Merge pull request #239 from PrincetonUniversity/feature/pySTEL

Feature/py stel

.gitignore

@@ -1,11 +1,11 @@
 *~
 *#
-
 *.o
 *.mod
 *.a
 *.so
 *.zip
+*.egg-info
 .DS*
 *.dSYM
 ._*
@@ -69,3 +69,9 @@ PB3D
 
 .vscode/
 LIBSTELL/.makefile.swp
+pySTEL/build
+pySTEL/dist
+
+*.sublime-project
+*.sublime-workspace
+fort.*

BEAMS3D/BEAMS3D.dep

@@ -10,7 +10,7 @@ beams3d_beam_density.o: \
       ../../LIBSTELL/$(LOCTYPE)/mpi_params.o 
 
 beams3d_interface_mod.o: \
-      beams3d_input_mod.o \
+      ../../LIBSTELL/$(LOCTYPE)/beams3d_input_mod.o \
       beams3d_runtime.o \
       beams3d_grid.o \
       beams3d_lines.o \
@@ -20,7 +20,7 @@ beams3d_interface_mod.o: \
 
 beams3d_imas_module.o: \
       beams3d_interface_mod.o \
-      beams3d_input_mod.o 
+      ../../LIBSTELL/$(LOCTYPE)/beams3d_input_mod.o 
 
 
 beams3d_fix_poloidal.o: \
@@ -143,7 +143,7 @@ beams3d_init.o: \
       ../../LIBSTELL/$(LOCTYPE)/adas_mod_parallel.o \
       beams3d_runtime.o \
       beams3d_grid.o \
-      beams3d_input_mod.o \
+      ../../LIBSTELL/$(LOCTYPE)/beams3d_input_mod.o \
       beams3d_lines.o\
       fidasim_input_mod.o \
 
@@ -260,16 +260,6 @@ beams3d_init_continuegrid.o: \
       beams3d_grid.o      
 
 
-beams3d_input_mod.o: \
-      ../../LIBSTELL/$(LOCTYPE)/stel_kinds.o \
-      ../../LIBSTELL/$(LOCTYPE)/safe_open_mod.o \
-      ../../LIBSTELL/$(LOCTYPE)/mpi_params.o \
-      ../../LIBSTELL/$(LOCTYPE)/mpi_inc.o \
-      beams3d_runtime.o \
-      beams3d_lines.o \
-      beams3d_grid.o 
-
-
 beams3d_lines.o: \
       ../../LIBSTELL/$(LOCTYPE)/stel_kinds.o 
 

BEAMS3D/ObjectList

@@ -46,7 +46,6 @@ beams3d_grid.o \
 backspace_out.o \
 beams3d_follow_gc.o \
 gauss_rand.o \
-beams3d_input_mod.o \
 beams3d_init_beams.o \
 fgc_rkh68.o \
 fgc_lsode.o 

BEAMS3D/Sources/beams3d_grid.f90

@@ -11,6 +11,19 @@ MODULE beams3d_grid
       USE stel_kinds, ONLY: rprec
       USE EZspline_obj
       USE EZspline
+      USE beams3d_globals, ONLY: nr, nphi, nz, rmin, rmax, zmin, zmax, &
+                                 phimin, phimax, vc_adapt_tol, nte, &
+                                 nne, nti,nzeff, npot, plasma_mass, &
+                                 plasma_Zmean, therm_factor, &
+                                 B_kick_min, B_kick_max, freq_kick, &
+                                 E_kick, rho_fullorbit, rmin_fida, &
+                                 rmax_fida, zmin_fida, zmax_fida, &
+                                 phimin_fida, phimax_fida, nr_fida, &
+                                 nphi_fida, nz_fida, nenergy_fida, &
+                                 npitch_fida, &
+                                 t_fida, dexionT, dexionD,dexionHe3, &
+                                 s_max,s_max_te, s_max_ne,s_max_zeff,&
+                                 s_max_ti, s_max_pot
 
