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Add sections to config doc #253

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23 changes: 18 additions & 5 deletions docs/configuration.md
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,8 @@ Apart from the base settings, there are three main sections in the configuration

## Coupling Parameters

This section is nested under `diagnostics`.

| Parameter | Description |
|----------------------------|--------------------------------------------------------------------------------|
| `precice_config_file_name` | Path to the preCICE XML configuration file from the current working directory. |
Expand All @@ -34,6 +36,8 @@ Apart from the base settings, there are three main sections in the configuration

## Simulation Parameters

This section is nested under `simulation_params`.

| Parameter | Description | Default |
| --- | --- | --- |
| `macro_domain_bounds` | Minimum and maximum bounds of the macro-domain, having the format `[xmin, xmax, ymin, ymax, zmin, zmax]` in 3D and `[xmin, xmax, ymin, ymax]` in 2D. | - |
Expand All @@ -50,6 +54,8 @@ Non-uniform domain decomposition is based on a geometric progression.

## Diagnostics

This section is nested under `diagnostics`.

| Parameter | Description | Default |
|------------------------|--------------------------------------------------------------------------------------------------------------------------------------------|---------|
| `data_from_micro_sims` | Dictionary with the names of the data from the micro simulation to be written to VTK files as keys and `"scalar"` or `"vector"` as values. | - |
Expand All @@ -73,7 +79,9 @@ If the parameter `data_from_micro_sims` is set, the data to be output needs to b

See the [adaptivity](tooling-micro-manager-adaptivity.html) documentation for a detailed explanation about the algorithm and variants.

To turn on adaptivity, set `"adaptivity": true` in `simulation_params`. Then under `adaptivity_settings` set the following variables:
This section is nested under `simulation_params`.
To turn on adaptivity, set `"adaptivity": true`.
Then under `adaptivity_settings` set the following variables:

| Parameter | Description | Default |
|-----------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------|
Expand Down Expand Up @@ -113,7 +121,9 @@ Example of adaptivity configuration is

See the [model adaptivity](tooling-micro-manager-model-adaptivity.html) documentation for a detailed explanation about the interface.

To turn on model adaptivity, set `"model_adaptivity": true` in `simulation_params`. Then under `model_adaptivity_settings` set the following variables:
This section is nested under `simulation_params`.
To turn on model adaptivity, set `"model_adaptivity": true`.
Then under `model_adaptivity_settings` set the following variables:

| Parameter | Description |
|----------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
Expand All @@ -129,7 +139,7 @@ Example of model adaptivity configuration is
"model_adaptivity_settings": {
"micro_file_names": ["python-dummy/micro_dummy", "python-dummy/micro_dummy", "python-dummy/micro_dummy"],
"switching_function": "mada_switcher",
"micro_stateless": [False, True, True]
"micro_stateless": [false, true, true]
}
}
```
Expand Down Expand Up @@ -160,8 +170,11 @@ The Micro Manager uses the output functionality of preCICE, hence these data set

## Load balancing

Load balancing can be activated by setting `load_balancing` to true.
It balances based on either the elapsed time required to solve the prior iteration `type="time""` or the number of active simulations `type=active`.
This section is nested under `simulation_params`.
To turn on load balancing, set `"load_balancing": true`.
Then under `load_balancing_setting` set the following configuration.

The load balancing balances based on either the elapsed time required to solve the prior iteration `type="time""` or the number of active simulations `type=active`.
One Initial load balancing step is performed, prior to any computation (assuming equal workload for time based load balancing or the current active counts for `active` load balancing.).
Subsequently, in the following iteration another load balancing step is performed based. (This is mainly for the time based balancing to use the just acquired timings.)
Afterwards balancing is performed `every_n_time_windows`.
Expand Down
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