<p><b>dwj07@fsu.edu</b> 2012-02-08 14:59:30 -0700 (Wed, 08 Feb 2012)</p><p><br>
-- BRANCH COMMIT --<br>
<br>
Updating test cases to use a checked out namelist input, and replace variables as required.<br>
This allows a test case to use a namelist.input that is valid for the trunk/branch that was checked out.<br>
</p><hr noshade><pre><font color="gray">Copied: branches/ocean_projects/ocean_test_cases_staging/ocean/advective_transport/MPAS-namelist.input.default (from rev 1487, branches/ocean_projects/ocean_test_cases_staging/ocean/advective_transport/MPAS-namelist.input.template)
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/advective_transport/MPAS-namelist.input.default (rev 0)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/advective_transport/MPAS-namelist.input.default 2012-02-08 21:59:30 UTC (rev 1488)
@@ -0,0 +1,111 @@
+&sw_model
+ config_test_case = 0
+ config_time_integration = 'RK4'
+ config_rk_filter_btr_mode = .false.
+ config_dt = *TIME_STEP
+ config_start_time = '0000-01-01_00:00:00'
+ config_run_duration = '0000_00:20:00'
+ config_stats_interval = 1
+ config_initial_stats = .true.
+ config_prescribe_velocities = .true.
+ config_prescribe_thickness = .true.
+/
+&io
+ config_input_name = 'grid.nc'
+ config_output_name = 'output.nc'
+ config_restart_name = 'restart.nc'
+ config_output_interval = '00_00:01:00'
+ config_frames_per_outfile = 1000000
+/
+&restart
+ config_do_restart = .false.
+ config_restart_interval = '120_00:00:00'
+/
+&grid
+ config_vert_grid_type = '*VERT_TYPE'
+ config_rho0 = 1000
+/
+&split_explicit_ts
+ config_n_ts_iter = 2
+ config_n_bcl_iter_beg = 1
+ config_n_bcl_iter_mid = 2
+ config_n_bcl_iter_end = 2
+ config_n_btr_subcycles = 10
+ config_n_btr_cor_iter = 2
+ config_u_correction = .true.
+ config_filter_btr_mode = .false.
+ config_btr_subcycle_loop_factor = 2
+ config_SSH_from = 'avg_flux'
+ config_new_btr_variables_from = 'btr_avg'
+ config_btr_gam1_uWt1 = 0.5
+ config_btr_gam2_SSHWt1 = 1.0
+ config_btr_gam3_uWt2 = 1.0
+ config_btr_solve_SSH2 = .false.
+/
+&hmix
+ config_h_mom_eddy_visc2 = *VISC_H
+ config_h_mom_eddy_visc4 = 0.0
+ config_visc_vorticity_term = .true.
+ config_h_tracer_eddy_diff2 = *VISC_H
+ config_h_tracer_eddy_diff4 = 0.0
+/
+&vmix
+ config_vert_visc_type = 'const'
+ config_vert_diff_type = 'const'
+ config_implicit_vertical_mix = .true.
+ config_convective_visc = 1.0
+ config_convective_diff = 1.0
+ config_bottom_drag_coeff = 1.0e-3
+/
+&vmix_const
+ config_vert_visc = *VISC_V
+ config_vert_diff = *VISC_V
+/
+&vmix_rich
+ config_bkrd_vert_visc = 1.0e-4
+ config_bkrd_vert_diff = 1.0e-4
+ config_rich_mix = 0.005
+/
+&vmix_tanh
+ config_max_visc_tanh = 2.5e-1
+ config_min_visc_tanh = 1.0e-4
+ config_max_diff_tanh = 2.5e-2
+ config_min_diff_tanh = 1.0e-5
+ config_zMid_tanh = -100
+ config_zWidth_tanh = 100
+/
+&eos
+ config_eos_type = 'linear'
+/
+&advection
+ config_vert_tracer_adv = 'spline'
+ config_vert_tracer_adv_order = 3
+ config_tracer_adv_order = 3
+ config_thickness_adv_order = 3
+ config_positive_definite = .false.
+ config_monotonic = .false.
+/
+&restore
+ config_restoreTS = .false.
+ config_restoreT_timescale = 30.0
+ config_restoreS_timescale = 30.0
+/
+&debug
+ config_thick_hadv_off = .true.
+ config_thick_vadv_off = .true.
+ config_tracer_hadv_off = .false.
+ config_tracer_vadv_off = .false.
+ config_tracer_hmix2_off = .false.
+ config_tracer_hmix4_off = .false.
+ config_tracer_vmix_off = .false.
+ config_vel_coriolis_off = .true.
+ config_vel_bottomdrag_off = .true.
+ config_vel_windstress_off = .true.
+ config_vel_rayleigh_off = .true.
+ config_vel_hmix2_off = .true.
+ config_vel_hmix4_off = .true.
+ config_vel_pressuregrad_off = .true.
+ config_vel_vadv_off = .true.
+ config_vel_vmix_off = .true.
+ config_restoring_off = .false.
+/
Deleted: branches/ocean_projects/ocean_test_cases_staging/ocean/advective_transport/MPAS-namelist.input.template
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/advective_transport/MPAS-namelist.input.template 2012-02-08 21:56:13 UTC (rev 1487)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/advective_transport/MPAS-namelist.input.template 2012-02-08 21:59:30 UTC (rev 1488)
@@ -1,111 +0,0 @@
-&sw_model
- config_test_case = 0
- config_time_integration = 'RK4'
- config_rk_filter_btr_mode = .false.
