New tutorial: two-scale mechanics problem on a 3D notch component

two-scale-notch/README.md

@@ -0,0 +1,73 @@
+---
+title: Two-scale notch
+permalink: tutorials-two-scale-notch.html
+keywords: Macro-micro, Micro Manager, CalculiX, FANS, FE-FFT
+summary: We solve a two-scale notch problem with a micro-structure based material. One macro simulation is coupled to several micro simulations using the Micro Manager.
+---
+
+{% note %}
+Get the [case files of this tutorial](https://github.com/precice/tutorials/tree/master/two-scale-notch). Read how in the [tutorials introduction](https://precice.org/tutorials.html).
+{% endnote %}
+
+## Setup
+
+This tutorial solves a linear elastic static problem on a 3D notch geometry which has an underlying micro-structure. The notch is fixed at one end and has a force boundary condition at the other end.
+
+<img class="img-responsive" src="images/tutorials-two-scale-notch-mesh-with-boundary-conditions.png" alt="Von Mises stress on macro scale" width=60% height=50%/>
+
+The micro-structure is a 3D sphere enclosed in a unit square box.
+
+<img class="img-responsive" src="images/tutorials-two-scale-notch-micro-structure.png" alt="Micro structure" width=30% height=40%/>
+
+The micro-structure needs to be evaluated to obtain the stresses and the material stiffness matrix, both necessary for solving the problem on the macro scale. This leads to a two-scale problem with one macro-scale simulation and several micro-scale simulations.
+
+At each Gauss point of the macro domain there exists a micro simulation. The macro problem is one participant, which is coupled to many micro simulations. Each micro simulation is not an individual coupling participant, instead we use the [Micro Manager](https://github.com/precice/micro-manager), which controls all the micro simulations and is itself a coupling participant.
+
+## Configuration
+
+preCICE configuration (image generated using the [precice-config-visualizer](https://precice.org/tooling-config-visualization.html)):
+
+![preCICE configuration visualization](images/tutorials-two-scale-notch-precice-config.png)
+
+## Available solvers and dependencies
+
+* The macro notch problem is solved using [CalculiX](https://www.calculix.de/), so it required the [CalculiX adapter](https://github.com/precice/calculix-adapter).
+* The micro problem is solved using [FANS](https://github.com/DataAnalyticsEngineering/FANS/tree/develop). FANS needs to be compiled in a Python-wrapped library form, check the [documentation](https://github.com/DataAnalyticsEngineering/FANS/blob/develop/pyfans/README.md) on how to do this.
+* The [Micro Manager](https://precice.org/tooling-micro-manager-installation.html) controls all micro-simulations and facilitates coupling via preCICE. Use the [develop](https://github.com/precice/micro-manager/tree/develop) branch of the Micro Manager.
+
+## Running the simulation
+
+You can find the corresponding `run.sh` script for running the case in the folders corresponding to the solvers you want to use.
+
+Run the macro problem:
+
+```bash
+cd macro-calculix
+./run.sh
+```
+
+Check the Micro Manager [configuration](https://precice.org/tooling-micro-manager-configuration.html) and [running](https://precice.org/tooling-micro-manager-running.html) documentation to understand how to set it up and launch it. The Micro Manager can be run via this script in serial or parallel. Run it in serial:
+
+```bash
+cd micro-fans
+./run.sh -s
+```
+
+## Running the simulation in parallel
+
+```bash
+cd micro-fans
+./run.sh -p <num_procs>
+```
+
+The `num_procs` needs to fit the decomposition specified in the `micro-manager-config.json` (default is serial). See the documentation on [how to set domain decomposition](https://precice.org/tooling-micro-manager-configuration.html#domain-decomposition) in the Micro Manager configuration.
+
+**NOTE**: When running `micro-fans`, even though the case setup and involved physics is simple, each micro simulation is a FANS simulation with a mesh of 32x32x32 nodes, which usually has a moderately high computation time. If the Micro Manager is run in serial, the total runtime is approximately 30 minutes.
+
+## Post-processing
+
+The final von Mises stress on the macro scale look like
+
+<img class="img-responsive" src="images/tutorials-two-scale-notch-von-mises-stress.png" alt="Von Mises stress on macro scale" width=30% height=10%/>
+
+The result is generated by converting the CalculiX `.frd` output file to a VTU or VTK file using [ccx2paraview](https://github.com/calculix/ccx2paraview), and visualizing it in ParaView.

two-scale-notch/clean-tutorial.sh

@@ -0,0 +1,11 @@
+#!/usr/bin/env sh
+set -e -u
+
+# shellcheck disable=SC1091
+. ../tools/cleaning-tools.sh
+
+clean_tutorial .
+clean_precice_logs .
+rm -fv ./*.log
+rm -fv ./*.vtu
+

two-scale-notch/macro-calculix/clean.sh

@@ -0,0 +1,6 @@
+#!/usr/bin/env sh
+set -e -u
+
+. ../../tools/cleaning-tools.sh
+
+clean_calculix .

two-scale-notch/macro-calculix/config.yml

@@ -0,0 +1,9 @@
+participants:
+    Notch:
+        interfaces:
+        - elements-mesh: notch-mesh
+          patch: Eall
+          read-data: [stresses1to3, stresses4to6, cmat1, cmat2, cmat3, cmat4, cmat5, cmat6, cmat7]
+          write-data: [strains1to3, strains4to6]
+
+precice-config-file: ../precice-config.xml