From c8bfca7eff03d7bee9cd7182e02f37081326f006 Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Wed, 17 Feb 2016 15:06:16 -0800
Subject: [PATCH 01/19] inserted no-megan clause to ED compset configurations

---
 cime/scripts/Tools/config_compsets.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cime/scripts/Tools/config_compsets.xml b/cime/scripts/Tools/config_compsets.xml
index 9c91719e67..3ee679ecdc 100644
--- a/cime/scripts/Tools/config_compsets.xml
+++ b/cime/scripts/Tools/config_compsets.xml
@@ -845,7 +845,7 @@ CAM[45]%L60  => CAM with 60 layers and full gravity wave spectrum:
 <CLM_BLDNML_OPTS compset="_CLM45%[^_]*BGCDV"     >-bgc bgc -dynamic_vegetation</CLM_BLDNML_OPTS>
 <CLM_BLDNML_OPTS compset="_CLM45%[^_]*CNDV-CROP" >-bgc cn -dynamic_vegetation -crop</CLM_BLDNML_OPTS>
 <CLM_BLDNML_OPTS compset="_CLM45%[^_]*BGCDV-CROP">-bgc bgc -dynamic_vegetation -crop</CLM_BLDNML_OPTS>
-<CLM_BLDNML_OPTS compset="_CLM45%[^_]*ED"        >-ed_mode</CLM_BLDNML_OPTS>
+<CLM_BLDNML_OPTS compset="_CLM45%[^_]*ED"        >-ed_mode -no-megan</CLM_BLDNML_OPTS>
 
 <CLM_BLDNML_OPTS compset="_CLM50%[^_]*SP"        >-bgc sp</CLM_BLDNML_OPTS>
 <CLM_BLDNML_OPTS compset="_CLM50%[^_]*BGC"       >-bgc bgc</CLM_BLDNML_OPTS>

From c61aaef0dab1669fcd16310337da5cf19d59d197 Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Wed, 17 Feb 2016 15:11:44 -0800
Subject: [PATCH 02/19] added use_century_decomp and use_vertsoilc to the
 ed_mode in components/clm/bld/CLMBuildNamelist.pm

---
 components/clm/bld/CLMBuildNamelist.pm | 38 +++++++++++++++++++++-----
 1 file changed, 31 insertions(+), 7 deletions(-)

diff --git a/components/clm/bld/CLMBuildNamelist.pm b/components/clm/bld/CLMBuildNamelist.pm
index d70e50c1b4..723aa468e4 100755
--- a/components/clm/bld/CLMBuildNamelist.pm
+++ b/components/clm/bld/CLMBuildNamelist.pm
@@ -159,7 +159,8 @@ OPTIONS
                               (can ONLY be turned on when BGC type is 'cn' or 'bgc')
                               This turns on the namelist variable: use_cndv
      -ed_mode                 Turn ED (Ecosystem Demography) : [on | off] (default is off)
-                              Sets the namelist variable use_ed and use_spit_fire.
+                              Sets the namelist variable use_ed, use_spit_fire, 
+                                   use_vertsoilc, use_century_decomp
      -glc_present             Set to true if the glc model is present (not sglc).
                               This is used for error-checking, to make sure other options are
                               set appropriately.
@@ -745,13 +746,36 @@ sub setup_cmdl_ed_mode {
         fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values\n");
       }
 
-      $var = "use_ed_spit_fire";
-      $nl->set_variable_value($group, $var, $val);
-      if ( ! $definition->is_valid_value($var, $val) ) {
-        my @valid_values   = $definition->get_valid_values( $var );
-        fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values\n");
-      }
+      # If the variable has already been set use it, if not set to the value defined by the ed_mode
+      my @list  = (  "use_ed_spit_fire", "use_vertsoilc", "use_century_decomp" );
+      my $ndiff = 0;
+      foreach my $var ( @list ) {
+	  if ( ! defined($nl->get_value($var))  ) {
+	      $nl_flags->{$var} = $setting;
+	  } else {
+	      if ( $nl->get_value($var) ne $setting ) {
+		  $ndiff += 1;
+	      }
+	      $nl_flags->{$var} = $nl->get_value($var);
+	  }
+	  $val = $nl_flags->{$var};
+	  my $group = $definition->get_group_name($var);
+	  $nl->set_variable_value($group, $var, $val);
+	  if (  ! $definition->is_valid_value( $var, $val ) ) {
+	      my @valid_values   = $definition->get_valid_values( $var );
+	      fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values\n");
+	  }
+      }
+
+#      $var = "use_ed_spit_fire";
+#      $nl->set_variable_value($group, $var, $val);
+#      if ( ! $definition->is_valid_value($var, $val) ) {
+#        my @valid_values   = $definition->get_valid_values( $var );
+#        fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values\n");
+#      }
+
     } else {
+	# we only dis-allow ed_spit_fire with non-ed runs
        $var = "use_ed_spit_fire";
        if ( defined($nl->get_value($var)) ) {
            fatal_error("$var is being set, but can ONLY be set when -ed_mode option is used.\n");

From c6185f2736873e85181962701fe2ecdcdde52fd3 Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Wed, 17 Feb 2016 15:38:55 -0800
Subject: [PATCH 03/19] updated the intel compiler for lr2/lr3

---
 cime/machines/env_mach_specific.lawrencium-lr2 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cime/machines/env_mach_specific.lawrencium-lr2 b/cime/machines/env_mach_specific.lawrencium-lr2
index 3de47efa2d..b13016ef30 100755
--- a/cime/machines/env_mach_specific.lawrencium-lr2
+++ b/cime/machines/env_mach_specific.lawrencium-lr2
@@ -23,9 +23,9 @@ module load cmake
 module load perl xml-libxml switch
 
 if ( $COMPILER == "intel" ) then
-    module load intel/2015.0.090
+    module load intel/2015.6.233
     module load openmpi
-    module load netcdf/4.3.2-intel-p
+    module load netcdf/4.4.0-intel-p
     module load mkl
 endif
 

From 89809d84d73de6d5d410b6e6ac3739237c5bfa64 Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Wed, 17 Feb 2016 20:03:28 -0800
Subject: [PATCH 04/19] Added env_mach_specific.lawrencium-lr3

---
 .../machines/env_mach_specific.lawrencium-lr3 | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100755 cime/machines/env_mach_specific.lawrencium-lr3

diff --git a/cime/machines/env_mach_specific.lawrencium-lr3 b/cime/machines/env_mach_specific.lawrencium-lr3
new file mode 100755
index 0000000000..b13016ef30
--- /dev/null
+++ b/cime/machines/env_mach_specific.lawrencium-lr3
@@ -0,0 +1,37 @@
+#! /bin/csh -f
+
+set CESM_REPO = `./xmlquery CCSM_REPOTAG -value`
+if($status == 0) then
+  set COMPILER            = `./xmlquery  COMPILER          -value`
+  set MPILIB              = `./xmlquery  MPILIB            -value`
+  set DEBUG               = `./xmlquery  DEBUG             -value`
+  set OS                  = `./xmlquery  OS                -value`
+  set PROFILE_PAPI_ENABLE = `./xmlquery  PROFILE_PAPI_ENABLE -value`
+  set PROJECT             = `./xmlquery  PROJECT           -value`
+else
+  echo $0 using settings from environment:
+endif
+echo "COMPILER=$COMPILER"
+echo "MPILIB=$MPILIB"
+echo "DEBUG=$DEBUG"
+echo "OS=$OS"
+echo "PROJECT=$PROJECT"
+
+source /etc/profile.d/modules.csh
+module purge
+module load cmake
+module load perl xml-libxml switch
+
+if ( $COMPILER == "intel" ) then
+    module load intel/2015.6.233
+    module load openmpi
+    module load netcdf/4.4.0-intel-p
+    module load mkl
+endif
+
+setenv NETCDF_PATH $NETCDF_DIR
+#-------------------------------------------------------------------------------
+
+limit coredumpsize 1000000
+limit stacksize unlimited
+

From a7ff225f552a40620df4775184207f0e73cee219 Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Wed, 17 Feb 2016 20:14:03 -0800
Subject: [PATCH 05/19] corrections to CLMBuildNamelist.pm, removed the setting
 variable and counter

---
 components/clm/bld/CLMBuildNamelist.pm | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/components/clm/bld/CLMBuildNamelist.pm b/components/clm/bld/CLMBuildNamelist.pm
index 723aa468e4..a86b36a09e 100755
--- a/components/clm/bld/CLMBuildNamelist.pm
+++ b/components/clm/bld/CLMBuildNamelist.pm
@@ -751,11 +751,8 @@ sub setup_cmdl_ed_mode {
       my $ndiff = 0;
       foreach my $var ( @list ) {
 	  if ( ! defined($nl->get_value($var))  ) {
-	      $nl_flags->{$var} = $setting;
+	      $nl_flags->{$var} = ".true.";
 	  } else {
-	      if ( $nl->get_value($var) ne $setting ) {
-		  $ndiff += 1;
-	      }
 	      $nl_flags->{$var} = $nl->get_value($var);
 	  }
 	  $val = $nl_flags->{$var};

From b4deebab25fb23c4b404310ffc03a19807bfd913 Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Thu, 18 Feb 2016 16:20:11 -0800
Subject: [PATCH 06/19] Initial tinkering with namelist unit tests of ed_mode

