ALCON

version 2014-05-24 13:22:42-04:00

ALCON has been rewritten in Python. All users including those of the former Fortran version are encouraged to read through this README to get familiar with the new Python version.

ALCON is a code for solving ideal MHD Alfven continua in tokamaks, i.e., Eq. (10) in Physics of Fluids 29, 3695 (1986), using a poloidal-spectral method described in Appendix A in Nuclear Fusion 52, 043006 (2012). When referencing ALCON in a publication, please cite:

@ARTICLE{Deng2012b,
	author = {W. Deng and Z. Lin and I. Holod and Z. Wang and Y. Xiao and H. Zhang},
	title = {Linear properties of reversed shear {A}lfv\'en eigenmodes in the {DIII-D} tokamak},
	journal = {Nuclear Fusion},
	year = {2012},
	volume = {52},
	pages = {043006},
	number = {4},
	doi = {10.1088/0029-5515/52/4/043006}
}

Copying

ALCON is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

ALCON is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with ALCON. If not, see http://www.gnu.org/licenses/.

System requirements

ALCON requires:

• Python 2 (2.7+) or 3 (3.4+)
• NumPy 1.8+
• SciPy 0.13+

Additionally, matplotlib 1.3+ is recommended for quickly plotting solved continua.

Unless you keep excessive (100+) poloidal m-harmonics and want excessive high radial resolution (solving 5000+ radial grid points), ALCON should be able to finish a run within half an hour on any desktop that has two or more physical cores. Running the default case on an Apple Mac Mini 2011 takes about 14 minutes with a single process and about 10 minutes with two processes.

Usage

Know about the files

• README.md -- This instruction.
• COPYING -- The license (GNU General Public License) for ALCON.
• alcon.sh -- A bash script for conveniently launching alcon.py without the need to type all the input parameters in the command line. This script can be used as an input file.
• alcon.py -- The main program file.
• alcon_input.py -- Module for managing input parameters.
• alcon_eqdata.py -- Module for managing equilibrium data.
• alcon_solver.py -- Module for solving Alfven continua.
• alcon_output.py -- Module for writing solutions to output files.
• wctimer.py -- Module for a wall-clock timer.
• alcon_plot.py -- Plotting utility for plotting output data from ALCON.
• alcon_plot_input.py -- Module for managing input parameters for the plotting utility.
• alcon_plot_core.py -- Module for core functionalities of the plotting utility.
• alcon.dat -- A sample equilibrium data input file. The equilibrium is taken from Physics of Plasmas 17, 112504 (2010). This file is for testing when you use ALCON for the first time. For practical use, you want to replace this file by your own alcon.dat file generated from your equilibrium. See acdgen_sample.F90 for a sample subroutine to generate alcon.dat.
• profile_sa.dat -- A sample equilibrium profiles for solving a simple analytic equilibrium. The profiles are taken from Physics of Plasmas 17, 112504 (2010). This file is for testing when you use ALCON for the first time. For practical use, you want to replace this file by your own profile_sa.dat file. See next section for preparing your own profile_sa.dat.
• acdgen_sample.F90 -- A sample subroutine to show how to generate alcon.dat.

Running

The main program file is alcon.py. To launch it, you can execute python alcon.py [options], or simply ./alcon.py [options] if your system supports direct script execution (with the script parser specified by the shebang in the script; supported by most UNIX and Linux systems including Mac OS X) and the execution permission is granted for alcon.py. To see all the available [options], use the -h option, i.e., execute python alcon.py -h. First-time user can simply run python alcon.py to try out ALCON with default parameters and a sample tokamak equilibrium. To get meaningful results from the execution of alcon.py, careful input preparation is needed.

Note that the above paragraph assumed the Python interpreter to be python. If this is not the case, you need to replace the interpreter specifier accordingly. For example, if you use Python 3 and its interpreter is named python3 instead of python, you need to execute python3 alcon.py [options] instead of python alcon.py [options], or replace the shebang line #!/usr/bin/env python by #!/usr/bin/env python3 in alcon.py for direct script execution. This also applies to the plotting utility alcon_plot.py.

Input preparation

ALCON (alcon.py) reads input parameters from the command line. Execute python alcon.py -h to see all the command line parameters.

