Adapt documentation

docs/README.md

@@ -11,6 +11,8 @@ The Micro Manager manages many simulations on a micro scale and couples them to
 
 ![Micro Manager strategy schematic](images/docs-tooling-micro-manager-manager-solution.png)
 
+The Micro Manager can also compute snapshots of micro simulations given macro input parameters in an offline manner without preCICE.
+
 ## What can it do?
 
 The Micro Manager couples many micro simulations with one macro simulation. This includes ...
@@ -21,9 +23,13 @@ The Micro Manager couples many micro simulations with one macro simulation. This
 
 ## Documentation
 
-To use the Micro Manager for a macro-micro coupling, your micro simulation code needs to be in a library format with a specific class name and functions with specific names. For a macro-micro coupled problem, the macro simulation code is coupled to preCICE directly. The section [couple your code](couple-your-code-overview.html) of the preCICE documentation gives more details on coupling existing codes. To setup a macro-micro coupled simulation using the Micro Manager, follow these steps:
+To use the Micro Manager for a macro-micro coupling, your micro simulation code needs to be in a library format with a specific class name and functions with specific names. For a macro-micro coupled problem, the macro simulation code is coupled to preCICE directly. The section [couple your code](couple-your-code-overview.html) of the preCICE documentation gives more details on coupling existing codes. To set up a macro-micro coupled simulation using the Micro Manager, follow these steps:
 
 - [Installation](tooling-micro-manager-installation.html)
 - [Preparing micro simulation](tooling-micro-manager-prepare-micro-simulation.html)
 - [Configuration](tooling-micro-manager-configuration.html)
 - [Running](tooling-micro-manager-running.html)
+
+To compute snapshots in an offline manner your simulation code also needs to be in a library format with a specific class name and functions with specific names. To set up a snapshot computation using the Micro Manager, follow these steps:
+
+- [Snapshot computation](tooling-micro-manager-snapshot-configuration.html)

docs/configuration.md

@@ -173,4 +173,4 @@ For more details on the interpolation see the [crash handling documentation](too
 
 ## Next step
 
-After creating a configuration file you are ready to [run the Micro Manager](tooling-micro-manager-running.html/#micro-manager).
+After creating a configuration file you are ready to [run the Micro Manager](tooling-micro-manager-running.html).

docs/installation.md

@@ -23,12 +23,6 @@ Unless already installed, the dependencies will be installed by `pip` during the
 pip install --user micro-manager-precice[sklearn]
 ```
 
-To perform snapshot computations, the optional dependency `h5py` is required. To install `micro-manager-precice` with `h5py`, run
-
-```bash
-pip install --user micro-manager-precice[snapshot]
-```
-
 preCICE itself needs to be installed separately. If you encounter problems in the direct installation, see the [dependencies section](#required-dependencies) and [optional dependency section](#optional-dependencies) below.
 
 ### Option 2: Install manually

docs/running.md

@@ -5,8 +5,6 @@ keywords: tooling, macro-micro, two-scale
 summary: Run the Micro Manager from the terminal with a configuration file as input argument or from a Python script.
 ---
 
-## Micro Manager
-
 The Micro Manager is run directly from the terminal by providing the path to the configuration file as an input argument in the following way
 
 ```bash
@@ -22,27 +20,3 @@ mpiexec -n micro-manager-precice micro-manager-config.json
 ### What happens when a micro simulation crashes?
 
 If a micro simulation crashes and the Micro Manager is configured to [interpolate a crashed micro simulation](tooling-micro-manager-configuration.html/#Interpolate-a-crashed-micro-simulation), the Micro Manager attempts to continue running. The error message from the micro simulation, along with the macro location are logged in the Micro Manager log file. The Micro Manager continues the simulation run even if a micro simulation crashes. Results of the crashed micro simulation are generated by interpolating results of a certain number of similar running simulations. The [inverse distance weighed](https://en.wikipedia.org/wiki/Inverse_distance_weighting) method is used. If more than 20% of global micro simulations crash or if locally no neighbors are available for interpolation, the Micro Manager terminates.
-
-## Snapshot Computation
-
-The Micro Manager snapshot computation is run directly from the terminal by adding the `--snapshot` argument and by providing the path to the configuration file as an input argument in the following way
-
-```bash
-micro-manager-precice --snapshot snapshot-config.json
-```
-
-The Micro Manager snapshot computation can also be run in parallel
-
-```bash
-mpiexec -n <number-of-processes> micro-manager-precice --snapshot snapshot-config.json
-```
-
-where `<number-of-processes>` must be replaced with the number of processes to be used.
-
-### Results
-
-The results of the snapshot computation is written into `output/` in HDF5-format. Each parameter is stored in a separate dataset. The dataset names correspond to the names specified in the configuration file. The first dimension of the datasets corresponds to the macro parameter index.
-
-### What happens when a micro mimulation crashes during snapshot computation?
-
-If the computation of a snapshot fails, the snapshot is skipped.

docs/snapshot_configuration.md

@@ -1,13 +1,31 @@
 ---
-title: Configure the Snapshot Computation
+title: 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.
+summary: Set up 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.
+## Installation
+
+To perform snapshot computations, the in the coupled case optional dependency `h5py` becomes mandatory. To install `micro-manager-precice` with `h5py`, run
+
+```bash
+pip install --user micro-manager-precice[snapshot]
+```
+
+If you have already installed `micro-manager-precice`, you can install `h5py` separately by running
+
+```bash
+pip install --user h5py
+```
+
+## Preparation
+
+To prepare a micro simulation for the Micro Manager, follow the instructions in the [Micro Manager preparation guide](tooling-micro-manager-preparation.html).
+
+Note: The `initialize()` method is not supported for the snapshot computation.
+
+## Configuration
 
 The Micro Manager snapshot computation is configured with a JSON file. An example configuration file is
 
@@ -43,7 +61,7 @@ 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.
+`write_data_names` | A Python dictionary with the names of the data to be written to the database as keys and `"scalar"` or `"vector"` as values depending on the nature of the data.
 
 ## Simulation Parameters
 
@@ -55,14 +73,38 @@ Parameter | Description
 
 Parameter | Description
 --- | ---
-`post_processing_file_name`| Path to the post-processing script from the current working directory.
+`post_processing_file_name`| Path to the post-processing Python script from the current working directory. Providing a post-processing script is optional
 
 ## 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.
+`output_micro_sim_solve_time` | If `True`, the Micro Manager writes the wall clock time of the `solve()` function of each micro simulation to the database.
 
 ## Next step
 
-After creating a configuration file you are ready to [run the Micro Manager snapshot computation](tooling-micro-manager-running.html/#snapshot-computation).
+After creating a configuration file you are ready to [run the Micro Manager snapshot computation](tooling-micro-manager-snapshot-configuration.html/#running).
+
+## Running
+
+The Micro Manager snapshot computation is run directly from the terminal by adding the `--snapshot` argument and by providing the path to the configuration file as an input argument in the following way
+
+```bash
+micro-manager-precice --snapshot snapshot-config.json
+```
+
+The Micro Manager snapshot computation can also be run in parallel
+
+```bash
+mpiexec -n <number-of-processes> micro-manager-precice --snapshot snapshot-config.json
+```
+
+where `<number-of-processes>` must be replaced with the number of processes to be used.
+
+### Results
+
+The results of the snapshot computation are written into `output/` in HDF5-format. Each parameter is stored in a separate dataset. The dataset names correspond to the names specified in the configuration file. The first dimension of the datasets corresponds to the macro parameter index.
+
+### What happens when a micro simulation crashes during snapshot computation?
+
+If the computation of a snapshot fails, the snapshot is skipped.