STELLOPT

https://princetonuniversity.github.io/STELLOPT
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STELLOPT is a stellarator optimization suite designed to optimize three-dimensional...
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### Install external dependencies via EPEL

Source: https://princetonuniversity.github.io/STELLOPT/STELLOPT%20Compilation%20Redhat

Download and install the EPEL repository, then install NetCDF, NCL, and HDF5 packages.

```bash
wget http://mirrors.mit.edu/epel/6/i386/epel-release-6-8.noarch.rpm
rpm -Uvh epel-release-6-8.noarch.rpm
yum -assumeyes install netcdf*
yum install ncl*
yum install hdf5*
```

--------------------------------

### NMORPH Execution Example

Source: https://princetonuniversity.github.io/STELLOPT/NMORPH

Example command line execution of NMORPH with specified input files and surface/mode parameters.

```bash
NMORPH -a axis.test -dom boundary.test -i iboundary.test -g extended_mesh -cf extended_field -c coils.test -s 99 -m_use 8 -n_use 6
```

--------------------------------

### Verify COILOPT++ Compilation Support

Source: https://princetonuniversity.github.io/STELLOPT/STELLOPT%20Coil%20Optimization%20Old

Example of the terminal output confirming that COILOPT++ libraries were detected during the STELLOPT setup process.

```bash
---------------------------------------------------
COILOPT++ libraries where located in /u/user/src/COILOPT++/
Build with COILOPT++ support? (default: y)
---------------------------------------------------
y / n : y Compiling with COILOPT++ support!
```

--------------------------------

### BOOTSJ Input File Example

Source: https://princetonuniversity.github.io/STELLOPT/BOOTSJ

Example input file content for calculating bootstrap current on surfaces 2, 5, and 37 for a VMEC run with the extension 'test'.

```fortran
test
2 5 37
```

--------------------------------

### Install Homebrew dependencies

Source: https://princetonuniversity.github.io/STELLOPT/STELLOPT%20Compilation%20OS%20X%20Brew

Install the required system packages for STELLOPT using Homebrew.

```bash
#  gcc10 : Working
#  gcc11 : Issue with hdf5 23.02.2024
#  gcc12 : Issue with hdf5 23.02.2024
#  gcc13 : Working as of 14.11.2024
#  gcc14 : Libraries still missing (14.11.2024)
brew install git
brew install gcc
brew install openmpi
brew install netcdf
brew install netcdf-fortran
brew install fftw
brew install openblas
brew install scalapack
brew install python3
# All other python modules should be handled durring 
# install using pip and setuptools
```

--------------------------------

### COBRAVMEC Input File Format (pre 4.1)

Source: https://princetonuniversity.github.io/STELLOPT/COBRAVMEC

Example of the legacy input file structure for COBRAVMEC, specifying starting angles and surfaces for growth rate calculations.

```text
    5
    5
    test
    0.00  1.58  3.14  4.78  5.46
    0.00  1.58  3.14  4.62  5.00
    5
    20  30  40  50  60
```

