Merge branch 'hotfix-v6.1'

This merge introduces v6.1 of MPAS.
Changes only occur in the sea ice model.

* hotfix-v6.1:
  Update README and LICENSE
  Increment version number to 6.1
  Removed reference to restartability_bgc in testing system.
  Added restart testing capability to restartability.py
  Added BGC testing and corrected 0 dimension
  Corrects iron uptake when carbon is active.
  Commented out two flags and updated bgc parameter defaults.

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2013,  Los Alamos National Security, LLC (LANS) (Ocean: LA-CC-13-047;
+Copyright (c) 2013-2018,  Los Alamos National Security, LLC (LANS) (Ocean: LA-CC-13-047;
 Land Ice: LA-CC-13-117) and the University Corporation for Atmospheric Research (UCAR).
 
 All rights reserved. 

README.md

@@ -1,4 +1,4 @@
-MPAS-v6.0
+MPAS-v6.1
 ====
 
 The Model for Prediction Across Scales (MPAS) is a collaborative project for
@@ -28,25 +28,29 @@ core's user's guide, which can be found at the following web sites:
 
 [MPAS-Atmosphere](http://mpas-dev.github.io/atmosphere/atmosphere_download.html)
 
-[MPAS-Land Ice](http://mpas-dev.github.io/land_ice/download.html)
+[MPAS-Albany Land Ice](http://mpas-dev.github.io/land_ice/download.html)
 
 [MPAS-Ocean](http://mpas-dev.github.io/ocean/releases.html)
 
+[MPAS-Seaice](http://mpas-dev.github.io/sea_ice/releases.html)
+
+
 Code Layout
 ----------
 
 Within the MPAS repository, code is laid out as follows. Sub-directories are
 only described below the src directory.
 
-	MPAS
-	└── src
-	    ├── registry -- Code for building Registry.xml parser (Shared)
-	    ├── driver -- Main driver for MPAS in stand-alone mode (Shared)
-	    ├── external -- External software for MPAS (Shared)
-	    ├── framework -- MPAS Framework (Includes DDT Descriptions, and shared routines. Shared)
-	    ├── operators -- MPAS Opeartors (Includes Operators for MPAS meshes. Shared)
-	    ├── inc -- Empty directory for include files that Registry generates (Shared)
-	    └── core_* -- Individual model cores.
+	MPAS-Model
+	├── src
+	│   ├── registry -- Code for building Registry.xml parser (Shared)
+	│   ├── driver -- Main driver for MPAS in stand-alone mode (Shared)
+	│   ├── external -- External software for MPAS (Shared)
+	│   ├── framework -- MPAS Framework (Includes DDT Descriptions, and shared routines. Shared)
+	│   ├── operators -- MPAS Opeartors (Includes Operators for MPAS meshes. Shared)
+	│   ├── inc -- Empty directory for include files that Registry generates (Shared)
+	│   └── core_* -- Individual model cores.
+        └────── testing_and_setup -- tools for setting up configurations and tests cases (Shared)
 
 Model cores are typically developed independently. For information about
 building and running a particular core, please refer to that core's user's

src/core_atmosphere/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="atmosphere" core_abbrev="atm" version="6.0">
+<registry model="mpas" core="atmosphere" core_abbrev="atm" version="6.1">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->

src/core_init_atmosphere/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="init_atmosphere" core_abbrev="init_atm" version="6.0">
+<registry model="mpas" core="init_atmosphere" core_abbrev="init_atm" version="6.1">
 
 <!-- **************************************************************************************** -->
 <!-- ************************************** Dimensions ************************************** -->

src/core_landice/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="landice" core_abbrev="li" version="6.0">
+<registry model="mpas" core="landice" core_abbrev="li" version="6.1">
 
 
 <!-- ======================================================================= -->

src/core_ocean/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="ocean" core_abbrev="ocn" version="6.0">
+<registry model="mpas" core="ocean" core_abbrev="ocn" version="6.1">
 
 	<dims>
 		<dim name="nCells" units="unitless"

src/core_seaice/column/ice_algae.F90

@@ -1278,7 +1278,7 @@ subroutine z_biogeochemistry (n_cat,        dt,        &
                 call add_warning(warning)
                 write(warning,*)'Category,mm:',n_cat,mm
                 call add_warning(warning)
-                l_stop = .true.
+!                l_stop = .true.
                 stop_label = 'zbgc FCT tracer solution failed'
             endif
             if (l_stop) return
@@ -1351,7 +1351,7 @@ subroutine z_biogeochemistry (n_cat,        dt,        &
                 call add_warning(warning)
                 write(warning, *)  react(k,m),iphin_N(k),biomat_brine(k,m)
                 call add_warning(warning)
-                l_stop = .true.
+!                l_stop = .true.
                 stop_label = 'very large bgc value'
             elseif (bio_tmp < c0) then
                 write(warning, *) 'negative bgc'
@@ -2036,7 +2036,8 @@ subroutine algal_dyn (dt,           &
           enddo    
         endif
         endif !Docin(1) > c0
-      elseif (tr_bgc_Fe) then
+      endif
+      if (tr_bgc_Fe) then
         do n = 1,n_fed
            Fed_r(n) = Fed_r(n) + rFed(n)*Fed_tot_r          ! scavenging + uptake
         enddo 

src/core_sw/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="sw" core_abbrev="sw" version="6.0">
+<registry model="mpas" core="sw" core_abbrev="sw" version="6.1">
 	<dims>
 		<dim name="nCells"/>
 		<dim name="nEdges"/>

src/core_test/Registry.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<registry model="mpas" core="test" core_abbrev="test" version="6.0">
+<registry model="mpas" core="test" core_abbrev="test" version="6.1">
 	<dims>
 		<dim name="nCells"/>
 		<dim name="nEdges"/>

testing_and_setup/seaice/configurations/standard_bgc/namelist.seaice

@@ -117,7 +117,7 @@
     config_use_vertical_tracers = true
     config_use_skeletal_biochemistry = false
     config_use_nitrate = true
-    config_use_carbon = true
+    config_use_carbon = false
     config_use_chlorophyll = false
     config_use_ammonium = true
     config_use_silicate = true

testing_and_setup/seaice/testing/tests/restartability.py

@@ -59,8 +59,18 @@ def restartability(mpasDevelopmentDir, domainsDir, domain, configuration, option
     # restart
     nProcs = 32
 
-    nmlChanges = {"seaice_model": {"config_start_time":"file"},
-                  "restart":    {"config_do_restart":True}}
+    bgcRestart = False
+    if ("bgc" in options.keys() and options["bgc"] == "True"):
+        bgcRestart = True
+
+    if (not bgcRestart):
+        nmlChanges = {"seaice_model": {"config_start_time":"file"},
+                      "restart": {"config_do_restart":True}}
+    else:
+        nmlChanges = {"seaice_model": {"config_start_time":"file"},
+                      "restart": {"config_do_restart":True,
+                                  "config_do_restart_bgc":True,
+                                  "config_do_restart_hbrine":True}}
     if (check):
         nmlChanges["unit_test"] = {"config_testing_system_test":True}
 

testing_and_setup/seaice/testing/testsuites/testsuite.standard_bgc.xml

@@ -4,7 +4,9 @@
 		<domain name="domain_QU240km">
 			<test name="regression"/>
 			<test name="parallelism"/>
-			<test name="restartability"/>
+			<test name="restartability">
+			      <option name="bgc" value="True"/>
+			    </test>
 		</domain>
 	</configuration>
 </testsuite>