- config_dt = *TIME_STEP
- config_start_time = '0000-01-01_00:00:00'
- config_run_duration = '0000_00:20:00'
- config_stats_interval = 1
- config_initial_stats = .true.
- config_prescribe_velocities = .true.
- config_prescribe_thickness = .true.
-/
-&io
- config_input_name = 'grid.nc'
- config_output_name = 'output.nc'
- config_restart_name = 'restart.nc'
- config_output_interval = '00_00:01:00'
- config_frames_per_outfile = 1000000
-/
-&restart
- config_do_restart = .false.
- config_restart_interval = '120_00:00:00'
-/
-&grid
- config_vert_grid_type = '*VERT_TYPE'
- config_rho0 = 1000
-/
-&split_explicit_ts
- config_n_ts_iter = 2
- config_n_bcl_iter_beg = 1
- config_n_bcl_iter_mid = 2
- config_n_bcl_iter_end = 2
- config_n_btr_subcycles = 10
- config_n_btr_cor_iter = 2
- config_u_correction = .true.
- config_filter_btr_mode = .false.
- config_btr_subcycle_loop_factor = 2
- config_SSH_from = 'avg_flux'
- config_new_btr_variables_from = 'btr_avg'
- config_btr_gam1_uWt1 = 0.5
- config_btr_gam2_SSHWt1 = 1.0
- config_btr_gam3_uWt2 = 1.0
- config_btr_solve_SSH2 = .false.
-/
-&hmix
- config_h_mom_eddy_visc2 = *VISC_H
- config_h_mom_eddy_visc4 = 0.0
- config_visc_vorticity_term = .true.
- config_h_tracer_eddy_diff2 = *VISC_H
- config_h_tracer_eddy_diff4 = 0.0
-/
-&vmix
- config_vert_visc_type = 'const'
- config_vert_diff_type = 'const'
- config_implicit_vertical_mix = .true.
- config_convective_visc = 1.0
- config_convective_diff = 1.0
- config_bottom_drag_coeff = 1.0e-3
-/
-&vmix_const
- config_vert_visc = *VISC_V
- config_vert_diff = *VISC_V
-/
-&vmix_rich
- config_bkrd_vert_visc = 1.0e-4
- config_bkrd_vert_diff = 1.0e-4
- config_rich_mix = 0.005
-/
-&vmix_tanh
- config_max_visc_tanh = 2.5e-1
- config_min_visc_tanh = 1.0e-4
- config_max_diff_tanh = 2.5e-2
- config_min_diff_tanh = 1.0e-5
- config_zMid_tanh = -100
- config_zWidth_tanh = 100
-/
-&eos
- config_eos_type = 'linear'
-/
-&advection
- config_vert_tracer_adv = 'spline'
- config_vert_tracer_adv_order = 3
- config_tracer_adv_order = 3
- config_thickness_adv_order = 3
- config_positive_definite = .false.
- config_monotonic = .false.
-/
-&restore
- config_restoreTS = .false.
- config_restoreT_timescale = 30.0
- config_restoreS_timescale = 30.0
-/
-&debug
- config_thick_hadv_off = .true.
- config_thick_vadv_off = .true.
- config_tracer_hadv_off = .false.
- config_tracer_vadv_off = .false.
- config_tracer_hmix2_off = .false.
- config_tracer_hmix4_off = .false.
- config_tracer_vmix_off = .false.
- config_vel_coriolis_off = .true.
- config_vel_bottomdrag_off = .true.
- config_vel_windstress_off = .true.
- config_vel_rayleigh_off = .true.
- config_vel_hmix2_off = .true.
- config_vel_hmix4_off = .true.
- config_vel_pressuregrad_off = .true.
- config_vel_vadv_off = .true.
- config_vel_vmix_off = .true.
- config_restoring_off = .false.
-/
Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/advective_transport/makeMeshes.sh
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/advective_transport/makeMeshes.sh 2012-02-08 21:56:13 UTC (rev 1487)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/advective_transport/makeMeshes.sh 2012-02-08 21:59:30 UTC (rev 1488)
@@ -9,17 +9,14 @@
VERTLEVS="1 10"
TCNAME="advective_transport"
-SPACINGS="2"
-VERTLEVS="1"
-
###############################################################
## Change reference spacing, time_step, and viscosities here ##
###############################################################
REF_TIME_STEP="5"
REF_VISC_H="0.0"
REF_VISC_V="0.0"
-REF_SPACING="10000.0"
-TOTAL_TIME="17280000" # in seconds
+REF_SPACING="10.0"
+TOTAL_TIME="7200" # in seconds
echo "Building ${TCNAME} meshes"
@@ -33,7 +30,27 @@
X_EXTENT="600"
Y_EXTENT="600"
+X_EXTENT="460"
+Y_EXTENT="460"
+############################################################
+## Setup Default namelist keys and values to update later ##
+############################################################
+
+KEYS[0]="config_time_integration"; VALUES[0]="'RK4'";
+KEYS[1]="config_run_duration"; VALUES[1]="'0200_00:00:00'";
+KEYS[2]="config_input_name"; VALUES[2]="'grid.nc'";
+KEYS[3]="config_output_name"; VALUES[3]="'output.nc'";
+KEYS[4]="config_restart_name"; VALUES[4]="'restart.nc'";
+KEYS[5]="config_output_interval"; VALUES[5]="'01_00:00:00'";
+KEYS[6]="config_do_restart"; VALUES[6]=".false.";
+KEYS[7]="config_vert_grid_type"; VALUES[7]="'zlevel'";
+KEYS[8]="config_rho0"; VALUES[8]="1000";
+KEYS[9]="config_bottom_drag_coeff"; VALUES[9]="1.0e-3";
+KEYS[10]="config_vert_visc_type"; VALUES[10]="'const'";
+KEYS[11]="config_vert_diff_type"; VALUES[11]="'const'";
+
+
#################################################
## Build perfect hex meshes using periodic_hex ##
#################################################
@@ -80,6 +97,25 @@
rm run_paths
fi
+########################################
+## Setup Template Namelist input file ##
+########################################
+if [ -a MPAS-namelist.input.repo ]; then
+ cp MPAS-namelist.input.repo MPAS-namelist.input.temporary
+else
+ cp MPAS-namelist.input.default MPAS-namelist.input.temporary
+fi
+
+i=1
+for ((i=0; i<${#KEYS[@]}; i++));
+do
+ cat MPAS-namelist.input.temporary | sed "s/${KEYS[$i]} .*/${KEYS[$i]} = ${VALUES[$i]}/g" > Temp
+ mv Temp MPAS-namelist.input.temporary
+done
+
+mv MPAS-namelist.input.temporary MPAS-namelist.input.template
+
+
touch run_paths
#################################################################
@@ -177,15 +213,21 @@
mv ${TCNAME}_${NAME}_${VERTLEV}levs* ${NAME}_${VERTLEV}levs/.
