Add new tutorial: opendihu-febio-muscle-contraction

muscle-contraction-with-fibres/.gitignore

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+fibers-opendihu/src/hodgkin_huxley-razumova.c
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muscle-contraction-with-fibres/README.md

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+---
+title: Muscle contraction with fibers
+permalink: 
+keywords: OpenDiHu, FEBio
+summary: The muscle contraction with fibers is a solid mechanics problem. The muscle participant, is a FEM solver is used to compute the deformation of the muscle due to internal active forces. The fibers participant takes care of the computation of active forces by solving the monodomain equation in each fiber. This tutorial contains OpenDiHu and FEBio variants of the FEM solver and an OpenDiHu fibers solvers.  
+---
+
+**Disclaimer:** This tutorial is built on the work of Silas Natterer et al. You can check out their work at their [repository](https://github.com/silasnatterer/bfp), including a student report. 
+
+## Setup
+
+## Available solvers
+
+The muscle and fibers participants are supported in:
+
+- *OpenDiHu*: Check [OpenDiHu's documentation](https://opendihu.readthedocs.io/en/latest/) and follow the installation instructions. 
+- *FEBio*: TODO
+
+Note: the fibers participant is only supported in OpenDiHu.
+
+Before running the OpenDiHu participants you first have to build it. In order to follow the following instructions you must have added `OPENDIHU_HOME` to your system variables as well as the aliases for `mkorn` and `sr`.
+
+```bash
+cd muscle-opendihu
+mkorn && sr
+```
+
+```bash
+cd fibers-opendihu
+mkorn && sr
+```
+
+## Running the Simulation
+
+### OpenDiHu
+
+Open two separate terminals and start each participant by calling the respective run script.
+
+```bash
+cd muscle-opendihu
+./run.sh
+```
+
+and
+
+```bash
+cd fibers-opendihu
+./run.sh
+```
+
+### FEBio
+
+TODO
+
+## Post-processing
+
+TODO
+
+## References
+
+TODO

muscle-contraction-with-fibres/fibers-opendihu/SConscript

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+# This script declares to SCons how to compile the example.
+# It has to be called from a SConstruct file.
+# The 'env' object is passed from there and contains further specification like directory and debug/release flags.
+#
+# Note: If you're creating a new example and copied this file, adjust the desired name of the executable in the 'target' parameter of env.Program.
+
+
+Import('env')     # import Environment object from calling SConstruct
+
+# if the option no_tests was given, quit the script
+if not env['no_examples']:
+
+  # create the main executable
+  env.Program(target = 'fibers', source= "src/fibers.cpp")

muscle-contraction-with-fibres/fibers-opendihu/SConstruct

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+# SConstruct file for a single example.
+#
+# Usage: `scons BUILD_TYPE=debug` will build debug version, `scons` will build release version.
+
+# Call the generic `SConstructGeneral` script that will configure everything. It is located at the top level directory of opendihu.
+# That script will then call a `SConscript` file that defines which sources to use.
+
+import os
+
+# get the directory where opendihu is installed (the top level directory of opendihu)
+opendihu_home = os.environ.get('OPENDIHU_HOME') or "../../.."
+
+# set path where the "SConscript" file is located (set to current path)
+path_where_to_call_sconscript = Dir('.').srcnode().abspath
+
+# call general SConstruct that will configure everything and then call SConscript at the given path
+SConscript(os.path.join(opendihu_home,'SConstructGeneral'), 
+           exports={"path": path_where_to_call_sconscript})

muscle-contraction-with-fibres/fibers-opendihu/run.sh

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+#!/bin/sh
+set -e -u
+
+./build_release/fibers settings_fibers.py