Merge pull request #1 from rgknox/ncar-ngeet-release-1

Ncar ngeet release 1

LICENSE.txt

@@ -1,34 +1,59 @@
-Copyright (c) 2013-2015, University Corporation for Atmospheric Research (UCAR)
-All rights reserved.
-
-Developed by: 
-              University Corporation for Atmospheric Research - National Center for Atmospheric Research
-              https://www2.cesm.ucar.edu/working-groups/sewg
-
-Permission is hereby granted, free of charge, to any person obtaining 
-a copy of this software and associated documentation files (the "Software"), 
-to deal with the Software without restriction, including without limitation 
-the rights to use, copy, modify, merge, publish, distribute, sublicense, 
-and/or sell copies of the Software, and to permit persons to whom 
-the Software is furnished to do so, subject to the following conditions:
-
-    - Redistributions of source code must retain the above copyright notice, 
-      this list of conditions and the following disclaimers.
-    - Redistributions in binary form must reproduce the above copyright notice, 
-      this list of conditions and the following disclaimers in the documentation 
-      and/or other materials provided with the distribution.
-    - Neither the names of UCAR, or NCAR, 
-      nor the names of its contributors may be used to endorse or promote 
-      products derived from this Software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
-ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 
-LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
-CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
-SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
-POSSIBILITY OF SUCH DAMAGE.		
+Functionally Assembled Terrestrial Ecosystem Simulator (“FATES”)
+
+Copyright (c) 2016-2017, The Regents of the University of California, through Lawrence
+Berkeley National Laboratory, University Corporation for Atmospheric Research, Los Alamos
+National Security, LLC (LANS), as operator of Los Alamos National Laboratory (LANL), and
+President and Fellows of Harvard College. All rights reserved.
+
+Copyright (c) 2013-2015, University Corporation for Atmospheric Research (UCAR). All
+rights reserved.
+
+If you have questions about your rights to use or distribute this software, please contact
+Berkeley Lab's Innovation & Partnerships Office at [email protected].
+
+NOTICE.  This Software was developed under funding from the U.S. Department of Energy and
+the U.S. Government consequently retains certain rights.  As such, the U.S. Government has
+been granted for itself and others acting on its behalf a paid-up, nonexclusive,
+irrevocable, worldwide license in the Software to reproduce, distribute copies to the
+public, prepare derivative works, and perform publicly and display publicly, and to permit
+other to do so.
+
+ Redistribution and use in source and binary forms, with or without modification, are
+ permitted provided that the following conditions are met:
+
+ (1) Redistributions of source code must retain the above copyright notice, this list of
+ conditions and the following disclaimer.
+
+ (2) Redistributions in binary form must reproduce the above copyright notice, this list
+ of conditions and the following disclaimer in the documentation and/or other materials
+ provided with the distribution.
+
+ (3) Neither the name of the University of California, Lawrence Berkeley National
+ Laboratory, University Corporation for Atmospheric Research, Los Alamos National
+ Security, LLC (LANS), as operator of Los Alamos National Laboratory (LANL), President and
+ Fellows of Harvard College, or the U.S. Dept. of Energy nor the names of its contributors
+ may be used to endorse or promote products derived from this software without specific
+ prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
+EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+You are under no obligation whatsoever to provide any bug fixes, patches, or upgrades to
+the features, functionality or performance of the source code ("Enhancements") to anyone;
+however, if you choose to make your Enhancements available either publicly, or directly to
+Lawrence Berkeley National Laboratory, without imposing a separate written license
+agreement for such Enhancements, then you hereby grant the following license to Lawrence
+Berkeley National Laboratory, University Corporation for Atmospheric Research, Los Alamos
+National Security, LLC (LANS), as operator of Los Alamos National Laboratory (LANL),
+President and Fellows of Harvard College, and the U.S. Dept. of Energy: a non-exclusive,
+royalty-free perpetual license to install, use, modify, prepare derivative works,
+incorporate into other computer software, distribute, and sublicense such enhancements or
+derivative works thereof, in binary and source code form.
+

README.md

@@ -1,9 +1,22 @@
-# FATES - Functionally Assembled Terrestrial Ecosystem Simulator
+# NGEE-T fates repository
+------------------------------
 
-This is a READ-ONLY mirror of the NGEE-Tropics FATES public
-release. Please contact the [NGEE-T](https://github.com/NGEET) group
-for details, support and on-going development.
+This is the developer repository of the Next Generation Ecosystem Experiment Tropics’ (NGEE-T) model: the Functionally Assembled Terrestrial Ecosystem Simulator (FATES).
 
-FATES compsets are experimental and under active development.
+For more information on the FATES model, see our wiki:  https://github.com/NGEET/fates/wiki
 
 
+## Important:
+------------------------------
+
+**Most users should not need to directly clone this repository.  FATES needs to be run through a host model, and all supported host-models are in charge of cloning and loading the fates software.**
+
+FATES has support to be run via the Accelerated Climate Model for Energy (ACME) and the Community Earth System Model (CESM).
+
+https://climatemodeling.science.energy.gov/projects/accelerated-climate-modeling-energy
+
+http://www.cesm.ucar.edu/
+
+The NGEE-T project maintains a mirror of CLM.  That software system will automatically pull in the FATES software, and is where most users should go to clone the code:
+
+https://github.com/NGEET/fates-clm

biogeochem/EDCanopyStructureMod.F90

@@ -383,10 +383,15 @@ subroutine canopy_structure( currentSite , bc_in )
           enddo
           currentPatch%ncl_p = min(z,nclmax)
 
-       enddo !is there still excess area in any layer?      
+       enddo !is there still excess area in any layer?
+
+       ! Remove cohorts that are incredibly sparse
+       call terminate_cohorts(currentSite, currentPatch, 1)
 
        call fuse_cohorts(currentPatch, bc_in)
-       call terminate_cohorts(currentSite, currentPatch)
+
+       ! Remove cohorts for various other reasons
+       call terminate_cohorts(currentSite, currentPatch, 2)
 
        ! ----------- Check cohort area ------------------------------!
        do i = 1,z
@@ -605,8 +610,13 @@ subroutine canopy_structure( currentSite , bc_in )
           endif
        enddo !is there still not enough canopy area in any layer?         
 
+       ! remove cohorts that are extremely sparse
+       call terminate_cohorts(currentSite, currentPatch, 1)
+
        call fuse_cohorts(currentPatch, bc_in)
-       call terminate_cohorts(currentSite, currentPatch)
+
+       ! remove cohorts for various other reasons
+       call terminate_cohorts(currentSite, currentPatch, 2)
 
        if(promswitch == 1)then
           !write(fates_log(),*) 'going into cohort check'
@@ -1223,7 +1233,7 @@ subroutine leaf_area_profile( currentSite , snow_depth_si, frac_sno_eff_si)
                 write(fates_log(), *) 'ED: canopy-area-profile wrong', &
                       sum(currentPatch%canopy_area_profile(L,1:numpft_ed,1)), &
                       currentPatch%patchno, L
-                write(fates_log(), *) 'ED: areas',currentPatch%canopy_area_profile(L,1:2,1),currentPatch%patchno
+                write(fates_log(), *) 'ED: areas',currentPatch%canopy_area_profile(L,1:numpft_ed,1),currentPatch%patchno
 
                 currentCohort => currentPatch%shortest