## Generate new namelist.input file for test case
- cat MPAS-namelist.input.template | sed "s/*VISC_H/${VISC_H}/g" \
- | sed "s/*VISC_V/${VISC_V}/g" | sed "s/*TIME_STEP/${TIME_STEP}/g" \
- | sed "s/*STATS/${STATS}/g" | sed "s/*VERT_TYPE/${VERT_TYPE}/g" > ${NAME}_${VERTLEV}levs/namelist.input
+ cat MPAS-namelist.input.template \
+ | sed "s/config_h_mom_eddy_visc2 .*/config_h_mom_eddy_visc2 = ${VISC_H}/g" \
+ | sed "s/config_h_tracer_eddy_diff2 .*/config_h_tracer_eddy_diff2 = ${VISC_H}/g" \
+ | sed "s/config_vert_visc .*/config_vert_visc = ${VISC_V}/g" \
+ | sed "s/config_vert_diff .*/config_vert_diff = ${VISC_V}/g" \
+ | sed "s/config_dt .*/config_dt = ${TIME_STEP}/g" \
+ | sed "s/config_stats_interval .*/config_stats_interval = ${STATS}/g" \
+ > ${NAME}_${VERTLEV}levs/namelist.input
done
rm map
done
+rm MPAS-namelist.input.template
rm ${TCNAME}*
rm fort.*
Copied: branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/MPAS-namelist.input.default (from rev 1477, branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/MPAS-namelist.input.template)
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/MPAS-namelist.input.default (rev 0)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/MPAS-namelist.input.default 2012-02-08 21:59:30 UTC (rev 1488)
@@ -0,0 +1,90 @@
+&sw_model
+ config_test_case = 0
+ config_time_integration = 'split_explicit'
+ config_rk_filter_btr_mode = .false.
+ config_dt = *TIME_STEP
+ config_start_time = '0000-01-01_00:00:00'
+ config_run_duration = '0200_00:00:00'
+ config_stats_interval = *STATS
+/
+&io
+ config_input_name = 'grid.nc'
+ config_output_name = 'output.nc'
+ config_restart_name = 'restart.nc'
+ config_output_interval = '00_00:30:00'
+ config_frames_per_outfile = 1000000
+/
+&restart
+ config_do_restart = .false.
+ config_restart_interval = '120_00:00:00'
+/
+&grid
+ config_vert_grid_type = 'zlevel'
+ config_rho0 = 1000
+/
+&split_explicit_ts
+ config_n_ts_iter = 2
+ config_n_bcl_iter_beg = 1
+ config_n_bcl_iter_mid = 2
+ config_n_bcl_iter_end = 2
+ config_n_btr_subcycles = 20
+ config_n_btr_cor_iter = 2
+ config_u_correction = .true.
+ config_filter_btr_mode = .false.
+ config_btr_mom_eddy_visc2 = 0.0
+ config_btr_subcycle_loop_factor = 2
+ config_SSH_from = 'avg_flux'
+ config_new_btr_variables_from = 'btr_avg'
+ config_btr_gam1_uWt1 = 0.5
+ config_btr_gam2_SSHWt1 = 1.0
+ config_btr_gam3_uWt2 = 1.0
+ config_btr_solve_SSH2 = .false.
+/
+&hmix
+ config_h_mom_eddy_visc2 = 0.0
+ config_h_mom_eddy_visc4 = 0.0
+ config_visc_vorticity_term = .true.
+ config_h_tracer_eddy_diff2 = 0.0
+ config_h_tracer_eddy_diff4 = 0.0
+/
+&vmix
+ config_vert_visc_type = 'const'
+ config_vert_diff_type = 'const'
+ config_implicit_vertical_mix = .true.
+ config_convective_visc = 1.0
+ config_convective_diff = 1.0
+ config_bottom_drag_coeff = 1.0e-2
+/
+&vmix_const
+ config_vert_visc = *VISC_V
+ config_vert_diff = *VISC_V
+/
+&vmix_rich
+ config_bkrd_vert_visc = 1.0e-4
+ config_bkrd_vert_diff = 1.0e-4
+ config_rich_mix = 0.005
+/
+&vmix_tanh
+ config_max_visc_tanh = 2.5e-1
+ config_min_visc_tanh = 1.0e-4
+ config_max_diff_tanh = 2.5e-2
+ config_min_diff_tanh = 1.0e-5
+ config_zMid_tanh = -100
+ config_zWidth_tanh = 100
+/
+&eos
+ config_eos_type = 'linear'
+/
+&advection
+ config_vert_tracer_adv = 'spline'
+ config_vert_tracer_adv_order = 3
+ config_tracer_adv_order = 3
+ config_thickness_adv_order = 2
+ config_positive_definite = .false.
