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PHITSExercises using Recommendation
Settings and Utilities
Multi-Purpose Particle and Heavy Ion Transport code System
title 1
Jun. 2013 revised
• Recommendation Settings
• Utilities
• Summary and Homework
Contents 2
• ParticleTherapy• H10mupliplier
• Animation of Particle Trajectories• SimpleGEO
Contents
What is Recommendation Settings?
3Recommendation Settings
I cannot understand the appropriate parameter setting even if I read PHITS manual carefully
We prepared several examples of PHITS input files for various calculation conditions, and uploaded to PHITS website
http://phits.jaea.go.jp/examples.html
FAQ
Our Reply
List of Recommendation Settings
4
DetectorResponse.inp Detector response calculation (event-by-event information) Shielding.inp Shielding calculation using [t-track], example of complex geometry ParticleTherapy.inp Dose & LET distribution calculation for charged particle therapy PhotonTherapy.inp Dose & particle fluence calculation for X-ray therapy SemiConductor.inp Dose calculation inside a tiny region for SER estimation NuclearReaction.inp Double differential cross sections by calculating fluence of secondaries H10multiplier.inp H*(10) in water using [t-track] in combination with [multiplier] Counter.inp Dose deposited from primary and secondary particles using [counter]
Recommendation Settings
• Recommendation Settings
• Utilities
• Summary and Homework
Contents 5
• ParticleTherapy• H10mupliplier
• Animation of Particle Trajectories• SimpleGEO
Contents
ParticleTherapy.inp
6ParticleTherapy
[t-deposit] (file=dose) Depth-dose distribution in water [t-deposit] (file=dose-equivalent.out) Depth-dose-equivalent distribution in water [t-LET] Probability density of LET in water [t-SED] Probability density of lineal energy in water
10 cm
10 c
m
Carbon 200 MeV/u
WaterPhantom
Tally
Dose and Dose Equivalent
7
r-z mesh
Dose.eps Dose-equivalent.eps[ T - Deposit ]mesh = r-z r-type = 2 rmin = 0.000000 rmax = 1.000000 nr = 1 z-type = 2 zmin = 0.000000 zmax = 10.00000 nz = 100 dedxfnc = 0
[ T - Deposit ]dedxfnc = 1
Z
R
Output quantities are weighted by the function written in usrdfn1.f
Q(L) relationship is given as default
Dose is converted into Dose equivalent!
ParticleTherapy
Probability Density of LET & y
8
LET-distribution.eps(page 1: front surface)
y-distribution.eps(page 1: front surface)
LET of C(200 MeV/u) = 16 keV/m y*f(y) broad distribution even for mono-energetic incidenceL*f(L) has Sharp peak
[T-LET] [T-SED]
ParticleTherapy
Change Incident Particle
9
[ S o u r c e ]s-type = 1 proj = 12C e0 = 200.00 r0 = 0.0000 x0 = 0.0000 y0 = 0.0000 z0 = -20.000 z1 = -20.000 dir = 1.0000
10 c
m
Carbon 200 MeV/u
WaterPhantom
10 cm
(0,0,-20)
Z
X
Y
Proton
Dose.eps
Execute
Proton
10cm water is too short to stop 200 MeV proton!
[ T - Deposit ]…
[ T - Deposit ]…
[ T – L E T ]...
[ T – S E D ]...
[ T - Deposit ]…
[ T - Deposit ] off…
[ T – L E T ] off...
[ T – S E D ] off...
ParticleTherapy
Change Geometry
10General description
[ C e l l ] 1 1 -1.0000000E+00 1 -2 -3 2 0 #1 -999 3 -1 999
[ S u r f a c e ] 1 pz 0.0000000E+00 2 pz 1.0000000E+01 3 cz 5.0000000E+00 999 so 1.0000000E+02
10 c
m
Carbon 200 MeV/u
WaterPhantom
10 cm
(0,0,-20)
Z
X
Y
3.0000000E+01
Dose.eps
Proton 10 c
m
30 cm
Forgot to change tally region!!!
Execute
Change Tally Region
11
[ T - Deposit ] title = depth-dose d mesh = r-z x0 = 0.000000 y0 = 0.000000 r-type = 2 rmin = 0.000000 rmax = 1.000000 nr = 1 z-type = 2 zmin = 0.000000 zmax = 10.00000 nz = 100
Dose.eps
[ C e l l ] 1 1 -1.0000000E+00 1 -2 -3 2 0 #1 -999 3 -1 999
[ S u r f a c e ] 1 pz 0.0000000E+00 2 pz 2.0000000E+01 3 cz 5.0000000E+00 999 so 1.0000000E+02
set: c1[30.0]
c1
c110
cm
Carbon 200 MeV/u
WaterPhantom(0,0,-20)
Z
X
Y
Proton 10 c
m
30 cm
Statistics is not
enough!!