 !-----------------------------------------------------------------------
 !     Module Variables
@@ -40,7 +53,6 @@ MODULE beams3d_grid
 !         plasma_Zmean   [Z] = sum(n*Z*Z*mi/mj)/sum(n*Z) sum over j ion species (mi: plasma mass)
 !-----------------------------------------------------------------------
       IMPLICIT NONE
-      INTEGER  ::    nr, nphi, nz, nte, nne, nti, nzeff, npot, dexionT, dexionD, dexionHe3
       INTEGER  ::    win_raxis, win_phiaxis, win_zaxis, win_B_R, win_B_PHI, win_B_Z,&
                      win_MODB, win_TE, win_NE, win_TI, win_ZEFF_ARR,&
                      win_S_ARR, win_U_ARR,win_X_ARR,win_Y_ARR, win_POT_ARR, win_BR4D, win_BPHI4D, &
@@ -49,16 +61,12 @@ MODULE beams3d_grid
                      win_wall_load, win_wall_shine, win_hr, win_hp, win_hz, &
                      win_hri, win_hpi, win_hzi, win_NI5D, win_NI, &
                      win_raxis_fida, win_phiaxis_fida, win_zaxis_fida, win_energy_fida, win_pitch_fida, &
-                     win_beam_density, win_NEUTRONS, win_E_NEUTRONS, &
-                     nr_fida, nphi_fida, nz_fida, nenergy_fida, npitch_fida
-      REAL(rprec) :: rmin, rmax, zmin, zmax, phimin, phimax, tmin, tmax, delta_t, &
-                     vc_adapt_tol, psiedge_eq, phiedge_eq, plasma_Zmean, plasma_mass, &
-                     reff_eq, therm_factor, B_kick_min, B_kick_max, &
-      E_kick, freq_kick, t_fida, rho_fullorbit, rho_help,&
-      s_max,s_max_te, s_max_ne,s_max_zeff,s_max_ti, s_max_pot
+                     win_beam_density, win_NEUTRONS, win_E_NEUTRONS 
+      REAL(rprec) :: emin_fida, pimin_fida
+      REAL(rprec) :: tmin, tmax, delta_t, psiedge_eq, phiedge_eq, &
+                     reff_eq, rho_help
       REAL(rprec), POINTER :: raxis(:), zaxis(:), phiaxis(:)
       REAL(rprec), POINTER :: req_axis(:), zeq_axis(:), E_NEUTRONS(:)
-      REAL :: rmin_fida, rmax_fida, zmin_fida, zmax_fida, phimin_fida, phimax_fida, emin_fida, pimin_fida
       REAL(rprec), POINTER :: raxis_fida(:), zaxis_fida(:), phiaxis_fida(:), energy_fida(:), pitch_fida(:)
       REAL(rprec), POINTER :: wall_load(:,:), wall_shine(:,:)
       REAL(rprec), POINTER :: B_R(:,:,:),B_PHI(:,:,:), B_Z(:,:,:), MODB(:,:,:),&

BEAMS3D/Sources/beams3d_lines.f90

@@ -10,6 +10,8 @@ MODULE beams3d_lines
 !     Libraries
 !-----------------------------------------------------------------------
       USE stel_kinds, ONLY: rprec
+      USE beams3d_globals, ONLY: nparticles, ns_prof1, ns_prof2, &
+                                 ns_prof3, ns_prof4, ns_prof5, partvmax
 