---
 .../bld/test_build_namelist/t/test_ed_mode.pm | 82 +++++++++++++++++++
 .../test_build_namelist/t/test_vichydro.pm    |  1 +
 2 files changed, 83 insertions(+)
 create mode 100644 components/clm/bld/test_build_namelist/t/test_ed_mode.pm

diff --git a/components/clm/bld/test_build_namelist/t/test_ed_mode.pm b/components/clm/bld/test_build_namelist/t/test_ed_mode.pm
new file mode 100644
index 0000000000..a1bc25ab8f
--- /dev/null
+++ b/components/clm/bld/test_build_namelist/t/test_ed_mode.pm
@@ -0,0 +1,82 @@
+package test_ed_mode;
+
+# Unit tests for function: ed_mode
+
+use Data::Dumper;
+use Test::More;
+use Test::Exception;
+
+use parent qw(Test::Class);
+
+#-------------------------------------------------------------------------------
+#
+# Common test fixture for all tests:
+#
+#-------------------------------------------------------------------------------
+sub startup : Test(startup => 4) {
+  my $self = shift;
+  # provide common fixture for all tests, only created once at the
+  # start of the tests.
+
+  $self->{cfg} = Build::Config->new("t/input/config_cache_clm4_5_test.xml");
+  isnt($self->{cfg}, undef, (caller(0))[3] . " : config object created.");
+
+  $self->{definition} = Build::NamelistDefinition->new("t/input/namelist_definition_clm4_5_test.xml");
+  isnt($self->{definition}, undef, (caller(0))[3] . " : namelist_definition object created.");
+
+  $self->{defaults} = Build::NamelistDefaults->new("t/input/namelist_defaults_clm4_5_test.xml");
+  isnt($self->{defaults}, undef,  (caller(0))[3] . " : namelist_defaults object created.");
+
+  $self->{physv} = config_files::clm_phys_vers->new( $self->{cfg}->get('phys') );
+  isnt($self->{physv}, undef,  (caller(0))[3] . " : phys_vers object created.");
+
+}
+
+sub shutdown : Test(shutdown) {
+  # cleanup the single instance test fixtures
+}
+
+sub setup : Test(setup => 1) {
+  my $self = shift;
+  # provide common fixture for all tests, create fresh for each test
+
+  $self->{nl} = Build::Namelist->new();
+  isnt($self->{nl}, undef, (caller(0))[3] . " : empty namelist object created.");
+}
+
+sub teardown : Test(teardown) {
+  # clean up after test
+}
+
+#-------------------------------------------------------------------------------
+#
+# tests
+# 
+# 1: test that use_century_decom is the default with ed_mode
+# 7: test that clm4.0 fails with ed_mode
+#
+#-------------------------------------------------------------------------------
+
+# Test 1: use_century_decomp is default with ed_mode
+sub test_ed_mode__use_century_decomp : Tests {
+  my $self = shift;
+
+  my $msg = "Test that the ed_mode set with use_century_decomp results success.\n";
+
+  use CLMBuildNamelist qw(setup_cmdl_ed_mode);
+
+  my $opts = { ed_mode => 1, };
+  my $nl_flags = { crop => 1, };  # eq "on"
+
+#  my $nl_flags = { phys => "clm4_5", };
+#  my $physv = config_files::clm_phys_vers->new( "clm4_5" );
+
+  CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+  my $group = $self->{definition}->get_group_name("use_century_decomp");
+  my $result = $self->{nl}->get_variable_value($group, "use_century_decomp");
+  is($result, '.true.' ) || diag($msg);
+  #isnt
+}
+
+
+1;
diff --git a/components/clm/bld/test_build_namelist/t/test_vichydro.pm b/components/clm/bld/test_build_namelist/t/test_vichydro.pm
index b49889b16c..16a3ebc59a 100644
--- a/components/clm/bld/test_build_namelist/t/test_vichydro.pm
+++ b/components/clm/bld/test_build_namelist/t/test_vichydro.pm
@@ -20,6 +20,7 @@ sub startup : Test(startup => 4) {
   $self->{cfg} = Build::Config->new("t/input/config_cache_clm4_5_test.xml");
   isnt($self->{cfg}, undef, (caller(0))[3] . " : config object created.");
 
+
   $self->{definition} = Build::NamelistDefinition->new("t/input/namelist_definition_clm4_5_test.xml");
   isnt($self->{definition}, undef, (caller(0))[3] . " : namelist_definition object created.");
 

From 73ba5c80004a8fee9164cfadc02cfed0a73ee8e4 Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Thu, 18 Feb 2016 22:35:49 -0800
Subject: [PATCH 07/19] completed a working prototype of ed_mode namelist
 unittests, 9 tests total

---
 components/clm/bld/CLMBuildNamelist.pm        |   3 +-
 .../bld/test_build_namelist/t/test_ed_mode.pm | 154 +++++++++++++++++-
 2 files changed, 148 insertions(+), 9 deletions(-)

diff --git a/components/clm/bld/CLMBuildNamelist.pm b/components/clm/bld/CLMBuildNamelist.pm
index a86b36a09e..495904958e 100755
--- a/components/clm/bld/CLMBuildNamelist.pm
+++ b/components/clm/bld/CLMBuildNamelist.pm
@@ -731,7 +731,6 @@ sub setup_cmdl_ed_mode {
     $var = "use_ed";
     $nl_flags->{$var} = ".false.";
     if ($nl_flags->{'ed_mode'} eq 1) {
-      message("Using ED (Ecosystem Demography).");
       $val = ".true.";
       $nl_flags->{$var} = $val;
     }
@@ -746,7 +745,7 @@ sub setup_cmdl_ed_mode {
         fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values\n");
       }
 
-      # If the variable has already been set use it, if not set to the value defined by the ed_mode
+      # If these variablse  not being set by user, default to true
       my @list  = (  "use_ed_spit_fire", "use_vertsoilc", "use_century_decomp" );
       my $ndiff = 0;
       foreach my $var ( @list ) {
diff --git a/components/clm/bld/test_build_namelist/t/test_ed_mode.pm b/components/clm/bld/test_build_namelist/t/test_ed_mode.pm
index a1bc25ab8f..c2043986e5 100644
--- a/components/clm/bld/test_build_namelist/t/test_ed_mode.pm
+++ b/components/clm/bld/test_build_namelist/t/test_ed_mode.pm
@@ -53,7 +53,14 @@ sub teardown : Test(teardown) {
 # tests
 # 
 # 1: test that use_century_decom is the default with ed_mode
-# 7: test that clm4.0 fails with ed_mode
+# 2: test that use_vertsoilc is the default with ed_mode
+# 3: test that use_ed_spit_fire is the default with ed_mode
+# 4: test that use_ed = .false. will fail for ed_mode
+# 5: test that crop = "on" will fail for ed_mode
+# 6: test that clm4_0 will fail for ed_mode (NOT AVAILABLE)
+# 7: test that use_ed_spit_fire = false generates a false
+# 8: test that use_versoilc = false generates a false
+# 9: test that use_century_decomp = false generates a false
 #
 #-------------------------------------------------------------------------------
 
@@ -61,22 +68,155 @@ sub teardown : Test(teardown) {
 sub test_ed_mode__use_century_decomp : Tests {
   my $self = shift;
 
-  my $msg = "Test that the ed_mode set with use_century_decomp results success.\n";
+  my $msg = "Test that use_century_decomp is the default on ed_mode.\n";
 
   use CLMBuildNamelist qw(setup_cmdl_ed_mode);
 
   my $opts = { ed_mode => 1, };
-  my $nl_flags = { crop => 1, };  # eq "on"
-
-#  my $nl_flags = { phys => "clm4_5", };
-#  my $physv = config_files::clm_phys_vers->new( "clm4_5" );
+  my $nl_flags = { crop => "off", }; # the setup_cmdl_ed_mode code requires this logic
 
   CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
   my $group = $self->{definition}->get_group_name("use_century_decomp");
   my $result = $self->{nl}->get_variable_value($group, "use_century_decomp");
   is($result, '.true.' ) || diag($msg);
-  #isnt
 }
 
