

elastic-tube-1d/fluid-python/FluidSolver.py

@@ -6,20 +6,40 @@
 from thetaScheme import perform_partitioned_implicit_trapezoidal_rule_step, perform_partitioned_implicit_euler_step
 import numpy as np
 import tubePlotting
-
 import matplotlib.pyplot as plt
 import matplotlib.animation as manimation
-
 from output import writeOutputToVTK
-
 import precice
-from precice import *
+from precice import action_write_initial_data, action_write_iteration_checkpoint, \
+    action_read_iteration_checkpoint
+
+# physical properties of the tube
+r0 = 1 / np.sqrt(np.pi)  # radius of the tube
+a0 = r0**2 * np.pi  # cross sectional area
+u0 = 10  # mean velocity
+ampl = 3  # amplitude of varying velocity
+frequency = 10  # frequency of variation
+t_shift = 0  # temporal shift of variation
+p0 = 0  # pressure at outlet
+kappa = 100
+
+L = 10  # length of tube/simulation domain
+N = 100
+dx = L / kappa
+# helper function to create constant cross section
+
+
+def velocity_in(t): return u0 + ampl * np.sin(frequency *
+                                              (t + t_shift) * np.pi)  # inflow velocity
+
+
+def crossSection0(N):
+    return a0 * np.ones(N + 1)
+
 
 parser = argparse.ArgumentParser()
 parser.add_argument("configurationFileName", help="Name of the xml precice configuration file.",
                     nargs='?', type=str, default="../precice-config.xml")
-parser.add_argument(
-    "--write-vtk", help="Save vtk files of each timestep in the 'VTK' folder.", action='store_true')
 parser.add_argument(
     "--enable-plot", help="Show a continuously updated plot of the tube while simulating.", action='store_true')
 parser.add_argument("--write-video", help="Save a video of the simulation as 'writer_test.mp4'. \
@@ -33,7 +53,6 @@
     print("Try '$ python FluidSolver.py precice-config.xml'")
     quit()
 
-output_mode = config.OutputModes.VTK if args.write_vtk else config.OutputModes.OFF
 plotting_mode = config.PlottingModes.VIDEO if args.enable_plot else config.PlottingModes.OFF
 if args.write_video and not args.enable_plot:
     print("")
@@ -42,41 +61,14 @@
     quit()
 writeVideoToFile = True if args.write_video else False
 
-print("Starting Fluid Solver...")
-
-configFileName = args.configurationFileName
-
-# physical properties of the tube
-r0 = 1 / np.sqrt(np.pi)  # radius of the tube
-a0 = r0**2 * np.pi  # cross sectional area
-u0 = 10  # mean velocity
-ampl = 3  # amplitude of varying velocity
-frequency = 10  # frequency of variation
-t_shift = 0  # temporal shift of variation
-p0 = 0  # pressure at outlet
-kappa = 100
-
-
-def velocity_in(t): return u0 + ampl * np.sin(frequency *
-                                              (t + t_shift) * np.pi)  # inflow velocity
-
-
-L = 10  # length of tube/simulation domain
-N = 100
-dx = L / kappa
-# helper function to create constant cross section
-
-
-def crossSection0(N):
-    return a0 * np.ones(N + 1)
+print("Plotting Mode: {}".format(plotting_mode))
 
+print("Starting Fluid Solver...")
 
 print("N: " + str(N))
 
-solverName = "Fluid"
-
 print("Configure preCICE...")
-interface = precice.Interface(solverName, configFileName, 0, 1)
+interface = precice.Interface("Fluid", args.configurationFileName, 0, 1)
 print("preCICE configured...")
 
 dimensions = interface.get_dimensions()
@@ -88,7 +80,6 @@ def crossSection0(N):
 crossSectionLength = a0 * np.ones(N + 1)
 crossSectionLength_old = a0 * np.ones(N + 1)
 
-
 if plotting_mode == config.PlottingModes.VIDEO:
     fig, ax = plt.subplots(1)
     if writeVideoToFile:
@@ -110,11 +101,10 @@ def crossSection0(N):
 vertexIDs = interface.set_mesh_vertices(meshID, grid)
 
 t = 0
-precice_dt = 0.01
 
 print("Fluid: init precice...")
 # preCICE defines timestep size of solver via precice-config.xml
-interface.initialize()
+precice_dt = interface.initialize()
 
 if interface.is_action_required(action_write_initial_data()):
     interface.write_block_scalar_data(pressureID, vertexIDs, pressure)
@@ -161,9 +151,8 @@ def crossSection0(N):
         velocity_old = np.copy(velocity)
         pressure_old = np.copy(pressure)
         crossSectionLength_old = np.copy(crossSectionLength)
-        if output_mode is config.OutputModes.VTK:
-            writeOutputToVTK(time_it, "out_fluid_", dx, datanames=["velocity", "pressure", "diameter"], data=[
-                             velocity_old, pressure_old, crossSectionLength_old])
+        writeOutputToVTK(time_it, "out_fluid_", dx, datanames=["velocity", "pressure", "diameter"], data=[
+            velocity_old, pressure_old, crossSectionLength_old])
         time_it += 1
 
 print("Exiting FluidSolver")

elastic-tube-1d/fluid-python/run.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 set -e -u
 
