Tutorial: NCSX Neutral Beam Deposition Example
This tutorial will walk the user through running the BEAMS3D code for neutral beam deposition run. Before beginning the user should run the VMEC free boundary tutorial tutorial to generate an input and wout file. Additionally, we will make use of coils file from that example.
Edit the input namelist text file.
The following namelist should be added to the VMEC input file. And for
clarity the input and wout file should be renamed input.ncsx_c09r00_free_birth
and wout_ncsx_c09r00_free_birth.nc. Additionally, a wall file with port
openings is requried: NCSX port wall.
&BEAMS3D_INPUT
NR = 128
NZ = 128
NPHI = 120
RMIN = 7.50000000000000E-01
RMAX = 2.40000000000000E+00
ZMIN = -1.00000000000000E+00
ZMAX = 1.00000000000000E+00
PHIMIN = 0.00000000000000E+00
PHIMAX = 2.09439510239320E+00
MU = 0.00000000000000E+00
NPOINC = 3
NPARTICLES_START = 65536
INT_TYPE = 'LSODE'
FOLLOW_TOL = 1.00000000000000E-08
VC_ADAPT_TOL = 1.00E-03
! Plasma Profiles
TE_AUX_S = 0.0000000000E+00 1.0204081633E-02 2.0408163265E-02 3.0612244898E-02 4.0816326531E-02
5.1020408163E-02 6.1224489796E-02 7.1428571429E-02 8.1632653061E-02 9.1836734694E-02
1.0204081633E-01 1.1224489796E-01 1.2244897959E-01 1.3265306122E-01 1.4285714286E-01
1.5306122449E-01 1.6326530612E-01 1.7346938776E-01 1.8367346939E-01 1.9387755102E-01
2.0408163265E-01 2.1428571429E-01 2.2448979592E-01 2.3469387755E-01 2.4489795918E-01
2.5510204082E-01 2.6530612245E-01 2.7551020408E-01 2.8571428571E-01 2.9591836735E-01
3.0612244898E-01 3.1632653061E-01 3.2653061224E-01 3.3673469388E-01 3.4693877551E-01
3.5714285714E-01 3.6734693878E-01 3.7755102041E-01 3.8775510204E-01 3.9795918367E-01
4.0816326531E-01 4.1836734694E-01 4.2857142857E-01 4.3877551020E-01 4.4897959184E-01
4.5918367347E-01 4.6938775510E-01 4.7959183673E-01 4.8979591837E-01 5.0000000000E-01
5.1020408163E-01 5.2040816327E-01 5.3061224490E-01 5.4081632653E-01 5.5102040816E-01
5.6122448980E-01 5.7142857143E-01 5.8163265306E-01 5.9183673469E-01 6.0204081633E-01
6.1224489796E-01 6.2244897959E-01 6.3265306122E-01 6.4285714286E-01 6.5306122449E-01
6.6326530612E-01 6.7346938776E-01 6.8367346939E-01 6.9387755102E-01 7.0408163265E-01
7.1428571429E-01 7.2448979592E-01 7.3469387755E-01 7.4489795918E-01 7.5510204082E-01
7.6530612245E-01 7.7551020408E-01 7.8571428571E-01 7.9591836735E-01 8.0612244898E-01
8.1632653061E-01 8.2653061224E-01 8.3673469388E-01 8.4693877551E-01 8.5714285714E-01
8.6734693878E-01 8.7755102041E-01 8.8775510204E-01 8.9795918367E-01 9.0816326531E-01
9.1836734694E-01 9.2857142857E-01 9.3877551020E-01 9.4897959184E-01 9.5918367347E-01
9.6938775510E-01 9.7959183673E-01 9.8979591837E-01 1.0000000000E+00