+ config_monotonic = .false.
+/
+&restore
+ config_restoreTS = .false.
+ config_restoreT_timescale = 30.0
+ config_restoreS_timescale = 30.0
+/
Deleted: branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/MPAS-namelist.input.template
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/MPAS-namelist.input.template 2012-02-08 21:56:13 UTC (rev 1487)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/MPAS-namelist.input.template 2012-02-08 21:59:30 UTC (rev 1488)
@@ -1,90 +0,0 @@
-&sw_model
- config_test_case = 0
- config_time_integration = 'split_explicit'
- config_rk_filter_btr_mode = .false.
- config_dt = *TIME_STEP
- config_start_time = '0000-01-01_00:00:00'
- config_run_duration = '0200_00:00:00'
- config_stats_interval = *STATS
-/
-&io
- config_input_name = 'grid.nc'
- config_output_name = 'output.nc'
- config_restart_name = 'restart.nc'
- config_output_interval = '00_00:30:00'
- config_frames_per_outfile = 1000000
-/
-&restart
- config_do_restart = .false.
- config_restart_interval = '120_00:00:00'
-/
-&grid
- config_vert_grid_type = 'zlevel'
- config_rho0 = 1000
-/
-&split_explicit_ts
- config_n_ts_iter = 2
- config_n_bcl_iter_beg = 1
- config_n_bcl_iter_mid = 2
- config_n_bcl_iter_end = 2
- config_n_btr_subcycles = 20
- config_n_btr_cor_iter = 2
- config_u_correction = .true.
- config_filter_btr_mode = .false.
- config_btr_mom_eddy_visc2 = 0.0
- config_btr_subcycle_loop_factor = 2
- config_SSH_from = 'avg_flux'
- config_new_btr_variables_from = 'btr_avg'
- config_btr_gam1_uWt1 = 0.5
- config_btr_gam2_SSHWt1 = 1.0
- config_btr_gam3_uWt2 = 1.0
- config_btr_solve_SSH2 = .false.
-/
-&hmix
- config_h_mom_eddy_visc2 = *VISC_H
- config_h_mom_eddy_visc4 = 0.0
- config_visc_vorticity_term = .true.
- config_h_tracer_eddy_diff2 = *VISC_H
- config_h_tracer_eddy_diff4 = 0.0
-/
-&vmix
- config_vert_visc_type = 'const'
- config_vert_diff_type = 'const'
- config_implicit_vertical_mix = .true.
- config_convective_visc = 1.0
- config_convective_diff = 1.0
- config_bottom_drag_coeff = 1.0e-2
-/
-&vmix_const
- config_vert_visc = *VISC_V
- config_vert_diff = *VISC_V
-/
-&vmix_rich
- config_bkrd_vert_visc = 1.0e-4
- config_bkrd_vert_diff = 1.0e-4
- config_rich_mix = 0.005
-/
-&vmix_tanh
- config_max_visc_tanh = 2.5e-1
- config_min_visc_tanh = 1.0e-4
- config_max_diff_tanh = 2.5e-2
- config_min_diff_tanh = 1.0e-5
- config_zMid_tanh = -100
- config_zWidth_tanh = 100
-/
-&eos
- config_eos_type = 'linear'
-/
-&advection
- config_vert_tracer_adv = 'spline'
- config_vert_tracer_adv_order = 3
- config_tracer_adv_order = 3
- config_thickness_adv_order = 2
- config_positive_definite = .false.
- config_monotonic = .false.
-/
-&restore
- config_restoreTS = .false.
