Initial commit of LPJmL4.0.001 as published in Schaphoff et al. 2017

AUTHORS

+Authors of LPJmL C-version
+
+Werner von Bloh         (Werner.von.Bloh@pik-potsdam.de)
+Sibyll Schaphoff        (Sibyll.Schaphoff@pik-potsdam.de)
+Stefanie Rost (Jachner) (Stefanie.Rost@pik-potsdam.de)
+Marlies Gumpenberger    (Marlies.Gumpenberger@pik-potsdam.de)
+Tim Beringer (Erbrecht) (Tim.Beringer@pik-potsdam.de)
+Christoph Mueller       (Christoph.Mueller@pik-potsdam.de)
+Hester Biemans          (Hester.Biemans@wur.nl)
+Jens Heinke             (Jens.Heinke@pik-potsdam.de)
+Ursula Heyder           (Ursula.Heyder@pik-potsdam.de)
+Kirsten Thonicke        (Kirsten.Thonike@pik-potsdam.de)
+Katharina Waha          (Katharina.Waha@csiro.au)
+Susanne Rolinski        (Susanne.Rolinski@pik-potsdam.de)
+Matthias Forkel         (mforkel@bgc-jena.mpg.de)
+Jonas Jaegermeyr        (jonasjae@pik-potsdam.de)
+Elke Stehfest           (Elke.Stehfest@pbl.nl)
+Liesbeth de Waal        (liesbeth.dewaal@pbl.nl) 
+
+Based on Fortran/C++ version
+
+Stephen Sitch    (S.A.Sitch@exeter.ac.uk)
+Ben Smith        (ben.smith@nateko.lu.se)
+Dieter Gerten    (Dieter.Gerten@pik-potsdam.de)
+Alberte Bondeau  (Alberte.Bondeau@imbe.fr)

