MCX v2022.10 - Special Edition for MCX 2022 Training Workshop

Monte Carlo eXtreme (MCX) - CUDA Edition

v2022.10

• Author: Qianqian Fang (q.fang at neu.edu)
• License: GNU General Public License version 3 (GPLv3)
• Version: 1.9.7 (v2022.10, Glossy Gluon)
• Website: http://mcx.space

MCX v2022.10 is a special release with only limited deployment to MCX 2022 (fNIRS 2022, Boston, Oct 2022) trainees.
The source code that was used to build the release package can be found at the bottom of this release.

To download the packages created for this release, please follow the registration link at https://mcx.space/register

What's New

MCX v2022.10 introduces a major new feature - split-voxel MC (SVMC), published in
Biomedical Optics Express recently by Shijie Yan and Qianqian Fang, see
Yan2020 for details.
Shortly, SVMC provides a level of accuracy close to mesh-based MC (MMC) in modeling
curved boundaries but it is 4x to 6x faster than MMC. Several demo scripts of SVMC
can be found in the MCXLAB package under examples/demo_svmc_*. In addition, MCX v2022.10
supports GPU-based polarized light simulation, see our JBO paper
Yan2022. This release also includes
both the web-client and server scripts for MCX Cloud - an in-browser MC simulator
as we reported in Fang2022. Moreover, MCX
v2022.10 provides an official pymcx module to run stream-lined MCX simulations in
Python, offering mcxlab-like interface.

• Introduced Split voxel MC (SVMC) to accurately model curved boundaries
• GPU polarized light modeling (Stokes) with 900x speedup
• Web-based MCX Cloud platform including web-client and server scripts
• pymcx - an mcxlab-like Python module for running MCX simulations in Python
• Added Debian/Ubuntu packages for easy installation
• Added a unified command line interface, photon, to call mcx/mcxcl/mmc
• Fine-tuned Windows installer
• Support CMake in Travis-CI automation

A detailed list of updates is summarized below (key features marked with “*”):