A bash script alcon.sh is provided for easily setting input parameters. You can directly edit the input parameters in this file, and then execute this file (bash alcon.sh or ./alcon.sh) in the command line to launch ALCON with your specified input parameters.

Depending on the parameter passed to the --eqtype option, ALCON reads equilibrium data from additional input data file. For currently implemented parameters for --eqtype, ALCON may read from alcon.dat or profile_sa.dat for equilibrium data. ALCON comes with a sample of each of these two files.

To prepare your own alcon.dat, see acdgen_sample.F90 for a sample subroutine to generate alcon.dat.

To prepare your own profile_sa.dat, follow this format: the first line puts one real number, which is the inverse aspect ratio a/R0; the second line puts two integers nrad and nprofile, nrad being the number of radial grid points for the profiles, nprofile being the number of profiles (for current version always put nprofile to be 4); starting from the third line is a nrad * nprofile matrix giving the profile data. The first column is the radial coordinate r/a. The second column is the q-profile. The third column is the pressure profile normalized as: (4 pi gamma P / B^2), where gamma is the specific heat ratio, P is the plasma pressure, B is the on-axis magnetic field, and P and B are in CGS units. The fourth column is the mass density normalized by proton mass times on-axis electron density (Eq. (A.35) in Nuclear Fusion 52, 043006 (2012)).

Output data and plotting

All output data files are put in the sub-directory specified by the --dirout option. Note that if the specified directory preexists, ALCON will exit with a "file exists" error, unless the --erasedirout option is specified, in which case the preexisting directory will be erased.

A plotting utility (alcon_plot.py) is provided for plotting and generating plotting scripts for other visualization softwares. It supports these operations:

• plotting on screen or saving a .png or .pdf figure through matplotlib;
• generating a .m script for MATLAB;
• generating a .pro script for IDL;
• generating a .gp script and a Makefile for gnuplot.

Run python alcon_plot.py -h for detailed usage information. First-time user can simply run python alcon_plot.py --dirout <directory of ALCON output> to get the continuum plot on screen, then gradually try out other options.

Known issue

ALCON can run in parallel by specifying an integer larger than 1 to the -n option. The parallelization is implemented using the multiprocessing module in the Python Standard Library. However, on Mac OS X, the subprocesses of a program that is parallelized in this way and has certain NumPy and SciPy function calls would crash, if NumPy and SciPy are built with Apple's Accelerate Framework. More information about this issue can be found at these links:

• numpy/numpy#654
• http://mail.scipy.org/pipermail/numpy-discussion/2012-August/063590.html

This issue does not apply if NumPy and SciPy are built with OpenBLAS. If you use Homebrew to install NumPy and SciPy, you can choose to build them with OpenBLAS by passing the --with-openblas option:

brew install numpy --with-openblas
brew install scipy --with-openblas

The above commands may complain:

Error: Operation already in progress for openblas
Another active Homebrew process is already using openblas.
Please wait for it to finish or terminate it to continue.

To work around this, run brew edit numpy, then the NumPy formula would be opened in the default text editor. In the editor, replace homebrew/science/openblas by openblas, save and quit. Then run brew edit scipy and do the same replacement. Afterwards, run the above commands to install NumPy and SciPy.

Contact

Get latest updates on the project website: http://wdeng.info/codes/alcon.

Report bugs, request new features at: https://github.com/wenjundeng/alcon/issues.

Contribute patches, new features by forking the project on GitHub: https://github.com/wenjundeng/alcon, applying your contributions to the forked project, and then submitting a pull request at: https://github.com/wenjundeng/alcon/pulls.

Acknowledgments

ALCON was originally developed when I was a graduate student at University of California, Irvine, where my research was supported by the U.S. Department of Energy (DOE) SciDAC Center for Gyrokinetic Simulation of Energetic Particle Turbulence and Transport (GSEP). The development continued after I became a postdoc at Princeton Plasma Physics Laboratory, where my research was supported by the U.S. DOE SciDAC Center for Nonlinear Simulation of Energetic Particles in Burning Plasmas (CSEP). I would like to acknowledge useful discussions with Eric Bass, Guo-Yong Fu, Zhihong Lin, Don Spong, Xin Wang, Zhixuan Wang, and Huasen Zhang.

Wenjun Deng