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Copy pathbeta_medium_topasfile.py
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329 lines (291 loc) · 16.8 KB
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import os
import math
def write_common_config(filename, InnerRadius, OuterRadius, HalfHeight, HLX, HLY, HLZ):
"""
通用配置部分，只需要写一次
"""
template_common = f"""
b:Ge/QuitIfOverlapDetected="false"
#### GENERAL ####
i:Ts/Seed = 656
i:Ts/NumberOfThreads = -1
#b:Ts/DumpParameters = "True"
#b:Ts/DumpNonDefaultParameters = "False"
#b:Ts/ListUnusedParameters = "True"
#Ts/PauseBeforeQuit = "True"
#b:Ts/ShowCPUTime = "True"
#### GUI ####
#s:Gr/ViewA/Type = "OpenGL"
#i:Gr/ViewA/WindowSizeX = 1200
#i:Gr/ViewA/WindowSizeY = 1000
#u:Gr/ViewA/Zoom = 2.
#Ts/UseQt = "True"
#d:Gr/view/Theta = 45 deg
#d:Gr/view/Phi = 30 deg
#s:Gr/view/ColorBy = "ParticleType"
#sv:Gr/view/ColorByParticleTypeNames = 4 "e-" "alpha" "proton" "neutron"
#sv:Gr/view/ColorByParticleTypeColors = 4 "green" "red" "blue" "grass"
#s:Gr/view/BackgroundColor = "White"
#### WORLD ####
s:Ge/World/Type = "TsBox"
d:Ge/World/HLX = 1.76 mm
d:Ge/World/HLY = 1.76 mm
d:Ge/World/HLZ = 1.76 mm
s:Ge/World/Material = "Vacuum"
#s:Ge/World/Color = "lightBlue"
#b:Ge/World/Invisible = "true"
#### MEDIUM ####
s:Ge/Medium/Type="TsMyMedium"
s:Ge/Medium/Material="G4_Lu"
s:Ge/Medium/Parent="World"
d:Ge/Medium/InnerRadius= {InnerRadius} mm # 内半径
d:Ge/Medium/OuterRadius= {OuterRadius} mm # 外半径
d:Ge/Medium/HalfHeight= {HalfHeight} mm # 半高
d:Ge/Medium/HLX= 141.5875 um
d:Ge/Medium/HLY= 124.575 um
d:Ge/Medium/HLZ= 2.3575 um
s:Ge/Medium/Color = "white"
d:Ge/Medium/transX= 0 um
d:Ge/Medium/transY= 0 um
d:Ge/Medium/transZ= 437.6425 um
# -- Materials
s:Ma/G4_HistoneMaterial/CloneFromMaterial = "G4_WATER"
d:Ma/G4_HistoneMaterial/CloneWithDensity = 1.407 g/cm3
s:Ma/G4_BaseMaterial/CloneFromMaterial = "G4_WATER"
d:Ma/G4_BaseMaterial/CloneWithDensity = 1.0 g/cm3
s:Ma/G4_BackboneMaterial/CloneFromMaterial = "G4_WATER"
d:Ma/G4_BackboneMaterial/CloneWithDensity = 1.0 g/cm3
s:Ma/G4_WATER_MODIFIED/CloneFromMaterial = "G4_WATER"
d:Ma/G4_WATER_MODIFIED/CloneWithDensity = 1.0 g/cm3
#### Physics and Chemistry ####
sv:Ph/Default/Modules = 4 "g4em-livermore" "g4decay" "g4radioactivedecay" "TsEmDNAChemistry"
d:Ph/Default/LowestElectronEnergy = 100 eV
d:Ph/Default/EMRangeMin = 100. eV
d:Ph/Default/ProductionCut = 0.2 um
d:Ph/Default/ForRegion/Nucleus/ProductionCut = 0.2 um
s:Ph/Default/ForRegion/G4DNA/ActiveG4EmModelFromModule = "g4em-dna_opt2"#g4em-dna,g4em-dna_opt2,g4em-dna-stationary_opt2