COPYRIGHT

+Copyright (C) 2007-2017 Potsdam Institute for Climate Impact Research

INSTALL

+ _     ____     _           _     
+| |   |  _ \   | |_ __ ___ | |    
+| |   | |_) |  | | '_ ` _ \| |    
+| |___|  __/ |_| | | | | | | |___ 
+|_____|_|   \___/|_| |_| |_|_____| Version 4.0.001
+
+
+Installation of LPJmL C Version 4.0.001
+=======================================
+
+Installation for Unix-like systems
+----------------------------------
+
+This text describes how to install LPJmL on your system. 
+The code has been tested for AIX, Linux, Mac OS X, and Windows 
+with cygwin and Microsoft C compiler (sequential version without MPI). 
+Cygwin is a Linux-like environment for Windows (http://www.cygwin.com)
+On Mac OS the xcode suite must be installed in order to have the gcc 
+compiler.
+
+create LPJmL directory:
+
+mkdir lpjml
+
+Go to LPJmL directory:
+
+cd lpjml
+
+untar source and data files
+
+gzip -cd lpjml-4.0.001.tar.gz|tar -xf -
+gzip -cd cru.tar.gz|tar -xf -
+
+Directory tree after extracting the tar files:
+
+--lpjml
+  |
+  +-config        : OS- and compiler-specific Makefiles
+  |
+  +-bin           : Directory for executables and shell scripts
+  |
+  +-R             : Scripts for R statistical package
+  |
+  +-man           : Manual pages root directory
+  | |
+  | +-man1        : Manual pages for programs and scripts
+  | |
+  | +-man3        : Manual pages for functions
+  | |
+  | +-man5        : Manual pages for file formats
+  |
+  +--html         : Documentation and man pages in HTML format
+  |
+  +--doc          : Documentation
+  |
+  +--par          : Parameter files for PFTs and soils
+  |
+  +--input        : input data set for climate
+  |
+  +--output       : output data (created by make test)
+  |
+  +--restart      : restart data (created by make test)
+  |
+  +--lib          : library files (created by make)
+  |
+  +--include      : include files
+  |
+  +--src          : source tree
+     |
+     +--numeric   : source for numerical routines
+     |
+     +--tools     : source for tools
+     |
+     +--pnet      : source for library for distributed networks
+     |
+     +--climate   : climate code 
+     |
+     +--lpj       : lpj functions
+     |
+     +--soil      : soil code
+     |
+     +--grass     : grass PFT code
+     |
+     +--tree      : tree PFT code
+     |
+     +--crop      : crop PFT code
+     |
+     +--landuse   : land use code
+     |
+     +--spitfire  : spitfire fire code
+     |
+     +--reservoir : reservoir code
+     |
+     +--socket    : socket communication library 
+     |
+     +--image     : coupler to IMAGE model 
+     |
+     +--netcdf    : NetCDF output functions
+     |
+     +--utils     : utility programs
+         
+Configure for your operating system
+
+On the HLRS2015 cluster at PIK you have to set several modules for compilation and linking:
+
+module load gmp/4.3.2
+module load mpi/intel/5.1.1
+module load compiler/intel/15.0.3
+module load compiler/gnu/4.9.2
+module load netcdf-c/4.3.3.1/serial udunits/2.2.19 expat/2.1.0
+
+./configure.sh
+
+If configure script exits with message "Unsupported operating system",
+Makefile.$osname is created from Makefile.gcc and probably has to be 
+modified for your operating system/compiler.
+If the configure script finds a MPI environment a parallel version of lpjml is built.
+The configure script creates a copy of the following OS-specific makefiles from
+directory config:
+
+Makefile.aix         - IBM AIX settings (xlc compiler)
+Makefile.aix_mpi     - IBM AIX and MPI environment
+Makefile.gcc         - GNU C-compiler settings
+Makefile.darwin_gcc  - GNU C-compiler settings for MacOS X
+Makefile.intel       - Intel C-compiler settings
+Makefile.intel_mpi   - Intel C-compiler and Intel MPI settings
+Makefile.cluster2015 - Intel C-compiler and Intel MPI on HLRS2015 cluster at PIK
+Makefile.mpich       - GNU C-Compiler and MPI Chameleon settings
+Makefile.win32       - Windows settings (used by configure.bat)
+
+Compilation flags
+
+Compilation of LPJmL is customized by definition of macros in the LPJFLAGS
+section of Makefile.inc:
+
+LPJFLAGS= -Dflag1 ...
+
+Flag                Description
+------------------- ------------------------------------------------------------
+COUPLING_WITH_FMS   enable coupling to FMS
+DAILY_ESTABLISHMENT Enable daily establishment 
+DEBUG               diagnostic output is generated for debugging purposes
+DOUBLE_HARVEST      adding correct sequencing of harvest events