+# Test 2: use_vertsoilc is default with ed_mode
+sub test_ed_mode__use_vertsoilc : Tests {
+    my $self = shift;
+
+    my $msg = "Tests that use_vertsoilc is default on ed_mode.\n";
+
+    use CLMBuildNamelist qw(setup_cmdl_ed_mode);
+
+    my $opts = { ed_mode => 1, };
+    my $nl_flags = { crop => "off", };
+
+    CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+    my $group = $self->{definition}->get_group_name("use_vertsoilc");
+    my $result = $self->{nl}->get_variable_value($group, "use_vertsoilc");
+    is($result, '.true.' ) || diag($msg);
+}
+
+# Test 3: use_ed_spit_fire is default with ed_mode
+sub test_ed_mode__use_ed_spit_fire : Tests {
+    my $self = shift;
+
+    my $msg = "Tests that use_ed_spit_fire is default on ed_mode.\n";
+
+    use CLMBuildNamelist qw(setup_cmdl_ed_mode);
+
+    my $opts = { ed_mode => 1, };
+    my $nl_flags = { crop => "off", };
+
+    CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+    my $group = $self->{definition}->get_group_name("use_ed_spit_fire");
+    my $result = $self->{nl}->get_variable_value($group, "use_ed_spit_fire");
+    is($result, '.true.' ) || diag($msg);
+}
+
+# Test 4: use_ed=false will crash on ed_mode
+sub test_ed_mode__use_ed_nl_contradicts_cmdl : Tests {
+    my $self = shift;
+
+    my $msg = "Tests that use_ed=false will fail on ed_mode.\n";
+
+    use CLMBuildNamelist qw(setup_cmdl_ed_mode);
+
+    my $opts = { ed_mode => 1, };
+    my $nl_flags = { crop => "off", use_ed => ".false."};
+
+    my $group = $self->{definition}->get_group_name("use_ed");
+    $self->{nl}->set_variable_value($group, "use_ed", '.false.' );
+
+    dies_ok(sub { CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl},
+							$self->{physv}) }) || diag($msg);
+}
+
+# Test 5: crop=on will crash on ed_mode
+sub test_ed_mode__crop_on_nl_contradicts_cmdl : Tests {
+    my $self = shift;
+
+    my $msg = "Tests that crop=on will fail on ed_mode.\n";
+
+    use CLMBuildNamelist qw(setup_cmdl_ed_mode);
+
+    my $opts = { ed_mode => 1, };
+    my $nl_flags = { crop => "on", };
+
+    my $group = $self->{definition}->get_group_name("crop");
+    $self->{nl}->set_variable_value($group, "crop", 'on' );
+
+    dies_ok(sub { CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl},
+						   $self->{physv}) }) || diag($msg);
+}
+
+# 7: test that use_ed_spit_fire = false generates a false
+sub test_ed_mode__use_ed_spit_fire_false : Tests {
+    my $self = shift;
+
+    my $msg = "Tests that use_ed_spit_fire can be turned to false.\n";
+
+    use CLMBuildNamelist qw(setup_cmdl_ed_mode);
+
+    my $opts = { ed_mode => 1, };
+    my $nl_flags = { crop => "off", };
+
+    my $group = $self->{definition}->get_group_name("use_ed_spit_fire");
+    $self->{nl}->set_variable_value($group, "use_ed_spit_fire", '.false.' );
+
+    CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl},
+						       $self->{physv});
+
+    my $result = $self->{nl}->get_variable_value($group, "use_ed_spit_fire");
+    is($result, '.false.' ) || diag($msg);
+
+}
+
+# 8: test that use_ed_spit_fire = false generates a false
+sub test_ed_mode__use_vertsoilc_false : Tests {
+    my $self = shift;
+
+    my $msg = "Tests that use_vertsoilc can be turned to false.\n";
+
+    use CLMBuildNamelist qw(setup_cmdl_ed_mode);
+
+    my $opts = { ed_mode => 1, };
+    my $nl_flags = { crop => "off", };
+
+    my $group = $self->{definition}->get_group_name("use_vertsoilc");
+    $self->{nl}->set_variable_value($group, "use_vertsoilc", '.false.' );
+
+    CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl},
+					 $self->{physv});
+
+    my $result = $self->{nl}->get_variable_value($group, "use_vertsoilc");
+    is($result, '.false.' ) || diag($msg);
+
+}
+
+# 9: test that use_ed_spit_fire = false generates a false
+sub test_ed_mode__use_century_decomp_false : Tests {
+    my $self = shift;
+
+    my $msg = "Tests that use_century_decomp can be turned to false.\n";
+
+    use CLMBuildNamelist qw(setup_cmdl_ed_mode);
+
+    my $opts = { ed_mode => 1, };
+    my $nl_flags = { crop => "off", };
+
+    my $group = $self->{definition}->get_group_name("use_century_decomp");
+    $self->{nl}->set_variable_value($group, "use_century_decomp", '.false.' );
+
+    CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl},
+                                         $self->{physv});
+
+    my $result = $self->{nl}->get_variable_value($group, "use_century_decomp");
+    is($result, '.false.' ) || diag($msg);
+
+}
+
+
 
 1;

From 109b32bbb5c54cabf2a073e3fd9de3e1d507d322 Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Mon, 22 Feb 2016 18:03:40 -0800
Subject: [PATCH 08/19] trying to integrate usage of namelist default files and
 calls to add_default

---
 components/clm/bld/CLMBuildNamelist.pm        | 119 +++++++++++-------
 .../namelist_defaults_clm4_5.xml              |  11 ++
 .../namelist_definition_clm4_5.xml            |   4 +-
 .../t/input/namelist_defaults_clm4_5_test.xml |   7 ++
 .../bld/test_build_namelist/t/test_ed_mode.pm |  16 ++-
 .../clm/edNoFire/include_user_mods            |   1 +
 .../testmods_dirs/clm/edNoFire/shell_commands |   1 +
 .../testmods_dirs/clm/edNoFire/user_nl_clm    |  11 ++
 8 files changed, 120 insertions(+), 50 deletions(-)
 create mode 100644 components/clm/cimetest/testmods_dirs/clm/edNoFire/include_user_mods
 create mode 100755 components/clm/cimetest/testmods_dirs/clm/edNoFire/shell_commands
 create mode 100644 components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm

diff --git a/components/clm/bld/CLMBuildNamelist.pm b/components/clm/bld/CLMBuildNamelist.pm
index 495904958e..ab955debfe 100755
--- a/components/clm/bld/CLMBuildNamelist.pm
+++ b/components/clm/bld/CLMBuildNamelist.pm
@@ -159,8 +159,9 @@ OPTIONS
                               (can ONLY be turned on when BGC type is 'cn' or 'bgc')
                               This turns on the namelist variable: use_cndv
      -ed_mode                 Turn ED (Ecosystem Demography) : [on | off] (default is off)
-                              Sets the namelist variable use_ed, use_spit_fire, 
-                                   use_vertsoilc, use_century_decomp
+                              Sets the namelist variable use_ed, checks for use_spit_fire, 
+                              use_vertsoilc, use_century_decomp and use_lch4
+			      Also specifies defaults for these
      -glc_present             Set to true if the glc model is present (not sglc).
                               This is used for error-checking, to make sure other options are
                               set appropriately.
@@ -745,31 +746,37 @@ sub setup_cmdl_ed_mode {
         fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values\n");
       }
 
-      # If these variablse  not being set by user, default to true
-      my @list  = (  "use_ed_spit_fire", "use_vertsoilc", "use_century_decomp" );
-      my $ndiff = 0;
+      # This section is a place-holder to test for modules that are not allowed with ED
+      # the defaults which are set in the logic section of the namelist builder will
+      # automatically set these correctly (well that is the assumption), but here we
+      # want to set a catch to fail and warn users if they explicitly set incompatible user namelist
+      # options
+      
+#      my $var = "use_somevar";
+#      $val = $nl_flags->{$var};
+#      if ( defined($nl->get_value($var))  ) {
+#	  if ( $nl->get_value($var) == ".true." ) { 
+#	      fatal_error("$var was set to .true., which is incompatible when -ed_mode option is used.\n");
+#	  }
+#      }
+
+      
+      # The following variables may be set by the user and are compatible with use_ed
+      # no need to set defaults, covered in a different routine
+      my @list  = (  "use_ed_spit_fire", "use_vertsoilc", "use_century_decomp", "use_lch4" );
       foreach my $var ( @list ) {
-	  if ( ! defined($nl->get_value($var))  ) {
-	      $nl_flags->{$var} = ".true.";
-	  } else {
+	  if ( defined($nl->get_value($var))  ) {
 	      $nl_flags->{$var} = $nl->get_value($var);
-	  }
-	  $val = $nl_flags->{$var};
-	  my $group = $definition->get_group_name($var);
-	  $nl->set_variable_value($group, $var, $val);
-	  if (  ! $definition->is_valid_value( $var, $val ) ) {
-	      my @valid_values   = $definition->get_valid_values( $var );
-	      fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values\n");
+	      $val = $nl_flags->{$var};
+	      my $group = $definition->get_group_name($var);
+	      $nl->set_variable_value($group, $var, $val);
+	      if (  ! $definition->is_valid_value( $var, $val ) ) {
+		  my @valid_values   = $definition->get_valid_values( $var );
+		  fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values\n");
+	      }
 	  }
       }
 
-#      $var = "use_ed_spit_fire";
-#      $nl->set_variable_value($group, $var, $val);
-#      if ( ! $definition->is_valid_value($var, $val) ) {
-#        my @valid_values   = $definition->get_valid_values( $var );
-#        fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values\n");
-#      }
-
     } else {
 	# we only dis-allow ed_spit_fire with non-ed runs
        $var = "use_ed_spit_fire";
@@ -791,6 +798,7 @@ sub setup_cmdl_bgc {
 
