SFINCS is a code that solves the drift-kinetic equation to compute many neoclassical quantities, such as the collisional radial fluxes, parallel flows, and bootstrap current. The code has a separate GitHub repository here https://github.com/landreman/sfincs and is not included in the main STELLOPT repository. This page describes one particular application of SFINCS: coupling to STELLOPT in order to obtain MHD equilibria with a self-consistent profile of bootstrap current. For other applications, you can refer directly to the SFINCS GitHub repository and the user manual there.
SFINCS requires a real (not complex) version of PETSc. There is basically no way for an executable to link to both real and complex versions of PETSc, and since GENE uses a complex version of PETSc, this means SFINCS and GENE cannot both be linked to STELLOPT at the same time. (Although perhaps GENE could be built without PETSc support?)
SFINCS requires that the PETSc library be built with either MUMPS or SuperLU_DIST, which are libraries for parallel direct solution of sparse linear systems. MUMPS is preferable to SuperLU_DIST, as it is faster and uses less memory.
SFINCS also requires the HDF5 and NetCDF libraries.
To get SFINCS, clone the git repository:
git clone https://github.com/landreman/sfincs.git
Compile SFINCS following the directions in the SFINCS user manual. A library file libsfincs.a will be generated that we will link into STELLOPT.
Next, in your STELLOPT repository, you must (at least for now) switch to
the "sfincs" branch of the repo. To do this, type
git checkout sfincs from anywhere in the STELLOPT repository.
In your stellopt
make_*.inc file, look for the section\
####################################################################### # SFINCS Options #######################################################################
LSFINCS = T Also, set
appropriately for your system. Now build STELLOPTV2. This should
generate an executable
xstelloptv2 that is linked to SFINCS.
To obtain a self-consistent profile of bootstrap current, each call to
(PAR)VMEC is replaced by an iteration between VMEC and a bootstrap
current code (SFINCS, or perhaps some other code like BOOTSJ). VMEC
takes a given profile of toroidal current and computes the magnetic
geometry. Then the bootstrap current code takes the given magnetic
geometry and computes an updated current profile. The process is
repeated until convergence. These iterations are coordinated by
STELLOPT, in the file
The switch to turn on this iteration in STELLOPTV2 is
equil_type = 'vboot' in the
&optimum namelist, instead of the usual
settings 'vmec2000' or 'parvmec'. To select which code is used to
compute the bootstrap current, you should include
bootcalc_type='bootsj' in the
namelist. In this namelist you should also specify
vboot_tolerance = 1.e-2 or some other value; this variable controls
the number of iterations that will be performed between VMEC and the
bootstrap current code, with a smaller tolerance leading to more
For further mathematical details of the vboot iteration, see the note
When SFINCS is run as a standalone code, it reads several namelists
(&general, &geometryParameters, etc.) from a file named input.namelist.
However when SFINCS is run via STELLOPT, these namelists should all be
appended to the main STELLOPT
input.* file. If there is an
input.namelist file present, it will not be read by SFINCS.
For detailed documentation of the SFINCS input namelists and parameters, see the SFINCS user manual. The following SFINCS input parameters are all filled in by STELLOPT, so they do not need to be specified in the input file, and any values that do appear in the input file will be over-written:\
geometryScheme VMECRadialOption inputRadialCoordinate inputRadialCoordinateForGradients psiN_wish equilibriumFile nHats THats dnHatdpsiNs dTHatdpsiNs
There are several parameters related to the SFINCS-STELLOPT interaction
that are not used with standalone SFINCS, and which should be specified
&optimum namelist. First,
sfincs_s should be set to a real
array with entries in (0,1], giving the radii (in terms of normalized
toroidal flux s) at which SFINCS will be run. Do not include 0 as a
radius, since the bootstrap current always vanishes on axis. Depending
on the density and temperature profiles, you may or may not wish to
include 1 as a radius; if either the density or temperature vanish at
s=1 then SFINCS will fail there.
sfincs_min_procs should be set to an integer giving the minimum
number of processors allocated to SFINCS for each magnetic surface.