• 2022-10-05 [dc42951] prevent nan where log(rand) is calculated
• 2022-10-05 [63ffc1e] fix nan in detected photon data when using hyperboloid src, see https://groups.google.com/g/mcx-users/c/vyfHbzEO-0M/m/JzlpEZ3TBwAJ
• 2022-09-07 [e281f3e] allow to preview continuously varying medium (4D cfg.vol)
• 2022-08-19 [10330ef] fix windows compilation error
• 2022-08-17 [bbb4425] prevent zero-valued mus creating nan, #133
• 2022-08-12 [51f42f5] fix mcxlab log printing caused by commit f3beb75
• 2022-08-12 [7058785] Lambertian launch for all focusable sources when focal-length is -inf
• 2022-07-28 [6d64c0b] fix incorrect flag for skipvoid
• 2022-06-27 [3d4fb26] partially fix rf replay
• 2022-06-04 [8af3631] fix line source
• 2022-05-22 [149b1ef] make code compile on windows
• 2022-05-20 [e87bb49] use consistent file naming convention, remove outdated units
• 2022-05-20 [45d84d3] complete reformat source code using astyle, always run make pretty before committing
• 2022-05-20 [aff8ff0] add source code formatting option
• 2022-05-20 [f3beb75] use MATLAB_MEX_FILE to determine container environment
• 2022-05-18 [1295024] fix incorrect trajectory id, fix #147
• 2022-05-18 [ccd2deb] fix macro condition
• 2022-05-18 [6f4ee88] use MCX_CONTAINER and env macros to replace extra PYMCX_CONTAINER
• 2022-05-16 [6fa1580] avoid using clear all and ~ in return value
• 2022-05-16 [21f9bd7] merge changes with @ShijieYan's svmc fix
• 2022-05-16 [8b2740f] debugging svmc crashes
• 2022-05-16 [7582a6e] fix svmc issue after patch f8da832
• 2022-05-15 [188ac2a] Added Pybind11's license info to README.md.
• 2022-05-15 [86529cf] Added PYMCX_CONTAINER compilation macro. Added support for extracting MCX_ERRORs like Mex + author fix.
• 2022-05-15 [b58ad88] Renamed gpu_info to gpuinfo for consistency.
• 2022-05-15 [0582974] changed issaveref to accept ints.
• 2022-05-15 [1cf1b3b] Added py::value_error handling + additional error checking for volume assurance.
• 2022-05-15 [7df8938] Added better + more informative exception handling for pymcx.
• 2022-05-15 [6a741e8] Changed reinterpret_casts to direct object construction + added the stat dict to the output dict + defined PYBIND11_DETAILED_ERROR_MESSAGES for easier debugging.
• 2022-05-15 [e4547ba] add pybind11 as submodule to build pymcx
• 2022-05-13 [f8da832] fix cyclic bc demo and srctype demo error, svmc still not working
• 2022-05-13 [4bd3974] report register counts on sm_60 using nvcc --ptxas-options=-v
• 2022-05-13 [e8f6a2d] fix cfg.unitinmm does not exist error
• 2022-05-13 [447975f] complete dda ray-marching, cube60 benchmark gain 40% speed, others are similar
• 2022-05-12 [b873f90] add integer voxel indices to avoid nextafter
• 2022-05-11 [32d46cd] merge additional updates from mcxcl version of json2mcx, #139
• 2022-05-11 [3d6d7df] fix bugs in json2mcx, #139
• 2022-05-08 [3b1c320] Removed nlhs argument left from Matlab.
• 2022-05-08 [61cc994] Fixed issue with std::cout and std::cerr flush.
• 2022-05-06 [d9793e9] Added working setup.py.
• 2022-05-03 [a3e47c8] Minor fix.
• 2022-05-02 [c9bedd6] Moved validate_config.
• 2022-05-02 [5427ece] Working prototype with different volume configs.
• 2022-05-02 [739b7ea] Moved some stuff to interface-common.cpp.
• 2022-05-02 [d852a87] Minor bug fixes.
• 2022-05-01 [f4cd3c3] Added kwargs version of mcx.
• 2022-05-01 [baa5fdd] Skeleton is done.
• 2022-04-24 [e919716] Prints GPU info.
• 2022-04-23 [0c7b6a7] Working interface and CMakeLists.txt file.
• 2022-04-19 [c710c3c] update ubj parser, update jnifti metadata
• 2022-04-15 [4033c54] mcxlab bug fix: digimouse atlas voxel size is 0.2mm, not 0.8mm
• 2022-04-15 [9b17eee] critical bug fix: digimouse atlas voxel size is 0.2mm, not 0.8mm
• 2022-03-31 [df6c311] Add viewing axis selection
• 2022-03-25 [04f1565] Add optimized isosurface rendering; add the ability to view cross-sectional slices of geometry
• 2022-03-23 [200decb] Remove testing files
• 2022-03-23 [e434553] Remove unnecessary variable
• 2022-03-22 [ebd5bee] update ubj to support BJData Draft 2, add JNIfTI DataInfo, fix #142
• 2022-03-21 [6de0855] Enable event-based repainting; re-add shader refinement, remove animation frame bugs; remove unnecessary shader branches and discards
