diff --git a/HEN_HOUSE/doc/src/irs.bib b/HEN_HOUSE/doc/src/irs.bib index f8b6f8463..1c05d9777 100644 --- a/HEN_HOUSE/doc/src/irs.bib +++ b/HEN_HOUSE/doc/src/irs.bib @@ -28993,6 +28993,17 @@ @article{AR08 pages={1527--43} } +@article{AR12, + author = {E. S. M. Ali and D. W. O. Rogers}, + title = {{Implementation of photonuclear attenuation in EGSnrc}}, + journal = {Carleton University Technical Report CLRP 12-01}, + year = {2012}, + url = {http://www.physics.carleton.ca/clrp/photonuclear}, + keywords = {EGSnrc BEAMnrc photonuclear}, + notes = {Describes implementation of photonuclear effect }, + location = { } +} + @article{MK08, author={Ernesto Mainegra-Hing and Iwan Kawrakow}, title={{Novel approach for the Monte Carlo calculation of free-air chamber correction factors}}, diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/figures/hen_house.fig b/HEN_HOUSE/doc/src/pirs509a-beamnrc/figures/hen_house.fig index 4baf818da..f2e63a616 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/figures/hen_house.fig +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/figures/hen_house.fig @@ -1,4 +1,4 @@ -#FIG 3.2 +#FIG 3.2 Produced by xfig version 3.2.7a Landscape Center Metric @@ -7,146 +7,118 @@ A4 Single -2 1200 2 -6 1032 6894 4302 9780 -6 1368 9364 4113 9780 +6 2272 6781 3167 7207 2 4 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a/HEN_HOUSE/doc/src/pirs509a-beamnrc/figures/omega_home.pdf b/HEN_HOUSE/doc/src/pirs509a-beamnrc/figures/omega_home.pdf index abc504e8c..a944d59be 100644 Binary files a/HEN_HOUSE/doc/src/pirs509a-beamnrc/figures/omega_home.pdf and b/HEN_HOUSE/doc/src/pirs509a-beamnrc/figures/omega_home.pdf differ diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM0.inp b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM0.inp index eb62aea23..a9908f1ee 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM0.inp +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM0.inp @@ -12,7 +12,7 @@ *********** In many CMs, the region about the central-axis or at the front or back of the CM, is assumed to be this medium. - It is thought of and refered to as air, but can be anything. + It is thought of and referred to as air, but can be anything. Default is VACUUM. MEDIUM must exactly match name in pegs4dat ----------------------------------------------------------------------------- \end{verbatim} diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM13.inp b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM13.inp index 937f21728..842ba80bb 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM13.inp +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM13.inp @@ -76,6 +76,6 @@ Next record (If ISOURC=21) *********** SPCNAM FILENAME (with EXT) contains phase space information - (maximum of 80 characters) + (maximum of 256 characters) ------------------------------------------------------------------------ \end{verbatim} diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM14.inp b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM14.inp index a70d1b616..dee56f292 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM14.inp +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM14.inp @@ -9,6 +9,6 @@ Next record (If ISOURC=31) *********** SPCNAM FILENAME (with EXT) contains information on beam model - (maximum of 80 characters) + (maximum of 256 characters) -------------------------------------------------------------------------- \end{verbatim} diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM15.inp b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM15.inp index f8275695d..3bc88bc10 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM15.inp +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM15.inp @@ -16,7 +16,7 @@ Next Record (IF MONOEN = 1) *********** - FILNAM(80A1) FILENAME(WITH EXT) contains spectrum information + FILNAM(256A1) FILENAME(WITH EXT) contains spectrum information which must be in NRC's ensrcV format. _______________________________________________________ FILE FORMAT: diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM2.inp b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM2.inp index 7cb5b3658..d20174164 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM2.inp +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM2.inp @@ -16,10 +16,8 @@ IBRSPL = 0 no brem splitting = 1 with uniform brem splitting = 2 with directional bremsstrahlung splitting (DBS) - = 29 with selective bremsstrahlung splitting - NBRSPL = (if IBRSPL = 1 or 2) brem splitting number AND + NBRSPL = brem splitting number AND annihilation splitting number (if IRRLTT=2) - = (if IBRSPL = 29) max. brem splitting number IRRLTT = 0 no Russian Roulette (the default). Also, no annihilation or higher-order splitting. = 1 no longer used. This defaults to IRRLTT=2 @@ -29,8 +27,7 @@ If the surviving particle undergoes another (higher- order) bremsstrahlung event or an annihilation, resulting photons are split again by NBRSPL for - IBRSPL=1. (ie uniform splitting) and by NMIN - for IBRSPL=29 (i.e. selective brem splitting) + IBRSPL=1. (ie uniform splitting) Note: The input IRRLTT is automatically set to 0 if IBRSPL=2 This is because Directional Bremsstrahlung Splitting @@ -42,24 +39,14 @@ of times as soon as they cross the arbitrary splitting plane at the top of this CM #. - Next record (if IBRSPL=2 or 29) + Next record (if IBRSPL=2) *********** - FS,SSD,(NMIN),(ICM_DBS,ZPLANE_DBS,IRAD_DBS,ZRR_DBS) (3F12.0 or 6F12.0) + FS,SSD,ICM_DBS,ZPLANE_DBS,IRAD_DBS,ZRR_DBS (6F12.0) FS = radius of field (cm) into which bremsstrahlung photons - must be directed if they are to be split (IBRSPL=2) - or length of side of square field (cm) in which - selective bremsstrahlung splitting probabilities are - calculated for IBRSPL=29. + must be directed if they are to be split. SSD = distance from bremsstrahlung target where FS - is defined. FS and SSD only define an angle which is - used (IBRSPL=29). - NMIN = background bremsstrahlung splitting number (ie even - outside the field, bremsstrahlung events will be - split into NMIN photons). Also equal to the - higher generation brem splitting number - and annihilation photon splitting number if IRRLTT=2. - NMIN is only required for IBRSPL=29. + is defined. ICM_DBS and These are only required to define the splitting plane if IBRSPL=2. As soon as ZPLANE_DBS a fat electron reaches ZPLANE_DBS within CM number diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM21.inp b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM21.inp index 7badd23d0..d1588845a 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM21.inp +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM21.inp @@ -20,7 +20,7 @@ *********** SPCNAM FILENAME (with EXT) containing description of the radial intensity distribution of the incident particles - (maximum 80 characters) + (maximum 256 characters) _______________________________________________________ FILE FORMAT for SPCNAM: NRDIST diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM24.inp b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM24.inp index 26b83cfda..29e815ace 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM24.inp +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM24.inp @@ -11,13 +11,13 @@ All input associated with selection of EGSnrc transport parameters is not crucial for the execution as there are default values set. Therefore, if some of the input options in this section are - missing/misspelled, this will be ignored and defualt parameter assumed + missing/misspelled, this will be ignored and default parameters assumed. As the transport parameter input routine uses get_inputs, a lot of error/warning messages may be produced on UNIT 15, though. If you don't have the intention of changing default settings, simply ignore the error messages. - The delimeters are + The delimiters are :start mc transport parameter: :stop mc transport parameter: diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM25.inp b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM25.inp index 4472d169d..0bf85d458 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM25.inp +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM25.inp @@ -1,12 +1,12 @@ \begin{verbatim} Global ECUT= Global (in all regions) electron transport cut - off energy (in MeV). If this imput is missing, + off energy (in MeV). If this input is missing, or is < ECUTIN from the main BEAMnrc inputs (See above) then ECUTIN is used for Global ECUT. Global ECUT defaults to AE(medium). [ ECUT ] Global PCUT= Global (in all regions) photon transport cut - off energy (in MeV). If this imput is missing, + off energy (in MeV). If this input is missing, or is < PCUTIN from the main BEAMnrc inputs (See above) then PCUTIN is used for Global PCUT. Global PCUT defaults to AP(medium). diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM26.inp b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM26.inp index 86fdc2ca6..4f569d009 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM26.inp +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM26.inp @@ -2,7 +2,7 @@ ESTEPE= Maximum fractional energy loss per step. Note that this is a global option only, no region-by-region setting is possible. If missing, - the defualt is 0.25 (25%). + the default is 0.25 (25%). [ ESTEPE ] XImax= Maximum first elastic scattering moment per step. Default is 0.5, NEVER use value greater than 1 as @@ -25,24 +25,18 @@ increase CPU time in most accelerators. [ bca_algorithm, exact_bca ] Skin depth for BCA= - If Boundary crossing algorithm= PRESTA-I - then this is the distance from the boundary (in - elastic MFP) at which lateral correlations will be - switched off. The default in this case is to - calculate a value based on the scattering power at - ECUT (same as PRESTA with EGS4). If - Boundary crossing algorithm= EXACT (default) then - this is the distance from the boundary (in elastic + Determines the distance from a boundary (in elastic MFP) at which the algorithm will go into single - scattering mode and defaults to 3 mfp. - Note that if you choose EXACT boundary crossing and - set Skin depth for BCA to a very large number (e.g. - 1e10), the entire calculation will be in SS mode. - If you choose PRESTA-I boundary crossing and make - Skin depth for BCA large, you will get default EGS4 - behaviour (no PRESTA). + scattering mode (if EXACT boundary crossing) or + switch off lateral correlations (if PRESTA-I boundary + crossing). Default value is 3 for EXACT or + exp(BLCMIN)/BLCMIN for PRESTA-I (see the PRESTA paper + for a definition of BLCMIN). Note that if you choose + EXACT boundary crossing and set Skin depth for BCA + to a very large number (e.g. 1e10), the entire + calculation will be in SS mode. If you choose + PRESTA-I boundary crossing and make Skin depth for + BCA large, you will get default EGS4 behaviours + (no PRESTA) [ skindepth_for_bca ] - - The new transport mechanics of EGSnrc are maintained away from - boundaries. \end{verbatim} diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM27.inp b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM27.inp index 6b8f4d097..4f217438b 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM27.inp +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM27.inp @@ -10,12 +10,12 @@ Spin effects= Off, On, (default is On) Turns off/on spin effects for electron elastic scattering. Spin On is ABSOLUTELY necessary for - good backscattering calculations. Will make a + good back-scattering calculations. Will make a difference even in `well conditioned' situations (e.g. depth dose curves for RTP energy range electrons). [ spin_effects ] - Brems angular sampling= Simple, KM, (default is Simple) + Brems angular sampling= Simple, KM, (default is KM) If Simple, use only the leading term of the Koch-Motz distribution to determine the emission angle of bremsstrahlung photons. If KM, complete @@ -31,20 +31,27 @@ cross section data base (which is the basis for the ICRU radiative stopping powers) will be employed. Differences are negligible for E > ,say, 10 MeV, - but signifficant in the keV energy range. If NRC is + but significant in the keV energy range. If NRC is selected, NIST data including corrections for electron-electron brems will be used (typically only significant for low values of the atomic number Z and for k/T < 0.005). - Bound Compton scattering= On, Off or Norej (Default is Off) + Triplet production= On or Off (default). Turns on/off simulation + of triplet production. If On, then Borsellino's + first Born approximation is used to sample triplet + events based on the triplet cross-section data. + [ itriplet ] + Bound Compton scattering= On, Off, Simple or norej (default) If Off, Compton scattering will be treated with Klein-Nishina, with On Compton scattering is treated in the Impulse approximation. - Make sure to turn on for low energy applications, - not necessary above, say, 1 MeV. Option Norej - uses full bound Compton cross section data - supplied in input below and does not reject - interactions. + With Simple, the impulse approximation incoherent + scattering function will be used (i.e., no Doppler + broadening). With norej the actual total bound + Compton cross section is used and there are no + rejections at run time. + Make sure to use for low energy applications, + not necessary above, say, 1 MeV. [ IBCMP ] Compton cross sections= Bound Compton cross-section data. User- supplied bound Compton cross-sections in the file diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM28.inp b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM28.inp index 2d9dab6a7..380c6cd59 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM28.inp +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM28.inp @@ -14,13 +14,13 @@ to NRC, then use NRC pair production cross-sections (in file $HEN_HOUSE/data/pair_nrc1.data). Only of interest at low energies, where the NRC cross- - sections take into account the assymmetry in the + sections take into account the asymmetry in the positron-electron energy distribution. [ pair_nrc ] - Photoelectron angular sampling= Off or On (Default is Off) + Photoelectron angular sampling= Off or On (Default is On) If Off, photo-electrons get the direction of the `mother' photon, with On, Sauter's furmula is - used (which is, striktly speaking, valid only for + used (which is, strictly speaking, valid only for K-shell photo-absorption). If the user has a better approach, replace the macro $SELECT-PHOTOELECTRON-DIRECTION; @@ -31,27 +31,45 @@ in a low energy photon beam. [ IPHTER ] Rayleigh scattering= Off, On, custom - If On, turned on coherent (Rayleigh) scattering. - Default is Off. Should be turned on for low energy - applications. Not set to On by default because - On requires a special PEGS4 data set. If set to - custom, then media for which custom form factors - are to be specified are listed in the input: - ff media names= - and the corresponding files containing custom data - are listed in: - ff file names= + If On, turn on coherent (Rayleigh) scattering. + Default is On. Should be turned on for low energy + applications. + If custom, user must provide media names and form + factor files for each desired medium. For the rest + of the media, default atomic FF are used. [ IRAYLR ] - Atomic relaxations= Off, On (Default is Off) - The effect of using On is twofold: + ff media names = A list of media names (must match media found in + PEGS4 data file) for which the user is going to + provide custom Rayleigh form factor data. + [ iray_ff_media($MXMED) ] + ff file names = A list of names of files containing the Rayleigh + form factor data for the media specified by + the ff media names = input above. Full directory + paths must be given for all files, and for each medium + specified, iray_ff_media(i), there must be a + corresponding file name, iray_ff_file(i). For + example files, see the directory + $HEN_HOUSE/data/molecular_form_factors. + [ iray_ff_file($MXMED) ] + Atomic relaxations= Off, On, eadl, simple + Default is eadl. On defaults to eadl. + When simulating atomic relaxations: - In photo-electric absorption events, the element (if material is mixture) and the shell the photon is interacting with are sampled from the - appropriate cross seections - - Shell vacancies created in photo-absorption events + appropriate cross sections + - Shell vacancies created in photoelectric, + compton and electron impact ionization events are relaxed via emission of fluorescent X-Rays, Auger and Koster-Cronig electrons. - Make sure to turn this option on for low energy + The eadl option features a more accurate treatment + of relaxation events and uses binding energies + consistent with those in of the photon cross + sections used in the simulation. If using + mcdf-xcom or mcdf-epdl photon cross sections, you + cannot use the simple option and this will + automatically get reset to eadl. + Make sure to use eadl or simple for low energy applications. [ IEDGFL ] \end{verbatim} diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM29.inp b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM29.inp index dfc7ea0fb..1a77df59b 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM29.inp +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM29.inp @@ -1,34 +1,59 @@ \begin{verbatim} - Electron impact ionization= Off, On, Casnati, Kolbenstvedt, Gryzinski - (Default is Off) - Determines which, if any, theory is used to model - electron impact ionization. If set to 'On' then the - theory of Kawrakow is used. Other settings use the - theory associated with the name given. See future - editions of the EGSnrc Manual (PIRS-701) for more - details. This is only of interest in keV X-Ray - simulations. Otherwise, leave it Off. - [ eii_flag ] - Photon cross sections= epdl,xcom,custom (Default is Storm-Israel - cross-sections from PEGS4) - The name of the cross-section data for photon - interactions. This input line must be left out - to access the default Storm-Israel cross-sections - from PEGS4. 'edpl' uses cross-sections from the - evaluated photon data library (EPDL) from Lawrence - Livermore. 'xcom' will use the XCOM cross-sections - from Burger and Hubbell. The user also has the - option of using their own customized cross-section - data. See the BEAMnrc manual for more details. - [ photon_xsections ] + Electron Impact Ionization= Off (default), On, casnati, kolbenstvedt, + gryzinski, penelope. If set to On or ik, then use + Kawrakow's theory to derive EII cross-sections. + If set to casnati, then + use the cross-sections of Casnati (contained in the + file ($HEN_HOUSE/data/eii_casnati.data). Similar for + kolbenstvedt, gryzinski and penelope. This is only of + interest in kV X-ray calculations. + Case-sensitive except for Off, On or ik options. + [ eii_flag ] + Photon cross sections= Photon cross-section data. Current options are + si (Storm-Israel), epdl (Evaluated Photon Data + Library), xcom (the default), pegs4, mcdf-xcom and + mcdf-epdl: + Allows the use of photon cross-sections other than + from the PEGS4 file (unless the pegs4 option is + specified). Options mcdf-xcom and mcdf-epdl use + Sabbatucci and Salvat's renormalized photoelectric + cross sections with either xcom or epdl for all other + cross sections. These are more accurate but can + increase CPU time by up to 6 %. + Note that the user can supply their own cross-section + data as well. The requirement is that the files + photon_xsections_photo.data, + photon_xsections_pair.data, + photon_xsections_triplet.data, and + photon_xsections_rayleigh.data exist in the + $HEN_HOUSE/data directory, where photon_xsections + is the name specified. + Hence this entry is case-sensitive. + [ photon_xsections ] Photon cross-sections output= Off (default) or On. If On, then a file $EGS_HOME/user_code/inputfile.xsections is output containing photon cross-section data used. [ xsec_out ] + Photonuclear attenuation= Off (default) or On + If On, models the photonuclear effect. Current + implementation is crude. Available on a + region-by-region basis (see below) + [ IPHOTONUCR ] + Photonuclear cross sections= Total photonuclear cross sections. User- + supplied total photonuclear cross-sections in + $HEN_HOUSE/data/photonuc_xsections_photonuc.data, + where photonuc_xsections is the name supplied for + this input (case sensitive). In the absence of + any user-supplied data, or if photonuc_xsections + is set to 'default', the default file is + iaea_photonuc.data. + [ photonuc_xsections ] Atomic relaxations, Rayleigh scattering, Photoelectron angular - sampling and Bound Compton scattering can also be turned On/Off - on a region-by-region basis. To do so, put e.g. + sampling, Bound Compton scattering and Photonuclear attenuation + can also be turned On/Off on a region-by-region basis. + To do so, put e.g. + Atomic relaxations= On in Regions or Atomic relaxations= Off in regions in your input file. Then use the relevant one of: @@ -43,6 +68,9 @@ or PE sampling start region= PE sampling stop region= + or + Photonuclear start region= + Photonuclear stop region= each followed by a list of one or more start and stop regions separated by commas. diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM31.inp b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM31.inp index 5f5f00826..fdbf7a67a 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM31.inp +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM31.inp @@ -39,7 +39,7 @@ energy dependent BCSE is modest (~20%). Note that if BCSE is used in conjunction with uniform bremsstrahlung - splitting (UBS) or selective bremsstrahlung splitting (SBS), then + splitting (UBS) then Russian Roulette is automatically turned on (IRRLTT=2--see above). BCSE is most efficient when used in conjunction with DBS or UBS diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM33.inp b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM33.inp index a3aae8d05..8e7a1c6a3 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM33.inp +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM33.inp @@ -22,13 +22,10 @@ Note restriction that if ALPHA24~=0 and/or BETA24 ~=0, then INIT_ICM must be > 1. This is because the rotation will result in some - particles incident within INIT_ICM-1. Also, the following CMs - currently do not handle the general case of a forward-directed particle - incident from within them: - APPLICAT,ARCCHM,CHAMBER,CIRCAPP,CONESTAK,DYNJAWS,JAWS,MESH,PYRAMIDS, - SIDETUBE - Thus, if ALPHA24~=0 and/or BETA24 ~=0 and INIT_ICM or INIT_ICM-1 is - one of these, negative ustep errors may result. + particles incident within INIT_ICM-1. Also, both INIT_ICM and + INIT_ICM-1 must be SLABS, SIDETUBE or FLATFILT, since these are the + only CMs currently capable of determining initial regions for particles + incident within them. Next record (If ISOURC=23) *********** diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM34.inp b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM34.inp index 2b4ded7c6..cbc89b6f2 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM34.inp +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM34.inp @@ -17,13 +17,10 @@ Note restriction that if ALPHA24~=0 and/or BETA24 ~=0, then INIT_ICM must be > 1. This is because the rotation will result in some - particles incident within INIT_ICM-1. Also, the following CMs - currently do not handle the general case of a forward-directed particle - incident from within them: - APPLICAT,ARCCHM,CHAMBER,CIRCAPP,CONESTAK,DYNJAWS,JAWS,MESH,PYRAMIDS, - SIDETUBE - Thus, if ALPHA24~=0 and/or BETA24 ~=0 and INIT_ICM or INIT_ICM-1 