   $val = $opts->{$var};
   $nl_flags->{'bgc_mode'} = $val;
+
   if ( $physv->as_long() == $physv->as_long("clm4_0") ) {
     if ( $nl_flags->{'bgc_mode'} ne "default" ) {
       fatal_error("-bgc option used with clm4_0 physics. -bgc can ONLY be used with clm4_5/clm5_0 physics");
@@ -822,29 +830,32 @@ sub setup_cmdl_bgc {
     if ( defined($nl->get_value("use_cn")) && ($nl_flags->{'use_cn'} ne $nl->get_value("use_cn")) ) {
       fatal_error("The namelist variable use_cn is inconsistent with the -bgc option");
     }
-    # If the variable has already been set use it, if not set to the value defined by the bgc_mode
-    my @list  = (  "use_lch4", "use_nitrif_denitrif", "use_vertsoilc", "use_century_decomp" );
-    my $ndiff = 0;
-    foreach my $var ( @list ) {
-       if ( ! defined($nl->get_value($var))  ) {
-          $nl_flags->{$var} = $setting;
-       } else {
-          if ( $nl->get_value($var) ne $setting ) {
-             $ndiff += 1;
-          }
-          $nl_flags->{$var} = $nl->get_value($var);
-       }
-       $val = $nl_flags->{$var};
-       my $group = $definition->get_group_name($var);
-       $nl->set_variable_value($group, $var, $val);
-       if (  ! $definition->is_valid_value( $var, $val ) ) {
-         my @valid_values   = $definition->get_valid_values( $var );
-         fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values\n");
-       }
-    }
-    # If all the variables are different report it as an error
-    if ( $ndiff == ($#list + 1) ) {
-       fatal_error("You are contradicting the -bgc setting with the namelist variables: @list" );
+
+    if ( $opts->{"ed_mode"} != 1) {
+	# If the variable has already been set use it, if not set to the value defined by the bgc_mode
+	my @list  = (  "use_lch4", "use_nitrif_denitrif", "use_vertsoilc", "use_century_decomp" );
+	my $ndiff = 0;
+	foreach my $var ( @list ) {
+	    if ( ! defined($nl->get_value($var))  ) {
+		$nl_flags->{$var} = $setting;
+	    } else {
+		if ( $nl->get_value($var) ne $setting ) {
+		    $ndiff += 1;
+		}
+		$nl_flags->{$var} = $nl->get_value($var);
+	    }
+	    $val = $nl_flags->{$var};
+	    my $group = $definition->get_group_name($var);
+	    $nl->set_variable_value($group, $var, $val);
+	    if (  ! $definition->is_valid_value( $var, $val ) ) {
+		my @valid_values   = $definition->get_valid_values( $var );
+		fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values\n");
+	    }
+	}
+	# If all the variables are different report it as an error
+	if ( $ndiff == ($#list + 1) ) {
+	    fatal_error("You are contradicting the -bgc setting with the namelist variables: @list" );
+	}
     }
 
     # Now set use_cn
@@ -1447,6 +1458,7 @@ sub process_namelist_inline_logic {
   setup_logic_supplemental_nitrogen($opts->{'test'}, $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_snowpack($opts->{'test'}, $nl_flags, $definition, $defaults, $nl, $physv);
   setup_logic_atm_forcing($opts->{'test'}, $nl_flags, $definition, $defaults, $nl, $physv);
+  setup_logic_ed($opts->{'test'}, $nl_flags, $definition, $defaults, $nl, $physv);
 
   #########################################
   # namelist group: clm_humanindex_inparm #
@@ -2756,6 +2768,23 @@ sub setup_logic_atm_forcing {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_ed {
+    #
+    # Set some default options related to Ecosystem Demography
+    #                                                                                                                                                            
+    my ($test_files, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
+
+    if ($physv->as_long() >= $physv->as_long("clm4_5")) {
+	add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_vertsoilc', 'use_ed'=>$nl_flags->{'use_ed'} );
+	add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_century_decomp', 'use_ed'=>$nl_flags->{'use_ed'} );
+	add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_ed_spit_fire', 'use_ed'=>$nl_flags->{'use_ed'} );
+	add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lch4', 'use_ed'=>$nl_flags->{'use_ed'} );
+	add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_nitrif_denitrif', 'use_ed'=>$nl_flags->{'use_ed'} );
+    }
+}
+
+#-------------------------------------------------------------------------------                     
+
 sub write_output_files {
   my ($opts, $nl_flags, $defaults, $nl, $physv) = @_;
 
diff --git a/components/clm/bld/namelist_files/namelist_defaults_clm4_5.xml b/components/clm/bld/namelist_files/namelist_defaults_clm4_5.xml
index 5937bcd3ba..6c56a214ce 100644
--- a/components/clm/bld/namelist_files/namelist_defaults_clm4_5.xml
+++ b/components/clm/bld/namelist_files/namelist_defaults_clm4_5.xml
@@ -1612,4 +1612,15 @@ lnd/clm2/surfdata_map/surfdata_ne30np4_simyr1850_c141219.nc</fsurdat>
 
 <use_aereoxid_prog use_cn=".true.">.true.</use_aereoxid_prog>
 
+<!-- =========================================  -->
+<!-- Defaults for use_ed = .true.               -->
+<!-- =========================================  -->
+
+<use_vertsoilc use_ed=".true."> .true. </use_vertsoilc>
+<use_century_decomp use_ed=".true."> .true. </use_century_decomp>
+<use_ed_spit_fire use_ed=".true."> .true. </use_ed_spit_fire>
+<use_lch4 use_ed=".true."> .false. </use_lch4>
+<use_nitrif_denitrif use_ed=".true."> .false. </use_nitrif_denitrif>
+
+
 </namelist_defaults>
diff --git a/components/clm/bld/namelist_files/namelist_definition_clm4_5.xml b/components/clm/bld/namelist_files/namelist_definition_clm4_5.xml
index d89038523c..9992e1e97f 100644
--- a/components/clm/bld/namelist_files/namelist_definition_clm4_5.xml
+++ b/components/clm/bld/namelist_files/namelist_definition_clm4_5.xml
@@ -427,13 +427,13 @@ Requires the CN model to work (either CN or CNDV).
 <entry id="use_vertsoilc" type="logical" category="bgc"
        group="clm_inparm" valid_values="" value=".false.">
 Turn on vertical soil carbon.
-Requires the CN model to work (either CN or CNDV).
+Requires the CN or ED model to work (either CN or CNDV).
 </entry>
 
 <entry id="use_century_decomp" type="logical" category="bgc"
        group="clm_inparm" valid_values="" value=".false.">
 Use parameters for decomposition from the CENTURY Carbon model
-Requires the CN model to work (either CN or CNDV).
+Requires the CN or ED model to work (either CN or CNDV).
 </entry>
 
 <entry id="use_extralakelayers" type="logical" category="physics"
diff --git a/components/clm/bld/test_build_namelist/t/input/namelist_defaults_clm4_5_test.xml b/components/clm/bld/test_build_namelist/t/input/namelist_defaults_clm4_5_test.xml
index 974f15acab..1b41e79f1e 100644
--- a/components/clm/bld/test_build_namelist/t/input/namelist_defaults_clm4_5_test.xml
+++ b/components/clm/bld/test_build_namelist/t/input/namelist_defaults_clm4_5_test.xml
@@ -1478,4 +1478,11 @@ lnd/clm2/surfdata_map/surfdata_ne30np4_simyr1850_c130927.nc</fsurdat>
 
 <use_aereoxid_prog use_cn=".true.">.true.</use_aereoxid_prog>
 
+<use_vertsoilc use_ed=".true."> .true. </use_vertsoilc>
+<use_century_decomp use_ed=".true."> .true. </use_century_decomp>
+<use_ed_spit_fire use_ed=".true."> .true. </use_ed_spit_fire>
+<use_lch4 use_ed=".true."> .false. </use_lch4>
+<use_nitrif_denitrif use_ed=".true."> .false. </use_nitrif_denitrif>
+
+
 </namelist_defaults>
diff --git a/components/clm/bld/test_build_namelist/t/test_ed_mode.pm b/components/clm/bld/test_build_namelist/t/test_ed_mode.pm
index c2043986e5..cc4ae7a8ec 100644
--- a/components/clm/bld/test_build_namelist/t/test_ed_mode.pm
+++ b/components/clm/bld/test_build_namelist/t/test_ed_mode.pm
@@ -8,6 +8,8 @@ use Test::Exception;
 
 use parent qw(Test::Class);
 
+use CLMBuildNamelist qw(setup_logic_lnd_frac);
+
 #-------------------------------------------------------------------------------
 #
 # Common test fixture for all tests:
@@ -30,6 +32,8 @@ sub startup : Test(startup => 4) {
   $self->{physv} = config_files::clm_phys_vers->new( $self->{cfg}->get('phys') );
   isnt($self->{physv}, undef,  (caller(0))[3] . " : phys_vers object created.");
 
+  $self->{test_files} = 0;
+
 }
 
 sub shutdown : Test(shutdown) {
@@ -71,14 +75,20 @@ sub test_ed_mode__use_century_decomp : Tests {
   my $msg = "Test that use_century_decomp is the default on ed_mode.\n";
 
   use CLMBuildNamelist qw(setup_cmdl_ed_mode);
+  use CLMBuildNamelist qw(setup_logic_ed);
 
-  my $opts = { ed_mode => 1, };
+  my $opts = { ed_mode => 1, bgc => "default" };
   my $nl_flags = { crop => "off", }; # the setup_cmdl_ed_mode code requires this logic
 
