Add snapshot configuration docs

docs/snapshot_configuration.md

@@ -0,0 +1,68 @@
+---
+title: Configure the Snapshot Computation
+permalink: tooling-micro-manager-snapshot-configuration.html
+keywords: tooling, macro-micro, two-scale, snapshot
+summary: Provide a JSON file to configure the Micro Manager snapshot computation.
+---
+
+> Note: To install the Micro Manager for the snapshot computation, follow the instructions in the [Micro Manager installation guide](tooling-micro-manager-installation.html).
+> To prepare a micro simulation for the Micro Manager, follow the instructions in the [Micro Manager preparation guide](tooling-micro-manager-preparation.html).
+> Currently, the Micro Manager Snapshot tool can not be used with an `initialize()` method.
+
+The Micro Manager snapshot computation is configured with a JSON file. An example configuration file is
+
+```json
+{
+    "micro_file_name": "python-dummy/micro_dummy",
+    "coupling_params": {
+        "parameter_file_name": "parameter.hdf5",
+        "read_data_names": {"macro-scalar-data": "scalar", "macro-vector-data": "vector"},
+        "write_data_names": {"micro-scalar-data": "scalar", "micro-vector-data": "vector"},
+    },
+    "simulation_params": {
+        "micro_dt": 1.0,
+    },
+    "snapshot_params": {
+        "post_processing_file_name": "snapshot_postprocessing"
+    },
+    "diagnostics": {
+        "output_micro_sim_solve_time": "True"
+    }
+}
+```
+
+This example configuration file is in [`examples/snapshot-config.json`](https://github.com/precice/micro-manager/tree/develop/examples/snapshot-config.json).
+
+The path to the file containing the Python importable micro simulation class is specified in the `micro_file_name` parameter. If the file is not in the working directory, give the relative path.
+
+There are four main sections in the configuration file, the `coupling_params`, the `simulations_params`, the `snapshot_params` and the optional `diagnostics`.
+
+## Coupling Parameters
+
+Parameter | Description
+--- | ---
+`parameter_file_name` | Path to the HDF5 file containing the parameter space from the current working directory. Each macro parameter must be given as a dataset. Macro data for the same micro simulation should have the same index in the first dimension. The name must correspond to the names given in the config file.
+`read_data_names` | A Python dictionary with the names of the data to be read from preCICE as keys and `"scalar"` or `"vector"` as values depending on the nature of the data.
+`write_data_names` | A Python dictionary with the names of the data to be written to preCICE as keys and `"scalar"` or `"vector"` as values depending on the nature of the data.
+
+## Simulation Parameters
+
+Parameter | Description
+--- | ---
+`micro_dt` | Initial time window size (dt) of the micro simulation. Must be set even if the micro simulation is time-independent.
+
+## Snapshot Parameters
+
+Parameter | Description
+--- | ---
+`post_processing_file_name`| Path to the post-processing script from the current working directory.
+
+## Diagnostics
+
+Parameter | Description
+--- | ---
+`output_micro_sim_solve_time` | If `True`, the Micro Manager writes the wall clock time of the `solve()` function of each micro simulation.
+
+## Next step
+
+After creating a configuration file you are ready to [run the Micro Manager snapshot computation](tooling-micro-manager-running.html/#snapshot-computation).