Add julia example in resonant circuit

.gitignore

@@ -40,6 +40,10 @@ __pycache__/
 Cargo.lock
 target/
 
+# Julia
+Manifest.toml
+Project.toml
+
 # OpenFOAM
 0.*/
 [1-9]*/

changelog-entries/658.md

@@ -0,0 +1 @@
+- Added Julia-based participants to the resonant-circuit tutorial [#658](https://github.com/precice/tutorials/pull/658)

resonant-circuit/README.md

@@ -1,14 +1,14 @@
 ---
-title: Resonant Circuit
+title: Resonant circuit
 permalink: tutorials-resonant-circuit.html
-keywords: MATLAB, Python
+keywords: MATLAB, Python, Julia
 summary: We simulate a two-element LC circuit (one inductor and one capacitor).
 ---
 
 
 ## Setup
 
-The purpose of this tutorial is to illustrate the usage of preCICE to couple MATLAB code. Two different MATLAB solvers will be coupled to simulate a two-element LC circuit. This type of circuit consists of a very simple system with one inductor and one capacitor:
+Two different solvers are coupled to simulate a two-element LC circuit. This type of circuit consists of a simple system with one inductor and one capacitor:
 
 ![LC circuit diagram [1]](images/tutorials-resonant-circuit-diagram.svg)
 
@@ -20,7 +20,7 @@ $I(t) = -C \frac{\text{d}U}{\text{d}t}$
 
 where $I$ is the current and $U$ the voltage of the circuit.
 
-Each of these equations is going to be solved by a different MATLAB solver. Note that, as only one scalar is solved per equation, this is a 0+1 dimensional problem.
+Each of these equations is solved by a different solver. Note that, as only one scalar is solved per equation, this is a 0+1 dimensional problem.
 
 ## Configuration
 
@@ -31,43 +31,42 @@ preCICE configuration (image generated using the [precice-config-visualizer](htt
 ## Available solvers
 
 * *MATLAB* A solver using the [MATLAB bindings](https://precice.org/installation-bindings-matlab.html).
- Before running this tutorial, follow the [instructions](https://precice.org/installation-bindings-matlab.html) to correctly install the MATLAB bindings.
 * *Python* A solver using the preCICE [Python bindings](https://precice.org/installation-bindings-python.html).
+* *Julia* A solver using the preCICE [Julia bindings](https://precice.org/installation-bindings-julia.html).
 
 ## Running the simulation
 
-### MATLAB
+All listed solvers can be used to run the simulation. Open two separate terminals and start the desired capacitor and coil participants by calling the respective run script. For example:
 
-For running this example, first get into one of the solver folders and open a MATLAB instance.
-Afterward, do the same for the second solver.
-After adding the MATLAB bindings to the MATLAB path (in both instances), run the following commands:
-
-In the first MATLAB instance, one can run the solver for the current:
-
-```MATLAB
-coil
+```bash
+cd capacitor-python
+./run.sh
 ```
 
-And in the second MATLAB instance, the solver for the voltage:
+and
 
-```MATLAB
-capacitor
+```bash
+cd coil-julia
+./run.sh
 ```
 
-The preCICE configuration file is hard-coded as `precice-config.xml` in the solvers.
+### Running the MATLAB participants
+
+For running this example in the MATLAB GUI, first get into each of the solver folders and open a MATLAB instance for each.
+After adding the MATLAB bindings to the MATLAB path (in both instances), run the `coil` and `capacitor` commands in the two windows.
 
-#### Running from terminal
+The path to the preCICE configuration file is hard-coded as `precice-config.xml` in the solvers.
 
-If you prefer to not open the MATLAB GUIs, you can alternatively use two shells instead.
+If you prefer not to use the MATLAB GUI, you can alternatively use two shells instead.
 For that, modify the path in the file `matlab-bindings-path.sh` found in the base directory of this tutorial to the path to your MATLAB bindings.
 
 By doing that, you can now open two shells and switch into the directories `capacitor-matlab` and `coil-matlab` and execute the `run.sh` scripts.
 
 ## Post-processing
 
-As we defined a watchpoint on the 'Capacitor' participant (see `precice-config.xml`), we can plot it with gnuplot using the script `plot-solution.sh.` You need to specify the directory of the selected solid participant as a command line argument, so that the script can pick-up the desired watchpoint file, e.g. `./plot-solution.sh capacitor-python`. The resulting graph shows the voltage and current exchanged between the two participants.
+As we defined a watchpoint on the 'Capacitor' participant (see `precice-config.xml`), we can plot it with gnuplot using the script `plot-solution.sh`. You need to specify the directory of the selected solid participant as a command line argument, so that the script can pick-up the desired watchpoint file, e.g., `./plot-solution.sh capacitor-python`. The resulting graph shows the voltage and current exchanged between the two participants.
 