ParticleTherapy
Restart Calculation
12
Dose.eps
[ P a r a m e t e r s ] icntl = 0 maxcas = 100 maxbch = 2 10
10 c
m
Carbon 200 MeV/u
WaterPhantom(0,0,-20)
Z
X
Y
Proton 10 c
m
30 cm
Finally, we obtained the depth-dose distribution in water irradiated by 200 MeV proton with enough statistics!!
Execute
ParticleTherapy
istdev = -1
• Recommendation Settings
• Utilities
• Summary and Homework
Contents 13
• ParticleTherapy• H10mupliplier
• Animation of Particle Trajectories• SimpleGEO
Contents
H10multiplier.inp
14H10multiplier
[t-track] Calculate dose from fluences of particle multiplied with dose conversion coefficients. In this case, dose conversion coefficients for H*(10) are defined in [multiplier] section [t-heat] Calculate dose using Kerma Approximation [t-deposit] Calculate dose from the ionization energy of charged particles
100 cm
100
cm
400 MeV NeutronConcrete
3 ways to calculate “Dose” in PHITS
100
cm
Air
Results of Each Tally
15
[T-Track] [T-Heat] [T-Deposit]
[t-track] Fluence multiplied with H*(10) dose conversion coefficients → No gap between concrete and air [t-heat] Kerma approximation for low-energy neutrons and photons → There is a gap between concrete and air [t-deposit] Ionizing energy of charged particles → There is a gap between concrete and air. Large uncertainties in air
*
0(10) ( ) ( )dH E d E E
H10multiplier
Calculation of H*(10) and Effective Dose
16
[ Multiplier ] number = -250 interpolation = log ne = 140 1.13000E-08 9.14000E+00*3600*1.0e-6 1.42000E-08 9.44000E+00*3600*1.0e-6 1.79000E-08 9.83000E+00*3600*1.0e-6...
[ T - T r a c k ] title = H*(10) in xyz mesh in uSv/h... multiplier = all part = neutron emax = 1000.0 mat mset1 mset2 all ( 1.0 -250 ) (1.0 -102) multiplier = all part = photon emax = 1000.0 mat mset1 mset2 all ( 1.0 -251) (1.0 -114)
Fluence calculated by [t-track] can be multiplied with several functions that are pre-defined or defined in [multiplier] section
• H*(10) conversion coefficient for neutron(-250) and photon (-251) defined in [multiplier]
• Predefined Effective dose conversion coefficients for neutron (-102) and photon (-114)
• H*(10) conversion coefficient for neutron(-250) and photon (-251) defined in [multiplier]
• Predefined Effective dose conversion coefficients for neutron (-102) and photon (-114)
Track.epsThey seem to be almost the same!
H*(10)(Page 1)
Effective Dose(Page 2)
H10multiplier
Change Axis
17
[ T - T r a c k ] title = H*(10) in xy part = ( neutron photon ) mesh = xyz x-type = 2 xmin = -60.0 xmax = 60.0 nx = 60 y-type = 2 ymin = -60.0 ymax = 60.0 ny = 1 z-type = 2 zmin = 0.0 zmax = 120.0 nz = 60 e-type = 1 ne = 1 1.00000E-10 1.00000E+03 unit = 1 material = all axis = xz file = track.out
2D-plot (contour map) to1D-plot (histogram)2D-plot (contour map) to1D-plot (histogram)
Track.epsTough to compare because each scale is automatically adjusted
1
z
H*(10)(Page 1)
Effective Dose(Page 2)
Avoid to output too much graphsAvoid to output too much graphs
Execute
H10multiplier
Adjust Scale
18
[ T - T r a c k ] title = H*(10) in xy part = ( neutron photon ) mesh = xyz x-type = 2 xmin = -60.0 xmax = 60.0 nx = 60 y-type = 2 ymin = -60.0 ymax = 60.0 ny = 1 z-type = 2 zmin = 0.0 zmax = 120.0 nz = 60 e-type = 1 ne = 1 1.00000E-10 1.00000E+03 unit = 1 material = all axis = xz file = track.out
Add ANGEL parameter(min & max for y-axis)Add ANGEL parameter(min & max for y-axis)
Track.eps
1
z
H*(10)(Page 1)
Effective Dose(Page 2)
angel = ymin(5.e-05) ymax(5.e-4)
H10multiplier
H*(10) < Effective dose
Execute
Execute Only ANGEL
19
#------------------------------------------------ 80 行目 #newpage:# no. = 1 ie = 1 ix = 1 iy = 1…x: z[cm]y: Flux [1/cm^2/source] p: xlin ylog afac(0.8) form(0.9)p: ymin(5.e-05) ymax(5.0e-4)h: n x y(p1-group),hh0l n # z-lower z-upper flux r.err 0.0000E+00 1.0000E+00 1.2809E-04 0.0263…#------------------------------------------------- 232 行目 newpage:# no. = 2 ie = 1 ix = 1 iy = 1…x: z[cm]y: Flux [1/cm^2/source] p: xlin ylog afac(0.8) form(0.9)p: ymin(5.e-05) ymax(5.0e-4)h: n x y(p1-group),hh0l n # z-lower z-upper flux r.err 0.0000E+00 1.0000E+00 1.9351E-04 0.0174...