- config_restoreT_timescale = 30.0
- config_restoreS_timescale = 30.0
-/
Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/makeMeshes.sh
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/makeMeshes.sh 2012-02-08 21:56:13 UTC (rev 1487)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/makeMeshes.sh 2012-02-08 21:59:30 UTC (rev 1488)
@@ -12,7 +12,7 @@
###############################################################
## Change reference spacing, time_step, and viscosities here ##
###############################################################
-REF_TIME_STEP="200"
+REF_TIME_STEP="400"
REF_VISC_H="10.0"
REF_VISC_V="0.0001"
REF_SPACING="10000.0"
@@ -31,6 +31,23 @@
X_EXTENT="160000"
Y_EXTENT="500000"
+############################################################
+## Setup Default namelist keys and values to update later ##
+############################################################
+
+KEYS[0]="config_time_integration"; VALUES[0]="'RK4'";
+KEYS[1]="config_run_duration"; VALUES[1]="'0200_00:00:00'";
+KEYS[2]="config_input_name"; VALUES[2]="'grid.nc'";
+KEYS[3]="config_output_name"; VALUES[3]="'output.nc'";
+KEYS[4]="config_restart_name"; VALUES[4]="'restart.nc'";
+KEYS[5]="config_output_interval"; VALUES[5]="'01_00:00:00'";
+KEYS[6]="config_do_restart"; VALUES[6]=".false.";
+KEYS[7]="config_vert_grid_type"; VALUES[7]="'zlevel'";
+KEYS[8]="config_rho0"; VALUES[8]="1000";
+KEYS[9]="config_bottom_drag_coeff"; VALUES[9]="1.0e-2";
+KEYS[10]="config_vert_visc_type"; VALUES[10]="'const'";
+KEYS[11]="config_vert_diff_type"; VALUES[11]="'const'";
+
#################################################
## Build perfect hex meshes using periodic_hex ##
#################################################
@@ -77,6 +94,24 @@
rm run_paths
fi
+########################################
+## Setup Template Namelist input file ##
+########################################
+if [ -a MPAS-namelist.input.repo ]; then
+ cp MPAS-namelist.input.repo MPAS-namelist.input.temporary
+else
+ cp MPAS-namelist.input.default MPAS-namelist.input.temporary
+fi
+
+i=1
+for ((i=0; i<${#KEYS[@]}; i++));
+do
+ cat MPAS-namelist.input.temporary | sed "s/${KEYS[$i]} .*/${KEYS[$i]} = ${VALUES[$i]}/g" > Temp
+ mv Temp MPAS-namelist.input.temporary
+done
+
+mv MPAS-namelist.input.temporary MPAS-namelist.input.template
+
touch run_paths
#################################################################
@@ -122,7 +157,7 @@
## Compute scaled spacing, time_step, and viscosities
D_SPACING=`echo "scale=4; ${SPACING}/${REF_SPACING}" | bc`
TIME_STEP=`echo "scale=4; $D_SPACING * $REF_TIME_STEP" | bc`
- VISC_H=`echo "scale=4; ($D_SPACING^4)*${REF_VISC_H}" | bc`
+ VISC_H=`echo "scale=4; ($D_SPACING^2)*${REF_VISC_H}" | bc`
VISC_H=`echo ${REF_VISC_H}` # No Scaling in Horizontal
VISC_V=`echo ${REF_VISC_V}` # No Scaling in Vertocal
STATS=`echo " $TOTAL_TIME / $TIME_STEP / 10 " | bc`
@@ -167,15 +202,21 @@
mv ${TCNAME}_${NAME}_${VERTLEV}levs* ${NAME}_${VERTLEV}levs/.
## Generate new namelist.input file for test case
- cat MPAS-namelist.input.template | sed "s/*VISC_H/${VISC_H}/g" \
- | sed "s/*VISC_V/${VISC_V}/g" | sed "s/*TIME_STEP/${TIME_STEP}/g" \
- | sed "s/*STATS/${STATS}/g" > ${NAME}_${VERTLEV}levs/namelist.input
+ cat MPAS-namelist.input.template \
+ | sed "s/config_h_mom_eddy_visc2 .*/config_h_mom_eddy_visc2 = ${VISC_H}/g" \
+ | sed "s/config_h_tracer_eddy_diff2 .*/config_h_tracer_eddy_diff2 = ${VISC_H}/g" \
+ | sed "s/config_vert_visc .*/config_vert_visc = ${VISC_V}/g" \
+ | sed "s/config_vert_diff .*/config_vert_diff = ${VISC_V}/g" \
+ | sed "s/config_dt .*/config_dt = ${TIME_STEP}/g" \
+ | sed "s/config_stats_interval .*/config_stats_interval = ${STATS}/g" \
+ > ${NAME}_${VERTLEV}levs/namelist.input
done
rm map
done
+rm MPAS-namelist.input.template
rm ${TCNAME}*
rm fort.*
Copied: branches/ocean_projects/ocean_test_cases_staging/ocean/idealized_acc/MPAS-namelist.input.default (from rev 1487, branches/ocean_projects/ocean_test_cases_staging/ocean/idealized_acc/MPAS-namelist.input.template)
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/idealized_acc/MPAS-namelist.input.default (rev 0)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/idealized_acc/MPAS-namelist.input.default 2012-02-08 21:59:30 UTC (rev 1488)
@@ -0,0 +1,90 @@
+&sw_model
+ config_test_case = 0
+ config_time_integration = 'split_explicit'
+ config_rk_filter_btr_mode = .false.
+ config_dt = *TIME_STEP
+ config_start_time = '0000-01-01_00:00:00'
+ config_run_duration = '0000_10:00:00'
+ config_stats_interval = *STATS
+/
+&io
+ config_input_name = 'grid.nc'
+ config_output_name = 'output.nc'
+ config_restart_name = 'restart.nc'
+ config_output_interval = '00_00:30:00'
+ config_frames_per_outfile = 1000000
+/
+&restart
+ config_do_restart = .false.
+ config_restart_interval = '120_00:00:00'
+/
+&grid
+ config_vert_grid_type = 'zlevel'
+ config_rho0 = 1000
+/
+&split_explicit_ts
+ config_n_ts_iter = 2
+ config_n_bcl_iter_beg = 1
+ config_n_bcl_iter_mid = 2
+ config_n_bcl_iter_end = 2
+ config_n_btr_subcycles = 20
+ config_n_btr_cor_iter = 2
+ config_u_correction = .true.
+ config_filter_btr_mode = .false.
+ config_btr_mom_eddy_visc2 = 0.0
+ config_btr_subcycle_loop_factor = 2
+ config_SSH_from = 'avg_flux'
+ config_new_btr_variables_from = 'btr_avg'
+ config_btr_gam1_uWt1 = 0.5
+ config_btr_gam2_SSHWt1 = 1.0
+ config_btr_gam3_uWt2 = 1.0
+ config_btr_solve_SSH2 = .false.
+/
+&hmix
+ config_h_mom_eddy_visc2 = 0.0
+ config_h_mom_eddy_visc4 = *VISC_H
+ config_visc_vorticity_term = .true.
