diff --git a/docs/source/tutorial1.ipynb b/docs/source/tutorial1.ipynb
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--- a/docs/source/tutorial1.ipynb
+++ b/docs/source/tutorial1.ipynb
@@ -1,11 +1,12 @@
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- "# DART-WRF introductory example\n",
+ "# Tutorial 1: The assimilation step\n",
"DART-WRF is a python package which automates many things like configuration, saving configuration and output, handling computing resources, etc.\n",
"\n",
"**Goal**: Using a predefined configuration file, run an example of Data Assimilation.\n",
diff --git a/docs/source/tutorial2.ipynb b/docs/source/tutorial2.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..054e068ffc482dc2e112ca583a8f388fc71a5612
--- /dev/null
+++ b/docs/source/tutorial2.ipynb
@@ -0,0 +1,121 @@
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+ "# Tutorial 2: Cycled experiment\n",
+ "\n",
+ "\n",
+ "**Goal**: To run a cycled data assimilation experiment.\n",
+ "[`cycled_exp.py`](https://github.com/lkugler/DART-WRF/blob/master/generate_free.py) contains an example which will be explained here:\n",
+ "\n",
+ "#### Configure your experiment\n",
+ "See tutorial 1.\n",
+ "\n",
+ "#### Prepare initial conditions (from input_sounding)\n",
+ "1) Define starting time:\n",
+ "`begin = dt.datetime(2008, 7, 30, 6)`\n",
+ "2) WRF needs directories with certain files:\n",
+ "`id = prepare_WRFrundir(begin)`\n",
+ "3) Create 3D initial conditions from input_sounding etc.:\n",
+ "`id = run_ideal(depends_on=id)`\n",
+ "\n",
+ "#### Run free forecast\n",
+ "Let's say you want to run a free forecast starting at 6z, which you want to use as prior for an assimilation at 9z. Then you need can use the above defined 3 steps to create initial conditions.\n",
+ "Then you can run an ensemble forecast using:\n",
+ "```\n",
+ "id = run_ENS(begin=begin, # start integration from here\n",
+ " end=end, # integrate until here\n",
+ " input_is_restart=False,\n",
+ " output_restart_interval=(end-begin).total_seconds()/60,\n",
+ " depends_on=id)\n",
+ "```\n",
+ "where `begin` & `end` are `dt.datetime` objects.\n",
+ "\n",
+ "#### Assimilate\n",
+ "To assimilate observations at dt.datetime `time` use this command:\n",
+ "\n",
+ "`id = assimilate(time, prior_init_time, prior_valid_time, prior_path_exp, depends_on=id)`\n",
+ "\n",
+ "#### Update initial conditions from Data Assimilation\n",
+ "In order to continue after assimilation you need the posterior = prior (1) + increments (2)\n",
+ "\n",
+ "1. Set prior with this function:\n",
+ "\n",
+ "`id = prepare_IC_from_prior(prior_path_exp, prior_init_time, prior_valid_time, depends_on=id)`\n",
+ "\n",
+ "where path is `str`, times are `dt.datetime`.\n",
+ "\n",
+ "2. To update the model state with assimilation increments, you need to update the WRF restart files by running\n",
+ "\n",
+ "`id = update_IC_from_DA(time, depends_on=id)`\n",
+ "\n",
+ "After this, the wrfrst files are updated with assimilation increments (filter_restart) and copied to the WRF's run directories so you can continue to run the ENS after assimilation using\n",
+ "\n",
+ "```\n",
+ "id = run_ENS(begin=time, # start integration from here\n",
+ " end=time + timedelta_integrate, # integrate until here\n",
+ " restart_path=cluster.archivedir+prior_init_time.strftime('/%Y-%m-%d_%H:%M/'),\n",
+ " output_restart_interval=timedelta_btw_assim.total_seconds()/60,\n",
+ " depends_on=id)\n",
+ "```\n",
+ "where times are `dt.datetime`; `timedelta` variables are `dt.timedelta`.\n",
+ "\n",
+ "\n",
+ "#### Job scheduling status\n",
+ "The script submits jobs into the SLURM queue with dependencies so that SLURM starts the jobs itself as soon as resources are available. Most jobs need only a few cores, but model integration is done across many nodes:\n",
+ "```\n",
+ "$ squeue -u `whoami` --sort=i\n",
+ " JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)\n",
+ " 1710274 mem_0384 prepwrfr lkugler PD 0:00 1 (Priority)\n",
+ " 1710275 mem_0384 IC-prior lkugler PD 0:00 1 (Dependency)\n",
+ " 1710276 mem_0384 Assim-42 lkugler PD 0:00 1 (Dependency)\n",
+ " 1710277 mem_0384 IC-prior lkugler PD 0:00 1 (Dependency)\n",
+ " 1710278 mem_0384 IC-updat lkugler PD 0:00 1 (Dependency)\n",
+ " 1710279 mem_0384 preWRF2- lkugler PD 0:00 1 (Dependency)\n",
+ " 1710280_[1-10] mem_0384 runWRF2- lkugler PD 0:00 1 (Dependency)\n",
+ " 1710281 mem_0384 pRTTOV-6 lkugler PD 0:00 1 (Dependency)\n",
+ " 1710282 mem_0384 Assim-3a lkugler PD 0:00 1 (Dependency)\n",
+ " 1710283 mem_0384 IC-prior lkugler PD 0:00 1 (Dependency)\n",
+ " 1710284 mem_0384 IC-updat lkugler PD 0:00 1 (Dependency)\n",
+ " 1710285 mem_0384 preWRF2- lkugler PD 0:00 1 (Dependency)\n",
+ " 1710286_[1-10] mem_0384 runWRF2- lkugler PD 0:00 1 (Dependency)\n",
+ " 1710287 mem_0384 pRTTOV-7 lkugler PD 0:00 1 (Dependency)\n",
+ "```\n",
+ "\n"
+ ]
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diff --git a/docs/source/tutorial2.rst b/docs/source/tutorial2.rst
deleted file mode 100644
index 254ae4b037d2a70e743689102d4865cb3f38aded..0000000000000000000000000000000000000000
--- a/docs/source/tutorial2.rst
+++ /dev/null
@@ -1,99 +0,0 @@
-Cycled experiment
-=================
-
-#### Configure your experiment
-Define simulation specific variables in [`config/cfg.py`](https://github.com/lkugler/DART-WRF/blob/master/config/cfg.py).