Change LegendDo not use “(“ and “)”
Change LegendDo not use “(“ and “)”
H10multiplier
H10
Effective
#
Right click “Track2.out” → Sendto → ANGEL
Comment out(Same format as PHITS input file)
Comment out(Same format as PHITS input file)
Specify line color(r: red, b: blue, g: green etc)Do not insert space between
“hh0l” and color ID
Specify line color(r: red, b: blue, g: green etc)Do not insert space between
“hh0l” and color ID
r
Track2.eps
Copy “Track.out” to “Track2.out”, and Edit
Contributions from High- and Low-Energy Particles
20
[ T - T r a c k ] title = H*(10) in xy part = ( neutron photon ) mesh = xyz x-type = 2 xmin = -60.0 xmax = 60.0 nx = 1 y-type = 2 ymin = -60.0 ymax = 60.0 ny = 1 z-type = 2 zmin = 0.0 zmax = 120.0 nz = 60 e-type = 1 ne = 1 1.00000E-10 1.00000E+03 unit = 1 material = all axis = z file = track.out H*(10) Effective Dose angel = ymin(1.e-05)
ymax(2.e-4)
H10multiplier
20.0 1.0E+03 2
Low Energy(page1)
High Energy(page2)
Low Energy(page3)
High Energy(page4)
Execute ≅
<Divide the energy bin
into high- and low-energy region
Divide the energy bin into high- and low-
energy region
• Recommendation Settings
• Utilities
• Summary and Homework
Contents 21
• ParticleTherapy• H10mupliplier
• Animation of Particle Trajectories• SimpleGEO
Contents
Contents of Utilities
22Utilities
Animation Create an animation of particle trajectories Rotate3dshow Rotate the geometry depicted by [t-3dshow] SimpleGEO Instruction for how to use SimpleGEO for PHITS input generator Autorun Shell script for successively executing PHITS by slightly changing calculation conditions
Animation Rotate3dshow SimpleGEO
• Recommendation Settings
• Utilities
• Summary and Homework
Contents 23
• ParticleTherapy• H10mupliplier
• Animation of Particle Trajectories• SimpleGEO
Contents
How to Create Animation
24Animation
Required Software ImageMagick (http://www.imagemagick.org/script/binary-releases.php) Software that can convert a multiple-page EPS file into a GIF animation Procedures
1. Execute PHITS Calculate the time-dependence of particle fluences or deposition energies by introducing “t-type” in PHITS input file2. Edit EPS file generated by PHITS 1. Open EPS file “track.eps” with your text editor 2. Search the word “PageBoundingBox” twice 3. Change the first 2 numbers to 0, and save the file
3. Convert the EPS file to GIF animation using ImageMagick 1. Open “command prompt” 2. Move to the folder including the EPS file 3. Type ‘convert -dispose background -rotate 90 XXX.eps XXX.gif‘
%%PageBoundingBox: 27 36 571 803
%%PageBoundingBox: 0 0 571 803
Increase the Time Resolution
25Animation
[ T - T r a c k ] C -- Contour figure Tally -- mesh = xyz ...t-type = 2 nt = 20 # Number of frame tmin = 0.00 # Initial time (nsec) tmax = 40 # Final time (nsec)... angel = cmin(1.e-05) cmax(1.e+00) epsout = 1
animation.inp
60
Increase the frame numberIncrease the frame number
Execute PHITSEdit EPS file
Convert EPS to GIF
20 frame
60 frame
• Recommendation Settings
• Utilities
• Summary and Homework
Contents 26
• ParticleTherapy• H10mupliplier
• Animation of Particle Trajectories• SimpleGEO
Contents
How to use SimpleGEO for PHITS
27SimpleGEO
Required Software SimpleGEO & Its plugin package (only for Windows) Download site: http://theis.web.cern.ch/theis/simplegeo/
Procedures
1. Make geometry using SimpleGEO You have to define void (or air) region too. See manual of SimpleGEO
2. Export the geometry to PHITS readable format (File → Export → PHITS) Only [cell] & [surface] sections are generated
3. Make PHITS input file except for [cell] & [surface] sections Include the exported file using “infl:” command
4. Execute PHITS using the input file