-Additionally, the MATLAB participant `capacitor-matlab` records the current and voltage over time. At the end of the simulation it creates a plot with the computed waveforms of current and voltage, as well as the analytical solution.
+Additionally, the `capacitor-matlab` case records the current and voltage over time. At the end of the simulation, it creates a plot with the computed waveforms of current and voltage, as well as the analytical solution.
 
 After successfully running the coupling, one can find the curves in the folder `capacitor-matlab` as `Curves.png`.
 

resonant-circuit/capacitor-julia/capacitor.jl

@@ -0,0 +1,82 @@
+using PreCICE
+using DifferentialEquations
+
+# Initialize and configure preCICE
+participant = PreCICE.createParticipant("Capacitor", "../precice-config.xml", 0, 1)
+
+# Geometry IDs. As it is a 0-D simulation, only one vertex is necessary.
+mesh_name = "Capacitor-Mesh"
+
+dimensions = PreCICE.getMeshDimensions(mesh_name)
+
+vertex_ids = PreCICE.setMeshVertices(mesh_name, zeros((1,dimensions)))
+
+let
+    # Data IDs
+    read_data_name = "Current"
+    write_data_name = "Voltage"
+
+    # Simulation parameters and initial condition
+    C = 2                         # Capacitance of the capacitor
+    L = 1                         # Inductance of the coil
+    t0 = 0                        # Initial simulation time
+    t_max = 10                    # End simulation time
+    Io = 1                        # Initial current
+    phi = 0                       # Phase of the signal
+
+    w0 = 1 / sqrt(L * C)          # Resonant frequency
+    U0 = -w0 * L * Io * sin(phi)  # Initial condition for U
+
+    function f_U(u, p, t)
+        (dt, C, mesh_name, read_data_name, vertex_ids) = p
+        I = PreCICE.readData(mesh_name, read_data_name, vertex_ids, dt)
+        return -I[1] / C      # Time derivative of U
+    end
+
+    # Initialize simulation
+    if PreCICE.requiresInitialData()
+        PreCICE.writeData(mesh_name, write_data_name, vertex_ids, I0)
+    end
+    PreCICE.initialize()
+
+    solver_dt = PreCICE.getMaxTimeStepSize()
+
+    # Start simulation
+    t = t0
+    U0_checkpoint = U0
+    t_checkpoint = t
+    while PreCICE.isCouplingOngoing()
+
+        # Record checkpoint if necessary
+        if PreCICE.requiresWritingCheckpoint()
+            U0_checkpoint = U0
+            t_checkpoint = t
+        end
+
+        # Make Simulation Step
+        precice_dt = PreCICE.getMaxTimeStepSize()
+        dt = min(precice_dt, solver_dt)
+        t_span = (t, t + dt)
+        params = (dt, C, mesh_name, read_data_name, vertex_ids)
+        prob = ODEProblem(f_U, U0, t_span, params)
+        # https://docs.sciml.ai/DiffEqDocs/stable/basics/common_solver_opts
+        sol = solve(prob, Tsit5(), reltol=1e-12, abstol=1e-12)
+
+        # Exchange data
+        evals = max(length(sol.t), 3)  # at least do 3 substeps to allow cubic interpolation
+        for i in range(1,evals)
+            U0 = sol(t_span[1] + i * dt / evals)
+            PreCICE.writeData(mesh_name, write_data_name, vertex_ids, fill(U0, (1,1)))
+            PreCICE.advance(dt / evals)
+        end
+        t = t + dt
+
+        # Recover checkpoint if not converged
+        if PreCICE.requiresReadingCheckpoint()
+            U0 = U0_checkpoint
+            t = t_checkpoint
+        end
+    end
+    # Stop coupling
+    PreCICE.finalize()
+end

resonant-circuit/capacitor-julia/clean.sh

@@ -0,0 +1,7 @@
+#!/bin/sh
+set -e -u
+
+. ../../tools/cleaning-tools.sh
+
+clean_precice_logs .
+clean_case_logs .

resonant-circuit/capacitor-julia/run.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+set -e -u
+
+. ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
+
+julia --project=Project.toml -e 'using Pkg; Pkg.add("DifferentialEquations"); Pkg.add("PreCICE"); Pkg.instantiate();'
+julia --project=Project.toml capacitor.jl
+
+close_log

resonant-circuit/capacitor-matlab/clean.sh

@@ -1,8 +1,7 @@
 #!/bin/sh
 set -e -u
 
-rm ./*.png ./*.mat
-
 . ../../tools/cleaning-tools.sh
 
 clean_matlab .
+rm -f ./*.png ./*.mat

resonant-circuit/capacitor-python/clean.sh

@@ -0,0 +1,7 @@
+#!/bin/sh
+set -e -u
+
+. ../../tools/cleaning-tools.sh
+
+clean_precice_logs .
+clean_case_logs .