+ config_h_tracer_eddy_diff2 = 0.0
+ config_h_tracer_eddy_diff4 = *VISC_H
+/
+&vmix
+ config_vert_visc_type = 'const'
+ config_vert_diff_type = 'const'
+ config_implicit_vertical_mix = .true.
+ config_convective_visc = 1.0
+ config_convective_diff = 1.0
+ config_bottom_drag_coeff = 1.0e-2
+/
+&vmix_const
+ config_vert_visc = *VISC_V
+ config_vert_diff = *VISC_V
+/
+&vmix_rich
+ config_bkrd_vert_visc = 1.0e-4
+ config_bkrd_vert_diff = 1.0e-4
+ config_rich_mix = 0.005
+/
+&vmix_tanh
+ config_max_visc_tanh = 2.5e-1
+ config_min_visc_tanh = 1.0e-4
+ config_max_diff_tanh = 2.5e-2
+ config_min_diff_tanh = 1.0e-5
+ config_zMid_tanh = -100
+ config_zWidth_tanh = 100
+/
+&eos
+ config_eos_type = 'linear'
+/
+&advection
+ config_vert_tracer_adv = 'spline'
+ config_vert_tracer_adv_order = 3
+ config_tracer_adv_order = 3
+ config_thickness_adv_order = 2
+ config_positive_definite = .false.
+ config_monotonic = .false.
+/
+&restore
+ config_restoreTS = .false.
+ config_restoreT_timescale = 30.0
+ config_restoreS_timescale = 30.0
+/
Deleted: branches/ocean_projects/ocean_test_cases_staging/ocean/idealized_acc/MPAS-namelist.input.template
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/idealized_acc/MPAS-namelist.input.template 2012-02-08 21:56:13 UTC (rev 1487)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/idealized_acc/MPAS-namelist.input.template 2012-02-08 21:59:30 UTC (rev 1488)
@@ -1,90 +0,0 @@
-&sw_model
- config_test_case = 0
- config_time_integration = 'split_explicit'
- config_rk_filter_btr_mode = .false.
- config_dt = *TIME_STEP
- config_start_time = '0000-01-01_00:00:00'
- config_run_duration = '0000_10:00:00'
- config_stats_interval = *STATS
-/
-&io
- config_input_name = 'grid.nc'
- config_output_name = 'output.nc'
- config_restart_name = 'restart.nc'
- config_output_interval = '00_00:30:00'
- config_frames_per_outfile = 1000000
-/
-&restart
- config_do_restart = .false.
- config_restart_interval = '120_00:00:00'
-/
-&grid
- config_vert_grid_type = 'zlevel'
- config_rho0 = 1000
-/
-&split_explicit_ts
- config_n_ts_iter = 2
- config_n_bcl_iter_beg = 1
- config_n_bcl_iter_mid = 2
- config_n_bcl_iter_end = 2
- config_n_btr_subcycles = 20
- config_n_btr_cor_iter = 2
- config_u_correction = .true.
- config_filter_btr_mode = .false.
- config_btr_mom_eddy_visc2 = 0.0
- config_btr_subcycle_loop_factor = 2
- config_SSH_from = 'avg_flux'
- config_new_btr_variables_from = 'btr_avg'
- config_btr_gam1_uWt1 = 0.5
- config_btr_gam2_SSHWt1 = 1.0
- config_btr_gam3_uWt2 = 1.0
- config_btr_solve_SSH2 = .false.
-/
-&hmix
- config_h_mom_eddy_visc2 = 0.0
- config_h_mom_eddy_visc4 = *VISC_H
- config_visc_vorticity_term = .true.
- config_h_tracer_eddy_diff2 = 0.0
- config_h_tracer_eddy_diff4 = *VISC_H
-/
-&vmix
- config_vert_visc_type = 'const'
- config_vert_diff_type = 'const'
- config_implicit_vertical_mix = .true.
- config_convective_visc = 1.0
- config_convective_diff = 1.0
- config_bottom_drag_coeff = 1.0e-2
-/
-&vmix_const
- config_vert_visc = *VISC_V
- config_vert_diff = *VISC_V
-/
-&vmix_rich
- config_bkrd_vert_visc = 1.0e-4
- config_bkrd_vert_diff = 1.0e-4
- config_rich_mix = 0.005
-/
-&vmix_tanh
- config_max_visc_tanh = 2.5e-1
- config_min_visc_tanh = 1.0e-4
- config_max_diff_tanh = 2.5e-2
- config_min_diff_tanh = 1.0e-5
- config_zMid_tanh = -100
- config_zWidth_tanh = 100
-/
-&eos
- config_eos_type = 'linear'
-/
-&advection
- config_vert_tracer_adv = 'spline'
- config_vert_tracer_adv_order = 3
- config_tracer_adv_order = 3
- config_thickness_adv_order = 2
- config_positive_definite = .false.
- config_monotonic = .false.
-/
-&restore
- config_restoreTS = .false.