-Define paths for python, ncks, etc. in [`config/clusters.py`](https://github.com/lkugler/DART-WRF/blob/master/config/clusters.py).
-Dependencies are `numpy, pandas, scipy, xarray, netCDF4`. Install non-standard packages with `pip install docopt slurmpy --user`.
-Workflow is defined using meta-routines (functions) like `run_ENS` which are defined in `scheduler.py`.
-
-#### Prepare initial conditions (from input_sounding)
-1) Define starting time:
-`begin = dt.datetime(2008, 7, 30, 6)`
-2) WRF needs directories with certain files:
-`id = prepare_WRFrundir(begin)`
-3) Create 3D initial conditions from input_sounding etc.:
-`id = run_ideal(depends_on=id)`
-
-### Run free forecast
-Let's say you want to run a free forecast starting at 6z, which you want to use as prior for an assimilation at 9z. Then you need can use the above defined 3 steps to create initial conditions.
-Then you can run an ensemble forecast using:
-```
-id = run_ENS(begin=begin, # start integration from here
- end=end, # integrate until here
- input_is_restart=False,
- output_restart_interval=(end-begin).total_seconds()/60,
- depends_on=id)
-```
-where `begin` & `end` are `dt.datetime` objects.
-
-### Assimilation experiment
-#### Assimilate
-To assimilate observations at dt.datetime `time` use this command:
-
-`id = assimilate(time, prior_init_time, prior_valid_time, prior_path_exp, depends_on=id)`
-
-#### Update initial conditions from Data Assimilation
-In order to continue after assimilation you need the posterior = prior (1) + increments (2)
-
-1. Set prior with this function:
-
-`id = prepare_IC_from_prior(prior_path_exp, prior_init_time, prior_valid_time, depends_on=id)`
-
-where path is `str`, times are `dt.datetime`.
-
-2. To update the model state with assimilation increments, you need to update the WRF restart files by running
-
-`id = update_IC_from_DA(time, depends_on=id)`
-
-After this, the wrfrst files are updated with assimilation increments (filter_restart) and copied to the WRF's run directories so you can continue to run the ENS after assimilation using
-
-```
-id = run_ENS(begin=time, # start integration from here
- end=time + timedelta_integrate, # integrate until here
- restart_path=cluster.archivedir+prior_init_time.strftime('/%Y-%m-%d_%H:%M/'),
- output_restart_interval=timedelta_btw_assim.total_seconds()/60,
- depends_on=id)
-```
-where times are `dt.datetime`; `timedelta` variables are `dt.timedelta`.
-
-### Examples
-[`scheduler.py`](https://github.com/lkugler/DART-WRF/blob/master/scheduler.py)
-[`generate_free.py`](https://github.com/lkugler/DART-WRF/blob/master/generate_free.py)
-
-## Finally
-
-### SLURM submissions
-`scheduler.py` submits jobs into the SLURM queue with dependencies, so that SLURM starts the jobs itself as soon as resources are available. Most jobs need only one node, but model integration is done in a SLURM job array across e.g. 10 nodes:
-```
-$ squeue -u `whoami` --sort=i
- JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
- 1710274 mem_0384 prepwrfr lkugler PD 0:00 1 (Priority)
- 1710275 mem_0384 IC-prior lkugler PD 0:00 1 (Dependency)
- 1710276 mem_0384 Assim-42 lkugler PD 0:00 1 (Dependency)
- 1710277 mem_0384 IC-prior lkugler PD 0:00 1 (Dependency)
- 1710278 mem_0384 IC-updat lkugler PD 0:00 1 (Dependency)
- 1710279 mem_0384 preWRF2- lkugler PD 0:00 1 (Dependency)
- 1710280_[1-10] mem_0384 runWRF2- lkugler PD 0:00 1 (Dependency)
- 1710281 mem_0384 pRTTOV-6 lkugler PD 0:00 1 (Dependency)
- 1710282 mem_0384 Assim-3a lkugler PD 0:00 1 (Dependency)
- 1710283 mem_0384 IC-prior lkugler PD 0:00 1 (Dependency)
- 1710284 mem_0384 IC-updat lkugler PD 0:00 1 (Dependency)
- 1710285 mem_0384 preWRF2- lkugler PD 0:00 1 (Dependency)
- 1710286_[1-10] mem_0384 runWRF2- lkugler PD 0:00 1 (Dependency)
- 1710287 mem_0384 pRTTOV-7 lkugler PD 0:00 1 (Dependency)
-```
-
-### Easily switch between clusters
-Define cluster specific variables in `config/clusters.py `:
-```python
-
-clusterA = ClusterConfig()
-clusterA.name = 'vsc'
-clusterA.userdir = '/home/pathA/myuser/'
-...
-clusterB = ClusterConfig()
-clusterB.name = 'jet'
-clusterB.userdir = '/home/pathB/myuser/'
-```
-