5. Visualize the tally results obtained from “mesh=xyz” in SimpleGEO Load “DaVis3D” in SimpleGEO (Macros → Load Plugins → DaVis3D) Select the xyz-mesh tally results, and visualize in SimpleGEO
[ S u r f a c e ]c Body1 RCC 0.00 0.00 0.00 0.00 0.00 10.00 5.00c Headball2 SPH 0.00 0.00 15.00 5.00c LeftEye3 SPH -3.00 4.00 16.00 1.00c OuterSphere4 SPH 0.00 0.00 0.00 100.00c Outmostsphere5 SPH 0.00 0.00 0.00 100.00c RightEye6 SPH 3.00 4.00 16.00 1.00
Change Geometry in SimpleGEO
28SimpleGEO
[ C e l l ]c Body 00001 26 -1 -1 c Eyes 00002 11 -7.87 -6 : -3 c Head 00003 6 -1.9 -2 #2 c Void 00004 0 -4 +1 #2 #3c Outervoid 00005 -1 -5 +4
[ S u r f a c e ]c Body1 RCC 0.00 0.00 0.00 0.00 0.00 10.00 5.00c Headball2 SPH 0.00 0.00 15.00 5.00c LeftEye3 SPH -3.00 4.00 16.00 1.00c OuterSphere4 SPH 0.00 0.00 0.00 100.00c Outmostsphere5 SPH 0.00 0.00 0.00 100.00c RightEye6 SPH 3.00 4.00 16.00 1.00c leg17 RCC -2.50 0.00 -10.00 0.00 0.00 10.00 2.00c leg28 RCC 2.50 0.00 -10.00 0.00 0.00 10.00 2.00
doll.pht[ C e l l ]c Body 00001 26 -1 -1 c Eyes 00002 11 -7.87 -6 : -3 c Head 00003 6 -1.9 -2 #2 c Void 00004 0 -4 +1 #2 #3 +7 +8 c Outervoid 00005 -1 -5 +4 c leg1 00006 26 -1 -7 c leg2 00007 26 -1 -8
Export to PHITS
Visualize Tally Result in 3D
29SimpleGEO
SimpleGEO.inp[ T - Deposit ] title = [t-deposit] in xyz mesh mesh = xyz # mesh type is xyz scoring mesh x-type = 2 # x-mesh is linear given by xmin, xmax and nx xmin = -5.000000 # minimum value of x-mesh points xmax = 5.000000 # maximum value of x-mesh points nx = 20 # number of x-mesh points y-type = 2 # y-mesh is linear given by ymin, ymax and ny ymin = -5.000000 # minimum value of y-mesh points ymax = 5.000000 # maximum value of y-mesh points ny = 20 # number of y-mesh points z-type = 2 # z-mesh is linear given by zmin, zmax and nz zmin = 0.000000 # minimum value of z-mesh points zmax = 20.00000 # maximum value of z-mesh points nz = 40 # number of z-mesh points
-10.00000
Extend the tally regionExtend the tally regionExecute
1. Select ‘Macros -> Load Plugins -> DaVis3D’ 2. Press ‘DaVis3D‘ button3. Select ‘deposity-xy.out’ and press ‘Load data’
SimpleGEO
• Recommendation Settings
• Utilities
• Summary and Homework
Contents 30
• ParticleTherapy• H10mupliplier
• Animation of Particle Trajectories• SimpleGEO
Contents
http://phits.jaea.go.jp 31
• It is difficult to make PHITS input file all by yourself
• It is better to select an appropriate recommendation setting, and edit the file for your calculation condition
• You can enjoy PHITS more using the utilities!
Summary
Dose distribution in PHITS-shaped water phantom irradiated by 1 GeV protons
Summary 32
1. Calculate the depth-dose distributions for various radial distances inside cylindrical water phantom irradiated by 11B 250 MeV/u beam
2. Separate the depth-dose distributions into the contributions from neutron, proton, He, Li, Be, B
3. Divide the phantom into 2 layers, composed of water and Aluminum (2.7 g/cm3) respectively.
4. Obtain better statistic data by increasing the history number or by using the restart function
Homework
Hints• Use 1st [t-deposit] tally in “ParticleTherapy” in “recommendation” folder• Increase the number of the radial bins in the [t-deposit] tally• Comment out unnecessary tallies using “off” command for speed up• Setup appropriate source particles and energy in [source] section• Specify particle type in the [t-deposit] tally• Add new material (Al), surface, and cells to set up geometry
Summary 33
Example of Simulation Results
Depth dose distributions for r < 1 cm and 1 cm < r < 2 cm
r < 1 cm 1 cm < r < 2 cm
Let’s think about …• What kinds of particles contribute to the dose behind Bragg peak?• Why dose suddenly increase at the depth of 5 cm?• Why we cannot see the neutron contributions in these graphs?