- config_restoreT_timescale = 30.0
- config_restoreS_timescale = 30.0
-/
Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/idealized_acc/makeMeshes.sh
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/idealized_acc/makeMeshes.sh 2012-02-08 21:56:13 UTC (rev 1487)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/idealized_acc/makeMeshes.sh 2012-02-08 21:59:30 UTC (rev 1488)
@@ -32,6 +32,24 @@
X_EXTENT="320000"
Y_EXTENT="160000"
+############################################################
+## Setup Default namelist keys and values to update later ##
+############################################################
+
+KEYS[0]="config_time_integration"; VALUES[0]="'RK4'";
+KEYS[1]="config_run_duration"; VALUES[1]="'0200_00:00:00'";
+KEYS[2]="config_input_name"; VALUES[2]="'grid.nc'";
+KEYS[3]="config_output_name"; VALUES[3]="'output.nc'";
+KEYS[4]="config_restart_name"; VALUES[4]="'restart.nc'";
+KEYS[5]="config_output_interval"; VALUES[5]="'01_00:00:00'";
+KEYS[6]="config_do_restart"; VALUES[6]=".false.";
+KEYS[7]="config_vert_grid_type"; VALUES[7]="'zlevel'";
+KEYS[8]="config_rho0"; VALUES[8]="1000";
+KEYS[9]="config_bottom_drag_coeff"; VALUES[9]="1.0e-3";
+KEYS[10]="config_vert_visc_type"; VALUES[10]="'const'";
+KEYS[11]="config_vert_diff_type"; VALUES[11]="'const'";
+
+
#################################################
## Build perfect hex meshes using periodic_hex ##
#################################################
@@ -78,6 +96,24 @@
rm run_paths
fi
+########################################
+## Setup Template Namelist input file ##
+########################################
+if [ -a MPAS-namelist.input.repo ]; then
+ cp MPAS-namelist.input.repo MPAS-namelist.input.temporary
+else
+ cp MPAS-namelist.input.default MPAS-namelist.input.temporary
+fi
+
+i=1
+for ((i=0; i<${#KEYS[@]}; i++));
+do
+ cat MPAS-namelist.input.temporary | sed "s/${KEYS[$i]} .*/${KEYS[$i]} = ${VALUES[$i]}/g" > Temp
+ mv Temp MPAS-namelist.input.temporary
+done
+
+mv MPAS-namelist.input.temporary MPAS-namelist.input.template
+
touch run_paths
#################################################################
@@ -170,9 +206,14 @@
mv ${TCNAME}_${NAME}_${VERTLEV}levs_${RIDGESIZE}ridge* ${NAME}_${VERTLEV}levs_${RIDGESIZE}ridge/.
## Generate new namelist.input file for test case
- cat MPAS-namelist.input.template | sed "s/*VISC_H/${VISC_H}/g" \
- | sed "s/*VISC_V/${VISC_V}/g" | sed "s/*TIME_STEP/${TIME_STEP}/g" \
- | sed "s/*STATS/${STATS}/g" > ${NAME}_${VERTLEV}levs_${RIDGESIZE}ridge/namelist.input
+ cat MPAS-namelist.input.template \
+ | sed "s/config_h_mom_eddy_visc2 .*/config_h_mom_eddy_visc2 = ${VISC_H}/g" \
+ | sed "s/config_h_tracer_eddy_diff2 .*/config_h_tracer_eddy_diff2 = ${VISC_H}/g" \
+ | sed "s/config_vert_visc .*/config_vert_visc = ${VISC_V}/g" \
+ | sed "s/config_vert_diff .*/config_vert_diff = ${VISC_V}/g" \
+ | sed "s/config_dt .*/config_dt = ${TIME_STEP}/g" \
+ | sed "s/config_stats_interval .*/config_stats_interval = ${STATS}/g" \
+ > ${NAME}_${VERTLEV}levs_${RIDGESIZE}ridge/namelist.input
done
@@ -180,6 +221,7 @@
done
done
+rm MPAS-namelist.input.template
rm ${TCNAME}*
rm fort.*
Copied: branches/ocean_projects/ocean_test_cases_staging/ocean/internal_waves/MPAS-namelist.input.default (from rev 1487, branches/ocean_projects/ocean_test_cases_staging/ocean/internal_waves/MPAS-namelist.input.template)
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/internal_waves/MPAS-namelist.input.default (rev 0)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/internal_waves/MPAS-namelist.input.default 2012-02-08 21:59:30 UTC (rev 1488)
@@ -0,0 +1,90 @@
+&sw_model
+ config_test_case = 0
+ config_time_integration = 'split_explicit'
+ config_rk_filter_btr_mode = .false.
+ config_dt = *TIME_STEP
+ config_start_time = '0000-01-01_00:00:00'
+ config_run_duration = '0000_06:00:00'
+ config_stats_interval = 1
+/
+&io
+ config_input_name = 'grid.nc'
+ config_output_name = 'output.nc'
+ config_restart_name = 'restart.nc'
+ config_output_interval = '00_00:00:30'
+ config_frames_per_outfile = 1000000
+/
+&restart
+ config_do_restart = .false.
+ config_restart_interval = '120_00:00:00'
+/
+&grid
+ config_vert_grid_type = 'zlevel'
+ config_rho0 = 1000
+/
+&split_explicit_ts
+ config_n_ts_iter = 2
+ config_n_bcl_iter_beg = 1
+ config_n_bcl_iter_mid = 2
+ config_n_bcl_iter_end = 2
+ config_n_btr_subcycles = 20
+ config_n_btr_cor_iter = 2
+ config_u_correction = .true.
+ config_filter_btr_mode = .false.
+ config_btr_mom_eddy_visc2 = 0.0
+ config_btr_subcycle_loop_factor = 2
+ config_SSH_from = 'avg_flux'
+ config_new_btr_variables_from = 'btr_avg'
+ config_btr_gam1_uWt1 = 0.5
+ config_btr_gam2_SSHWt1 = 1.0
+ config_btr_gam3_uWt2 = 1.0
+ config_btr_solve_SSH2 = .false.