resonant-circuit/coil-julia/clean.sh

@@ -0,0 +1,7 @@
+#!/bin/sh
+set -e -u
+
+. ../../tools/cleaning-tools.sh
+
+clean_precice_logs .
+clean_case_logs .

resonant-circuit/coil-julia/coil.jl

@@ -0,0 +1,85 @@
+using PreCICE
+using DifferentialEquations
+
+# Initialize and configure preCICE
+participant = PreCICE.createParticipant("Coil", "../precice-config.xml", 0, 1)
+
+# Geometry IDs. As it is a 0-D simulation, only one vertex is necessary.
+mesh_name = "Coil-Mesh"
+
+dimensions = PreCICE.getMeshDimensions(mesh_name)
+
+vertex_ids = PreCICE.setMeshVertices(mesh_name, zeros((1,dimensions)))
+
+let
+    # Data IDs
+    read_data_name = "Voltage"
+    write_data_name = "Current"
+
+    # Simulation parameters and initial condition
+    C = 2                      # Capacitance of the capacitor
+    L = 1                      # Inductance of the coil
+    t0 = 0                     # Initial simulation time
+    Io = 1                     # Initial current
+    phi = 0                    # Phase of the signal
+
+    w0 = 1 / sqrt(L * C)       # Resonant frequency
+    I0 = Io * cos(phi)         # Initial condition for I
+
+    # to estimate cost
+    f_evals = 0
+
+    function f_I(u, p, t)
+        f_evals += 1
+        (dt, L, mesh_name, read_data_name, vertex_ids) = p
+        U = PreCICE.readData(mesh_name, read_data_name, vertex_ids, dt)
+        return U[1] / L  # Time derivative of I; ODE determining capacitor
+    end
+
+    # Initialize simulation
+    if PreCICE.requiresInitialData()
+        PreCICE.writeData(mesh_name, write_data_name, vertex_ids, I0)
+    end
+    PreCICE.initialize()
+
+    solver_dt = PreCICE.getMaxTimeStepSize()
+
+    # Start simulation
+    t = t0
+    I0_checkpoint = I0
+    t_checkpoint = t
+    while PreCICE.isCouplingOngoing()
+
+        # Record checkpoint if necessary
+        if PreCICE.requiresWritingCheckpoint()
+            I0_checkpoint = I0
+            t_checkpoint = t
+        end
+
+        # Make Simulation Step
+        precice_dt = PreCICE.getMaxTimeStepSize()
+        dt = min(precice_dt, solver_dt)
+        t_span = (t, t + dt)
+        params = (dt, L, mesh_name, read_data_name, vertex_ids)
+        prob = ODEProblem(f_I, I0, t_span, params)
+        # https://docs.sciml.ai/DiffEqDocs/stable/basics/common_solver_opts
+        sol = solve(prob, Tsit5(), reltol=1e-12, abstol=1e-12)
+
+        # Exchange data
+        evals = max(length(sol.t), 3)  # at least do 3 substeps to allow cubic interpolation
+        for i in range(1,evals)
+            I0 = sol(t_span[1] + i * dt / evals)
+            PreCICE.writeData(mesh_name, write_data_name, vertex_ids, fill(I0, (1,1)))
+            PreCICE.advance(dt / evals)
+        end
+        t = t + dt
+
+        # Recover checkpoint if not converged
+        if PreCICE.requiresReadingCheckpoint()
+            I0 = I0_checkpoint
+            t = t_checkpoint
+        end
+    end
+    # Stop coupling
+    PreCICE.finalize()
+end

resonant-circuit/coil-julia/run.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+set -e -u
+
+. ../../tools/log.sh
+exec > >(tee --append "$LOGFILE") 2>&1
+
+julia --project=Project.toml -e 'using Pkg; Pkg.add("DifferentialEquations"); Pkg.add("PreCICE"); Pkg.instantiate();'
+julia --project=Project.toml coil.jl
+
+close_log

resonant-circuit/coil-python/clean.sh

@@ -0,0 +1,7 @@
+#!/bin/sh
+set -e -u
+
+. ../../tools/cleaning-tools.sh
+
+clean_precice_logs .
+clean_case_logs .

resonant-circuit/precice-config.xml

@@ -1,5 +1,12 @@
 <?xml version="1.0" encoding="UTF-8" ?>
 <precice-configuration>
+  <log>
+    <sink
+      filter="%Severity% > debug and %Rank% = 0"
+      format="---[precice] %ColorizedSeverity% %Message%"
+      enabled="true" />
+  </log>
+
   <data:scalar name="Current" waveform-degree="3" />
   <data:scalar name="Voltage" waveform-degree="3" />