is - one of these, negative ustep errors may result. + particles incident within INIT_ICM-1. Also, both INIT_ICM and + INIT_ICM-1 must be SLABS, SIDETUBE or FLATFILT, since these are the + only CMs currently capable of determining initial regions for particles + incident within them. The initial idea and much of the coding for Source 24 is courtesy of Patrick Downes at University of Cardiff, Wales. diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM5.inp b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM5.inp index ae9faf06c..0d5010bdf 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM5.inp +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/BEAM5.inp @@ -3,7 +3,7 @@ ********** Circular: Vertical ring centred on Z-axis or horizontal cylinder centred parallel to X-axis - IQIN,ISOURC,RMINBM,RBEAM,ZSMIN,ZSMAX + IQIN,ISOURC,RMINBM,RBEAM,ZSMIN,ZSMAX,i_dsb,splitcm_dsb,dsb_delta IQIN charge of particles from source (defaults to 0) ISOURC = 3 RMINBM inner radius of vertical ring (RBEAM >= 0) (cm) @@ -19,13 +19,35 @@ ZSMAX Z of bottom of vertical ring (RBEAM >= 0) (cm) or: max. X of horizontal cylinder (RBEAM < 0) (cm) + i_dsb Set to 1 to use directional source biasing. Note that + directional bremsstrahlung splitting (IBRSPL=2) must + also be used. Splitting number (NBRSPL), splitting + field radius (FS), source to surface distance + (SSD) and electron splitting parameters (if e- + contamination is desired) are read from the DBS + inputs. + splitcm_dsb The CM no. at which primary photons are split and + radially redistributed about the Z-axis. Photons + are split/redistributed immediately upon entering + CM no. splitcm_dsb. Note that this should be the + the no. of the first CM in the treatment head without + radial symmetry. The number of times a photon is + split depends upon the radial bin into which it + is directed. Bin radii are determined by the input + dsb_delta below. Set splitcm_dsb=0 for no splitting/ + redistribution. + dsb_delta The min. linear distance, in cm, between split/ + redistributed photons, projected to the SSD of the + splitting field. dsb_delta is used to divide the + splitting field into radial bins, where photons + directed into bin i are split i times. NOTE: The sign of RBEAM determines if the source will be a vertical ring a horizontal cylinder. The Z-span of the source must be in the range Z_min_CM(1)-Z_min_CM(MAX_CMs+1). Currently, this source is limited to being placed within - CONESTAK, FLATFILT or SIDETUBE. + CONESTAK, FLATFILT or SIDETUBE ------------------------------------------------------------------------ ISOURC = 3a A cylindrical, isotropically radiating Co60 source within CMs ********** using directional source biasing (DSB). diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/update.sh b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/update.sh index 1e0c47601..cf6f7e202 100755 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/update.sh +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats/update.sh @@ -42,7 +42,7 @@ fi OMEGA_HOME="$HEN_HOUSE/omega" BEAM_DIR="$OMEGA_HOME/beamnrc" CMs="$OMEGA_HOME/beamnrc/CMs" -OUTDIR="$HEN_HOUSE/doc/pirs509a-beamnrc/inputformats" +OUTDIR="$HEN_HOUSE/doc/src/pirs509a-beamnrc/inputformats" $ECHO "Update APPLICAT input description? [n] \c" read response @@ -274,4 +274,10 @@ egrep '"I>|"%A31' $BEAM_DIR/beamnrc.mortran | sed -e '/"%A31/,$!d' | sed -e '1,$ $ECHO "Done updating BEAMnrc input description." fi +# remove eol white space from *.inp files +for f in $(grep -El '\s+$' *.inp); do + echo "Removing end-of-line whitespace in $f"; + sed -i 's/[[:space:]]*$//' $f; +done + # chmod g+w *.inp diff --git a/HEN_HOUSE/doc/src/pirs509a-beamnrc/pirs509a-beamnrc.tex b/HEN_HOUSE/doc/src/pirs509a-beamnrc/pirs509a-beamnrc.tex index b3ee4e314..27ec49abd 100644 --- a/HEN_HOUSE/doc/src/pirs509a-beamnrc/pirs509a-beamnrc.tex +++ b/HEN_HOUSE/doc/src/pirs509a-beamnrc/pirs509a-beamnrc.tex @@ -180,21 +180,18 @@ sources which was developed as part of the OMEGA project to develop 3-D treatment planning for radiotherapy (with the University of Wisconsin). BEAMnrc is built on the -EGSnrc Code System\cite{KR03}. Until 2004, BEAMnrc could only -be run on Unix/Linux systems. However, with the recent port -of BEAMnrc to the EGSnrcMP system\cite{Ka03}, BEAMnrc can also -run on Windows-based systems. +EGSnrc Code System\cite{KR03} and, as of 2004\cite{Ka03}, can run on Unix/Linux, +Windows and macOS systems. The purpose of this manual is to be a reference/guide to someone using the BEAMnrc system. This user's manual covers general BEAMnrc inputs and component module (CM) -geometries and inputs. It discusses how to use the various variance -reduction techniques which are part of the system, most importantly, -range rejection, bremsstrahlung splitting, photon forcing in a specific -region and Russian Roulette. -It also covers the structure of the directory system used for the -BEAMnrc system, the utility codes available (readphsp, addphsp, checkCM8 \etc), -the installation procedure, the phase space file definition and it +geometries and inputs. It discusses how to use the variance reduction techniques +which are part of the system; specifically, range rejection, bremsstrahlung +splitting, photon forcing and Russian Roulette. It also covers the directory +structure within which the BEAMnrc system resides, the utility codes available +(readphsp, addphsp, checkCM8 \etc), the installation procedure, the phase space +file definition, and it has cross references to all related BEAMnrc documentation. Appendix A gives a specification for writing new component modules. @@ -232,9 +229,9 @@ \section{Overview of BEAMnrc} October 2001 and generally released in Feb 2002. In spring 2004 a version of the code was released to course participants with Directed Brem Splitting available. In fall 2004 this version of the code was made -available generally with a port to the EGSnrcMP system which allows the -code system to be run on Windows systems as well as the traditional -Unix/Linux systems. There is a `new version' +available generally with a port to the multi-platform version of EGSnrc +(originally dubbed EGSnrcMP) which allows the code system to be run on Windows +as well as Unix/Linux and MacOS. There is a `new version' of this manual with each release of the code (usually with the annual course) and there have been five major revisions\cite{Ro95b,Ro97,Ro98a,Ro01b,Ro04} with changes in authorship to @@ -289,7 +286,7 @@ \subsection{Other documents available} \index{BEAMnrc GUI} \index{GUI} \item [BEAMnrc, DOSXYZnrc and BEAMDP GUI User's Manual:] Describes how to -install and use these graphical user interfaces to BEAMnrc and +install and use the graphical user interfaces for BEAMnrc and related codes\cite{Tr04}. \index{BEAMDP} @@ -305,7 +302,7 @@ \subsection{Other documents available} at NRC but describes the extensive QA program carried out on component modules, variance reduction options and source routines. It also describes -the automated system for on-going QA\cite{WR95a}. +the automated system for ongoing QA\cite{WR95a}. \index{DOSXYZnrc} \item [DOSXYZnrc User's Manual:] DOSXYZnrc is an associated code for doing dose @@ -324,11 +321,11 @@ \subsection{Other documents available} \index{EGS\_Windows\_4.0} \item[The EGSnrc Code System Manual- PIRS-701:] Complete manual describing -the use of the EGSnrc simulation system\cite{KR03}. +the EGSnrc simulation system including the physics and inputs for Monte Carlo +simulation parameters\cite{KR03}. \item[EGSnrcMP: the multi-platform environment for EGSnrc- PIRS-877:] Manual -describing the EGSnrcMP system\cite{Ka03}. Essential reading to understand -how the current version of BEAMnrc is compiled and run. +describing the EGSnrcMP system\cite{Ka03}. \item[History by history statistical estimators in the BEAM code system:] Med Phys {\bf 29} (2002) 2745--2752: In-depth description of the method used @@ -380,8 +377,10 @@ \subsection{Overview of the directory structure} \end{figure} {\tt \$OMEGA\_HOME} resides (as directory {\tt omega}) -within the {\tt \$HEN\_HOUSE}, which contains the EGSnrcMP system. -This is shown in more detail in fig~\ref{fig_hen_house}. +within the {\tt \$HEN\_HOUSE}, which contains the EGSnrc system. +This is shown in more detail in fig~\ref{fig_hen_house}. By default, +{\tt \$HEN\_HOUSE} is sudirectory {\tt EGSnrc/HEN\_HOUSE} off the +directory into which you downloaded/cloned the EGSnrc distribution. \index{examin} \index{directory structure!HEN\_HOUSE} \begin{figure}[hbp] @@ -390,33 +389,27 @@ \subsection{Overview of the directory structure} \mbox{} \hspace*{-1cm} \includegraphics[width=19cm]{figures/hen_house} -\caption[Structure of EGSnrcMP directory, {\em i.e~} the {\tt \$HEN\_HOUSE}.] +\caption[Structure of EGSnrc directory, {\em i.e.~} the {\tt \$HEN\_HOUSE}.] {The structure of the EGSnrc system. Note that the {\tt \$OMEGA\_HOME} subsystem shown in fig~\ref{fig_omega_home} is included in this structure. } -\index{HEN\_HOUSE} \index{NRC EGSnrcMP system} +\index{HEN\_HOUSE} \index{NRC EGSnrc system} \label{fig_hen_house} \end{center} \end{figure} \index{HEN\_HOUSE} Originally, EGSnrc was a Unix-based script system developed primarily by -Alex Bielajew and Dave Rogers at NRC. With the advent of EGSnrcMP\cite{Ka03} -and the -requirement for compiling on Windows-based systems in addition to Unix-based -systems, we have largely eliminated the scripts and, in the case of -compilation, replaced them with the GNU {\tt make} utility. -For more detail about the EGSnrcMP system and how it works, see the -EGSnrcMP manual~\cite{Ka03}. For users of the previous BEAM/BEAMnrc -systems, note that in the past the {\tt \$HEN\_HOUSE} was a component of -{\tt \$OMEGA\_HOME} since the EGS system was distributed as a component of -BEAM whereas in the EGSnrcMP system, BEAMnrc is a special subcomponent of -{\tt \$HEN\_HOUSE} and DOSXYZnrc is treated as just another user-code. - -The final component of the OMEGA/BEAM structure is the user's area which +Alex Bielajew and Dave Rogers at NRC. With the advent of the multi-platform +EGSnrc system (EGSnrcMP\cite{Ka03}) and the requirement for compiling on +Windows-based systems in addition to Unix-based systems, we have largely +eliminated the scripts and, in the case of compilation, replaced them with the +GNU {\tt make} utility. + +The final component of the EGSnrc directory structure is the user's area which is shown in fig~\ref{fig_users_area}. This is known as {\tt \$EGS\_HOME} -and is usually the subdirectory {\tt \$HOME/egsnrc\_mp}. The BEAM -installation will set +and is subdirectory {\tt EGSnrc/egs\_home} off the directory in which you +downloaded/cloned the EGSnrc installation. \index{directory structure!users area} \index{user's area} \begin{figure}[hbpt] @@ -427,7 +420,7 @@ \subsection{Overview of the directory structure} \includegraphics[width=17cm]{figures/nrc_users_area} \index{user's area} \caption[The user's \$EGS\_HOME area.]{The user's {\tt \$EGS\_HOME} - area (usually {\tt \$HOME/egsnrc\_mp}). A $*$ indicates an executable + area. A $*$ indicates an executable file. In the example shown, the user has 3 accelerator models and the disk system is being used with three different configurations, \eg, gcc, pgf77 and Windows. The complete directory contents are only shown @@ -436,11 +429,10 @@ \subsection{Overview of the directory structure} \label{fig_users_area} \end{center} \end{figure} -up much of this automatically if it is not in place. One of the main complications is that the -EGSnrcMP and BEAMnrcMP systems are +EGSnrc system is set up to use one disk system to support multiple configurations and -their associated compilers. +associated compilers. \index{multiple configurations} \index{script!egsnrc} Thus, all execute modules and various compiler options @@ -448,7 +440,6 @@ \subsection{Overview of the directory structure} Within the \verb+bin+ area, the modules within each subdirectory apply only to the configuration shown. -\clearpage \subsection{Overview of running BEAMnrc} \index{overview} @@ -463,7 +454,7 @@ \subsection{Overview of running BEAMnrc} \begin{center} \leavevmode \mbox{}\hspace{0cm} -\includegraphics[width=15cm]{figures/flow} +\includegraphics[width=12cm]{figures/flow} \index{building accelerators}\index{specifying accelerators} \caption[Steps involved in using the BEAMnrc code] {The steps involved in using the BEAMnrc system, from ref~\cite{Ro95}.} @@ -482,14 +473,14 @@ \subsection{Overview of running BEAMnrc} which specifies all the details about the particular accelerator (\eg, there are 4 scattering foils located at specified distances from the vacuum exit window, -made of certain materials and of particular thickness). Also the user +made of certain materials and of particular thickness). In addition, the user must specify all the parameters controlling the radiation transport modelling and must also select and control the various variance reduction techniques being used. The final stage of the simulation is the analysis of the outputs which -consist of raw phase space files (measured in tens if not hundreds of -Mbytes), an output listing and optionally a 3D graphics file to be displayed +consist of raw phase space files (which may be on the order of GBytes), +an output listing and optionally a 3D graphics file to be displayed by {\tt EGS\_Windows}\cite{TR99a}. \index{EGS\_Windows} @@ -511,8 +502,8 @@ \section{Building/compiling/running BEAMnrc} \index{EGS\_HOME} \index{EGS\_CONFIG} \begin{verbatim} -setenv EGS_HOME /full directory path to $HOME/egsnrc_mp/ -(or export EGS_HOME=/full directory path to $HOME/egsnrc_mp for .bashrc) +setenv EGS_HOME /full directory path to $EGS_HOME/ +(or export EGS_HOME=/full directory path to $EGS_HOME/ .bashrc) setenv EGS_CONFIG /full directory path to $HEN_HOUSE/specs/config.conf/ (or export EGS_CONFIG=/full directory path to $HEN_HOUSE/specs/config.conf/ for .bashrc) @@ -521,29 +512,18 @@ \section{Building/compiling/running BEAMnrc} for .bashrc) \end{verbatim} where {\tt config} is the name of the particular configuration -(eg {\tt gcc}, {\tt pgf77}) that you have installed BEAMnrc on. The -first three statements are required for the -EGSnrcMP system (see the EGSnrcMP Users Manual\cite{Ka03}), while -{\tt \$HEN\_HOUSE/scripts/egsnrc\_cshrc\_additions} -(or {\tt \$HEN\_HOUSE/scripts/egsnrc\_cshrc\_additions}) define aliases -for the OMEGA/BEAM system. Once you have added these statements you -must source the {\tt .cshrc} -(or {\tt .bashrc}) file to bring them into effect. +(eg {\tt gcc}, {\tt pgf77}) that you have installed BEAMnrc on. +Once you have added these statements you must source the {\tt .cshrc} +(or {\tt .bashrc}) file or start a new terminal window to bring them into effect. Instructions for adding these statements are given explicitly at the -end of the EGSnrcMP and BEAMnrc installations (see section~\ref{installbeam}) +end of the EGSnrc/BEAMnrc installation (see section~\ref{installbeam}). No such additions are required when installing BEAMnrc on a Windows system. -Previous to the current version of BEAM (BEAMnrcMP), the user had the -option to specify, build, compile and run a BEAM simulation -from within a Linux/Unix script, called {\tt beamnrc}. \index{beamnrc script} -This script was eliminated with the advent of BEAMnrcMP as it was seen to -be of limited use for a system that is also required to work on -Windows (which does not support scripts). However, you will note -in the descriptions that follow that all of the functions of the -{\tt beamnrc} script can be performed (in a much more user-friendly -manner) from within the BEAM GUI. +The following subsections define the processes of specifying, building and +compiling an accelerator. In general, these are carried out via the BEAM GUI. +However, command-line options are also given. \subsection{``Specifying'' Accelerators} \index{specifying accelerators} @@ -576,7 +556,7 @@ \subsection{``Specifying'' Accelerators} it is useful to have {\tt myaccel} indicate the machine you are modeling. -The {\tt myaccel.module} file created from scratch using the +The {\tt myaccel.module} file can created from scratch using the BEAM GUI (just select ``Specify a new accelerator" from the ``File" menu), or you can copy an existing {\tt .module} file (eg one of the examples included with the distribution) into {\tt myaccel.module} @@ -604,9 +584,9 @@ \subsection{Building an Accelerator: The {\tt beam\_build} Code} \index{prefix} \index{BEAM\_} are just the name of the specification module with the prefix \verb+BEAM_+. -If you are modifying the code at all, an accelerator must be re-built -every time any of the \verb+CMs+ are modified, but not when the main -\verb+beamnrc.mortran+ code is modified. +An accelerator must be re-built any time one of its component source files +({\em e.g.}, the code for one of its CMs, or {\tt beamnrc.mortran}) is +modified. An accelerator is built using the MORTRAN code {\tt beam\_build.mortran}. The command for running this code to build the accelerator specified @@ -631,9 +611,8 @@ \subsection{Building an Accelerator: The {\tt beam\_build} Code} are given in section~\ref{makefilesect}, on page~\pageref{makefilesect}, below. -If the {\tt beam\_build} utility has not already been compiled for your particular -configuration (this may be the case if you have switched configurations -after installing BEAMnrc), then before typing the above command line, go into +If the {\tt beam\_build} utility should be compiled when configuring your +system. However, if it has not, then before typing the above command line, go into {\tt \$HEN\_HOUSE/omega/beamnrc/tools/beam\_build} and type {\tt make}. This will put a copy of the {\tt beam\_build.exe} executable in the appropriate subdirectory of {\tt \$HEN\_HOUSE/bin}. @@ -649,11 +628,8 @@ \subsection{Compiling an Accelerator using {\tt make}} \index{Fortran} \index{make} -In previous versions of BEAM, compiling of accelerators was completely -driven by Unix scripts. However, with the necessity to run on non-Unix -platforms, EGSnrcMP now uses the GNU -{\tt make} utility. For more detailed information on {\tt make}, see -the EGSnrcMP manual~\cite{Ka03}. +Compilation of BEAMnrc (and all other EGSnrc codes) uses the GNU +{\tt make} utility. To compile an accelerator, go into the {\tt BEAM\_myaccel} subdirectory and type: @@ -680,7 +656,7 @@ \subsection{Compiling an Accelerator using {\tt make}} \end{verbatim} Upon typing {\tt make} you will see output to the screen indicating files -that are being concatenated together to create the final .mortran code +that are being concatenated together to create the final MORTRAN code that is then compiled. After compiling an accelerator, the following files will be left behind: @@ -757,16 +733,6 @@ \subsubsection{Compiling an Accelerator as a Shared Library} unix/Linux machines) or {\tt BEAM\_myaccel.dll} (for Windows machines) in directory {\tt \$EGS\_HOME/bin/config}. -Note that previous versions of BEAMnrc required -\index{libg2c.a} -the static g2c library, {\tt libg2c.a}, when compiling shared -libraries on Unix/Linux machines. Use of this library prevented -confusion of I/O units between BEAM and the code using BEAM as a source -(the ``driving'' code). -In the current version of BEAMnrc, however, the opening of I/O units -has been recoded so that only those units not already being used by -the driving code are available to BEAMnrc. - When using the BEAM shared library as a source, you must also supply a working input file and the pegs data for the BEAM simulation. The input file must exist in your {\tt \$EGS\_HOME/BEAM\_myaccel} directory and @@ -891,11 +857,14 @@ \subsection{Running an Accelerator Simulation} \index{PEGS4} \index{cross section data} -In order to run an accelerator, you also have to enter the name -of the {\tt .peg4dat} file containing the cross section data for the -materials in the model. Note that all of the material names used -in the input file must exist in the {\tt .pegs4dat} file used. -There is more information in section~\ref{CSDP} +In order to run an accelerator, the code must have access to electron stopping +power and interaction cross section data. This can be supplied either vi a +separate {\tt .peg4dat} file or, if running in ``pegsless'' mode, it can be +calculated on the fly based on media inputs in the {\tt .egsinp} file. Note that +all media used in a simulation must be defined, either in the {\tt. pegs4dat} +file or in the {\tt media definition} section of the {\tt .egsinp} file. + +There is more information on PEGS4 files in section~\ref{CSDP} but basically the files \verb+700icru.pegs4dat+ and \verb+521icru.pegs4dat+ \index{.pegs4dat}\index{700icru.pegs4dat}\index{521icru.pegs4dat} @@ -910,6 +879,9 @@ \subsection{Running an Accelerator Simulation} these files can be put either on that area, or on the user's pegs4 area, \viz\ \verb+$EGS_HOME/pegs4/data+. +For more information on pegsless runs, the user is referred to +section~\ref{pegsless_sect} in this manual. + \subsubsection{Batch Runs} \label{batchsect} \index{batch runs} @@ -933,7 +905,7 @@ \subsubsection{Batch Runs} Submitting a batch job uses the {\tt exb} command, which is aliased \index{egs\_batch\_run} to the Unix script {\tt \$HEN\_HOUSE/scripts/run\_user\_code\_batch}. The -syntax of the {\tt exb} command is: +basic syntax of the {\tt exb} command is: \begin{verbatim} exb BEAM_myaccel inputfile pegsdata [short|medium|long] [batch=batch_system] [p=N] \end{verbatim} @@ -952,18 +924,29 @@ \subsubsection{Batch Runs} the batch submission commands for the particular queuing system chosen and may redefine the names of the queues available on that system (this means that the queue names {\tt short|medium|long} are not -necessarily general). Currently, {\tt batch\_system} can be set to +necessarily general). Currently, {\tt batch\_system} can be set to: +\begin{itemize} \index{at} \index{PBS} \index{NQS} -{\tt at} (the standard Unix batch command), {\tt pbs} (for the -PBS queuing system) or {\tt nqs} (for the NQS queuing system). +\index{PBSDSH} +\index{KEG} +\item {\tt at} (the standard Unix batch command) +\item {\tt pbs} (for the +PBS queuing system) +\item {\tt nqs} (for the NQS queuing system) +\item {\tt pbsdsh} (PBS in distributed shell mode) +\item {\tt keg} (SUN SGE scheduler) +\end{itemize} This means that the files \index{batch\_options.at} \index{batch\_options.pbs} \index{atch\_options.nqs} -{\tt batch\_options.at}, {\tt batch\_options.pbs} and -{\tt batch\_options.nqs} are included with the EGSnrcMP distribution. However, +\index{atch\_options.pbsdsh} +\index{atch\_options.keg} +{\tt batch\_options.at}, {\tt batch\_options.pbs}, +{\tt batch\_options.nqs}, {\tt batch\_options.pbsdsh}, and +{\tt batch\_options.keg} are included with the EGSnrc distribution. However, the batch submission commands in these files are for our system at the NRC and you may have to make some changes for your system. The default value for {\tt batch\_system} is {\tt at}, unless you have the environment @@ -989,8 +972,6 @@ \subsubsection{Batch Runs} contain clues to the problem. More information on BEAM output files is given in section~\ref{outputfilessect}, page~\pageref{outputfilessect} below. -For more information on submitting batch jobs, see the EGSnrcMP manual~\cite{Ka03}. - \subsection{Running BEAMnrc using the GUI} \index{running BEAMnrc!with the GUI} @@ -1125,16 +1106,20 @@ \subsection{BEAMnrc Output Files} \index{scoring plane!average energy} \index{scoring plane!average angle} This section summaries the results for all scoring planes in -the geometry. BEAMnrc outputs a summary of each scoring plane, including +the geometry. For the purpose of {\tt .egslst} output, each +scoring plane is divided into a user specified number of +square or annular scoring zones with the zone half-widths +(square) or radii (annular) also specified by the user. +BEAMnrc outputs a summary of each scoring plane, including the plane's Z-position, the number of particles that crossed it, and the -radii (half-widths) of the scoring zones, followed by the actual fluence -results for the plane. The fluence is taken as the weighted +radii or half-widths of the scoring zones, followed by the actual fluence +results for the scoring zones. The fluence is taken as the weighted sum of 1/cos$\theta$ \index{fluence} where $\theta$ is the angle of the particle with respect to the z-axis. The number averaged energy and number averaged angle are also output. Scoring zones are numbered in order of -increasing radius (half-width). Note that the fluence results may be +increasing radius or half-width. Note that the fluence results may be output for one more scoring zone than the number of scoring zones input by the user. This ``extra'' scoring zone represents the area of the scoring plane not covered by the scoring zones. Fluence results for @@ -1157,23 +1142,21 @@ \subsection{BEAMnrc Output Files} \item [Dose Results] The first table shows the total dose and total energy deposited in each -of the dose scoring zones set up in the accelerator. +of the dose scoring zones that the user set up in the accelerator. \index{dose scoring zones} Note that each dose scoring zone may include several geometric regions. The second table (if contaminant dose calculations are asked for) shows the dose in each region due to the contaminant particles which are defined as the -charge state selected by the user as the particles cross a certain -planar boundary. This was designed for calculation of dose in a phantom +charge state selected by the user as the particles cross a user-defined +planar boundary. This option was originally designed for calculation of dose in a phantom but is applied in general. Finally, the doses in each region with bit filters applied are given. -Note that these dose components are +These are called ``dose components'' and are numbered to correspond to the order +of the bit filters in the {\tt .egsinp} file. For more information about bit filters +and dose components see section~\ref{dosecompsect} below. \index{dose components} \index{bit filters} -not exclusive; that is, dose components from particles that have -been in a specified scraper include contributions from particles that -have been in other scrapers before and/or after passing -through/interacting in the specified scraper. \end{description} @@ -1195,9 +1178,9 @@ \subsection{BEAMnrc Output Files} \verb+USTEP+\index{negative USTEP errors} errors, occurred. When using a phase space file for the source, the log file contains a warning -line every time the particles in the phase space source are -all used and the source file is reused from the beginning. -\index{phase space files!when reused} +line every time all particles in the phase space source have been +used, necessitating a restart of the source from the beginning. +\index{phase space sources!when restarted} \item [.egsdat] This file contains all of the information required to restart a run and @@ -1236,9 +1219,10 @@ \subsection{BEAMnrc Output Files} This file contains the complete state of the random number generator at the start the current batch (\verb+ISTORE=0+) or current history (\verb+ISTORE=1+) in a simulation. -This is only used for debugging problems which occur. +This is only used for debugging when problems occur. These data are used to restart the run with this RNG -when \verb+ISTORE+ is set to -1. +when \verb+ISTORE+ is set to -1. Note that running with \verb+ISTORE=1+ slows +down a simulation significantly. \index{ISTORE} \index{random number generator} \index{batches} @@ -1247,7 +1231,7 @@ \subsection{BEAMnrc Output Files} \index{.egsplot} This file contains dose {\em vs} depth for all dose components when a CHAMBER CM is used as a depth dose phantom. The format of the file is suitable -for plotting with {\tt xmgr} or {\tt xmgrace}. Note that the output +for plotting with {\tt xmgrace}. Note that the output of the file only makes sense for doses scored in a CHAMBER depth dose phantom. \index{xmgr} \index{xmgrace} @@ -1283,6 +1267,12 @@ \subsection{BEAMnrc Output Files} \item [.eo] Contains output from the network queuing system (batch job submissions only). +\index{.mederr} +\item [.mederr] Output from pegsless routines including errors, warnings and +information regarding where the medium composition and density are being read +from ({\em i.e.}, a density correction file or the {\tt .egsinp} file itself). +This file is only output for pegsless runs (see section~\ref{pegsless_sect}). + \end{description} Since the {\tt .egsphsp} files are often very large, and may exceed the @@ -1331,7 +1321,7 @@ \subsection{Changing the defaults} \verb+Max stack+ should have a value at least 4 times greater than \verb+Max bremsstrahlung split+. Nonetheless, the user should feel free to vary these parameters if they need to. The default settings should be OK -using directional bremsstrahlung splitting. +using directional bremsstrahlung splitting in an MV photon beam. Once any of the parameters in {\tt beamnrc\_user\_macros.mortran} have been changed, the accelerator must be recompiled to make the changes @@ -1383,8 +1373,6 @@ \subsubsection{The {\tt BEAM\_myaccel.io} File} specified here are ALWAYS opened (ie there are no conditions on whether the file is created or not), so if no quantity is written an empty file will be created. -For more information about {\tt .io} files, see the EGSnrcMP -Manual~\cite{Ka03}. \subsubsection{What's in {\tt BEAM\_myaccel\_macros.mortran} and {\tt BEAM\_myaccel\_cm.mortran}} @@ -1450,10 +1438,9 @@ \subsubsection{Files used during Compilation with {\tt make}} \label{makefilesect} The {\tt make} command uses several different files to direct the -concatenation and compilation of the final MORTRAN code. This section +concatenation and compilation of the final MORTRAN code. This section describes those files, along with their functions, which are likely to be relevant -to BEAM users. For a more complete description of the files involved in -the {\tt make} command, see the EGSnrcMP manual~\cite{Ka03}. +to BEAM users. \begin{description} \index{Makefile} @@ -1533,7 +1520,7 @@ \subsubsection{Files used during Compilation with {\tt make}} \index{all\_common.spec} \item [{\tt all\_common.spec}] Contains definitions common to all systems. This including the mortran sources and macros required to compile a -generic EGSnrcMP user code. This file also defines the variable +generic EGSnrc user code. This file also defines the variable {\tt RANDOM}, for the random number generator, but the definition of {\tt RANDOM} in {\tt beamnrc.spec} (see below) overrides this one. \index{beamnrc.spec} @@ -1547,7 +1534,8 @@ \subsubsection{Files used during Compilation with {\tt make}} \index{C preprocessor} \index{Fortran extension} the compiler to use the C-preprocessor before compiling the code. This is -necessary for the new implementation of parallel processing in BEAM. If, for some reason, you do not have a C compiler on your system, then the installation +necessary for the implementation of parallel processing in BEAM. If, +for some reason, you do not have a C compiler on your system, then the installation will set {\tt FEXT = f}. In addition, the variable {\tt SOURCES} in {\tt beamnrc.spec} defines all the MORTRAN macros and codes \index{mortjob.mortran} @@ -1573,7 +1561,7 @@ \subsubsection{Files used during Compilation with {\tt make}} \index{random number generators} {\tt RANDOM}, which determines the random number generator to be used in the simulation. Two random number generators, {\tt RANLUX} and -{\tt RANMAR} are included in the EGSnrcMP system. Currently, +{\tt RANMAR} are included in the EGSnrc system. Currently, {\tt RANMAR} is the default random number generator. See section~\ref{rngsect} for more information about the random number generators and how to switch from the default RANMAR @@ -1602,7 +1590,6 @@ \subsubsection{Files used during Compilation with {\tt make}} the accelerator. It is through the {\tt modules.make} file that {\tt beam\_makefile} has access to the individual CM macros and MORTRAN codes and can, thus, rebuild the accelerator if any of the CM coding changes. -The user should not modify this file since it \index{sources.make} \item[{\tt sources.make}] Located in {\tt \$EGS\_HOME/BEAM\_myaccel} and created by {\tt beam\_build} when the accelerator is built. This file @@ -1654,7 +1641,7 @@ \subsubsection{Files Concatenated to Create {\tt mortjob.mortran}} \index{egsnrc.mortran} \index{MORTRAN} \index{mortjob.mortran} -\includegraphics{figures/mortjob-mortran} +\includegraphics[width=12cm]{figures/mortjob-mortran} \caption[Files making up the complete BEAM source code.] {Files concatenated to form the complete BEAM source code, {\tt mortjob.mortran}, where {\tt BEAM\_myaccel\_cm.mortran} @@ -1692,8 +1679,7 @@ \subsubsection{Files Concatenated to Create {\tt mortjob.mortran}} \item [{\tt machine.macros}] Machine/compiler-dependent macros. Defines {\tt \$LONG\_INT} as {\tt integer*8} if it is available on this machine, the record length factor ({\tt \$RECL-FACTOR}) for -a 4-byte record in a phase space file, etc. See the EGSnrcMP Manual\cite{Ka03} -for more details. +a 4-byte record in a phase space file, etc. \index{ranmar.macros} \index{ranlux.macros} \item [{\tt ranmar.macros} (or {\tt ranlux.macros})] Macros used by @@ -1705,6 +1691,15 @@ \subsubsection{Files Concatenated to Create {\tt mortjob.mortran}} define text patterns searched for in the EGSnrc input section of a BEAMnrc input file (see section~\ref{egsnrc_inputs}). \index{beamnrc\_user\_macros.mortran} +\item{pegs4\_macros.mortran} +\item{pegsless mode} +\item [{\tt pegs4\_macros.mortran}] Macros required for running in pegsless +mode. This file contains common block definitions of variables used to +calculate and store electron stopping powers and interaction cross sections as +well as definitions of the macros, {\tt \$INIT-PEGS4-VARIABLES} and {\tt +\$GET-PEGSLESS-XSECTIONS}, used in the {\tt HATCH} subroutine to initialize data +arrays and compute stopping powers and cross sections, respectively. For more +information on pegsless mode, see section~\ref{pegsless_sect}. \item[{\tt beamnrc\_user\_macros.mortran}] Macros defining many default BEAMnrc parameters such as the maximum number of dose/fluence scoring zones, the maximum stack depth, etc. These parameters often need to be @@ -1752,9 +1747,12 @@ \subsubsection{Files Concatenated to Create {\tt mortjob.mortran}} with CM names replaced by their identifiers as specified in {\tt myaccel.module}. See section~\ref{beambuildsect} for more details. \index{get\_inputs.mortran} -\item [{\tt get\_inputs.mortran}] Coding for reading EGSnrc inputs from +\item [{\tt get\_inputs.mortran}] Coding for reading Monte Carlo transport parameters from the BEAMnrc input file. See section~\ref{egsnrc_inputs} for more about these inputs. +\index{get\_media\_inputs.mortran} +\item[{\tt get\_media\_inputs.mortran}] Coding for reading media definitions from the +{\tt .egsinp} file when running in pegsless mode. \index{ranmar.mortran} \index{ranlux.mortran} \item [{\tt ranmar.mortran} (or {\tt ranlux.mortran})] Subroutines used @@ -1775,12 +1773,16 @@ \subsubsection{Files Concatenated to Create {\tt mortjob.mortran}} \index{machine.mortran} \item [{\tt machine.mortran}] Machine/configuration-dependent routines such as date/time routines and system calls. This file is created during -EGSnrcMP installation. See the EGSnrc Users Manual\cite{KR03} and -EGSnrcMP Users Manual\cite{Ka03} for more info. +EGSnrc installation. \index{egs\_parallel.mortran} \item [{\tt egs\_parallel.mortran}] Subroutines for creating, opening, reading from and writing to the job control ({\tt .lock}) file during a parallel run (see section~\ref{parallelcalc}). +\item [{\tt pegs4\_routines.mortran}] Subroutines for calculating electron +stopping powers and cross sections when running in pegsless mode. With the +exception of some variable definitions, these routines have been copied verbatim +from their counterparts in {\tt pegs4.mortran}. See section~\ref{pegsless_sect} +for more information on running in pegsless mode. \index{egsnrc.mortran} \item [{\tt egsnrc.mortran}] EGSnrc subroutines. See the EGSnrc Manual\cite{KR03} for more details. @@ -1988,6 +1990,8 @@ \section{Description of main BEAMnrc input file} \index{comp\_xsections} \index{radiative Compton corrections} \index{radc\_flag} +\index{triplet production} +\index{itriplet} \input{./inputformats/BEAM27.inp} \index{pair angular sampling} \index{IPRDST} @@ -2007,8 +2011,14 @@ \section{Description of main BEAMnrc input file} \index{photon cross-sections!EPDL} \index{photon cross-sections!XCOM} \index{photon cross-sections!Storm-Israel} +\index{photon cross-sections!PEGS} +\index{photon cross-sections!Sabbatucci \& Salvat's photoelectric cross sections} \index{photon cross-sections output} \index{xsec\_out} +\index{photonuclear effect} +\index{photonuclear cross sections} +\index{iphotonucr} +\index{photonuc\_xsections} \input{./inputformats/BEAM29.inp} \index{rejection plane inputs} \index{USE\_REJPLN} @@ -2054,14 +2064,14 @@ \subsection{Sample input files} immediately (but the script only works on Linux/Unix and there is no corresponding replacement for Windows). \index{test\_BEAMnrc} -\clearpage + \section{Source Routines} \index{source!general remarks} In general, the incident particles move in the direction of the z-axis. With the exception of ISOURC=3 (internal isotropic source), =10 and 13 (x-ray -tube sources) or =21 and 31 (phase space -inputs), the particles start being transported on the \verb+Z_min_CM(1)+ +tube sources) or =21, 23, 24, 31 (phase space source, BEAMnrc simulation source, or +source model), the particles start being transported on the \verb+Z_min_CM(1)+ plane. Conceptually, some of them originate at a point outside the accelerator model and are essentially transported through vacuum to the accelerator which starts at the \verb+Z_min_CM(1)+ plane. @@ -2112,7 +2122,7 @@ \section{Source Routines} \item [ISOURC=31] Beam characterization Model \end{description} - +\clearpage \subsection{ISOURC=0: Parallel Circular Beam} \cen{IQIN, 0, RBEAM, UINC, VINC, WINC} \index{UINC} \index{VINC} \index{WINC} @@ -2276,6 +2286,14 @@ \subsection{ISOURC=3: Interior Isotropic Cylindrical Source} \end{center} \end{figure} +\index{Directional Source Biasing} +Source 3 also has an option to split photons that are emitted into a user +specified treatment field. This option, called directional source biasing (DSB), +can increase the efficiency of Cobalt-60 treatment head simulations by factors +on the order of 100 and, in general, can be used to increase the efficiency of +any photon beam with an isotropically emitting source. A detailed explanation +of DSB is given in section~\ref{DSB}. + \clearpage \subsection{ISOURC=5: NRC Swept BEAM} \cen{IQIN, 5, GAMMA, RBEAM} @@ -2659,7 +2677,8 @@ \subsection{ISOURC=15: NRC Swept Beam (Radial Variation, by bin area before sampling. \end{description} %\vspace{-3mm} -Some sample radial intensity distribution files are found in {\tt \$OMEGA\_HOME/beamnrc/radial\_source\_distributions}. +Some sample radial intensity distribution files are found in\\ + {\tt \$OMEGA\_HOME/beamnrc/radial\_source\_distributions}. \end{description} The radial position of an incident particle, RIN, is chosen based on the radial intensity distribution. The divergence angle, {\tt THETAI}, of the @@ -3204,8 +3223,8 @@ \subsection{ISOURC=31: Phase Space Reconstructed Using Beam\\ Models} \section{Monoenergetic vs Energy Spectrum Sources} \index{source!monoenergetic} \index{source!energy spectrum} -In any of the above sources, with the exception of the phase space source -(ISOURC=21), incident beam energy can be either monoenergetic or described by an energy +In any of the above sources, with the exception of the phase space and beam simulation +sources (ISOURC=21,23,24), incident beam energy can be either monoenergetic or described by an energy spectrum. Inputs associated with incident beam energy are: \begin{description} @@ -3250,9 +3269,9 @@ \section{Monoenergetic vs Energy Spectrum Sources} The code randomly distributes incident particle energies equally across each energy bin. -On \verb+$HEN_HOUSE/ensrc_spectra+ there are a collection of spectra -developed at NRC over the years in various situations. We intend to -augment this collection with time, and will happily add any other +In \verb+$HEN_HOUSE/spectra/egsnrc/+ there are a collection of spectra +developed at NRC over the years for various applications. We will +happily add any other spectra sent to us in the correct format, and with some semi-adequate documentation. \index{ensrc\_spectra} @@ -3274,10 +3293,12 @@ \subsection{Range Rejection} This section contains a brief description of how range rejection is performed and describes the input variables used to control range -rejection. +rejection. Range rejection is used to save computing time, in the process +introducing approximations in the simulation (see below). Thus, it really falls +under the category of an ``approximate efficiency improvement technique'' (AEIT) +as opposed to being a true variance reduction technique (VRT). -Range rejection is used to save computing time during simulations. The -basic method is to calculate the range of a charged particle and +The basic method for range rejection is to calculate the range of a charged particle and terminate its history (depositing all of its energy at that point) if it cannot leave the current region with energy $>$ {\tt ECUTRR}. {\tt ECUTRR} is the range @@ -3317,11 +3338,12 @@ \subsection{Range Rejection} boundary, the particle is terminated and energy deposited in the current region. \verb+IREJCT_GLOBAL=1+ can save more time than -\verb+IREJCT_GLOBAL=2+ but can only be used if -there is only 1 scoring plane and it is at the very bottom of the -accelerator. One can approximate \verb+IREJCT_GLOBAL=1+ for other -situations by using \verb+IREJCT_GLOBAL=2+ and carefully selecting -\verb+ECUT+ for different regions throughout the accelerator. +\verb+IREJCT_GLOBAL=2+ but is generally only useful for the case where the user +is only interested in phase space data at the bottom of the accelerator, since +the higher values of \verb+ECUTRR+ higher up in the accelerator may lead to +inaccuracies in scored quanties ({\em e.g.}, dose) in these regions. +Note, one can increase the time saved by \verb+IREJCT_GLOBAL=2+ by +judicious setting of \verb+ECUT+ in different regions throughout the accelerator. \index{range rejection} Range rejection introduces an approximation because, in @@ -3343,11 +3365,12 @@ \subsection{Range Rejection} this is because this CM is used for bremsstrahlung targets and we thought we might need more control). -The actual rejection of particles based on range to {\tt ECUTRR} -is performed in a BEAMnrc macro and does -not make use of the internal range rejection macro available in EGSnrc. -This is because the EGSnrc macro only performs range rejection based on -range to {\tt AE}. +Rejection of particles based on range to {\tt ECUTRR}, as described above, is +defined in the BEAMnrc macro, {\tt \$USER-RANGE-DISCARD}. This is implemented +immediately after EGSnrc's intrinsic range rejection routine, which is based on +particle range to {\tt AE}, the lower energy limit for cross section and +stopping power data, and which, in general, is not as stringent a rejection +criterion. \index{ESAVE} \index{ESAVE!ESAVEIN} @@ -3368,11 +3391,9 @@ \subsection{Photon Forcing} Briefly, a photon forced to interact in a CM is ``split'' into a scattered photon whose weight is equal to the probability of interaction and an unscattered photon carrying the remaining weight. The unscattered -photon proceeds as if an interaction did not take place, and it cannot be -forced to interact any more within the specified forcing zone, which can -consist of one or several component modules. However, once the -unscattered photon gets out of the forcing zone, it may interact again -depending on the sampled pathlength. The scattered photon can be forced +photon proceeds as if an interaction did not take place and is transported +directly through the forcing zones with no further interaction. +The scattered photon can be forced again in the forcing zone depending on how many interactions are allowed to be forced. @@ -3397,23 +3418,35 @@ \subsection{Photon Forcing} \end{description} \index{forcing} \index{photon forcing} -Photon forcing parameters are passed onto secondary photons, so that -if the parent particle has not yet been forced to interact {\tt NFMAX} -times, each secondary photon is forced to interact the remaining number -of times (\ie\ {\tt NFMAX} - \# of times parent particle forced) as long -as it is within the forcing CMs. Forcing of secondary photons does not -affect the number of times the parent particle is forced to interact -if it is a photon as well. The feature of passing forcing parameters -to secondary photons is particularly useful to get good statistics for -bremsstrahlung photon interactions. The incident electron creating the -photons will not be forced at all, so each bremsstrahlung photon will be -forced to interact {\tt NFMAX} times. This feature makes Photon Forcing +Briefly, a photon forced to interact in a CM is ``split'' into a scattered +photon whose weight is equal to the probability of interaction and an +unscattered photon carrying the remaining weight. The unscattered photon +proceeds as if an interaction did not take place and is transported directly +through the forcing zone ({\em i.e.}, the forcing CMs) with no further +interaction. This process is repeated along the path of the scattered photon +(and its descendants) until a total of {\tt NFMAX} interactions have been +forced. In each case, the weight of the scattered photon is equal to the weight +of the parent photon times the probability of interaction, and the weight of the +unscattered photon is equal to the weight of the parent photon times (1 - the +probability of interaction). Note that, depending on the setting of {\tt +NFMAX}, this can lead to a broad distribution of particle weights at the bottom +of the forcing zone. + +The number of times interactions have been forced is passed onto higher-order +photons arising from non-forced events ({\em e.g.}, bremsstrahlung, positron +annihilation). Thus, if the parent photon has not yet undergone {\tt NFMAX} +forced interactions, or if the parent is a charged particle, these higher-order +photons will be forced to interact the remaining number of times (\ie\ {\tt +NFMAX} - \# of times parent particle forced) as long as they are within the +forcing zone. This does not affect any remaining forced interactions of the +parent photon. This feature is useful for getting good statistics on +bremsstrahlung photon interactions and makes Photon Forcing a powerful tool for improving statistics when used in conjunction with bremsstrahlung splitting (see next section). -Note that forcing in restricted regions with low mass can lead to a few -electrons created outside the forcing region having much larger weights than -those created inside the forcing region and thereby distorting results +Note that forcing in regions with low mass can lead to a few secondary electrons +created outside the forcing region having much larger weights than those created +inside the forcing region and thereby distort results which are sensitive to these weight variations. \subsection[Brem Splitting and Russian Roulette] @@ -3456,22 +3489,22 @@ \subsubsection{Uniform Bremsstrahlung Splitting} underwent the bremsstrahlung event. The energies and directions of each photon are sampled individually according to the relevant probability distributions. The energy of the primary electron is decremented by -the energy of just one of the photons. This must be done in order to -preserve the effects on energy straggling but it does mean that energy is -not conserved on a given history (the energy would have to be decremented -by the average energy of the photons created) but it is conserved ``on +the energy of just one of these photons. This must be done in order to preserve +energy straggling and means that, while energy is not conserved for a single +history (the energy would have to be decremented by the average energy of the +photons created to achieve this), it is conserved ``on average'' over many histories. -The splitting number, {\tt NBRSPL}, is not applied to higher-order +The splitting number, {\tt NBRSPL}, is not applied to higher-order bremsstrahlung and annihilation photons unless Russian Roulette is turned on (see section~\ref{rusrousect} below). This prevents wasting simulation time by tracking many higher-order photons of vanishing weight. -Uniform bremsstrahlung splitting in BEAMnrc is now handled by the EGSnrc -system using a more efficient internal bremsstrahlung splitting feature. -So, other than input, there is no longer any coding in BEAMnrc related -to this except for the feature which turns it off for higher orders. +Uniform bremsstrahlung splitting in BEAMnrc is handled by the EGSnrc +system using an efficient internal bremsstrahlung splitting algorithm. +So, other than input, the only coding in BEAMnrc related +to UBS involves turning off splitting for higher-order events. \subsubsection{Selective Bremsstrahlung Splitting} \label{sbssect} @@ -3979,6 +4012,28 @@ \subsubsection{Directional Bremsstrahlung Splitting (DBS)} generates only those photons that are directed into the splitting field plus one fat photon representing the statistics of photons directed away from the field. +\index{directional source biasing!schematic} +\begin{figure}[ht] +\begin{center} +\includegraphics[width=10cm]{figures/dsb} +\end{center} +\caption[Schematic of DSB] +{A schematic of directional source biasing (DSB) in a Co-60 treatment head +simulation. The splitting field is defined by the user inputs, {\tt FS} and {\tt +SSD} and contains the treatment field. If there is radial symmetry above CM +number {\tt splitcm\_dsb}, the number of primary photons tracked in this region +can be reduced by dividing the splitting field into {\tt nbin} radial bins. The +number of split primary photons directed into bin i, defined by minimum radius, +r$_i$, is reduced by a factor of i and the weight of each photon is i/{\tt +NBRSPL}. Upon entering {\tt splitcm\_dsb}, photons are split i times and +radially redistributed about the beam central axis, and their weight is +decreased by a factor of i to become 1/{\tt NBRSPL}. The individual r$_i$ are +determined by the user input, {\tt dsb\_delta}, defining the minimum linear +distance between radially redistributed photons ({\em i.e.} for photons directed +exactly at r$_i$).} +\label{dsb_fig} +\end{figure} + \index{directional source biasing!use of radial symmetry} \index{directional source biasing!r$_i$} \index{directional source biasing!splitcm\_dsb} @@ -4016,29 +4071,6 @@ \subsubsection{Directional Bremsstrahlung Splitting (DBS)} {\tt \$OMEGA\_HOME/beamnrc/beamnrc\_user\_macros.mortran}. Currently, {\tt \$DSB\_MAX\_BIN} is set to 1000. -\clearpage -\index{directional source biasing!schematic} -\begin{figure}[H] -\begin{center} -\includegraphics[width=9cm]{figures/dsb} -\end{center} -\caption[Schematic of DSB] -{A schematic of directional source biasing (DSB) in a Co-60 treatment head simulation. -The splitting field is -defined by the user inputs, {\tt FS} and -{\tt SSD} and contains the treatment field. If there is radial symmetry -above CM number {\tt splitcm\_dsb}, the number of primary photons tracked in -this region can be reduced by dividing the splitting field into {\tt nbin} radial bins. -The number of split primary photons directed into bin i, defined by minimum radius, r$_i$, is -reduced by a factor of i and the weight of each photon is i/{\tt NBRSPL}. Upon -entering {\tt splitcm\_dsb}, photons are split i times and radially redistributed about the -beam central axis, and their weight is decreased by a factor of i to become 1/{\tt NBRSPL}. -The individual r$_i$ are determined by the user input, {\tt dsb\_delta}, defining -the minimum linear distance between radially redistributed photons ({\em i.e.} for -photons directed exactly at r$_i$).} -\label{dsb_fig} -\end{figure} - \index{directional source biasing!dsb\_delta} Since {\tt dsb\_delta} defines the minimum linear distance, projected to {\tt SSD}, between split, radially-redistributed photons, the actual linear distance between redistributed photons directed towards radius, r, in bin i is {\tt dsb\_delta}+$\delta_i(r)$, where $\delta_i(r)$ increases linearly with r from 0 at r=r$_i$ to @@ -4369,20 +4401,16 @@ \subsection{Description of Phase Space Files} \index{binary format -phase space} \index{byte order} \index{byte swapping} -The phase space files are binary files and thus suffer from the problem of -being being one of two types which depend on which machine they were -written on (little-endians and big-endians). The utility program -\verb+readphsp+ can be used to convert between these formats. Files from -DEC alpha and PC Linux machines have the same byte order as each other and -may be interchanged. Files from SUNs, SGIs, RS6000s, and HP9000s are the -same and can be interchanged. We have also slightly compressed the files -to save space. +The phase space files are binary and, thus, byte order (big endian or little +endian) will depend on which type of architecture they were written on. The +utility program \verb+readphsp+ can be used to swap bytes between these two +formats. \index{readphsp} \index{phase space files!binary format} \index{binary format -phase space} \index{MODE} -The first record in a file is different from the others and contains +The first record in a phase space file is different from the others and contains the following information. \begin{description} \item [MODE\_RW] The file mode: it can be either 'MODE0' or 'MODE2' depending @@ -4415,28 +4443,28 @@ \subsection{Description of Phase Space Files} because they were multiple passers, {\tt NFAT\_ph\_sp} is the number of fat photons rejected from the source (only if directional bremsstrahlung is used--see section~\ref{dbssect}), and {\tt NRCYCL} is the number -of times each particle in the source is recycled (see section~\ref{phspsrcsect}). The value of -\verb+NINCPHSP+ is stored -in any phase space files generated by the phase space source -and is also used to normalize doses and fluences resulting from the phase -space source. -Thus, \verb+NINCPHSP+, doses and fluences are traceable back to -the original source. For example, consider a model of a $^{60}Co$ unit +of times each particle in the source is recycled (see +section~\ref{phspsrcsect}). Thus, regardless of the number of upstream phase +space sources, the value of \verb+NINCPHSP+ in a phase space file is always +traceable back to the number of histories from the primary, non-phase space +source. Since quantities scored during a simulation that uses a phase space +source are normalized by \verb+NINCPHSP+, they, too, are traceable back to the +original, primary source. For example, consider a model of a $^{60}Co$ unit which is broken into 2 components. In the first part, the source capsule is modelled and a phase space file created with all the particles leaving the surface of the capsule. Here all outputs are normalized -per photon from the $^{60}Co$. In the second stage, the phase +per photon from the $^{60}Co$ capsule. In the second stage, the phase space file from the first part is used as input to a model of the collimator system. Here again the outputs are normalized per photon -from the $^{60}Co$, thus automatically maintaining the +from the $^{60}Co$ capsule, thus automatically maintaining the ``natural'' normalization. \index{normalization!of dose and fluence when using ISOURC=21} \index{dose!normalization when using ISOURC=21} \index{fluence!normalization when using ISOURC=21} Each record in a phase space file contains the following information -about a particle (in this order):\\ -\verb+LATCH, E, X, Y, U, V, WT, (ZLAST)+\\ +about the particle scored (in this order):\\ +\verb+LATCH, E, X, Y, U, V, WT, [ZLAST]+\\ where: \vspace*{-4mm} \index{LATCH!in phase space} @@ -4447,27 +4475,27 @@ \subsection{Description of Phase Space Files} the particle has crossed the scoring plane, \verb+NPASS+, and information \index{NPASS} which allows the particle's history to be traced (see section~\ref{LATCH} -below). The value of \verb+LATCH+ in the phase space file is not the -same as that internal to BEAMnrc or other analysis codes -because of the compression used. +below). Note that because it is also used to store IQ and {\tt NPASS}, +the value of \verb+LATCH+ written to the phase space file is not the +same as that during transport. \index{LATCH!in phase space} -\item [E] is the particle total energy (kinetic and rest mass, single -precision). This is set negative if this is the first particle scored -from a new primary (ie from a non-phase space source) history. -\item [X] is the particle X-position (cm) -\item [Y] is the particle Y-position (cm) -\item [U] is the X-direction cosine -\item [V] is the Y-direction cosine +\item [E] is the particle total energy (kinetic plus rest mass) in single +precision. This is set negative if this is the first particle scored +from a new primary (ie non-phase space source) history. +\item [X] is the particle X-position (cm). +\item [Y] is the particle Y-position (cm). +\item [U] is the X-direction cosine. +\item [V] is the Y-direction cosine. \item [WT] is the particle's weight; WT also carries the -sign of W, the Z-direction cosine -\item [ZLAST] is the Z-position of last interaction for photons and is -the Z-position of where an electron or its ancestor was set in motion by -a photon (i.e. it does not flag the creation site of delta rays. This -variable is in brackets because its inclusion in the phase space file +sign of W, the Z-direction cosine, W. +\item [ZLAST] For scored photons, this is the Z-position of last interaction; +for charged particles, it is the Z-position where the charged particle or its +ancestor was set in motion by a photon ({\em i.e.}, it does not flag the +creation site of delta rays). If a particle does not interact, then {\tt ZLAST} +stores Z-position on entering the simulation ({\em i.e.}, {\tt ZIN}). This +quantity is in brackets because its inclusion in the phase space file depends upon the setting of the input variable -\verb+IZLAST+ (see section~\ref{IZLAST} on \verb+IZLAST+). If a -particle does not interact, ZLAST is the value it had as it entered the -simulation ({\tt ZIN}). +\verb+IZLAST+ (see section~\ref{IZLAST} on \verb+IZLAST+). \index{ZLAST} \index{IZLAST} \index{phase space files!description} @@ -4497,25 +4525,24 @@ \subsection{Description of Phase Space Files} {\tt E} markers as a source, scored quantities will be grouped according to incident particle instead of primary history. BEAMnrc will output a warning that uncertainties may be underestimated because correlations -between incident particles cannot be accounted for. However, we have -shown that in most cases the underestimates in uncertainty caused by -not taking correlations into account are -not significant~\cite{Wa02a}. +between incident particles cannot be accounted for. The underestimates in +uncertainty caused by not taking correlations into account may be significant in +cases where variance reduction techniques result in many correlated particles +scoring quantities in the same volume (dose) or area (fluence)~\cite{Wa02a}. An +example of a case where this could happen is when directional bremsstrahlung +splitting is used with a large splitting number (see section~\ref{dbssect}). When BEAMnrc writes a phase space file, it opens the file using\\ \verb+ACCESS = 'direct', FORM = 'unformatted', RECL = 'length'+.\\ -The \verb+FORM='unformatted'+ statement ensures that -the file will be stored in a -compressed format, requiring less disk space. The record length, -'length', depends on the machine being used to run BEAMnrc; on SUN -stations and Linux PC's, 'length' is the number of bytes/record -(28 or 32 [with {\tt ZLAST}]); -on SGI and DEC alpha -machines, 'length' is the number of variables stored in a -record (7 or 8 [with {\tt ZLAST}]). Internally `length' is determined as -7*\verb+$RECL_FACTOR+ or 8*\verb+$RECL_FACTOR+ (with {\tt ZLAST}), -where the value of the macro is 1 or 4 and is defined in -\verb+$HEN_HOUSE/lib/${my_machine}/machine.mortran+. +The \verb+FORM='unformatted'+ statement ensures that the file will be stored in +binary format. Specification of the record length, 'length', depends on the +machine being used. For most architectures, 'length' is the number of +bytes/record ({\em i.e.}, 28 or 32 with {\tt ZLAST}). However, given that some +architectures specify record length in 4-byte units, 'length' is represented +internally as 7*\verb+$RECL_FACTOR+ or 8*\verb+$RECL_FACTOR+ (with {\tt ZLAST}), +where \verb+$RECL_FACTOR+ is 4 or 1, depending on architecture. Note that +\verb+$RECL_FACTOR+ is defined in\\ +\verb+$HEN_HOUSE/lib/${my_machine}/machine.macros+. \index{machine.mortran} \index{ZLAST} @@ -4527,18 +4554,7 @@ \subsection{Description of Phase Space Files} \verb+ZLAST+ is not scored and 'MODE2' if \verb+ZLAST+ is scored. The 'MODE0' or 'MODE2' -designation appears in the first record of a phase space file along -with the total number of particles contained in the file, the number -of photons, maximum kinetic energy of any particle in the file, -minimum kinetic energy of electrons, and the number of particles incident -from the original source. - -An older version of BEAM opened files in compressed format but with\\ -\verb+ACCESS='sequential'+. These older files are designated 'MODE1' without -\verb+ZLAST+ and\\ 'MODE3' with \verb+ZLAST+. The current version of BEAM requires -conversion of files in the older format to access='direct' format before adding -new phase space data to them. The \verb+readphsp+ program described below -performs this conversion. +identifier is the first quantity written to the first record of a phase space file. \index{.egsphsp1} Phase space files have extension \verb+.egsphsp#+ where \verb+#+ @@ -4556,13 +4572,12 @@ \subsection{Description of Phase Space Files} optimisations that could be made, however, in a normal accelerator simulation, only a small fraction of the simulation time is taken up reading from and writing to phase space files. -The source for these macros is kept separately so that users may -utilise them in their own codes to read or write phase space files. -The same macros are used uniformly throughout the -BEAMnrc system (DOSXYZnrc, BEAMDP, BEAMnrc \etc). -\index{phsp\_macros.mortran} +The source for these macros is kept separately to preserve commonality between +the methods used by all Mortran applications (BEAMnrc, DOSXYZnrc, BEAMDP, etc) +to access phase space files. In addition, they may be used in the user's own +applications. \index{phsp\_macros.mortran} -\subsection{Maximum size of Phase Space Files} +\subsection{Maximum Size of Phase Space Files} \index{Phase space files!maximum size} Note that the variable written to header storing the number of particles in a phase space file, {\tt NPPHSP}, is a 4-byte integer. This puts a @@ -4682,9 +4697,10 @@ \subsubsection{IAEA format} \item {\tt \$RECORD\_CONTENTS}: A block indicating the data that is stored in the {\tt .IAEAphsp} file. A ``1'' beside a variable indicates that this is stored in the {\tt .IAEAphsp} file. This block also indicates how many extra long integers -and extra floating point variables are stored. In the case of BEAMnrc, two extra long integers, -{\tt LATCH} and the number of primary histories between this particle and the last -particle scored, are always stored. In addition, if the input {\tt IZLAST=1} +and extra floating point variables are stored. In the case of an IAEA-format +phase space file written by BEAMnrc, {\tt LATCH} is always stored as an extra +long integer variable. In addition, if the input {\tt IZLAST=1} + (See Section~\ref{IZLAST}) then {\tt ZLAST}, the Z of the last interaction site for photons and the creation site for secondary charged particles, is stored as an extra floating point variable. @@ -4780,10 +4796,10 @@ \subsubsection{Reading IAEA phase space data} same directory as the phase space data file. As with BEAMnrc format phase space sources, the Z-direction cosine, {\tt W} is -calculated from $\sqrt{{\tt U}^2+{\tt V}^2}$. The sign of {\tt type} is then -applied to {\tt W}. On reading a negative -energy value, the primary history counter in BEAMnrc is incremented by one, and {\tt E} is set -to its absolute value before being used in a simulation. +calculated from $\sqrt{{\tt U}^2+{\tt V}^2}$. The sign of {\tt W} is determined +from {\tt type}, the {\tt CHAR*1} variable storing particle type. First, {\tt type} +is converted to {\tt INTEGER*2}, and then its sign is applied to {\tt W}, after which +the integer form of {\tt type} is set to its absolute value. Note that BEAMnrc automatically handles 3-D IAEA format phase space sources in which the (X,Y,Z) position of each particle is stored and 4-D phase space data in which fractional monitor unit index ({\tt MU}) is stored. @@ -4820,18 +4836,18 @@ \subsection{readphsp} space files generated on another type of machine become compatible with the type of machine that \verb+readphsp+ is being run on. -The \verb+readphsp+ program also allows selection of a particular charge -from a phase space file, or a subset of a file can be extracted. +The \verb+readphsp+ program also allows extraction of a subset of +phase space data from a file based on charge and/or maximum number +of particles. \index{phase space files!binary format} \index{binary format -phase space} Before converting phase space files \verb+readphsp+ prints a summary of -the file contents. If this is nonsense, then very likely the file has -the wrong binary format (\ie\ was generated on a machine which uses a -different binary format). The user should use the option of +the file contents. If this is nonsense, then it is very likely the file +was generated on a machine with a different byte order. The user should use the option of \verb+readphsp+ to swap the bytes of the phase space data to make it -compatible with the current machine before otherwise converting the phase -space data to its new form. When using \verb+readphsp+ for byte +compatible with the current machine before otherwise manipulating phase +space data. When using \verb+readphsp+ for byte swapping, the name of the output file can be the same as that of the input file however the swapped data will overwrite the original data. \index{readphsp} @@ -4900,15 +4916,14 @@ \section{Tracking a Particle's History using LATCH} The \verb+LATCH+ variable, associated with each particle in a simulation, is a 32-bit variable used to track the particle's history. In the input files there is an opportunity to define a mapping from geometric regions to -bits (\ie\ bit regions) +bits (\ie\ define bit regions) using the \verb+IREGION_to_BIT+ variable. Thus, \eg\ it is possible that bit 5 corresponds to geometric region 3, and more importantly, one bit, say 3, can correspond to multiple geometric -regions, \eg\ 1,5,8. Thus, although the JAWS may consist of 6 different -geometric regions, they can all be associated with a single bit or bit -region. All regions which are not associated with a bit/bit region by the -user are associated with bit region 23 by default. -Each bit is designated as follows: +regions, \eg\ 1,5,8. This is convenient for accelerator structures comprising +multiple regions. All regions which are not explicitly associated with a bit +number by the user are assigned bit number 23 by default. Each bit of the {\tt +LATCH} variable is designated as follows: \index{bit region} \index{IREGION\_to\_BIT} \begin{description} @@ -4922,10 +4937,10 @@ \section{Tracking a Particle's History using LATCH} \item [bit 1-23] Used to record the bit region where a particle has been and/or has interacted (Note that the bit set for a region is determined by \verb+IREGION_TO_BIT+ for that region) -\item [bit 24-28] Stores the bit region number (as opposed to geometric -region) in which a secondary particle -is created; if these bits are all 0, the particle is a primary -particle (not for \verb+LATCH_OPTION+ = 1). +\item [bit 24-28] When downshifted by 24 bits (see paragraph below), these store the bit +region in which a secondary particle +is created; if no bit number is stored, the particle is a primary +particle. Note these bits are not used if \verb+LATCH_OPTION+ = 1. \item [bit 29-30] Store the charge of a particle when \verb+LATCH+ is output to a phase space file (see section~\ref{PSF} on phase space files). During a simulation, bit 30 is used to identify a contaminant particle @@ -4933,16 +4948,14 @@ \section{Tracking a Particle's History using LATCH} the particle is a contaminant particle; 0 otherwise. Note that if \verb+LATCH+ is not inherited (\ie\ when \verb+LATCH_OPTION+ = 1), bit 30 loses its meaning. - - \item [bit 31] Set to 1 if a particle has crossed a scoring plane more than once when \verb+LATCH+ is output to a phase space file (see section~\ref{PSF} on phase space files above) \end{description} -For secondary particles, recording the region number in which they were -created in bits 24-28 is equivalent to multiplying the region number by -2$^{24}$, or 16777216. Thus, to retrieve the region of origin of a +For secondary particles, recording the bit region in which they were +created in bits 24-28 is equivalent to multiplying the bit region number by +2$^{24}$, or 16777216. Thus, to retrieve the bit region of origin of a secondary particles, the \verb+LATCH+ value of the particle must be divided by 16777216 (\ie\ taking the value \verb+INT(LATCH/16777216))+. @@ -4954,41 +4967,40 @@ \section{Tracking a Particle's History using LATCH} \begin{description} \item [LATCH\_OPTION = 1 (Non-Inherited LATCH Setting):] -secondaries do not inherit \verb+LATCH+ -values from the primaries that created them; +{\tt LATCH} bits 1-23 store bit regions where a particle +has been. Secondaries do not inherit \verb+LATCH+ +values from the primaries that created them ({\em i.e.}, bits 1-23 of a secondary particle carry no information about the -regions its primary parent(s) has(ve) been. This option must NOT be +the transport history of its ancestors). This option must NOT be used if \verb+ICM_CONTAM+ is non-zero since the \verb+ICM_CONTAM+ option needs bit 30. \index{ICM\_CONTAM} \item [LATCH\_OPTION = 2 (Comprehensive LATCH Setting --default):] -\verb+LATCH+ values\\ are passed on to -secondary particles from the primaries that created them; bits 1-23 -for a secondary particle include all regions in which the secondary +Bits 1-23 store bit regions where a particle +has been. \verb+LATCH+ values are passed on to +secondary particles from the primaries that created them. Thus, bits 1-23 +for a secondary particle include all bit regions in which the secondary particle has been plus those in which its ancestors have been -up to the point where the secondary was created; uses -bits 24-28 to record the bit region -where secondary particles are created and bit 0 to -record whether or not a bremsstrahlung photon was involved in a +up to the point where the secondary was created. Bits +24-28 are used to record the bit region +where a secondary particle is created. Bit 0 +is set if a bremsstrahlung photon is involved in a \index{LATCH!LATCH\_OPTION} \index{bremsstrahlung!bit 0 flag} \index{bremsstrahlung!testing for} particle's history. \item [LATCH\_OPTION = 3 (Comprehensive LATCH Setting 2):] -similar to 2, but for\\ photons -bits 1-23 record the regions in which the particles have interacted, -rather than simply the regions in which they have been. After a Compton, -pair or photo-electric event, the charged particles, and in the latter -case, also the fluorescent photons, have the bits 1--23 set for the region -in which they are created to treat the case in which they are created -below cutoff in a manner similar to being created above cutoff (where the -bits would be set on the first step). +Similar to {\tt LATCH\_OPTION}=2, but, for a photon, +bits 1-23 record the bit regions in which the particle has interacted, +rather than simply where it has been. Secondary particles +resulting from these interactions have bits 1-23 set for the +bit regions in which they were created. \end{description} To clarify further the setting of \verb+LATCH+ bits under various \verb+LATCH_OPTION+ values, fig~\ref{fig_latch} and table~\ref{table_latch} \index{LATCH!LATCH\_OPTION} -summarise the situation for a simple photon accelerator. Two electrons -enter the simulation and produce bremsstrahlung photons in the target, -bit (and geometric) region 1. One photon goes all the way to the scoring +summarize the situation for a simple photon accelerator. Two electrons +enter the simulation and produce bremsstrahlung photons in the target (bit region 1). +One photon goes all the way to the scoring plane without interacting and the second undergoes a pair production event in the flattening filter (bit region 3). The electron escapes from the flattening filter an gets to the scoring plane and the positron @@ -4999,7 +5011,40 @@ \section{Tracking a Particle's History using LATCH} \index{ICM\_CONTAM} \index{IQ\_CONTAM} \verb+IQ_CONTAM=-1+). -\clearpage +For {\tt LATCH\_OPTION}=1 (non-inherited), bits 1-23 are set for bit regions +where a particle has been. Note that all particles have bit 23 set because they +have all been in air, which defaults to bit region 23 unless the user explicitly +sets it to some other bit region number. Bits 24-28 store nothing because the +bit regions where secondary particles are created are not recorded. Contaminant +particles are not marked, so bit 30 is not used, and bremsstrahlung events are +not recorded in bit 0. + +For {\tt LATCH\_OPTION}=2 (comprehensive inherited where been), bits 1-23 for a +particle are set for bit regions where it and all of its ancestors have been. +Thus, all particles have bit 1 set since they are all descendants of the +bremsstrahlung interaction in bit region 1. Particles 2 and 3 both have bit 3 +set since they are descendants of the pair event in bit region 3. Again, bit 23 +is set for all particles because they (and their ancestors) all pass through +air. In addition, bit 0 is set for all particles because they (or their +ancestors) are products of a bremsstrahlung event (in bit region 1). Bits +24-28, when downshifted by 24 bits, store the bit region where secondary +particles were created. Thus, these bits store the number "3" for particles 2 +and 3 and the number "1" for particle 1. Finally, bit 30 is used to identify +contaminant particles and their descendants, where, in this example, contaminant +particles are defined as any charged particle crossing the contaminant plane +shown. Thus, bit 30 for particle 3, an electron reaching the scoring plane from +above the contaminant plane, is set. + +{\tt LATCH\_OPTION}=3 (comprehensive inherited where interacted) is similar to +{\tt LATCH\_OPTION}=2 except that bits 1-23 are set for bit regions in which +photons (and ancestral photons) have interacted, as opposed to regions they have +simply passed through. Note that charged particles interact at every step +(although only a small fraction of these interactions are explicitly simulated!) +and so they can be treated the same as with {\tt LATCH\_OPTION}=2. In the +example shown, the only difference in bit settings between {\tt LATCH\_OPTION}=2 +and {\tt LATCH\_OPTION}=3 is that bit 23 is not set for particles 1 and 2, +because these photons have not interacted in air, nor are they descendants of +photons that have interacted in air. \begin{figure}[H] \vspace*{-0.3cm} @@ -5013,7 +5058,8 @@ \section{Tracking a Particle's History using LATCH} the phase space file after 2 electrons are incident. Contamination is defined as charged particles crossing the contamination plane. Table~\ref{table_latch} shows the bit settings in {\tt LATCH} as the particles -reach the scoring plane. The bit region numbers are shown in circles.} +reach the scoring plane. The bit numbers associated with the geometric regions +(bit regions) are shown in circles.} \label{fig_latch} \end{center} \end{figure} @@ -5021,7 +5067,8 @@ \section{Tracking a Particle's History using LATCH} \vspace*{-1cm} \begin{center} \caption{Bit settings in LATCH for the simple example shown in -fig~\ref{fig_latch}.} +fig~\ref{fig_latch}. In the +case of bits 24-28, the table gives the numbers stored after downshifting by 24 bits.} \label{table_latch} \begin{tabular}{|r|c|ccccccc|c|c|} \hline @@ -5062,8 +5109,8 @@ \section{Calculating Dose Components} to be broken down into their components. In any dose zone, BEAMnrc is able to break dose down in 2 ways: dose from contaminant particles (identified on -the basis of their charge only); or dose including only and/or excluding -only contributions arising from particles with certain user-specified +the basis of their charge only); dose +arising only from particles with a certain user-specified combination of \verb+LATCH+ bit settings (this is called ``bit filtering''). \index{ITDOSE\_ON} @@ -5081,30 +5128,25 @@ \section{Calculating Dose Components} and are only required if \verb+ITDOSE_ON = 1+. \begin{description} \item [ICM\_CONTAM] contaminant particles are identified upon entering -the top of \verb+CM+ number \verb+ICM_CONTAM+ if 1 $\leq$ \verb+ICM_CONTAM+ -$\leq$ total number of \verb+CM+s (previously, this range was restricted to -1 $<$ \verb+ICM_CONTAM+ $\leq$ total number of \verb+CM+s); -if it is set to 0, no contaminant dose will be calculated. +the top of \verb+CM+ number \verb+ICM_CONTAM+, where 1 $\leq$ \verb+ICM_CONTAM+ +$\leq$ total number of \verb+CM+s. If \verb+ICM_CONTAM+ +is set to 0, no contaminant dose will be calculated. \index{LATCH!LATCH\_OPTION} \item [IQ\_CONTAM] The charge of the contaminant particles (0 for photons and 1 for charged particles); all particles with this charge will be marked as contaminant particles (by setting -\verb+LATCH+ bit 30 of the particles to 1) +\verb+LATCH+ bit 30) upon entering the front of \verb+CM+ number \verb+ICM_CONTAM+. \end{description} -Contaminant dose is scored in every dose zone. However it is traced back only -to those particles identified as having contaminant charge upon entering CM -number \verb+ICM_CONTAM+. For example, if \verb+IQ_CONTAM+ = 1, all the charged -particles entering CM number \verb+ICM_CONTAM+ will be marked as contaminant -particles and this mark will be passed onto their descendants via -\verb+LATCH+ bit 30. The dose -contributed by the contaminant particles and their descendants is then scored -as the contaminant dose. Note that if \verb+LATCH_OPTION = 1+ +Contaminant dose is scored in every dose zone and is the dose due to particles +having the contaminant charge entering CM number \verb+ICM_CONTAM+ and their +descendants. For example, if \verb+IQ_CONTAM+ = 1, all the charged particles +entering CM number \verb+ICM_CONTAM+ and their descendants will contribute to +contaminant dose. Note that if \verb+LATCH_OPTION = 1+ \verb+LATCH+ values are not transferred to descendants (secondaries), and contaminant dose calculations will be meaningless. Thus, the contaminant dose option is automatically -turned off if \verb+LATCH_OPTION = 1+. Note also that prior to Sept 2002, -contamination was defined as it entered the CM from the front or the back. +turned off if \verb+LATCH_OPTION = 1+. The following variables are associated with bit filtering of dose and are only required if \verb+ITDOSE_ON+ = 1: @@ -5115,47 +5157,34 @@ \section{Calculating Dose Components} \index{LNINC} \index{L\_N\_INC} \begin{description} -\item [LNEXC] number of dose components that -exclude contributions from particles with user-specified \verb+LATCH+ bits -set (bit filters). \verb+LNEXC+ = 0 is allowed. \verb+LNEXC <= $MAXIT - 3+ +\item [LNEXC] number of dose components using an exclusive {\tt LATCH} bit +filter. Note that\\ +\verb+0 <= LNEXC <= $MAXIT - 3+, where \verb+$MAXIT+ can be changed from its default value of 12 (as described in section~\ref{ctd}). -\item [L\_N\_EXC(I,31) (I = 1,2,...,LNEXC)] Bit filter for determining -which particles to exclude -from dose component I; each of the LNEXC components requires input of a -separate bit filter; a bit filter consists of a sequence of up to 31 -\verb+LATCH+ -bit numbers on a single record (range 1-31), separated by commas; -particles with any of the listed bits set -are excluded from dose component I. -\item [LNINC] number of dose components with contributions only from -particles with user specified bit filters which are a combination of -inclusive and possibly exclusive patterns. \verb+LNINC+ = 0 is allowed. -\verb+LNINC <= $MAXIT - LNEXC - 3+. -%For example, if the inputs for \verb+L\_N\_EXC(I,31)+ are 2,3,5,0,..., -%then the dose component I will exclude the contributions from the -%particles with any of the LATCH bits 2,3,5 set high (=1) - -\item [L\_N\_INC(I,31) (I = 1,2,...,LNINC)] Bit filter for determining -which particles to include in dose component I; each of the LNINC -components requires input of a separate bit filter which consists of 2 groups -of \verb+LATCH+ bit numbers (range 1-31) separated by a 0; -contributions from the particles with any of the \verb+LATCH+ bits in the -first group of \verb+L_N_INC(I,31)+ set and none of those in the second -group set are included in dose component I. - -For example, if the inputs for -\verb+L_N_INC(I,31)+ are 2,3,5,0,1,4,0,..., then dose component I will -include the contributions from the particles with {\bf any} of the \verb+LATCH+ -bits 2, 3 or 5 set (=1) {\bf and} both \verb+LATCH+ bits 1 and 4 not set (=0); -the status of other \verb+LATCH+ bits will have no effect on this -dose component. +\item [L\_N\_EXC(I,31) (I = 1,2,...,LNEXC)] Exclusive bit filter for dose +component I. An exclusive bit filter consists of a sequence of up to 31 bit +numbers (range 1-31) on a single record separated by commas. Particles with any +of the bits set are excluded from dose component I. +\item [LNINC] number of dose components using an inclusive/exclusive {\tt LATCH} +bit filter. Note \verb+0 <= LNINC <= $MAXIT - LNEXC - 3+. \item [L\_N\_INC(I,31) +(I = 1,2,...,LNINC)] Inclusive/exclusive bit filter for dose component I+LNEXC +(inclusive/exclusive components are listed after exclusive components). An +inclusive/exclusive bit filter consists of up to 31 bit numbers (range 1-31) +split into 2 groups input on one record. Bit numbers are separated by commas, +with ",0," denoting the end of the first (inclusive) group and the beginning of +the second (exclusive) group. Dose component I+LNEXC then includes contributions +from particles with \verb+LATCH+ having any of the bits in the first group set +and none of those in the second group set. For example, if the input for +\verb+L_N_INC(I,31)+ is 2,3,5,0,1,4, then dose component I will include the +contributions from the particles with {\bf any} of \verb+LATCH+ bits 2, 3 or 5 +set {\bf and} neither of bits 1 and 4 set. The status of other \verb+LATCH+ bits +will have no effect on this dose component. If the inputs are 1,2,3,0,0,...,(equivalently 1,2,3,) the dose component will include -the contributions from the particles with any of the \verb+LATCH+ +the contributions from the particles with any of \verb+LATCH+ bits 1, 2 or 3 -set (=1). Note that no dose will be scored if one inputs 0,2,3,5,0,... - +set, and there are no exclusive bit settings. \end{description} @@ -5166,10 +5195,15 @@ \section{Calculating Dose Components} Bit filtering of dose provides a particularly powerful tool for determining dose contributions. In view of the information stored in \verb+LATCH+ (see section above), dose contributions can be separated -according to what regions particles have passed through/interacted in, -whether the particle is a primary or secondary, if the particle is a -secondary then where it was created, whether or not the particle is a -contaminant, and any combination of these. +according to: +\begin{enumerate} +\item What regions particles have passed through/interacted in +\item Whether the particle is a primary or secondary +\item Where a secondary was created +\item Whether or not the particle is a +contaminant +\item Any combination of the above +\end{enumerate} \index{fat particles} It should be noted that if directional bremsstrahlung splitting (DBS) @@ -5344,23 +5378,23 @@ \subsection{IZLAST} \item [= 0] (default) BEAMnrc does not score \verb+ZLAST+ in phase space files; this means that phase space files are read and -written in compressed ``mode0'' +written in compressed ``MODE0'' \item [= 1] BEAMnrc scores the Z position of last interaction in phase -space files; phase space files are read and written in compressed ``mode2''; -``mode2'' files are approximately 14\% larger than ``mode0'' files; when +space files; phase space files are read and written in compressed ``MODE2.'' +``MODE2'' files are approximately 14\% larger than ``MODE0'' files; when plotting phase space data with paw, \verb+ZLAST+ replaces the radial position of a photon (r) -\item [= 2] Same as option 1 and in Addison, BEAMnrc writes the X-Y-Z positions +\item [= 2] Same as option 1 and, in addition, BEAMnrc writes the X-Y-Z positions of the last site of interaction for photons into the \verb+.egsgph+ file. These last sites of interaction can be viewed in 3-D using -{\tt EGS\_Windows}\cite{TR99a}. {\tt IWATCH}=4 -must not be turned on at the same time since it also writes to the +{\tt EGS\_Windows}\cite{TR99a}. Note that {\tt IWATCH}=4 must not be turned on +at the same time since particle tracks are also written to the \verb+.egsgph+ file. \index{EGS\_Windows} \end{description} -Note that the utility BEAMDP has an option to present graphs of {\tt ZLAST} +Note that the utility BEAMDP has an option to plot graphs of {\tt ZLAST} in 2-D. \subsection{NCASE} @@ -5424,12 +5458,12 @@ \subsection{IXXIN, JXXIN} of the previous run is read from the {\tt .egsdat} file and is used at the beginning of the restart. Thus, a restarted run with a total of, eg, 10000+10000 histories should generate results identical to a single run -of the same simulation with 20000 histories. Also note that -when running parallel -simulations with BEAMnrc (see section~\ref{parallelcalc}), {\tt JXXIN} must have -a different value for each of the individual jobs that make up the simulation. -A property of the random number generators being used is that this simple -change guarantees random number sequences which are independent. +of the same simulation with 20000 histories. Also note that when running +parallel simulations with BEAMnrc (see section~\ref{parallelcalc}), {\tt IXXIN} +and/or {\tt JXXIN} must have different values for each of the individual jobs +that make up the simulation. A property of the random number generators being +used is that this simple change guarantees random number sequences which are +independent. \index{random number generator!changing from RANMAR to RANLUX} To switch from the default RANMAR to RANLUX in your BEAM code, either go into @@ -5515,6 +5549,10 @@ \subsection{ ECUTIN} although for electrons which are moving isotropically, this can be a very conservative requirement. +If the global value of \verb+ECUT+ is left blank or set to 0, then it defaults +to \verb+AE+ of the default medium, unless the default is VACUUM, in which +case it defaults to the maximum \verb+AE+ of all media in the accelerator. + \subsection{ PCUTIN} \index{PCUTIN} \label{PCUTIN} \index{PCUT} {\tt PCUT} is the photon equivalent of {\tt ECUT}. As soon as a @@ -5536,6 +5574,10 @@ \subsection{ PCUTIN} \index{PCUTIN} \label{PCUTIN} \index{PCUT} that low values do not take much more time. A value of 0.01 MeV should generally be used. +The global value of \verb+PCUT+ defaults to \verb+AP+ of the default +medium, unless this is VACUUM, in which case it defaults to the maximum +\verb+AP+ of all media in the accelerator. + \subsection{ ESTEPIN, SMAX, IDORAY, IFLUOR} \label{dummyinputs} \index{ESTEPIN} @@ -5550,7 +5592,7 @@ \subsection{ ESTEPIN, SMAX, IDORAY, IFLUOR} ({\tt IDORAY}), and a switch to turn on K-shell X-ray fluorescence ({\tt IFLUOR}). Now all of these transport parameters are handled in the EGSnrc inputs (see section~\ref{egsnrc_inputs}), however, -the dummy inputs are retained for compatibility with older EGS4 BEAM +the dummy inputs are retained for compatibility with older BEAM input files. \subsection{ ICM\_SPLIT, NSPLIT\_PHOT, NSPLIT\_ELEC} @@ -5559,25 +5601,22 @@ \subsection{ ICM\_SPLIT, NSPLIT\_PHOT, NSPLIT\_ELEC} \index{NSPLIT\_PHOT} \index{NSPLIT\_ELEC} -{\tt ICM\_SPLIT} is used to split photons and electrons at an arbitrary -plane within an accelerator. To use this option, the user sets -{\tt ICM\_SPLIT} equal to the CM \# at the top of which the photons and electrons -are to be split. When {\tt ICM\_SPLIT}$>$0, then the user must -input {\tt NSPLIT\_PHOT} and {\tt NSPLIT\_ELEC}, the splitting number for -photons -and electrons, respectively, upon entering the CM. If -{\tt NSPLIT\_PHOT} or {\tt NSPLIT\_ELEC} is $\leq$1, then the relevant -particle type is not split at all. Once a particle -has been split, the resultant particles carry weight -1/{\tt NSPLIT\_PHOT} or 1/{\tt NSPLIT\_ELEC}. A particle is only split -upon entering the user-specified CM from the top (\ie\ {\tt W(NP) > 0}) -and if it has not been split by this option before. +These inputs are used to split photons and electrons by an arbitrary splitting +number upon entering a CM. The CM number is specified by {\tt ICM\_SPLIT}, with +the restriction\\ +1$<${\tt ICM\_SPLIT}$\leq${\tt MAX\_CMs}, and {\tt NSPLIT\_PHOT} and {\tt +NSPLIT\_ELEC} are the splitting numbers for photons and electrons, respectively. +If the splitting number is $\leq$1 then particles are not split. Once a particle +has been split, the resultant particles carry weight 1/{\tt NSPLIT\_PHOT} or +1/{\tt NSPLIT\_ELEC}. A particle is only split upon entering the user-specified +CM from the top (\ie\ {\tt W(NP) > 0}) and if it has not been split by this +option before. Splitting at an arbitrary plane was designed primarily for improving statistics in dose calculations in a phantom, -in which case particles (usually photons) would be split upon entering a -phantom at the bottom of the accelerator. Use of this option near the +in which case particles are split upon entering the CM modeling +the phantom. Use of this option near the top of an accelerator may produce undesirable correlations, without much gain in efficiency. @@ -5587,49 +5626,32 @@ \subsection{ ICM\_SPLIT, NSPLIT\_PHOT, NSPLIT\_ELEC} to the plane at which photon forcing is to begin), the photons are split BEFORE they are forced to interact. -Currently, if {\tt ICM\_SPLIT}=1, then the -option is turned on, but no splitting will occur. We hope to remove this -restriction, but if you wish to split particles in CM 1, you can -get around the problem, by inserting a dummy CM 1 and setting -{\tt ICM\_SPLIT}=2. - -\section{EGSnrc inputs} +\section{EGSnrc Monte Carlo Transport Parameters} \label{egsnrc_inputs} \index{EGSnrc inputs} -The use of EGSnrc to simulate charged particle and photon transport -in BEAMnrc allows the user a greater degree of control over the -transport physics -than was previously available in EGS4 versions of BEAM. For most -accelerator applications, the default settings in the BEAMnrc code for the EGSnrc -parameters should be adequate (these are not the same as the EGSnrc -standard defaults). However, there are some cases, such -as low energy applications, in which the user will want to vary -the EGSnrc transport parameters using the EGSnrc inputs. - -EGSnrc inputs appear at the end of a BEAMnrc input file using the new -format used with the general purpose user EGSnrc user codes. The input -occurs between the +EGSnrc allows the user extensive control over the Monte Carlo (MC) parameters +governing transport physics in BEAMnrc. The default settings of these +parameters in BEAMnrc are currently identical to those for EGSnrc applications +in general and will result in accurate simulations at both high (MV) and low +(kV) energies. However, if the user is interested only in MV simulations, then +CPU time can be saved by adjusting some of these parameters without sacrificing +accuracy. These parameters and their recommended settings for MV applications +will be noted in the subsections below. + +EGSnrc inputs generally appear at the end of a BEAMnrc input file +between the delimiters {\tt :start mc transport parameter:} and -{\tt :stop mc transport parameter:}. +{\tt :stop mc transport parameter:} and have the format:\\ +{\tt PARAMETER NAME = parameter value}\\ +If you are using the BEAMnrc GUI, then the EGSnrc parameters +(including defaults) are written to the input file when you save it. -In general, EGSnrc inputs must appear in the input file in -the format:\\ -{\tt PARAMETER NAME= parameter value}\\ -Note that there is a space between the ``='' sign and the parameter value -but not before the ``='' sign. -If you are using the BEAMnrc GUI to set the EGSnrc inputs, then -the above format is written to the input file automatically when you save -the input parameters. - -If any or all of the EGSnrc input parameters is missing, then the default -setting will be used. This feature allows BEAM input files to be used -directly with BEAMnrc. A better approach is to read the old BEAM input -file into the {\tt beamnrc\_gui} and then save it since this will explicitly -add the required EGSnrc inputs to the file. - -The following sections describe the EGSnrc inputs required in -BEAMnrc. For more information, see the EGSnrc manual\cite{KR03}. The +If an MC transport parameter does not appear in the input file, +then its default value is used. + +The following subsections describe each EGSnrc MC transport parameter. +For more information, see the EGSnrc manual\cite{KR03}. The actual internal variable name associated with each input appears in brackets. \subsection{ {\tt Global ECUT} ({\tt ECUT})} @@ -5741,8 +5763,7 @@ \subsection{{\tt Skin depth for BCA} ({\tt skindepth\_for\_bca})} (in elastic mean free paths) from the boundary at which lateral pathlength corrections are turned off and the particle is transported in a straight line until it reaches the boundary. -By default the distance at which to switch off -lateral corrections is a fixed value calculated by EGSnrc to be +In this case, the default is a fixed value calculated by EGSnrc to be the same as that used in the original implementation of PRESTA in EGS4 and depends on the value of {\tt ECUT}. @@ -5766,7 +5787,7 @@ \subsection{{\tt Electron-step algorithm} ({\tt transport\_algorithm})} This input determines the algorithm used to calculate lateral and longitudinal corrections to account for elastic scattering in a condensed history electron step. There are 2 possible settings: {\tt PRESTA-II} -(the default) and {\tt PRESTA-I}. {\tt PRESTA-II} is the new, +(the default) and {\tt PRESTA-I}. {\tt PRESTA-II} is the newer, more accurate, algorithm developed for use with EGSnrc\cite{KR03}. {\tt PRESTA-I} is the original PRESTA algorithm with some modifications\cite{BR87}. The original {\tt PRESTA-I} is known @@ -5780,7 +5801,7 @@ \subsection{{\tt Spin effects} ({\tt spin\_effects})} \index{spin effects} \index{spin\_effects} -If {\tt Spin effects= on} (the default), then elastic scattering +If {\tt Spin effects= On} (the default), then elastic scattering cross-sections that take into account relativistic spin effects are used in electron transport. If {\tt Spin effects= off}, then screened Rutherford cross-sections (similar to EGS4) are used for elastic @@ -5799,18 +5820,19 @@ \subsection{ {\tt Brems angular sampling} ({\tt IBRDST})} \label{bremssect} This input determines the type of angular sampling that is done when -a bremsstrahlung photon is created. If {\tt Brems angular sampling= Simple} -(the default) then bremsstrahlung angles are sampled using only the leading +a bremsstrahlung photon is created. The possible settings for +{\tt Brems angular sampling} are {\tt Simple} and {\tt KM} (the default). +If {\tt Simple} is used, then bremsstrahlung angles are sampled using only the leading term of modified equation 2BS of Koch and Motz\cite{Bi89,KM59}. If {\tt Brems angular sampling= KM}, then the bremsstrahlung angles are sampled -using the entire modified equation. +using the entire modified equation. Note that {\tt Brems angular sampling= KM} +is similar to the bremsstrahlung angular sampling scheme used by the latest +version of EGS4/BEAM, with some modifications. + {\tt Brems angular sampling= Simple} is adequate at high energies, however, there is little increase in simulation time associated with using -the entire modified 2BS equation and the entire equation is recommended +the entire modified 2BS equation, and the entire equation is recommended at low energies. -Note that {\tt Brems angular sampling= KM} is similar to the bremsstrahlung -angular sampling scheme used by the latest version of EGS4/BEAM, with some -modifications. \subsection{ {\tt Brems cross sections} ({\tt IBR\_NIST})} \index{bremsstrahlung cross sections} @@ -5840,8 +5862,9 @@ \subsection{ {\tt Bound Compton scattering} ({\tt IBCMP})} The {\tt Bound Compton scattering} input is used to determine whether binding effects and Doppler broadening are simulated in Compton -(incoherent) scattering events. If this input is set to {\tt Off} -(the default), then the Klein-Nishina formula\cite{KN29} is used to +(incoherent) scattering events. It has four possible settings: {\tt Off}, {\tt +On}, {\tt Simple} and {\tt Norej} (the default). If this input is set to {\tt +Off}, then the Klein-Nishina formula\cite{KN29} is used to determine differential cross-sections for Compton scattering. This is similar to the treatment of Compton scattering in EGS4/BEAM. If {\tt Bound Compton scattering= On}, then the original Klein-Nishina formula is @@ -5849,13 +5872,19 @@ \subsection{ {\tt Bound Compton scattering} ({\tt IBCMP})} effects and Doppler broadening. Simulation of binding effects and Doppler broadening takes extra time and is only important below 1 MeV and/or if Rayleigh scattering is being simulated (see section~\ref{rayleighsect}). -A third option, {\tt Bound Compton scattering= Norej}, is provided which -uses the total bound Compton cross sections ({em i.e.} no impulse -approximation) and does not reject any Compton interactions at run -time. - -Bound Compton scattering may also be turned on in selected regions -(off everywhere else) using +The {\tt Simple} setting uses the impulse approximation to simulate binding +effects but neglects doppler broadening. Finally, the default {\tt Norej} +option uses the total bound Compton cross sections ({em i.e.} no impulse +approximation) resulting in no rejected Compton interactions at run time. + +For MV applications, {\tt Bound Compton scattering} can be set to {\tt Off} with +little impact on simulation accuracy but with a potentially significant decrease +in CPU time. Directional bremsstrahlung splitting (see section~\ref{dbssect}), +in particular, makes use of a more efficient Compton splitting routine if {\tt +Bound Compton scattering} is {\tt Off}. + +Bound Compton scattering may also be turned {\tt On} in selected regions +({\tt Off} everywhere else) using {\tt Bound Compton scattering= On in regions} together with the inputs {\tt Bound Compton start region} and {\tt Bound Compton stop region} to define the region ranges for which bound Compton is to be turned on. @@ -5872,7 +5901,7 @@ \subsection{ {\tt Compton cross sections} ({\tt comp\_xsections})} \index{Compton cross section data} \index{comp\_xsections} -If the {\tt Bound Compton scattering= Norej} option is selected (see above), then +If the {\tt Bound Compton scattering= Simple} option is selected (see above), then the user also has the option of specifying their own Compton cross section data using the {\tt Compton cross sections} input. Cross section data must exist @@ -5886,14 +5915,15 @@ \subsection{ {\tt Compton cross sections} ({\tt comp\_xsections})} \end{verbatim} Default Compton cross section \index{Compton cross section data!default} -data is contained in the file {\tt compton\_sigma.data} and is included with -the EGSnrc system. +data is contained in the file {\tt compton\_sigma.data} included with +the EGSnrc system. Note that this default data is also used +if {\tt Bound Compton scattering} is not set to {\tt Simple}. \subsection{{\tt Radiative Compton corrections} ({\tt radc\_flag})} \index{radiative Compton corrections} \index{radc\_flag} -If set to {\tt Radiative Compton corrections= On}, then radiative +If set to {\tt On}, then radiative corrections for Compton scattering based on the equations of Brown and Feynman (Phys. Rev. 85, p 231--1952) are used. If set to {\tt Off} (the default) no corrections are done. @@ -5908,17 +5938,16 @@ \subsection{ {\tt Pair angular sampling} ({\tt IPRDST})} This input determines the method used to sample the positron/electron emission angles (relative to the incoming photon) in a pair production event. There -are three possible settings of this input: {\tt Off}, {\tt Simple} and {\tt KM}. +are three possible settings: {\tt Off}, {\tt Simple} (the default) and {\tt KM}. If it is set to {\tt Off}, then the positron and electron created by pair production have fixed polar angles, $\theta_{\pm}$, given by $\theta_{\pm}=\frac{m}{E_{\gamma}}$, where m is the electron rest energy and $E_{\gamma}$ - is the energy of the original photon. This is similar to method used to determine -positron/electron emission angles in the original version of EGS4. +is the energy of the original photon. If {\tt Pair angular sampling= KM}, then equation 3D-2003 in an article by Motz et al\cite{Mo69} is used to determine the positron/electron emission -angles. This option is similar to the sampling technique used by the current -version of EGS4/BEAM. Finally if {\tt Pair angular sampling= Simple} (the default), then only +angles. This option is similar to the sampling technique used by +EGS4/BEAM. Finally if {\tt Pair angular sampling= Simple} (the default), then only the first term in the the Motz et al equation 3D-2003 is used. The {\tt KM} option becomes less efficient with increasing accelerator energies and, moreover, involves assumptions that are questionable at low energy. For these reasons, the default @@ -5942,12 +5971,12 @@ \subsection{ {\tt Photoelectron angular sampling} ({\tt IPHTER})} The {\tt Photoelectron angular sampling} input determines the sampling method used by EGSnrc to determine the angle of emission of photoelectrons. -If {\tt Photoelectron angular sampling= Off} (the default), then - photoelectrons inherit the direction of the incident photon. If -{\tt Photoelectron angular sampling= On}, then Sauter's formula +If {\tt Photoelectron angular sampling= Off}, then +photoelectrons inherit the direction of the incident photon. If\\ +{\tt Photoelectron angular sampling= On} (the default), then Sauter's formula \cite{Sa31} is used to determine the angle of the photoelectron. Note that, in most applications, we have not observed any difference between -the ``Off" and ``On" settings of this parameters. Also note that, +the {\tt Off} and {\tt On} settings of this parameters. Also note that, strictly speaking, Sauter's formula is only valid for K-shell photo-absorption and is also derived from extreme relativistic approximations. Thus, if the user has a better approach, they can insert it in the @@ -5961,140 +5990,223 @@ \subsection{ {\tt Photoelectron angular sampling} ({\tt IPHTER})} {\tt Photoelectron angular sampling= Off in regions} together with the inputs {\tt PE sampling start region} and {\tt PE sampling stop region} to define the region ranges for which -photoelectron angular sampling is to be turned on or off. +photoelectron angular sampling is to be turned {\tt On} or {\tt Off}. \subsection{ {\tt Rayleigh scattering} ({\tt IRAYLR})} \index{Rayleigh scattering} \index{IRAYLR} \label{rayleighsect} -This input determines whether Rayleigh (coherent) scattering is -simulated or not. Note that this replaces the {\tt IDORAY} input +This input determines the simulation of Rayleigh (coherent) scattering. +Its possible settings are {\tt On} (the default), {\tt Off} and {\tt Custom}. +Note that this replaces the {\tt IDORAY} input in the BEAM main inputs (see section~\ref{dummyinputs}). -If {\tt Rayleigh scattering= On}, then Rayleigh events are simulated +If {\tt Rayleigh scattering= On} (the default), then Rayleigh events are simulated using the total coherent cross-sections from Storm and Israel\cite{SI70} and atomic form factors from Hubbell and {\O}verb{\o}\cite{HO79}. -This data must be included in the PEGS4 material data set. -If {\tt Rayleigh scattering= Off} (the default), then Rayleigh -events are not simulated. Rayleigh scattering is only recommended for -low energy ($<$ 1 MeV) simulations. Also, for proper simulation -with Rayleigh events included, bound Compton scattering (see section~\ref{bcsect} above) -should also be turned on. - -Rayleigh scattering can be turned on or off in selected regions + +If {\tt Rayleigh scattering= Off}, then Rayleigh events are not simulated. The +{\tt Custom} setting \index{custom Rayleigh form factors} allows the user to +specify custom Rayleigh form factors for specified media. To do this, the user +must specify the list of media in additional input {\tt ff media names= } and +the list of files containing custom form factors for each medium in the +additional input {\tt ff file names= }. For media not included in {\tt ff media +names}, Rayleigh scattering is turned {\tt On} and uses default atomic form +factors. + +Rayleigh scattering is recommended for low energy ($<$ 1 MeV) simulations. +Also, for proper simulation of Rayleigh events, bound Compton scattering (see +section~\ref{bcsect} above) should also be simulated. + +Rayleigh scattering can be turned {\tt Off} for MV applications with little to +no effect on simulation accuracy. + +Note that if Rayleigh scattering is turned {\tt On} and PEGS4 photon cross +sections are used (see section~\ref{photxsectsect} below) then the option to +include Rayleigh data must have been turned on when generating the PEGS4 data. + +Rayleigh scattering can be turned {\tt On} or {\tt Off} in selected regions (with the opposite setting everywhere else) using {\tt Rayleigh scattering= On in regions} or {\tt Rayleigh scattering= Off in regions} and the inputs {\tt Relaxations start region} and {\tt Relaxations stop region} to define the region ranges for turning Rayleigh scattering on or off. -\index{custom Rayleigh form factors} -EGSnrc also allows the user to specify custom Rayleigh form factors for -specified media. To do this, the user must -set {\tt Rayleigh scattering= custom} and then specify the list of -PEGS4 media in additional input {\tt ff media names= } and the list of -files containing custom form factors for each specified -medium in the additional input {\tt ff file names= }. +\subsection{{\tt Photon cross sections} ({\tt photon\_xsections})} +\label{photxsectsect} +\index{photon cross-sections} +\index{photon\_xsections} + +\index{photon cross-sections!Storm-Israel} +\index{photon cross-sections!EPDL} +\index{photon cross-sections!XCOM} +This input determines the photon cross section data used. Current possible +settings (and the data source used) are: {\tt xcom} (XCOM), {\tt si} +(Storm-Israel), {\tt epdl} (Evaluated Photon Data Library), {\tt pegs4} (PEGS4), +{\tt mcdf-xcom}, and {\tt mcdf-epdl}. The current default is {\tt xcom}. +However, this can be changed using the {\tt \$XDATA\_DEFAULT} macro in {\tt +\$HEN\_HOUSE/src/egsnrc.macros}. Note that if {\tt PEGS4} cross sections are +either supplied by a PEGS4 data file or are calculated on the fly in pegsless +mode. + +\index{Sabbatucci \& Salvat!renormalized photoelectric cross sections} The +inputs, {\tt mcdf-xcom} and {\tt mcdf-epdl}, instruct the code to use Sabbatucci +\& Salvat's renormalized cross sections when simulating photoelectric events, +with either the XCOM ({\tt mcdf-xcom}) or Evaluated Photon Data Library ({\tt +mcdf-epdl}) used for all other cross sections. The more accurate modeling of +photoelectric events allowed by the the Sabbatucci \& Salvat cross sections does +incur a CPU time penalty (up to 6\% for a 30 kV beam) and so this option is only +of interest for low energy simulations. Use of these renormalized cross sections +is necessary for agreement with PENELOPE results in ICRU90\cite{ICRU90}. + +If the user has their own photon cross section data, {\tt x}, then this can be +used as an input for {\tt Photon cross sections} provided that the files: {\tt +x\_photo.data} (photoelectric cross sections), {\tt x\_pair.data} (pair +production event cross sections), {\tt x\_triplet.data} (triplet event cross +sections) and {\tt x\_rayleigh.data} (rayleigh cross sections) exist in the {\tt +\$HEN\_HOUSE/data} directory. Once these files are in place, then ``x'' will +appear in the pull-down menu in the GUI where photon cross-sections are +specified. Alternatively, if you are editing the {\tt .egsinp} file directly, +you can enter the line: +\begin{verbatim} +Photon cross sections= x +\end{verbatim} +inside the block of EGSnrc transport parameter inputs. + +\subsection{{\tt Photon cross-sections output} ({\tt xsec\_out})} +\index{Photon cross-sections output} +\index{xsec\_out} + +The input {\tt Photon cross-sections output} can be set to {\tt Off} (the +default) or {\tt On}. If set to {\tt On}, then the simulation outputs the file +{\tt \$EGS\_HOME/BEAM\_accelname/inputfile.xsections} which contains the photon +cross section data used in the simulation. \subsection{ {\tt Atomic Relaxations} ({\tt IEDGFL})} \index{atomic relaxations} \index{IEDGFL} -This input determines whether or not the relaxation of atoms to their -ground state after Compton and photoelectric events is simulated. -If {\tt Atomic Relaxations= On}, then relaxation after -Compton and photoelectric events is simulated via the -emission of any combination of K-, L-, M- and N-shell fluorescent photons, Auger electrons -and Coster-Kronig electrons. The lower energy limit for relaxation processes +This input determines how the relaxation of atoms to their ground state after +Compton, photoelectric and electron impact ionization events is simulated. +Possible settings are {\tt Off}, {\tt On}, {\tt eadl} (the default) and {\tt +simple}. The {\tt On} option defaults to {\tt eadl}. + +If set to {\tt Off} then relaxations are not simulated. In this case, when +there is a photoelectric event, EGSnrc transfers all of the photon energy to the +photoelectron. This is different from EGS4/BEAM, where the binding energy of +the electron is subtracted and deposited on the spot. Both approaches are +approximations, but the EGSnrc approach is more accurate. + +If set to {\tt simple} then a simplified relaxation scheme based on the +transition probabilities in the Evaluated Atomic Data Library (EADL) is used. +Relaxation after Compton, electron impact ionization and photoelectric events is +simulated via the emission of K-, L-, M- and N-shell fluorescent photons, Auger +electrons and Coster-Kronig electrons. In this option, the EADL is also used as +a ``one size fits all'' library of binding energies, independent of the photon +cross sections used (see section~\ref{photxsectsect} above). This can result in +a mismatch between the energies of the fluorescent photons emitted and the +binding energies used for interactions. Note that this was the only relaxation +scheme implemented until the 2018 release of EGSnrc/BEAMnrc. + +If set to {\tt eadl} then a more detailed relaxation scheme, also based on the +EADL transition probabilities, is used. This differs from the {\tt simple} +relaxation scheme in that: 1) initial $\langle$M$\rangle$ shell vacancies are +not considered; 2) for final vacancies, exact M- and N-shells replace +$\langle$M$\rangle$ and $\langle$N$\rangle$. Moreover, the {\tt eadl} +relaxation algorithm uses binding energies consistent with the photon cross +sections selected (see section~\ref{photxsectsect} above), eliminating the +mismatch between the energies of fluorescent photons and these binding energies. +If the user has opted to use Sabbatucci \& Salvat's renormalized photoelectric +cross sections ({\tt Photon cross sections = mcdf-xcom} or {\tt mcdf-epdl}--see +section~\ref{photxsectsect} above)--then {\tt simple} relaxation cannot be used, +and the code will automatically default to {\tt eadl} relaxation. + +The lower energy limit for relaxation processes is 1 keV. Thus, only relaxation in shells with binding energy $>$ 1 keV is simulated. -If {\tt Atomic Relaxations= Off} (the default), then atomic relaxations -are not simulated. In this case, when there is a -photoelectric event, EGSnrc transfers all of the photon energy to the -photoelectron. This is different from EGS4/BEAM, where the binding energy -of the electron is subtracted and deposited on the spot. Both approaches -are approximations, but the EGSnrc approach is more accurate. -{\tt Atomic Relaxations= On} is only recommended for low energy applications. + +Simulation of atomic relaxations is essential for accurate transport in low +energy (kV) applications. However, it can be turned {\tt Off} for MV +applications to reduce simulation time at no significant reduction in accuracy. + Note that the {\tt Atomic Relaxations} option supersedes the {\tt IFLUOR} option in EGS4/BEAM (see section~\ref{dummyinputs}), which only simulates emission of K-shell fluorescent photons after photoelectric events. -Similar to bound Compton, photoelectric angular sampling and -Rayleigh scattering, atomic relaxations can be turned on/off in +Atomic relaxations can be turned {\tt On}/{\tt Off} in selected regions (with the opposite setting everywhere else) using {\tt Atomic Relaxations= On in regions} or {\tt Atomic Relaxations= Off in regions} and the inputs {\tt Relaxations start region} and {\tt Relaxations stop region} to define -the region ranges for which relaxations are to be turned on/off. +the region ranges for which relaxations are to be turned {\tt On}/{\tt Off}. +Since the {\tt On} setting defaults to {\tt eadl}, the detailed {\tt eadl} +relaxation algorithm will be used in regions where atomic relaxations are set +{\tt On}. \subsection{ {\tt Electron impact ionization} ({\tt eii\_flag})} \index{electron impact ionization} \index{eii\_flag} -This input determines what, if any, theory is used to simulate -electron impact ionization. The possible values are +This input determines the cross sections used to simulate electron impact +ionization (EII). The possible values of {\tt Electron impact ionization} are: +{\tt Off} (the default), {\tt On}, {\tt ik}, {\tt casnati}, {\tt gryzinski}, +{\tt kolbenstvedt}, and {\tt penelope}. \index{Casnati} \index{Kolbenstvedt} \index{Gryzinski} -``off'' (the default), ``on'', ``Casnati'', ``Kolbenstvedt'', -and ``Gryzinski''. When ``on'' is selected, Kawrakow's electron -impact ionization theory\cite{Ka02b} is used. For the other selections, -the theory associated with the name given is used. See -the EGSnrc Manual\cite{KR03} for more details. - -Since the details of electron impact ionization are only relevant -at keV X-Ray energies, the default ``off'' setting should be used -in most linac simulations. - -\subsection{ {\tt Photon cross sections} ({\tt photon\_xsections})} -\index{photon cross-sections} -\index{photon\_xsections} - -This selects the photon interaction cross-sections to use in -the simulation. Cross-sections included with the BEAMnrc/DOSXYZnrc -distribution (and, thus, the possible settings of -{\tt photon\_xsections} immediately after installation are): -\index{photon cross-sections!Storm-Israel} -\index{photon cross-sections!EPDL} -\index{photon cross-sections!XCOM} -``Storm-Israel'' (the default), ``epdl'' and ``xcom''. -The Storm-Israel cross-sections are the standard PEGS4 cross-sections. -The ``epdl'' setting will use cross-sections from -the evaluated photon data library (EPDL) from Lawrence Livermore\cite{Cu90}. -The ``xcom'' setting will use the XCOM -photon cross-sections from Burger and Hubbell\cite{BH87}. Note that -the EGSnrc transport parameter input routine is coded in such a way that, -if you are editing the {\tt .egsinp} file directly instead of using -the BEAMnrc GUI, the default Storm-Israel cross-sections can only be -specified by leaving out the {\tt Photon cross sections} input line -altogether. This is taken care of automatically if you are using the -GUI to set this parameter. - -\index{photon cross-sections!customized} -You can also use your own customized photon cross-section data. To do this, -you must create the files {\tt x\_pair.data}, {\tt x\_photo.data}, {\tt x\_rayleigh.data} and -{\tt x\_triplet.data} (where ``x'' is the name of your cross-section data) -which contain cross-sections for pair production, photoelectric events, rayleigh scattering and triplet production, respectively. These files must be in -your {\tt \$HEN\_HOUSE/data} directory. Once these files are in place, then -``x'' will appear in the pull-down menu in the GUI where photon -cross-sections are specified. Alternatively, if you are editing the -{\tt .egsinp} file directly, you can enter the line: -\begin{verbatim} -Photon cross sections= x -\end{verbatim} -inside the block of EGSnrc transport parameter inputs. - -\subsection{{\tt Photon cross-sections output} ({\tt xsec\_out})} -\index{Photon cross-sections output} -\index{xsec\_out} +\index{Penelope} + +If set to {\tt Off} EII is not simulated. If set to {\tt On}, then it defaults +to {\tt ik}, and cross sections from Kawrakow's electron impact ionization +theory\cite{Ka02b} are used. The selections, {\tt casnati}, {\tt gryzinski}, +and {\tt kolbenstvedt}, use EII cross sections derived from the theories +associated with the respective names, and {\tt penelope} uses the cross sections +identical to those used to simulate EII in the Penelope code. See the EGSnrc +Manual\cite{KR03} for more details. -The input {\tt Photon cross-sections output} can be set to {\tt On} to -output the file\\ - {\tt \$EGS\_HOME/BEAM\_accelname/inputfile.xsections} which -contains the photon cross section data used in the simulation. Default -is {\tt Off}. +EII cross section data is stored in the files \verb+$HEN_HOUSE/data/eii_x.data+, +where \verb+x+ specifies the theory/source of the data and is identical to the +{\tt Electron impact ionization} input (Note: inputs are case sensitive). Thus, +it is possible for the user to use their own EII cross section data provided it +is in the supplied in a file having the same format as those already included +with the distribution. + +EII is only of interest for low energy X-ray applications. + +\subsection{ {\tt Triplet production} ({\tt itriplet})} +\index{triplet production} +\index{itriplet} + +This input turns on/off the simulation of triplet production. Possible values of +{\tt Triplet production} are {\tt Off} (the default) and {\tt On}. If set to +{\tt On} then Borsellino's first Born approximation\cite{Mo69} is used to sample +triplet events based on the triplet cross section data in +\verb+$HEN_HOUSE/data/triplet.data+. + +\subsection{ {\tt Photonuclear attenuation} ({\tt iphotonucr}) and\\ +{\tt Photonuclear cross sections} ({\tt photonuc\_xsections})} +\index{photonuclear attenuation} +\index{photonuclear cross sections} + +First implemented in EGSnrc 2012\cite{AR12}, inclusion of the photonuclear +effect in simulations been found to have a significant effect on transmitted +photon spectra in the MV energy range. Though it is not necessary for most +applications, it should be included in the high-accuracy simulations used in +standards work. + +The input, {\tt Photonuclear attenuation}, determines whether the photonuclear +effect is included in the simulation. Possible settings are {\tt Off} (the +default) and {\tt On}. If set to {\tt On} then, if present, the input {\tt +Photonuclear cross sections} specifies the cross sections used. + +Cross sections must exist in the file \verb+$HEN_HOUSE/data/x_photonuc.data+, +where \verb+x+ is the name of the cross section database and corresponds to the +input for {\tt Photonuclear cross sections}. The distribution includes the +default photonuclear cross sections,\\ +\verb+iaea_photonuc.data+, which are used in the absence of any input for {\tt +Photonuclear cross sections}. \section{Custom user inputs} \label{custom_inputs} @@ -6137,9 +6249,9 @@ \section{Custom user inputs} A BEAMnrc simulation can be split into smaller jobs which can then be run on different processors in parallel to reduce the elapsed time required -for a simulation. Parallel processing requires that you be running -in Unix/Linux and that you have a network queuing system such as PBS or -NQS. +for a simulation. In general, parallel processing requires that you be running +on a system that supports a job queuing utility, such as {\tt at}, or, if +sending jobs to multiple cores over a network, PBS or NQS. \index{pprocess} \index{pprocess!limitations} @@ -6151,10 +6263,10 @@ \section{Custom user inputs} source inputs, {\tt IPARALLEL} and {\tt PARNUM}). This method of parallel processing had a major limitation, though, in that each job consisted of the same number of histories, making the total -simulation time dependent on the slowest CPU. +simulation time dependent on the slowest computing core. In the current version of BEAMnrc, parallel processing -is accomplished much more efficiently using a built-in +is accomplished more efficiently using a built-in parallel processing functionality. \index{exb} @@ -6163,10 +6275,18 @@ \section{Custom user inputs} {\tt exb} (discussed in detail in section~\ref{batchsect}). The command syntax for a parallel job is: \begin{verbatim} -exb BEAM_myaccel inputfile pegsdata [short|medium|long] [batch=batch_system] p=N +exb BEAM_myaccel inputfile pegsdata [short|medium|long] [batch=batch_system] ... + ... [start=first_job] p=N (or stop=last_job) [fresh=yes/no] \end{verbatim} -where {\tt N} is the number of parallel jobs to submit (see -Section~\ref{batchsect} for a detailed discussion of the other inputs). + +{\tt first\_job} is the number of the first parallel job minus 1 ({\tt +first\_job} defaults to 0), {\tt N} is the number of parallel jobs, and {\tt +last\_job} is the number of the last job (only used if {\tt N} is not input). +Note that the numbering convention of {\tt first\_job} is historical and may be +changed in future releases. The input {\tt fresh} can be used to specify whether +this is an independent batch of parallel jobs ({\tt yes}--the default) or +whether they are to be added to parallel jobs currently running ({\tt no}). The +other batch inputs above are covered in more detail in section~\ref{batchsect}. Once this command is entered, the script \index{exb} @@ -6175,35 +6295,51 @@ \section{Custom user inputs} aliased) enters a loop which submits BEAM\_myaccel to the batch queue {\tt N} times. Each submission has the form: \begin{verbatim} -BEAM_myaccel -i inputfile -p pegsdata -P n_parallel -j i_parallel +BEAM_myaccel -i inputfile -p pegsdata -P n_parallel -j i_parallel [-f first_job+1] \end{verbatim} \index{i\_parallel} \index{n\_parallel} -where {\tt n\_parallel}={\tt N} and {\tt i\_parallel} takes on values 1,2,..., -{\tt n\_parallel}, depending on which job is being submitted. +where {\tt n\_parallel}={\tt N}, {\tt i\_parallel} takes on values 1,2,..., +{\tt n\_parallel}, depending on which job is being submitted, and +{\tt first\_job}+1 is the number of the first parallel job. The last argument +is omitted if the batch submission script is run with {\tt fresh=no}. For each parallel job, BEAMnrc will create a temporary working directory (see section~\ref{twdsect} for more on temporary working directories), and the output files from the {\tt i\_parallel}th run will have the naming scheme -{\tt inputfile\_w[i\_parallel].egslog}, {\tt inputfile\_w[i\_parallel].egslst}, -{\tt inputfile\_w[i\_parallel].egsphsp1}, \\ +{\tt inputfile\_w[i\_parallel].egslog}, {\tt inputfile\_w[i\_parallel].egslst},\\ +{\tt inputfile\_w[i\_parallel].egsphsp1}, {\tt inputfile\_w[i\_parallel].egsdat}, etc. Note that {\tt N} different input files are not created, and that all parallel runs make use of the original input file. \index{.lock file} \index{job control file} -On submission of the first job ({\tt i\_parallel}=1) BEAMnrc will create +The first job submitted ({\tt first\_job}+1) creates a file, {\tt inputfile.lock}, in the {\tt BEAM\_myaccel} directory. The {\tt .lock} file, or job control file, is accessed and updated by all parallel -jobs and contains +jobs and contains: \index{n\_left} \index{n\_job} -the number of histories remaining to be run, {\tt n\_left}, and the total -number of jobs running, {\tt n\_job}, among other quantities. +\index{n\_tot} +\begin{itemize} +\item {\tt n\_left}: The number of histories remaining to be run after the current +job is submitted. +\item {\tt n\_tot}: The total number of histories already completed +\item {\tt n\_job}: The number of jobs currently running +\item {\tt sum} and {\tt sum2}: Scored quantity of interest and (quantity of +interest)$^2$ from all previous runs ({\em i.e.}, runs completed before +submitting the current parallel run) \item {\tt res} and {\tt dres}: scored +quantity of interest and relative uncertainty on quantity of interest (\%) after +the completion of {\tt n\_tot} histories in the current parallel run plus all +previous runs. +\end{itemize} + +Note that the {\tt .lock} file created by BEAMnrc during parallel runs currently +does not keep track of any quantity of interest, and +{\tt res}=0.0 and {\tt dres}=99.9\%. -Before -beginning a run, a parallel job opens the {\tt .lock} file and +Before running any history, a parallel job opens the {\tt .lock} file and reads {\tt n\_left} (the file cannot be read by more than one job at a time). If {\tt n\_left}$>$0, then there are still histories to run, and the job begins execution. @@ -6226,8 +6362,8 @@ \section{Custom user inputs} chunk of histories needs to be run. Doing parallel simulations in chunks like this prevents jobs that are -running on slower CPU's from tying up large portions of the simulation -and, hence, dominating the total elapsed time required. +running on slower cores from tying up large portions of the simulation +and, hence, determining the total elapsed time required. \index{lock file} \index{.lock file} If, on opening the {\tt .lock} file, a parallel job finds that @@ -6238,7 +6374,7 @@ \section{Custom user inputs} and decrements {\tt n\_job}. If, after decrementing {\tt n\_job}, {\tt n\_job}=0, then this is the last job to stop running, and it \index{egs\_combine\_runs} -automatically calls the EGSnrcMP subroutine {\tt egs\_combine\_runs} +automatically calls the subroutine {\tt egs\_combine\_runs} to combine the results from all parallel jobs (see section~\ref{recombinesect} below). @@ -6308,7 +6444,7 @@ \subsection{Combining Results from Parallel Jobs} \index{combining results\\ from parallel runs} The last parallel job to finish running automatically combines -the results of all parallel runs by calling the EGSnrcMP subroutine +the results of all parallel runs by calling the EGSnrc subroutine \index{egs\_combine\_runs} {\tt egs\_combine\_runs}. This subroutine loops through {\tt i\_parallel}=1,...,{\tt n\_parallel} and, for each value @@ -6350,7 +6486,7 @@ \subsection{Combining Results from Parallel Jobs} with the input variable {\tt IRESTART}=4 (in the GUI, this is equivalent to setting the Run option to ``analyze parallel jobs") after all parallel jobs have finished. Use of {\tt IRESTART}=4 is generally not necessary -now that the last job automatically combines parallel results, however, +since the last job automatically combines parallel results, however, it may be useful if, for some reason, all of the {\tt .egsdat} files were not moved out of their temporary working directories or if you wish to add more {\tt .egsdat} files from a separate group of parallel runs. @@ -6384,12 +6520,12 @@ \subsection{Combining Phase Space Files from Parallel Runs using {\tt addphsp}} for the concatenated phase space data (a {\tt .egsphsp[iscore]} extension is added automatically), {\tt ipar} is the number of parallel jobs being added, {\tt istart} is the job number at which adding begins -(ie the first value of {\tt i\_parallel})--defaults to 1, +(ie the first value of {\tt i\_parallel}--defaults to 1), {\tt iscore} is the scoring plane number for which you are combining phase space files (\ie\ are -you adding {\tt .egsphsp1}, {\tt .egsphsp2} or {\tt .egsphsp3} files?)--defaults -to 1, and {\tt i\_iaea} is set to 1 if you are adding IAEA-format phase -space files--default is 0. +you adding {\tt .egsphsp1}, {\tt .egsphsp2} or {\tt .egsphsp3} files?--defaults +to 1), and {\tt i\_iaea} is set to 1 if you are adding IAEA-format phase +space files (default is 0 for EGSnrc-format phase space files). {\tt addphsp} then concatenates the phase space files {\tt inputfile\_w[istart].egsphsp[iscore]}, @@ -6705,8 +6841,7 @@ \subsubsubsection{SYNCMLCE} \index{SYNCHDMLC} \subsubsubsection{SYNCHDMLC} SYNCHDMLC is a version of SYNCVMLC optimized for modeling the High-definition Multileaf -Collimator (HDMLC 120) and the Millenium MLC (120 MLC) available on TrueBeam and Novalis linacs. -SYNCHDMLC features five +Collimator (HDMLC 120) available on TrueBeam and Novalis linacs. SYNCHDMLC features five possible leaf cross sections: FULL, HALF TARGET/HALF ISOCENTER pairs, and QUARTER TARGET/QUARTER ISOCENTER pairs. FULL leaves are similar to FULL leaves in DYNVMLC/SYNCVMLC. HALF TARGET/HALF ISOCENTER leaves are equivalent to the TARGET/ISOCENTER leaves in DYNVMLC/SYNCVMLC. QUARTER TARGET/QUARTER ISOCENTER have the @@ -6863,8 +6998,6 @@ \subsubsection{SLABS} \end{center} \end{figure} -\clearpage - The input format for SLABS, and an example of the input file are given as follows. @@ -6883,7 +7016,7 @@ \subsubsection{SLABS} %} %\markboth{CONS3R Users Manual}{~~~~last edited 2004/11/19 20:21:18 %~~~~printed \today} - +\clearpage %\vspace*{1.5cm} \subsubsection{CONS3R} \renewcommand{\rightmark}{CONS3R CM} @@ -6980,8 +7113,6 @@ \subsubsection{CONESTAK} \end{center} \end{figure} -\clearpage - The input format for CONESTAK, and an example of input file are given as follows. \begin{small} @@ -7027,8 +7158,6 @@ \subsubsection{FLATFILT} \end{figure} -\clearpage - \begin{small} \index{FLATFILT!inputs} \input{./inputformats/FLATFILT.inp} @@ -7042,6 +7171,8 @@ \subsubsection{FLATFILT} %\markboth{CHAMBER Users Manual}{~~~~last edited 2004/11/19 20:21:18 %~~~~printed \today} +\clearpage + \subsubsection{CHAMBER} \label{chamber_cm} \renewcommand{\rightmark}{CHAMBER CM} @@ -7441,6 +7572,8 @@ \subsubsection{CIRCAPP} %\markboth{PYRAMIDS Users Manual}{~~~~last edited 2004/11/19 20:21:18 %~~~~printed \today} +\clearpage + \subsubsection{PYRAMIDS} \renewcommand{\rightmark}{PYRAMIDS CM} \index{PYRAMIDS} @@ -7456,13 +7589,11 @@ \subsubsection{PYRAMIDS} This CM has a square outer boundary centered on the beam axis. -\newpage - -\begin{figure}[tp] +\begin{figure}[htp] \htmlimage{scale=1.5} \leavevmode \hfill -\includegraphics[height=10.5cm]{figures/pyramidsd} +\includegraphics[height=10cm]{figures/pyramidsd} \vspace{0.1cm} \includegraphics[height=6.0cm]{figures/pyramidstop} \caption[PYRAMIDS CM geometry] @@ -7499,7 +7630,7 @@ \subsubsection{PYRAMIDS} %\setlength{\textheight}{10.1in} -%\clearpage +\clearpage %\markboth{BLOCK Users Manual}{~~~~last edited 2004/11/19 20:21:18 %~~~~printed \today} @@ -7531,8 +7662,7 @@ \subsubsection{BLOCK} is because John Antolak of the M.D. Anderson Cancer Center found and corrected some serious errors in this CM. -\newpage -\begin{figure}[tp] +\begin{figure}[htp] \begin{center} \leavevmode \begin{latexonly} @@ -7578,7 +7708,7 @@ \subsubsection{BLOCK} %\setlength{\textheight}{10.0in} -%\clearpage +\clearpage %\markboth{MLC Users Manual}{~~~~last edited 2004/11/19 20:21:18 %~~~~printed \today} @@ -7652,7 +7782,7 @@ \subsubsection{MLC} %\setlength{\textheight}{10.0in} -%\clearpage +\clearpage %\markboth{MLCQ Users Manual}{~~~~last edited 2004/11/19 20:21:18 %~~~~printed \today} @@ -7715,7 +7845,7 @@ \subsubsection{MLCQ} %\setlength{\textheight}{10.0in} -%\clearpage +\clearpage %\markboth{VARMLC Users Manual}{~~~~last edited 2004/11/19 20:21:18 %~~~~printed \today} @@ -8332,15 +8462,12 @@ \subsubsection{SYNCHDMLC} \index{SYNCHDMLC} SYNCHDMLC is a CM coded by Lobo \& Popescu and based on an earlier code by Borges et al\cite{Bo12} for -modeling the high-definition micro mlc (HD120) and the Millenium MLC (MLC 120) available on TrueBeam and Novalis linacs. In overall +modeling the high-definition micro mlc (HD120) available on TrueBeam and Novalis linacs. In overall design it is similar to DYNVMLC/SYNCVMLC but features two different types of TARGET/ISOCENTER leaf pairs: HALF TARGET/HALF ISOCENTER and QUARTER TARGET/QUARTER ISOCENTER. In terms of leaf cross-section (perpendicular to the opening direction), these are similar to the TARGET/ISOCENTER leaves in DYNVMLC, with HALF TARGET/HALF ISOCENTER leaves being -wider than the QUARTER TARGET/QUARTER ISOCENTER leaves. The five available leaf types are intended to facilitate -modeling of either the HD120 MLC (HALF TARGET/ISOCENTER and QUARTER TARGET/ISOCENTER leaves) or the MLC 120 -(FULL and HALF TARGET/ISOCENTER leaves). However, the user is free to use any combination of leaf types to model -their MLC, provided that TARGET/ISOCENTER leaves are always used in pairs. +wider than the QUARTER TARGET/QUARTER ISOCENTER leaves. \begin{figure}[htpb] \begin{center} @@ -8357,7 +8484,7 @@ \subsubsection{SYNCHDMLC} \end{center} \vspace*{-1.0cm} \caption[SYNCHDMLC CM geometry] -{Example SYNCHDMLC using all leaf types with 12 leaves opening in the Y +{Example SYNCHDMLC with 12 leaves opening in the Y direction ({\tt ORIENT}=0). The X cross-sections of the five leaf types show the dimensions that the user must input (see Table~\ref{dynvmlc_tab} for label key). @@ -8400,9 +8527,10 @@ \subsubsection{SYNCHDMLC} of adjacent leaves all having the same type. Since HALF TARGET/HALF ISOCENTER leaves and QUARTER TARGET/QUARTER ISOCENTER leaves must always occur in pairs, there are really only three types to choose from. This also means there must be an even number of -HALF or QUARTER TARGET/ISOCENTER leaves. Also note that, even though an input line must -exist for all cross-sections, the values on this line can be blanks, zeroes, or nonsense real -numbers for leaves not being used in the MLC model. +HALF or QUARTER TARGET/ISOCENTER leaves. Also note that, even though the user +must specify cross-sections for all leaf types, they need not use all types in a +given MLC simulation. Thus, there may be no FULL leaves, HALF TARGET/ISOCENTER +pairs, or QUARTER TARGET/ISOCENTER pairs in the simulation. Similar to DYNVMLC and SYNCVMLC, leaf ends can be straight, focused ({\tt ENDTYPE}=1) or cylindrical ({\tt ENDTYPE}=0). For straight, focused ends, the user must specify the Z-position of the @@ -8748,6 +8876,8 @@ \subsubsection{ARCCHM} %\markboth{BEAMnrc Users Manual}{~~~~~~last edited 2004/11/19 20:21:18 %~~~~printed \today} +\clearpage + \renewcommand{\rightmark}{Cross-section data-PEGS4} \section{Cross-Section Data -- PEGS4} \label{CSDP} @@ -8836,15 +8966,12 @@ \subsection{Creating additional cross section data} An much easier way to create PEGS4 data is to run PEGS4 from the {\tt egs\_gui} (invoked simply by typing ``{\tt egs\_gui}''). A screen shot of the PEGS4 option in the {\tt egs\_gui} is shown in -Figure~\ref{fig_pegs4_screen}. For more information on {\tt egs\_gui} -see the EGSnrcMP Manual\cite{Ka03}. +Figure~\ref{fig_pegs4_screen}. Note that {\tt egs\_gui} offers an option to append newly-created PEGS4 data to an existing {\tt .pegs4dat} file. -\clearpage - -\begin{figure}[ht] +\begin{figure}[htb] \htmlimage{scale=2.5} \leavevmode \begin{center} @@ -8917,6 +9044,7 @@ \subsection{Choice of AE,AP} \end{figure} \subsection{Pegsless Mode} +\label{pegsless_sect} \index{pegsless mode} As of 2013, the user has the option of running BEAMnrc (and other EGSnrc user codes) in pegsless mode, thus obviating the requirement for a-priori calculation of cross-section data and generation @@ -9106,7 +9234,7 @@ \section{Distribution and Installation} available on the github page: \htmladdnormallink{{\tt https://github.com/nrc-cnrc/EGSnrc/wiki/Installation-overview}}{https://github.com/nrc-cnrc/EGSnrc/wiki/Installation-overview} -In order to install and run EGSnrcMP and OMEGA/BEAM, your system must have: +In order to install and run EGSnrc and BEAMnrc, your system must have: \index{system requirements} \begin{enumerate} \index{Fortran compiler} @@ -9138,8 +9266,8 @@ \section{Distribution and Installation} \index{Qt} \index{Qt!how to get it} \item The Qt4 development tools. This is necessary for -compiling the GUIs for the EGSnrcMP user codes and is, thus, -not strictly necessary for the OMEGA/BEAM codes or if you can use the +compiling the GUIs for the EGSnrc user codes and is, thus, +not strictly necessary for BEAMnrc codes or if you can use the pre-compiled versions provided online. Pre-compiled versions of the Qt GUIs are available on the EGSnrc release page. Note that many current Linux distributions @@ -9213,11 +9341,11 @@ \section{Distribution and Installation} % the distribution website before installation. Note that ``Method 1'' and % ``Method 2'' for % EGSnrc installation are -% not available for the Mac OSX. +% not available for the MacOS. % % The third method, ``Method 3'', of installing EGSnrcMP is for % \index{EGSnrcMP!installation script} -% Unix/Linux systems and Mac OSX systems and uses the installation script +% Unix/Linux systems and MacOS systems and uses the installation script % {\tt install\_egs}. In addition to the script, you must also download % \index{EGSnrcMP!.tar files} % the {\tt tar} files (which may be in compressed format) @@ -9233,7 +9361,7 @@ \section{Distribution and Installation} % directory before running the {\tt install\_egs} script. This method % of installation may be necessary if your Linux/Unix system cannot % run the installation wizard and is currently the only way of -% installing EGSnrcMP on Mac OSX. Note that when you use this +% installing EGSnrcMP on MacOS. Note that when you use this % method of installation, you must % run the script {\tt \$HEN\_HOUSE/scripts/finalize\_egs\_foruser} % at the end ({\tt install\_egs} gives you an option to do this @@ -9253,7 +9381,7 @@ \section{Distribution and Installation} % also be asked to define the Fortran compiler that % you want to use (defaults are suggested if found on your system). % \index{installation!C compiler}. -% On Unix/Linux/Mac OSX systems, if you wish to use functionality that requires a C compiler such +% On Unix/Linux/MacOS systems, if you wish to use functionality that requires a C compiler such % as the built-in parallel processing functionality % (see Section~\ref{parallelcalc}) or BEAMnrc shared % library sources (see Section~\ref{sharedlibsect}), @@ -9289,7 +9417,7 @@ \section{Distribution and Installation} % EGSnrc C++ class library, egspp (see the egspp Manual\cite{Ka05a} for more % details). % -% Note that, on Unix/Linux/Mac OSX machines, if you supply a working C compiler +% Note that, on Unix/Linux/MacOS machines, if you supply a working C compiler % during EGSnrcMP installation % and the C routines for built-in parallel processing and/or BEAM shared % library sources are compiled successfully, then the installation automatically @@ -9311,7 +9439,7 @@ \section{Distribution and Installation} % {\tt config} is the prefix you have chosen for % the {\tt .conf} file). It is recommended that % you do this to avoid having to add them manually. When installing -% on Unix/Linux/Mac OSX, on the other hand, you do not have the option to set +% on Unix/Linux/MacOS, on the other hand, you do not have the option to set % these variables automatically. Instead, you will be directed to % add the statements: % \index{.cshrc} @@ -9347,7 +9475,7 @@ \section{Distribution and Installation} % % If you wish to use a second compiler or operating system, you can either % run the installation wizard (self-extracting or stand-alone) and -% select the ``Configure existing EGSnrc'' option or, if on a Unix/Linux/Mac OSX +% select the ``Configure existing EGSnrc'' option or, if on a Unix/Linux/MacOS % system, you can run the % script\\ % {\tt \$HEN\_HOUSE/scripts/configure} from the {\tt @@ -9391,7 +9519,7 @@ \section{Distribution and Installation} % Similar to EGSnrcMP, there are 3 methods for installing the OMEGA/BEAM system: % using the self-extracting installation wizard (Linux/Unix and Windows), % using the installation wizard with files downloaded separately -% (Linux/Unix and Windows) and using an installation script (Linux/Unix and Mac OSX). +% (Linux/Unix and Windows) and using an installation script (Linux/Unix and MacOS). % % \subsubsection{Using the Self-extracting Wizard} % \index{installing!with self-extracting wizard} @@ -9488,7 +9616,7 @@ \section{Distribution and Installation} % If setting up on Windows, then {\tt \$OMEGA\_HOME} % will automatically be set (to \\ % {\tt /full\_directory\_path\_to\_\$HEN\_HOUSE/omega}). -% If set up is on Unix/Linux/Mac OSX, {\tt \$OMEGA\_HOME} will not automatically be +% If set up is on Unix/Linux/MacOS, {\tt \$OMEGA\_HOME} will not automatically be % set, but you will be instructed (in the installation wizard display window) % to add the statement: % \index{beamnrc\_cshrc\_additions} @@ -10111,7 +10239,8 @@ \subsection{Changes from {\tt BEAMnrc03} to {\tt BEAMnrc05}} \begin{itemize} -\item Ported the entire set of codes to work with the EGSnrcMP system. +\item Ported the entire set of codes to work with the new multi-platform +EGSnrc system (EGSnrcMP). \item Electron impact ionization added to the EGSnrc system. diff --git a/HEN_HOUSE/omega/beamnrc/beamnrc.mortran b/HEN_HOUSE/omega/beamnrc/beamnrc.mortran index 3aa16beb5..f279e1d85 100644 --- a/HEN_HOUSE/omega/beamnrc/beamnrc.mortran +++ b/HEN_HOUSE/omega/beamnrc/beamnrc.mortran @@ -239,7 +239,7 @@ WITH {,' ',} "I> *********** "I> In many CMs, the region about the central-axis or at the "I> front or back of the CM, is assumed to be this medium. -"I> It is thought of and refered to as air, but can be anything. +"I> It is thought of and referred to as air, but can be anything. "I> Default is VACUUM. MEDIUM must exactly match name in pegs4dat "I>----------------------------------------------------------------------------- ; @@ -1133,13 +1133,13 @@ WITH {,' ',} "I> All input associated with selection of EGSnrc transport parameters "I> is not crucial for the execution as there are default values set. "I> Therefore, if some of the input options in this section are -"I> missing/misspelled, this will be ignored and defualt parameter assumed +"I> missing/misspelled, this will be ignored and default parameters assumed. "I> As the transport parameter input routine uses get_inputs, a lot "I> of error/warning messages may be produced on UNIT 15, though. "I> If you don't have the intention of changing default settings, "I> simply ignore the error messages. "I> -"I> The delimeters are +"I> The delimiters are "I> :start mc transport parameter: "I> :stop mc transport parameter: "I> @@ -1148,13 +1148,13 @@ WITH {,' ',} "I> "%A24 "I> Global ECUT= Global (in all regions) electron transport cut -"I> off energy (in MeV). If this imput is missing, +"I> off energy (in MeV). If this input is missing, "I> or is < ECUTIN from the main BEAMnrc inputs "I> (See above) then ECUTIN is used for Global ECUT. "I> Global ECUT defaults to AE(medium). "I> [ ECUT ] "I> Global PCUT= Global (in all regions) photon transport cut -"I> off energy (in MeV). If this imput is missing, +"I> off energy (in MeV). If this input is missing, "I> or is < PCUTIN from the main BEAMnrc inputs "I> (See above) then PCUTIN is used for Global PCUT. "I> Global PCUT defaults to AP(medium). @@ -1175,7 +1175,7 @@ WITH {,' ',} "I> ESTEPE= Maximum fractional energy loss per step. "I> Note that this is a global option only, no "I> region-by-region setting is possible. If missing, -"I> the defualt is 0.25 (25%). +"I> the default is 0.25 (25%). "I> [ ESTEPE ] "I> XImax= Maximum first elastic scattering moment per step. "I> Default is 0.5, NEVER use value greater than 1 as @@ -1198,26 +1198,20 @@ WITH {,' ',} "I> increase CPU time in most accelerators. "I> [ bca_algorithm, exact_bca ] "I> Skin depth for BCA= -"I> If Boundary crossing algorithm= PRESTA-I -"I> then this is the distance from the boundary (in -"I> elastic MFP) at which lateral correlations will be -"I> switched off. The default in this case is to -"I> calculate a value based on the scattering power at -"I> ECUT (same as PRESTA with EGS4). If -"I> Boundary crossing algorithm= EXACT (default) then -"I> this is the distance from the boundary (in elastic +"I> Determines the distance from a boundary (in elastic "I> MFP) at which the algorithm will go into single -"I> scattering mode and defaults to 3 mfp. -"I> Note that if you choose EXACT boundary crossing and -"I> set Skin depth for BCA to a very large number (e.g. -"I> 1e10), the entire calculation will be in SS mode. -"I> If you choose PRESTA-I boundary crossing and make -"I> Skin depth for BCA large, you will get default EGS4 -"I> behaviour (no PRESTA). +"I> scattering mode (if EXACT boundary crossing) or +"I> switch off lateral correlations (if PRESTA-I boundary +"I> crossing). Default value is 3 for EXACT or +"I> exp(BLCMIN)/BLCMIN for PRESTA-I (see the PRESTA paper +"I> for a definition of BLCMIN). Note that if you choose +"I> EXACT boundary crossing and set Skin depth for BCA +"I> to a very large number (e.g. 1e10), the entire +"I> calculation will be in SS mode. If you choose +"I> PRESTA-I boundary crossing and make Skin depth for +"I> BCA large, you will get default EGS4 behaviours +"I> (no PRESTA) "I> [ skindepth_for_bca ] -"I> -"I> The new transport mechanics of EGSnrc are maintained away from -"I> boundaries. "%A26 "I> Electron-step algorithm= "I> PRESTA-II (the default), the name is @@ -1230,12 +1224,12 @@ WITH {,' ',} "I> Spin effects= Off, On, (default is On) "I> Turns off/on spin effects for electron elastic "I> scattering. Spin On is ABSOLUTELY necessary for -"I> good backscattering calculations. Will make a +"I> good back-scattering calculations. Will make a "I> difference even in `well conditioned' situations "I> (e.g. depth dose curves for RTP energy range "I> electrons). "I> [ spin_effects ] -"I> Brems angular sampling= Simple, KM, (default is Simple) +"I> Brems angular sampling= Simple, KM, (default is KM) "I> If Simple, use only the leading term of the Koch-Motz "I> distribution to determine the emission angle of "I> bremsstrahlung photons. If KM, complete @@ -1251,20 +1245,27 @@ WITH {,' ',} "I> cross section data base (which is the basis for "I> the ICRU radiative stopping powers) will be employed. "I> Differences are negligible for E > ,say, 10 MeV, -"I> but signifficant in the keV energy range. If NRC is +"I> but significant in the keV energy range. If NRC is "I> selected, NIST data including corrections for "I> electron-electron brems will be used (typically only "I> significant for low values of the atomic number Z "I> and for k/T < 0.005). -"I> Bound Compton scattering= On, Off or Norej (Default is Off) +"I> Triplet production= On or Off (default). Turns on/off simulation +"I> of triplet production. If On, then Borsellino's +"I> first Born approximation is used to sample triplet +"I> events based on the triplet cross-section data. +"I> [ itriplet ] +"I> Bound Compton scattering= On, Off, Simple or norej (default) "I> If Off, Compton scattering will be treated with "I> Klein-Nishina, with On Compton scattering is "I> treated in the Impulse approximation. -"I> Make sure to turn on for low energy applications, -"I> not necessary above, say, 1 MeV. Option Norej -"I> uses full bound Compton cross section data -"I> supplied in input below and does not reject -"I> interactions. +"I> With Simple, the impulse approximation incoherent +"I> scattering function will be used (i.e., no Doppler +"I> broadening). With norej the actual total bound +"I> Compton cross section is used and there are no +"I> rejections at run time. +"I> Make sure to use for low energy applications, +"I> not necessary above, say, 1 MeV. "I> [ IBCMP ] "I> Compton cross sections= Bound Compton cross-section data. User- "I> supplied bound Compton cross-sections in the file @@ -1300,13 +1301,13 @@ WITH {,' ',} "I> to NRC, then use NRC pair production cross-sections "I> (in file $HEN_HOUSE/data/pair_nrc1.data). Only "I> of interest at low energies, where the NRC cross- -"I> sections take into account the assymmetry in the +"I> sections take into account the asymmetry in the "I> positron-electron energy distribution. "I> [ pair_nrc ] -"I> Photoelectron angular sampling= Off or On (Default is Off) +"I> Photoelectron angular sampling= Off or On (Default is On) "I> If Off, photo-electrons get the direction of the "I> `mother' photon, with On, Sauter's furmula is -"I> used (which is, striktly speaking, valid only for +"I> used (which is, strictly speaking, valid only for "I> K-shell photo-absorption). "I> If the user has a better approach, replace the macro "I> $SELECT-PHOTOELECTRON-DIRECTION; @@ -1317,60 +1318,103 @@ WITH {,' ',} "I> in a low energy photon beam. "I> [ IPHTER ] "I> Rayleigh scattering= Off, On, custom -"I> If On, turned on coherent (Rayleigh) scattering. -"I> Default is Off. Should be turned on for low energy -"I> applications. Not set to On by default because -"I> On requires a special PEGS4 data set. If set to -"I> custom, then media for which custom form factors -"I> are to be specified are listed in the input: -"I> ff media names= -"I> and the corresponding files containing custom data -"I> are listed in: -"I> ff file names= +"I> If On, turn on coherent (Rayleigh) scattering. +"I> Default is On. Should be turned on for low energy +"I> applications. +"I> If custom, user must provide media names and form +"I> factor files for each desired medium. For the rest +"I> of the media, default atomic FF are used. "I> [ IRAYLR ] -"I> Atomic relaxations= Off, On (Default is Off) -"I> The effect of using On is twofold: +"I> ff media names = A list of media names (must match media found in +"I> PEGS4 data file) for which the user is going to +"I> provide custom Rayleigh form factor data. +"I> [ iray_ff_media($MXMED) ] +"I> ff file names = A list of names of files containing the Rayleigh +"I> form factor data for the media specified by +"I> the ff media names = input above. Full directory +"I> paths must be given for all files, and for each medium +"I> specified, iray_ff_media(i), there must be a +"I> corresponding file name, iray_ff_file(i). For +"I> example files, see the directory +"I> $HEN_HOUSE/data/molecular_form_factors. +"I> [ iray_ff_file($MXMED) ] +"I> Atomic relaxations= Off, On, eadl, simple +"I> Default is eadl. On defaults to eadl. +"I> When simulating atomic relaxations: "I> - In photo-electric absorption events, the element "I> (if material is mixture) and the shell the photon "I> is interacting with are sampled from the -"I> appropriate cross seections -"I> - Shell vacancies created in photo-absorption events +"I> appropriate cross sections +"I> - Shell vacancies created in photoelectric, +"I> compton and electron impact ionization events "I> are relaxed via emission of fluorescent X-Rays, "I> Auger and Koster-Cronig electrons. -"I> Make sure to turn this option on for low energy +"I> The eadl option features a more accurate treatment +"I> of relaxation events and uses binding energies +"I> consistent with those in of the photon cross +"I> sections used in the simulation. If using +"I> mcdf-xcom or mcdf-epdl photon cross sections, you +"I> cannot use the simple option and this will +"I> automatically get reset to eadl. +"I> Make sure to use eadl or simple for low energy "I> applications. "I> [ IEDGFL ] "%A28 -"I> Electron impact ionization= Off, On, Casnati, Kolbenstvedt, Gryzinski -"I> (Default is Off) -"I> Determines which, if any, theory is used to model -"I> electron impact ionization. If set to 'On' then the -"I> theory of Kawrakow is used. Other settings use the -"I> theory associated with the name given. See future -"I> editions of the EGSnrc Manual (PIRS-701) for more -"I> details. This is only of interest in keV X-Ray -"I> simulations. Otherwise, leave it Off. -"I> [ eii_flag ] -"I> Photon cross sections= epdl,xcom,custom (Default is Storm-Israel -"I> cross-sections from PEGS4) -"I> The name of the cross-section data for photon -"I> interactions. This input line must be left out -"I> to access the default Storm-Israel cross-sections -"I> from PEGS4. 'edpl' uses cross-sections from the -"I> evaluated photon data library (EPDL) from Lawrence -"I> Livermore. 'xcom' will use the XCOM cross-sections -"I> from Burger and Hubbell. The user also has the -"I> option of using their own customized cross-section -"I> data. See the BEAMnrc manual for more details. -"I> [ photon_xsections ] +"I> Electron Impact Ionization= Off (default), On, casnati, kolbenstvedt, +"I> gryzinski, penelope. If set to On or ik, then use +"I> Kawrakow's theory to derive EII cross-sections. +"I> If set to casnati, then +"I> use the cross-sections of Casnati (contained in the +"I> file ($HEN_HOUSE/data/eii_casnati.data). Similar for +"I> kolbenstvedt, gryzinski and penelope. This is only of +"I> interest in kV X-ray calculations. +"I> Case-sensitive except for Off, On or ik options. +"I> [ eii_flag ] +"I> Photon cross sections= Photon cross-section data. Current options are +"I> si (Storm-Israel), epdl (Evaluated Photon Data +"I> Library), xcom (the default), pegs4, mcdf-xcom and +"I> mcdf-epdl: +"I> Allows the use of photon cross-sections other than +"I> from the PEGS4 file (unless the pegs4 option is +"I> specified). Options mcdf-xcom and mcdf-epdl use +"I> Sabbatucci and Salvat's renormalized photoelectric +"I> cross sections with either xcom or epdl for all other +"I> cross sections. These are more accurate but can +"I> increase CPU time by up to 6 %. +"I> Note that the user can supply their own cross-section +"I> data as well. The requirement is that the files +"I> photon_xsections_photo.data, +"I> photon_xsections_pair.data, +"I> photon_xsections_triplet.data, and +"I> photon_xsections_rayleigh.data exist in the +"I> $HEN_HOUSE/data directory, where photon_xsections +"I> is the name specified. +"I> Hence this entry is case-sensitive. +"I> [ photon_xsections ] "I> Photon cross-sections output= Off (default) or On. If On, then "I> a file $EGS_HOME/user_code/inputfile.xsections is "I> output containing photon cross-section data used. "I> [ xsec_out ] +"I> Photonuclear attenuation= Off (default) or On +"I> If On, models the photonuclear effect. Current +"I> implementation is crude. Available on a +"I> region-by-region basis (see below) +"I> [ IPHOTONUCR ] +"I> Photonuclear cross sections= Total photonuclear cross sections. User- +"I> supplied total photonuclear cross-sections in +"I> $HEN_HOUSE/data/photonuc_xsections_photonuc.data, +"I> where photonuc_xsections is the name supplied for +"I> this input (case sensitive). In the absence of +"I> any user-supplied data, or if photonuc_xsections +"I> is set to 'default', the default file is +"I> iaea_photonuc.data. +"I> [ photonuc_xsections ] "I> "I> Atomic relaxations, Rayleigh scattering, Photoelectron angular -"I> sampling and Bound Compton scattering can also be turned On/Off -"I> on a region-by-region basis. To do so, put e.g. +"I> sampling, Bound Compton scattering and Photonuclear attenuation +"I> can also be turned On/Off on a region-by-region basis. +"I> To do so, put e.g. +"I> "I> Atomic relaxations= On in Regions or "I> Atomic relaxations= Off in regions "I> in your input file. Then use the relevant one of: @@ -1385,6 +1429,9 @@ WITH {,' ',} "I> or "I> PE sampling start region= "I> PE sampling stop region= +"I> or +"I> Photonuclear start region= +"I> Photonuclear stop region= "I> "I> each followed by a list of one or more "I> start and stop regions separated by commas. @@ -1586,23 +1633,28 @@ REPLACE {$USER-CONTROLS-NEGATIVE-USTEP;} WITH { " ]" "};" -"the following change the defaults for the EGSnrc input parameters" -"override the values in egsnrc.macros" +"uncomment the following to change the defaults for certain EGSnrc input" +"parameters in egsnrc.macros. The settings below can speed up MV simulations" +"at little/no cost to accuracy" "Brems angular sampling= Simple" -REPLACE {$IBRDST-DEFAULT} WITH {0} +"REPLACE {$IBRDST-DEFAULT} WITH {0} ; "Bound Compton scattering= Off" -REPLACE {$IBCMP-DEFAULT} WITH {0} +"REPLACE {$IBCMP-DEFAULT} WITH {0} ; "Atomic relaxations= Off" -REPLACE {$IEDGFL-DEFAULT} WITH {0} +"REPLACE {$IEDGFL-DEFAULT} WITH {0} ; "Photoelectron angular sampling= Off" -REPLACE {$IPHTER-DEFAULT} WITH {0} +"REPLACE {$IPHTER-DEFAULT} WITH {0} +; + +"Rayleigh scattering = Off" +"REPLACE {$IRAYLR-DEFAULT} WITH {0} ; "required to prevent needless calls to interaction subroutines" @@ -6435,7 +6487,8 @@ ELSEIF(IBRSPL=2) ["directional bremsstrahlung splitting" "a fat electron" call do_compton; count_kill_comp = count_kill_comp + count_kill_tmp; - ] ELSE [ + ] ELSE +"at little/no cost to accuracy"[ IF(LATCH_OPTION=3)LATCH(np)=LATCHIN;"pass on LATCHIN" IF(IZLAST=1)zlast(np)=z(np); call do_smart_compton; diff --git a/HEN_HOUSE/omega/progs/gui/beamnrc/beamnrc_params.tcl b/HEN_HOUSE/omega/progs/gui/beamnrc/beamnrc_params.tcl index 2fbceadb6..49da3ee74 100644 --- a/HEN_HOUSE/omega/progs/gui/beamnrc/beamnrc_params.tcl +++ b/HEN_HOUSE/omega/progs/gui/beamnrc/beamnrc_params.tcl @@ -1435,7 +1435,7 @@ makes 2BS almost the same as 2BN at low energies). set numopts(ibrdst) 2 set options(ibrdst,0) "Simple" set options(ibrdst,1) "KM" -set values(ibrdst) $options(ibrdst,0) +set values(ibrdst) $options(ibrdst,1) set ibr_nist {} set names(ibr_nist) "Brems cross sections" @@ -1611,7 +1611,7 @@ set options(iphter,0) "Off" set options(iphter,1) "On" set options(iphter,2) "On in regions" set options(iphter,3) "Off in regions" -set values(iphter) $options(iphter,0) +set values(iphter) $options(iphter,1) set level(iphter) 0 set iraylr {} diff --git a/HEN_HOUSE/specs/beamnrc.spec b/HEN_HOUSE/specs/beamnrc.spec index 9035cf431..cbf87cc1e 100644 --- a/HEN_HOUSE/specs/beamnrc.spec +++ b/HEN_HOUSE/specs/beamnrc.spec @@ -81,11 +81,11 @@ SOURCES = $(EGS_SOURCEDIR)egsnrc.macros \ $(BEAM_HOME)beamnrc_user_macros.mortran \ $(EGS_UTILS)phsp_macros.mortran $(IAEA_PHSP_MACROS)\ $(BEAM_CODE)_macros.mortran \ - $(EGS_SOURCEDIR)egs_utilities.mortran \ $(BEAM_HOME)beam_main.mortran\ $(BEAM_HOME)beamnrc.mortran \ $(EGS_UTILS)xvgrplot.mortran \ $(BEAM_CODE)_cm.mortran \ + $(EGS_SOURCEDIR)egs_utilities.mortran \ $(EGS_SOURCEDIR)get_inputs.mortran \ $(EGS_SOURCEDIR)get_media_inputs.mortran \ $(RANDOM).mortran \ diff --git a/HEN_HOUSE/src/egsnrc.macros b/HEN_HOUSE/src/egsnrc.macros index 03882085f..832a69bdc 100644 --- a/HEN_HOUSE/src/egsnrc.macros +++ b/HEN_HOUSE/src/egsnrc.macros @@ -674,6 +674,7 @@ REPLACE {$MXESHLL} WITH {30} "max. number of shells for an element" REPLACE {$MAXSHELL} WITH {3000}"max. number of shells" REPLACE {$MAXRELAX} WITH {10000}"max. number of relaxations channels" REPLACE {$MAXVAC} WITH {100} "max. number of vacancies" +REPLACE {$MAXTRANS} WITH {300} "max. number of transitions per element" "============================================================" " Set input key 'Atomic relaxations' to 'simple' to recover original " implementation which allows photoelectric interactions with and diff --git a/HEN_HOUSE/src/egsnrc.mortran b/HEN_HOUSE/src/egsnrc.mortran index 0bb18cd69..df1f30058 100644 --- a/HEN_HOUSE/src/egsnrc.mortran +++ b/HEN_HOUSE/src/egsnrc.mortran @@ -5825,9 +5825,8 @@ character data_dir*128,relax_file*144; $INTEGER ish,medio,iZ,ntran; $REAL Ec, Pc, tmp, min_be, sumw,Ex; $LOGICAL is_open, is_there; -REPLACE {$MAXTMP} WITH {250} -$REAL wtmp($MAXTMP); -$INTEGER itmp($MAXTMP); +$REAL wtmp($MAXTRANS); +$INTEGER itmp($MAXTRANS); integer*4 pos, curr_rec, sh_eadl; integer*4 nz, nshell, tr_type; diff --git a/HEN_HOUSE/src/get_inputs.mortran b/HEN_HOUSE/src/get_inputs.mortran index d2f42d61c..47e4efae7 100644 --- a/HEN_HOUSE/src/get_inputs.mortran +++ b/HEN_HOUSE/src/get_inputs.mortran @@ -936,7 +936,7 @@ subroutine get_transport_parameter(ounit); " Brems angular sampling= Simple, KM, default is KM " If Simple, use only the leading term of the Koch-Motz " distribution to determine the emission angle of -" bremsstrahlung photons. If On, complete +" bremsstrahlung photons. If KM, complete " modified Koch-Motz 2BS is used (modifications " concern proper handling of kinematics at low energies, " makes 2BS almost the same as 2BN at low energies). @@ -969,7 +969,7 @@ subroutine get_transport_parameter(ounit); " broadenning). With norej the actual total bound " Compton cross section is used and there are no " rejections at run time. -" Make sure to turn on for low energy applications, +" Make sure to use for low energy applications, " not necessary above, say, 1 MeV. " [ IBCMP ] " Radiative Compton corrections= On or Off (default). If on, then @@ -1011,10 +1011,16 @@ subroutine get_transport_parameter(ounit); " positron-electron energy distribution. " [ pair_nrc ] " Photon cross sections= Photon cross-section data. Current options are -" si (Storm-Israel--the default), epdl (Evaluated Photon -" Data Library), xcom and pegs4. Allows the use of -" photon cross-sections other than from the PEGS4 file -" unless the pegs4 option is specified. +" si (Storm-Israel), epdl (Evaluated Photon Data +" Library), xcom (the default), pegs4, mcdf-xcom and +" mcdf-epdl: +" Allows the use of photon cross-sections other than +" from the PEGS4 file (unless the pegs4 option is +" specified). Options mcdf-xcom and mcdf-epdl use +" Sabbatucci and Salvat's renormalized photoelectric +" cross sections with either xcom or epdl for all other +" cross sections. These are more accurate but can +" increase CPU time by up to 6 %. " Note that the user can supply their own cross-section " data as well. The requirement is that the files " photon_xsections_photo.data, @@ -1039,10 +1045,9 @@ subroutine get_transport_parameter(ounit); " of any user-supplied data) is compton_sigma.data. " [ comp_xsections ] " Rayleigh scattering= Off, On, custom -" If On, turned on coherent (Rayleigh) scattering. -" Default is Off. Should be turned on for low energy -" applications. Not set to On by default for historical -" reasons since a PEGS4 data set is not required anymore. +" If On, turn on coherent (Rayleigh) scattering. +" Default is On. Should be turned on for low energy +" applications. " If custom, user must provide media names and form " factor files for each desired medium. For the rest " of the media, default atomic FF are used. @@ -1089,16 +1094,25 @@ subroutine get_transport_parameter(ounit); " in a low energy photon beam. " Default is On " [ IPHTER ] -" Atomic relaxations= Off, On -" Default is On. The effect of using On is twofold: +" Atomic relaxations= Off, On, eadl, simple +" Default is eadl. On defaults to eadl. +" When simulating atomic relaxations: " - In photo-electric absorption events, the element " (if material is mixture) and the shell the photon " is interacting with are sampled from the appropriate -" cross seections -" - Shell vacancies created in photo-absorption events +" cross sections +" - Shell vacancies created in photoelectric, +" compton and electron impact ionization events " are relaxed via emission of fluorescent X-Rays, " Auger and Koster-Cronig electrons. -" Make sure to turn this option on for low energy +" The eadl option features a more accurate treatment +" of relaxation events and uses binding energies +" consistent with those in of the photon cross sections +" used in the simulation. If using mcdf-xcom or +" mcdf-epdl photon cross sections, you cannot use +" the simple option and this will automatically get +" reset to eadl. +" Make sure to use eadl or simple for low energy " applications. " [ IEDGFL ] "