+IMAGE               include coupler to IMAGE model
+LINEAR_DECAY        use linearized functions for litter decay
+MICRO_HEATING       Enable microbial heating
+SAFE                code is compiled with additional checks
+STORECLIMATE        store climate data in memory for spin up phase
+USE_MPI             compile parallel version of LPJmL
+USE_NETCDF          enable NetCDF input/output
+USE_NETCDF4         enable NetCDF version 4 input/output
+USE_RAND48          use drand48() random number generator
+USE_UDUNITS         enable unit conversion in NetCDF files
+WITH_FPE            floating point exceptions are enabled for debugging purposes
+------------------- ------------------------------------------------------------
+
+Create executables:
+
+make    
+
+One executable in directory bin is created: 
+
+lpjml    - LPJmL simulation code
+
+Utility programs are compiled by 
+
+make utils
+
+The following programs are created in the bin directory:
+
+lpjcat      - concatenates LPJmL restart files.
+lpjcheck    - checks syntax of LPJmL configuration files.
+cru2clm     - converts CRU data into file format suitable for LPJmL.
+printheader - prints file header of LPJmL input data files.
+lpjprint    - prints content of restart file to stdout.
+txt2clm     - converts CRU data files into LPJmL climate data files.
+              CRU data files have to be in the format specified in
+              http://www.cru.uea.ac.uk/~timm/grid/CRU_TS_2_1.html. 
+
+The binaries can be copied in an installation directory by invoking
+
+make install
+
+The necessary parameter and include files will be copied, too.
+The target directory must be specified by setting the environment variable LPJROOT:
+
+export LPJROOT=<installation directory>
+
+
+Environment variables
+
+The following environment variables are used by LPJmL:
+
+LPJCONFIG      - default LPJmL configuration filename
+LPJPREP        - defines preprocessor command for LPJmL configuration  file, default
+                 is "cpp -P"
+LPJROOT        - defines the root directory for LPJmL. This directory is added to the 
+                 include directories of the preprocessor
+LPJIMAGE       - sets host where IMAGE is running
+LPJWAITIMAGE   - sets time to wait for connection to IMAGE model
+LPJINPATH      - Path append to the input filenames. Only done for filenames
+                 without absolute path.
+LPJRESTARTPATH - Path append to the restart filenames. Only done for filenames
+                 without absolute path.
+LPJOPTIONS     - cpp runtime options for LPJmL
+LPJOUTPATH     - Path appended to the output filenames. Only done for filenames
+                 without absolute path.
+LPJOUTPUT      - Default method for generating output files. Valid values
+                 are write, mpi2, gather, and socket. 
+
+Create output and restart directory:
+
+make test
+
+On the compute cluster at PIK it is better to create symbolic links of the 
+input, output, and restart directory to the parallel GPFS filesystem /scratch.
+This improves performance in particular for the parallel code. 
+
+Man pages
+---------
+
+Manual pages for the man command are located in the $LPJROOT/man directory. Setting the
+environment variable MANPATH to:
+
+export MANPATH=$MANPATH:$LPJROOT/man
+
+will enable help.
+
+Invoking
+
+apropos lpj
+
+yields list of man pages related to LPJmL.
+
+Running the code
+---------------- 
+ 
+Sequential version can be started by invoking:
+
+./bin/lpjml 
+
+If you run lpjml outside the root directory of LPJmL, the following environment
+variable should be set:
+
+export LPJROOT=$HOME/lpjml
+
+Then all includes are found. You can include the bin directory in the search path:
+
+export PATH=$PATH:$LPJROOT/bin
+
+Script lpj_paths.sh is defined in bin setting all environment variables. Put
+
+. <Path to LPJmL root dir>/lpj_paths.sh
+
+in your profile. Then LPJROOT, PATH and MANPATH are set accordingly.
+
+Runtime options of lpjml
+
+The following runtime options are defined: 
+
+-Iincludepath     - Adds include path for LPJmL configuration file
+-Dmacro[=value]   - Defines macro
+-h                - print usage of lpjml
+-l                - print license
+-v                - print compiler used and LPJmL flags set
+-vv               - verbosely print the actual values during reading of the
+                    configuration files
+-param            - print LPJmL parameter for soils and PFTs
