adding test for collision operators using ionbalance data from Eric H…

…ollmann

test/CMakeLists.txt

@@ -23,6 +23,7 @@ set_property(TARGET xtest PROPERTY LINKER_LANGUAGE Fortran)
 configure_file(${CMAKE_SOURCE_DIR}/test/egyro/korc_egyro.sh.in ${CMAKE_BINARY_DIR}/egyro_test/korc_egyro.sh)
 configure_file(${CMAKE_SOURCE_DIR}/test/mars/korc_mars.sh.in ${CMAKE_BINARY_DIR}/mars_test/korc_mars.sh)
 configure_file(${CMAKE_SOURCE_DIR}/test/aorsa/korc_aorsa.sh.in ${CMAKE_BINARY_DIR}/aorsa_test/korc_aorsa.sh)
+configure_file(${CMAKE_SOURCE_DIR}/test/hollmann/korc_hollmann.sh.in ${CMAKE_BINARY_DIR}/hollmann_test/korc_hollmann.sh)
 
 #if(USE_PSPLINE)
 #  add_test (NAME mars_test_1
@@ -34,6 +35,7 @@ configure_file(${CMAKE_SOURCE_DIR}/test/aorsa/korc_aorsa.sh.in ${CMAKE_BINARY_DI
 file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/bin/egyro_test)
 file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/bin/mars_test)
 file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/bin/aorsa_test)
+file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/bin/hollmann_test)
 
 foreach(RANK IN ITEMS 1 2 4 8) #16)
   if(${RANK} LESS_EQUAL ${MPIEXEC_MAX_NUMPROCS})
@@ -52,6 +54,11 @@ foreach(RANK IN ITEMS 1 2 4 8) #16)
       COMMAND ${CMAKE_BINARY_DIR}/aorsa_test/korc_aorsa.sh ${RANK}
             WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
       set_tests_properties (aorsa_test_${RANK} PROPERTIES PROCESSORS ${RANK} ENVIRONMENT OMP_NUM_THREADS=1)
+
+      add_test (NAME hollmann_test_${RANK}
+      COMMAND ${CMAKE_BINARY_DIR}/hollmann_test/korc_hollmann.sh ${RANK}
+            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
+      set_tests_properties (hollmann_test_${RANK} PROPERTIES PROCESSORS ${RANK} ENVIRONMENT OMP_NUM_THREADS=1)
     endif()
 
