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Diffusion FENNECS: Finite Element Non-Neutral Electron Cloud Simulator (breakdown) Browse

fennecs/wk/T-REX/run.sh
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run.sh
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#!/bin/bash -l
#SBATCH --job-name=fennecs
#SBATCH --time=1:00:00
#SBATCH -n 1
#SBATCH -c 36
#SBATCH --mem=144G
module purge
module restore espic2d-intel
espicsrc='${HOME}/espic2master/src'
espicwk='${HOME}/espic2master/wk'
res_folder='/scratch/${USER}/experiment/upper_electrode_ellipse/'
mkdir -p $res_folder
cat > job.in << EOM
General input parameters for the FENNECS code
=========================================
T.M. Tran SPC/EPFL
G. Le Bars SPC/EPFL
&BASIC
job_time=43000.0, ! FENNECS run time in [s]
extra_time=200.0, ! time to save to file and tidy up at the end of the simulatio [s]
nrun=100, !# of steps
nlres=f, ! Resume from existing simulation
newres=f, ! Overwrite the result file in resume
dt=1E-12 ! Time step in [s]
! Mesh and Poisson parameters
femorder=3,3, ! degree of the b-spline polynomia in z and r direction
ngauss=6,6, ! number of points for the gauss integration in z and r direction
nlppform=.TRUE. ! evaluate the electrostatic potential in ppform instead of spline form
nz=480, ! # of intervals in z
lz=0.249,0.481, ! axial dimensions of the mesh
radii=0, 0.008, 0.019, 0.033,0.038,0.0505 ! Limits of the subregions of mesh in radial direction [m]
nnr=20, 60,130,35,40 ! Number of grid cell in r direction for each radii sub-region
! Diagnostic variables
nlxg=f, ! Display graphical interface (need compilation with xgrafix)
it0d=10, ! # of time steps between each save of scalar variables
it2d=100, ! # of time steps between each save of grid variables
ittext=100, ! # of time steps between each write of the simulation status to standard output
itparts=50000,! # of time steps between each save of the particles position and velocity
ittracer=10, ! # of time steps between each save of the particles position and velocity if they have is_test=t
itgraph=100, ! # of time steps between each update of the graphical interface
nbcelldiag=0, ! # of cells being diagnosed with celldiag (see &celldiagparams)
itcelldiag=20,! # of time steps between each save of the cell diagnostics
resfile='${res_folder}resultfast.h5' ! result file filename
rstfile='${res_folder}restartfast.h5' ! restart file filename containing only the last time-step status
! Particles properties and loading
partperiodic=f ! Set periodic boundary conditions in z for the particles
nlclassical=t, ! Solve classical equations of motion or relativistic
nbspecies=3, ! # of species to load using particle files
partfile='electrons_gauss.in','electron_tracers.in','ion_tracers.in', ! Name of the particle files to load
distribtype=7 ! Type of distribution function for particle loading
! 1: uniform RZ gaussian in V, 2: stable eq 4.85 from Davidson,... 7: use partfile
! see beam_mod.f90 for more details
nplasma=2116800, ! # of particles to load in case of loading with distribtype != 7
n0=-3e17 ! density of plasma in [m-3] in case of loading with distribtype != 7
! Other modules parameters
nlmaxwellsource=t, ! use an ad-hoc source defined in &maxwellparams
! Geometry configuration, combined with &geomparams and &spldomain
nlPhis=t, ! if false deactivate calculation of space-charge effects and onsider only external field
potinn=-0000, ! potential at inner wall [V]
potout=0, ! potential at outer wall [V]
! Magnetic field configuration
B0=0.28, ! Normalization variable for magnetic field [T]
! and maximum magnetic field amplitude if bscaling!=0
magnetfile='10T_DNPW.h5' ! .h5 filename of the magnetic field configuration takes precedence over R and
! such a file can be created using matlab/savemagtoh5.m
bscaling=0, ! rescaling of the magnetic field amplitude imported from magnetfile
! -1 rescale before evaluation to the grid, 0 no rescaling, 1 rescaling after evaluation to the grid points
/
&maxwellsourceparams
! see maxwellsrce_mod.f90 for more information
frequency=5E11, ! # of macro particles genereated per s [Hz]
temperature=22000, ! temperature of the maxwellian source [K]
rlimits=0.01,0.027,! radial limits of the source [m]
zlimits=0.35,0.4 ! axial limits of the source [m]
time_start=-1.0, ! time at which the source starts [s]
radialtype=2 ! type of radial distribution
time_end=-1.0 ! time at which the source stops [s]
/
&celldiagparams
! set-up of cell diagnostics
specieid=1, ! id of specie to save
rindex=112, ! radial index of the cell to save
zindex=117, ! axial index of the cell to save
/
&geomparams
! parameters defining the system geometry in case of analytical Rvachev weight functions
r_a=0.01
r_bLeft=0.02358
alpha=0.1745
z_0=0.375
r_0=0.028
z_r=0.025
r_r=0.005
r_b=0.028
r_bRight=0.0375
above2=-1
above1=1
interior=-1
! Type of geometric weight to use negative values use a test source term for Poisson
! to test if the resolution of the grid is sufficient
walltype=9 ! 9: use a spline domain defined in &spldomain
! More walltypes are defined in weighttypes_mod.f90
nlweb=t ! use web-splines ( should always be true)
testkr=10 ! in case of negative walltype, set the electrostatic test function radial wave vector
testkz=10 ! in case of negative walltype, set the electrostatic test function axial wave vector
/
&spldomain
! set the parameters for a geometry defined from spline curves boundaries
dist_extent=5e-3, ! distance to the boundary over which the geometric weight goes to 1 [m]
h5fname='exp_outer_with_vessel_geom.h5', ! name of the h5 file containing the geometry
! such a file can be created using matlab/savegeomtoh5.m
Dvals=0,-20000,0,0 ! Potential set on the surface of each spline curve [V]
/
&neutcolparams
! Defines the parameters for collisions with neutrals see neutcol_mod.f90
neutdens=2.5e20, ! density of the neutrals
! Here Neon parameters are used
Eion=21.56, ! Ionisation energy of [eV]
scatter_fac=24.2, ! parameter defining the energy splitting between scattered and released electrons [eV]
! see Opal 1971 https://doi.org/10.1063/1.1676707
nlcol=t, ! activate the collisions
io_cross_sec_file='${espicwk}/Ne_io_cross_sec.in', ! file containing the tables for ionisation cross-sections
ela_cross_sec_file='${espicwk}/Ne_ela_cross_sec.in', ! file containing the tables for elastic collision cross-sections for momentum exchange
/
EOM
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
srun $espicsrc/fennecs job.in
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