+  # include bgc because they have mutually exclusive functionality that needs to be tested
+  CLMBuildNamelist::setup_cmdl_bgc($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{cfg},$self->{physv});
   CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
-  my $group = $self->{definition}->get_group_name("use_century_decomp");
+  $nl_flags->{"use_ed"} = $self->{nl}->get_value("use_ed");
+
+  CLMBuildNamelist::setup_logic_ed($self->{test_files}, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
   my $result = $self->{nl}->get_variable_value($group, "use_century_decomp");
   is($result, '.true.' ) || diag($msg);
+  
 }
 
 # Test 2: use_vertsoilc is default with ed_mode
@@ -173,7 +183,7 @@ sub test_ed_mode__use_ed_spit_fire_false : Tests {
 
 }
 
-# 8: test that use_ed_spit_fire = false generates a false
+# 8: test that use_versoilc = false generates a false
 sub test_ed_mode__use_vertsoilc_false : Tests {
     my $self = shift;
 
diff --git a/components/clm/cimetest/testmods_dirs/clm/edNoFire/include_user_mods b/components/clm/cimetest/testmods_dirs/clm/edNoFire/include_user_mods
new file mode 100644
index 0000000000..fe0e18cf88
--- /dev/null
+++ b/components/clm/cimetest/testmods_dirs/clm/edNoFire/include_user_mods
@@ -0,0 +1 @@
+../default
diff --git a/components/clm/cimetest/testmods_dirs/clm/edNoFire/shell_commands b/components/clm/cimetest/testmods_dirs/clm/edNoFire/shell_commands
new file mode 100755
index 0000000000..d81ed7dbc5
--- /dev/null
+++ b/components/clm/cimetest/testmods_dirs/clm/edNoFire/shell_commands
@@ -0,0 +1 @@
+./xmlchange CLM_BLDNML_OPTS="-no-megan" --append
diff --git a/components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm b/components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm
new file mode 100644
index 0000000000..ca8ec28614
--- /dev/null
+++ b/components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm
@@ -0,0 +1,11 @@
+use_cn            = .false. 
+use_ed_spit_fire  = .false.
+finidat           = ''
+hist_mfilt        = 365
+hist_nhtfrq       = -24
+hist_empty_htapes = .true.
+hist_fincl1       = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN','LITTER_OUT',
+   'STORVEGC','FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','fire_fuel_mef',
+   'fire_fuel_bulkd','fire_fuel_sav','FIRE_NESTEROV_INDEX','PFTbiomass',
+   'PFTleafbiomass','FIRE_ROS','WIND','TFC_ROS','DISPVEGC','AREA_TREES','AREA_PLANT' 
+

From 69e3efbfc039fd7f5574da2a08732db66011994a Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Tue, 23 Feb 2016 16:45:29 -0800
Subject: [PATCH 09/19] unit tests now working correctly and calling
 add_defaults via defaults xml

---
 components/clm/bld/CLMBuildNamelist.pm        |   7 +-
 .../t/input/namelist_defaults_clm4_5_test.xml |  18 ++-
 .../t/template_test_XXX.pm                    |   8 +-
 .../bld/test_build_namelist/t/test_ed_mode.pm | 148 ++++++++++++------
 4 files changed, 127 insertions(+), 54 deletions(-)

diff --git a/components/clm/bld/CLMBuildNamelist.pm b/components/clm/bld/CLMBuildNamelist.pm
index ab955debfe..91394b1f0c 100755
--- a/components/clm/bld/CLMBuildNamelist.pm
+++ b/components/clm/bld/CLMBuildNamelist.pm
@@ -777,6 +777,9 @@ sub setup_cmdl_ed_mode {
 	  }
       }
 
+#      add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_vertsoilc', 'use_ed'=>$nl_flags->{'use_ed'} );
+
+
     } else {
 	# we only dis-allow ed_spit_fire with non-ed runs
        $var = "use_ed_spit_fire";
@@ -2777,7 +2780,7 @@ sub setup_logic_ed {
     if ($physv->as_long() >= $physv->as_long("clm4_5")) {
 	add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_vertsoilc', 'use_ed'=>$nl_flags->{'use_ed'} );
 	add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_century_decomp', 'use_ed'=>$nl_flags->{'use_ed'} );
-	add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_ed_spit_fire', 'use_ed'=>$nl_flags->{'use_ed'} );
+ 	add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_ed_spit_fire', 'use_ed'=>$nl_flags->{'use_ed'} );
 	add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lch4', 'use_ed'=>$nl_flags->{'use_ed'} );
 	add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_nitrif_denitrif', 'use_ed'=>$nl_flags->{'use_ed'} );
     }
@@ -2889,6 +2892,7 @@ sub add_default {
     $var = $1;
   }
   # Query the definition to find which group the variable belongs to.  Exit if not found.
+
   my $group = $definition->get_group_name($var);
   unless ($group) {
     my $fname = $definition->get_file_name();
@@ -2909,6 +2913,7 @@ sub add_default {
     # in %settings to the get_value method to be used as attributes that are matched
     # when looking for default values.
     else {
+
       $val = $defaults->get_value($var, \%settings);
 
       # Truncate model_version appropriately
diff --git a/components/clm/bld/test_build_namelist/t/input/namelist_defaults_clm4_5_test.xml b/components/clm/bld/test_build_namelist/t/input/namelist_defaults_clm4_5_test.xml
index 1b41e79f1e..25e3d47e65 100644
--- a/components/clm/bld/test_build_namelist/t/input/namelist_defaults_clm4_5_test.xml
+++ b/components/clm/bld/test_build_namelist/t/input/namelist_defaults_clm4_5_test.xml
@@ -75,6 +75,18 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- Plant function types (relative to {csmdata}) -->
 <paramfile       >lnd/clm2/paramdata/clm_params.c130821.nc</paramfile>
 
+
+<!--- ========================================  -->
+<!--- Defaults for use_ed = .true.              -->
+<!--  ========================================  -->
+
+<use_vertsoilc use_ed=".true.">.true.</use_vertsoilc>
+<use_century_decomp use_ed=".true."  >.true.</use_century_decomp>
+<use_ed_spit_fire use_ed=".true.">.true.</use_ed_spit_fire>
+<use_lch4 use_ed=".true.">.false.</use_lch4>
+<use_nitrif_denitrif use_ed=".true.">.false.</use_nitrif_denitrif>
+
+
 <!--
 
      Original initial condition file at 1 degree resolution
@@ -1478,11 +1490,5 @@ lnd/clm2/surfdata_map/surfdata_ne30np4_simyr1850_c130927.nc</fsurdat>
 
 <use_aereoxid_prog use_cn=".true.">.true.</use_aereoxid_prog>
 
-<use_vertsoilc use_ed=".true."> .true. </use_vertsoilc>
-<use_century_decomp use_ed=".true."> .true. </use_century_decomp>
-<use_ed_spit_fire use_ed=".true."> .true. </use_ed_spit_fire>
-<use_lch4 use_ed=".true."> .false. </use_lch4>
-<use_nitrif_denitrif use_ed=".true."> .false. </use_nitrif_denitrif>
-
 
 </namelist_defaults>
diff --git a/components/clm/bld/test_build_namelist/t/template_test_XXX.pm b/components/clm/bld/test_build_namelist/t/template_test_XXX.pm
index dab237ee11..cf43818044 100644
--- a/components/clm/bld/test_build_namelist/t/template_test_XXX.pm
+++ b/components/clm/bld/test_build_namelist/t/template_test_XXX.pm
@@ -23,8 +23,14 @@ sub startup : Test(startup => 3) {
   $self->{definition} = Build::NamelistDefinition->new("t/input/namelist_definition_clm4_5_test.xml");
   isnt($self->{definition}, undef, (caller(0))[3] . " : namelist_definition object created.");
 
-  $self->{defaults} = Build::NamelistDefaults->new("t/input/namelist_defaults_clm4_5_test.xml");
+  $self->{defaults} = Build::NamelistDefaults->new("t/input/namelist_defaults_clm4_5_test.xml",$self->{cfg});
   isnt($self->{defaults}, undef,  (caller(0))[3] . " : namelist_defaults object created.");
+
+#  The next line may be usefull (set startup => 4) in arg call above:
+#  $self->{physv} = config_files::clm_phys_vers->new( $self->{cfg}->get('phys') );
+#  isnt($self->{physv}, undef,  (caller(0))[3] . " : phys_vers object created.");
+
+
 }
 
 sub shutdown : Test(shutdown) {
diff --git a/components/clm/bld/test_build_namelist/t/test_ed_mode.pm b/components/clm/bld/test_build_namelist/t/test_ed_mode.pm
index cc4ae7a8ec..07cd3c8813 100644
--- a/components/clm/bld/test_build_namelist/t/test_ed_mode.pm
+++ b/components/clm/bld/test_build_namelist/t/test_ed_mode.pm
@@ -8,7 +8,9 @@ use Test::Exception;
 
 use parent qw(Test::Class);
 
-use CLMBuildNamelist qw(setup_logic_lnd_frac);
+use CLMBuildNamelist qw(setup_cmdl_ed_mode);
+use CLMBuildNamelist qw(setup_logic_ed);
+
 
 #-------------------------------------------------------------------------------
 #
@@ -26,7 +28,7 @@ sub startup : Test(startup => 4) {
   $self->{definition} = Build::NamelistDefinition->new("t/input/namelist_definition_clm4_5_test.xml");
   isnt($self->{definition}, undef, (caller(0))[3] . " : namelist_definition object created.");
 