--------------------------------

### Interactive Execution Example

Source: https://princetonuniversity.github.io/STELLOPT/DESCUR

Example of an interactive session running the DESCUR executable.

```text
>~/bin/xcurve
 Enter spectral convergence parameter
 = 0 for polar,  = 1 for equal arclength
 >1 for smaller spectral width
 = 4 corresponds to STELLOPT choice): 4
 Use (default) VMEC-compatible compression (V)
 or Advanced Hirshman-Breslau compression (A): V
 Select source of curve data to be fit:
 0 :  Points from file
 1 :  Fourier coeffs from file (wout file allowed)
 2 :  Solove'ev Equilibrium
 3 :  Assorted 2-D shapes

3
  Shape to fit: 1=ellipse; 2=D; 3=bean; 4=belt; 5=square; 6=heliac)
3
 ORDERING SURFACE POINTS
 Average elongation = 1.2850E+00
 Raxis =   3.0000E+00 Zaxis =  -6.4514E-17
 Number of Theta Points Matched =   400
 Number of Phi Planes =     1
 Max Poloidal Mode Number =    19
 Max Toroidal Mode Number =     1

                  Fitting toroidal plane #   1

 RAXIS =  3.000E+00 ZAXIS = -6.451E-17 R10 =  1.697E+00

 ITERATIONS    RMS ERROR    FORCE GRADIENT    <M>    MAX m   DELT
       1       1.604E-02       8.625E-04      1.66      19  9.70E-01
     100       3.179E-05       2.417E-05      1.69      19  9.70E-01
     114       1.161E-05       8.099E-06      1.69      19  9.70E-01

 ANGLE CONSTRAINTS WERE APPLIED
 BASED THE POLAR DAMPING EXPONENT (PEXP) =  4
 RM**2 + ZM**2 SPECTRUM COMPUTED WITH P =     4.00 AND Q =     1.00
 TIME:   6.21E-02 SEC.

  OUTPUTTING FOURIER COEFFICIENTS TO OUTCURVE FILE

 Do you wish to plot this data (Y/N)? N
```

--------------------------------

### TORLINES Execution Example

Source: https://princetonuniversity.github.io/STELLOPT/TORLINES

An example of running TORLINES using mpirun, showing the resulting console output and parameter summary.

```bash
>mpirun -np 64 ~/bin/xtorlines -vmec ncsx_c09r00_free -coil coils.c09r00 -auto
TORLINES Version 1.00
 -----TORLINES File Parameters-----
          k:  70
         nu:  90   nv:  60
  bound_sep:    1.200
 -----VMEC File Parameters-----
        file: ncsx_c09r00_free
           m:  11   nu:  90
           n:   6   nv:  60
       mnmax:  137
         nfp:   3
          ns:  99
       Total Current: -178.653 [kA]
 ----- Vacuum Grid Info. -----
           Eq. Surface:     59
           Grid Points:  59400
 ----- COILS Information -----
       FILE: coils.c09r00
       Coil Periodicity:   3
       Current Systems:  10
       Current Type:      SCALED
       Num Coils  =    6  EXTCUR =  652.272 [kA]
       Num Coils  =    6  EXTCUR =  651.869 [kA]
       Num Coils  =    6  EXTCUR =  537.744 [kA]
       Num Coils  =    8  EXTCUR =    0.000 [A]
       Num Coils  =    8  EXTCUR =    0.000 [A]
       Num Coils  =    8  EXTCUR =   28.095 [kA]
       Num Coils  =   12  EXTCUR =  -54.805 [kA]
       Num Coils  =    4  EXTCUR =   30.123 [kA]
       Num Coils  =    2  EXTCUR =   94.241 [kA]
       Num Coils  =   18  EXTCUR =   45.514 [kA]
         Vacuum Field Calculation [ 99]%
 ----- Virtual Casing Information -----
       INTEGRAL TYPE: Surface Current
       MIN_GRID_DISTANCE =  6.0493E-02
       NORMAL_AREA =  2.4595E+01
       NR =    1;   NU =  128;  NV =  128;  NFP =   3
       NUVP =  49152
       ABS_TOL =  0.0000E+00;   REL_TOL =  5.0000E-03
       MIN_CLS =      0   (16777216)
         Plasma Field Calculation [ 99]%
 ---------- EXECUTION ----------
 ----     Rough GRID     ----
       rho   = [ 0.00000, 1.00000];
      ----- FOLLOWING FIELD LINES -----
          Method: NAG
           Lines:    201
           Steps:  180000   Delta-phi: 0.3491E-01
             Tol: 0.1000E-08  Type: M
         Fieldline Calculation [ 75]%
 ----     Edge GRID     ----
       rho   = [ 0.78824, 1.00000];
      ----- FOLLOWING FIELD LINES -----
          Method: NAG
           Lines:    201
           Steps:  180000   Delta-phi: 0.3491E-01
             Tol: 0.1000E-08  Type: M
         Fieldline Calculation [ 75]%
 ----     Final GRID     ----
       rho   = [ 0.00000, 1.00000];
      ----- FOLLOWING FIELD LINES -----
          Method: NAG
           Lines:    201
           Steps:  180000   Delta-phi: 0.3491E-01
             Tol: 0.1000E-08  Type: M
         Fieldline Calculation [ 83]%
 ---------- TORLINES DONE ----------
```