+-fpe              - enable floating point exceptions
+-image host       - set host where IMAGE model is running. Option is only
+                    available for the IMAGE version
+-wait time        - set time to wait for connection to IMAGE model
+-output method    - Method for generating output files. Valid values for method
+                    are mpi2, gather, and socket. Methods mpi2 and
+                    gather are only available for the MPI version
+-inpath dir       - input directory path
+-outpath dir      - output directory path
+-restartpath dir  - restart directory path
+
+The first two options will be sent to the preprocessor.
+
+For the parallel version SLURM and LoadLeveler files for Linux and AIX are provided. 
+A job can be submitted by invoking the bin/lpjsubmit script:
+
+bin/lpjsubmit ntasks LPJmL_args...
+
+Templates for customized LoadLeveler job control files are in the
+loadl directory:
+
+lpjml_aix.jcf    -- for AIX with POE
+lpjml_intel.jcf  -- for Linux with Intel MPI
+lpjml_mpich.jcf  -- for Linux with MPICH
+
+Depending on your MPI version installed the program can be started interactively:
+
+mpirun -np 32 ./bin/lpjml
+
+Error codes
+-----------
+
+If lpjml fails an error message is displayed in the following format
+
+ERRORxxx: message
+
+where xxx is the error code returned. The following error codes are defined:
+
+Error code Description                                 Error type
+---------- ------------------------------------------- ----------
+         1 Error reading configuration                   External
+         2 Error initializing input data                 External
+         3 Error initializing grid                       External
+         4 Invalid carbon balance                        Internal
+         5 Invalid water balance                         Internal
+         6 Negative discharge                            Internal
+         7 Negative fire probability                     Internal
+         8 Negative soil moisture                        Internal
+         9 Error allocating memory                       External
+        10 Negative stand fraction                       Internal
+        11 Stand fraction sum error                      Internal
+        12 List is empty in dellistitem                  Internal
+        13 Index out of range in dellistitem             Internal
+        15 Invalid year in getco2()                      External
+        16 Crop fraction >1                              Internal
+        17 No natural stand for deforest                 Internal
+        18 Wrong cultivation type                        Internal
+        19 Floating point error                          Internal
+        21 PFT list is not empty in setaside             Internal
+        22 Negative establishment rate                   Internal
+        23 Output channel is broken in socket connection External
+        24 Sending data to IMAGE model failed            External
+        25 Opening connection to IMAGE model failed      External
+        26 Not enough setaside stand created             Internal
+        27 Forest left after deforestation               Internal
+        28 Outflow reservoir error                       Internal
+        29 Permafrost error                              Internal
+        30 Global waterbalance error                     Internal
+        31 Cannot store climate data                     External
+        32 NO FMS coupler                                External
+        33 Cannot initialize soil temperature            External
+---------- --------------------------------------------- --------
+
+External errors are caused by invalid or missing input files while internal 
+errors are caused by problems inside the LPJ code. The latter will cause a core
+dump and have to be fixed by program changes. Some errors will only be generated
+if -DSAFE is set in the compile options of Makefile.inc.
+
+Installation for Windows XP without cygwin
+------------------------------------------
+
+The code without MPI has been tested on Windows XP using the free Microsoft 
+C++ compiler and nmake. The Microsoft SDK has to be installed, too.  All necessary
+programs can be downloaded from the Microsoft webpage.
+
+Unzip the source and data files
+
+configure makefile:
+
+configure.bat
+
+If the compiler does not find the system libraries, the library path defined in 
+Makefile.inc has to be modified. 
+
+create lpjml executable:
+
+nmake 

