def set_geometry(input_file):
"""
Add simple geometry, consisting of water target, surrounded with air.
:param input_file: Fluka input file object, will be modified
:return:
"""
# geometry description starts here http://www.fluka.org/fluka.php?id=man_onl&sub=38
geo_begin = Card("GEOBEGIN", comment="geometry description starts here")
geo_begin.setSdum(
"COMBNAME"
) # SDUM = COMBNAME : Combinatorial geometry is used in free format,
# and names can be used instead of body and region numbers
input_file.addCard(geo_begin)
# list of bodies, see http://www.fluka.org/fluka.php?id=man_onl&sub=94
# 1. black body sphere, centered around (0,0,0), radius 10m
blkbody_sph = Card("SPH", comment="black body sphere")
blkbody_sph.setSdum("blkbody") # SDUM - name of the body
blkbody_sph.setWhat(
1, 0.0) # WHAT(1) - x-coordinate of the centre (in free format)
blkbody_sph.setWhat(
2, 0.0) # WHAT(2) - y-coordinate of the centre (in free format)
blkbody_sph.setWhat(
3, 0.0) # WHAT(3) - z-coordinate of the centre (in free format)
blkbody_sph.setWhat(4, 10000.0) # WHAT(4) - radius (in free format)
input_file.addCard(blkbody_sph)
# 2. air sphere, centered around (0,0,0), radius 1m
air_sph = blkbody_sph.clone() # see comments above
air_sph.setSdum("air")
air_sph.setWhat(4, 100.0)
air_sph.setComment("air shpere")
input_file.addCard(air_sph)
# 3. target cylinder, bottom center at (0,0,0), height 10cm, radius 5cm, positioned along Z axis
target_rcc = Card("RCC", comment="target cylinder")
target_rcc.setSdum("target") # SDUM - name of the body
target_rcc.setWhat(
1, 0.0
) # WHAT(1) - x-coordinate of the centre of circular plane, bottom (in free format)
target_rcc.setWhat(
2, 0.0
) # WHAT(2) - y-coordinate of the centre of circular plane, bottom (in free format)
target_rcc.setWhat(
3, 0.0
) # WHAT(3) - z-coordinate of the centre of circular plane, bottom (in free format)
target_rcc.setWhat(
4, 0.0) # WHAT(4) - x-coordinate of the height vector (in free format)
target_rcc.setWhat(
5, 0.0) # WHAT(5) - y-coordinate of the height vector (in free format)
target_rcc.setWhat(
6,
10.0) # WHAT(6) - z-coordinate of the height vector (in free format)
target_rcc.setWhat(7, 5.0) # WHAT(7) - radius (in free format)
input_file.addCard(target_rcc)
# end of body region
input_file.addCard(Card("END"))
# list of regions, see http://www.fluka.org/fluka.php?id=man_onl&sub=94
# 1. outer black body region
blk_body_zone = Card("REGION")
blk_body_zone.setComment("outer black body region")
blk_body_zone.setSdum("Z_BBODY") # SDUM - name of the region
blk_body_zone.addZone('+blkbody -air') # logical formula
input_file.addCard(blk_body_zone)
# 2. inner air region
air_zone = Card("REGION")
air_zone.setComment("inner air region")
air_zone.setSdum("Z_AIR")
air_zone.addZone('+air -target')
input_file.addCard(air_zone)
# 3. target region
target_zone = Card("REGION")
target_zone.setComment("target region")
target_zone.setSdum("Z_TARGET")
target_zone.addZone('+target')
input_file.addCard(target_zone)
# end of target region
input_file.addCard(Card("END"))
# geometry description ends here http://www.fluka.org/fluka.php?id=man_onl&sub=39
geo_end = Card("GEOEND", comment="geometry description ends here")
input_file.addCard(geo_end)
# material assignment, see http://www.fluka.org/fluka.php?id=man_onl&sub=10
blk_body_mat = Card("ASSIGNMA")