--------------------------------

### Install STELLOPT dependencies via apt-get

Source: https://princetonuniversity.github.io/STELLOPT/STELLOPT%20Compilation%20Debian

Use these commands to install the required compilers, libraries, and tools on a Debian system.

```bash
sudo apt-get install git
sudo apt-get install gcc
sudo apt-get install gfortran
sudo apt-get install openmpi-bin
sudo apt-get install libopenmpi-dev
sudo apt-get install libopenblas-dev
sudo apt-get install libscalapack-openmpi-dev
sudo apt-get install libnetcdf-dev
sudo apt-get install libnetcdff-dev
sudo apt-get install libhdf5-openmpi-dev
sudo apt-get install hdf5-tools
sudo apt-get install python3 pip
######### FOR MANGO #############
sudo apt-get install libnlopt-dev
sudo apt-get install libnlopt-cxx-dev
sudo apt-get install libeigen3-dev
sudo apt-get install libgsl-dev
```

--------------------------------

### TERPSICHORE Input Configuration

Source: https://princetonuniversity.github.io/STELLOPT/Tutorial%20TERPSICHORE%20NCSX

Example configuration file for TERPSICHORE, defining Fourier coefficients and equilibrium parameters.

```text
               ncsx_c09r00_fixed
C
C        MM  NMIN  NMAX   MMS NSMIN NSMAX NPROCS INSOL
       32   -16    16    55    -7     7     1     0
C
C     TABLE OF FOURIER COEFFIENTS FOR BOOZER COORDINATES
C     EQUILIBRIUM SETTINGS ARE COMPUTED FROM FIT/VMEC
C
C M= 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6  N
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 -16
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 -15
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 -14
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 -13
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 -12
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 -11
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 -10
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 -9
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 -8
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 -7
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 -6
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 -5
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 -4
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 -3
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 -2
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 -1
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 1
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 2
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 3
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 4
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 5
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 6
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 7
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 8
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 9
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 10
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 11
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 12
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 13
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 14
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 15
     1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 16
C
      LLAMPR      LVMTPR      LMETPR      LFOUPR
           0           0           0           0
      LLHSPR      LRHSPR      LEIGPR      LEFCPR
           9           9           1           1
      LXYZPR      LIOTPL      LDW2PL      LEFCPL
           0           1           1           1
      LCURRF      LMESHP      LMESHV      LITERS
           1           1           3           1
      LXYZPL      LEFPLS      LEQVPL      LPRESS
           1           1           0           2
C
C    PVAC        PARFAC      QONAX        QN         DSVAC       QVAC    NOWALL
  1.0001E+00  0.0000E+00  2.8323E+00  0.0000E+00  1.0000E+00  1.0001E+00     -2
C
C    AWALL       EWALL       DWALL       GWALL       DRWAL       DZWAL   NPWALL
  1.5000E+00  1.0000E+00  5.0000E-01  1.4960E+00  0.0000E+00  0.0000E+00      3
C
C    RPLMIN       XPLO      DELTAJP       WCT      CURFAC
  1.0000E-05  1.0000E-06  4.0000E-02  1.0578E-01  1.0000E+00
C
C                                                             MODELK =      1
C
C     NUMBER OF EQUILIBRIUM FIELD PERIODS PER STABILITY PERIOD: NSTA =      3
C
C     TABLE OF FOURIER COEFFIENTS FOR STABILITY DISPLACEMENTS
C
C M= 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5  N
     0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -7
     0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -6
```

--------------------------------

### Execution Command

Source: https://princetonuniversity.github.io/STELLOPT/EXTENDER

Example command to execute EXTENDER on 4 processors using mpirun.

```bash
> mpirun -np 4 ./bin/EXTENDER -vmec2000 wout.test -i extender_in.test -c coils.test_machine -NU 360 -NV 72 -s test
```