d:Ph/Default/CutForElectron = 0.2 um
d:Ph/Default/ForRegion/G4DNA/CutForElectron = 0.2 um
d:Ph/Default/ForRegion/G4DNA/LowestElectronEnergy = 0 eV
includeFile = /home/liangkun/topas-nbio/TOPAS-nBio-latest/examples/processes/TOPASChemistry.txt
#includeFile = /home/tdw/MyTOPAS-nBio/TOPAS-nBio/examples/geometry/nucleusModel/supportFiles/TOPASChemistry.txt
s:Ch/ChemistryName = "TOPASChemistry"
b:Ch/TOPASChemistry/ChemicalStageTransportActive = "True"
i:Ph/Verbosity = 0
d:Ch/TOPASChemistry/ChemicalStageTimeEnd = 2.5 ns
dv:Ch/TOPASChemistry/ChemicalStageTimeStepsHighEdges = 1 999999 ps
dv:Ch/TOPASChemistry/ChemicalStageTimeStepsResolutions = 1 2.5 ns
b:Ch/TOPASChemistry/TestForContactReactions = "True"
b:Ph/Default/Fluorescence = "True"
b:Ph/Default/Auger = "True"
b:Ph/Default/AugerCascade = "True"
b:Ph/Default/DeexcitationIgnoreCut = "True"
b:Ph/Default/PIXE = "True"
Ts/ShowHistoryCountAtInterval = 1
#### Radionuclide Source for Medium ####
s:So/RadionuclideSource/Type = "Volumetric"
s:So/RadionuclideSource/Component = "Medium" # 如果只是放射性核素在培养基的话，这里可以指定为上面的Medium
s:So/RadionuclideSource/ActiveMaterial = "G4_Lu"
b:So/RadionuclideSource/RecursivelyIncludeChildren = "T"
i:So/RadionuclideSource/NumberOfHistoriesInRun = 1000000000
i:So/RadionuclideSource/MaxNumberOfPointsToSample = 10000000
#s:So/RadionuclideSource/BeamEnergySpectrumType = "Discrete"
s:So/RadionuclideSource/BeamEnergySpectrumType = "Continuous"
s:So/RadionuclideSource/BeamParticle = "e-"
dv:So/RadionuclideSource/BeamEnergySpectrumValues = 101 0.00000 0.00010 0.00011 0.00012 0.00013 0.00014 0.00015 0.00016 0.00018 0.00020 0.00022 0.00024 0.00026 0.00028 0.00030 0.00032 0.00036 0.00040 0.00045 0.00050 0.00055 0.00060 0.00065 0.00070 0.00075 0.00080 0.00085 0.00090 0.00100 0.00110 0.00120 0.00130 0.00140 0.00150 0.00160 0.00180 0.00200 0.00220 0.00240 0.00260 0.00280 0.00300 0.00320 0.00360 0.00400 0.00450 0.00500 0.00550 0.00600 0.00650 0.00700 0.00750 0.00800 0.00850 0.00900 0.01000 0.01100 0.01200 0.01300 0.01400 0.01500 0.01600 0.01800 0.02000 0.02200 0.02400 0.02600 0.02800 0.03000 0.03200 0.03600 0.04000 0.04500 0.05000 0.05500 0.06000 0.06500 0.07000 0.07500 0.08000 0.08500 0.09000 0.10000 0.11000 0.12000 0.13000 0.14000 0.15000 0.16000 0.18000 0.20000 0.22000 0.24000 0.26000 0.28000 0.30000 0.32000 0.36000 0.40000 0.45000 0.49780 MeV
