https://github.com/turtlesoupy/abm-u-and-abm-b-cpp

Scientific model for simulating light transport in unifacial/bifacial plant leaves (C++ version)
https://github.com/turtlesoupy/abm-u-and-abm-b-cpp

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Scientific model for simulating light transport in unifacial/bifacial plant leaves (C++ version)

• Host: GitHub
• URL: https://github.com/turtlesoupy/abm-u-and-abm-b-cpp
• Owner: turtlesoupy
• License: other
• Created: 2010-12-13T02:22:46.000Z (over 15 years ago)
• Default Branch: master
• Last Pushed: 2011-01-30T22:34:07.000Z (over 15 years ago)
• Last Synced: 2025-04-04T11:47:19.783Z (over 1 year ago)
• Language: C++
• Homepage: http://www.npsg.uwaterloo.ca/models/ABMU.php
• Size: 129 KB
• Stars: 2
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README
  • License: LICENSE

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README

          
ABM-B and ABM-U (C++ version)

This is a reference implementation of the ABM-B and ABM-U models described in

http://www.npsg.uwaterloo.ca/resources/docs/rse2006.pdf, with modifications

described in http://www.npsg.uwaterloo.ca/resources/docs/ieee07-8.pdf

For detailed information, visit the online pages for:

    - ABM-U: http://www.npsg.uwaterloo.ca/models/ABMU.php

    - ABM-B: http://www.npsg.uwaterloo.ca/models/ABMB.php

The package is licensed under a BSD license, described in LICENSE. 

This was released by the Natural Phenomenon Simulation Group at University of

Waterloo in Waterloo, Ontario, Canada. Please visit http://www.npsg.uwaterloo.ca

for more information.

Usage:

    - Run "make abmu" to make an abmu executible. Run "make abmb" to 

      make an abmb executible. Afterwards,

      run "./abmb samples/lopex_0219-0220.json output.csv" 

      or  "./abmu samples/lopex_0141-0142.json output.csv". You can specify more

      detailed options too, just run "./abmu" to see them all.

Command line flags:

    - -n : Specifies the number of samples to run the monte carlo simulation.

                We recommend 10^5 to get asymptotic convergence

    - -a : Azimuthal angle in degrees to fire rays from.

    - -p : Polar angle in degrees to fire rays from. Values from 0 to 90

                  correspond to the abaxial surface, while values from 90 to 180

                  correspond to the adaxial surface.

    - -s : Wavelength step in nm. Output will occur with every  wavelengths

    - -w : Wavelength start in nm. Output will start with this wavelength.

    - -e : Wavelength endin nm. Output will end with this wavelength.

    - -d : Data directory. The data is outlined in the Code Organization section

                 below.

    - -t :  Number of threads. Rule of thumb is double the number of parallel processing

                 units in your computer.

    - -q: Disable sieve and detour effects. This is an in-vivo Vs. in-vitro modelling issue that is

          outlined in the paper here: http://www.npsg.uwaterloo.ca/resources/docs/ieee07-8.pdf

Requirements:

    - The yajl JSON parsing library headers: http://lloyd.github.com/yajl/

      (available in Ubuntu under libyajl-dev)

    - pthreads

Code Organization:

    - 'src/': This folder contains all the code files necessary for ABM-U/ABM-B to run.

    - 'include/': This folder contains all the header files necessary for ABM-U/ABM-B to run.

    - 'data/': This folder contains the data files (e.g., refractive indices) that are needed

               to run ABM-B or ABM-U. All are available here: http://www.npsg.uwaterloo.ca/data/leaves.php

               - 'caro-PAS-400-2500.txt': Specific absorption coefficient of carotenoids (400-2500nm)

               - 'cellulose400-2500.txt': Specific absorption coefficient of cellulose (400-2500nm)

               - 'chloAB-DFA-400-2500.txt': Specific absorption coefficient of chlorophyll a+b (400-2500nm)

               - 'sacwH400-2500.txt': Specific absorption coefficient of water (400-2500nm)

               - 'raH400-2500.txt': Refractive index (real part) of antidermal cell wall (400-2500nm)

               - 'rcH400-2500.txt': Refractive index (real part) of epicuticular wax (400-2500nm)

               - 'rmH400-2500.txt': Refractive index (real part) of wet mesophyll wall (400-2500nm)

    - 'samples/': This folder contains data definitions for samples used for testing of ABM-U/ABM-B.

                  All samples correspond to those mentioned in http://www.npsg.uwaterloo.ca/resources/docs/rse2006.pdf.

                  Samples are specified in a json-like format. 

               - 'lopex_0141_0142.json': Soybean (Soja hispida or Glycine max), a bifacial leaf for ABM-B

               - 'lopex_0219_0220.json': Corn (Zea mays L.), a unifacial leaf for ABM-U

Notes:

    - All concentrations are specified in g/cm^3, and lengths in meters.

    - Data is piecewise-constant interpolated accross 400-2500nm, with data points

      every five nanometers.