Changes between Version 11 and Version 12 of WikiStart


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Timestamp:
Oct 13, 2016, 5:06:08 PM (10 years ago)
Author:
henrik
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  • WikiStart

    v11 v12  
    4949Physics group at Lund University and the Computational Morphodynamics group at the Sainsbury Laboratory, University of Cambridge. Contact: henrik.jonsson@slcu.cam.ac.uk.
    5050
     51Developers (incomplete list): Henrik Jönsson, Patrik Sahlin, Pontus Melke, Pau Formosa-Jordan, Laura Brown, Pawel Krupinski, Behruz Bozorg
     52
    5153= Binaries =
    5254
    … …  
    6062
    6163* model file: this file defines the model. Information of its format can be
    62 found in the documentation of Organism::readModel().
     64found in the documentation of Organism::readModel() [for tissue it is Tissue::readModel()].
    6365
    6466* init file: this file holds the initial variable values. Information of
    … …  
    7678A common command line execution of the simulator binary is then:
    7779
    78 $ORGANISM/bin/simulator example.model example.init example.rk5 > example.data
     80simulator example.model example.init example.rk5 > example.data
    7981
    80 which generates the system output in the file example.data.
     82which generates the system output in the file example.data. Note that the simulator binary is in the bin directory of the organism (or tissue) main directory. This needs to be in your PATH or you will need to specify the full path to the binary.
    8183
    8284'''Optimizer'''
    … …  
    98100= Compilation =
    99101
    100 The code can be compiled by using make. A Makefile can be found in the $ORGANISM/src directory (to compile: 'cd src; make' will generate the binaries in the bin directory) . The
     102The code can be compiled by using make. A Makefile can be found in the 'src' directory (to compile: 'cd src; make' will generate the binaries in the bin directory) . The
    101103code is ANSI-compatible and has been tested to compile on Linux (default for the provided Makefile), Mac OS X and
    102104Windows (using Cygwin) platforms. It is dependent on boost and for plotting OpenGL.
    … …  
    104106= Documentation =
    105107
    106 Documentation is generated via Doxygen (http://www.doxygen.org) and a Makefile is found in the $ORGANISM/doc directory. 'cd doc; make' will generate a html version in the doc/html directory and the introductory page is doc/html/index.html. PDF documentation can be generated by 'cd doc/latex; make' which generates doc/latex/refman.pdf. Other formats are also available via Doxygen.
     108Documentation is generated via Doxygen (http://www.doxygen.org) and a Makefile is found in the 'doc' directory. 'cd doc; make' will generate a html version in the doc/html directory and the introductory page is doc/html/index.html. PDF documentation can be generated by 'cd doc/latex; make' which generates doc/latex/refman.pdf. Other formats are also available via Doxygen.
    107109
    108110= Download =