Hi, I have a question. What I would like to do with galprop is that I want to propagate HE electrons within small 3D space placing SNR sources. I have downloaded v50p, and I am able to run galdef_50p_999726 without any problem. Then, I have changed a few options (especially n_spatial_dimentions = 3 and be careful with not blowing up memory.) in galdef file. I have played around with different parameters and gives me always the following message with segmentation fault in the end.


<<<<create_gcr>>>>propagate_particles
Particle = primary_electrons
Distribution.init:generated 3D array of spectra 56 76 81 54
Particle create_transport_arrays primary_electrons
Distribution.init:generated 3D array of spectra 56 76 81 54
Distribution.init:generated 3D array of spectra 56 76 81 54
Distribution.init:generated 3D array of spectra 56 76 81 54
Distribution.init:generated 3D array of spectra 56 76 81 54
Distribution.init:generated 3D array of spectra 56 76 81 54
Distribution.init:generated 3D array of spectra 56 76 81 54
Distribution.init:generated 3D array of spectra 56 76 81 54
Distribution.init:generated 3D array of spectra 56 76 81 54
Distribution.init:generated 3D array of spectra 56 76 81 54
Network iteration 1

Particle = Helium_4
>>>> create_transport_arrays Helium_4
assigning primary source function
Helium_4 g_0=0 rigid_br0= 0 g_1=2.3 rigid_br= 40000 g_2=2.15
>>>>>>>>>>>>>>>>>>> norm 1 >>>>>>>>>>>>>>>>>>>
assigning diffusion coefficient
beta at break rigidity=0.847871 rigidity_br=3000?= galdef.D_rigid_br=3000
Segmentation fault


my typecial galdef files is:

1234567890123456789012
======================value
Title = Plain diffusion model/2D 4 kpc tuned to agree with ACE
Title = source isotopic distr. of an element = solar isot. abund. distr.
n_spatial_dimensions = 3
r_min =00.0 min r
r_max =20.00 max r
dr = 1.0 delta r
z_min =-4.0 min z
z_max =+4.0 max z
dz = 0.1 delta z

x_min =- 4.0 min x
x_max =+ 4.0 max x
dx = 0.2 delta x
y_min =- 4.0 min y
y_max =+ 4.0 max y
dy = 0.2 delta y

p_min =1000 min momentum (MV)
p_max =4000 max momentum
p_factor =1.50 momentum factor

Ekin_min =1.0e1 min kinetic energy per nucleon (MeV)
Ekin_max =1.0e7 max kinetic energy per nucleon
Ekin_factor =1.3 kinetic energy per nucleon factor

p_Ekin_grid = Ekin p||Ekin alignment

E_gamma_min = 1.e0 min gamma-ray energy (MeV)
E_gamma_max = 1.e8 max gamma-ray energy (MeV)
E_gamma_factor = 1.4 gamma-ray energy factor
integration_mode = 1 integr.over part.spec.: =1-old E*logE; 0=1-PL analyt.

nu_synch_min = 1.0e6 min synchrotron frequency (Hz)
nu_synch_max = 1.0e10 max synchrotron frequency (Hz)
nu_synch_factor = 2.0 synchrotron frequency factor

long_min = 0.50 gamma-ray intensity skymap longitude minimum (deg)
long_max =359.50 gamma-ray intensity skymap longitude maximum (deg)
lat_min =-89.50 gamma-ray intensity skymap latitude minimum (deg)
lat_max =+89.50 gamma-ray intensity skymap latitude maximum (deg)
d_long = 1.00 gamma-ray intensity skymap longitude binsize (deg)
d_lat = 1.00 gamma-ray intensity skymap latitude binsize (deg)

