Remove options not used, e.g. use_fates, use_cndv, and many more

bld/configure

@@ -47,7 +47,7 @@ OPTIONS
      or double leading dashes.  A consequence of this is that single letter options may
      NOT be bundled.
 
-     -bgc <name>            Build CLM with BGC package [ none | cn | cndv ] 
+     -bgc <name>            Build CLM with BGC package [ none | cn ] 
                             (default is none).
      -cache <file>          Name of output cache file (default: config_cache.xml).
      -cachedir <file>       Name of directory where output cache file is written 
@@ -58,30 +58,20 @@ OPTIONS
      -cppdefs <string>      A string of user specified CPP defines.  Appended to
                             Makefile defaults.  e.g. -cppdefs '-DVAR1 -DVAR2'
      -crop <name>           Toggle for prognostic crop model. [on | off] (default is off) 
-                            (can ONLY be turned on when BGC type is CN or CNDV)
+                            (can ONLY be turned on when BGC type is CN)
      -comp_intf <name>      Component interface to use (ESMF or MCT) (default MCT)
      -defaults <file>       Specify full path to a configuration file which will be used 
                             to supply defaults instead of the defaults in bld/config_files.
                             This file is used to specify model configuration parameters only.
                             Parameters relating to the build which are system dependent will
                             be ignored.
      -help [or -h]          Print usage to STDOUT.
-     -nofire                Turn off wildfires for BGC setting of CN 
-                            (default includes fire for CN)
      -noio                  Turn history output completely off (typically for testing).
      -phys <name>           Value of clm4_5, or clm5_0 (default is clm4_5)   
      -silent [or -s]        Turns on silent mode - only fatal messages issued.
      -sitespf_pt <name>     Setup for the given site specific single-point resolution.
      -snicar_frc <name>     Turn on SNICAR radiative forcing calculation. [on | off] 
                             (default is off)
-     -spinup <name>         CLM 4.0 Only. For CLM 4.5, spinup is controlled from build-namelist.
-                            Turn on given spinup mode for BGC setting of CN		  (level)
-                              AD            Turn on Accelerated Decomposition from	      (2)
-                                            bare-soil
-                              exit          Jump directly from AD spinup to normal mode	      (1)
-                              normal        Normal decomposition ("final spinup mode")	      (0)
-                                            (default)
-                            The recommended sequence is 2-1-0
      -usr_src <dir1>[,<dir2>[,<dir3>[...]]]
                             Directories containing user source code.
      -verbose [or -v]       Turn on verbose echoing of settings made by configure.
@@ -121,14 +111,11 @@ my $commandline = "$cfgdir/configure @ARGV";
 my %opts = (
 	    cache       => "config_cache.xml",
             phys        => "clm4_5",
-            nofire      => undef,
             noio        => undef,
             cimeroot    => undef,
             clm_root    => undef,
-            spinup      => "normal",
 	    );
 GetOptions(
-    "spinup=s"                  => \$opts{'spinup'}, 
     "bgc=s"                     => \$opts{'bgc'}, 
     "cache=s"                   => \$opts{'cache'},
     "cachedir=s"                => \$opts{'cachedir'},
@@ -140,7 +127,6 @@ GetOptions(
     "defaults=s"                => \$opts{'defaults'},
     "clm4me=s"                  => \$opts{'clm4me'},
     "h|help"                    => \$opts{'help'},
-    "nofire"                    => \$opts{'nofire'},
     "noio"                      => \$opts{'noio'},
     "phys=s"                    => \$opts{'phys'},
     "snicar_frc=s"              => \$opts{'snicar_frc'}, 

bld/namelist_files/namelist_defaults.xsl

@@ -20,17 +20,15 @@
     </ul>
     <h3>Miscellaneous items include:</h3>
     <ol>
-       <li>Biogeochemistry (BGC) type (none, CN, CNDV)</li>
+       <li>Biogeochemistry (BGC) type (none, CN)</li>
        <li>Initial condition date (ymd - year month day)</li>
        <li>Initial condition time of day (tod) (sec)</li>
        <li>Maximum number of Plant Function Types (maxpft)</li>
-       <li>Number of glacier multiple elevation classes (glc_nec)</li>
        <li>Site specific point name (sitespf_pt)</li>
        <li>Crop model (crop)</li>
        <li>Data model forcing source (forcing)</li>
        <li>Representative concentration pathway for future scenarios (rcp)</li>
        <li>New good wood harvest (newwoodharv)</li>
-       <li>CN Spin-up mode (spinup)</li>
        <li>Type of file (type)</li>
        <li>Grid mapping to (to_hgrid)</li>
        <li>Land-mask mapping to (to_lmask)</li>
@@ -121,9 +119,6 @@
         <xsl:if test="string-length(@maxpft)>0">
         maxpft=<xsl:value-of select="@maxpft"/>
         </xsl:if>
-        <xsl:if test="string-length(@glc_nec)>0">
-        glc_nec=<xsl:value-of select="@glc_nec"/>
-        </xsl:if>
         <xsl:if test="string-length(@sitespf_pt)>0">
         sitespf_pt=<xsl:value-of select="@sitespf_pt"/>
         </xsl:if>
@@ -133,12 +128,6 @@
         <xsl:if test="string-length(@crop)>0">
         crop=<xsl:value-of select="@crop"/>
         </xsl:if>
-        <xsl:if test="string-length(@irrig)>0">
-        irrig=<xsl:value-of select="@irrig"/>
-        </xsl:if>
-        <xsl:if test="string-length(@spinup)>0">
-        spinup=<xsl:value-of select="@spinup"/>
-        </xsl:if>
         <xsl:if test="string-length(@source)>0">
         forcing=<xsl:value-of select="@source"/>
         </xsl:if>