• 2022-03-19 [7ef65a8] Added event-based repainting; shader optimizations
• 2022-03-05 [a93f6fa] save user info in local storage to avoid retyping
• 2022-03-05 [34d9afa] fix SaveDataFlag invisible bug
• 2022-02-18 [f051314] add missing voxel unit
• 2022-02-03 [23bf5b2] lowering default photon number so it can be launched on most gpus
• 2022-01-31 [220d9c2] fix incorrect type for gsmatrix
• 2022-01-31 [28e20d6] fix windows vs warning
• 2022-01-29 [6a9ad2f] update mcx_utils to use the Mie interface
• 2022-01-29 [13679e9] fix compilation issue of mcx_mie.cpp using MSVC, close #138
• 2022-01-28 [d7daf57] manually resolve complaint in CUDA 9
• 2022-01-28 [e99edb2] update .travis.yml
• 2022-01-28 [533c8ce] manually add mcx_mie in Makefile
• 2022-01-28 [e56b5cb] improve complex arithmetic compatablity with MSVC
• 2022-01-27 [a0ed0e7] add Mie function modules into cmake
• 2022-01-27 [c350c67] seperate Mie scattering functions from mcx_utils.h
• 2022-01-27 [0d51bb7] add missing i detflag in command line
• 2022-01-27 [9b74e4b] fix: add save detector flag for Stokes vectors
• 2022-01-26 [077060a] use static_cast in mcxlab so that cfg.vol can be realloc in mcx_shapes
• 2022-01-26 [8503125] do not reset cfg.vol when rasterizing cfg.shapes
• 2022-01-26 [3f22070] fix normalization in multiple detector RF replay
• 2022-01-26 [cdfd468] apply normalization to both real and imaginary jacobain for RF replay
• 2022-01-26 [87a310e] one can use ~ to ignore fluence output in octave, not in matlab
• 2022-01-26 [d45f084] allow users to explicitly disable fluence output by accepting cfg.issave2pt
• 2022-01-25 [376a730] partial fix to RF Jacobian calculation, need verification
• 2022-01-25 [d6e2b9e] NaN value in mua_float and muamus_float signifies a 0-value voxel
• 2022-01-24 [c9f2ad9] force threejs version to avoid breaking update in R136
• 2022-01-14 [51483eb] add template specialization for polarized mode
• 2022-01-12 [3487dfe] update the example for the polarized MCX
• 2021-12-15 [b9e046a] fix out of bounds error due to limited precision of R_PI
• 2021-12-15 [3b10265] fix the built-in example to match the update in e5dfd78
• 2021-12-15 [dbe17af] no Stoke vector output for unpolarized MCX simulation
• 2021-12-15 [99293dd] add sanity check for incident Stokes vector
• 2021-12-13 [f1537bd] no need to check constant memory usage in polarized mode
• 2021-12-13 [61281ae] use prop.g to return the anisotropy computed from Mie
• 2021-12-12 [3b0ecc0] fix #133, handling underflowing denorms in float to half conversion for muamus_float
• 2021-12-11 [979f691] Move scattering matrix from constant memory to global memory
• 2021-11-29 [5c13f4b] avoid divided by zero on windows cygwin gcc
• 2021-11-29 [ef57f4b] allow make double to compile
• 2021-11-28 [0c96fe8] accept JData styled NaN in the JSON input for srcdir
• 2021-11-26 [a4545a4] fix #131, mcxplotshapes now plots shapes with correct scale
• 2021-11-04 [2585471] making svmc matlab demos compatible with Octave 5
• 2021-11-03 [5976811] replace matlab-only function with more portable code
• 2021-11-01 [37e121c] update preprint version url
• 2021-10-21 [7a77bf7] display rendering frame rate
• 2021-10-18 [99592c1] fix: #114 improve robustness to unknown boundry conditions
• 2021-10-14 [1aa2922] feat: Add one-sheet hyperboloid gaussian beam
• 2021-10-07 [86d56c2] feat: output prop. along with det. photon profile
• 2021-10-07 [24f4698] fix: ensure the largest grid to be accumulated
• 2021-10-06 [e5dfd78] feat: Support target mus or musp in polarized MCX
• 2021-10-06 [ae9216d] remove old det photon data after a new simulation
• 2021-10-05 [8cb21b5] support downloading detected photon data in mcxcloud
• 2021-10-04 [81ff4b1] fix rf replay bugs reported by Pauliina Hirvi
• 2021-09-24 [833bf6a] Reorganize some kernel code to optimize SVMC speed
• 2021-09-20 [605c15f] Fix numerical error of intersection test in SVMC
• 2021-09-20 [392ee87] Reorder code to fix photon detection for SVMC
• 2021-09-07 [5c44c6e] fix trajectory saving buffer length bug
• 2021-08-20 [99ea2b6] avoid continuous mua/mus inputs be treated as 0-label if mua=mus=0