TE_AUX_F = 2.9000000000E+03 2.8996980425E+03 2.8987921699E+03 2.8972823823E+03 2.8951686797E+03
2.8924510621E+03 2.8891295294E+03 2.8852040816E+03 2.8806747189E+03 2.8755414411E+03
2.8698042482E+03 2.8634631404E+03 2.8565181175E+03 2.8489691795E+03 2.8408163265E+03
2.8320595585E+03 2.8226988755E+03 2.8127342774E+03 2.8021657643E+03 2.7909933361E+03
2.7792169929E+03 2.7668367347E+03 2.7538525614E+03 2.7402644731E+03 2.7260724698E+03
2.7112765514E+03 2.6958767180E+03 2.6798729696E+03 2.6632653061E+03 2.6460537276E+03
2.6282382341E+03 2.6098188255E+03 2.5907955019E+03 2.5711682632E+03 2.5509371095E+03
2.5301020408E+03 2.5086630571E+03 2.4866201583E+03 2.4639733444E+03 2.4407226156E+03
2.4168679717E+03 2.3924094127E+03 2.3673469388E+03 2.3416805498E+03 2.3154102457E+03
2.2885360267E+03 2.2610578925E+03 2.2329758434E+03 2.2042898792E+03 2.1750000000E+03
2.1451062057E+03 2.1146084965E+03 2.0835068721E+03 2.0518013328E+03 2.0194918784E+03
1.9865785090E+03 1.9530612245E+03 1.9189400250E+03 1.8842149105E+03 1.8488858809E+03
1.8129529363E+03 1.7764160766E+03 1.7392753020E+03 1.7015306122E+03 1.6631820075E+03
1.6242294877E+03 1.5846730529E+03 1.5445127030E+03 1.5037484382E+03 1.4623802582E+03
1.4204081633E+03 1.3778321533E+03 1.3346522282E+03 1.2908683882E+03 1.2464806331E+03
1.2014889629E+03 1.1558933778E+03 1.1096938776E+03 1.0628904623E+03 1.0154831320E+03
9.6747188671E+02 9.1885672636E+02 8.6963765098E+02 8.1981466056E+02 7.6938775510E+02
7.1835693461E+02 6.6672219908E+02 6.1448354852E+02 5.6164098292E+02 5.0819450229E+02
4.5414410662E+02 3.9948979592E+02 3.4423157018E+02 2.8836942940E+02 2.3190337359E+02
1.7483340275E+02 1.1715951687E+02 5.8881715952E+01 0.0000000000E+00
TI_AUX_S = 0.0000000000E+00 1.0204081633E-02 2.0408163265E-02 3.0612244898E-02 4.0816326531E-02
5.1020408163E-02 6.1224489796E-02 7.1428571429E-02 8.1632653061E-02 9.1836734694E-02
1.0204081633E-01 1.1224489796E-01 1.2244897959E-01 1.3265306122E-01 1.4285714286E-01
1.5306122449E-01 1.6326530612E-01 1.7346938776E-01 1.8367346939E-01 1.9387755102E-01
2.0408163265E-01 2.1428571429E-01 2.2448979592E-01 2.3469387755E-01 2.4489795918E-01
2.5510204082E-01 2.6530612245E-01 2.7551020408E-01 2.8571428571E-01 2.9591836735E-01
3.0612244898E-01 3.1632653061E-01 3.2653061224E-01 3.3673469388E-01 3.4693877551E-01
3.5714285714E-01 3.6734693878E-01 3.7755102041E-01 3.8775510204E-01 3.9795918367E-01
4.0816326531E-01 4.1836734694E-01 4.2857142857E-01 4.3877551020E-01 4.4897959184E-01
4.5918367347E-01 4.6938775510E-01 4.7959183673E-01 4.8979591837E-01 5.0000000000E-01
5.1020408163E-01 5.2040816327E-01 5.3061224490E-01 5.4081632653E-01 5.5102040816E-01
5.6122448980E-01 5.7142857143E-01 5.8163265306E-01 5.9183673469E-01 6.0204081633E-01