blk_body_mat.setWhat(
1, 'BLCKHOLE') # WHAT(1) - material index, or material name
blk_body_mat.setWhat(2, blk_body_zone.sdum(
)) # WHAT(2) - lower bound (or name corresponding to it) of the region
# indices with material index equal or corresponding to WHAT(1).
# upper bound is set to WHAT(2) by default
input_file.addCard(blk_body_mat)
air_mat = Card("ASSIGNMA") # see comments above
air_mat.setWhat(1, 'AIR')
air_mat.setWhat(2, air_zone.sdum())
input_file.addCard(air_mat)
target_mat = Card("ASSIGNMA") # see comments above
target_mat.setWhat(1, 'WATER')
target_mat.setWhat(2, target_zone.sdum())
input_file.addCard(target_mat)
def add_scoring(input_file):
"""
Add scoring of deposited energy and neutron fluence on 4 different mesh types (8 scorers in total)
:param input_file: Fluka input_file object, will be modified
:return:
"""
# Dictionary of scoring type (generalized particle)
# keys will be used as parts of output filenames, this is why they are short
# for list of all possible generalized particles, see: http://www.fluka.org/fluka.php?id=man_onl&sub=7
det_types = {"en": "ENERGY", "n": "NEUTRON"}
# Define 4 different scoring meshes (1D and 2D), using pymchelper classes
msh_z = CarthesianMesh()
msh_z.set_axis(axis_no=0, start=-0.5, stop=0.5, nbins=1)
msh_z.set_axis(axis_no=1, start=-0.5, stop=0.5, nbins=1)
msh_z.set_axis(axis_no=2, start=0.0, stop=5.0, nbins=500)
msh_xy = CarthesianMesh()
msh_xy.set_axis(axis_no=0, start=-5.0, stop=5.0, nbins=500)
msh_xy.set_axis(axis_no=1, start=-5.0, stop=5.0, nbins=500)
msh_xy.set_axis(axis_no=2, start=2.8, stop=2.9, nbins=1)
msh_yz = CarthesianMesh()
msh_yz.set_axis(axis_no=0, start=-0.1, stop=0.1, nbins=1)
msh_yz.set_axis(axis_no=1, start=-5.0, stop=5.0, nbins=500)
msh_yz.set_axis(axis_no=2, start=0.0, stop=5.0, nbins=500)
msh_zx = CarthesianMesh()
msh_zx.set_axis(axis_no=0, start=-5.0, stop=5.0, nbins=500)
msh_zx.set_axis(axis_no=1, start=-0.1, stop=0.1, nbins=1)
msh_zx.set_axis(axis_no=2, start=0.0, stop=5.0, nbins=500)
mesh_types = {"z": msh_z, "xy": msh_xy, "yz": msh_yz, "zx": msh_zx}
# Fluka is using concept of output unit numbers, this is starting number,
# for each new scorer will be decreased by one
output_unit = -21
# scoring, see http://www.fluka.org/fluka.php?id=man_onl&sub=84
# template cards for USRBIN scorers:
usrbin_card1 = Card("USRBIN")
usrbin_card1.setWhat(
1, 0.0
) # WHAT(1) - type of binning selected (0.0 : Mesh Cartesian, no sym.)