• 2021-08-01 [943197a] Reorder preprocessing code to allow detector in SVMC Mask detector voxels only after the volume has been fully prepared!
• 2021-07-27 [65359f7] avoid extra level of square brackets for Optode.Detector
• 2021-07-27 [6b2f074] accept 3-element param1
• 2021-07-27 [2633bfb] avoid param1 missing error if not present
• 2021-07-23 [192613b] fix offset of cylinder along the axis direction, close #119
• 2021-07-17 [fc0465d] add tutorial 2 link
• 2021-07-17 [8c72d17] restore accidentally removed analytics tag
• 2021-07-13 [566df5e] provide flags to help access the detp.jdat file
• 2021-07-12 [b97c0f6] return metadata when loading simulation from library
• 2021-07-12 [3be6603] add default tab in the direct link,return mcx error if failed
• 2021-07-12 [70fb2a7] fix mixlabel byte order
• 2021-07-11 [24df0c3] add comment on raw voxel binary data layout
• 2021-07-07 [53d7ac0] fix shared mem misalignment error, close #118
• 2021-07-06 [7f8a2ac] allow ArrayZipSize to accept 1x2 array
• 2021-07-05 [9b00fa3] fix initial tab
• 2021-07-05 [2737853] deep copy data.options to avoid script error
• 2021-07-05 [0398b95] fix several bug while recording utorials
• 2021-07-04 [f5974ed] add preprint link
• 2021-07-04 [5d21a0d] create mcx cloud tutorial, add link
• 2021-07-03 [df0a48b] support tab param in url to open default tab
• 2021-07-03 [4c3f240] link json in direct link, remove schema
• 2021-07-03 [da6595e] add newline to json file download
• 2021-07-03 [cc3c06d] fix X/Y/ZSlabs parsing, restore original schemas
• 2021-07-03 [7c5054d] internal normalization of srcdir
• 2021-07-02 [877e9fe] get user id and group at runtime
• 2021-07-02 [22d6ffe] fix X/Y/ZSlabs schemas
• 2021-07-01 [270bb7c] prepare for beta testing
• 2021-06-30 [4b6df28] rename mcxone to mcxcloud, add help info
• 2021-06-30 [66b77fb] partial fix of json2mcx.m conversion issues
• 2021-06-25 [c399efa] enable negative g value support
• 2021-06-23 [3c642ce] set maximum characters to read for fscanf, fix #117
• 2021-06-23 [606b3d1] handle empty detector array in json2mcx
• 2021-06-22 [b537143] give a warning if the output type is not jacobian in replay
• 2021-06-17 [363d2d8] support reading .jdat file for replay
• 2021-06-04 [7191ca3] make thumbnail the same size when updating
• 2021-06-04 [5a2e13e] add tab overflow control
• 2021-06-04 [59e6be2] layout adjustments
• 2021-06-04 [4b55c88] minor polishing
• 2021-06-03 [1c29578] fix regression
• 2021-06-03 [3aedee6] add LengthUnit, MediaFormat in schema, support number and string for DebugFlag/SaveDataMask
• 2021-06-03 [64c5dd0] fix unnecessary shared memory allocation related to invcdf
• 2021-06-03 [ebf1ea1] support user-defined phase functions via cfg.invcdf, close #13
• 2021-06-03 [0731511] revert back to no restarting policy so that overtime jobs can be killed
• 2021-06-02 [4d2a891] process cache,fix fullname,fix job status,fix server-side limit,kill overtime job
• 2021-06-02 [a08d676] update the skinvessel benchmark
• 2021-06-02 [168db14] feat: save Mie function outputs mus, g to a file
• 2021-06-02 [57a44c5] feat: Add anisotropy g as an output of Mie func.
• 2021-06-02 [7387394] finally fix crossdomain post, change jsonp to json,test simu lib edit
• 2021-06-01 [95c6e1d] test:use default BC for all polarizedMC benchmarks
• 2021-06-01 [98697de] Add a three-layer slab demo for polarizedMC
• 2021-06-01 [7d86804] Add visualization for polarized MC example(MATLAB)
• 2021-05-31 [7d82a51] fix: resolve valgrind complaint: uninit. values
• 2021-05-31 [d6c9743] Add outputs in mcx2json.m to support polarizedMC
• 2021-05-31 [5088678] Add an example for polarized MC
• 2021-05-31 [d3054fd] Add document for polarized MC in mcxlab
• 2021-05-31 [44e0e9c] fea: extend loadmch.m to load output Stokes vector
• 2021-05-31 [a51cb52] feat: support polarized MC in command line (JSON)
• 2021-05-30 [d7921fe] skip checklimit if json is directly loaded from lib
• 2021-05-30 [65870f5] gui fine adjustment,use hash to update runcount,enable restart on fail,permit mcxpub update
• 2021-05-30 [692adfb] fix broken link
• 2021-05-30 [7a159ab] merge css
• 2021-05-30 [55bb1ea] initial drag and drop support, not working
• 2021-05-30 [fc9ca38] add meta headers, other minor adjustments
