of the `reaction` part. It must follow the syntax of `d<var_i>_d<var_j>`, which
reads as the *partial derivate of `<var_i>` with respect to `<var_j>`*.
* The `operator` subsection is an experimental feature and we recommend to set all variables to the
same index, e.g. 0.
* Finally, the subsection `writer` will define the file name for the vtk output.
For example, the following `mode.nucleous` section defines a [Gray-Scott
model with `F=0.0420` and `k=0.0610`](http://mrob.com/pub/comp/xmorphia/F420/F420-k610.html):
```ini
[model.nucleous.initial]
u=0.5
v=(x>0) && (x<0.5) && (y>0.) && (y<0.5) ? 1 : 0
[model.nucleous.diffusion]
u=2e-5
v=2e-5/2
[model.nucleous.reaction]
u=-u*v^2+0.0420*(1-u)
v=u*v^2-(0.0420+0.0610)*v
[model.nucleous.reaction.jacobian]
du_du=-v^2-0.0420
du_dv=-2*u*v
dv_du=v^2
dv_dv=2*u*v-(0.0420+0.0610)
[model.nucleous.operator]
u=0
v=0
[model.nucleous.writer]
file_name=nucleous_output
```
The `model.cytoplasm` would have to be defined in similar way. An important aspect when working
with different compartments is the interface fluxes. In `dune-copasi` thex fluxes are set
automatically to [dirichlet-dirichlet](https://en.wikipedia.org/wiki/Dirichlet_boundary_condition)
boundary conditions iff the variable is shared between the two intersecting domains. Further
improvements will come for interface treatment.
#### Logging
The logging settings are directly forwarded to the `dune-logging` module. Please check
its doxygen documentation for detailed information. A simple configuration is the following:
```ini
[logging]
# possible levels: off, critical, error, waring, notice, info, debug, trace, all
default.level=trace
The full build system is described in the `dune-common/doc/buildsystem` (Git version) or under `share/doc/dune-common/buildsystem` if you installed DUNE! -->
@@ -7,15 +7,15 @@ RUN ln -s /duneci/toolchains/${TOOLCHAIN} /duneci/toolchain
RUN echo'CMAKE_FLAGS+=" -DDUNE_PYTHON_VIRTUALENV_SETUP=1 -DDUNE_PYTHON_VIRTUALENV_PATH=/duneci/modules/dune-python-venv"'>> /duneci/cmake-flags/enable_virtualenv
RUN echo'CMAKE_FLAGS+=" -DCMAKE_GENERATOR="Ninja'>> /duneci/cmake-flags/cmake_generator
RUN duneci-install-module -b support/dune-copasi https://gitlab.dune-project.org/santiago.ospina/dune-common.git \