uv:So/RadionuclideSource/BeamEnergySpectrumWeightsUnscaled = 101 5.707E+00 5.705E+00 5.704E+00 5.704E+00 5.704E+00 5.704E+00 5.703E+00 5.703E+00 5.703E+00 5.702E+00 5.702E+00 5.701E+00 5.701E+00 5.700E+00 5.700E+00 5.699E+00 5.698E+00 5.697E+00 5.696E+00 5.694E+00 5.693E+00 5.692E+00 5.691E+00 5.689E+00 5.688E+00 5.687E+00 5.685E+00 5.684E+00 5.682E+00 5.679E+00 5.676E+00 5.674E+00 5.671E+00 5.669E+00 5.666E+00 5.661E+00 5.656E+00 5.651E+00 5.646E+00 5.641E+00 5.636E+00 5.630E+00 5.625E+00 5.615E+00 5.605E+00 5.592E+00 5.579E+00 5.566E+00 5.554E+00 5.541E+00 5.528E+00 5.515E+00 5.503E+00 5.490E+00 5.477E+00 5.452E+00 5.426E+00 5.401E+00 5.375E+00 5.357E+00 5.338E+00 5.319E+00 5.280E+00 5.240E+00 5.201E+00 5.161E+00 5.122E+00 5.082E+00 5.042E+00 5.002E+00 4.922E+00 4.841E+00 4.739E+00 4.638E+00 4.536E+00 4.434E+00 4.333E+00 4.232E+00 4.131E+00 4.031E+00 3.932E+00 3.834E+00 3.642E+00 3.456E+00 3.276E+00 3.106E+00 2.946E+00 2.797E+00 2.661E+00 2.433E+00 2.223E+00 2.009E+00 1.793E+00 1.578E+00 1.367E+00 1.161E+00 9.643E-01 6.102E-01 3.285E-01 8.584E-02 0.000E+00
uv:So/RadionuclideSource/BeamEnergySpectrumWeights = 1.0 * So/RadionuclideSource/BeamEnergySpectrumWeightsUnscaled
"""
with open(filename, 'w') as file:
file.write(template_common)
def append_cell_config(filename, cell_number, x, y, z, nucleus_radius, nucleus_radiusX, nucleus_radiusY, nucleus_radiusZ):
"""
动态生成每个细胞的配置，并追加到文件中
"""
cell_template = f"""
#### Cell {cell_number} ####
#### MEMBRANE ####
s:Ge/Membrane{cell_number}/Type="TsEllipsoidalShell"
s:Ge/Membrane{cell_number}/Material="G4_Lu"
s:Ge/Membrane{cell_number}/Parent="World"
d:Ge/Membrane{cell_number}/OuterX= 28.3175 um
d:Ge/Membrane{cell_number}/OuterY= 12.4575 um
d:Ge/Membrane{cell_number}/OuterZ= 2.3575 um
d:Ge/Membrane{cell_number}/InnerX= 28.31 um
d:Ge/Membrane{cell_number}/InnerY= 12.45 um
d:Ge/Membrane{cell_number}/InnerZ= 2.35 um
s:Ge/Membrane{cell_number}/Color = "white"
d:Ge/Membrane{cell_number}/transX= {x} um
d:Ge/Membrane{cell_number}/transY= {y} um
d:Ge/Membrane{cell_number}/transZ= {z} um
#### CYTOPLASM ####
s:Ge/Cytoplasm{cell_number}/Type="TsEllipsoidalShell"
s:Ge/Cytoplasm{cell_number}/Material="G4_Lu"
s:Ge/Cytoplasm{cell_number}/Parent="World"
d:Ge/Cytoplasm{cell_number}/OuterX= 28.31 um
d:Ge/Cytoplasm{cell_number}/OuterY= 12.45 um
d:Ge/Cytoplasm{cell_number}/OuterZ= 2.35 um
d:Ge/Cytoplasm{cell_number}/InnerX= 12 um
d:Ge/Cytoplasm{cell_number}/InnerY= 8.5 um
d:Ge/Cytoplasm{cell_number}/InnerZ= 1.9 um
s:Ge/Cytoplasm{cell_number}/Color = "green"
d:Ge/Cytoplasm{cell_number}/transX= {x} um
d:Ge/Cytoplasm{cell_number}/transY= {y} um
d:Ge/Cytoplasm{cell_number}/transZ= {z} um