-  $self->{defaults} = Build::NamelistDefaults->new("t/input/namelist_defaults_clm4_5_test.xml");
+  $self->{defaults} = Build::NamelistDefaults->new("t/input/namelist_defaults_clm4_5_test.xml",$self->{cfg});
   isnt($self->{defaults}, undef,  (caller(0))[3] . " : namelist_defaults object created.");
 
   $self->{physv} = config_files::clm_phys_vers->new( $self->{cfg}->get('phys') );
@@ -46,26 +48,28 @@ sub setup : Test(setup => 1) {
 
   $self->{nl} = Build::Namelist->new();
   isnt($self->{nl}, undef, (caller(0))[3] . " : empty namelist object created.");
+
+  $self->set_value('crop', 'off');
+
 }
 
 sub teardown : Test(teardown) {
   # clean up after test
 }
 
+sub set_value {
+    # Set the value of a namelist option
+    my ($self, $var, $value) = @_;
+    my $group = $self->{definition}->get_group_name($var);
+    $self->{nl}->set_variable_value($group, $var, $value);
+}
+
+
+
 #-------------------------------------------------------------------------------
 #
 # tests
 # 
-# 1: test that use_century_decom is the default with ed_mode
-# 2: test that use_vertsoilc is the default with ed_mode
-# 3: test that use_ed_spit_fire is the default with ed_mode
-# 4: test that use_ed = .false. will fail for ed_mode
-# 5: test that crop = "on" will fail for ed_mode
-# 6: test that clm4_0 will fail for ed_mode (NOT AVAILABLE)
-# 7: test that use_ed_spit_fire = false generates a false
-# 8: test that use_versoilc = false generates a false
-# 9: test that use_century_decomp = false generates a false
-#
 #-------------------------------------------------------------------------------
 
 # Test 1: use_century_decomp is default with ed_mode
@@ -74,18 +78,15 @@ sub test_ed_mode__use_century_decomp : Tests {
 
   my $msg = "Test that use_century_decomp is the default on ed_mode.\n";
 
-  use CLMBuildNamelist qw(setup_cmdl_ed_mode);
-  use CLMBuildNamelist qw(setup_logic_ed);
-
   my $opts = { ed_mode => 1, bgc => "default" };
   my $nl_flags = { crop => "off", }; # the setup_cmdl_ed_mode code requires this logic
 
   # include bgc because they have mutually exclusive functionality that needs to be tested
   CLMBuildNamelist::setup_cmdl_bgc($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{cfg},$self->{physv});
   CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
-  $nl_flags->{"use_ed"} = $self->{nl}->get_value("use_ed");
-
   CLMBuildNamelist::setup_logic_ed($self->{test_files}, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+
+  my $group = $self->{definition}->get_group_name("use_century_decomp");
   my $result = $self->{nl}->get_variable_value($group, "use_century_decomp");
   is($result, '.true.' ) || diag($msg);
   
@@ -97,12 +98,13 @@ sub test_ed_mode__use_vertsoilc : Tests {
 
     my $msg = "Tests that use_vertsoilc is default on ed_mode.\n";
 
-    use CLMBuildNamelist qw(setup_cmdl_ed_mode);
-
-    my $opts = { ed_mode => 1, };
+    my $opts = { ed_mode => 1, bgc => "default"};
     my $nl_flags = { crop => "off", };
 
+    CLMBuildNamelist::setup_cmdl_bgc($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{cfg},$self->{physv});
     CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+    CLMBuildNamelist::setup_logic_ed($self->{test_files}, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+
     my $group = $self->{definition}->get_group_name("use_vertsoilc");
     my $result = $self->{nl}->get_variable_value($group, "use_vertsoilc");
     is($result, '.true.' ) || diag($msg);
@@ -114,25 +116,60 @@ sub test_ed_mode__use_ed_spit_fire : Tests {
 
     my $msg = "Tests that use_ed_spit_fire is default on ed_mode.\n";
 
-    use CLMBuildNamelist qw(setup_cmdl_ed_mode);
-
-    my $opts = { ed_mode => 1, };
+    my $opts = { ed_mode => 1, bgc => "default"};
     my $nl_flags = { crop => "off", };
 
+    CLMBuildNamelist::setup_cmdl_bgc($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{cfg},$self->{physv});
     CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+    CLMBuildNamelist::setup_logic_ed($self->{test_files}, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+
     my $group = $self->{definition}->get_group_name("use_ed_spit_fire");
     my $result = $self->{nl}->get_variable_value($group, "use_ed_spit_fire");
     is($result, '.true.' ) || diag($msg);
 }
 
-# Test 4: use_ed=false will crash on ed_mode
+# Test 4: use_nitrif_denitrif is not default with ed_mode                                                                       
+sub test_ed_mode__use_nitrif_denitrif: Tests {
+    my $self = shift;
+
+    my $msg = "Tests that us_nitrif_denitfif e i nots default on ed_mode.\n";
+
+    my $opts = { ed_mode => 1, bgc => "default"};
+    my $nl_flags = { crop => "off", };
+
+    CLMBuildNamelist::setup_cmdl_bgc($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{cfg},$self->{physv});
+    CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+    CLMBuildNamelist::setup_logic_ed($self->{test_files}, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+
+    my $group = $self->{definition}->get_group_name("use_nitrif_denitrif");
+    my $result = $self->{nl}->get_variable_value($group, "use_nitrif_denitrif");
+    is($result, '.false.' ) || diag($msg);
+}
+
+# Test 5: use_lch4 is not default with ed_mode                                                                       
+sub test_ed_mode__use_lch4: Tests {
+     my $self = shift;
+     
+     my $msg = "Tests that use_lch4 is not default on ed_mode.\n";
+
+     my $opts = { ed_mode => 1, bgc => "default"};
+     my $nl_flags = { crop => "off", };
+
+     CLMBuildNamelist::setup_cmdl_bgc($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{cfg},$self->{physv});
+     CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+     CLMBuildNamelist::setup_logic_ed($self->{test_files}, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+
+     my $group = $self->{definition}->get_group_name("use_lch4");
+     my $result = $self->{nl}->get_variable_value($group, "use_lch4");
+     is($result, '.false.' ) || diag($msg);
+}
+
+# Test 6: use_ed=false will crash on ed_mode
 sub test_ed_mode__use_ed_nl_contradicts_cmdl : Tests {
     my $self = shift;
 
     my $msg = "Tests that use_ed=false will fail on ed_mode.\n";
 
-    use CLMBuildNamelist qw(setup_cmdl_ed_mode);
-
     my $opts = { ed_mode => 1, };
     my $nl_flags = { crop => "off", use_ed => ".false."};
 
@@ -143,14 +180,12 @@ sub test_ed_mode__use_ed_nl_contradicts_cmdl : Tests {
 							$self->{physv}) }) || diag($msg);
 }
 
-# Test 5: crop=on will crash on ed_mode
+# Test 7: crop=on will crash on ed_mode
 sub test_ed_mode__crop_on_nl_contradicts_cmdl : Tests {
     my $self = shift;
 
     my $msg = "Tests that crop=on will fail on ed_mode.\n";
 
-    use CLMBuildNamelist qw(setup_cmdl_ed_mode);
-
     my $opts = { ed_mode => 1, };
     my $nl_flags = { crop => "on", };
 
@@ -161,72 +196,93 @@ sub test_ed_mode__crop_on_nl_contradicts_cmdl : Tests {
 						   $self->{physv}) }) || diag($msg);
 }
 
-# 7: test that use_ed_spit_fire = false generates a false
+# Test 8: test that use_ed_spit_fire = false generates a false
 sub test_ed_mode__use_ed_spit_fire_false : Tests {
     my $self = shift;
 
     my $msg = "Tests that use_ed_spit_fire can be turned to false.\n";
 
-    use CLMBuildNamelist qw(setup_cmdl_ed_mode);
-
     my $opts = { ed_mode => 1, };
     my $nl_flags = { crop => "off", };
 
     my $group = $self->{definition}->get_group_name("use_ed_spit_fire");
     $self->{nl}->set_variable_value($group, "use_ed_spit_fire", '.false.' );
 
-    CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl},
-						       $self->{physv});
+    CLMBuildNamelist::setup_cmdl_bgc($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{cfg},$self->{physv});
+    CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+    CLMBuildNamelist::setup_logic_ed($self->{test_files}, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
 
     my $result = $self->{nl}->get_variable_value($group, "use_ed_spit_fire");
     is($result, '.false.' ) || diag($msg);
 
 }
 
-# 8: test that use_versoilc = false generates a false
+# Test 9: test that use_versoilc = false generates a false
 sub test_ed_mode__use_vertsoilc_false : Tests {
     my $self = shift;
 
     my $msg = "Tests that use_vertsoilc can be turned to false.\n";
 
-    use CLMBuildNamelist qw(setup_cmdl_ed_mode);
+    use CLMBuildNamelist qw(setup_cmdl_ed_mode);	
+    use CLMBuildNamelist qw(setup_logic_ed);	
 
-    my $opts = { ed_mode => 1, };
+    my $opts = { ed_mode => 1, bgc => "default"};
     my $nl_flags = { crop => "off", };
 
     my $group = $self->{definition}->get_group_name("use_vertsoilc");
     $self->{nl}->set_variable_value($group, "use_vertsoilc", '.false.' );
 
