From 3c87f3d66a2f6f2e943d20637aee2e03e63107fc Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Thu, 19 Jan 2023 09:28:18 -0500
Subject: [PATCH 01/18] For GEOS runs with gigatraj

---
 AGCM.rc.tmpl   | 9 +++++++++
 CMakeLists.txt | 2 ++
 2 files changed, 11 insertions(+)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index b812362f..cbf0f320 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -719,6 +719,15 @@ SEAICETHERMO_INTERNAL_CHECKPOINT_TYPE:  @CHECKPOINT_TYPE
 @COUPLEDOCEAN_INTERNAL_CHECKPOINT_FILE:            ocean_internal_checkpoint
 @COUPLEDOCEAN_INTERNAL_CHECKPOINT_TYPE:            @CHECKPOINT_TYPE
 
+# GIGATRAJ RUN CONFIG
+# -------------------------
+GIGATRAJ_INTERNAL_RESTART_FILE:        gigatraj_internal_rst
+GIGATRAJ_INTERNAL_CHECKPOINT_FILE:      gigatraj_internal_checkpoint
+GIGATRAJ_INTERNAL_CHECKPOINT_TYPE:      @CHECKPOINT_TYPE
+GIGATRAJ_PARCELS_FILE:                  parcels.nc4
+GIGATRAJ_REBALANCE_MINUTES:             15
+GIGATRAJ_OUTPUT_MINUTES:                15
+
 # Boundary Datasets
 # -----------------
 TOPO_MEAN_FILE:     topo_dynave.data
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 42f35741..144ff8ef 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -2,12 +2,14 @@ ecbuild_add_executable (
   TARGET GEOSgcm.x
   SOURCES GEOSgcm.F90
   LIBS GEOSgcm_GridComp esmf OpenMP::OpenMP_Fortran
+  LINKER_LANGUAGE Fortran
   )
 
 ecbuild_add_executable (
   TARGET idfupd.x
   SOURCES idfupd.F90
   LIBS GEOSgcm_GridComp esmf
+  LINKER_LANGUAGE Fortran
   )
 
 set (CMAKE_Fortran_FLAGS_RELEASE "${GEOS_Fortran_FLAGS_VECT}")

From 1bf19af3d8df788053e00ff03a63a38ea4123e57 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Thu, 19 Jan 2023 10:20:51 -0500
Subject: [PATCH 02/18] provide parces' initial position

---
 gcm_run.j | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gcm_run.j b/gcm_run.j
index 76c2b3da..1f693f16 100755
--- a/gcm_run.j
+++ b/gcm_run.j
@@ -245,6 +245,7 @@ cd $SCRDIR
 /bin/rm -rf *
                              cp -f  $EXPDIR/RC/* .
                              cp     $EXPDIR/cap_restart .
+                             cp     $EXPDIR/parcels.nc4 .
                              cp -f  $HOMDIR/*.rc .
                              cp -f  $HOMDIR/*.nml .
                              cp -f  $HOMDIR/*.yaml .

From 92f1b14985b75b92754862295cbfe7afa1571865 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Wed, 8 Feb 2023 15:12:53 -0500
Subject: [PATCH 03/18] add extra field configuration

---
 AGCM.rc.tmpl | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index cbf0f320..8d15e8c4 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -721,12 +721,14 @@ SEAICETHERMO_INTERNAL_CHECKPOINT_TYPE:  @CHECKPOINT_TYPE
 
 # GIGATRAJ RUN CONFIG
 # -------------------------
-GIGATRAJ_INTERNAL_RESTART_FILE:        gigatraj_internal_rst
+GIGATRAJ_INTERNAL_RESTART_FILE:         gigatraj_internal_rst
 GIGATRAJ_INTERNAL_CHECKPOINT_FILE:      gigatraj_internal_checkpoint
 GIGATRAJ_INTERNAL_CHECKPOINT_TYPE:      @CHECKPOINT_TYPE
 GIGATRAJ_PARCELS_FILE:                  parcels.nc4
 GIGATRAJ_REBALANCE_MINUTES:             15
 GIGATRAJ_OUTPUT_MINUTES:                15
+# using ";" to separate fields
+GIGATRAJ_EXTRA_FIELDS:                  T;TH
 
