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Channel transport with particles (#700)
* Add initial setup * Configure the case properly * Add preliminary README * Add config-visualization * Update note * Add a changelog entry * Add a setup image * MercuryDPM cleaning utility * Add a run script * Extend the README
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‎changelog-entries/700.md‎

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- Added a tutorial for particle tracing with MercuryDPM, Nutils, and OpenFOAM, highlighting the just-in-time mappings in preCICE.

‎channel-transport-particles/README.md‎

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---
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title: Channel transport with particles
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permalink: tutorials-channel-transport-particles.html
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keywords: volume coupling, particles, OpenFOAM, MercuryDPM, transport, just-in-time mapping
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summary: A CFD problem is coupled to a particles in a uni-directional way for particles tracing.
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---
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{% note %}
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Get the [case files of this tutorial](https://github.com/precice/tutorials/tree/develop/channel-transport-particles), as continuously rendered here, or see the [latest released version](https://github.com/precice/tutorials/tree/master/channel-transport-particles) (if there is already one). Read how in the [tutorials introduction](https://precice.org/tutorials.html).
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{% endnote %}
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## Setup
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We model a two-dimensional incompressible fluid flowing through a channel with an obstacle. The fluid problem is coupled to a particle participant for particle tracing. Similar to the transport problem (see the [channel-transport tutorial](tutorials-channel-transport.html)), particles are arranged in a circular blob close to the inflow. The particles then move along with the flow as depicted in the following figure
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![preCICE configuration visualization](images/tutorials-channel-transport-particles-setup.png)
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Note that this scenario features a unidirectional coupling, where the fluid velocity affects the particles, but the particles do not affect the fluid.
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## Configuration
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preCICE configuration (image generated using the [precice-config-visualizer](https://precice.org/tooling-config-visualization.html)):
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![preCICE configuration visualization](images/tutorials-channel-transport-particles-precice-config.pdf
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)
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## Available solvers
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Fluid participant:
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* Nutils. For more information, have a look at the [Nutils adapter documentation](https://precice.org/adapter-nutils.html). This Nutils solver requires at least Nutils v7.0.
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* OpenFOAM (pimpleFoam). For more information, have a look at the [OpenFOAM adapter documentation](https://precice.org/adapter-openfoam-overview.html).
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Particle participant:
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* MercuryDPM. The specific case is available as part of MercuryDPM. To use it, compile MercuryDPM with support for preCICE (`-D MercuryDPM_PreCICE_COUPLING="ON"`). You can compile the relevant executable only using `make ChannelTransport`. Afterwards, the executable `ChannelTransport` is available in the build tree. The `run.sh` script can pick-up the executable, if a `MERCURYDPM_BUILD_DIR` has been exported. Copying the executable or providing it as a command line argument is also possible. Use `run.sh --help` for detailed information. Note that the drag model is mostly an arbitrary choice to validate the technical correctness, but it has no physical background.
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## Running the simulation
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For the fluid solver, use Nutils for ease of installation and OpenFOAM for speed.
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Open two separate terminals and start one fluid and one transport participant by calling the respective run scripts `run.sh` located in each of the participants' directory. For example:
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```bash
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cd fluid-nutils
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./run.sh
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```
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and the particle solver
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```bash
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cd particles-mercurydpm
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./run.sh
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```
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## Post-processing
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All solvers generate `vtk` files which can be visualized using, e.g., ParaView.

‎channel-transport-particles/clean-tutorial.sh‎

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../tools/clean-tutorial-base.sh

‎channel-transport-particles/fluid-nutils/clean.sh‎

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#!/usr/bin/env sh
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set -e -u
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. ../../tools/cleaning-tools.sh
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clean_nutils .