 !-----------------------------------------------------------------------
 !     Module Variables
@@ -22,15 +24,16 @@ MODULE beams3d_lines
 !-----------------------------------------------------------------------
       IMPLICIT NONE
       LOGICAL  ::  ltherm
-      INTEGER  ::  ns_prof1, ns_prof2, ns_prof3, ns_prof4, ns_prof5, nsh_prof4
-      INTEGER  :: nparticles, nsteps, myline, mybeam, mytdex, myend, mystart_save, myend_save
+      INTEGER  :: nsh_prof4
+      INTEGER  :: nsteps, myline, mybeam, mytdex, myend, mystart_save, myend_save
       INTEGER  :: win_epower, win_ipower, win_ndot, win_dense, win_jprof, win_dist5d, win_dist5d_fida
       REAL(rprec) :: xlast,ylast,zlast ! for storing position
       REAL(rprec) :: moment, mycharge, myZ, mymass, myv_neut(3), my_end, &
                      myqm, rand_prob, cum_prob, tau, next_t, &
-                     partvmax, fact_crit, fact_pa, fact_vsound, fact_kick, &
+                     fact_crit, fact_pa, fact_vsound, fact_kick, &
                      fact_coul, fact_crit_pro, &
-                     partpmax, h2_prof, h3_prof, h4_prof, h5_prof, r_h, z_h, p_h, e_h, pi_h, E_by_v
+                     partpmax, h2_prof, h3_prof, h4_prof, h5_prof, r_h, &
+                     z_h, p_h, e_h, pi_h, E_by_v
       LOGICAL, ALLOCATABLE     :: neut_lines(:,:)
       INTEGER, ALLOCATABLE     :: end_state(:)
       REAL(rprec), ALLOCATABLE :: shine_through(:), shine_port(:), GFactor(:), t_last(:)

BEAMS3D/Sources/beams3d_runtime.f90

@@ -51,12 +51,35 @@
 !     v4.07 01/11/24 - Added ability to specifiy weights in the input
 !-----------------------------------------------------------------------
 MODULE beams3d_runtime
-    !-----------------------------------------------------------------------
+    !-------------------------------------------------------------------
     !     Libraries
-    !-----------------------------------------------------------------------
+    !-------------------------------------------------------------------
     USE stel_kinds, ONLY: rprec
     USE mpi_params
     USE EZspline
+    USE beams3d_globals, ONLY: r_start_in, z_start_in, phi_start_in, &
+                              vll_start_in, mu_start_in, vr_start_in, &
+                              vphi_start_in, vz_start_in, t_end_in, &
+                              mass_in, charge_in, Zatom_in, weight_in, &
+                              NE_AUX_S, TE_AUX_S, NI_AUX_S, TI_AUX_S, &
+                              NE_AUX_F, TE_AUX_F, NI_AUX_F, TI_AUX_F, &
+                              ZEFF_AUX_S, POT_AUX_S, ZEFF_AUX_F, &
+                              POT_AUX_F, NI_AUX_M, NI_AUX_Z, &
+                              Adist_beams, Asize_beams, DIV_BEAMS, &
+                              DEX_BEAMS, R_BEAMS, Z_BEAMS, PHI_BEAMS, &
+                              E_BEAMS, MASS_BEAMS, CHARGE_BEAMS, &
+                              ZATOM_BEAMS, P_BEAMS, nparticles_start, &
+                              npoinc, follow_tol, int_type, ne_scale, &
+                              te_scale, ti_scale, zeff_scale, &
+                              fusion_scale, lendt_m, te_col_min, &
+                              duplicate_factor, ldebug, lbeam, &
+                              MAXBEAMS, lbeam, MAXBEAMS, nbeams, &
+                              pi2, NION, &
+                              MAXPROFLEN, MAXPARTICLES, lverb, &
+                              lbbnbi, lcollision, lfusion, &
+                              lrestart_particles, lfusion_alpha, &
+                              lfusion_He3, lfusion_proton, &
+                              lfusion_tritium, lkick, lgcsim, id_string
     !-----------------------------------------------------------------------
     !     Module Variables
     !          lverb         Logical to control screen output
@@ -123,46 +146,26 @@ MODULE beams3d_runtime
     INTEGER, PARAMETER :: MPI_BCAST_ERR = 83
     INTEGER, PARAMETER :: MPI_FINE_ERR = 89
 
