cpp/README.md

# Download

1. Clone repository with `git clone https://gitea.pkm.physik.tu-darmstadt.de/NMRRWSims/cpp.git` 
2. After download, change permissions of build.sh in terminal with `chmod a+x build.sh`

# Build

# Running

## Command line

To run a random walk simulation Execute `rwsim` in the command line with 

```bash
  ./rwsim /path/to/config.txt MotionModel DistributionModel --ste --spectrum -ARG1 1 -ARG2 2
```

It needs three positional arguments: the path to your basic configuration file (see below) and the names of the motional model and of the distribution of correlation times.
Set the optional arguments `--ste` and/or `--spectrum` to create Stimulated Echos or normal echo spectra, respectively.
You can overwrite any parameter given in the configuration file by adding it as optional argument with a numerical value, e.g. `-TAU 1e-3` for a correlation time of 1 ms.


## Configuration file `config.txt`

Change the values of delta, eta, mixing times, echo times,... in this file. If a paramter is defined multiple times, only the last one is used.  

### General parameter 

This list of general parameter are necessary for all simulations:

| Parameter  | Description                |
|------------|----------------------------|
| num_walker | Number of trajectories     |
| delta      | Anisotropy parameter in Hz |
| eta        | Asymmetry parameter        |

### Distribution of correlation times

Two distributions are available: A delta distribution `Delta`, i.e. the same correlation time for every walker, and a log-normal distribution `LogNormal`.

+ Parameters for delta distribution `Delta`

  | Parameter | Description           |
  |-----------|-----------------------|
  | tau       | Jump time in s        |

+ Parameters for log-normal distribution `LogNormal`

  | Parameter | Description                                |
  |-----------|--------------------------------------------|
  | tau       | Maximum jump time of the distribution in s |
  | sigma     | Standard deviation of the distribution     |

### Motion models

Four different jump models are implemented: Isotropic random jump `RandomJump`, isotropic jump with a certain angle, isotropic jump with a bimodal distribution of angles, and a tetrahedral jump `TetrahedralJump`.

+ Isotropic random jump `RandomJump` does not have additional parameters. 
+ Tetrahedral jump `TetrahedralJump` does not have additional parameters.
+ Parameters for isotropic jump by an angle `IsotropicAngle`

  | Parameter | Description          |
  |-----------|----------------------|
  | angle     | Jump angle in degree |

+ Parameters for isotropic jump with bimodal angle distribution `BimodalAngle`

  | Parameter    | Description                          |
  |--------------|--------------------------------------|
  | angle1       | First jump angle in degree           |
  | angle2       | Second jump angle in degree          |
  | probability1 | Probality that jump has angle1 (0-1) |  






# Running

**Because filenames are always the same, previous simulations and results are overwritten!**

1. Execute `build.sh` (in terminal with `./build.sh`). It compiles the source code and executes test.py