‎channel-transport-particles/fluid-nutils/fluid.py‎

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#! /usr/bin/env python3
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#
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# Incompressible NSE solved within a channel geometry with parabolic inflow profile and an obstacle attached to the bottom towards the middle of the domain. The fluid field is initialized with a Stokes solution. The resulting velocity field is written to preCICE on the complete volume.
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#
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from nutils import function, mesh, cli, solver, export
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import treelog as log
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import numpy as np
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import precice
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from mpi4py import MPI
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def main():
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print("Running Nutils")
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# define the Nutils mesh
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nx = 48
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ny = 16
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step_start = nx // 3
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step_end = nx // 2
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step_hight = ny // 2
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grid = np.linspace(0, 6, nx + 1), np.linspace(0, 2, ny + 1)
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domain, geom = mesh.rectilinear(grid)
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domain = domain.withboundary(inflow="left", outflow="right", wall="top,bottom") - domain[
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step_start:step_end, :step_hight
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].withboundary(wall="left,top,right")
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# cloud of Gauss points
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gauss = domain.sample("gauss", degree=4)
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# Nutils namespace
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ns = function.Namespace()
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ns.x = geom
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ns.ubasis = domain.basis("std", degree=2).vector(2)
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ns.pbasis = domain.basis("std", degree=1)
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ns.u_i = "ubasis_ni ?u_n" # solution
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ns.p = "pbasis_n ?p_n" # solution
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ns.dudt_i = "ubasis_ni (?u_n - ?u0_n) / ?dt" # time derivative
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ns.μ = 0.5 # viscosity
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ns.σ_ij = "μ (u_i,j + u_j,i) - p δ_ij"
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ns.uin = "10 x_1 (2 - x_1)" # inflow profile
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# define the weak form, Stokes problem
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ures = gauss.integral("ubasis_ni,j σ_ij d:x" @ ns)
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pres = gauss.integral("pbasis_n u_k,k d:x" @ ns)
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# define Dirichlet boundary condition
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sqr = domain.boundary["inflow"].integral("(u_0 - uin)^2 d:x" @ ns, degree=2)
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sqr += domain.boundary["inflow,outflow"].integral("u_1^2 d:x" @ ns, degree=2)
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sqr += domain.boundary["wall"].integral("u_k u_k d:x" @ ns, degree=2)
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cons = solver.optimize(["u"], sqr, droptol=1e-15)
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# preCICE setup
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participant = precice.Participant("Fluid", "../precice-config.xml", 0, 1)
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# define coupling mesh
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mesh_name = "Fluid-Mesh"
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vertices = gauss.eval(ns.x)
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vertex_ids = participant.set_mesh_vertices(mesh_name, vertices)
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# coupling data
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data_name = "Velocity"
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participant.initialize()
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timestep = 0
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solver_dt = 0.005
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precice_dt = participant.get_max_time_step_size()
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dt = min(precice_dt, solver_dt)
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state = solver.solve_linear(("u", "p"), (ures, pres), constrain=cons) # initial condition
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# add convective term and time derivative for Navier-Stokes
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ures += gauss.integral("ubasis_ni (dudt_i + μ (u_i u_j)_,j) d:x" @ ns)
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while participant.is_coupling_ongoing():
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if timestep % 1 == 0: # visualize
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bezier = domain.sample("bezier", 2)
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x, u, p = bezier.eval(["x_i", "u_i", "p"] @ ns, **state)
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with log.add(log.DataLog()):
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export.vtk("Fluid_" + str(timestep), bezier.tri, x, u=u, p=p)
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precice_dt = participant.get_max_time_step_size()
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# potentially adjust non-matching timestep sizes
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dt = min(solver_dt, precice_dt)
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# solve Nutils timestep
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state["u0"] = state["u"]
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state["dt"] = dt
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state = solver.newton(("u", "p"), (ures, pres), constrain=cons, arguments=state).solve(1e-10)
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velocity_values = gauss.eval(ns.u, **state)
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participant.write_data(mesh_name, data_name, vertex_ids, velocity_values)
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# do the coupling
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participant.advance(dt)
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# advance variables
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timestep += 1
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participant.finalize()
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if __name__ == "__main__":
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cli.run(main)

‎channel-transport-particles/fluid-nutils/requirements.txt‎

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setuptools # required by nutils
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nutils==7
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numpy >1, <2
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pyprecice~=3.0
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setuptools

‎channel-transport-particles/fluid-nutils/run.sh‎

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#!/usr/bin/env bash
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set -e -u
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. ../../tools/log.sh
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exec > >(tee --append "$LOGFILE") 2>&1
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if [ ! -v PRECICE_TUTORIALS_NO_VENV ]
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then
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python3 -m venv .venv
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. .venv/bin/activate
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pip install -r requirements.txt && pip freeze > pip-installed-packages.log
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fi
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python3 fluid.py
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close_log

‎channel-transport-particles/fluid-openfoam/0/U‎

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FoamFile
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{
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version 2.0;
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format ascii;
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class volVectorField;
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object U;
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}
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dimensions [0 1 -1 0 0 0 0];
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internalField uniform (10 0 0);
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boundaryField
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{
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inlet
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{
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type fixedValue;
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value $internalField;
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}
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outlet
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{
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type zeroGradient;
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}
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obstacle
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{
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type noSlip;
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}
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upperWall
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{
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type noSlip;
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}
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lowerWall
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{
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type noSlip;
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}
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frontAndBack
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{
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type empty;
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}
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}

‎channel-transport-particles/fluid-openfoam/0/p‎

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FoamFile
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{
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version 2.0;
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format ascii;
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class volScalarField;
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object p;
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}
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dimensions [0 2 -2 0 0 0 0];
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internalField uniform 0;
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boundaryField
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{
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inlet
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{
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type zeroGradient;
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}
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outlet
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{
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type fixedValue;
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value uniform 0;
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}
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obstacle
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{
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type zeroGradient;
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}
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upperWall
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{
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type zeroGradient;
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}
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lowerWall
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{
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type zeroGradient;
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}
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frontAndBack
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{
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type empty;
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}
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}

‎channel-transport-particles/fluid-openfoam/clean.sh‎

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#!/usr/bin/env sh
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set -e -u
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. ../../tools/cleaning-tools.sh
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clean_openfoam .

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