updated the models folder readme file

Author: jorindevandevis

Models/README.md

@@ -2,101 +2,31 @@
 
 ## Overview
 
-To run specific models, each folder contains a
-Makefile that can simply be run inside a specific model folder.
-The workflow includes running WolframScript to generate matrix elements, using Python to generate collision data, and finally processing the data with the main Python script.
+This folder contains individual model directories, each equipped with a Python script to calculate the wall velocity specific to that model. Additional files within each model directory support the computation of matrix elements and collision integrations.
 
 ## Directory Structure
 
-- `MatrixElements/` - Contains the script and data files for matrix element generation.
-- `CollisionOutput/` - Directory where collision data files are stored.
+Each model directory includes the following files and subdirectories:
+- `<nameOfModel>.py' - Contains the model definition and the commands for finding the wall velocity.
+- `<nameOfModel>Config.ini' - An optional configuration file containing model-specific configuration settings. (Note: This file is not included for the Yukawa model.)
+- `exampleCollisionDefs.py' - Defines collision generation settings specific to the model.
+- `MatrixElements/` - A subdirectory holding scripts (with .m extensions) used for generating matrix elements, as well as a .json file containing the computed matrix elements.
+- `CollisionOutput_N<spatialGridSize>/` - Subdirectories for storing collision data files for each pair of out-of-equilibrium particles, with each folder corresponding to a specific spatial grid size. 
 
+Additionally, the Models folder contains a common utility file:
 
-## Makefile Targets
+- `wallGoExampleBase.py' - This script provides a shared template for wall velocity computations. It is used by all models except the Yukawa model.
 
-### `all`
+## Running a model
 
-This is the default target which runs the `model` target.
+The examples can be run directly with e.g.
 
-### `generateMatrixElements`
-Generates matrix Elements at `MatrixElements.txt` from
-`MatrixElements/<Model>.m`
-as sometimes only the matrix elements need to be generated.
+    python3 Models/SingletStandardModel_Z2/singletStandardModelZ2.py
+    
+For models that use the common `wallGoExampleBase.py', additional command line arguments are available to (re)calculate matrix elements and collisions, and adjust the momentum grid size e.g.
 
-### `model`
-Runs only the model file
-`<model-name>.py`
-as sometimes no new matrix elements or collision integrals need to be generated.
+    python3 Models/SingletStandardModel_Z2/singletStandardModelZ2.py --recalculateMatrixElements -- recalculateCollisions --momentumGridSize 5
 
-### `generate_collisions`
+## Requirements
 
-Generates collision data files using the matrix elements. This target depends on `MatrixElements.txt`, which is generated by running a WolframScript file.
-
-### `clean`
-
-Removes the `CollisionOutput` and `MatrixElements` directories and all their contents.
-
-## Dependencies
-
-- `python3` - Required for running Python scripts.
-- `wolframscript` - Required for running the WolframScript file to generate matrix elements.
-
-
-- `matrixElements.m` -
-    MatrixElement script based on DRalgo.
-    See [https://github.com/Wall-Go/MatrixElements](https://github.com/Wall-Go/MatrixElements). 
-- `DRalgo` - See [https://github.com/DR-algo/DRalgo](https://github.com/DR-algo/DRalgo).
-
-Both `matrixElements.m` and the `DRalgo` folder should be placed in a directory visible to Mathematica. The best options are to place it in the Applications subfolder of
-`$BaseDirectory` or `$UserBaseDirectory`.
-Often, the paths are the following:
-
-### For Linux
-
-    /usr/share/Mathematica/Applications
-    /home/<computer-name>/.Mathematica/Applications
-
-### For Windows
-
-    C:\ProgramData\Mathematica\Applications
-    C:\Users\<computer-name>\AppData\Roaming\Mathematica\Applications
-
-## Usage
-
-### Full pipeline
-1. **Generate Collisions**:
-    Ensure that the matrix elements data file `MatrixElements.txt` exists, then generate collision data by running:
-   ```sh
-   make generate_collisions
-   ```
-
-2. **Run Main (Model) Script**:
-    Once collision data files are generated, run the main Python script:
-   ```sh
-   make model
-   ```
-
-4. **Clean Up**:
-    To clean up the generated collision data files and matrix elements:
-   ```sh
-   make clean
-   ```
-
-### Matrix Elements
-1. **Generate Matrix Elements**:
-    In that case it suffices to run:
-   ```sh
-   make generateMatrixElements
-   ```
-
-## File Descriptions
-
-- `MatrixElements/matrixElements.qcd.m` - WolframScript file for generating matrix elements.
-- `MatrixElements.txt` - Output data file containing matrix elements.
-- `collisionGenerator.py` - Python script for generating collision data.
-- `<model-name>.py` - Main Python Model script that uses the collision data e.g. `SingletStandardModel_Z2.py`
-
-## Notes
-
-- Ensure that the necessary Python and WolframScript dependencies are installed and properly configured in your environment.
-- The `CollisionOutput` directory is automatically created if it does not exist when running the `generate_collisions` target.
+Running the model files requires a valid installation of [**WallGo**](https://github.com/Wall-Go/WallGo) . Generation of new matrix elements and collisions furthermore requires installations of [**WallGoMatrix**](https://github.com/Wall-Go/WallGoMatrix) and  [**WallGoCollision**](https://github.com/Wall-Go/WallGoCollision) respectively.