New cost functions in coil complexity and coil-coil separation

(Please update the develop branch)

Updates:

• A new cost function on the so-called "Nissin" coil complexity has been implemented. For details, please check this documentation.
• A new cost function on the coil-coil separation has been (re-)implemented. Please check here.
• The curvature function has been revised. Please check here.
• There is also a cost function on the coil torsion, but documentation is underway.
• A new example of ATEN using the new cost functions has been prepared. Please check the example folder.
• The screen output has been re-organized. If you want to see the evolution of each cost function, please use IsQuiet = -2/-1.
• Some bugs have been fixed.

Some notes:

• The input namelist has been modified. A quick way to get a template of the latest namelist is to run xfocus -i. You can also have a look at input.html.
• Because of using exponential functions, the curvature, torsion, and nissin constrained functions might cause an error of floating-point-overflow (observed with Intel compilers). Please revised the corresponding exponential factors.
• According to @thomasgbkruger, the new functions will tend to use a relatively high resolution for coils.

Thanks to @thomasgbkruger for the contribution!

Curvature metric implemented and python wrapper provided

Two major updates:

1. The coil curvature penalty function has been implemented, see #51 .
2. Python wrapper using f90wrap has been utilized. Documentation is limited but will be provided in the future.

Two main bug fix:

1. Fixed the stellarator symmetry bug for Nfp>3.
2. Fixed the coil-surface separation calculation.

Other minor updates:

• Two more examples are provided.
• Temporarily fixed writing updated plasma boundary.

Stellarator symmetry enabled and separate limiter surface

It has been a long time since the last release (v0.5.3), although the version number has been keeping evolving. If you have missed all the changes, please check the full list here.

Here is a brief summary of major changes by chronological order.

• Field-line tracing (in vacuum) and rotational transform calculation were available as post-processing. #25
• 1/R toroidal field and vertical field were available as a special coil type.
• Added magnetic dipole as a new coil type (recommend to use the dipole branch directly).
• Added flexible interface for I/O, now can specify file names for all the inputs.
• Added new function for writing MGRID file.
• Added different normalization for Bn harmonics. #40
• Allowed to specify a limiter surface for coil-surface separation. #17
• Allowed for specifying stellarator symmetry and debugged the toroidal periodicity. #46
• Many bug fixes.

Add SPEC interface and enable Bn normalization

Main changes:

1. Add SPEC interface for future free-boundary SPEC calculations (case_postproc=2).
2. Enable Bn normalized to mod B (case_bnormal=1).
3. Fix several bugs.

Levenberg-Marquardt optimizer and new diagnostic terms available

Please view #21 for more details.

1. Levenberg-Marquardt algorithm is now available.
   Levenberg-Marquardt algorithm is one of the most famous minimization algorithms. The calculation of chi-squared and the packing of jacobian are different from the present optimization algorithms (DF, CG). Please view lmalg.pdf
2. More diagnostic terms in diagnos.h.
   • calculate the overlap rate between the present Bn harmonics and the target harmonics
   • compute a coil importance array (coil_importance in hdf5 file) for each coil
3. Several bugs are fixed.
   • add warnings about reset weights below machine precision
   • fix nfp reset issue
   • decompose Bn from coils only
   • update ellipse example

Coil-surface separation and organize the repository structure

Related pull request #20 , please view for more details.

• Repository structure #19
• Coil-surface separation #17

NAG dependance and other bugs fixed

In th past half year, no big changes have been made. Basically, this version is bugs fixing. For more details please view #16.

The first tag

Begin to use tag for better controlling the versions. This is the v0.1.0. Updates are copied from previous issues.

updates on 07/22/2017

• add version tag in both git and the code hdf5 output file;
• add exit option when CG line search not converge;
• add LHD helical coil case in examples;
• update coil.py;

updates on 07/20/2017

• Add options to freely control the optimization focus : currents or geometries
• Add additional criteria to exit optimizations
• Replace the repeated output information in CG
• fixed other minor stuffs

updates on 07/18/2017

• Transplant coil diagnostic subroutine
• Implement plasma and coil periodicity
• Minor improvements

update nots on 06/26/2017

• current availability

  • coil representation
    Fourier series.
  • optimizers
    Differential Flow and Nonlinear Conjugate Gradient method.
  • cost functions
    Bn surface integral; Bn Fourier spectrum (in VMEC polar coordinate); toroidal magnetic flux; coil length.
  • post-processers
    OMFIT FOCUS Interface (if you are interested, please contact Dr. Nikolas Logan). There are also some scripts in the python package coil.py.

• examples
  Two illustrating cases, designing modular coils for l=2 rotating ellipse and designing RMP coils for DIII-D are placed in examples.

• I/O related
  The input files needed for a run are listed here, while you can also find detailed explanations of each variable in initial.pdf.

• plotting
  There are 14 plotting functions in coilpy. For time reasons, I haven't written detailed instructions. But you are free to explore the functions.