DOSXYZnrc [plot profile] #1169

Mona99-del · 2024-08-19T10:49:15Z

Mona99-del
Aug 19, 2024

When trying to plot profile after completing the simulation, this error appears as shown in the picture. Do you know how I can solve it? This information file demo.egslst. Can you help me?
NRCC/UW EGSnrc user-code DOSXYZnrc
ON win3264 16:09:59 Aug 18 2024

** DOSXYZnrc **
** Z pronounced zed **

** Code developed at the National Research Council of Canada and **
** University of Wisconsin as part of the OMEGA project **

 The following parameters may be adjusted in dosxyz_user_macros.mortran

$MXMED: Max number of media: 20
$MXSTACK: Max stack size: 900000
$IMAX,etc: Max dose scoring regions in x,y,z directions: 128 128 128
$MAXDOSE: Max dose scoring regions consistent with above:2097153
$DOSEZERO(=1) 1=> all doses with uncert > 50% are zeroed in .3ddose file

The following parameters may be adjusted in srcxyz.macros
$INVDIM: number of elements in inverse CPD for input energy spectra = 1000
$NENSRC: number of bins in input energy spectrum = 200

===============================================================================

Title: 6Mv 10cm*10cm

===============================================================================

Number of media (min = 1, max = 20, 0 => CT data): 2
Medium 1: H2O700ICRU
Medium 2: AIR700ICRU

ECUTIN,PCUTIN,(ESTEPE,SMAX--DUMMY INPUTS):
0.000 0.000 0.000 0.000 0.000

regions in x (max= 128),y (max= 128),z (max= 128) directions

(if<0,implies # groups of reg), IPHANT (1 to output a .egsphant
file for dosxyz_show, 0[default] to not output this file)
: -3 -3 -2 1

Input boundaries in the x-direction

Initial boundary: -15.000
Width in this group, number of regions in group: 1.000 5
Width in this group, number of regions in group: 0.200 100
Width in this group, number of regions in group: 1.000 5
Boundaries
-15.000 -14.000 -13.000 -12.000 -11.000 -10.000
-9.800 -9.600 -9.400 -9.200 -9.000 -8.800
-8.600 -8.400 -8.200 -8.000 -7.800 -7.600
-7.400 -7.200 -7.000 -6.800 -6.600 -6.400
-6.200 -6.000 -5.800 -5.600 -5.400 -5.200
-5.000 -4.800 -4.600 -4.400 -4.200 -4.000
-3.800 -3.600 -3.400 -3.200 -3.000 -2.800
-2.600 -2.400 -2.200 -2.000 -1.800 -1.600
-1.400 -1.200 -1.000 -0.800 -0.600 -0.400
-0.200 -0.000 0.200 0.400 0.600 0.800
1.000 1.200 1.400 1.600 1.800 2.000
2.200 2.400 2.600 2.800 3.000 3.200
3.400 3.600 3.800 4.000 4.200 4.400
4.600 4.800 5.000 5.200 5.400 5.600
5.800 6.000 6.200 6.400 6.600 6.800
7.000 7.200 7.400 7.600 7.800 8.000
8.200 8.400 8.600 8.800 9.000 9.200
9.400 9.600 9.800 10.000 11.000 12.000
13.000 14.000 15.000

Input boundaries in the y-direction

Initial boundary: -15.000
Width in this group, number of regions in group: 1.000 5
Width in this group, number of regions in group: 0.200 100
Width in this group, number of regions in group: 1.000 5
Boundaries
-15.000 -14.000 -13.000 -12.000 -11.000 -10.000
-9.800 -9.600 -9.400 -9.200 -9.000 -8.800
-8.600 -8.400 -8.200 -8.000 -7.800 -7.600
-7.400 -7.200 -7.000 -6.800 -6.600 -6.400
-6.200 -6.000 -5.800 -5.600 -5.400 -5.200
-5.000 -4.800 -4.600 -4.400 -4.200 -4.000
-3.800 -3.600 -3.400 -3.200 -3.000 -2.800
-2.600 -2.400 -2.200 -2.000 -1.800 -1.600
-1.400 -1.200 -1.000 -0.800 -0.600 -0.400
-0.200 -0.000 0.200 0.400 0.600 0.800
1.000 1.200 1.400 1.600 1.800 2.000
2.200 2.400 2.600 2.800 3.000 3.200
3.400 3.600 3.800 4.000 4.200 4.400
4.600 4.800 5.000 5.200 5.400 5.600
5.800 6.000 6.200 6.400 6.600 6.800
7.000 7.200 7.400 7.600 7.800 8.000
8.200 8.400 8.600 8.800 9.000 9.200
9.400 9.600 9.800 10.000 11.000 12.000
13.000 14.000 15.000

