doc: AI-generated doc of master.conf inputs

Author: jjokella

doc/user_guide/usage_wfe/running.md

@@ -22,3 +22,167 @@ Start simulation
 ``` bash
 ./control_tsmp2.sh
 ```
+
+## master.conf
+
+The `master.conf` file contains general configuration settings for the
+workflow engine. It is located in `ctl/master.conf`.
+
+### Main Settings
+
+#### MODEL_ID
+Specifies which model components to use. Options include but are not
+restriced to:
+- `ParFlow` - ParFlow only
+- `ICON-eCLM` - ICON atmosphere with eCLM land surface
+- `ICON-eCLM-ParFlow` - Fully coupled system
+- `ICON` - ICON atmosphere only
+
+#### EXP_ID
+Experiment identifier (e.g., `"eur-11u"`). Used for naming and
+organizing simulation outputs.
+
+#### CASE_ID
+Optional identifier for specific cases within an experiment.
+
+#### conf_file
+Path to case-specific configuration file. If left empty, the system
+will look for `${ctl_dir}/expid.conf`.
+
+### Main Switches
+
+Each workflow stage has three boolean flags: `config`, `run`,
+`cleanup`.
+
+#### lpre
+Preprocessing stage switches: `( config run cleanup )`
+- `config`: Configure preprocessing
+- `run`: Execute preprocessing
+- `cleanup`: Clean up preprocessing files
+
+#### lsim
+Simulation stage switches: `( config run cleanup )`
+- `config`: Configure simulation
+- `run`: Execute simulation
+- `cleanup`: Clean up simulation files
+
+#### lpos
+Post-processing stage switches: `( config run cleanup )`
+- `config`: Configure post-processing
+- `run`: Execute post-processing
+- `cleanup`: Clean up post-processing files
+
+#### lvis
+Visualization stage switches: `( config run cleanup )`
+- `config`: Configure visualization
+- `run`: Execute visualization
+- `cleanup`: Clean up visualization files
+
+### Time Information
+
+#### cpltsp_atmsfc
+Coupling time step between atmosphere and surface (eCLM timestep) in
+seconds. Default: `900`.
+
+#### cpltsp_sfcss
+Coupling time step between surface and subsurface (ParFlow timestep)
+in seconds. Default: `900`.
+
+#### simlength
+Length of each simulation step (e.g., `"1 day"`, `"23 hours"`).
+
+#### startdate
+Start date of the simulation in ISO 8601 format (e.g.,
+`"2017-07-01T00:00Z"`).
+
+#### inidate
+Initial date for the entire simulation in ISO 8601 format. Default:
+same as `startdate`.
+
+#### numsimstep
+Number of simulation steps. 
+
+Total simulation time = `numsimstep * simlength`.
+
+Each simulation step is a queued job on the machine. The next job is
+only executed once the previous is done.
+
+### Mail Notification
+
+#### mailtype
+Email notification trigger for SLURM jobs. Options: `NONE`, `BEGIN`,
+`END`, `FAIL`, `REQUEUE`, `ALL`.
+
+#### mailaddress
+Email address for job notifications. Leave empty if `mailtype=NONE`.
+
+### User Settings
+
+#### prevjobid
+Previous job ID for job chaining. Leave empty by default; system will
+manage this automatically.
+
+#### npnode
+Number of cores per node. Leave empty to use machine defaults.
+
+#### partition
+Compute partition to use. Leave empty to use machine defaults.
+
+#### account
+Compute account for billing. If not set, `$BUDGET_ACCOUNTS` or `slts`
+will be used.
+
+### Wallclock Times
+
+Wallclock time limits for each workflow stage in `hh:mm:ss` format.
+
+#### pre_wallclock
+Time limit for preprocessing jobs (e.g., `00:35:00`).
+
+#### sim_wallclock
+Time limit for simulation jobs (e.g., `00:25:00`).
+
+#### pos_wallclock
+Time limit for post-processing jobs (e.g., `00:05:00`).
+
+#### vis_wallclock
+Time limit for visualization jobs (e.g., `00:05:00`).
+
+### File/Directory Paths
+
+#### tsmp2_dir
+Path to TSMP2 directory. Uses `$TSMP2_DIR` environment variable.
+
+#### tsmp2_install_dir
+Path to TSMP2 installation directory. Leave empty to use default.
+
+#### tsmp2_env
+Path to TSMP2 environment file. Leave empty to use default.
+
+### Node Allocation
+
+Number of nodes allocated to each model component. Components not
+indicated in `MODEL_ID` will have their node count set to zero.
+
+#### ico_node
+Number of nodes for ICON atmosphere component. Default: `3`.
+
+#### clm_node
+Number of nodes for eCLM land surface component. Default: `1`.
+
+#### pfl_node
+Number of nodes for ParFlow subsurface component. Default: `2`.
+
+### Debug and Logging
+
+#### debugmode
+If set to `true`, no job submission is carried out. Works only for
+`config` steps. 
+
+Useful for testing configuration without running jobs.
+
+Useful for running single tasks, e.g. namelist creation.
+
+#### joblog
+If set to `true`, job status will be logged. Default: `true`.
+