usrbin_card2 = Card("USRBIN")
usrbin_card2.setSdum("&") # continuation card
# loop over all possible detectors and meshes
for det_type, mesh_type in product(det_types.keys(), mesh_types.keys()):
# make copies of template cards
card1 = usrbin_card1.clone()
card2 = usrbin_card2.clone()
# generate comment
card1.setComment("scoring {:s} on mesh {:s}".format(
det_types[det_type], mesh_type))
card1.setSdum("{:s}_{:s}".format(
det_type, mesh_type)) # SDUM - identifying the binning detector
card1.setWhat(
2, det_types[det_type]
) # WHAT(2) - particle (or particle family) type to be scored
card1.setWhat(
3, output_unit
) # WHAT(3) - output unit (> 0.0 : formatted data, < 0.0 : unformatted data)
msh = mesh_types[mesh_type]
card1.setWhat(
4, msh.axis[0].stop) # WHAT(4) - For Cartesian binning: Xmax
card1.setWhat(
5, msh.axis[1].stop) # WHAT(5) - For Cartesian binning: Ymax
card1.setWhat(
6, msh.axis[2].stop) # WHAT(6) - For Cartesian binning: Zmax
card2.setWhat(
1, msh.axis[0].start) # WHAT(1) - For Cartesian binning: Xmin
card2.setWhat(
2, msh.axis[1].start) # WHAT(2) - For Cartesian binning: Ymin
card2.setWhat(
3, msh.axis[2].start) # WHAT(3) - For Cartesian binning: Zmin
card2.setWhat(4, msh.axis[0].nbins
) # WHAT(4) - For Cartesian binning: number of X bins
card2.setWhat(5, msh.axis[1].nbins
) # WHAT(5) - For Cartesian binning: number of Y bins
card2.setWhat(6, msh.axis[2].nbins
) # WHAT(6) - For Cartesian binning: number of Z bins
output_unit -= 1
# finally add generated cards to input structure
input_file.addCard(card1)
card1.appendWhats(card2.whats()[1:])
def generate_fluka_file(output_filename):
"""
Compose programatically fl_sim.inp Fluka input file
with many combinations of estimator and mesh types.
Fluka input file is saved in the default format (as Flair saves it), namely:
- fixed format is used everywhere, except:
- free format for geometry, forced by COMBNAME paramater in GEOBEGIN card
- names instead of numbers are used as identifies of particles, materials and regions
:param output_filename: output filename
:return: generated Fluka object
"""
# create empty input file object
input_configuration = Input.Input()
# add title
input_configuration.addCard(Card("TITLE", extra="proton beam simulation"))
# add default physics settings
input_configuration.addCard(
Card("DEFAULTS",
what=["HADROTHE"],
comment="default physics for hadron therapy"))
# add beam characteristics, see http://www.fluka.org/fluka.php?id=man_onl&sub=12
beam = Card("BEAM", comment="beam characteristics")
beam.setSdum("PROTON") # SDUM = beam particle name.
beam.setWhat(1,
-0.06) # WHAT(1) < 0.0 : average beam kinetic energy in GeV
beam.setWhat(
4, 2.0
) # WHAT(4) > 0.0 : If WHAT(6) > 0.0, beam width in x-direction in cm,
# The beam profile is assumed to be rectangular
beam.setWhat(
5, 2.0
) # WHAT(5) > 0.0 : If WHAT(6) > 0.0, beam width in y-direction in cm.
# The beam profile is assumed to be rectangular.
input_configuration.addCard(
Card("BEAM",
what=["PROTON", -0.06, 0.0, 0.0, -2.0, -2.0],
comment="beam source"))
# add beam source position, see http://www.fluka.org/fluka.php?id=man_onl&sub=14
beam_pos = Card("BEAMPOS", comment="beam source position")
beam_pos.setWhat(1, 0.0) # WHAT(1) = x-coordinate of the spot centre.
beam_pos.setWhat(2, 0.0) # WHAT(2) = y-coordinate of the spot centre.
beam_pos.setWhat(3, -100.0) # WHAT(3) = z-coordinate of the spot centre.
input_configuration.addCard(beam_pos)
# set geometry, in separate function
set_geometry(input_configuration)
# add scoring, in separate function
add_scoring(input_configuration)
# random number generator settings, see http://www.fluka.org/fluka.php?id=man_onl&sub=66
rng_card = Card("RANDOMIZ")
rng_card.setComment("random number generator settings")
rng_card.setWhat(
2, 137
) # Different numbers input as WHAT(2) will initialise different and independent
# random number sequences, allowing the user to run several jobs in parallel for the same problem
input_configuration.addCard(rng_card)
# number of particles to simulate, see http://www.fluka.org/fluka.php?id=man_onl&sub=73
start_card = Card("START")
start_card.setComment("number of particles to simulate")
start_card.setWhat(
1, 1000
) # WHAT(1) - maximum number of primary histories simulated in the run
input_configuration.addCard(start_card)
# end of input configuration http://www.fluka.org/fluka.php?id=man_onl&sub=76
input_configuration.addCard(Card("STOP"))
# write file to the disk
input_configuration.write(output_filename)
return input_configuration
def set_geometry(input_file):
"""
Add simple geometry, consisting of water target, surrounded with air.