D0_xx =2.2e28 diffusion coefficient at reference rigidity
D_rigid_br =3.0e3 reference rigidity for diffusion coefficient in MV
D_g_1 = 0. diffusion coefficient index below reference rigidity
D_g_2 = 0.60 diffusion coefficient index above reference rigidity
diff_reacc =-2 1,2=incl.diff.reacc.; 11=Kolmogorov+damping; 12=Kraichnan+dampi
ng; -2 - plain diffusion
v_Alfven = 0. Alfven speed in km s-1

damping_p0 = 1.e6 MV -some rigidity (where CR density is low)
damping_const_G = 0.02 a const derived from fitting B/C
damping_max_path_L = 3.e21 Lmax~1 kpc, max free path

convection =0 1=include convection
v0_conv =0. km s-1 v_conv=v0_conv+dvdz_conv*dz
dvdz_conv =3. km s-1 kpc-1 v_conv=v0_conv+dvdz_conv*dz

nuc_rigid_br =4.e4 reference rigidity for nucleus injection index in MV
nuc_g_1 =2.30 nucleus injection index below reference rigidity
nuc_g_2 =2.15 nucleus injection index index above reference rigidity

inj_spectrum_type = rigidity rigidity||beta_rig||Etot nucleon injection spectrum type

electron_g_0 =2.40 electron injection index below electron_rigid_br0
electron_rigid_br0 =4.0e2 reference rigidity0 for electron injection inde
electron_g_1 =2.40 electron injection index below reference rigidity
electron_rigid_br =1.0e3 reference rigidity for electron injection index in MV
electron_g_2 =2.40 electron injection index index above reference rigidity

He_H_ratio =0.11 He/H of ISM, by number
X_CO =1.9E20,1.9E20,1.9E20,1.9E20,1.9E20,1.9E20,1.9E20,1.9E20,1.9E20 conversio
n factor from CO integrated temperature to H2 column density
X_CO_variable =0.4E20,0.4E20,0.6E20,0.8E20,1.5E20,10.0E20,10.0E20,10.0E20,10.0E20 -put
here to remember (X_CO_variable-doesn't exist)
fragmentation =1 1=include fragmentation
momentum_losses =1 1=include momentum losses
radioactive_decay =1 1=include radioactive decay
K_capture =1 1=include K-capture

start_timestep =1.0e7
end_timestep =1.0e2
timestep_factor =0.25
timestep_repeat =20 number of repeats per timestep in timetep_mode=1
timestep_repeat2 =0 number of timesteps in timetep_mode=2
timestep_print =10000 number of timesteps between printings
timestep_diagnostics =10000 number of timesteps between diagnostics
control_diagnostics =0 control detail of diagnostics

network_iterations = 2 number of iterations of entire network

prop_r = 1 1=propagate in r (2D)
prop_x = 1 1=propagate in x (2D,3D)
prop_y = 1 1=propagate in y (3D)
prop_z = 1 1=propagate in z (3D)
prop_p = 1 1=propagate in momentum

use_symmetry = 0 0=no symmetry, 1=optimized symmetry, 2=xyz symmetry by copying(3D)

vectorized = 0 0=unvectorized code, 1=vectorized code

source_specification = 0 2D::1:r,z=0 2:z=0 3D::1:x,y,z=0 2:z=0 3:x=0 4:y=0
source_model = 1 0=zero 1=parameterized 2=Case&B 3=pulsars 4= 5=S&Mattox 6=S&Mattox
with cutoff
source_parameters_1 = 0.5 model 1:alpha
source_parameters_2 = 1.0 model 1:beta
source_parameters_3 = 20.0 model 1:rmax


n_cr_sources = 0 number of pointlike cosmic-ray sources 3D only!
cr_source_x_01 = 10.0 x position of cosmic-ray source 1 (kpc)
cr_source_y_01 = 10.0 y position of cosmic-ray source 1
cr_source_z_01 = 0.1 z position of cosmic-ray source 1
cr_source_w_01 = 0.1 sigma width of cosmic-ray source 1
cr_source_L_01 = 1.0 luminosity of cosmic-ray source 1
cr_source_x_02 = 3.0 x position of cosmic-ray source 2
cr_source_y_02 = 4.0 y position of cosmic-ray source 2
cr_source_z_02 = 0.2 z position of cosmic-ray source 2
cr_source_w_02 = 2.4 sigma width of cosmic-ray source 2
cr_source_L_02 = 2.0 luminosity of cosmic-ray source 2


