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README

==========================================================
           QUICK GUIDE FOR GETTING STARTED  
==========================================================

-------------------------------------------------------
  Prerequisites:
-------------------------------------------------------

Check that your system has the necessary ressources installed
  1) gmake 
  2) python2
  3) a fortran 90+ compiler
  
gmake and python2 should be standard in a linux environment. IBMlib has been
compiled in various configurations with these compilers: 
  ifort (Intel),
  gfortran (GNU)
  pg (Portland Group)
other compilers should work, but you may need to translate some compiler options
to the specific compiler. Cross compilation Windows (static build) has been achieved with gfortran

In addition to gmake, python2 and a fortran compiler, you may need other ressources,
depending on the configuration you build IBMlib for; often, you need netCDF, if you read/write  
netCDF data sets. If netCDF is not locatable by the compiler, you need to set the environment variables
or compiler options (compiler_defaults.mk) as. needed

-------------------------------------------------------
  IBMlib configuration
-------------------------------------------------------

Before you build the code, you must configure IBVMlib to the situation where it should be used:

1) Select overall configuration of code by copying the 
   file config.mk into the base directory (where this file is)
   The file config.mk tells which modules should be used for
   PHYSICAL_FIELDS, PARTICLE_STATE and TASK
   There are a set of examples in directory setups/configurations

2) Select a compiler by copying a file compiler_defaults.mk  into the 
   base directory (where this file is). compiler_defaults.mk
   contains defaults compiler/link flags, and auxillary software references
   if you need to link up IBMlib with outher packages.
   There are a set of examples in the directory setups/compilers


If a standard setup is applied steps 1-2 above can be accelerated
by running a standard script doing steps 1-2. 
There are some examples in setups/combo_scripts.
Run these in the base directory (where this file is) e.g. type:
   setups/combo_scripts/quick_ifort_minimal
at the command line. You can then edit files config.mk and compiler_defaults.mk as needed


-------------------------------------------------------
  IBMlib compilation
-------------------------------------------------------

3) Build the selected configuration by typing:

     make ibmrun
     
   at the command line (assuming you name the executable ibmrun in config.mk)



-------------------------------------------------------
  Testing IBMlib: 
-------------------------------------------------------

   IBMlib comes with a self test suite. If testing is the first thing you do, 
   you can just put an empty file for config.mk by typing "touch config.mk" 
   instead of step 1 above (but any file will work).
   Then select a compiler (step 2 above) and finally type:
   "make test" at the command line. A summary of the self test will be 
   printed at the screen at the end of (a successful) self test.
   So, if you use e.g. the ifort compiler you just type these three lines:

     touch config.mk
     ln -s setups/compilers/ifort/compiler_defaults.mk
     make test


-------------------------------------------------------
  Further reading
-------------------------------------------------------

  A user guide is available in directory doc. To build it type

    latex IBMlib_manual.tex
    dvipdf IBMlib_manual.dvi

 to generate the user guide IBMlib_manual.pdf
 
 An anthology of selected works using IBMlib along with framework design considerations is avaliable in this 
 open access reference:
 
    A. Christensen,P. Mariani, M. R. Payne:
    A generic framework for individual-based modelling and physical-biological interaction
    PLoS ONE 13(1) 2018: e0189956. https://doi.org/10.1371/journal.pone.0189956
 

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