--------------------------------

### Compile pySTEL

Source: https://princetonuniversity.github.io/STELLOPT/pySTEL

Builds LIBSTELL and installs Python components using pip and setuptools.

```bash
make pystel
```

--------------------------------

### Install optional dependencies

Source: https://princetonuniversity.github.io/STELLOPT/STELLOPT%20Compilation%20OS%20X%20Brew

Additional packages required for specific codes like TRAVIS and SFINCS.

```bash
############ TRAVIS ############
brew install netcdf-cxx
############ SFINCS ############
brew install superlu
brew install petsc
```

--------------------------------

### Set environment variables and build

Source: https://princetonuniversity.github.io/STELLOPT/STELLOPT%20Compilation%20OS%20X%20Brew

Configure the environment and execute the build script.

```bash
export STELLOPT_PATH=<path to your repository>
export MACHINE=osx_brew
./build_all
```

```bash
./build_all >& stellopt_build.log
```

--------------------------------

### Example cobra_grate.ext output format

Source: https://princetonuniversity.github.io/STELLOPT/COBRAVMEC

The output file contains growth rates for each surface, grouped by starting zeta and theta positions.

```text
     0.000E+00 0.000E+00   4
       2 -5.35845793E-02
       3 -6.64339650E-02
       4 -7.78813285E-02
       5 -8.61553492E-02
     3.140E+00 0.000E+00   4
       2 -5.19600197E-02
       3 -6.72031207E-02
       4 -7.57780371E-02
       5 -8.64640971E-02
```

--------------------------------

### Configure STELLOPT Input File for COILOPT++

Source: https://princetonuniversity.github.io/STELLOPT/STELLOPT%20Coil%20Optimization%20Old

Example of the &OPTIMUM namelist configuration including coil optimization parameters like NPOPULATION, NU_BNORM, and TARGET_COIL_BNORM.

```fortran
&OPTIMUM
!--------------------------------------------------------------------
! Optimizer Run Control Parameters
!--------------------------------------------------------------------
NFUNC_MAX = 100 EQUIL_TYPE = 'vmec2000' OPT_TYPE = 'lmdif' FTOL = 1.000000000000E-006 XTOL = 1.000000000000E-030 GTOL = 1.000000000000E-030 EPSFCN = 1.000000000000E-005 FACTOR = 1.000000000000E+002 MODE = 1 NPOPULATION = 10
!--------------------------------------------------------------------
! OPTIMIZED QUANTITIES
!--------------------------------------------------------------------
LRHO_OPT(-5:5,0) = 11*T LRHO_OPT(-5:5,1) = 11*T LRHO_OPT(-5:5,2) = 11*T LRHO_OPT(-5:5,3) = 11*T LRHO_OPT(-5:5,4) = 11*T
LRHO_OPT(-5:5,5) = 11*T LRHO_OPT(-5:5,6) = 11*T LRHO_OPT(-5:5,7) = 11*T LBOUND_OPT(1:4,0) = 4*T RHO_EXP = 4
!--------------------------------------------------------------------
! COIL OPTIMIZATION
!--------------------------------------------------------------------
NU_BNORM = 256 NV_BNORM = 64 TARGET_COIL_BNORM = 0.000000000000E+000
SIGMA_COIL_BNORM = 1.000000000000E+000 / &END
```