-    INTEGER, PARAMETER :: MAXPARTICLES = 2**18
-    INTEGER, PARAMETER :: MAXBEAMS = 32
-    INTEGER, PARAMETER :: MAXPROFLEN = 512
-    INTEGER, PARAMETER :: NION = 4
-
     DOUBLE PRECISION, PARAMETER :: one           = 1.0D0 ! 1.0
-
-    LOGICAL :: lverb, lvmec, lpies, lspec, lcoil, lmgrid, &
-               lvessel, lvac, lcontinue_grid, lrestart_particles, lneut, &
-               lbeam, lhitonly, lread_input, lplasma_only, lraw,&
-               ldepo, lbeam_simple, ldebug, lcollision, lw7x, lsuzuki, &
-               lascot, lascot4, lbbnbi, lfidasim, lfidasim_cyl, lsplit, lvessel_beam, lascotfl, lrandomize, &
-               lfusion, lfusion_alpha, leqdsk, lhint, lkick, lgcsim, &
-               lboxsim, limas, lfieldlines, lfusion_tritium, lfusion_proton, lfusion_He3, lbeamdensity
-    INTEGER :: nextcur, npoinc, nbeams, nparticles_start, nprocs_beams, &
-               ndt, ndt_max, duplicate_factor
-    INTEGER, DIMENSION(MAXBEAMS) :: Dex_beams
+    LOGICAL :: lvmec, lpies, lspec, lcoil, lmgrid, &
+               lvessel, lvac, lcontinue_grid, lneut, &
+               lhitonly, lread_input, lplasma_only, lraw, &
+               ldepo, lbeam_simple, lw7x, lsuzuki, &
+               lascot, lascot4, lfidasim, lfidasim_cyl, lsplit, &
+               lvessel_beam, lascotfl, lrandomize, leqdsk, lhint, &
+               lboxsim, limas, lfieldlines, lbeamdensity
+    INTEGER :: nextcur, nprocs_beams, ndt, ndt_max
     INTEGER, ALLOCATABLE :: beam(:)
-    REAL(rprec) :: dt, follow_tol, pi, pi2, invpi2, mu0, to3, dt_save, &
-                   ne_scale, te_scale, ti_scale, zeff_scale, fusion_scale, &
-                   lendt_m, te_col_min, rminor_norm
-    REAL(rprec), DIMENSION(MAXBEAMS) :: Adist_beams, Asize_beams, Div_beams, E_beams, mass_beams, &
-                                        charge_beams, Zatom_beams, P_beams
-    REAL(rprec), DIMENSION(MAXBEAMS, 2) :: r_beams, z_beams, phi_beams
-    REAL(rprec), DIMENSION(MAXPROFLEN) :: TE_AUX_S, TE_AUX_F, NE_AUX_S, NE_AUX_F, TI_AUX_S, TI_AUX_F,&
-                                            POT_AUX_S, POT_AUX_F, ZEFF_AUX_S, ZEFF_AUX_F
-    REAL(rprec), DIMENSION(MAXPROFLEN) :: NI_AUX_S
-    REAL(rprec), DIMENSION(NION,MAXPROFLEN) :: NI_AUX_F
-    INTEGER, DIMENSION(NION) :: NI_AUX_Z
-    REAL(rprec), DIMENSION(NION) :: NI_AUX_M
-    REAL(rprec), DIMENSION(MAXPARTICLES) :: r_start_in, phi_start_in, z_start_in, vll_start_in, &
-                                            & mu_start_in, charge_in, Zatom_in, mass_in, t_end_in, &
-                                            vr_start_in, vphi_start_in, vz_start_in, weight_in
+    REAL(rprec) :: dt, pi, invpi2, mu0, to3, dt_save, rminor_norm
     LOGICAL, ALLOCATABLE :: lgc2fo_start(:)
     REAL(rprec), ALLOCATABLE :: R_start(:), phi_start(:), Z_start(:), vll_start(:), mu_start(:), &
                                 & mass(:), charge(:), Zatom(:), t_end(:), weight(:), vr_start(:), vphi_start(:), vz_start(:)
     REAL(rprec), ALLOCATABLE :: extcur(:)
     CHARACTER(LEN=10) ::  qid_str_saved ! For ASCOT5
-    CHARACTER(256) :: id_string, mgrid_string, coil_string, &
-    vessel_string, int_type, restart_string, continue_grid_string, bbnbi_string, eqdsk_string
+    CHARACTER(256) :: mgrid_string, coil_string, &
+                      vessel_string, restart_string, &
+                      continue_grid_string, bbnbi_string, &
+                      eqdsk_string
 