:param input_file: Fluka input file object, will be modified
:return:
"""
# geometry description starts here http://www.fluka.org/fluka.php?id=man_onl&sub=38
geo_begin = Card("GEOBEGIN", comment="geometry description starts here")
geo_begin.setSdum("COMBNAME") # SDUM = COMBNAME : Combinatorial geometry is used in free format,
# and names can be used instead of body and region numbers
input_file.addCard(geo_begin)
# list of bodies, see http://www.fluka.org/fluka.php?id=man_onl&sub=94
# 1. black body sphere, centered around (0,0,0), radius 10m
blkbody_sph = Card("SPH", comment="black body sphere")
blkbody_sph.setSdum("blkbody") # SDUM - name of the body
blkbody_sph.setWhat(1, 0.0) # WHAT(1) - x-coordinate of the centre (in free format)
blkbody_sph.setWhat(2, 0.0) # WHAT(2) - y-coordinate of the centre (in free format)
blkbody_sph.setWhat(3, 0.0) # WHAT(3) - z-coordinate of the centre (in free format)
blkbody_sph.setWhat(4, 10000.0) # WHAT(4) - radius (in free format)
input_file.addCard(blkbody_sph)
# 2. air sphere, centered around (0,0,0), radius 1m
air_sph = blkbody_sph.clone() # see comments above
air_sph.setSdum("air")
air_sph.setWhat(4, 100.0)
air_sph.setComment("air shpere")
input_file.addCard(air_sph)
# 3. target cylinder, bottom center at (0,0,0), height 10cm, radius 5cm, positioned along Z axis
target_rcc = Card("RCC", comment="target cylinder")
target_rcc.setSdum("target") # SDUM - name of the body
target_rcc.setWhat(1, 0.0) # WHAT(1) - x-coordinate of the centre of circular plane, bottom (in free format)
target_rcc.setWhat(2, 0.0) # WHAT(2) - y-coordinate of the centre of circular plane, bottom (in free format)
target_rcc.setWhat(3, 0.0) # WHAT(3) - z-coordinate of the centre of circular plane, bottom (in free format)
target_rcc.setWhat(4, 0.0) # WHAT(4) - x-coordinate of the height vector (in free format)
target_rcc.setWhat(5, 0.0) # WHAT(5) - y-coordinate of the height vector (in free format)
target_rcc.setWhat(6, 10.0) # WHAT(6) - z-coordinate of the height vector (in free format)
target_rcc.setWhat(7, 5.0) # WHAT(7) - radius (in free format)
input_file.addCard(target_rcc)
# end of body region
input_file.addCard(Card("END"))
# list of regions, see http://www.fluka.org/fluka.php?id=man_onl&sub=94
# 1. outer black body region
blk_body_zone = Card("REGION")
blk_body_zone.setComment("outer black body region")
blk_body_zone.setSdum("Z_BBODY") # SDUM - name of the region
blk_body_zone.addZone('+blkbody -air') # logical formula
input_file.addCard(blk_body_zone)
# 2. inner air region
air_zone = Card("REGION")
air_zone.setComment("inner air region")
air_zone.setSdum("Z_AIR")
air_zone.addZone('+air -target')
input_file.addCard(air_zone)
# 3. target region
target_zone = Card("REGION")
target_zone.setComment("target region")
target_zone.setSdum("Z_TARGET")
target_zone.addZone('+target')
input_file.addCard(target_zone)
# end of target region
input_file.addCard(Card("END"))
# geometry description ends here http://www.fluka.org/fluka.php?id=man_onl&sub=39
geo_end = Card("GEOEND", comment="geometry description ends here")
input_file.addCard(geo_end)
# material assignment, see http://www.fluka.org/fluka.php?id=man_onl&sub=10
blk_body_mat = Card("ASSIGNMA")
blk_body_mat.setWhat(1, 'BLCKHOLE') # WHAT(1) - material index, or material name
blk_body_mat.setWhat(2, blk_body_zone.sdum()) # WHAT(2) - lower bound (or name corresponding to it) of the region