#### Nucleus ####
s:Ge/Nucleus{cell_number}/Type = "TsNucleus"
s:Ge/Nucleus{cell_number}/Parent = "World"
s:Ge/Nucleus{cell_number}/Material = "G4_WATER"
s:Ge/Nucleus{cell_number}/Color = "White"
s:Ge/Nucleus{cell_number}/DNAModel = "Sphere"#QuarterCylinder ，HalfCylinder，Sphere
s:Ge/Nucleus{cell_number}/NucleusType = "Ellipsoid" # Sphere:球体 Ellipsoid:椭球形
#d:Ge/Nucleus{cell_number}/NucleusRadius = {nucleus_radiusX} um
d:Ge/Nucleus{cell_number}/NucleusRadiusX = {nucleus_radiusX} um
d:Ge/Nucleus{cell_number}/NucleusRadiusY = {nucleus_radiusY} um
d:Ge/Nucleus{cell_number}/NucleusRadiusZ = {nucleus_radiusZ} um
d:Ge/Nucleus{cell_number}/VoxelAdd = 75.3 nm
i:Ge/Nucleus{cell_number}/HilbertCurveLayer = 4
i:Ge/Nucleus{cell_number}/HilbertCurve3DRepeatX = 63
i:Ge/Nucleus{cell_number}/HilbertCurve3DRepeatY = 45
i:Ge/Nucleus{cell_number}/HilbertCurve3DRepeatZ = 10
s:Ge/Nucleus{cell_number}/HilbertCurveFileName = "/home/liangkun/PaperReproduction/geometry/nucleusModel/supportFiles/HilbertPoints_iteration1.dat"
#s:Ge/Nucleus{cell_number}/HilbertCurveFileName = "/home/tdw/MyTOPAS-nBio/TOPAS-nBio/examples/geometry/nucleusModel/supportFiles/HilbertPoints_iteration1.dat"
s:Ge/Nucleus{cell_number}/Voxel/Material = "G4_WATER"
b:Ge/Nucleus{cell_number}/ShowDNAVoxels = "false"
s:Ge/Nucleus{cell_number}/ChromatinFiber/Material = "G4_WATER"
b:Ge/Nucleus{cell_number}/ShowChromatinCylinders = "false"
s:Ge/Nucleus{cell_number}/Histone/Material = "G4_HistoneMaterial"
b:Ge/Nucleus{cell_number}/OnlyBuildOneHistone = "false"
b:Ge/Nucleus{cell_number}/HistoneAsScavenger = "true"
b:Ge/Nucleus{cell_number}/AddBases = "true"
s:Ge/Nucleus{cell_number}/Base1/Material = "G4_BaseMaterial"
s:Ge/Nucleus{cell_number}/Base2/Material = "G4_BaseMaterial"
b:Ge/Nucleus{cell_number}/AddBackbones = "true"
s:Ge/Nucleus{cell_number}/Backbone1/Material = "G4_BackboneMaterial"
s:Ge/Nucleus{cell_number}/Backbone2/Material = "G4_BackboneMaterial"
b:Ge/Nucleus{cell_number}/AddHydrationShell = "true"
s:Ge/Nucleus{cell_number}/HydrationShell1/Material = "G4_WATER_MODIFIED"
s:Ge/Nucleus{cell_number}/HydrationShell2/Material = "G4_WATER_MODIFIED"
d:Ge/Nucleus{cell_number}/transX = {x} um
d:Ge/Nucleus{cell_number}/transY = {y} um
d:Ge/Nucleus{cell_number}/transZ = {z} um
#### Physics and Chemistry ####
s:Ge/Nucleus{cell_number}/AssignToRegionNamed = "G4DNA"
"""
with open(filename, 'a') as file: # 'a' 模式表示追加写入
file.write(cell_template)
def append_center_cell_config(filename, cell_number, x, y, z, nucleus_radius, nucleus_radiusX, nucleus_radiusY, nucleus_radiusZ):