     REAL(rprec), PARAMETER :: BEAMS3D_VERSION = 4.07 ! this is the full orbit test version
 

BENCHMARKS/BEAMS3D_TEST/input.ORBITS_slow

@@ -52,32 +52,20 @@ RBC(  0,  1) =  1.0000000000e+00  ZBS(  0,  1) =  1.0000000000e+00
   INT_TYPE = 'LSODE'
   FOLLOW_TOL =  1.00000000000000E-08
   VC_ADAPT_TOL =  1.00E-03
-  R_START_IN = 40*10.5
   Z_START_IN = 40*0.0
   PHI_START_IN = 40*0.0
   CHARGE_IN = 40*1.60217733E-19
-  MASS_IN = 40*1.6726231E-27
+  MASS_IN = 40*3.3434954106E-27
   ZATOM_IN = 40*1.0
   T_END_IN = 40*1.0E-3
   NPOINC = 1000
-  NE_AUX_S =     0.0     0.2     0.4     0.6     0.8    1.0
-  NE_AUX_F =  1.2E20  1.0E20  0.8E20  0.6E20  0.4E20 0.2E20
-  TE_AUX_S =     0.0     0.2     0.4     0.6     0.8    1.0
-  TE_AUX_F =  1.0E04  0.8E04  0.6E04  0.4E04  0.2E04 0.0E04
-  TI_AUX_S =     0.0     0.2     0.4     0.6     0.8    1.0
-  TI_AUX_F =  1.0E04  0.8E04  0.6E04  0.4E04  0.2E04 0.0E04
-  VLL_START_IN = 4.3767277259E+04     8.7521428600E+04     1.3124934778E+05     1.7493796783E+05     2.1857428054E+05     2.6214535568E+05
-     3.0563836005E+05     3.4904057609E+05     3.9233942017E+05     4.3552246036E+05     4.7857743375E+05     5.2149226315E+05
-     5.6425507318E+05     6.0685420574E+05     6.4927823469E+05     6.9151597983E+05     7.3355652011E+05     7.7538920600E+05
-     8.1700367103E+05     8.5838984243E+05     8.9953795097E+05     9.4043853987E+05     9.8108247275E+05     1.0214609408E+06
-     1.0615654689E+06     1.1013879211E+06     1.1409205047E+06     1.1801557741E+06     1.2190866335E+06     1.2577063383E+06
-     1.2960084967E+06     1.3339870693E+06     1.3716363692E+06     1.4089510599E+06     1.4459261541E+06     1.4825570104E+06
-                                                1.5188393303E+06     1.5547691543E+06     1.5903428569E+06     1.6255571421E+06
-  MU_START_IN  = 3.2040342566E-15     3.2030734306E-15     3.2014733340E-15     3.1992358826E-15     3.1963637506E-15     3.1928603627E-15
-     3.1887298836E-15     3.1839772059E-15     3.1786079357E-15     3.1726283762E-15     3.1660455093E-15     3.1588669756E-15
-     3.1511010522E-15     3.1427566301E-15     3.1338431883E-15     3.1243707683E-15     3.1143499465E-15     3.1037918055E-15
-     3.0927079046E-15     3.0811102500E-15     3.0690112633E-15     3.0564237505E-15     3.0433608700E-15     3.0298361006E-15
-     3.0158632094E-15     3.0014562196E-15     2.9866293783E-15     2.9713971254E-15     2.9557740614E-15     2.9397749174E-15
-     2.9234145242E-15     2.9067077830E-15     2.8896696366E-15     2.8723150412E-15     2.8546589399E-15     2.8367162358E-15
-                                                2.8185017680E-15     2.8000302866E-15     2.7813164309E-15     2.7623747069E-15
+  NE_AUX_S =     0.0     0.2     0.4     0.6     0.8     1.0
+  NE_AUX_F =  1.2E19  1.2E19  1.2E19  1.2E19  1.2E19  1.2E19
+  TE_AUX_S =     0.0     0.2     0.4     0.6     0.8     1.0