Input boundaries in the z-direction

Initial boundary: 0.000
Width in this group, number of regions in group: 0.100 100
Width in this group, number of regions in group: 1.000 10
Boundaries
0.000 0.100 0.200 0.300 0.400 0.500
0.600 0.700 0.800 0.900 1.000 1.100
1.200 1.300 1.400 1.500 1.600 1.700
1.800 1.900 2.000 2.100 2.200 2.300
2.400 2.500 2.600 2.700 2.800 2.900
3.000 3.100 3.200 3.300 3.400 3.500
3.600 3.700 3.800 3.900 4.000 4.100
4.200 4.300 4.400 4.500 4.600 4.700
4.800 4.900 5.000 5.100 5.200 5.300
5.400 5.500 5.600 5.700 5.800 5.900
6.000 6.100 6.200 6.300 6.400 6.500
6.600 6.700 6.800 6.900 7.000 7.100
7.200 7.300 7.400 7.500 7.600 7.700
7.800 7.900 8.000 8.100 8.200 8.300
8.400 8.500 8.600 8.700 8.800 8.900
9.000 9.100 9.200 9.300 9.400 9.500
9.600 9.700 9.800 9.900 10.000 11.000
12.000 13.000 14.000 15.000 16.000 17.000
18.000 19.000 20.000

Total # regions including exterior = 1331001

Input groups of regions for which density and medium are not defaults
Lower,upper i, j, k, MEDIUM, DENSITY ( 1 110)( 1 110)( 1 110) 1 0.000
Lower,upper i, j, k, MEDIUM, DENSITY ( 46 65)( 51 60)( 11 20) 2 0.000
Lower,upper i, j, k, MEDIUM, DENSITY
Found blank line => end of this input

Input groups of regions for which ECUT and PCUT are not defaults
NB This option is disabled, just input 8 zeros.
Dummy values of lower,upper i, j, k, ECUT, PCUT
Found blank line => end of this input

Enter 8 numbers on one line
3 pairs defininglower,upper x,y,z indicies of dose regions
for which results are to be output
IZSCAN: non-zero for z-scan/page
MAX20: if any one = 1, output summary of max 20 doses.
end signaled by first pair both zero
forno dose printed, MAX20 is still read from first line

Found blank line => end of this input

No doses will be output to egslst file

The material in the region outside the phantom is:AIR700ICRU
The thickness of this region (in x, y & z direction) is: 50.000 cm

NCASE,IWATCH,TIMMAX,INSEED1,INSEED2,BEAM_SIZE,ISMOOTH,IRESTART,IDAT,
IREJECT,ESAVE_GLOBAL,NRCYCL,IPARALLEL,PARNUM,n_split,ihowfarless,i_phsp_out,
i_bindos
:
6000000 0 500.00 33 97 100.00 0 0 0 0 0.00 0 0 0 1 0 0

================================================================================

               Electron/Photon transport parameter

================================================================================

Photon cross sections xcom
Compton cross sections default
Photon transport cutoff(MeV) 0.1000E-01
Pair angular sampling SIM
Pair cross sections BH
Triplet production Off
Bound Compton scattering OFF
Radiative Compton corrections Off
Rayleigh scattering OFF
Atomic relaxations OFF
Photoelectron angular sampling OFF

Electron transport cutoff(MeV) 0.7000
Bremsstrahlung cross sections BH
Bremsstrahlung angular sampling SIM
Spin effects On
Electron Impact Ionization Off
Maxium electron step in cm (SMAX) 0.1000E+11
Maximum fractional energy loss/step (ESTEPE) 0.2500
Maximum 1st elastic moment/step (XIMAX) 0.5000
Boundary crossing algorithm EXACT
Skin-depth for boundary crossing (MFP) 3.000
Electron-step algorithm PRESTA-II

================================================================================

     Summary of source parameters (srcxyznrc)

           BEAM treatment head simulation used as source:

      x-coordinate of the isocenter,                         0.0000 cm
      y-coordinate of the isocenter,                         0.0000 cm
      z-coordinate of the isocenter,                         0.0000 cm
      Polar angle of beam axis:                            180.0000 degrees
      Azimuthal angle of beam axis:                          0.0000 degrees
      Distance from isocenter to centre of scoring plane:   -0.0000 cm
      Rotation angle about beam axis,                        0.0000 degrees
      BEAM simulation: BEAM_EX16MVp
           input file: demo
       pegs data file: 700icru

      Fat photons from DBS will not be rejected.

Particles to be simulated: all

Medium AE AP
H2O700ICRU 0.700 0.010
AIR700ICRU 0.700 0.010

No range rejection.