"""
动态生成每个细胞的配置，并追加到文件中
"""
cell_template = f"""
#### Cell {cell_number} ####
#### MEMBRANE ####
s:Ge/Membrane{cell_number}/Type="TsEllipsoidalShell"
s:Ge/Membrane{cell_number}/Material="G4_Lu"
s:Ge/Membrane{cell_number}/Parent="World"
d:Ge/Membrane{cell_number}/OuterX= 28.3175 um
d:Ge/Membrane{cell_number}/OuterY= 12.4575 um
d:Ge/Membrane{cell_number}/OuterZ= 2.3575 um
d:Ge/Membrane{cell_number}/InnerX= 28.31 um
d:Ge/Membrane{cell_number}/InnerY= 12.45 um
d:Ge/Membrane{cell_number}/InnerZ= 2.35 um
s:Ge/Membrane{cell_number}/Color = "white"
d:Ge/Membrane{cell_number}/transX= {x} um
d:Ge/Membrane{cell_number}/transY= {y} um
d:Ge/Membrane{cell_number}/transZ= {z} um
#### CYTOPLASM ####
s:Ge/Cytoplasm{cell_number}/Type="TsEllipsoidalShell"
s:Ge/Cytoplasm{cell_number}/Material="G4_Lu"
s:Ge/Cytoplasm{cell_number}/Parent="World"
d:Ge/Cytoplasm{cell_number}/OuterX= 28.31 um
d:Ge/Cytoplasm{cell_number}/OuterY= 12.45 um
d:Ge/Cytoplasm{cell_number}/OuterZ= 2.35 um
d:Ge/Cytoplasm{cell_number}/InnerX= 12 um
d:Ge/Cytoplasm{cell_number}/InnerY= 8.5 um
d:Ge/Cytoplasm{cell_number}/InnerZ= 1.9 um
s:Ge/Cytoplasm{cell_number}/Color = "green"
d:Ge/Cytoplasm{cell_number}/transX= {x} um
d:Ge/Cytoplasm{cell_number}/transY= {y} um
d:Ge/Cytoplasm{cell_number}/transZ= {z} um
#### Nucleus ####
s:Ge/Nucleus{cell_number}/Type = "TsEllipsoid"
s:Ge/Nucleus{cell_number}/Parent = "World"
s:Ge/Nucleus{cell_number}/Material = "G4_WATER"
d:Ge/Nucleus{cell_number}/Dx = {nucleus_radiusX} um
d:Ge/Nucleus{cell_number}/Dy = {nucleus_radiusY} um
d:Ge/Nucleus{cell_number}/Dz = {nucleus_radiusZ} um
d:Ge/Nucleus{cell_number}/TransX = {x} um
d:Ge/Nucleus{cell_number}/TransY = {y} um
d:Ge/Nucleus{cell_number}/TransZ = {z} um
s:Ge/Nucleus{cell_number}/Color = "skyblue"
s:Sc/PhaseSpaceAtVacFilm/Quantity = "PhaseSpace"
b:Sc/PhaseSpaceAtVacFilm/OutputToConsole = "True"
s:Sc/PhaseSpaceAtVacFilm/Surface = "Nucleus{cell_number}/OuterCurvedSurface"
s:Sc/PhaseSpaceAtVacFilm/OutputType = "ASCII" # ASCII, Binary, Limited or ROOT
s:Sc/PhaseSpaceAtVacFilm/OutputFile = "ASCIIOutput"
i:Sc/PhaseSpaceAtVacFilm/OutputBufferSize = 1000
#s:Sc/PhaseSpaceAtVacFilm/OnlyIncludeParticlesGoing = "In"
b:Sc/PhaseSpaceAtVacFilm/IncludeTOPASTime = "True"
b:Sc/PhaseSpaceAtVacFilm/IncludeTimeOfFlight = "True"
b:Sc/PhaseSpaceAtVacFilm/IncludeRunID = "True"
b:Sc/PhaseSpaceAtVacFilm/IncludeEventID = "True"
b:Sc/PhaseSpaceAtVacFilm/IncludeTrackID = "True"
b:Sc/PhaseSpaceAtVacFilm/IncludeParentID = "True"