The SFINCS calculations at different radii are essentially independent
of each other, and so STELLOPT can efficiently parallelize calculations
over radius. At the same time, SFINCS can take advantage of multiple
processors for the calculation at each radius. An important
consideration is that at each radius, SFINCS requires a substantial
amount of memory (typically 30 GB - 1 TB for experimentally relevant
parameters), and so enough processors must be devoted to each radius or
else SFINCS will crash with an out-of-memory error. Due to this issue,
the STELLOPT parameter
sfincs_min_procs is provided. STELLOPT will
divide up the processors among radii ensuring that each radius has at
sfincs_min_procs processors. If your SFINCS jobs are running out
of memory but you do not wish to request more processors, raise
As an example, suppose you are running on the IPP computer Draco or on
NERSC Cori Haswell, either of which has nodes with 32 processors/node
and 128 GB/node, so 4 GB/processor. Suppose further that you are running
SFINCS at a resolution that requires 64 GB per solve, so you need
64/4=16 processors for each instance of SFINCS. Setting
sfincs_min_procs = 16 is then appropriate. Suppose also that
sfincs_s contains 8 radii. If you can request 4 nodes (=4*32=128
processors), then SFINCS can run for all 8 radii in parallel. If you run
on 2 nodes, then SFINCS will run for radii 1, 3, 5, and 7 in parallel,
and afterwards SFINCS will run for the remaining 4 radii. If you run on
1 node, then SFINCS will first run for radii 1 and 5 in parallel, after
which SFINCS will run for the radii 2 and 6, then radii 3 and 7, then
radii 4 and 8.
There is no restriction that the number of processors must be a multiple
of any particular number related to the number of radii in
sfincs_min_procs. Therefore as long as SFINCS does not run out of
memory, any number of processors should be allowed. For optimal load
balancing, you can request a number of processors equal to the number of
sfincs_s times the number of processors you want SFINCS to
use at each radius.
It is important to tune the SFINCS resolution parameters Ntheta, Nzeta, Nxi, and Nx based on the magnetic geometry and collisionality. If these values are too low, the SFINCS calculation will be under-resolved. If these resolution parameters are too high, the SFINCS calculations will take unnecessary computational time and memory. It is recommended that you do convergence testing using standalone SFINCS (not using STELLOPT) any time you make significant changes to the density, temperature, or magnetic geometry. (Small modifications to magnetic geometry, as arise during optimization, will not require changes to SFINCS resolution, but major changes such as switching from W7-X to NCSX will require resolution changes.) For detailed instructions on resolution convergence testing, see the chapter of the SFINCS user manual on `Numerical resolution parameters.'
The radial electric field Er typically has a small effect on the
bootstrap current, on the order of 10% for W7-X and NCSX. Accurate
computation of Er requires running SFINCS several times at each radius
for various values of Er to solve for the ambipolar value. However,
accurate calculation of Er may not be necessary due to its weak effect
on the bootstrap current. The parameter
sfincs_Er_option in the
&optimum namelist controls how Er is determined in the
STELLOPT-SFINCS system. Presently, two options are available. If
sfincs_Er_option="zero", Er is set to zero. (Actually Er is set to a
very small nonzero value, since SFINCS is slightly more robust when Er
is not exactly zero.) Alternatively, if
Er is set to an estimate for the ambipolar radial electric field based
on the sqrt(nu)-regime radial ion flux:
d phi / d s = - (1/e) [(T_i / n) (d n / d s) + 1.34 (d T_i / d s)]
where phi is the electrostatic potential and s is any radial coordinate. (This formula is obtained from eq (74.a) of Ho & Kulsrud, Phys Fluids 30, 442 (1987).) Full calculation of the ambipolar Er is not available yet within STELLOPT, but will be available in the future.
Several example input files are provided in subdirectories
of the BENCHMARKS directory. The first few lines of each input file
provides some information about the number of processors required,
expected output, etc. Each of the subdirectories also contains a .pdf
file showing the expected convergence of the vboot iterations.
Once a vboot calculation (using either BOOTSJ or SFINCS) has run, you
can plot several quantities using the
vbootPlot script in the
directory. This script will plot, for instance, how the total toroidal
current and the profile of toroidal current vary over the vboot
iterations. Some of the data this script plots is saved in the
boot_fit.<extension> file. The syntax for calling the plotting script
vboot_plot boot_fit.<extension> wout_<extension>_vboot0000.nc You