 # Boundary Datasets
 # -----------------

From 0d56e0e22ebf0f7ebc723fe431564260d92d15c1 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Tue, 28 Feb 2023 13:51:30 -0500
Subject: [PATCH 04/18] add more output fields

---
 AGCM.rc.tmpl | 1 +
 1 file changed, 1 insertion(+)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index 8d15e8c4..b5bb75c6 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -728,6 +728,7 @@ GIGATRAJ_PARCELS_FILE:                  parcels.nc4
 GIGATRAJ_REBALANCE_MINUTES:             15
 GIGATRAJ_OUTPUT_MINUTES:                15
 # using ";" to separate fields
+#fields supported: CA.bcDP;CA.ocWT;CA.bcphobic;CA.ocphobic;CA.bcphilic;CA.ocphilic
 GIGATRAJ_EXTRA_FIELDS:                  T;TH
 
 # Boundary Datasets

From 10543c9689ffadf8c383cde67ac9e2e5618d1cf0 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Tue, 14 Mar 2023 13:32:15 -0400
Subject: [PATCH 05/18] add GIGATRAJ_LON_START option

---
 AGCM.rc.tmpl | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index b5bb75c6..dcdf9764 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -724,6 +724,8 @@ SEAICETHERMO_INTERNAL_CHECKPOINT_TYPE:  @CHECKPOINT_TYPE
 GIGATRAJ_INTERNAL_RESTART_FILE:         gigatraj_internal_rst
 GIGATRAJ_INTERNAL_CHECKPOINT_FILE:      gigatraj_internal_checkpoint
 GIGATRAJ_INTERNAL_CHECKPOINT_TYPE:      @CHECKPOINT_TYPE
+# 0--360 or -180--180 
+GIGATRAJ_LON_START:                     0
 GIGATRAJ_PARCELS_FILE:                  parcels.nc4
 GIGATRAJ_REBALANCE_MINUTES:             15
 GIGATRAJ_OUTPUT_MINUTES:                15

From 56b793c26fd8b247cc9c359f6be57b91faf37f99 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Wed, 26 Jul 2023 10:14:18 -0400
Subject: [PATCH 06/18] change longitude start default to -180

---
 AGCM.rc.tmpl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index dcdf9764..391192a8 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -725,13 +725,13 @@ GIGATRAJ_INTERNAL_RESTART_FILE:         gigatraj_internal_rst
 GIGATRAJ_INTERNAL_CHECKPOINT_FILE:      gigatraj_internal_checkpoint
 GIGATRAJ_INTERNAL_CHECKPOINT_TYPE:      @CHECKPOINT_TYPE
 # 0--360 or -180--180 
-GIGATRAJ_LON_START:                     0
+GIGATRAJ_LON_START:                     -180.
 GIGATRAJ_PARCELS_FILE:                  parcels.nc4
 GIGATRAJ_REBALANCE_MINUTES:             15
 GIGATRAJ_OUTPUT_MINUTES:                15
 # using ";" to separate fields
-#fields supported: CA.bcDP;CA.ocWT;CA.bcphobic;CA.ocphobic;CA.bcphilic;CA.ocphilic
-GIGATRAJ_EXTRA_FIELDS:                  T;TH
+# fields supported: CA.bcDP;CA.ocWT;CA.bcphobic;CA.ocphobic;CA.bcphilic;CA.ocphilic
+# GIGATRAJ_EXTRA_FIELDS:                  T;TH
 
 # Boundary Datasets
 # -----------------

From 074058f4151812f2c06f1369a4fae6bfd359eb39 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Tue, 5 Sep 2023 11:21:59 -0400
Subject: [PATCH 07/18] add regrid option

---
 AGCM.rc.tmpl | 1 +
 1 file changed, 1 insertion(+)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index 391192a8..04bdcc28 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -724,6 +724,7 @@ SEAICETHERMO_INTERNAL_CHECKPOINT_TYPE:  @CHECKPOINT_TYPE
 GIGATRAJ_INTERNAL_RESTART_FILE:         gigatraj_internal_rst
 GIGATRAJ_INTERNAL_CHECKPOINT_FILE:      gigatraj_internal_checkpoint
 GIGATRAJ_INTERNAL_CHECKPOINT_TYPE:      @CHECKPOINT_TYPE
+GIGATRAJ_REGRID_TO_LATLON:              YES
 # 0--360 or -180--180 
 GIGATRAJ_LON_START:                     -180.
 GIGATRAJ_PARCELS_FILE:                  parcels.nc4

From 6ae858263257fd8ba43864e510a4f2d4c23abaf9 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Tue, 12 Sep 2023 11:02:57 -0400
Subject: [PATCH 08/18] add more comments

---
 AGCM.rc.tmpl | 3 +++
 gcm_run.j    | 6 +++++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index 04bdcc28..844c1874 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -728,8 +728,11 @@ GIGATRAJ_REGRID_TO_LATLON:              YES
 # 0--360 or -180--180 
 GIGATRAJ_LON_START:                     -180.
 GIGATRAJ_PARCELS_FILE:                  parcels.nc4
+# time interval (minutes) to rebalance the parcels, i.e, the process keeps its own parcels
 GIGATRAJ_REBALANCE_MINUTES:             15
+# time interval (minutes) to write output
 GIGATRAJ_OUTPUT_MINUTES:                15
+
 # using ";" to separate fields
 # fields supported: CA.bcDP;CA.ocWT;CA.bcphobic;CA.ocphobic;CA.bcphilic;CA.ocphilic
 # GIGATRAJ_EXTRA_FIELDS:                  T;TH
diff --git a/gcm_run.j b/gcm_run.j
index 1f693f16..864a3ff9 100755
--- a/gcm_run.j
+++ b/gcm_run.j
@@ -237,6 +237,8 @@ cat CAP.tmp | sed -e "s?$oldstring?$newstring?g" > CAP.rc
 
 endif
 
+set GIGATRAJ  = `grep '^\s*GIGATRAJ_PARCELS_FILE:'     AGCM.rc | cut -d: -f2`
+
 #######################################################################
 #   Move to Scratch Directory and Copy RC Files from Home Directory
 #######################################################################
@@ -245,7 +247,9 @@ cd $SCRDIR
 /bin/rm -rf *
                              cp -f  $EXPDIR/RC/* .
                              cp     $EXPDIR/cap_restart .
-                             cp     $EXPDIR/parcels.nc4 .
+                             if ($GIGATRAJ != "") then
+                               cp   $EXPDIR/$GIGATRAJ .
+                             endif
                              cp -f  $HOMDIR/*.rc .
                              cp -f  $HOMDIR/*.nml .
                              cp -f  $HOMDIR/*.yaml .

From 5278034c8399c23d2d78e9fafea569ad8a39202f Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Mon, 30 Oct 2023 14:33:41 -0400
Subject: [PATCH 09/18] added gigatraj collection

---
 AGCM.rc.tmpl         |  2 +-
 HISTORY.AGCM.rc.tmpl | 21 +++++++++++++++++++++
 2 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index 844c1874..b917f523 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -721,7 +721,7 @@ SEAICETHERMO_INTERNAL_CHECKPOINT_TYPE:  @CHECKPOINT_TYPE
 
 # GIGATRAJ RUN CONFIG
 # -------------------------
-GIGATRAJ_INTERNAL_RESTART_FILE:         gigatraj_internal_rst
+#GIGATRAJ_INTERNAL_RESTART_FILE:         gigatraj_internal_rst
 GIGATRAJ_INTERNAL_CHECKPOINT_FILE:      gigatraj_internal_checkpoint
 GIGATRAJ_INTERNAL_CHECKPOINT_TYPE:      @CHECKPOINT_TYPE
 GIGATRAJ_REGRID_TO_LATLON:              YES
diff --git a/HISTORY.AGCM.rc.tmpl b/HISTORY.AGCM.rc.tmpl
index 36cb0049..da415568 100644
--- a/HISTORY.AGCM.rc.tmpl
+++ b/HISTORY.AGCM.rc.tmpl
@@ -6,6 +6,7 @@ EXPSRC: @EXPSRC
 
 COLLECTIONS: 'geosgcm_prog'
 #             'prog.eta'
+             'geosgcm_gigatraj'
              'geosgcm_surf'
              'geosgcm_ocn'
              'geosgcm_moist'
@@ -74,6 +75,26 @@ PC@HIST_IMx@HIST_JM-DC.LM: @AGCM_LM
                                  'O3'     , 'CHEMISTRY'  ,
                                   ::
 
+  geosgcm_gigatraj.template:         '%y4%m2%d2_%h2%n2z.nc4' ,
+  geosgcm_gigatraj.archive:          '%c/Y%y4' ,
+  geosgcm_gigatraj.format:           'CFIO' ,
+  geosgcm_gigatraj.deflate:           1 ,
+  geosgcm_gigatraj.grid_label:        PC@HIST_IMx@HIST_JM-DC ,
+  geosgcm_gigatraj.regrid_method:    'BILINEAR',
+  geosgcm_gigatraj.frequency:         240000 ,
+  geosgcm_gigatraj.vscale:            100.0 ,
+  geosgcm_gigatraj.vunit:            'hPa' ,
+  geosgcm_gigatraj.vvars:            'log(PLE)' , 'DYN' ,
+  geosgcm_gigatraj.levels:            1000 975 950 925 900 875 850 825 800 775 750 725 700 650 600 550 500 450 400 350 300 250 200 150 100 70 50 40 30 20 10 7 5 4 3 2 1 0.7 0.5 0.4 0.3 0.2 0.1 0.07 0.05 0.04 0.03 0.02 ,
+  geosgcm_gigatraj.fields:           'CA.bcphobic', 'CA.bc',
+                                 'CA.ocphobic', 'CA.oc',
+                                 'CA.bcphilic', 'CA.bc',
+                                 'CA.ocphilic', 'CA.oc',
+                                 'CA.bcDP'    , 'CA.bc'  , 'CA.bcDP001;CA.bcDP002',
+                                 'CA.ocWT'    , 'CA.oc'  , 'CA.ocWT001;CA.ocWT002',
+                                  ::
+
+  prog.eta.template:             '%y4%m2%d2_%h2%n2z.nc4' ,
   prog.eta.template:             '%y4%m2%d2_%h2%n2z.nc4' ,
   prog.eta.archive:              '%c/Y%y4' ,
   prog.eta.format:               'CFIO' ,

From 1af2388d5f5027acb05b801406a1089b86d73140 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Tue, 7 Nov 2023 12:32:25 -0500
Subject: [PATCH 10/18] comment out some collections

---
 HISTORY.AGCM.rc.tmpl | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/HISTORY.AGCM.rc.tmpl b/HISTORY.AGCM.rc.tmpl
index da415568..906bf49c 100644
--- a/HISTORY.AGCM.rc.tmpl
+++ b/HISTORY.AGCM.rc.tmpl
@@ -7,18 +7,18 @@ EXPSRC: @EXPSRC
 COLLECTIONS: 'geosgcm_prog'
 #             'prog.eta'
              'geosgcm_gigatraj'
-             'geosgcm_surf'
-             'geosgcm_ocn'
-             'geosgcm_moist'
-             'geosgcm_turb'
-             'geosgcm_gwd'
-             'geosgcm_tend'
-             'geosgcm_budi'
-             'geosgcm_buda'
-             'geosgcm_landice'
-             'geosgcm_meltwtr'
-             'geosgcm_snowlayer'
-             'geosgcm_tracer'
+#             'geosgcm_surf'
+#             'geosgcm_ocn'
+#             'geosgcm_moist'
+#             'geosgcm_turb'
+#             'geosgcm_gwd'
+#             'geosgcm_tend'
+#             'geosgcm_budi'
+#             'geosgcm_buda'
+#             'geosgcm_landice'
+#             'geosgcm_meltwtr'
+#             'geosgcm_snowlayer'
+#             'geosgcm_tracer'
 >>>HIST_GOCART<<<             'tavg2d_aer_x'
 >>>HIST_GOCART<<<             'tavg3d_aer_p'
 #             'geosgcm_iau'

From ff02924bc895322eee38180b0edad8255e2474c6 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Tue, 7 Nov 2023 14:43:52 -0500
Subject: [PATCH 11/18] add entry for integration interval

---
 AGCM.rc.tmpl | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index b917f523..ed73ad16 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -728,6 +728,8 @@ GIGATRAJ_REGRID_TO_LATLON:              YES
 # 0--360 or -180--180 
 GIGATRAJ_LON_START:                     -180.
 GIGATRAJ_PARCELS_FILE:                  parcels.nc4
+# time interval (minutes) for integration. Default is heart beat and it must be a multiple of heart beat. 
+# GIGATRAJ_INTEGRATE_MINUTES:
 # time interval (minutes) to rebalance the parcels, i.e, the process keeps its own parcels
 GIGATRAJ_REBALANCE_MINUTES:             15
 # time interval (minutes) to write output

From 0ed52d2a8601f05457a975b3dafa33ec46997fc8 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Tue, 5 Dec 2023 12:38:29 -0500
Subject: [PATCH 12/18] remove lon_start. all are from -180 to 180

---
 AGCM.rc.tmpl | 2 --
 1 file changed, 2 deletions(-)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index ed73ad16..b27a7230 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -725,8 +725,6 @@ SEAICETHERMO_INTERNAL_CHECKPOINT_TYPE:  @CHECKPOINT_TYPE
 GIGATRAJ_INTERNAL_CHECKPOINT_FILE:      gigatraj_internal_checkpoint
 GIGATRAJ_INTERNAL_CHECKPOINT_TYPE:      @CHECKPOINT_TYPE
 GIGATRAJ_REGRID_TO_LATLON:              YES
-# 0--360 or -180--180 
-GIGATRAJ_LON_START:                     -180.
 GIGATRAJ_PARCELS_FILE:                  parcels.nc4
 # time interval (minutes) for integration. Default is heart beat and it must be a multiple of heart beat. 
 # GIGATRAJ_INTEGRATE_MINUTES:

From 452291442512bab627be72ec98aaef24a534bbf6 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Mon, 26 Feb 2024 09:29:26 -0500
Subject: [PATCH 13/18] change rc tmpl

---
 AGCM.rc.tmpl | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index b27a7230..d72f38be 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -727,11 +727,14 @@ GIGATRAJ_INTERNAL_CHECKPOINT_TYPE:      @CHECKPOINT_TYPE
 GIGATRAJ_REGRID_TO_LATLON:              YES
 GIGATRAJ_PARCELS_FILE:                  parcels.nc4
 # time interval (minutes) for integration. Default is heart beat and it must be a multiple of heart beat. 
-# GIGATRAJ_INTEGRATE_MINUTES:
-# time interval (minutes) to rebalance the parcels, i.e, the process keeps its own parcels
-GIGATRAJ_REBALANCE_MINUTES:             15
-# time interval (minutes) to write output
-GIGATRAJ_OUTPUT_MINUTES:                15
+# format hhmmss
+# GIGATRAJ_INTEGRATE_DT:
+# time interval to rebalance the parcels, i.e, the process keeps its own parcels
+# format hhmmss
+GIGATRAJ_REBALANCE_DT:      001500
+# time interval to write output
+# format hhmmss
+GIGATRAJ_OUTPUT_DT:         001500
 
 # using ";" to separate fields
 # fields supported: CA.bcDP;CA.ocWT;CA.bcphobic;CA.ocphobic;CA.bcphilic;CA.ocphilic

From 811b37adb69df3dd90f609147bccf38f7390e7ec Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Mon, 23 Sep 2024 12:22:15 -0400
Subject: [PATCH 14/18] convention for other fields

---
 AGCM.rc.tmpl |  4 ++--
 gcm_setup    | 11 +----------
 2 files changed, 3 insertions(+), 12 deletions(-)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index 839d9512..d2ca9cb0 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -804,8 +804,8 @@ GIGATRAJ_REBALANCE_DT:      001500
 GIGATRAJ_OUTPUT_DT:         001500
 
 # using ";" to separate fields
-# fields supported: CA.bcDP;CA.ocWT;CA.bcphobic;CA.ocphobic;CA.bcphilic;CA.ocphilic
-# GIGATRAJ_EXTRA_FIELDS:                  T;TH
+# format: COMP%%[BUNDLE%]FIELD[|ALIAS]
+# GIGATRAJ_EXTRA_FIELDS:                  DYN%%TH|Theta
 
 
 # IGNI Restart Files
diff --git a/gcm_setup b/gcm_setup
index b05a7c7d..f8b0e42c 100755
--- a/gcm_setup
+++ b/gcm_setup
@@ -2599,20 +2599,11 @@ foreach rsname ($RSNAMES)
    set  test = `eval echo \$$rsname`
    if( $test == FALSE ) then
        foreach type ($RSTYPES)
-          #set  TMPCMD = `mktemp`
           set  string = ${name}_${type}
-          /bin/rm -f $LOCDIR/$FILE.tmp
-          /bin/mv -f $LOCDIR/$FILE $LOCDIR/$FILE.tmp
-          echo `cat $LOCDIR/$FILE.tmp | awk '{if ( $1 ~ "${string}" )  {sub ( /${string}/ ,"#${string}"  );print} else print}' > $LOCDIR/$FILE`
-          #echo cat   $LOCDIR/$FILE.tmp \| awk \'\{if \( \$1 \~ \"${string}\" \) \
-          #     \{sub \( \/${string}\/ ,\"\#${string}\"  \)\;print\} else print\}\' \> $LOCDIR/$FILE > $TMPCMD
-          #chmod +x   $TMPCMD
-          #           $TMPCMD
-          #/bin/rm -f $TMPCMD
+          sed -i -e "s/${string}/#${string}/g" $LOCDIR/$FILE
        end
    endif
 end
-/bin/rm -f $LOCDIR/$FILE.tmp
 
 
 # Delete or Enable EXP Configuration Variables

From f01034dbbbd616c6c4ea05183c949027f617bdac Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Fri, 6 Dec 2024 14:12:28 -0500
Subject: [PATCH 15/18] more changes and comments on gigatraj section

---
 AGCM.rc.tmpl | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index d2ca9cb0..bed3e1e4 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -791,9 +791,9 @@ SEAICETHERMO_INTERNAL_CHECKPOINT_TYPE:  @CHECKPOINT_TYPE
 #GIGATRAJ_INTERNAL_RESTART_FILE:         gigatraj_internal_rst
 GIGATRAJ_INTERNAL_CHECKPOINT_FILE:      gigatraj_internal_checkpoint
 GIGATRAJ_INTERNAL_CHECKPOINT_TYPE:      @CHECKPOINT_TYPE
-GIGATRAJ_REGRID_TO_LATLON:              YES
+GIGATRAJ_REGRID_TO_LATLON:              NO
 GIGATRAJ_PARCELS_FILE:                  parcels.nc4
-# time interval (minutes) for integration. Default is heart beat and it must be a multiple of heart beat. 
+# time interval (minutes) for integration. Default is heart beat and it must be a multiple of heart beat.
 # format hhmmss
 # GIGATRAJ_INTEGRATE_DT:
 # time interval to rebalance the parcels, i.e, the process keeps its own parcels
@@ -801,12 +801,16 @@ GIGATRAJ_PARCELS_FILE:                  parcels.nc4
 GIGATRAJ_REBALANCE_DT:      001500
 # time interval to write output
 # format hhmmss
-GIGATRAJ_OUTPUT_DT:         001500
-
-# using ";" to separate fields
-# format: COMP%%[BUNDLE%]FIELD[|ALIAS]
-# GIGATRAJ_EXTRA_FIELDS:                  DYN%%TH|Theta
-
+GIGATRAJ_OUTPUT_DT:         003000
+# format :: comp[%%bundle]%field[|alias], [] is optional
+GIGATRAJ_VERTICAL_COORD: DYN%PL|P
+#GIGATRAJ_VERTICAL_COORD: DYN%TH|Theta
+#GIGATRAJ_VERTICAL_COORD: DYN%ZL|PAlt
+# using ";" to separate fields. NO blank space between chars
+# format :: comp[%%bundle]%field[|alias], [] is optional
+GIGATRAJ_EXTRA_FIELDS:       DYN%TH|Theta;DYN%ZL|PAlt
+#GIGATRAJ_EXTRA_FIELDS:       DYN%PL|P;DYN%ZL|PAlt
+#GIGATRAJ_EXTRA_FIELDS:       DYN%PL|P;DYN%TH|Theta
 
 # IGNI Restart Files
 # ------------------

From 9377220f77edaac8c8beb86387c6b8a2f1e59c32 Mon Sep 17 00:00:00 2001
From: Weiyuan Jiang <weiyuan.jiang@nasa.gov>
Date: Fri, 6 Dec 2024 14:55:13 -0500
Subject: [PATCH 16/18] remove history template change

---
 AGCM.rc.tmpl         |  2 +-
 HISTORY.AGCM.rc.tmpl | 21 ---------------------
 2 files changed, 1 insertion(+), 22 deletions(-)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index bed3e1e4..289b6ab4 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -792,7 +792,7 @@ SEAICETHERMO_INTERNAL_CHECKPOINT_TYPE:  @CHECKPOINT_TYPE
 GIGATRAJ_INTERNAL_CHECKPOINT_FILE:      gigatraj_internal_checkpoint
 GIGATRAJ_INTERNAL_CHECKPOINT_TYPE:      @CHECKPOINT_TYPE
 GIGATRAJ_REGRID_TO_LATLON:              NO
-GIGATRAJ_PARCELS_FILE:                  parcels.nc4
+#GIGATRAJ_PARCELS_FILE:                  parcels.nc4
 # time interval (minutes) for integration. Default is heart beat and it must be a multiple of heart beat.
 # format hhmmss
 # GIGATRAJ_INTEGRATE_DT:
diff --git a/HISTORY.AGCM.rc.tmpl b/HISTORY.AGCM.rc.tmpl
index a8401c0b..e1932d6f 100644
--- a/HISTORY.AGCM.rc.tmpl
+++ b/HISTORY.AGCM.rc.tmpl
@@ -22,7 +22,6 @@ COLLECTIONS: 'geosgcm_prog'
              'geosgcm_tracer'
 @HIST_GOCART             'tavg2d_aer_x'
 @HIST_GOCART             'tavg3d_aer_p'
-#             'geosgcm_gigatraj'
 #             'geosgcm_iau'
 #             'geosgcm_conv'
 #             'goswim_catch'
@@ -77,26 +76,6 @@ PC@HIST_IMx@HIST_JM-DC.LM: @AGCM_LM
                                  'O3'     , 'CHEMISTRY'  ,
                                   ::
 
-  geosgcm_gigatraj.template:         '%y4%m2%d2_%h2%n2z.nc4' ,
-  geosgcm_gigatraj.archive:          '%c/Y%y4' ,
-  geosgcm_gigatraj.format:           'CFIO' ,
-  geosgcm_gigatraj.deflate:           1 ,
-  geosgcm_gigatraj.grid_label:        PC@HIST_IMx@HIST_JM-DC ,
-  geosgcm_gigatraj.regrid_method:    'BILINEAR',
-  geosgcm_gigatraj.frequency:         240000 ,
-  geosgcm_gigatraj.vscale:            100.0 ,
-  geosgcm_gigatraj.vunit:            'hPa' ,
-  geosgcm_gigatraj.vvars:            'log(PLE)' , 'DYN' ,
-  geosgcm_gigatraj.levels:            1000 975 950 925 900 875 850 825 800 775 750 725 700 650 600 550 500 450 400 350 300 250 200 150 100 70 50 40 30 20 10 7 5 4 3 2 1 0.7 0.5 0.4 0.3 0.2 0.1 0.07 0.05 0.04 0.03 0.02 ,
-  geosgcm_gigatraj.fields:           'CA.bcphobic', 'CA.bc',
-                                 'CA.ocphobic', 'CA.oc',
-                                 'CA.bcphilic', 'CA.bc',
-                                 'CA.ocphilic', 'CA.oc',
-                                 'CA.bcDP'    , 'CA.bc'  , 'CA.bcDP001;CA.bcDP002',
-                                 'CA.ocWT'    , 'CA.oc'  , 'CA.ocWT001;CA.ocWT002',
-                                  ::
-
-  prog.eta.template:             '%y4%m2%d2_%h2%n2z.nc4' ,
   prog.eta.template:             '%y4%m2%d2_%h2%n2z.nc4' ,
   prog.eta.archive:              '%c/Y%y4' ,
   prog.eta.format:               'CFIO' ,

From efcf218026779020849b8687f88c9400697484db Mon Sep 17 00:00:00 2001
From: Matthew Thompson <matthew.thompson@nasa.gov>
Date: Tue, 10 Dec 2024 11:32:24 -0500
Subject: [PATCH 17/18] Set linker language to Fortran

---
 CMakeLists.txt | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 59e43e66..36a33063 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -3,12 +3,18 @@ ecbuild_add_executable (
   SOURCES GEOSgcm.F90
   LIBS GEOSgcm_GridComp ESMF::ESMF OpenMP::OpenMP_Fortran
   )
+# NOTE Due to Gigatraj being a C++ code, CMake apparently
+# gets confused if building with it and thinks GEOSgcm.x
+# is a C++ code and tries to link as C++. This will fail.
+# To fix this, we explicitly set the linker language to Fortran.
+set_target_properties (GEOSgcm.x PROPERTIES LINKER_LANGUAGE Fortran)
 
 ecbuild_add_executable (
   TARGET idfupd.x
   SOURCES idfupd.F90
   LIBS GEOSgcm_GridComp ESMF::ESMF
   )
+set_target_properties (idfupd.x PROPERTIES LINKER_LANGUAGE Fortran)
 
 set (CMAKE_Fortran_FLAGS_RELEASE "${GEOS_Fortran_FLAGS_VECT}")
 

From 07d99acc780b64d6ddc606851c6070eb1cd0e990 Mon Sep 17 00:00:00 2001
From: Matthew Thompson <matthew.thompson@nasa.gov>
Date: Fri, 20 Dec 2024 13:44:01 -0500
Subject: [PATCH 18/18] Comment out Gigatraj checkpoints

---
 AGCM.rc.tmpl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/AGCM.rc.tmpl b/AGCM.rc.tmpl
index 289b6ab4..acbd78c5 100644
--- a/AGCM.rc.tmpl
+++ b/AGCM.rc.tmpl
@@ -789,8 +789,8 @@ SEAICETHERMO_INTERNAL_CHECKPOINT_TYPE:  @CHECKPOINT_TYPE
 # GIGATRAJ RUN CONFIG
 # -------------------------
 #GIGATRAJ_INTERNAL_RESTART_FILE:         gigatraj_internal_rst
-GIGATRAJ_INTERNAL_CHECKPOINT_FILE:      gigatraj_internal_checkpoint
-GIGATRAJ_INTERNAL_CHECKPOINT_TYPE:      @CHECKPOINT_TYPE
+#GIGATRAJ_INTERNAL_CHECKPOINT_FILE:      gigatraj_internal_checkpoint
+#GIGATRAJ_INTERNAL_CHECKPOINT_TYPE:      @CHECKPOINT_TYPE
 GIGATRAJ_REGRID_TO_LATLON:              NO
 #GIGATRAJ_PARCELS_FILE:                  parcels.nc4
 # time interval (minutes) for integration. Default is heart beat and it must be a multiple of heart beat.