diff --git a/.gitmodules b/.gitmodules
index d253f6966..9dcb203ef 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,12 +1,12 @@
 [submodule "atmos_cubed_sphere"]
 	path = atmos_cubed_sphere
-	url = https://github.com/NOAA-EMC/GFDL_atmos_cubed_sphere
-	branch = dev/emc
+	url = https://github.com/XiaqiongZhou-NOAA/GFDL_atmos_cubed_sphere
+	branch = dev/emc_nest
 [submodule "ccpp/framework"]
 	path = ccpp/framework
 	url = https://github.com/NCAR/ccpp-framework
 	branch = master
 [submodule "ccpp/physics"]
 	path = ccpp/physics
-	url = https://github.com/NCAR/ccpp-physics
+	url = https://github.com/XiaqiongZhou-NOAA/ccpp-physics
 	branch = master
diff --git a/atmos_cubed_sphere b/atmos_cubed_sphere
index a56907a44..c80bebb81 160000
--- a/atmos_cubed_sphere
+++ b/atmos_cubed_sphere
@@ -1 +1 @@
-Subproject commit a56907a44461c7151e0ba266e160c8f1a1685882
+Subproject commit c80bebb813eb9eabd6204486372982e3ab1b6cc5
diff --git a/atmos_model.F90 b/atmos_model.F90
index 9a73e0151..1bbedf55b 100644
--- a/atmos_model.F90
+++ b/atmos_model.F90
@@ -78,7 +78,7 @@ module atmos_model_mod
 use atmosphere_mod,     only: atmosphere_scalar_field_halo
 use atmosphere_mod,     only: atmosphere_get_bottom_layer
 use atmosphere_mod,     only: set_atmosphere_pelist
-use atmosphere_mod,     only: Atm, mytile
+use atmosphere_mod,     only: Atm, mygrid
 use block_control_mod,  only: block_control_type, define_blocks_packed
 use DYCORE_typedefs,    only: DYCORE_data_type, DYCORE_diag_type
 #ifdef CCPP
@@ -599,8 +599,8 @@ subroutine atmos_model_init (Atmos, Time_init, Time, Time_step)
    Init_parm%area            => Atmos%area
    Init_parm%tracer_names    => tracer_names
 #ifdef CCPP
-   Init_parm%restart         = Atm(mytile)%flagstruct%warm_start
-   Init_parm%hydrostatic     = Atm(mytile)%flagstruct%hydrostatic
+   Init_parm%restart         = Atm(mygrid)%flagstruct%warm_start
+   Init_parm%hydrostatic     = Atm(mygrid)%flagstruct%hydrostatic
 #endif
 
 #ifdef INTERNAL_FILE_NML
@@ -663,7 +663,7 @@ subroutine atmos_model_init (Atmos, Time_init, Time, Time_step)
                              Atm_block%blksz(1))
    endif
 
-   Atm(mytile)%flagstruct%do_skeb = IPD_Control%do_skeb
+   Atm(mygrid)%flagstruct%do_skeb = IPD_Control%do_skeb
 
 !  initialize the IAU module
    call iau_initialize (IPD_Control,IAU_data,Init_parm)
@@ -684,7 +684,7 @@ subroutine atmos_model_init (Atmos, Time_init, Time, Time_step)
    call FV3GFS_diag_register (IPD_Diag, Time, Atm_block, IPD_Control, Atmos%lon, Atmos%lat, Atmos%axes)
    call IPD_initialize_rst (IPD_Control, IPD_Data, IPD_Diag, IPD_Restart, Init_parm)
 #ifdef CCPP
-   call FV3GFS_restart_read (IPD_Data, IPD_Restart, Atm_block, IPD_Control, Atmos%domain, Atm(mytile)%flagstruct%warm_start)
+   call FV3GFS_restart_read (IPD_Data, IPD_Restart, Atm_block, IPD_Control, Atmos%domain, Atm(mygrid)%flagstruct%warm_start)
 #else
    call FV3GFS_restart_read (IPD_Data, IPD_Restart, Atm_block, IPD_Control, Atmos%domain)
 #endif
diff --git a/ccpp/physics b/ccpp/physics
index 01ed01fb0..0af8bba2e 160000
--- a/ccpp/physics
+++ b/ccpp/physics
@@ -1 +1 @@
-Subproject commit 01ed01fb0b3112e96eb619e0339d88fb0201982f
+Subproject commit 0af8bba2eb28424b5473121d496ba18ea4bb5d34