############################################################################### # Mesh-based Monte Carlo (MMC) # # Copyright (c) 2010-2018 Qianqian Fang <q.fang at neu.edu> # # http://mcx.space/#mmc # # # #Computational Optics & Translational Imaging (COTI) Lab [http://fanglab.org]# # Department of Bioengineering, Northeastern University # # # # Research funded by NIH/NIGMS grant R01-GM114365 # ############################################################################### $Rev::feab0b $ Last $Date::2018-08-19 19:32:18 -04$ by $Author::Qianqian Fang $ ############################################################################### usage: mmc <param1> <param2> ... where possible parameters include (the first item in [] is the default value) == Required option == -f config (--input) read an input file in .inp or .json format == MC options == -n [0.|float] (--photon) total photon number, max allowed value is 2^32-1 -b [0|1] (--reflect) 1 do reflection at int&ext boundaries, 0 no ref. -U [1|0] (--normalize) 1 to normalize the fluence to unitary,0 save raw -m [0|1] (--mc) 0 use MCX-styled MC method, 1 use MCML style MC -C [1|0] (--basisorder) 1 piece-wise-linear basis for fluence,0 constant -u [1.|float] (--unitinmm) define the mesh data length unit in mm -E [1648335518|int|mch](--seed) set random-number-generator seed; if an mch file is followed, MMC "replays" the detected photons; the replay mode can be used to calculate the mua/mus Jacobian matrices -P [0|int] (--replaydet) replay only the detected photons from a given detector (det ID starts from 1), use with -E -M [H|PHBSG] (--method) choose ray-tracing algorithm (only use 1 letter) P - Plucker-coordinate ray-tracing algorithm H - Havel's SSE4 ray-tracing algorithm B - partial Badouel's method (used by TIM-OS) S - branch-less Badouel's method with SSE G - dual-grid MMC (DMMC) with voxel data output -e [1e-6|float](--minenergy) minimum energy level to trigger Russian roulette -V [0|1] (--specular) 1 source located in the background,0 inside mesh -k [1|0] (--voidtime) when src is outside, 1 enables timer inside void --atomic [1|0] 1 use atomic operations, 0 use non-atomic ones == Output options == -O [X|XFEJLP] (--outputtype) X - output flux, F - fluence, E - energy deposit J - Jacobian, L - weighted path length, P - weighted scattering count (J,L,P: replay mode) -s sessionid (--session) a string used to tag all output file names -S [1|0] (--save2pt) 1 to save the fluence field, 0 do not save -d [0|1] (--savedet) 1 to save photon info at detectors,0 not to save -x [0|1] (--saveexit) 1 to save photon exit positions and directions setting -x to 1 also implies setting '-d' to 1 -q [0|1] (--saveseed) 1 save RNG seeds of detected photons for replay -F format (--outputformat)'ascii', 'bin' (in 'double'), 'json' or 'ubjson' == User IO options == -i (--interactive) interactive mode -h (--help) print this message -v (--version) print MMC version information -l (--log) print messages to a log file instead == Debug options == -D [0|int] (--debug) print debug information (you can use an integer or or a string by combining the following flags) -D [''|MCBWDIOXATRPE] 1 M photon movement info 2 C print ray-polygon testing details 4 B print Bary-centric coordinates 8 W print photon weight changes 16 D print distances 32 I entering a triangle 64 O exiting a triangle 128 X hitting an edge 256 A accumulating weights to the mesh 512 T timing information 1024 R debugging reflection 2048 P show progress bar 4096 E exit photon info combine multiple items by using a string, or add selected numbers together --debugphoton [-1|int] to print the debug info specified by -D only for a single photon, followed by its index (start 0) == Additional options == --momentum [0|1] 1 to save photon momentum transfer,0 not to save == Example == mmc -n 1000000 -f input.json -s test -b 0 -D TP