cesm_1_2_2.patch

Index: models/atm/cam/bld/Makefile.in
===================================================================
--- models/atm/cam/bld/Makefile.in	(revision 65288)
+++ models/atm/cam/bld/Makefile.in	(working copy)
@@ -42,6 +42,8 @@
 #               Use this to replace default Fortran compiler optimization.
 # COSP_LIBDIR   Directory where COSP library will be built.
 # MCT_LIBDIR    Directory where MCT library will be built.
+# CATALYST_LDFLAGS Catalyst linking flags
+# CATALYST_INC  Search path for Catalyst mod file
 #
 # Note: An internal implementation of the ESMF time-manager interface is provided
 #       with the sequential CCSM distribution in models/utils/esmf_wrf_timemgr.
@@ -68,7 +70,7 @@
 dirs := . $(shell cat Filepath)
 
 # Set cpp search path, include netcdf
-cpp_dirs := $(dirs) $(INC_NETCDF) $(INC_MPI) $(INC_PNETCDF)
+cpp_dirs := $(dirs) $(INC_NETCDF) $(INC_MPI) $(INC_PNETCDF) $(CATALYST_INC)
 cpp_path := $(foreach dir,$(cpp_dirs),-I$(dir)) # format for command line
 
 # Expand any tildes in directory names. Change spaces to colons.
@@ -113,7 +115,7 @@
 endif
 
 $(MODEL_EXEDIR)/$(EXENAME): $(OBJS)
-	$(LINKER) -o $@ $(OBJS) $(NC_LDFLAGS) $(LDFLAGS)
+	$(LINKER) -o $@ $(OBJS) $(NC_LDFLAGS) $(LDFLAGS) $(CATALYST_LDFLAGS)
 
 ifneq ($(strip $(COSP_LIBDIR)),)
 # Rules to build COSP in its own library.  Add abortutils dependency so
Index: models/atm/cam/bld/configure
===================================================================
--- models/atm/cam/bld/configure	(revision 65288)
+++ models/atm/cam/bld/configure	(working copy)
@@ -187,6 +187,7 @@
 
      -cache <file>      Name of output cache file (default: config_cache.xml).
      -cachedir <file>   Name of directory where output cache file is written (default: CAM build directory).
+     -catalyst          Link with ParaView Catalyst.
      -ccsm_seq          Switch to specify that CAM is being built from within sequential CCSM scripts.
      -help [or -h]      Print usage to STDOUT.
      -silent [or -s]    Turns on silent mode - only fatal messages issued.
@@ -289,6 +290,7 @@
     "cache=s"                   => \$opts{'cache'},
     "cachedir=s"                => \$opts{'cachedir'},
     "carma=s"                   => \$opts{'carma'},
+    "catalyst"                  => \$opts{'catalyst'},
     "cam_bld=s"                 => \$opts{'cam_bld'},
     "cam_exe=s"                 => \$opts{'cam_exe'},
     "cam_exedir=s"              => \$opts{'cam_exedir'},
@@ -514,6 +516,8 @@
 my $ccsm_seq = (defined $opts{'ccsm_seq'}) ? 1 : 0;
 $cfg_ref->set('ccsm_seq', $ccsm_seq);
 
+my $catalyst = (defined $opts{'catalyst'}) ? 1 : 0;
+
 # Note that when building within the CCSM scripts the CAM Makefile is not written
 # since the CCSM build does not use it.  Many of the checks to ensure that a working
 # CAM Makefile is produced are disabled when the ccsm option is set.  Use the $cam_build
@@ -1952,6 +1956,10 @@
     $cfg_cppdefs .= " -DCLUBB_REAL_TYPE=dp";
 }
 
+if ($catalyst) {
+    $cfg_cppdefs .= " -DCATALYST";    
+}
+
 #-----------------------------------------------------------------------------------------------
 # External libraries ###########################################################################
 #-----------------------------------------------------------------------------------------------
@@ -2086,6 +2094,18 @@
     }
 }
 
+# Catalyst
+my $catalyst_ldflags = "";
+my $catalyst_inc = "";
+if ($catalyst) {
+    my $catalyst_build_dir = "cam_catalyst_adapter";
+    $catalyst_ldflags = "-L${catalyst_build_dir} -lcam_catalyst_adapter";
+    my $catalyst_src_dir = "${cam_root}/models/atm/cam/cam_catalyst_adapter/";
+    $catalyst_inc = "${catalyst_build_dir} $catalyst_src_dir";
+}
+
+
+
 # PNetCDF library
 my $pnc_lib = '';
 if ($cam_build) {
@@ -2812,6 +2832,8 @@
 INC_NETCDF   := $nc_inc
 LIB_NETCDF   := $nc_lib
 NC_LDFLAGS   := $nc_ldflags
+CATALYST_LDFLAGS := $catalyst_ldflags
+CATALYST_INC := $catalyst_inc
 MOD_NETCDF   := $nc_mod
 INC_PNETCDF  := $pnc_inc
 LIB_PNETCDF  := $pnc_lib
Index: models/atm/cam/src/cpl_mct/atm_comp_mct.F90
===================================================================
--- models/atm/cam/src/cpl_mct/atm_comp_mct.F90	(revision 65288)
+++ models/atm/cam/src/cpl_mct/atm_comp_mct.F90	(working copy)
@@ -50,6 +50,9 @@
   use runtime_opts     , only: read_namelist
   use phys_control     , only: cam_chempkg_is
   use scamMod          , only: single_column,scmlat,scmlon
+#if (defined CATALYST )
+  use fv_catalyst_adapter  , only: catalyst_init, catalyst_finalize
+#endif
 
 !
 ! !PUBLIC TYPES:
@@ -174,6 +177,12 @@
       call memmon_dump_fort('memmon.out','atm_init_mct:start::',lbnum)
     endif                      
 #endif                         
+#if (defined CATALYST )
+    ! call catalsyt_init only once (the second time atm_init_mct is called)
+    if(.not. present(NLFilename)) then
+       call catalyst_init()
+    endif
+#endif
     call seq_cdata_setptrs(cdata_a, ID=ATMID, mpicom=mpicom_atm, &
          gsMap=gsMap_atm, dom=dom_a, infodata=infodata)
 
@@ -650,6 +659,10 @@
     type(mct_aVect)             ,intent(inout) :: x2a_a
     type(mct_aVect)             ,intent(inout) :: a2x_a
 
+#if (defined CATALYST )
+       call catalyst_finalize()
+#endif
+
     call cam_final( cam_out, cam_in )
 
   end subroutine atm_final_mct
Index: models/atm/cam/src/physics/cam/physpkg.F90
===================================================================
--- models/atm/cam/src/physics/cam/physpkg.F90	(revision 65288)
+++ models/atm/cam/src/physics/cam/physpkg.F90	(working copy)
@@ -821,6 +821,11 @@
 
 end subroutine phys_init
 
+#if (defined CATALYST)
+include "fv_add_and_coprocess.F90"
+#endif
+
+
   !
   !-----------------------------------------------------------------------
   !
@@ -958,6 +963,10 @@
 #endif
     end if
 
+#if (defined CATALYST )
+    call fv_add_and_coprocess(phys_state);
+#endif
+
 end subroutine phys_run1
 
   !