Pisces1d-Genetic-Algorithm-Usage.md

-## Before starting
+## 1. Before starting
 
 Before starting to use this tool, one should first have NEMO 4.0 installed to be deployed in MN4 and be able to execute the PISCES1D configuration. The following links provide how to do this:
 
@@ -6,12 +6,12 @@ Before starting to use this tool, one should first have NEMO 4.0 installed to be
 
 [Configure Pisces1D](https://earth.bsc.es/gitlab/mgalitap/pisces_offline/wikis/pisces-offline)
 
-## Setting up the workflow (nohup recommended for large experime)and configuration
+## 2. Setting up the workflow and configuration
 
-The fastest way to set up the workflow is to copy it from an existing experiment, a1yt: 
+The fastest way to set up the workflow is to copy it from an existing experiment, a27e: 
 
 ```
-autosubmit expid -y a1yt -H marenostrum4 -d Description
+autosubmit expid -y a27e -H marenostrum4 -d Description
 ```
 
 Otherwise, create a new experiment
@@ -20,7 +20,26 @@ autosubmit expid -H marenostrum4 -d Description
 ```
 and replace the conf files there with the ones [here](https://earth.bsc.es/gitlab/mfalls/genetic_algorithm_pisces1d/tree/master/conf). 
 
-Next, copy the [workflow](https://earth.bsc.es/gitlab/mfalls/genetic_algorithm_pisces1d/tree/master/workflow) onto your local machine. 
+From here, you can either prepare the scripts via your local machine or via git.
+
+## 2.1 Git (Recommended)
+
+Open expdef_xxxx.conf and
+
+1. change PROJECT_TYPE from local to git
+2. change PROJECT_ORIGIN (line 43) to https://earth.bsc.es/gitlab/cp/genetic_algorithm_pisces1d.git
+3. change PROJECT_BRANCH to master
+4. Edit MEMBERS. This corresponds to the number of generations that you want the genetic algorithm to run for. This should always be of the form `fc[0000-xxxx]` (fc + 4 digits). 
+5. Edit NUMCHUNKS. This corresponds to the number of sets of parameters of each generation. Minimum 2, maximum 10,000.
+
+then autosubmit refresh xxxx
+
+Finally, edit the following configuration files: 
+* platforms.conf: Under marenostrum4, change USER to your HPC username (bsc32xxx).  
+
+## 2.2 Local
+
+Copy the [workflow](https://earth.bsc.es/gitlab/mfalls/genetic_algorithm_pisces1d/tree/master/workflow) onto your local machine. 
 
 Finally, edit the following configuration files: 
 * platforms.conf: Under marenostrum4, change USER to your HPC username (bsc32xxx).  
@@ -31,7 +50,7 @@ Finally, edit the following configuration files:
 3. Ensure that PROJECT_TYPE = local
 4. Under local, change PROJECT_PATH to the directory where you downloaded the workflow scripts.
 
-## Inputs
+## 3. Inputs
 
 Here is the full list of input files that you need:
 *  nemo executable, .xml files and namelists, found in EXP00
@@ -49,17 +68,17 @@ Once you have these, edit the variables and paths at the start of each script on
 6. VARIABLES: Path and file name of variables.csv
 7. MODELFILE: Name of the netcdf output that you want to compare the observed data to.
 
-## Running the experiment
+## 4. Running the experiment
 
 On the autosubmit terminal, run:
 
-```autosubmit refresh xxxx``` (only for the first time)
-
 ```autosubmit create xxxx``` (-np flag recommended for large experiments)
 
 ```nohup autosubmit run xxxx &>log &```
 
-## Postprocessing
+The outputs of the experiment will appear in /gpfs/scratch/bsc32/bsc32xxx/xxxx
+
+## 5. Postprocessing
 
 The postprocessing script can be found [here](https://earth.bsc.es/gitlab/cp/genetic_algorithm_pisces1d/-/tree/master/postproc).