# indices with material index equal or corresponding to WHAT(1).
# upper bound is set to WHAT(2) by default
input_file.addCard(blk_body_mat)
air_mat = Card("ASSIGNMA") # see comments above
air_mat.setWhat(1, 'AIR')
air_mat.setWhat(2, air_zone.sdum())
input_file.addCard(air_mat)
target_mat = Card("ASSIGNMA") # see comments above
target_mat.setWhat(1, 'WATER')
target_mat.setWhat(2, target_zone.sdum())
input_file.addCard(target_mat)
def add_scoring(input_file):
"""
Add scoring of deposited energy and neutron fluence on 4 different mesh types (8 scorers in total)
:param input_file: Fluka input_file object, will be modified
:return:
"""
# Dictionary of scoring type (generalized particle)
# keys will be used as parts of output filenames, this is why they are short
# for list of all possible generalized particles, see: http://www.fluka.org/fluka.php?id=man_onl&sub=7
det_types = {"en": "ENERGY", "n": "NEUTRON"}
# Define 4 different scoring meshes (1D and 2D), using pymchelper classes
msh_z = CarthesianMesh()
msh_z.set_axis(axis_no=0, start=-0.5, stop=0.5, nbins=1)
msh_z.set_axis(axis_no=1, start=-0.5, stop=0.5, nbins=1)
msh_z.set_axis(axis_no=2, start=0.0, stop=5.0, nbins=500)
msh_xy = CarthesianMesh()
msh_xy.set_axis(axis_no=0, start=-5.0, stop=5.0, nbins=500)
msh_xy.set_axis(axis_no=1, start=-5.0, stop=5.0, nbins=500)
msh_xy.set_axis(axis_no=2, start=2.8, stop=2.9, nbins=1)
msh_yz = CarthesianMesh()
msh_yz.set_axis(axis_no=0, start=-0.1, stop=0.1, nbins=1)
msh_yz.set_axis(axis_no=1, start=-5.0, stop=5.0, nbins=500)
msh_yz.set_axis(axis_no=2, start=0.0, stop=5.0, nbins=500)
msh_zx = CarthesianMesh()
msh_zx.set_axis(axis_no=0, start=-5.0, stop=5.0, nbins=500)
msh_zx.set_axis(axis_no=1, start=-0.1, stop=0.1, nbins=1)
msh_zx.set_axis(axis_no=2, start=0.0, stop=5.0, nbins=500)
mesh_types = {"z": msh_z, "xy": msh_xy, "yz": msh_yz, "zx": msh_zx}
# Fluka is using concept of output unit numbers, this is starting number,
# for each new scorer will be decreased by one
output_unit = -21
# scoring, see http://www.fluka.org/fluka.php?id=man_onl&sub=84
# template cards for USRBIN scorers:
usrbin_card1 = Card("USRBIN")
usrbin_card1.setWhat(1, 0.0) # WHAT(1) - type of binning selected (0.0 : Mesh Cartesian, no sym.)