-    CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl},
-					 $self->{physv});
+    CLMBuildNamelist::setup_cmdl_bgc($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{cfg},$self->{physv});
+    CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+    CLMBuildNamelist::setup_logic_ed($self->{test_files}, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
 
     my $result = $self->{nl}->get_variable_value($group, "use_vertsoilc");
     is($result, '.false.' ) || diag($msg);
 
 }
 
-# 9: test that use_ed_spit_fire = false generates a false
+# Test 10: test that use_century_decomp = false generates a false
 sub test_ed_mode__use_century_decomp_false : Tests {
     my $self = shift;
 
-    my $msg = "Tests that use_century_decomp can be turned to false.\n";
-
-    use CLMBuildNamelist qw(setup_cmdl_ed_mode);
+    my $msg = "Tests that use_vertsoilc can be turned to false.\n";
 
-    my $opts = { ed_mode => 1, };
+    my $opts = { ed_mode => 1, bgc => "default"};
     my $nl_flags = { crop => "off", };
 
     my $group = $self->{definition}->get_group_name("use_century_decomp");
     $self->{nl}->set_variable_value($group, "use_century_decomp", '.false.' );
 
-    CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl},
-                                         $self->{physv});
+    CLMBuildNamelist::setup_cmdl_bgc($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{cfg},$self->{physv});
+    CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+    CLMBuildNamelist::setup_logic_ed($self->{test_files}, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
 
     my $result = $self->{nl}->get_variable_value($group, "use_century_decomp");
     is($result, '.false.' ) || diag($msg);
 
 }
 
+# Test 11: test that use_lch4 = true generates a true
+sub test_ed_mode__use_lch4_true : Tests {
+    my $self = shift;
+
+    my $msg = "Tests that use_vertsoilc can be turned to false.\n";
+
+    my $opts = { ed_mode => 1, bgc => "default"};
+    my $nl_flags = { crop => "off", };
+
+    my $group = $self->{definition}->get_group_name("use_lch4");
+    $self->{nl}->set_variable_value($group, "use_lch4", '.true.' );
 
+    CLMBuildNamelist::setup_cmdl_bgc($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{cfg},$self->{physv});
+    CLMBuildNamelist::setup_cmdl_ed_mode($opts, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+    $nl_flags->{"use_ed"} = $self->{nl}->get_value("use_ed");
+
+    CLMBuildNamelist::setup_logic_ed($self->{test_files}, $nl_flags, $self->{definition}, $self->{defaults}, $self->{nl}, $self->{physv});
+
+    my $result = $self->{nl}->get_variable_value($group, "use_lch4");
+    is($result, '.true.' ) || diag($msg);
+
+}
 
 1;

From 476dccb8079c9bc56f9b3477662e4e0fc0a91fb6 Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Tue, 23 Feb 2016 17:55:58 -0800
Subject: [PATCH 10/19] syntax corrections on namelist_default xml, reverted H
 variables in tests

---
 .../bld/namelist_files/namelist_defaults_clm4_5.xml    | 10 +++++-----
 .../cimetest/testmods_dirs/clm/edNoFire/user_nl_clm    |  2 +-
 .../clm/cimetest/testmods_dirs/clm/edTest/user_nl_clm  |  2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/components/clm/bld/namelist_files/namelist_defaults_clm4_5.xml b/components/clm/bld/namelist_files/namelist_defaults_clm4_5.xml
index 6c56a214ce..72182e92de 100644
--- a/components/clm/bld/namelist_files/namelist_defaults_clm4_5.xml
+++ b/components/clm/bld/namelist_files/namelist_defaults_clm4_5.xml
@@ -1616,11 +1616,11 @@ lnd/clm2/surfdata_map/surfdata_ne30np4_simyr1850_c141219.nc</fsurdat>
 <!-- Defaults for use_ed = .true.               -->
 <!-- =========================================  -->
 
-<use_vertsoilc use_ed=".true."> .true. </use_vertsoilc>
-<use_century_decomp use_ed=".true."> .true. </use_century_decomp>
-<use_ed_spit_fire use_ed=".true."> .true. </use_ed_spit_fire>
-<use_lch4 use_ed=".true."> .false. </use_lch4>
-<use_nitrif_denitrif use_ed=".true."> .false. </use_nitrif_denitrif>
+<use_vertsoilc use_ed=".true.">.true.</use_vertsoilc>
+<use_century_decomp use_ed=".true.">.true.</use_century_decomp>
+<use_ed_spit_fire use_ed=".true.">.true.</use_ed_spit_fire>
+<use_lch4 use_ed=".true.">.false.</use_lch4>
+<use_nitrif_denitrif use_ed=".true.">.false.</use_nitrif_denitrif>
 
 
 </namelist_defaults>
diff --git a/components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm b/components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm
index ca8ec28614..ac4a70b39e 100644
--- a/components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm
+++ b/components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm
@@ -7,5 +7,5 @@ hist_empty_htapes = .true.
 hist_fincl1       = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN','LITTER_OUT',
    'STORVEGC','FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','fire_fuel_mef',
    'fire_fuel_bulkd','fire_fuel_sav','FIRE_NESTEROV_INDEX','PFTbiomass',
-   'PFTleafbiomass','FIRE_ROS','WIND','TFC_ROS','DISPVEGC','AREA_TREES','AREA_PLANT' 
+   'PFTleafbiomass','FIRE_ROS','WIND','TFC_ROS','DISPVEGC','AREA_TREES','AREA_PLANT'
 
diff --git a/components/clm/cimetest/testmods_dirs/clm/edTest/user_nl_clm b/components/clm/cimetest/testmods_dirs/clm/edTest/user_nl_clm
index 2c11d3b5ad..ab9cea3aeb 100644
--- a/components/clm/cimetest/testmods_dirs/clm/edTest/user_nl_clm
+++ b/components/clm/cimetest/testmods_dirs/clm/edTest/user_nl_clm
@@ -6,5 +6,5 @@ hist_empty_htapes = .true.
 hist_fincl1       = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN','LITTER_OUT',
    'STORVEGC','FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','fire_fuel_mef',
    'fire_fuel_bulkd','fire_fuel_sav','FIRE_NESTEROV_INDEX','PFTbiomass',
-   'PFTleafbiomass','FIRE_ROS','WIND','TFC_ROS','DISPVEGC','AREA_TREES','AREA_PLANT' 
+   'PFTleafbiomass','FIRE_ROS','WIND','TFC_ROS','DISPVEGC','AREA_TREES','AREA_PLANT'
 

From 6bd1285f3bf39337f20f06fccb43b536cc93f53c Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Tue, 23 Feb 2016 18:53:25 -0800
Subject: [PATCH 11/19] Added test
 ERS_D_Ld5.f10_f10.ICLM45ED.ed_ed.clm-edNoFire

This adds a regression test ofor ED without spitfire

Followed directions here: https://github.com/bandre-ucar/cime-testing-tools#adding-a-new-test
---
 components/clm/cimetest/testlist_clm.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/components/clm/cimetest/testlist_clm.xml b/components/clm/cimetest/testlist_clm.xml
index 2b753cea9d..4cdb759184 100644
--- a/components/clm/cimetest/testlist_clm.xml
+++ b/components/clm/cimetest/testlist_clm.xml
@@ -725,6 +725,7 @@
     <grid name="f10_f10">
       <test name="ERS_D_Ld5">
         <machine compiler="ed" testtype="ed" testmods="clm/edTest">ed</machine>
+        <machine compiler="ed" testtype="ed" testmods="clm/edNoFire">ed</machine>
       </test>
       <test name="SMS_D_Ld5">
         <machine compiler="ed" testtype="ed" testmods="clm/edTest">ed</machine>

From d9d1bda77b0eaf49e67a36e10e2787e7d991519c Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Wed, 24 Feb 2016 00:43:18 -0800
Subject: [PATCH 12/19] added conditional to the add_default namelist building
 for ed logic, modified test user_nl_clm to match baselines

---
 components/clm/bld/CLMBuildNamelist.pm                       | 2 +-
 components/clm/cimetest/testmods_dirs/clm/edTest/user_nl_clm | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/components/clm/bld/CLMBuildNamelist.pm b/components/clm/bld/CLMBuildNamelist.pm
index 91394b1f0c..2a9bc7d606 100755
--- a/components/clm/bld/CLMBuildNamelist.pm
+++ b/components/clm/bld/CLMBuildNamelist.pm
@@ -2777,7 +2777,7 @@ sub setup_logic_ed {
     #                                                                                                                                                            
     my ($test_files, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
 
-    if ($physv->as_long() >= $physv->as_long("clm4_5")) {
+    if ($physv->as_long() >= $physv->as_long("clm4_5") && value_is_true( $nl_flags->{'use_ed'})  ) {
 	add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_vertsoilc', 'use_ed'=>$nl_flags->{'use_ed'} );
 	add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_century_decomp', 'use_ed'=>$nl_flags->{'use_ed'} );
  	add_default($test_files, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_ed_spit_fire', 'use_ed'=>$nl_flags->{'use_ed'} );
diff --git a/components/clm/cimetest/testmods_dirs/clm/edTest/user_nl_clm b/components/clm/cimetest/testmods_dirs/clm/edTest/user_nl_clm
index ab9cea3aeb..7f7867def7 100644
--- a/components/clm/cimetest/testmods_dirs/clm/edTest/user_nl_clm
+++ b/components/clm/cimetest/testmods_dirs/clm/edTest/user_nl_clm
@@ -1,4 +1,6 @@
 use_cn            = .false. 
+use_century_decomp = .false.
+use_vertsoilc    = .false.
 finidat           = ''
 hist_mfilt        = 365
 hist_nhtfrq       = -24

