NeutPy - A neutrals code for tokamak fusion reactors
Project description
NeutPy - A code for the calculation of neutral particle transport in plasmas based on the transmission and escape probability method
NeutPy is the Python 2.x port of GTNEUT, which was written by John Mandrekas.
GTNEUT is a two-dimensional code for the calculation of the transport of neutral particles in fusion plasmas. It is based on the Transmission and Escape Probabilities (TEP) method and can be considered a computationally efficient alternative to traditional Monte Carlo methods. The code has been benchmarked extensively against Monte Carlo and has been used to model the distribution of neutrals in fusion experiments.
The original physics background can be found at
Mandrekas, John. (2004). GTNEUT: A code for the calculation of neutral particle transport in plasmas based on the Transmission and Escape Probability method. Computer Physics Communications. 161. 36-64. 10.1016/j.cpc.2004.04.009.
The original FORTRAN 95 GTNEUT code can be found at The Fusion Research Center GitHub at https://github.com/gt-frc/GTNEUT
Installation
- Triangle Installation
The Triangle 2D mesh generator is required for NeutPy mesh generation. This will install Triangle locally. If you imagine using triangle otherwise, consider following the steps below but with consideration for global installation (e.g., cloning to /opt/ instead of your home directory). Ensure that you have a C compiler installed. Download the Triangle zip file from https://www.cs.cmu.edu/~quake/triangle.html or
$ cd ~
$ git clone https://github.com/libigl/triangle.git
$ cd triangle
Make your bin directory
$ mkdir bin
Read the README file for instructions on how to compile. It's pretty basic. We recommend simply compiling triangle alone with (using GCC) since we do not use showme.
$ gcc -O -o bin/triangle triangle.c -lm
If you want to fully compile triangle and showme, edit the makefile, noting any special options from the README.
Keep SRC = ./
and set BIN = ./bin/
Make triangle
$ make
After triangle is compiled, set executable
$ cd bin
$ sudo chmod +x triangle
Set link (this allows triangle to be called on command line as triangle)
$ sudo ln -s /full/path/to/triangle /usr/local/bin/triangle
Install NeutPy
Using pip
$ pip install neutpy
From GitHub
$ cd /your/future/neutpy/home/
- Master branch
Clone master branch from github
$ git clone https://github.com/gt-frc/neutpy.git
- Other branches
You can clone another branch from github as follows:
$ git clone -b <branch> https://github.com/gt-frc/neutpy.git
Enter NeutPy
$ cd neutpy
Setup your virtual environment (install virtualenv using apt, yum, etc.)
$ virtualenv --python=/usr/bin/python2.7 venv
Activate it
$ source venv/bin/activate
Install packages
$ pip install -r requirements.txt
Usage
NeutPy requires 6 input files and 2 configuration files.
Configuration files:
toneutpy.conf
is the main input file. This file will change with each shot.
neutpy.conf
is the main NeutPy configuration file and includes parameters that probably wouldn't change between
shots and other variables. This file needs to be in the current working directory and cannot be renamed.
Data files:
The names of the data files included follow the GT3 gt3_shotid_timeid_profile.dat convention but can be defined
differently in your toneutpy
file.
Ion/Electron density and temperature data are X/Y (normalized rho/value) two-column data. Temperatures are in keV. Densities should be given in #/m^3. Psi data are non-normalized 3-column R/Z/value data, with R/Z in meters.
gt3_shotid_timeid_ne.dat
(Electron density profile)
gt3_shotid_timeid_ni.dat
(Ion density profile)
gt3_shotid_timeid_Te.dat
(Electron temperature profile)
gt3_shotid_timeid_Ti.dat
(Ion temperature profile)
gt3_shotid_timeid_psirz.dat
(Non-normalized psi grid)
gt3_diid_wall.dat
(Machine wall coordinates (R/Z))
Import the neutrals class.
from neutpy import neutrals
There are three main entry points into NeutPy: from_file
, from_mesh
, and from_gt3
. The usage of
from_file
is as follows:
neuts = neutrals() INITIALIZING NEUTPY neuts.from_file('/relative/path/to/your/toneutpy.conf')
where the filename is relative to the CWD.
The from_mesh
and from_gt3
methods are in development.
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