--------------------------------

### COILOPT++ Input Configuration

Source: https://princetonuniversity.github.io/STELLOPT/COILOPT

Example of the text-based input file used to define file paths, optimization parameters, and physical constraints for the COILOPT++ code.

```C++
cwsfilename[0] = cws  // Coil winding surface file (multiple may be specified)
modsplinename[0] = fd.spline  // Modular coil spline file (number matches surface)
Bmatch.woutname = wout.vmec_test // Text VMEC file name
Bmatch.cdfname = wout_vmec_test.nc // netCDF VMEC file name
Bmatch.bnormname = bnorm.vmec_test // Normal field file (as calculated by BNORM code)
Bmatch.bgridname = bgrid.dat // Normal field file (B on grid?)
Bmatch.beqoutname = b_norm_eq.dat // Equilibrium normal field grid file (produced by COILOPT++)
Bmatch.bcoiloutprefix = b_norm_final // Prefix for final coil normal field (produced by COILOPT++)
tvinname = tv.in
tvoutprefix = tv
xyzname = coilxyz.dat
uvroot = uv
xyzfized[0] = coils.machine_aux // Auxilliary coils file (one for each auxilliary current group)
Bmatch.normalize = 1; // On by default.
Bmatch.nu = 16; // Number of pts in u direction at which to compare
                               // B_normal_plasma with B_normal_coils
                               // Note: if this is left at zero, it will be reset to
                               // 4 times the maximum poloidal mode number in the
                               // Fourier expansion of the plasma field.
Bmatch.nv = 32; // Number of pts in v direction at which to compare
                                // B_normal_plasma with B_normal_coils
                                // Note: if this is left at zero, it will be reset to
                                // 4 times the maximum toroidal mode number in the
                                // Fourier expansion of the plasma field.

ncwss = 1;      // Just one winding surface by default.

Ip_targ = 0.0;  // Use plasma equilibrium value by default.
curscale[0] = 1.0 // Rescale current by specified amount (number matches surface)
targlenfactor[0] = 0.0; // coil length to target
lmodcur[0] = 1 // Vary coil current
lmodgeom = 1 // Vary coil geometry
lconstrainIp = 1
curscal[iws] = 1.0;   // Rescale currents by specified amount
targlenfactor[iws] = 0.0; // Make coils as short as possible
lmodcur[iws] = 1;
lmodgeom = 1;
lconstrainIp[iws] = 0;
lsamecur[iws] = 0;
sadcircvurat[iws] = 0.0;
curvar = 0.04;
curautoscal = 1; // Rescale currents to match target R BT at plasma surface
bgtfR0B0 = 0.0;  // Note: I_TF = 5e+06 * bgtfR0B0
nfixedgeom = 0;  // By default, don't read in fixed unsplined coilsets.
lccfixed[0] = 0;    // By default, fixed geom. coil current can vary.
lverbose = 0;


nseg_curv = 400;
nseg_coil = 100;
dphiguess = 0.1;
maxcurv = -0.105; // Set negative to use constant coil spacing (faster)
smartcc = 0;
minccsep = 0.0; // No penalty for touching coils
powccsep = 2.0;
ssexcfracw = 0.1;
  for (int icoil=0; icoil<MAXSC; icoil++) { // No bounds on saddle pos. by default
  sadmodl[icoil] = settings.sadmodr[icoil] = -1;
  sadrectumin[icoil] = settings.sadrectvmin[icoil] = 0.0;
  sadrectumax[icoil] = settings.sadrectvmax[icoil] = 1.0;
  }
sadmodws = 0;
sadmodwf = 0.04;
sadrectpfw = 0.02;
```

--------------------------------

### Configure BOOTIN Namelist in Input File

Source: https://princetonuniversity.github.io/STELLOPT/Bootstrap%20Calculation%20for%20NCSX-Like%20configuration

Define the BOOTIN namelist within the input file to set simulation parameters like temperature profiles and density.

```fortran
&INDATA
  MGRID_FILE = 'none'
  LFREEB = F
  DELT =   9.00E-01
  TCON0 =   2.00E+00
  .
  .
  .
  RBC(1,10) = -1.08453911913102E-06     ZBS(1,10) =  8.60890353665843E-05
  RBC(2,10) =  1.04051545504927E-04     ZBS(2,10) = -2.17661420286656E-04
  RBC(3,10) = -5.21965328013036E-04     ZBS(3,10) = -2.67111216700977E-04
  RBC(4,10) = -4.95991087393098E-04     ZBS(4,10) =  2.43875640076056E-05
  RBC(5,10) = -1.94520415280627E-04     ZBS(5,10) =  1.55759001593971E-04
  RBC(6,10) = -6.94143617569942E-05     ZBS(6,10) =  4.40565098025554E-05
/
&BOOTIN
  MBUSE = 72  ! From Boozer Transformation
  NBUSE = 24  ! From Boozer Transformation
  ZEFF1 = 1.0
  DAMP_BS = 0.001 
  TEMPRES = 1.0 ! Coefficient Te=P^TEMPRES
  TETI    = 1.0 ! Te/Ti
  DENS0   = 1.0 ! 10^20 [m^-3]
/
```

