MMC 2017.7 command line help

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#                         Mesh-based Monte Carlo (MMC)                        #
#          Copyright (c) 2010-2017 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              #
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$Rev::bd02e9 $ Last $Date::2017-07-07 18:24:18 -04$ by $Author::Qianqian Fang $
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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|PHBS]  (--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
 -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

== 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

== Additional options ==
 --momentum     [0|1]          1 to save photon momentum transfer,0 not to save

== Example ==
       mmc -n 1000000 -f input.inp -s test -b 0 -D TP
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