84 lines
3.1 KiB
Markdown
84 lines
3.1 KiB
Markdown
# Download
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1. Clone repository with `git clone https://gitea.pkm.physik.tu-darmstadt.de/NMRRWSims/cpp.git`
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2. After download, change permissions of build.sh in terminal with `chmod a+x build.sh`
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# Build
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# Running
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## Command line
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To run a random walk simulation Execute `rwsim` in the command line with
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```bash
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./rwsim /path/to/config.txt MotionModel DistributionModel --ste --spectrum -ARG1 1 -ARG2 2
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```
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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.
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Set the optional arguments `--ste` and/or `--spectrum` to create Stimulated Echos or normal echo spectra, respectively.
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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.
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## Configuration file `config.txt`
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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.
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### General parameter
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This list of general parameter are necessary for all simulations:
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| Parameter | Description |
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|------------|----------------------------|
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| num_walker | Number of trajectories |
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| delta | Anisotropy parameter in Hz |
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| eta | Asymmetry parameter |
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### Distribution of correlation times
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Two distributions are available: A delta distribution `Delta`, i.e. the same correlation time for every walker, and a log-normal distribution `LogNormal`.
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+ Parameters for delta distribution `Delta`
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| Parameter | Description |
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|-----------|-----------------------|
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| tau | Jump time in s |
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+ Parameters for log-normal distribution `LogNormal`
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| Parameter | Description |
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|-----------|--------------------------------------------|
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| tau | Maximum jump time of the distribution in s |
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| sigma | Standard deviation of the distribution |
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### Motion models
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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`.
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+ Isotropic random jump `RandomJump` does not have additional parameters.
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+ Tetrahedral jump `TetrahedralJump` does not have additional parameters.
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+ Parameters for isotropic jump by an angle `IsotropicAngle`
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| Parameter | Description |
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|-----------|----------------------|
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| angle | Jump angle in degree |
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+ Parameters for isotropic jump with bimodal angle distribution `BimodalAngle`
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| Parameter | Description |
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|--------------|--------------------------------------|
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| angle1 | First jump angle in degree |
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| angle2 | Second jump angle in degree |
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| probability1 | Probality that jump has angle1 (0-1) |
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# Running
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**Because filenames are always the same, previous simulations and results are overwritten!**
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1. Execute `build.sh` (in terminal with `./build.sh`). It compiles the source code and executes test.py
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