usrbin_card2 = Card("USRBIN")
usrbin_card2.setSdum("&") # continuation card
# loop over all possible detectors and meshes
for det_type, mesh_type in product(det_types.keys(), mesh_types.keys()):
# make copies of template cards
card1 = usrbin_card1.clone()
card2 = usrbin_card2.clone()
# generate comment
card1.setComment("scoring {:s} on mesh {:s}".format(det_types[det_type], mesh_type))
card1.setSdum("{:s}_{:s}".format(det_type, mesh_type)) # SDUM - identifying the binning detector
card1.setWhat(2, det_types[det_type]) # WHAT(2) - particle (or particle family) type to be scored
card1.setWhat(3, output_unit) # WHAT(3) - output unit (> 0.0 : formatted data, < 0.0 : unformatted data)
msh = mesh_types[mesh_type]
card1.setWhat(4, msh.axis[0].stop) # WHAT(4) - For Cartesian binning: Xmax
card1.setWhat(5, msh.axis[1].stop) # WHAT(5) - For Cartesian binning: Ymax
card1.setWhat(6, msh.axis[2].stop) # WHAT(6) - For Cartesian binning: Zmax
card2.setWhat(1, msh.axis[0].start) # WHAT(1) - For Cartesian binning: Xmin
card2.setWhat(2, msh.axis[1].start) # WHAT(2) - For Cartesian binning: Ymin
card2.setWhat(3, msh.axis[2].start) # WHAT(3) - For Cartesian binning: Zmin
card2.setWhat(4, msh.axis[0].nbins) # WHAT(4) - For Cartesian binning: number of X bins
card2.setWhat(5, msh.axis[1].nbins) # WHAT(5) - For Cartesian binning: number of Y bins
card2.setWhat(6, msh.axis[2].nbins) # WHAT(6) - For Cartesian binning: number of Z bins
output_unit -= 1
# finally add generated cards to input structure
input_file.addCard(card1)
card1.appendWhats(card2.whats()[1:])
def generate_fluka_file(output_filename):
"""
Compose programatically fl_sim.inp Fluka input file
with many combinations of detector and mesh types.
Fluka input file is saved in the default format (as Flair saves it), namely:
- fixed format is used everywhere, except:
- free format for geometry, forced by COMBNAME paramater in GEOBEGIN card
- names instead of numbers are used as identifies of particles, materials and regions
:param output_filename: output filename
:return: generated Fluka object
"""
# create empty input file object
input_configuration = Input.Input()
# add title
input_configuration.addCard(Card("TITLE", extra="proton beam simulation"))
# add default physics settings
input_configuration.addCard(Card("DEFAULTS", what=["HADROTHE"], comment="default physics for hadron therapy"))
# add beam characteristics, see http://www.fluka.org/fluka.php?id=man_onl&sub=12
beam = Card("BEAM", comment="beam characteristics")
beam.setSdum("PROTON") # SDUM = beam particle name.
beam.setWhat(1, -0.06) # WHAT(1) < 0.0 : average beam kinetic energy in GeV
beam.setWhat(4, 2.0) # WHAT(4) > 0.0 : If WHAT(6) > 0.0, beam width in x-direction in cm,
# The beam profile is assumed to be rectangular
beam.setWhat(5, 2.0) # WHAT(5) > 0.0 : If WHAT(6) > 0.0, beam width in y-direction in cm.
# The beam profile is assumed to be rectangular.
input_configuration.addCard(Card("BEAM", what=["PROTON", -0.06, 0.0, 0.0, -2.0, -2.0], comment="beam source"))
# add beam source position, see http://www.fluka.org/fluka.php?id=man_onl&sub=14
beam_pos = Card("BEAMPOS", comment="beam source position")
beam_pos.setWhat(1, 0.0) # WHAT(1) = x-coordinate of the spot centre.
beam_pos.setWhat(2, 0.0) # WHAT(2) = y-coordinate of the spot centre.
beam_pos.setWhat(3, -100.0) # WHAT(3) = z-coordinate of the spot centre.
input_configuration.addCard(beam_pos)
# set geometry, in separate function
set_geometry(input_configuration)
# add scoring, in separate function
add_scoring(input_configuration)
# random number generator settings, see http://www.fluka.org/fluka.php?id=man_onl&sub=66
rng_card = Card("RANDOMIZ")
rng_card.setComment("random number generator settings")
rng_card.setWhat(2, 137) # Different numbers input as WHAT(2) will initialise different and independent
# random number sequences, allowing the user to run several jobs in parallel for the same problem
input_configuration.addCard(rng_card)
# number of particles to simulate, see http://www.fluka.org/fluka.php?id=man_onl&sub=73
start_card = Card("START")
start_card.setComment("number of particles to simulate")
start_card.setWhat(1, 1000) # WHAT(1) - maximum number of primary histories simulated in the run
input_configuration.addCard(start_card)
# end of input configuration http://www.fluka.org/fluka.php?id=man_onl&sub=76
input_configuration.addCard(Card("STOP"))
# write file to the disk
input_configuration.write(output_filename)
return input_configuration