Makefile

+#################################################################################
+##                                                                             ##
+##               M  a  k  e  f  i  l  e                                        ##
+##                                                                             ##
+##   Makefile for C implementation of LPJmL                                    ##
+##   The call of ./configure.sh copies os-specific makefile.* in               ##
+##   directory config to Makefile.inc                                          ##
+##                                                                             ##
+## (C) Potsdam Institute for Climate Impact Research (PIK), see COPYRIGHT file ##
+## authors, and contributors see AUTHORS file                                  ##
+## This file is part of LPJmL and licensed under GNU AGPL Version 3            ##
+## or later. See LICENSE file or go to http://www.gnu.org/licenses/            ##
+## Contact: https://gitlab.pik-potsdam.de/lpjml                                ##
+##                                                                             ##
+#################################################################################
+
+include Makefile.inc
+
+INC     = include
+
+HDRS    = $(INC)/buffer.h $(INC)/cell.h $(INC)/climate.h $(INC)/conf.h\
+          $(INC)/config.h $(INC)/coord.h $(INC)/crop.h $(INC)/cropdates.h\
+          $(INC)/date.h $(INC)/discharge.h $(INC)/param.h $(INC)/input.h\
+          $(INC)/errmsg.h $(INC)/grass.h $(INC)/header.h $(INC)/landuse.h\
+          $(INC)/list.h $(INC)/lpj.h $(INC)/manage.h $(INC)/managepar.h\
+          $(INC)/numeric.h $(INC)/tree.h $(INC)/image.h $(INC)/biomes.h\
+          $(INC)/output.h $(INC)/pft.h $(INC)/pftlist.h $(INC)/pftpar.h\
+          $(INC)/soil.h $(INC)/soilpar.h $(INC)/stand.h $(INC)/swap.h\
+          $(INC)/types.h $(INC)/units.h $(INC)/climbuf.h $(INC)/intlist.h\
+          $(INC)/queue.h $(INC)/pnet.h $(INC)/channel.h\
+          $(INC)/natural.h $(INC)/grassland.h $(INC)/agriculture.h\
+          $(INC)/reservoir.h $(INC)/spitfire.h $(INC)/biomass_tree.h\
+          $(INC)/biomass_grass.h $(INC)/cdf.h $(INC)/outfile.h $(INC)/cpl.h
+
+CONF	= lpjml.conf input.conf param.conf lpj.conf\
+          lpjml_image.conf\
+          lpjml_netcdf.conf input_netcdf.conf lpjml_fms.conf input_fms.conf
+
+DATA    = par/*.par
+
+SCRIPTS	= configure.bat configure.sh\
+          bin/output_bsq bin/lpjsubmit_aix bin/lpjsubmit_intel\
+          bin/lpjsubmit_mpich bin/lpjrun bin/backtrace\
+          bin/filetypes.vim bin/regridlpj
+
+FILES	= Makefile config/* AUTHORS INSTALL VERSION LICENSE magic.mgc\
+          $(CONF) $(DATA) $(HDRS) $(SCRIPTS)
+
+main: 
+	$(MKDIR) lib
+	(cd src && $(MAKE))
+utils:
+	(cd src && $(MAKE) libs)
+	(cd src/utils && $(MAKE) all)
+
+all: main utils
+
+install: all
+	$(MKDIR) $(LPJROOT)/bin
+	$(MKDIR) $(LPJROOT)/include
+	$(MKDIR) $(LPJROOT)/lib
+	$(MKDIR) $(LPJROOT)/par
+	$(MKDIR) $(LPJROOT)/man/man1
+	$(MKDIR) $(LPJROOT)/man/man5
+	$(MKDIR) $(LPJROOT)/man/man3
+	chmod 755 $(LPJROOT)
+	chmod 755 $(LPJROOT)/bin
+	chmod 755 $(LPJROOT)/include
+	chmod 755 $(LPJROOT)/lib
+	chmod 755 $(LPJROOT)/par
+	chmod 755 $(LPJROOT)/man
+	chmod 755 $(LPJROOT)/man/man1
+	chmod 755 $(LPJROOT)/man/man5
+	chmod 755 $(LPJROOT)/man/man3
+	install bin/* $(LPJROOT)/bin
+	install -m 644 $(HDRS) $(LPJROOT)/include
+	install -m 644 lib/* $(LPJROOT)/lib
+	install -m 644 $(DATA) $(LPJROOT)/par
+	install -m 644 INSTALL VERSION AUTHORS Makefile.inc config/Makefile.template\
+                       $(JCFFILE) lpjml.conf input.conf param.conf $(LPJROOT)
+	install -m 644 man/whatis $(LPJROOT)/man
+	install -m 644 man/man1/*.1 $(LPJROOT)/man/man1
+	install -m 644 man/man5/*.5 $(LPJROOT)/man/man5
+	install -m 644 man/man3/*.3 $(LPJROOT)/man/man3
+
+test: main
+	$(MKDIR) output
+	$(MKDIR) restart
+
+clean:
+	(cd src  && $(MAKE) clean)
+
+tar: 
+	tar -cf lpjml-4.0.001.tar $(FILES) src/Makefile src/*.c\
+	    src/climate/Makefile src/climate/*.c\
+            man/man1/*.1 man/man3/*.3 man/man5/*.5 man/whatis\
+            man/man1/Makefile man/man3/Makefile man/man5/Makefile man/Makefile\
+	    src/crop/*.c src/crop/Makefile src/grass/*.c src/grass/Makefile\
+	    src/image/Makefile src/image/*.c\
+	    src/landuse/*.c src/landuse/Makefile src/lpj/*.c src/lpj/Makefile\
+	    src/numeric/*.c src/numeric/Makefile src/soil/*.c src/soil/Makefile\
+	    src/tools/*.c src/tools/Makefile src/tree/*.c src/tree/Makefile\
+            src/lpj/FILES src/pnet/*.c src/pnet/FILES src/socket/Makefile\
+            src/socket/*.c html/*.html html/*.css src/reservoir/Makefile\
+            src/image/Makefile src/image/*.c src/reservoir/*.c\
+            src/pnet/Makefile REFERENCES COPYRIGHT README doc/* src/utils/*.c src/utils/Makefile\
+            src/spitfire/Makefile src/spitfire/*.c R/*.r src/netcdf/Makefile src/netcdf/*.c\
+            src/cpl/Makefile src/cpl/*.c
+	    gzip -f lpjml-4.0.001.tar
+
+zipfile: 
+	zip -l lpjml-4.0.001.zip $(FILES) src/Makefile src/*.c\
+	    src/climate/Makefile src/climate/*.c config/* man/* man/man1/*.1\
+            man/man3/*.3 man/man5/*.5\
+	    src/crop/*.c src/crop/Makefile src/grass/*.c src/grass/Makefile\
+	    src/image/Makefile src/image/*.c R/*.r\
+	    src/landuse/*.c src/landuse/Makefile src/lpj/*.c src/lpj/Makefile\
+	    src/numeric/*.c src/numeric/Makefile src/soil/*.c src/soil/Makefile\
+	    src/tools/*.c src/tools/Makefile src/tree/*.c src/tree/Makefile\
+            src/lpj/FILES src/pnet/*.c src/pnet/FILES src/socket/Makefile\
+            src/socket/*.c src/reservoir/Makefile\
+            src/image/*.c src/image/Makefile src/reservoir/*.c\
+            src/pnet/Makefile REFERENCES COPYRIGHT README doc src/utils/*.c src/utils/Makefile\
+            src/spitfire/Makefile src/spitfire/*.c src/netcdf/Makefile src/netcdf/*.c\
+            src/cpl/Makefile src/cpl/*.c