SNR_events = 0 handle stochastic SNR events
SNR_interval = 1.0e4 time interval in years between SNR in 1 kpc^-3 volume
SNR_livetime = 1.0e4 CR-producing live-time in years of an SNR
SNR_electron_sdg = 0.00 delta electron source index Gaussian sigma
SNR_nuc_sdg = 0.00 delta nucleus source index Gaussian sigma
SNR_electron_dgpivot = 5.0e3 delta electron source index pivot rigidity (MeV)
SNR_nuc_dgpivot = 5.0e3 delta nucleus source index pivot rigidity (MeV)

HI_survey = 9 HI survey 8=orig 8 rings 9=new 9 rings
CO_survey = 9 CO survey 8=orig 8 rings 9=new 9 rings

B_field_model = 050100020 bbbrrrzzz bbb=10*B(0) rrr=10*rscale zzz=10*zscale
ISRF_file = MilkyWay_DR0.5_DZ0.1_DPHI10_RMAX20_ZMAX5_galprop_format.fits i
nput ISRF file
ISRF_factors = 1.0,1.0,1.0 ISRF factors for IC calculation: optical, FIR, CMB

proton_norm_Ekin = 1.00e+5 proton kinetic energy for normalization (MeV)
proton_norm_flux = 4.90e-9 to renorm nuclei/flux of protons at norm energy (cm^-2 sr^-1 s^
-1 MeV^-1)

electron_norm_Ekin = 34.5e3 electron kinetic energy for normalization (MeV)
electron_norm_flux = .40e-9 flux of electrons at normalization energy (cm^-2 sr^-1 s^-1 MeV
^-1)

max_Z = 2 maximum number of nucleus Z listed
use_Z_1 = 1
use_Z_2 = 1
use_Z_3 = 0
use_Z_4 = 0
use_Z_5 = 0
use_Z_6 = 0
use_Z_7 = 0
use_Z_8 = 0
use_Z_9 = 0
use_Z_10 = 0
use_Z_11 = 0
use_Z_12 = 0
use_Z_13 = 0
use_Z_14 = 0
use_Z_15 = 0
use_Z_16 = 0
use_Z_17 = 0
use_Z_18 = 0
use_Z_19 = 0
use_Z_20 = 0
use_Z_21 = 0
use_Z_22 = 0
use_Z_23 = 0
use_Z_24 = 0
use_Z_25 = 0
use_Z_26 = 0
use_Z_27 = 0
use_Z_28 = 0
use_Z_29 = 0
use_Z_30 = 0

iso_abundance_01_001 = 1.054e6 H
iso_abundance_01_002 = 0.
iso_abundance_02_004 = 0.703e5 He
iso_abundance_02_003 = 0.
iso_abundance_03_006 = 0. Li
iso_abundance_03_007 = 0.
iso_abundance_04_007 = 0. Be
iso_abundance_04_009 = 0.
iso_abundance_04_010 = 0.
iso_abundance_05_010 = 0. B
iso_abundance_05_011 = 0.
iso_abundance_06_012 = 2700.25 C
iso_abundance_06_013 = 0.
iso_abundance_07_014 = 190.5 N
iso_abundance_07_015 = 0.8
iso_abundance_08_016 = 3450. O
iso_abundance_08_017 = 1.5
iso_abundance_08_018 = 8.4
iso_abundance_09_019 = 0.0 F
iso_abundance_10_020 = 360.1 Ne
iso_abundance_10_021 = 1.2
iso_abundance_10_022 = 52.2
iso_abundance_11_023 = 25.0 Na
iso_abundance_12_024 = 570.3 Mg
iso_abundance_12_025 = 76.6
iso_abundance_12_026 = 87.7
iso_abundance_13_027 = 54.5 Al
iso_abundance_14_028 = 642.3 Si
iso_abundance_14_029 = 33.9
iso_abundance_14_030 = 23.1
iso_abundance_15_031 = 7.28 P
iso_abundance_16_032 = 94.40 S
iso_abundance_16_033 = 0.8
iso_abundance_16_034 = 4.45
iso_abundance_16_036 = 0.02
iso_abundance_17_035 = 2.11 Cl
iso_abundance_17_037 = 0.72
iso_abundance_18_036 = 11.17 Ar
iso_abundance_18_038 = 2.22
iso_abundance_19_039 = 4.47 K
iso_abundance_20_040 = 39.87 Ca
iso_abundance_20_042 = 0.28
iso_abundance_20_044 = 0.93
iso_abundance_20_048 = 0.09
iso_abundance_21_045 = 0.121 Sc
iso_abundance_22_046 = 0.17 Ti
iso_abundance_22_047 = 0.16
iso_abundance_22_048 = 1.64
iso_abundance_22_049 = 0.124
iso_abundance_22_050 = 0.12
iso_abundance_23_051 = 0.0 V
iso_abundance_24_050 = 0.72 Cr
iso_abundance_24_052 = 14.51
iso_abundance_24_053 = 1.69
iso_abundance_24_054 = 0.43
iso_abundance_25_055 = 16.15 Mn
iso_abundance_26_054 = 38.00 Fe
iso_abundance_26_056 = 620.2
iso_abundance_26_057 = 15.07
iso_abundance_26_058 = 2.31
iso_abundance_27_059 = 1.24 Co
iso_abundance_28_058 = 26.21 Ni
iso_abundance_28_060 = 10.44
iso_abundance_28_061 = 0.48
iso_abundance_28_062 = 1.51
iso_abundance_28_064 = 0.46