+  TE_AUX_F =  1.0E03  1.0E03  1.0E03  1.0E03  1.0E03  1.0E03
+  TI_AUX_S =     0.0     0.2     0.4     0.6     0.8     1.0
+  TI_AUX_F =  1.0E02  1.0E02  1.0E02  1.0E02  1.0E02  1.0E02
+  R_START_IN  = 1.0200000000E+01      1.0215384615E+01      1.0230769231E+01      1.0246153846E+01      1.0261538462E+01      1.0276923077E+01      1.0292307692E+01      1.0307692308E+01      1.0323076923E+01      1.0338461538E+01      1.0353846154E+01      1.0369230769E+01      1.0384615385E+01      1.0400000000E+01      1.0415384615E+01      1.0430769231E+01      1.0446153846E+01      1.0461538462E+01      1.0476923077E+01      1.0492307692E+01      1.0507692308E+01      1.0523076923E+01      1.0538461538E+01      1.0553846154E+01      1.0569230769E+01      1.0584615385E+01      1.0600000000E+01      1.0615384615E+01      1.0630769231E+01      1.0646153846E+01      1.0661538462E+01      1.0676923077E+01      1.0692307692E+01      1.0707692308E+01      1.0723076923E+01      1.0738461538E+01      1.0753846154E+01      1.0769230769E+01      1.0784615385E+01      1.0800000000E+01
+  VLL_START_IN = 2.9409892275E+05      3.5702255112E+05      4.1040958524E+05      4.5761004502E+05      5.0037773626E+05      5.3976736155E+05      5.7647179483E+05      6.1097516798E+05      6.4363155728E+05      6.7470920194E+05      7.0441708726E+05      7.3292179560E+05      7.6035865492E+05      7.8683937990E+05      8.1245746683E+05      8.3729210020E+05      8.6141104398E+05      8.8487282269E+05      9.0772839439E+05      9.3002245330E+05      9.7541577801E+05      1.1647286686E+06      1.3273092340E+06      1.4720416890E+06      1.6037654646E+06      1.7254624299E+06      1.8391241199E+06      1.9461588989E+06      2.0476062588E+06      2.1442593879E+06      2.2367398717E+06      2.3255455672E+06      2.4110825611E+06      2.4936872394E+06      2.5736419680E+06      2.6511865100E+06      2.7265265160E+06      2.7998399550E+06      2.8712820664E+06      2.9409892275E+06
+  MU_START_IN  = 3.1896056946E-18      4.7081133792E-18      6.2315977198E-18      7.7601060613E-18      9.2936866557E-18      1.0832387855E-17      1.2376258535E-17      1.3925348047E-17      1.5479706129E-17      1.7039381490E-17      1.8604425960E-17      2.0174891379E-17      2.1750824724E-17      2.3332282145E-17      2.4919310716E-17      2.6511966656E-17      2.8110298441E-17      2.9714358526E-17      3.1324201032E-17      3.2939878046E-17      3.6298197246E-17      5.1847620675E-17      6.7452916238E-17      8.3114598332E-17      9.8833182498E-17      1.1460919764E-16      1.3044312906E-16      1.4633550987E-16      1.6228686521E-16      1.7829770574E-16      1.9436854291E-16      2.1049989802E-16      2.2669231404E-16      2.4294627705E-16      2.5926231508E-16      2.7564097855E-16      2.9208279343E-16      3.0858830244E-16      3.2515807667E-16      3.4179263442E-16
 /