README

+README LPJmL
+
+This file contains some basic information on the open source distribution of the computer simulation model LPJmL.
+LPJmL is developed and maintained at the Potsdam Institute for Climate Impact Research (PIK) in Potsdam, Germany.
+
+All source code, configuration and parameter files are subject to 
+copyright (C) by the Potsdam Institute for Climate Impact Research, see the file COPYRIGHT
+and are licensed under the GNU AFFERO GENERAL PUBLIC LICENSE Version 3, see the file LICENSE
+and is the result of collaborative work, see the file AUTHORS
+
+For setting up the model, see the file INSTALL
+
+The source code is distributed via a git repository at https://gitlab.pik-potsdam.de/lpjml/lpjml after registration.
+The registration is free of costs.
+
+Outside joint collaborative agreements with PIK, there is absolutely no support in model download, setup, development, application or similar. 
+
+New model development can be submitted to the LPJmL git repository in separate repository branches and pull requests can be issued. There is no guarantee or obligation that external model features, bug fixes or other developemnts will be merged into the standard LPJmL distribution at PIK.
+Discussions on model development features can only be initiated via issues at https://gitlab.pik-potsdam.de/lpjml/lpjml after registration.
+
+We strongly encourrage considering the coding standards and style recommendations in LPJmL. For details see the file STYLESHEET

REFERENCES

+ -----------------------------------------------------------------------------
+                                 REFERENCES
+ -----------------------------------------------------------------------------
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+   Global Change Biology 13, doi: 10.1111/j.1365-2486.2006.01305.x
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+ Jury WA, Gardner WR & Gardner WH 1991 Soil Physics 5th ed, John Wiley, NY
+ Larcher W 1983 Physiological Plant Ecology, 2nd ed, Springer-Verlag, Berlin
+ Lloyd, J & Taylor JA 1994 On the temperature dependence of soil respiration
+   Functional Ecology 8: 315-323
+ Monsi, M & Saeki, T 1953 Ueber den Lichtfaktor in den Pflanzengesellschaften
+   und seine Bedeutung fuer die Stoffproduktion. Japanese Journal of Botany
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