--------------------------------

### Install system packages via yum

Source: https://princetonuniversity.github.io/STELLOPT/STELLOPT%20Compilation%20Redhat

Install the required GNU compilers, OpenMPI, and LAPACK libraries using the yum package manager.

```bash
yum install gcc*
yum install openmpi*
yum install lapack*
```

--------------------------------

### NEO Input Configuration File

Source: https://princetonuniversity.github.io/STELLOPT/NEO%20tutorial

Example of a standalone NEO input file. The file uses a specific text format rather than a Fortran namelist.

```text
this line is ignored
this line is ignored
this line is ignored
this line is ignored
neo_out
10 ! no_fluxs = Number of flux surfaces to analyze.
9 19 29 39 49 59 69 79 89 99  ! fluxs_arr = Indices of flux surfaces to analyze.
200 ! theta_n
200 ! phi_n
0 ! max_m_mode
0 ! max_n_mode
75 ! npart
1 ! multra
0.01 ! acc_req
100 ! no_bins
75 ! nstep_per
500 ! nstep_min
2000 ! nstep_max
0 ! calc_nstep_max
1 ! eout_swi
0 ! lab_swi
0 ! inp_swi
2 ! ref_swi
1 ! write_progress
0 ! write_output_files
0 ! spline_test
0 ! write_integrate
0 ! write_diagnostic
this line is ignored
this line is ignored
this line is ignored
0 ! calc_cur
neo_cur
0 ! npart_cur
0 ! alpha_cur
0 ! write_cur_inte
```

--------------------------------

### Install Dependencies via MacPorts

Source: https://princetonuniversity.github.io/STELLOPT/STELLOPT%20Compilation%20OS%20X%20MacPorts

Commands to install required compilers, libraries, and Python modules. Replace gccXX and pythonYYY with the desired versions.

```bash
#  gcc10 : Working
#  gcc11 : Issue with hdf5 23.02.2024
#  gcc12 : Issue with hdf5 23.02.2024
#  gcc13 : Working as of 14.11.2024
#  gcc14 : Working as of 18.09.2025
#  gcc15 : No OpenMPI as of 18.09.2025
export MACOSX_DEPLOYMENT_TARGET=26.0 # Needed at the 10.15->26.0 phase
sudo port install git
sudo port install gccXX        (gccXX should be gcc10 or another gcc variant)
sudo port install openmpi-gccXX +fortran
# The next two are needed for hdf5 and netcdf to build properly
sudo port install llvm-18
sudo port install clang-18 +analyzer +libstdcxx
sudo port select --set mpi openmpi-gccXX-fortran
sudo port select --set gcc mp-gccXX
sudo port select --set clang mp-clang-17
sudo port select --set llvm mp-llvm-18
# Because of dependencies if HDF5 can't be built with +openmpi neither can netcdf
sudo port install hdf5 +fortran +hl +gccXX (+openmpi issue with libc++)
sudo port install netcdf (+openmpi issue with libc++)
sudo port install netcdf-fortran +gccXX (+openmpi issue with libc++)
sudo port install fftw-3 +openmpi +gccXX
# This section for using OpenBLAS
sudo port install OpenBLAS +lapack +native +gccXX
sudo port install scalapack +openmpi +openblas +gccXX
# This section for using the Accelerate Framework
sudo port install scalapack +openmpi +accelerate +gccXX
sudo port install pythonYYY
sudo port select --set python pythonYYY
sudo port select --set python3 pythonYYY
sudo port install pyYYY-pip
sudo port select --set pip pipYYY
sudo port select --set pip3 pipYYY
# All other python modules should be handled durring 
# install using pip and setuptools
```
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