From 04f948155d7e7e1f2a63f853e6868c5e4ec991a0 Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Wed, 24 Feb 2016 13:43:09 -0800
Subject: [PATCH 13/19] modified the edNoFire regression tests to use
 pre-existing use_century_decomp and use_vertsoilc settings

---
 components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm | 2 ++
 components/clm/cimetest/testmods_dirs/clm/edTest/user_nl_clm   | 3 +--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm b/components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm
index ac4a70b39e..5c15d95828 100644
--- a/components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm
+++ b/components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm
@@ -1,5 +1,7 @@
 use_cn            = .false. 
 use_ed_spit_fire  = .false.
+use_vertsoilc     = .false.
+use_century_decomp = .false.
 finidat           = ''
 hist_mfilt        = 365
 hist_nhtfrq       = -24
diff --git a/components/clm/cimetest/testmods_dirs/clm/edTest/user_nl_clm b/components/clm/cimetest/testmods_dirs/clm/edTest/user_nl_clm
index 7f7867def7..12415896e2 100644
--- a/components/clm/cimetest/testmods_dirs/clm/edTest/user_nl_clm
+++ b/components/clm/cimetest/testmods_dirs/clm/edTest/user_nl_clm
@@ -8,5 +8,4 @@ hist_empty_htapes = .true.
 hist_fincl1       = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN','LITTER_OUT',
    'STORVEGC','FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','fire_fuel_mef',
    'fire_fuel_bulkd','fire_fuel_sav','FIRE_NESTEROV_INDEX','PFTbiomass',
-   'PFTleafbiomass','FIRE_ROS','WIND','TFC_ROS','DISPVEGC','AREA_TREES','AREA_PLANT'
-
+   'PFTleafbiomass','FIRE_ROS','WIND','TFC_ROS','DISPVEGC','AREA_TREES','AREA_PLANT' 
\ No newline at end of file

From 63a2773480f827ba621314825a74ce8d6456d6c0 Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Wed, 24 Feb 2016 15:58:50 -0800
Subject: [PATCH 14/19] removed inherited default namelist variables in the
 edNoFire test cases

---
 .../clm/cimetest/testmods_dirs/clm/edNoFire/include_user_mods    | 1 -
 1 file changed, 1 deletion(-)
 delete mode 100644 components/clm/cimetest/testmods_dirs/clm/edNoFire/include_user_mods

diff --git a/components/clm/cimetest/testmods_dirs/clm/edNoFire/include_user_mods b/components/clm/cimetest/testmods_dirs/clm/edNoFire/include_user_mods
deleted file mode 100644
index fe0e18cf88..0000000000
--- a/components/clm/cimetest/testmods_dirs/clm/edNoFire/include_user_mods
+++ /dev/null
@@ -1 +0,0 @@
-../default

From 48631c51ec7350b4b820ca32842d8c7158ce80e3 Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Wed, 24 Feb 2016 16:56:30 -0800
Subject: [PATCH 15/19] edNoFire updated to get inherited namelist from edTest

---
 .../cimetest/testmods_dirs/clm/edNoFire/user_nl_clm   | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm b/components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm
index 5c15d95828..05070adc21 100644
--- a/components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm
+++ b/components/clm/cimetest/testmods_dirs/clm/edNoFire/user_nl_clm
@@ -1,13 +1,2 @@
-use_cn            = .false. 
 use_ed_spit_fire  = .false.
-use_vertsoilc     = .false.
-use_century_decomp = .false.
-finidat           = ''
-hist_mfilt        = 365
-hist_nhtfrq       = -24
-hist_empty_htapes = .true.
-hist_fincl1       = 'NPP','GPP','BTRAN','H2OSOI','TLAI','LITTER_IN','LITTER_OUT',
-   'STORVEGC','FIRE_AREA','SCORCH_HEIGHT','FIRE_INTENSITY','FIRE_TFC_ROS','fire_fuel_mef',
-   'fire_fuel_bulkd','fire_fuel_sav','FIRE_NESTEROV_INDEX','PFTbiomass',
-   'PFTleafbiomass','FIRE_ROS','WIND','TFC_ROS','DISPVEGC','AREA_TREES','AREA_PLANT'
 

From a0661656dd7426477ef7b9e1a6b8435ec9bb8fde Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Wed, 24 Feb 2016 16:57:51 -0800
Subject: [PATCH 16/19] git added include_user_mods

---
 .../clm/cimetest/testmods_dirs/clm/edNoFire/include_user_mods    | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 components/clm/cimetest/testmods_dirs/clm/edNoFire/include_user_mods

diff --git a/components/clm/cimetest/testmods_dirs/clm/edNoFire/include_user_mods b/components/clm/cimetest/testmods_dirs/clm/edNoFire/include_user_mods
new file mode 100644
index 0000000000..53cabb16d0
--- /dev/null
+++ b/components/clm/cimetest/testmods_dirs/clm/edNoFire/include_user_mods
@@ -0,0 +1 @@
+../edTest

From 1703aa1cc84fc4d15b8be12ee7ed84ece25ff5d6 Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Thu, 25 Feb 2016 11:41:34 -0800
Subject: [PATCH 17/19] fixed error on the spit_fire=false namelist unit test

---
 components/clm/bld/test_build_namelist/t/test_ed_mode.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/clm/bld/test_build_namelist/t/test_ed_mode.pm b/components/clm/bld/test_build_namelist/t/test_ed_mode.pm
index 07cd3c8813..4c5ebb1359 100644
--- a/components/clm/bld/test_build_namelist/t/test_ed_mode.pm
+++ b/components/clm/bld/test_build_namelist/t/test_ed_mode.pm
@@ -202,7 +202,7 @@ sub test_ed_mode__use_ed_spit_fire_false : Tests {
 
     my $msg = "Tests that use_ed_spit_fire can be turned to false.\n";
 
-    my $opts = { ed_mode => 1, };
+    my $opts = { ed_mode => 1, bgc => "default"};
     my $nl_flags = { crop => "off", };
 
     my $group = $self->{definition}->get_group_name("use_ed_spit_fire");

From 72680279a0f6d5bd3156cc82e590c1520fc758d3 Mon Sep 17 00:00:00 2001
From: rgknox <rgknox@gmail.com>
Date: Thu, 25 Feb 2016 13:36:39 -0800
Subject: [PATCH 18/19] uncommented the initialization of the physics namelist
 variable in the unit test template

---
 components/clm/bld/test_build_namelist/t/template_test_XXX.pm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/components/clm/bld/test_build_namelist/t/template_test_XXX.pm b/components/clm/bld/test_build_namelist/t/template_test_XXX.pm
index cf43818044..d212e1ea2a 100644
--- a/components/clm/bld/test_build_namelist/t/template_test_XXX.pm
+++ b/components/clm/bld/test_build_namelist/t/template_test_XXX.pm
@@ -27,8 +27,8 @@ sub startup : Test(startup => 3) {
   isnt($self->{defaults}, undef,  (caller(0))[3] . " : namelist_defaults object created.");
 
 #  The next line may be usefull (set startup => 4) in arg call above:
-#  $self->{physv} = config_files::clm_phys_vers->new( $self->{cfg}->get('phys') );
-#  isnt($self->{physv}, undef,  (caller(0))[3] . " : phys_vers object created.");
+  $self->{physv} = config_files::clm_phys_vers->new( $self->{cfg}->get('phys') );
+  isnt($self->{physv}, undef,  (caller(0))[3] . " : phys_vers object created.");
 
 
 }

From 3d6f43d137b7f8571b8b7525e9cb0a42a4aab8bb Mon Sep 17 00:00:00 2001
From: Ben Andre <andre@ucar.edu>
Date: Thu, 25 Feb 2016 16:10:07 -0700
Subject: [PATCH 19/19] Update the clm build-namelist unit test to remove
 warning.

Update the number of tests in template_test_XXX : startup to remove a
warning from the test system.

Fixes: Part of #19

User interface changes?: no

Code review: self

Test suite: test_build_namelist.pl - pass
Test baseline: n/a
Test namelist changes: n/a
Test answer changes: n/a
Test summary: n/a
---
 components/clm/bld/test_build_namelist/t/template_test_XXX.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/clm/bld/test_build_namelist/t/template_test_XXX.pm b/components/clm/bld/test_build_namelist/t/template_test_XXX.pm
index d212e1ea2a..faef3d9cb7 100644
--- a/components/clm/bld/test_build_namelist/t/template_test_XXX.pm
+++ b/components/clm/bld/test_build_namelist/t/template_test_XXX.pm
@@ -13,7 +13,7 @@ use parent qw(Test::Class);
 # Common test fixture for all tests:
 #
 #-------------------------------------------------------------------------------
-sub startup : Test(startup => 3) {
+sub startup : Test(startup => 4) {
   my $self = shift;
   # provide common fixture for all tests, only created once at the
   # start of the tests.