b:Sc/PhaseSpaceAtVacFilm/IncludeCreatorProcess = "True"
b:Sc/PhaseSpaceAtVacFilm/IncludeVertexInfo = "True"
b:Sc/PhaseSpaceAtVacFilm/IncludeSeed = "True"
#sv:Sc/PhaseSpaceAtVacFilm/OnlyIncludeParticlesNamed = 1 "Proton"
#d:Sc/MyScorer/OnlyIncludeParticlesWithInitialKEAbove = 100. MeV
s:Sc/PhaseSpaceAtVacFilm/IfOutputFileAlreadyExists = "Overwrite"
"""
with open(filename, 'a') as file: # 'a' 模式表示追加写入
file.write(cell_template)
def create_cells_in_box(n, HLX, HLY, HLZ, cell_radius_x, cell_radius_y, cell_radius_z, nucleus_radius, nucleus_radiusX, nucleus_radiusY, nucleus_radiusZ, InnerRadius, OuterRadius, HalfHeight):
"""
生成 n 个细胞的配置文件，所有细胞写在一个文件中
"""
filename = "./topas_file/topas_cells.txt" # 输出文件
# 写入通用的配置（World 和其他物理、化学参数）
write_common_config(filename, InnerRadius, OuterRadius, HalfHeight, HLX, HLY, HLZ)
# 计算可放置的细胞数量
numCellsX = int(2 * HLX / (2 * cell_radius_x))
numCellsY = int(2 * HLY / (2 * cell_radius_y))
numCellsZ = int(2 * HLZ / (2 * cell_radius_z))
cell_count = 0
center_index= math.ceil(n / 2)
for i in range(numCellsX):
for j in range(numCellsY):
for k in range(numCellsZ):
if cell_count >= n:
break
x = -HLX + cell_radius_x + i * 2 * cell_radius_x
y = -HLY + cell_radius_y + j * 2 * cell_radius_y
z = -HLZ + cell_radius_z + k * 2 * cell_radius_z
cell_number= cell_count + 1
# 追加写入每个细胞的参数
if cell_number == center_index:
append_center_cell_config(filename, cell_count + 1, x, y, z, nucleus_radius, nucleus_radiusX, nucleus_radiusY, nucleus_radiusZ)
print(f"Generated **Center** cell {cell_count + 1} at position ({x}, {y}, {z})")
else:
append_cell_config(filename, cell_count + 1, x, y, z, nucleus_radius, nucleus_radiusX, nucleus_radiusY, nucleus_radiusZ)
print(f"Generated cell {cell_count + 1} at position ({x}, {y}, {z})")
cell_count += 1
print("x方向细胞个数：{}个，y方向细胞个数：{}个，z方向的细胞个数：{}个".format(numCellsX, numCellsY, numCellsZ))
# Example usage
n_cells = 50 # 需要生成的细胞数目
HLX = 141.5875 # 外部方框X方向半长
HLY = 124.575 # 外部方框Y方向半长
HLZ = 2.3575 # 外部方框Z方向半长
cell_radius_x = 28.3175 # 每个细胞 x方向的半长
cell_radius_y = 12.4575 # 每个细胞 y方向的半长
cell_radius_z = 2.3575 # 每个细胞 z方向的半长
nucleus_radius = 12 # 细胞核半径
nucleus_radiusX = 12 # 细胞核半径
nucleus_radiusY = 8.5
nucleus_radiusZ = 1.9
# 以下长度单位为mm
InnerRadius = 0 # 内半径，默认0，表示我们要的是个完整的圆柱
OuterRadius = 0.44 # 外半径，圆柱底面的半径
HalfHeight = 0.44 # 圆柱的半高，圆柱的高是这个的两倍
create_cells_in_box(n_cells, HLX, HLY, HLZ, cell_radius_x, cell_radius_y, cell_radius_z, nucleus_radius, nucleus_radiusX, nucleus_radiusY, nucleus_radiusZ, InnerRadius, OuterRadius, HalfHeight)