• 2021-05-29 [96cf071] support embedding src pattern in the all-in-one json/jdata file
• 2021-05-28 [450462c] Add document for functions used in polarized MC
• 2021-05-28 [cbc3340] Optimize Stokes vector computation
• 2021-05-28 [9bd2ce0] Remove redundant code in preprocessing
• 2021-05-28 [06a9c6b] fix: resolve nan results due to numerical error
• 2021-05-28 [d9d1d0a] rewrite some code to save computation
• 2021-05-28 [9195141] Add an example to show polarized photon simulation
• 2021-05-27 [2b87275] fix: rewrite code for better readability
• 2021-05-26 [d836c81] fix: correct formula for stokes parameter update
• 2021-05-25 [105d5a9] feat: Add stokes parameter output in MCXLAB
• 2021-05-25 [87d8847] feat: add polarized photon simulation
• 2021-05-23 [d398cc9] add simulation restrictions for initial public testing of mcx cloud
• 2021-05-23 [26536d3] feat: add preprocessing for polarized MC in mcxlab
• 2021-05-22 [f0975c5] support ring/annulus shaped source via disk source
• 2021-05-21 [6ed9727] support svmc in command line;add svmc example
• 2021-05-21 [3d0a793] reading 8-byte svmc volume format from input file
• 2021-05-20 [4010d99] move svmc repacking to mcx_preprocess
• 2021-05-20 [3214c1b] remove duplicated preprocessing codes in mcx and mcxlab,fix detbc bug in command line
• 2021-05-20 [54b0602] run batch of jobs in each call to fill all GPU devices
• 2021-05-20 [de9850c] add -K short option and svmc mediatype
• 2021-05-19 [660a8b8] relocate db and workspace folder to non www-data accessible paths
• 2021-05-19 [64f3008] update acknowledgement list
• 2021-05-19 [c168a87] can update thumbnail, add credit links
• 2021-05-19 [b9361a1] update to mcxcloud scripts
• 2021-05-15 [cef630b] save volume in jdata format by default
• 2021-05-15 [c50f871] define Frequency in json file instead of Omega
• 2021-05-15 [b4e7b57] initial support RF mua Jacobian in replay, thx Ilkka Nissilä, formula based on Juha Heiskala PhD thesis p45
• 2021-05-10 [073b168] mcxcloud initial preview at JBO hot-topics
• 2021-05-05 [5732e6a] update front and backends
• 2021-05-01 [ee3f88d] update and rename mcxcloudd and mcxserver.cgi
• 2021-05-01 [eac952d] fix cylinder schema, add footer
• 2021-04-14 [aaa1eab] add download, fix jsonp callback, render output volume
• 2021-04-10 [aaef1f3] draw 3d fluence,use orth camera,add cancel
• 2021-04-04 [4ab8105] add src rendering, fix material color
• 2021-04-02 [1ed5272] fix cylinder and layer object drawing bug
• 2021-04-02 [f4ba0b4] add md5 digest for each submitted json for cache lookup
• 2021-03-31 [2c55c3b] change basic tab name
• 2021-03-31 [3c466a1] now mcxcloud can render 3D volumes, float32 buffer only
• 2021-03-29 [b379b2b] initial support in rendering 3d volume, add schema to support jdata ND array
• 2021-03-28 [31345a1] support Domain.Volume to encode JData-formatted 3D array
• 2021-03-28 [9c2e8c7] rendering all shape types, bbx as dashed box,add tag based material color
• 2021-03-27 [9f6e82c] avoid repainting preview
• 2021-03-26 [5109d29] add normal material, add box, subgrid and cylinder
• 2021-03-25 [ad0b814] draw grid from Domain.Dim
• 2021-03-25 [9b0cf95] fine tune fonts, add big tab initial screen, add svg background, add funding info
• 2021-03-25 [77f8f7a] add three.js for 3d preview
• 2021-03-24 [4274c77] rename mcxcloud.txt to mcxcloud
• 2021-03-24 [dc25a87] add mcx cloud service server and client files, partially working
• 2021-03-22 [f9bc07c] use tabs in mcxone, add jquery by default
• 2021-03-18 [d8b88e1] fix unwanted double-precision math functions
• 2021-03-11 [f6ce5bd] update variable and function name to follow the convention
• 2021-03-11 [ca2ce60] add example: comparison of surface diffuse reflectance between MC and Diffusion
• 2021-03-05 [bcbb324] change window sizes using 96dpi default setting
• 2021-03-05 [5c8d27f] fix Name shape object schema
• 2021-03-03 [02add69] MCX json schema and json editor are working, added more Shapes objects
• 2021-03-01 [940d725] wrapping up json input import feature in mcxstudio
• 2021-02-28 [64d629c] parse src/detector, media and shape
• 2021-02-27 [a3b8457] * open/import JSON input file in MCX Studio