     add_test (NAME unit_testing_${RANK}

test/hollmann/input_file_JET_95128_TEST15b.korc

@@ -0,0 +1,170 @@
+&input_parameters
+  restart = F
+    ! Restart simulation that exited before simulation_time reached
+  proceed = F
+    ! Append simulation results after previous simulation_time reached
+  reinit = F
+    ! Begin a new simulation, reinitializing from restart file state
+  simulation_time = 1.E-8
+    ! Total aimed simulation time in seconds   
+    ! Run 10 mu s If transients exist put 5 extra mu s.
+  snapshot_frequency = 1.E-9
+    ! Time between snapshots in seconds
+  restart_overwrite_frequency = 1.E-1	
+    ! Time between overwritting of restart file in seconds
+  dt = 1.58E0
+    ! Time step as fraction of relativistic gyro-period
+  num_species = 1
+  minimum_particle_energy = 1.0E2 
+    ! Minimum energy of simulated particles in eV
+  radiation = T
+  GC_rad_model='SDE'
+  collisions = T
+  LargeCollisions = F
+  collisions_model = 'SINGLE_SPECIES' 
+    ! Options are: 'NONE','SINGLE_SPECIES' and 'MULTIPLE_SPECIES'
+  bound_electron_model = 'HESSLOW' 
+    ! Options are: 'NO_BOUND', 'HESSLOW', and 'ROSENBLUTH'
+  field_model = 'EXTERNAL-PSI'	
+  profile_model = 'EXTERNAL_Hdt'	
+    ! The two options for this parameter are 'ANALYTICAL' or 'EXTERNAL'.
+    ! For 'ANALYTICAL', the magnetic field is calculated based on
+    ! the parameters given in the "analytic_mag_field_params" section.
+    ! For 'EXTERNAL', the magnetic field is loaded from the file
+    ! specified in "filename".
+    ! 'UNIFORM' A uniform magnetic field used to advance only electrons' 
+    ! velocity.
+  magnetic_field_filename = 'EFIT_JET_95128_Hratio.h5'
+  outputs_list = '{X,Y,V,B,E,g,eta,flagCon,flagCol,PSIp}' 
+    ! List of outputs
+    !'{X,Y,V,E,B,g,mu,eta,Prad,Pin,flagCon,flagCol,gradB,
+    !  curlb,ne,Te,Zeff,PSIp,nimp}'
+  HDF5_error_handling = T
+  orbit_model = 'GC'
+    ! 'FO' for full orbit, 'GCpre' for guiding center with pre-computed
+    ! auxiliary fields, 'GCgrad' for guiding center with auxiliary
+    ! fields computed with PSPLINE.
+  field_eval = 'interp'
+    ! Set for plasma_model='ANALYTICAL'. Can be 'interp' or 'eqn',
+    ! where 'eqn' evaluates particle fields at particle positions and
+    ! 'interp' interpolates precomputed fields.
+  SameRandSeed = T
+  !pchunk = 1
+/
+
+&plasma_species
+  runaway = T
+  ppp = 100
+    ! Number of particles per process (mpi)
+  q = -1.0
+    ! Electric charge
+  m = 1.0
+    ! In units of electron mass
+  spatial_distribution = 'HOLLMANN-1DTRANSPORT'
+    ! Options are: 'UNIFORM', 'DISK', 'TORUS', 'EXPONENTIAL-TORUS',
+    ! 'GAUSSIAN-TORUS', 'ELLIPTIC-TORUS', 'EXPONENTIAL-ELLIPTIC-TORUS',
+    ! 'GAUSSIAN-ELLIPTICAL-TORUS', '2D-GAUSSIAN-ELLIPTIC-TORUS-MH',
+    ! 'AVALANCHE-4D','TRACER','SPONG-3D','HOLLMANN-3D'
+  Ro = 2.6
+  PHIo = 0.0
+    ! In degrees
+  Zo = 0.0
+  sigmaR = 1.e6
+  sigmaZ = 0.2
+  theta_gauss = 0.0
+  psi_max=1.
+    ! goes as R^2 for HOLLMANN-3D, is psiN_max for HOLLMANN-3D-PSI
+  energy_distribution = 'HOLLMANN-1DTRANSPORT'
+    ! Options are: 'MONOENERGETIC', 'THERMAL', 'AVALANCHE', 
+    ! 'EXPERIMENTAL', and 'UNIFORM'
+  pitch_distribution = 'HOLLMANN-1DTRANSPORT'
+    ! Options are: 'MONOPITCH', 'AVALANCHE', 'EXPERIMENTAL', and 'UNIFORM'.
+  Eno = 10.0E6
+    ! Initial energy in eV
+  etao = 170.0
+    ! Initial pitch angle
+  Eo_lims = 1.0E6,50.0E6
+    ! Lower and upper limit of simulated energy range, in eV.
+  etao_lims = 0.0,20.0
+    ! Lower and upper limit of simulated pitch-angle range, in degrees.
+  Xtrace = 2.6,0.0,0.0
+    ! Initial position of tracer particle for debugging with
+    ! spatial_distribution='TRACER'
+  dth = 3.
+    ! Variance of sampling normal variate for pitch angle
+  dgam = 3.
+    ! Variance of sampling normal variate for pitch angle
+  dR = 0.1
+    ! Variance of sampling normal variate for R location
+  dZ = 0.1
+    ! Variance of sampling normal variate for Z location
+/
+
+&analytical_fields_params
+/
+
+&externalPlasmaModel
+  Bfield = F
+  B1field = F
+  E1field = F
+  dBfield = F
+  axisymmetric_fields = T
+  Bflux = F
+  Bflux3D = T
+  Efield = T
+  Dim2x1t =T
+  ReInterp_2x1t = T
+  PSIp_lim= 1.046608805604306e+00
+  PSIp_0= 8.838935617719927e-01
+  psip_conv=-1.
+    ! sign appended to \nabla\phi\times\nabla\psi_p for definition of
+    ! poloidal magnetic field. +1 for DIII-D, -1 for JET
+/
+
+&plasmaProfiles
+  axisymmetric = T
+  filename = 'EFIT_JET_95128_Hratio.h5' 
+/
+
+&CollisionParamsSingleSpecies
+  Te_sing = 3.e0
+    ! Background electron temperature in eV
+  Ti_sing = 3.e0
+    ! Background ion temperature in eV
+  ne_sing = 9.63E19 
+    ! Background electron density in m^-3
+  Zeff_sing = 3.84 
+    ! Effective atomic number
+  dTau_sing = 5.e-2
+    ! Subcycling time step in collisional time units (Tau)
+  !p_therm = 1.
+  !min_secRE  = 'CRIT'
+  !ConserveLA = T
+  !Clog_model = 'MCDEVITT'
+  !sample_test = F
+/
+
+&CollisionParamsMultipleSpecies
+  num_impurity_species = 1
+  Te_mult = 3.e0 
+    ! Background electron temperature in eV
+  ne_mult = 9.36E19 
+    ! Background electron density in 1/m^3
+/
+
+&HollmannPDF
+  filename_Hollmann = 'Hollmann_PDF_JET_95128_3.h5'
+  rho_ind = 7
+  max_pitch_angle_Hollmann = 90. 
+    ! In degrees
+  min_pitch_angle_Hollmann = 0. 
+    ! In degrees
+  min_energy_Hollmann = 2.E3 
+    ! In eV
+  max_energy_Hollmann = 8.4E6
+    ! For Hollmann_PDF_HR.h5, needs to be less than 80 MeV
+    ! In eV
+  current_direction_Hollmann = 'PARALLEL'
+
+/
+

test/hollmann/korc_hollmann.sh.in

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+set -ex
+
+#define input file
+INPUT_FILE="${CMAKE_SOURCE_DIR}/test/hollmann/input_file_JET_95128_TEST15b.korc"
+#define output directory
+OUT_DIR="hollmann_test/rank_$1"
+
+#check that output directory doesn't exist so bash doesn't complain
+if [ ! -d $OUT_DIR ]; then
+  mkdir -p $OUT_DIR
+fi
+if [ ! -f EFIT_JET_95128_Hratio.h5 ]; then
+  ln -s ${CMAKE_SOURCE_DIR}/test/hollmann/EFIT_JET_95128_Hratio.h5 EFIT_JET_95128_Hratio.h5
+fi
+if [ ! -f Hollmann_PDF_JET_95128_3.h5 ]; then
+  ln -s ${CMAKE_SOURCE_DIR}/test/hollmann/Hollmann_PDF_JET_95128_3.h5 Hollmann_PDF_JET_95128_3.h5
+fi
+
+${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} $1 ./xkorc $INPUT_FILE $OUT_DIR/
+
+for i in $(seq 0 $(($1-1)));
+do
+  h5diff -r -p 0.000008 $OUT_DIR/file_$i.h5 ${CMAKE_SOURCE_DIR}/test/hollmann/rank_$1/file_$i.h5
+done