Histories to be simulated for this run 6000000

Histories to be analyzed after this run 6000000

Elapsed wall clock time to this point= 1.985 s

CPU time so far for this run = 1.062 s

BATCH # TIME-ELAPSED TOTAL CPUTIME RATIO TIME OF DAY RNG pointers

 1          0.0            0.0      0.00    16:10:01   ixx jxx =   97  33 
 2       6793.4         6732.4      1.01    18:03:14   ixx jxx =   33  66 
 3      13737.5        13570.5      1.01    19:58:58   ixx jxx =   60  93 
 4      20599.4        20337.0      1.01    21:53:20   ixx jxx =   65   1 
 5      27814.4        27279.4      1.02    23:53:35   ixx jxx =    7  40 
 6      34748.5        34085.2      1.02    01:49:09   ixx jxx =    8  41 
 7      42278.5        41308.9      1.02    03:54:39   ixx jxx =   41  74 
 8      49056.1        48080.7      1.02    05:47:37   ixx jxx =   43  76 
 9      55776.1        54799.9      1.02    07:39:37   ixx jxx =   62  95 
10      62497.3        61519.8      1.02    09:31:38   ixx jxx =   21  54

Total CPU time for run = 68239.0 s = 18.955 hr => 316535. hist/hr
On win3264

of particles read from BEAM simulation (N_read) = 6000000

of primary particles incident in BEAM simulation = 345512880

of particles discarded dueto charge/LATCH/W/multiple passer = 0

of particles discarded because beyond BEAM_SIZE = 0

of photons rejected because beyond DBS splitting radius = 0

of particles that missed geometry = 0

of particles simulated in DOSXYZnrc (N_used) = 6000000

                    N_used/N_read       =       1.000

Fraction of incident energy deposited in the phantom = 0.3919

Fraction of incident energy deposited in the region surrounding
the phantom when incident particles go through it = 0.0010

Number of charged particle steps simulated, N_step = 543280982
Number of charged particle steps/incident fluence = 1.57239E+00
No. of PRESTA-II steps/total no. of charged particle steps = 0.56934

1

The dose values in 798005 voxels had error > 50% and have been
zeroed in the .3ddose file.

Total CPU time for this run = 68253.8 s = 18.959 hr

END OF RUN Aug 19 2024 11:23:55

rtownson · 2024-08-19T14:11:18Z

rtownson
Aug 19, 2024
Maintainer

The error you're seeing from xmgrace is just to do with the plotting, nothing concerning. It's just adjusting your y-axis since all the numbers are squished together.

0 replies

Mona99-del · 2024-08-19T14:21:09Z

Mona99-del
Aug 19, 2024
Author

Thanks for your reply how can i adjust y-axis؟

…

On Mon, Aug 19, 2024, 5:11 PM Reid Townson ***@***.***> wrote: The error you're seeing from xmgrace is just to do with the plotting, nothing concerning. It's just adjusting your y-axis since all the numbers are squished together. — Reply to this email directly, view it on GitHub <#1169 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BJLSEJRAQCFME5CYHPCS4Y3ZSH4JZAVCNFSM6AAAAABMXSFZXWVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTAMZYGQ2TENI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

2 replies

rtownson Aug 19, 2024
Maintainer

Probably under Plot->Axis properties. Or just copy/paste the data into a plotting/spreadsheet tool that you're familiar with.

Mona99-del Aug 19, 2024
Author

ok, thank you so much

Mona99-del · 2024-08-22T17:10:10Z

Mona99-del
Aug 22, 2024
Author

I tried using VICTORIA and this is the result is the simulation correct?

1 reply

rtownson Aug 22, 2024
Maintainer

It looks reasonable to me, if you wanted an air pocket in a water box. The uncertainties look pretty large.

Mona99-del · 2024-08-22T19:47:18Z

Mona99-del
Aug 22, 2024
Author

ok, thank you for the replay. if I put another material instead of air, such as silicone, will reduce the uncertainty?

1 reply

rtownson Aug 23, 2024
Maintainer

Denser materials will have more interactions, so yes there would be a lower uncertainty on the dose deposited. But the best way to reduce the uncertainty is just to run longer simulations of more particles.

Mona99-del · 2024-08-23T13:44:41Z

Mona99-del
Aug 23, 2024
Author

Ok, thanks for the clarification.

…

On Fri, Aug 23, 2024, 4:37 PM Reid Townson ***@***.***> wrote: Denser materials will have more interactions, so yes there would be a lower uncertainty on the dose deposited. But the best way to reduce the uncertainty is just to run longer simulations of more particles. — Reply to this email directly, view it on GitHub <#1169 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BJLSEJXFZNE7HHT5IUQCCY3ZS43JLAVCNFSM6AAAAABMXSFZXWVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANBTGA3TGNY> . You are receiving this because you authored the thread.Message ID: ***@***.***>

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DOSXYZnrc [plot profile] #1169

Mona99-del Aug 19, 2024

===============================================================================

Title: 6Mv 10cm*10cm

regions in x (max= 128),y (max= 128),z (max= 128) directions

Input boundaries in the x-direction

Input boundaries in the y-direction

Input boundaries in the z-direction

of particles read from BEAM simulation (N_read) = 6000000

of primary particles incident in BEAM simulation = 345512880

of particles discarded dueto charge/LATCH/W/multiple passer = 0

of particles discarded because beyond BEAM_SIZE = 0

of photons rejected because beyond DBS splitting radius = 0

of particles that missed geometry = 0

of particles simulated in DOSXYZnrc (N_used) = 6000000

Replies: 5 comments · 4 replies

rtownson Aug 19, 2024 Maintainer

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