• 2021-01-07 [9811c83] reorder the input data layout to match the change in preprocessing
• 2020-10-22 [991910e] add function comment and revert unnecessary changes
• 2020-10-22 [3343338] * add benchmarks from SVMC paper to mcxlab
• 2020-10-19 [de87cbf] resolve code alignment issue
• 2020-10-18 [5acd287] fix photon detection issue for SVMC mode
• 2020-10-18 [61dbf63] fix ray-tracing issue after the initial template implementation
• 2020-10-17 [fbb4f8c] initial implementation of template for SVMC mode
• 2020-10-08 [dad83c6] resolve conflict between two branches to elimate mismatch in demo_focus_mirror_bc.m
• 2020-10-08 [fb61782] * sync master branch into nuvox(SVMC) branch
• 2020-09-20 [75f08c5] remove empty depends
• 2020-09-20 [fa98229] fix incorrect dependency
• 2020-09-20 [d748d29] add octave package files for mcxlab and mcxtools
• 2020-09-16 [cf3b1f0] fix typo, change default exe path
• 2020-09-16 [15e9946] * fix warnings found by debian packaging at https://mentors.debian.net/package/mcx/
• 2020-09-16 [04bb0e7] add man pages for other binaries
• 2020-09-14 [aca9f97] remove additional debian packging warnings
• 2020-09-14 [ce4e341] add desktop icon files
• 2020-09-14 [eb0aa9f] allow new lines in string values in json
• 2020-09-14 [4b1301a] set default exe folder to /usr/libexec, fall back to ~/bin/
• 2020-09-14 [643e4a1] * add photon as unified cmd for mcx/mcxcl/mmc,polish for debian packaging
• 2020-09-14 [a67bc6d] updates to ease debian packaging
• 2020-09-08 [8983305] Inno Installer Setup paths and file details fixed
• 2020-09-07 [a6bc5a9] another attempt to fix #105
• 2020-09-07 [ca303dd] change default shortcut group name, fix #105
• 2020-09-06 [0313d4c] install mcxstudio to 64bit folder, close #105
• 2020-09-04 [37b4914] add demo script for mirror bc
• 2020-09-04 [e561890] make mcxplotvol work in matlab 2010 or earlier
• 2020-09-04 [9518cfa] handle mirror bc correctly, close #104
• 2020-09-04 [64896aa] * reset pattern center position following a failed launch, fix #103
• 2020-09-02 [5af2e76] fix -geometry 0x0 error, see https://forum.lazarus.freepascal.org/index.php?topic=40593.0
• 2020-09-01 [dd4be78] add cubesph60b to match example/benchmark2
• 2020-08-30 [971ffac] fix extended ascii letters
• 2020-08-29 [6eb9596] update mcxcreate.m, add mcxplotshapes.m to render json shapes
• 2020-08-29 [0199dad] clean up code and add comments for SVMC
• 2020-08-29 [94d55a7] * add mcxcreate, force mcxlab return one output
• 2020-08-28 [d917751] give an error for unsupported single dash option
• 2020-08-28 [093c9ba] * add pre-processing for SVMC mode
• 2020-08-28 [a79e116] add mode delphi in carbon unit
• 2020-08-27 [63e5a5f] handle det radii less than or equal to 0.5, fix #101
• 2020-08-27 [8f93ee2] fix make mex link error
• 2020-08-26 [65f0fe4] fix issrcfrom0 offset
• 2020-08-26 [79f9d70] * multiply voxelsize with det radius
• 2020-08-26 [d5c3c11] fix mcxpreview det radis issue, require srcpos and tend in mcxlab
• 2020-08-24 [1af5507] avoid error on mac
• 2020-08-24 [2fce8e5] add missing carbon unit for mac
• 2020-08-24 [6f11857] add command line option cheatsheet
• 2020-08-24 [5046de0] fix cmake command
• 2020-08-24 [cea663b] test cmake in travis
• 2020-08-24 [782b4a3] massive update of documentation
• 2020-08-24 [041e386] massive update to README to describe all output formats

Between 2020 and 2022, three new journal papers have been published as the
result of this project, including [Yan2020]. Please see the full list at
http://mcx.space/#publication

• [Yan2020] Shijie Yan and Qianqian Fang* (2020), "Hybrid mesh and voxel based Monte Carlo
  algorithm for accurate and efficient photon transport modeling in complex bio-tissues,"
  Biomed. Opt. Express, 11(11) pp. 6262-6270.
• [Fang2022] Qianqian Fang, Shijie Yan, "MCX Cloud—a modern, scalable, high-performance
  and in-browser Monte Carlo simulation platform with cloud computing," J. Biomed. Opt.
  27(8) 083008, 2022
• [Yan2022] Shijie Yan, Steven L. Jacques, Jessica C. Ramella-Roman, Qianqian Fang,
  "Graphics processing unit-accelerated Monte Carlo simulation of polarized light in
  complex three-dimensional media," J. of Biomedical Optics, 27(8), 083015 (2022)