6.1224489796E-01 6.2244897959E-01 6.3265306122E-01 6.4285714286E-01 6.5306122449E-01
6.6326530612E-01 6.7346938776E-01 6.8367346939E-01 6.9387755102E-01 7.0408163265E-01
7.1428571429E-01 7.2448979592E-01 7.3469387755E-01 7.4489795918E-01 7.5510204082E-01
7.6530612245E-01 7.7551020408E-01 7.8571428571E-01 7.9591836735E-01 8.0612244898E-01
8.1632653061E-01 8.2653061224E-01 8.3673469388E-01 8.4693877551E-01 8.5714285714E-01
8.6734693878E-01 8.7755102041E-01 8.8775510204E-01 8.9795918367E-01 9.0816326531E-01
9.1836734694E-01 9.2857142857E-01 9.3877551020E-01 9.4897959184E-01 9.5918367347E-01
9.6938775510E-01 9.7959183673E-01 9.8979591837E-01 1.0000000000E+00
TI_AUX_F = 2.0000000000E+03 1.9997917534E+03 1.9991670137E+03 1.9981257809E+03 1.9966680550E+03
1.9947938359E+03 1.9925031237E+03 1.9897959184E+03 1.9866722199E+03 1.9831320283E+03
1.9791753436E+03 1.9748021658E+03 1.9700124948E+03 1.9648063307E+03 1.9591836735E+03
1.9531445231E+03 1.9466888796E+03 1.9398167430E+03 1.9325281133E+03 1.9248229904E+03
1.9167013744E+03 1.9081632653E+03 1.8992086631E+03 1.8898375677E+03 1.8800499792E+03
1.8698458975E+03 1.8592253228E+03 1.8481882549E+03 1.8367346939E+03 1.8248646397E+03
1.8125780925E+03 1.7998750521E+03 1.7867555185E+03 1.7732194919E+03 1.7592669721E+03
1.7448979592E+03 1.7301124531E+03 1.7149104540E+03 1.6992919617E+03 1.6832569763E+03
1.6668054977E+03 1.6499375260E+03 1.6326530612E+03 1.6149521033E+03 1.5968346522E+03
1.5783007080E+03 1.5593502707E+03 1.5399833403E+03 1.5201999167E+03 1.5000000000E+03
1.4793835902E+03 1.4583506872E+03 1.4369012911E+03 1.4150354019E+03 1.3927530196E+03
1.3700541441E+03 1.3469387755E+03 1.3234069138E+03 1.2994585589E+03 1.2750937110E+03
1.2503123698E+03 1.2251145356E+03 1.1995002082E+03 1.1734693878E+03 1.1470220741E+03
1.1201582674E+03 1.0928779675E+03 1.0651811745E+03 1.0370678884E+03 1.0085381091E+03
9.7959183673E+02 9.5022907122E+02 9.2044981258E+02 8.9025406081E+02 8.5964181591E+02
8.2861307788E+02 7.9716784673E+02 7.6530612245E+02 7.3302790504E+02 7.0033319450E+02
6.6722199084E+02 6.3369429404E+02 5.9975010412E+02 5.6538942107E+02 5.3061224490E+02
4.9541857559E+02 4.5980841316E+02 4.2378175760E+02 3.8733860891E+02 3.5047896710E+02
3.1320283215E+02 2.7551020408E+02 2.3740108288E+02 1.9887546855E+02 1.5993336110E+02
1.2057476052E+02 8.0799666805E+01 4.0608079967E+01 0.0000000000E+00
NE_AUX_S = 0.0000000000E+00 1.0204081633E-02 2.0408163265E-02 3.0612244898E-02 4.0816326531E-02
5.1020408163E-02 6.1224489796E-02 7.1428571429E-02 8.1632653061E-02 9.1836734694E-02
1.0204081633E-01 1.1224489796E-01 1.2244897959E-01 1.3265306122E-01 1.4285714286E-01
1.5306122449E-01 1.6326530612E-01 1.7346938776E-01 1.8367346939E-01 1.9387755102E-01
2.0408163265E-01 2.1428571429E-01 2.2448979592E-01 2.3469387755E-01 2.4489795918E-01
2.5510204082E-01 2.6530612245E-01 2.7551020408E-01 2.8571428571E-01 2.9591836735E-01
3.0612244898E-01 3.1632653061E-01 3.2653061224E-01 3.3673469388E-01 3.4693877551E-01
3.5714285714E-01 3.6734693878E-01 3.7755102041E-01 3.8775510204E-01 3.9795918367E-01
4.0816326531E-01 4.1836734694E-01 4.2857142857E-01 4.3877551020E-01 4.4897959184E-01
4.5918367347E-01 4.6938775510E-01 4.7959183673E-01 4.8979591837E-01 5.0000000000E-01
5.1020408163E-01 5.2040816327E-01 5.3061224490E-01 5.4081632653E-01 5.5102040816E-01
5.6122448980E-01 5.7142857143E-01 5.8163265306E-01 5.9183673469E-01 6.0204081633E-01
6.1224489796E-01 6.2244897959E-01 6.3265306122E-01 6.4285714286E-01 6.5306122449E-01
6.6326530612E-01 6.7346938776E-01 6.8367346939E-01 6.9387755102E-01 7.0408163265E-01
7.1428571429E-01 7.2448979592E-01 7.3469387755E-01 7.4489795918E-01 7.5510204082E-01
7.6530612245E-01 7.7551020408E-01 7.8571428571E-01 7.9591836735E-01 8.0612244898E-01
8.1632653061E-01 8.2653061224E-01 8.3673469388E-01 8.4693877551E-01 8.5714285714E-01
8.6734693878E-01 8.7755102041E-01 8.8775510204E-01 8.9795918367E-01 9.0816326531E-01
9.1836734694E-01 9.2857142857E-01 9.3877551020E-01 9.4897959184E-01 9.5918367347E-01
9.6938775510E-01 9.7959183673E-01 9.8979591837E-01 1.0000000000E+00
NE_AUX_F = 8.0000000000E+19 7.9991670137E+19 7.9966680550E+19 7.9925031237E+19 7.9866722199E+19
7.9791753436E+19 7.9700124948E+19 7.9591836735E+19 7.9466888796E+19 7.9325281133E+19
7.9167013744E+19 7.8992086631E+19 7.8800499792E+19 7.8592253228E+19 7.8367346939E+19
7.8125780925E+19 7.7867555185E+19 7.7592669721E+19 7.7301124531E+19 7.6992919617E+19
7.6668054977E+19 7.6326530612E+19 7.5968346522E+19 7.5593502707E+19 7.5201999167E+19
7.4793835902E+19 7.4369012911E+19 7.3927530196E+19 7.3469387755E+19 7.2994585589E+19
7.2503123698E+19 7.1995002082E+19 7.1470220741E+19 7.0928779675E+19 7.0370678884E+19
6.9795918367E+19 6.9204498126E+19 6.8596418159E+19 6.7971678467E+19 6.7330279050E+19
6.6672219908E+19 6.5997501041E+19 6.5306122449E+19 6.4598084132E+19 6.3873386089E+19
6.3132028322E+19 6.2374010829E+19 6.1599333611E+19 6.0807996668E+19 6.0000000000E+19
5.9175343607E+19 5.8334027489E+19 5.7476051645E+19 5.6601416077E+19 5.5710120783E+19
5.4802165764E+19 5.3877551020E+19 5.2936276551E+19 5.1978342357E+19 5.1003748438E+19
5.0012494794E+19 4.9004581424E+19 4.7980008330E+19 4.6938775510E+19 4.5880882965E+19
4.4806330696E+19 4.3715118701E+19 4.2607246980E+19 4.1482715535E+19 4.0341524365E+19
3.9183673469E+19 3.8009162849E+19 3.6817992503E+19 3.5610162432E+19 3.4385672636E+19
3.3144523115E+19 3.1886713869E+19 3.0612244898E+19 2.9321116202E+19 2.8013327780E+19
2.6688879633E+19 2.5347771762E+19 2.3990004165E+19 2.2615576843E+19 2.1224489796E+19
1.9816743024E+19 1.8392336526E+19 1.6951270304E+19 1.5493544357E+19 1.4019158684E+19
1.2528113286E+19 1.1020408163E+19 9.4960433153E+18 7.9550187422E+18 6.3973344440E+18
4.8229904207E+18 3.2319866722E+18 1.6243231987E+18 0.0000000000E+00
ADIST_BEAMS( 1) = 2.00000000000000E+00
ADIST_BEAMS( 2) = 2.00000000000000E+00
ASIZE_BEAMS( 1) = 1.50000000000000E-01
ASIZE_BEAMS( 2) = 1.50000000000000E-01
DIV_BEAMS( 1) = 1.00000000000000E-01
DIV_BEAMS( 2) = 1.00000000000000E-01
E_BEAMS( 1) = 6.40800000000000E-15 ! In [J] multiply by electron charge to get [eV]
E_BEAMS( 2) = 6.40800000000000E-15
MASS_BEAMS( 1) = 1.67300000000000E-27
MASS_BEAMS( 2) = 1.67300000000000E-27
CHARGE_BEAMS( 1) = 1.60200000000000E-19
CHARGE_BEAMS( 2) = 1.60200000000000E-19
R_BEAMS(1,1) = 2.00000000000000E+00
R_BEAMS(1,2) = 1.40000000000000E+00
R_BEAMS(2,1) = 2.00000000000000E+00
R_BEAMS(2,2) = 1.40000000000000E+00
PHI_BEAMS(1,1) = 0.00000000000000E+00
PHI_BEAMS(1,2) = 1.04719755120000E+00
PHI_BEAMS(2,1) = 0.00000000000000E+00
PHI_BEAMS(2,2) = -1.04719755120000E+00
Z_BEAMS(1,1) = 0.00000000000000E+00
Z_BEAMS(1,2) = 0.00000000000000E+00
Z_BEAMS(2,1) = 0.00000000000000E+00
Z_BEAMS(2,2) = 0.00000000000000E+00
P_BEAMS(1) = 1.0E+06
P_BEAMS(2) = 1.0E+06
T_END_IN(1:2) = 2*100.0E-3
/
&END
Execute the code.
To execute the code, we first
invoke the MPI execution command with the number of processors we
wish to use. The BEAMS3D executable is passed next with the VMEC run
extension next. The coils option is passed next with the coil name
(this will be used for calculation of the vacuum field). The full
path may be specified here. This will be a deposition only run
so we supply the -depo flag to indicate this. We also supply
a vessel via the vessel flag.
>mpirun -np 32 ~/bin/xbeams3d -vmec ncsx_c09r00_free_birth -coil /u/sul/pub/coils/coils.c09r00 -vessel /u/sul/Sims/NCSX/NCSX_wall_nbiport_acc.dat -depo
BEAMS3D Version 4.07
----- HDF5 (Parallel) Parameters -----
HDF5_version: 1.12 release: 02
----- MPI Parameters -----
MPI_version: 3.01
Intel(R) MPI Library 2021.9 for Linux* OS
Nproc_total: 640
Nproc_shared: 40
----- GIT Repository -----
Repository: git@github.com:PrincetonUniversity/STELLOPT.git
Branch: develop
Version: v3.00-110-g6f274
Built-on: 30.01.2024 13:28:38
Hash: 512375ce3582efa57910c336c83409577d760d6b
----- Input Parameters -----
FILE: input.ncsx_c09r00_free_birth
R = [ 0.75000, 2.40000]; NR: 128
PHI = [ 0.00000, 2.09440]; NPHI: 120
Z = [-1.00000, 1.00000]; NZ: 128
# of Particles to Start: 65920
# of Beams: 2
VESSEL: /u/sul/Sims/NCSX/NCSX_wall_nbiport_acc.dat
COIL: /u/sul/pub/coils/coils.c09r00
COLLISION OPERATOR ON!
DEPOSITION ONLY!
----- Plasma Parameters -----
Te = [ 0.00000, 2.90000] keV; NTE: 99; S_MAX_TE: 1.00000
Ti = [ 0.00000, 2.00000] keV; NTI: 99; S_MAX_TI: 1.00000
Ne = [ 0.00000, 0.80000] E20 m^-3; NNE: 99; S_MAX_NE: 1.00000
Ni(1)= [ 0.00000, 0.80000] E20 m^-3; M: 1 amu; Z: 1; S_MAX_NI: 1.00000
Zeff = [ 1.00000, 1.00000]; NZEFF: 6; S_MAX_ZEFF: 1.00000
PLASMA_MASS = 1.00728 amu
PLASMA_ZMEAN = 1.00000 [Z]
----- COILS Information -----
FILE: /u/sul/pub/coils/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 [100]%
----- VMEC Information -----
FILE: ncsx_c09r00_free_birth
R = [ 1.02249, 1.77878]
Z = [-0.64066, 0.64066]
BETA = 0.04; I = -0.18 [MA]
AMINOR = 0.32 [m]
PHIEDGE = 0.50 [Wb]
VOLUME = 2.96 [m^3]
NYQUIST DETECTED IN WOUT FILE!
----- Virtual Casing Information -----
INTEGRAL TYPE: Surface Current (DCUHRE)
MIN_GRID_DISTANCE = 6.0439E-02
NORMAL_AREA = 2.4584E+01
NR = 1; NU = 128; NV = 128; NFP = 3
NUVP = 49152
ABS_TOL = 0.0000E+00; REL_TOL = 1.0000E-03
MIN_CLS = 0 (16777216)
Plasma Field Calculation [100]%
----- Loading wall data -----
----- Constructing Splines -----
R = [ 0.75000, 2.40000]; NR: 128
PHI = [ 0.00000, 2.09440]; NPHI: 120
Z = [-1.00000, 1.00000]; NZ: 128
HERMITE FORM: 1
----- INITIALIZING BEAMS -----
nbeams: 2
nparticles_start: 65920
E_BEAM( 1): 40 [keV] P_BEAM( 1): 1.000 [MW]
E_BEAM( 2): 40 [keV] P_BEAM( 2): 1.000 [MW]
----- Vessel Information -----
Wall Name : NCSX NBI WALL
Date : : 09-04-11
Faces : 35874
Blocks : 720
Mean faces per block: 839.00
Highest faces per block: 2932
R_WALL = [ 0.92003, 2.35994]
Z_WALL = [ -0.89111, 0.89111]
----- FOLLOWING NEUTRAL TRAJECTORIES -----
----- BEAM Density Calc. -----
----- BEAM DIAGNOSTICS -----
BEAMLINE E [keV] Q [e] M [Mp] Markers [#] NDIST [#] Orbit [%] Lost [%] Shine. [%] Port [%] T_MIN [s] T_MAX [s]
1 40 1 1 65920 2.1E+12 76.6 0.0 23.4 0.0 279.9E-09 100.0E-03
2 40 1 1 65920 2.1E+12 76.6 0.0 23.4 0.0 276.7E-09 100.0E-03
----- BEAMS3D DONE -----
>
Examine the output. The BEAMS3D code only generates one HDF5 file as output. This file contains all information about the backgroud grids, particles, particle orbits and In this example two files will be created: beams3d_ncsx_c09r00.h5. The first is an HDF5 file containing the saved particle trajectory information for the run with the magnetic field grid information. Here is a sample plot:
