From 3d72650187f7c75a9e46752d070965e30f7a5dd7 Mon Sep 17 00:00:00 2001
From: Wuyin Lin <wlin@bnl.gov>
Date: Thu, 7 Dec 2023 21:54:27 -0800
Subject: [PATCH 1/2] Enable rough topograph and add remaining atm and lnd
 settings for v3b02

Rough topography for atm is enabled by replacing 16x topography with x6t ones.
This PR replaces the default topo file for ne30pg2 and ne120pg2. x6t topo for
other production grids are pending. Companion settings to go with rough topo
are set with pgrad_correction = 1 and hv_ref_profiles = 6. These options can
also be beneficial when using smoother topography.

The PR also reset dust_emis_fact and first and last year of pdepdyn stream files
for 2010 and 1950 compsets to match the stream file used.

[Non-BFB]
[NML]
---
 components/eam/bld/build-namelist                      |  6 ++++++
 .../eam/bld/namelist_files/namelist_defaults_eam.xml   | 10 +++++++---
 .../elm/bld/namelist_files/namelist_defaults.xml       |  4 ++++
 .../namelist_files/use_cases/1950_CMIP6_control.xml    |  4 ++--
 .../namelist_files/use_cases/2010_CMIP6_control.xml    |  4 ++--
 5 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/components/eam/bld/build-namelist b/components/eam/bld/build-namelist
index a448608ab378..be37559d1e31 100755
--- a/components/eam/bld/build-namelist
+++ b/components/eam/bld/build-namelist
@@ -879,6 +879,12 @@ if ($sim_year =~ /(\d+)-(\d+)/) {
 
 # Topography
 add_default($nl, 'bnd_topo', 'nofail'=>1);
+if (defined($defaults->get_value('pgrad_correction'))) {
+   add_default($nl, 'pgrad_correction', 'val' =>$nl->get_value('pgrad_correction'));
+}
+if (defined($defaults->get_value('hv_ref_profiles'))) {
+   add_default($nl, 'hv_ref_profiles', 'val' =>$nl->get_value('hv_ref_profiles'));
+}
 
 # Tropopause climatology
 add_default($nl, 'tropopause_climo_file');
diff --git a/components/eam/bld/namelist_files/namelist_defaults_eam.xml b/components/eam/bld/namelist_files/namelist_defaults_eam.xml
index bc29d28ebf05..11c67575505a 100755
--- a/components/eam/bld/namelist_files/namelist_defaults_eam.xml
+++ b/components/eam/bld/namelist_files/namelist_defaults_eam.xml
@@ -133,13 +133,13 @@
 <bnd_topo hgrid="ne16np4"  npg="0">atm/cam/topo/USGS-gtopo30_ne16np4_16xconsistentSGH.c20160612.nc</bnd_topo>
 <bnd_topo hgrid="ne16np4"  npg="2">atm/cam/topo/USGS-gtopo30_ne16np4pg2_16xdel2_20200527.nc</bnd_topo>
 <bnd_topo hgrid="ne30np4"  npg="0">atm/cam/topo/USGS-gtopo30_ne30np4_16xdel2-PFC-consistentSGH.nc</bnd_topo>
-<bnd_topo hgrid="ne30np4"  npg="2">atm/cam/topo/USGS-gtopo30_ne30np4pg2_16xdel2.c20200108.nc</bnd_topo>
+<bnd_topo hgrid="ne30np4"  npg="2">atm/cam/topo/USGS-gtopo30_ne30np4pg2_x6t-SGH.c20210614.nc</bnd_topo>
 <bnd_topo hgrid="ne30np4"  npg="3">atm/cam/topo/USGS-gtopo30_ne30np4pg3_16xdel2.c20200504.nc</bnd_topo>
 <bnd_topo hgrid="ne30np4"  npg="4">atm/cam/topo/USGS-gtopo30_ne30np4pg4_16xdel2.c20200504.nc</bnd_topo>
 <bnd_topo hgrid="ne45np4"  npg="2">atm/cam/topo/USGS-gtopo30_ne45np4pg2_16xdel2.c20200615.nc</bnd_topo>
 <bnd_topo hgrid="ne60np4"  npg="0">atm/cam/topo/USGS-gtopo30_ne60np4_16xconsistentSGH.c20140517.nc</bnd_topo>
 <bnd_topo hgrid="ne120np4" npg="0">atm/cam/topo/USGS-gtopo30_ne120np4_16xdel2-PFC-consistentSGH.nc</bnd_topo>
-<bnd_topo hgrid="ne120np4" npg="2">atm/cam/topo/USGS-gtopo30_ne120np4pg2_16xdel2.nc</bnd_topo>
+<bnd_topo hgrid="ne120np4" npg="2">atm/cam/topo/USGS-gtopo30_ne120np4pg2_x6t_20230404.nc</bnd_topo>
 <bnd_topo hgrid="ne240np4" npg="0">atm/cam/topo/USGS-gtopo30_ne240np4_16xconsistentSGH.c20130724.nc</bnd_topo>
 <bnd_topo hgrid="ne512np4"  npg="0">atm/cam/topo/USGS-gtopo30_ne512np4_16xconsistentSGH_20190212.nc</bnd_topo>
 <bnd_topo hgrid="ne1024np4" npg="0">atm/cam/topo/USGS-gtopo30_ne1024np4_16xconsistentSGH_20190528.nc</bnd_topo>
@@ -1887,7 +1887,7 @@ with se_tstep, dt_remap_factor, dt_tracer_factor set to -1
 <use_gw_energy_fix phys="default"> .true.      </use_gw_energy_fix>
 <clubb_C14 phys="default"> 2.5D0      </clubb_C14>
 <clubb_tk1 phys="default"> 268.15D0   </clubb_tk1>
-<dust_emis_fact phys="default"> 12.8D0     </dust_emis_fact>
+<dust_emis_fact phys="default"> 13.8D0     </dust_emis_fact>
 <linoz_psc_T               > 198.0D0    </linoz_psc_T>
 <lght_no_prd_factor        > 5.0D0    </lght_no_prd_factor>
 <micro_mincdnc phys="default" microphys="mg2"> 10.D6      </micro_mincdnc>
@@ -1942,4 +1942,8 @@ with se_tstep, dt_remap_factor, dt_tracer_factor set to -1
 <cflx_cpl_opt phys="default"> 2 </cflx_cpl_opt>
 <tropopause_E90_thrd phys="default"> 80.0e-9 </tropopause_E90_thrd>
 
+<!-- set following parameters to go with rough topography -->
+<pgrad_correction phys="default"> 2 </pgrad_correction>
+<hv_ref_profiles phys="default"> 6 </hv_ref_profiles>
+
 </namelist_defaults>
diff --git a/components/elm/bld/namelist_files/namelist_defaults.xml b/components/elm/bld/namelist_files/namelist_defaults.xml
index 0d2bfbc4b326..5befd66792f8 100644
--- a/components/elm/bld/namelist_files/namelist_defaults.xml
+++ b/components/elm/bld/namelist_files/namelist_defaults.xml
@@ -670,8 +670,12 @@ this mask will have smb calculated over the entire global land surface
 
 
 <!-- Phosphorus deposition streams namelist defaults -->
+<stream_year_first_pdep use_cn=".true."   sim_year="2010" >2000</stream_year_first_pdep>
+<stream_year_last_pdep  use_cn=".true."   sim_year="2010" >2000</stream_year_last_pdep>
 <stream_year_first_pdep use_cn=".true."   sim_year="2000" >2000</stream_year_first_pdep>
 <stream_year_last_pdep  use_cn=".true."   sim_year="2000" >2000</stream_year_last_pdep>
+<stream_year_first_pdep use_cn=".true."   sim_year="1950" >2000</stream_year_first_pdep>
+<stream_year_last_pdep  use_cn=".true."   sim_year="1950" >2000</stream_year_last_pdep>
 <stream_year_first_pdep use_cn=".true."   sim_year="1850" >2000</stream_year_first_pdep>
 <stream_year_last_pdep  use_cn=".true."   sim_year="1850" >2000</stream_year_last_pdep>
 <stream_year_first_pdep use_cn=".true."   sim_year="1000" >2000</stream_year_first_pdep>
diff --git a/components/elm/bld/namelist_files/use_cases/1950_CMIP6_control.xml b/components/elm/bld/namelist_files/use_cases/1950_CMIP6_control.xml
index 600094f80ca9..8943baee8006 100644
--- a/components/elm/bld/namelist_files/use_cases/1950_CMIP6_control.xml
+++ b/components/elm/bld/namelist_files/use_cases/1950_CMIP6_control.xml
@@ -11,8 +11,8 @@
 <stream_year_first_ndep phys="elm" use_cn=".true." ndepsrc="stream" >1950</stream_year_first_ndep>
 <stream_year_last_ndep  phys="elm" use_cn=".true." ndepsrc="stream" >1950</stream_year_last_ndep>
 
-<stream_year_first_pdep phys="elm" use_cn=".true." ndepsrc="stream" >1950</stream_year_first_pdep>
-<stream_year_last_pdep  phys="elm" use_cn=".true." ndepsrc="stream" >1950</stream_year_last_pdep>
+<stream_year_first_pdep phys="elm" use_cn=".true." ndepsrc="stream" >2000</stream_year_first_pdep>
+<stream_year_last_pdep  phys="elm" use_cn=".true." ndepsrc="stream" >2000</stream_year_last_pdep>
 
 <stream_year_first_popdens phys="elm" use_cn=".true." ndepsrc="stream" >1950</stream_year_first_popdens>
 <stream_year_last_popdens  phys="elm" use_cn=".true." ndepsrc="stream" >1950</stream_year_last_popdens>
diff --git a/components/elm/bld/namelist_files/use_cases/2010_CMIP6_control.xml b/components/elm/bld/namelist_files/use_cases/2010_CMIP6_control.xml
index fb7c037822c7..807b7ae07c32 100644
--- a/components/elm/bld/namelist_files/use_cases/2010_CMIP6_control.xml
+++ b/components/elm/bld/namelist_files/use_cases/2010_CMIP6_control.xml
@@ -11,8 +11,8 @@
 <stream_year_first_ndep phys="elm" use_cn=".true." ndepsrc="stream" >2010</stream_year_first_ndep>
 <stream_year_last_ndep  phys="elm" use_cn=".true." ndepsrc="stream" >2010</stream_year_last_ndep>
 
-<stream_year_first_pdep phys="elm" use_cn=".true." ndepsrc="stream" >2010</stream_year_first_pdep>
-<stream_year_last_pdep  phys="elm" use_cn=".true." ndepsrc="stream" >2010</stream_year_last_pdep>
+<stream_year_first_pdep phys="elm" use_cn=".true." ndepsrc="stream" >2000</stream_year_first_pdep>
+<stream_year_last_pdep  phys="elm" use_cn=".true." ndepsrc="stream" >2000</stream_year_last_pdep>
 
 <stream_year_first_popdens phys="elm" use_cn=".true." ndepsrc="stream" >2010</stream_year_first_popdens>
 <stream_year_last_popdens  phys="elm" use_cn=".true." ndepsrc="stream" >2010</stream_year_last_popdens>

From a2072b0add3fb98c00ee3fcf639eab907674d4a1 Mon Sep 17 00:00:00 2001
From: Wuyin Lin <wlin@bnl.gov>
Date: Mon, 18 Dec 2023 07:39:17 -0800
Subject: [PATCH 2/2] Fix default value for pgrad_correction

---
 components/eam/bld/namelist_files/namelist_defaults_eam.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/components/eam/bld/namelist_files/namelist_defaults_eam.xml b/components/eam/bld/namelist_files/namelist_defaults_eam.xml
index 11c67575505a..60e3199c4b22 100755
--- a/components/eam/bld/namelist_files/namelist_defaults_eam.xml
+++ b/components/eam/bld/namelist_files/namelist_defaults_eam.xml
@@ -1943,7 +1943,7 @@ with se_tstep, dt_remap_factor, dt_tracer_factor set to -1
 <tropopause_E90_thrd phys="default"> 80.0e-9 </tropopause_E90_thrd>
 
 <!-- set following parameters to go with rough topography -->
-<pgrad_correction phys="default"> 2 </pgrad_correction>
+<pgrad_correction phys="default"> 1 </pgrad_correction>
 <hv_ref_profiles phys="default"> 6 </hv_ref_profiles>
 
 </namelist_defaults>