-python3 ./FluidSolver.py ../precice-config.xml --write-vtk
+python3 ./FluidSolver.py ../precice-config.xml

elastic-tube-1d/plot-diameter.sh

@@ -1,15 +1,17 @@
 #!/bin/sh
 set -e -u
 
+# File check solution from: https://stackoverflow.com/questions/91368/checking-from-shell-script-if-a-directory-contains-files
+
 # Plot diameter from fluid-cpp
-if [ -d "./fluid-cpp/output/" ]; then
+if [ -n "$(ls -A ./fluid-cpp/output/*.vtk 2>/dev/null)" ]; then
     python3 plot-vtk.py diameter fluid-cpp/output/out_fluid_ &
 else
     echo "No results to plot from fluid-cpp."
 fi
 
 # Plot diameter from fluid-python
-if [ -d "./fluid-python/output/" ]; then
+if [ -n "$(ls -A ./fluid-python/output/*.vtk 2>/dev/null)" ]; then
     python3 plot-vtk.py diameter fluid-python/output/out_fluid_ &
 else
     echo "No results to plot from fluid-python."

elastic-tube-1d/solid-cpp/src/SolidSolver.cpp

@@ -45,11 +45,10 @@ int main(int argc, char **argv)
 
   std::vector<int> vertexIDs(chunkLength);
   interface.setMeshVertices(meshID, chunkLength, grid.data(), vertexIDs.data());
-  std::cout << "Initialize preCICE..." << std::endl;
-  interface.initialize();
 
   double t  = 0;
-  double dt = 0.01;
+  std::cout << "Initialize preCICE..." << std::endl;
+  double dt = interface.initialize();
 
   if (interface.isActionRequired(actionWriteInitialData())) {
     interface.writeBlockScalarData(crossSectionLengthID, chunkLength, vertexIDs.data(), crossSectionLength.data());

elastic-tube-1d/solid-python/SolidSolver.py

@@ -5,7 +5,8 @@
 import argparse
 import numpy as np
 import precice
-from precice import *
+from precice import action_write_initial_data, action_read_iteration_checkpoint, \
+    action_write_iteration_checkpoint
 
 
 r0 = 1 / np.sqrt(np.pi)  # radius of the tube
@@ -21,8 +22,6 @@
 def crossSection0(N):
     return a0 * np.ones(N + 1)
 
-###############
-
 
 print("Starting Solid Solver...")
 
@@ -38,14 +37,10 @@ def crossSection0(N):
     print("Try '$ python SolidSolver.py precice-config.xml'")
     quit()
 
-configFileName = args.configurationFileName
-
 print("N: " + str(N))
 
-solverName = "Solid"
-
 print("Configure preCICE...")
-interface = precice.Interface(solverName, configFileName, 0, 1)
+interface = precice.Interface("Solid", args.configurationFileName, 0, 1)
 print("preCICE configured...")
 
 dimensions = interface.get_dimensions()

multiple-perpendicular-flaps/README.md

@@ -111,4 +111,7 @@ After the simulation has finished, you can visualize your results using e.g. Par
 
 ## References
 
-[1] H. Bungartz, F. Linder, M. Mehl, B. Uekerman. A plug-and-play coupling approach for parallel multi-field simulations. 2014.
+<!-- markdownlint-configure-file {"MD034": false } -->
+[1] H. Bungartz, F. Linder, M. Mehl, B. Uekermann. A plug-and-play coupling approach for parallel multi-field simulations. _Comput Mech_ **55**, 1119-1129 (2015). https://doi.org/10.1007/s00466-014-1113-2
+
+{% include disclaimer.html content="This offering is not approved or endorsed by OpenCFD Limited, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM®  and OpenCFD®  trade marks." %}

perpendicular-flap/README.md

@@ -71,3 +71,5 @@ Reasons for the differences:
 
 * The CalculiX adapter only supports linear finite elements (deal.II uses 4th order, FEniCS 2nd order).
 * SU2 models a compressible fluid, OpenFOAM and Nutils an incompressible one.  
+
+{% include disclaimer.html content="This offering is not approved or endorsed by OpenCFD Limited, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM®  and OpenCFD®  trade marks." %}

quickstart/README.md

@@ -110,6 +110,8 @@ You may be curious what displacements OpenFOAM received from the rigid body solv
 
 ![result](images/quickstart-result.png)
 
+{% include disclaimer.html content="This offering is not approved or endorsed by OpenCFD Limited, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM®  and OpenCFD®  trade marks." %}
+
 ## What's next?
 
 To become a preCICE pro:

tools/openfoam-remove-empty-dirs.sh

@@ -6,15 +6,15 @@ openfoam_remove_empty_dirs() {
 		echo "Looking for any time directories without results (e.g. stray functionObjectProperties files, see openfoam-adapter issue #26 on GitHub)..."
 
 		for f in [0-9]* [0-9]*.[0-9]*; do
-			if ! [ -f "${f}/U" ] && ! [ -f "${f}/T" ]; then
+			if ! [ -f "${f}/U" ] && ! [ -f "${f}/T" ] && ! [ -f "${f}/U.gz" ] && ! [ -f "${f}/T.gz" ]; then
 				rm -rfv "${f}"
 			fi
 		done
 		if [ -d processor0 ]; then
 			for d in processor*; do
 				cd "${d}"
 				for f in [0-9]* [0-9]*.[0-9]*; do
-					if ! [ -f "${f}"/U ] && ! [ -f "${f}"/T ]; then
+					if ! [ -f "${f}/U" ] && ! [ -f "${f}/T" ] && ! [ -f "${f}/U.gz" ] && ! [ -f "${f}/T.gz" ]; then
 						rm -rfv "${f}"
 					fi
 				done