total_cross_section = 2 total cross section option: 0=L83 1=WA96 2=BP01
cross_section_option = 012 100*i+j i=1: use Heinbach-Simon C,O->B j=kopt j=11=Webber, 21=S
T

t_half_limit = 1.0e4 year - lower limit on radioactive half-life for explicit inclusio
n

primary_electrons = 1
secondary_positrons = 0
secondary_electrons = 0
secondary_antiproton = 0 0 1 2
tertiary_antiproton = 0
secondary_protons = 0

gamma_rays = 0 1=compute gamma rays, 2=compute HI,H2 skymaps separately
pi0_decay = 0 1= old formalism 2=Blattnig et al.
IC_isotropic = 0 1,2= compute isotropic IC: 1=compute full, 2=store skymap componen
ts
IC_anisotropic = 0 1,2,3= compute anisotropic IC: 1=full, 2=approx., 3=isotropic
bremss = 0 1=compute bremsstrahlung
synchrotron = 0 1=compute synchrotron

comment = the dark matter (DM) switches and user-defined parameters
DM_positrons = 0 1=compute DM positrons
DM_electrons = 0 1=compute DM electrons
DM_antiprotons = 0 1=compute DM antiprotons
DM_gammas = 0 1=compute DM gammas

DM_double0 = 2.8 core radius, kpc
DM_double1 = 0.43 local DM mass density, GeV cm-3
DM_double2 = 80. neutralino mass, GeV
DM_double3 = 40. positron width distribution, GeV
DM_double4 = 40. positron branching
DM_double5 = 40. electron width distribution, GeV
DM_double6 = 30. electron branching
DM_double7 = 50. pbar width distribution, GeV
DM_double8 = 40. pbar branching
DM_double9 =3.e-25 <cross_sec>-thermally overaged, cm3 s-1

DM_int0 = 1 isothermal profile
DM_int1 = 1
DM_int2 = 1
DM_int3 = 1
DM_int4 = 1
DM_int5 = 1
DM_int6 = 1
DM_int7 = 1
DM_int8 = 1
DM_int9 = 1

output_gcr_full = 0 output full galactic cosmic ray array
warm_start = 0 read in nuclei file and continue run

verbose = 0 verbosity: 0=min,10=max <0: selected debugs
test_suite = 0 run test suite instead of normal run

After experiencing the same problem I traced the error back to line 44 in D_xx.cc. The problem is that regardless of the value of n_spatial_dimensions the array Dxx.d2[ir][iz].s[ip] is filled.

If the user specified n_spatial_dimensions = 3, Dxx.d3[ix][iy][iz] will be created rather than Dxx.d2[ir][iz]. But D_xx.cc tries to fill d2[...] which obviously can not work. What I did was insert if (n_spatial_dimensions == 3) ... and if (n_spatial_dimensions == 2) statements into the code.

Here's my updated version of the file:



Regards
Bastian

Attched is my version of the D_xx.cc routine. Please, note that there is also another bug in
a routine create_transport_arrays.cc. I am attaching a version with this bug fixed: