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Progress on cgyro_json
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@jcandy
jcandy committed Oct 18, 2024
1 parent 6fb8034 commit 00628bd
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48 changes: 34 additions & 14 deletions cgyro/bin/cgyro_json
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Original file line number Diff line number Diff line change
Expand Up @@ -28,27 +28,37 @@ for i in range(sim.n_species):

d = {}

with open('/home/candy/GIT/gacode/cgyro/bin/input.json','r') as file:
default = json.load(file)

# Determine non-default values in input.cgyro
with open('input.cgyro.gen','r') as file:
for line in file:
u = line.split()
key = u[1]
value = u[0]
if key in default.keys():
if str(value) != str(default[key]):
d[key] = value

# Code-specific parameters
d['N_ENERGY'] = sim.n_energy
d['N_XI'] = sim.n_xi
d['N_THETA'] = sim.n_theta
d['N_RADIAL'] = sim.n_theta
d['N_RADIAL'] = sim.n_radial
d['N_TOROIDAL'] = sim.n_n
d['N_FIELD'] = sim.n_field

# Physics parameters
d['RMIN'] = sim.rmin
d['RMAJ'] = sim.rmaj
d['Q'] = sim.q
d['SHEAR'] = sim.shear
d['S'] = sim.shear
d['MACH'] = sim.mach
d['GAMMA_E'] = sim.gamma_e
d['GAMMA_P'] = sim.gamma_p
d['BETAE_UNIT'] = sim.betae_unit

d['Z'] = sim.z[:].tolist()
d['MASS'] = sim.mass[:].tolist()
d['DENS'] = sim.dens[:].tolist()
d['TEMP'] = sim.temp[:].tolist()
d['DLNNDR'] = sim.dlnndr[:].tolist()
d['DLNTDR'] = sim.dlntdr[:].tolist()

d['ZMAG'] = sim.zmag
d['DZMAG'] = sim.dzmag
d['SHIFT'] = sim.shift
Expand All @@ -60,9 +70,15 @@ d['ZETA'] = sim.zeta
d['S_ZETA'] = sim.s_zeta

d['SHAPE_SIN'] = sim.shape_sin[:].tolist()

d['SHAPE_COS'] = sim.shape_cos[:].tolist()

d['Z'] = sim.z[:].tolist()
d['MASS'] = sim.mass[:].tolist()
d['DENS'] = sim.dens[:].tolist()
d['TEMP'] = sim.temp[:].tolist()
d['DLNNDR'] = sim.dlnndr[:].tolist()
d['DLNTDR'] = sim.dlntdr[:].tolist()

# JSON output
with open('json.cgyro.localdump','w') as f:
json.dump(d,f,indent=2,sort_keys=True)
Expand Down Expand Up @@ -129,6 +145,10 @@ d['velocity_tor_gradient_norm'] = lref/vthref*sim.gamma_p
d['collisionality_norm'] = (lref/vthref)*sim.nu[ielec]
# electron beta
d['beta_reference'] = sim.betae_unit/bref**2
# pressure gradient
d['pressure_gradient_norm'] = -lref*sim.beta_star/bref**2
# Debye length (normalized to lref)
d['debye_length_reference'] = sim.lambda_star*sim.rho_star_norm/lref
#-----------------------------------------------------------------------

#-----------------------------------------------------------------------
Expand All @@ -143,14 +163,14 @@ d['delongation_dr_minor_norm'] = sim.s_kappa*sim.kappa*lref/sim.rmin
# Shape coefficients (cn,sn)
d['shapecoefficients_c'] = sim.shape_cos[:nmax].tolist()
d['shapecoefficients_s'] = sim.shape_sin[:nmax].tolist()
d['shapecoefficients_s'][1] = np.arcsin(sim.delta)
d['shapecoefficients_s'][2] = -sim.zeta
#d['shapecoefficients_s'][1] = np.arcsin(sim.delta)
#d['shapecoefficients_s'][2] = -sim.zeta

# Derivatives of (cn,sn)
d['dc_dr_minor_norm'] = (sim.shape_s_cos[:nmax]*lref/sim.rmin).tolist()
d['ds_dr_minor_norm'] = (sim.shape_s_sin[:nmax]*lref/sim.rmin).tolist()
d['ds_dr_minor_norm'][1] = sim.s_delta*lref/sim.rmin/np.cos(np.arcsin(sim.delta))
d['ds_dr_minor_norm'][2] = -sim.s_zeta*lref/sim.rmin
#d['ds_dr_minor_norm'][1] = sim.s_delta*lref/sim.rmin/np.cos(np.arcsin(sim.delta))
#d['ds_dr_minor_norm'][2] = -sim.s_zeta*lref/sim.rmin
#-----------------------------------------------------------------------

with open('json.cgyro.imas','w') as f:
Expand Down
1 change: 1 addition & 0 deletions cgyro/bin/input.json
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@@ -0,0 +1 @@
{"N_ENERGY":8,"N_XI":16,"N_THETA":24,"N_RADIAL":4,"N_TOROIDAL":1,"N_FIELD":1,"E_MAX":8.0,"ALPHA_POLY":0.0,"E_FIX":2,"DELTA_T_METHOD":0,"DELTA_T":0.01,"ERROR_TOL":6e-5,"MAX_TIME":100.0,"PRINT_STEP":100,"RESTART_STEP":10,"RESTART_PRESERVATION_MODE":3,"MPIIO_STRIPE_FACTOR":0,"MPIIO_SMALL_STRIPE_FACTOR":0,"FREQ_TOL":0.001,"UP_RADIAL":1.0,"UP_THETA":1.0,"UP_ALPHA":0.0,"NUP_RADIAL":3,"NUP_THETA":3,"NUP_ALPHA":3,"N_WAVE":2,"CONSTANT_STREAM_FLAG":1,"EXPLICIT_TRAP_FLAG":0,"KY":0.3,"BOX_SIZE":1,"IPCCW":-1.0,"BTCCW":-1.0,"SILENT_FLAG":0,"PROFILE_MODEL":1,"EQUILIBRIUM_MODEL":2,"COLLISION_MODEL":4,"COLLISION_MOM_RESTORE":1,"COLLISION_ENE_RESTORE":1,"COLLISION_ENE_DIFFUSION":1,"COLLISION_KPERP":1,"COLLISION_FIELD_MODEL":1,"COLLISION_ION_MODEL":0,"COLLISION_PRECISION_MODE":0,"COLLISION_TEST_MODE":0,"COLLISION_FIELD_MAX_L":-2,"COLLISION_TEST_MAX_L":-2,"Z_EFF":1.0,"Z_EFF_METHOD":2,"ZF_TEST_MODE":0,"NONLINEAR_FLAG":0,"AE_FLAG":0,"TEMP_AE":1.0,"DENS_AE":1.0,"MASS_AE":0.0002724486,"DLNTDR_AE":1.0,"DLNNDR_AE":1.0,"LAMBDA_STAR":0.0,"H_PRINT_FLAG":0,"MOMENT_PRINT_FLAG":0,"GFLUX_PRINT_FLAG":0,"FIELD_PRINT_FLAG":0,"AMP0":0.0,"AMP":0.1,"GAMMA_E":0.0,"GAMMA_P":0.0,"MACH":0.0,"ROTATION_MODEL":1,"TOROIDALS_PER_PROC":1,"MPI_RANK_ORDER":2,"VELOCITY_ORDER":1,"HIPREC_FLAG":0,"UDSYMMETRY_FLAG":0,"SHEAR_METHOD":2,"GLOBAL_FLAG":0,"N_GLOBAL":4,"NU_GLOBAL":15.0,"THETA_PLOT":1,"GPU_BIGMEM_FLAG":1,"UPWIND_SINGLE_FLAG":0,"PX0":0.0,"STREAM_TERM":0,"STREAM_FACTOR":1.0,"EXCH_FLAG":0,"RES_WEIGHT_POWER":1.0,"RMIN":0.5,"RMAJ":3.0,"Q":2.0,"S":1.0,"SHIFT":0.0,"KAPPA":1.0,"S_KAPPA":0.0,"DELTA":0.0,"S_DELTA":0.0,"ZETA":0.0,"S_ZETA":0.0,"ZMAG":0.0,"DZMAG":0.0,"SHAPE_SIN3":0.0,"SHAPE_S_SIN3":0.0,"SHAPE_SIN4":0.0,"SHAPE_S_SIN4":0.0,"SHAPE_SIN5":0.0,"SHAPE_S_SIN5":0.0,"SHAPE_SIN6":0.0,"SHAPE_S_SIN6":0.0,"SHAPE_COS0":0.0,"SHAPE_S_COS0":0.0,"SHAPE_COS1":0.0,"SHAPE_S_COS1":0.0,"SHAPE_COS2":0.0,"SHAPE_S_COS2":0.0,"SHAPE_COS3":0.0,"SHAPE_S_COS3":0.0,"SHAPE_COS4":0.0,"SHAPE_S_COS4":0.0,"SHAPE_COS5":0.0,"SHAPE_S_COS5":0.0,"SHAPE_COS6":0.0,"SHAPE_S_COS6":0.0,"BETAE_UNIT":0.0,"N_SPECIES":1,"NU_EE":0.1,"Z":[1,1,1,1,1,1,1,1,1,1,1],"MASS":[1,1,1,1,1,1,1,1,1,1,1],"DENS":[0,0,0,0,0,0,0,0,0,0,0],"TEMP":[1,1,1,1,1,1,1,1,1,1,1],"DLNNDR":[1,1,1,1,1,1,1,1,1,1,1],"DLNTDR":[1,1,1,1,1,1,1,1,1,1,1],"SDLNNDR":[0,0,0,0,0,0,0,0,0,0,0],"SDLNTDR":[0,0,0,0,0,0,0,0,0,0,0],"SBETA":[0,0,0,0,0,0,0,0,0,0,0],"DLNNDR_SCALE":[1,1,1,1,1,1,1,1,1,1,1],"DLNTDR_SCALE":[1,1,1,1,1,1,1,1,1,1,1],"QUASINEUTRAL_FLAG":1,"LAMBDA_STAR_SCALE":0.0,"GAMMA_E_SCALE":1.0,"GAMMA_P_SCALE":1.0,"MACH_SCALE":1.0,"BETA_STAR_SCALE":1.0,"BETAE_UNIT_SCALE":1.0,"NU_EE_SCALE":1.0,"ZF_SCALE":1.0}
16 changes: 8 additions & 8 deletions cgyro/src/cgyro_make_profiles.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -188,7 +188,7 @@ subroutine cgyro_make_profiles
! Debye length (from NRL plasma formulary):
! Use input lambda_debye as scaling parameter

lambda_star = 7.43 * sqrt((1e3*temp_norm)/(1e13*dens_norm))/rhos
lambda_star = 7.434*sqrt((1e3*temp_norm)/(1e13*dens_norm))/rhos

! Normalize
do is=1,n_species
Expand All @@ -212,14 +212,14 @@ subroutine cgyro_make_profiles

! Re-scaling
lambda_star = lambda_star * lambda_star_scale
gamma_e = gamma_e * gamma_e_scale
gamma_p = gamma_p * gamma_p_scale
mach = mach * mach_scale
betae_unit = betae_unit * betae_unit_scale
gamma_e = gamma_e * gamma_e_scale
gamma_p = gamma_p * gamma_p_scale
mach = mach * mach_scale
betae_unit = betae_unit * betae_unit_scale
do is=1,n_species
dlnndr(is) = dlnndr(is) * dlnndr_scale(is)
dlntdr(is) = dlntdr(is) * dlntdr_scale(is)
nu(is) = nu(is) * nu_ee_scale
dlnndr(is) = dlnndr(is) * dlnndr_scale(is)
dlntdr(is) = dlntdr(is) * dlntdr_scale(is)
nu(is) = nu(is) * nu_ee_scale
enddo

! Set beta_* consistent with re-scaled beta and gradients and then re-scale
Expand Down

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