+/
+&hmix
+ config_h_mom_eddy_visc2 = *VISC_H
+ config_h_mom_eddy_visc4 = 0.0
+ config_visc_vorticity_term = .true.
+ config_h_tracer_eddy_diff2 = *VISC_H
+ config_h_tracer_eddy_diff4 = 0.0
+/
+&vmix
+ config_vert_visc_type = 'const'
+ config_vert_diff_type = 'const'
+ config_implicit_vertical_mix = .true.
+ config_convective_visc = 1.0
+ config_convective_diff = 1.0
+ config_bottom_drag_coeff = 1.0e-3
+/
+&vmix_const
+ config_vert_visc = *VISC_V
+ config_vert_diff = *VISC_V
+/
+&vmix_rich
+ config_bkrd_vert_visc = 1.0e-4
+ config_bkrd_vert_diff = 1.0e-4
+ config_rich_mix = 0.005
+/
+&vmix_tanh
+ config_max_visc_tanh = 2.5e-1
+ config_min_visc_tanh = 1.0e-4
+ config_max_diff_tanh = 2.5e-2
+ config_min_diff_tanh = 1.0e-5
+ config_zMid_tanh = -100
+ config_zWidth_tanh = 100
+/
+&eos
+ config_eos_type = 'linear'
+/
+&advection
+ config_vert_tracer_adv = 'spline'
+ config_vert_tracer_adv_order = 3
+ config_tracer_adv_order = 3
+ config_thickness_adv_order = 3
+ config_positive_definite = .false.
+ config_monotonic = .false.
+/
+&restore
+ config_restoreTS = .false.
+ config_restoreT_timescale = 30.0
+ config_restoreS_timescale = 30.0
+/
Deleted: branches/ocean_projects/ocean_test_cases_staging/ocean/internal_waves/MPAS-namelist.input.template
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/internal_waves/MPAS-namelist.input.template 2012-02-08 21:56:13 UTC (rev 1487)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/internal_waves/MPAS-namelist.input.template 2012-02-08 21:59:30 UTC (rev 1488)
@@ -1,90 +0,0 @@
-&sw_model
- config_test_case = 0
- config_time_integration = 'split_explicit'
- config_rk_filter_btr_mode = .false.
- config_dt = *TIME_STEP
- config_start_time = '0000-01-01_00:00:00'
- config_run_duration = '0000_06:00:00'
- config_stats_interval = 1
-/
-&io
- config_input_name = 'grid.nc'
- config_output_name = 'output.nc'
- config_restart_name = 'restart.nc'
- config_output_interval = '00_00:00:30'
- config_frames_per_outfile = 1000000
-/
-&restart
- config_do_restart = .false.
- config_restart_interval = '120_00:00:00'
-/
-&grid
- config_vert_grid_type = 'zlevel'
- config_rho0 = 1000
-/
-&split_explicit_ts
- config_n_ts_iter = 2
- config_n_bcl_iter_beg = 1
- config_n_bcl_iter_mid = 2
- config_n_bcl_iter_end = 2
- config_n_btr_subcycles = 20
- config_n_btr_cor_iter = 2
- config_u_correction = .true.
- config_filter_btr_mode = .false.
- config_btr_mom_eddy_visc2 = 0.0
- config_btr_subcycle_loop_factor = 2
- config_SSH_from = 'avg_flux'
- config_new_btr_variables_from = 'btr_avg'
- config_btr_gam1_uWt1 = 0.5
- config_btr_gam2_SSHWt1 = 1.0
- config_btr_gam3_uWt2 = 1.0
- config_btr_solve_SSH2 = .false.
-/
-&hmix
- config_h_mom_eddy_visc2 = *VISC_H
- config_h_mom_eddy_visc4 = 0.0
- config_visc_vorticity_term = .true.
- config_h_tracer_eddy_diff2 = *VISC_H
- config_h_tracer_eddy_diff4 = 0.0
-/
-&vmix
- config_vert_visc_type = 'const'
- config_vert_diff_type = 'const'
- config_implicit_vertical_mix = .true.
- config_convective_visc = 1.0
- config_convective_diff = 1.0
- config_bottom_drag_coeff = 1.0e-3
-/
-&vmix_const
- config_vert_visc = *VISC_V
- config_vert_diff = *VISC_V
-/
-&vmix_rich
- config_bkrd_vert_visc = 1.0e-4
- config_bkrd_vert_diff = 1.0e-4
- config_rich_mix = 0.005
-/
-&vmix_tanh
- config_max_visc_tanh = 2.5e-1
- config_min_visc_tanh = 1.0e-4
- config_max_diff_tanh = 2.5e-2
- config_min_diff_tanh = 1.0e-5
- config_zMid_tanh = -100
- config_zWidth_tanh = 100
-/
-&eos
- config_eos_type = 'linear'
-/
-&advection
- config_vert_tracer_adv = 'spline'
- config_vert_tracer_adv_order = 3
- config_tracer_adv_order = 3
- config_thickness_adv_order = 3
- config_positive_definite = .false.
- config_monotonic = .false.
-/
-&restore
- config_restoreTS = .false.
- config_restoreT_timescale = 30.0
- config_restoreS_timescale = 30.0
-/
Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/internal_waves/makeMeshes.sh
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/internal_waves/makeMeshes.sh 2012-02-08 21:56:13 UTC (rev 1487)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/internal_waves/makeMeshes.sh 2012-02-08 21:59:30 UTC (rev 1488)
@@ -32,6 +32,24 @@
Y_EXTENT="250000"
AMPLITUDES="2 0.2"
+############################################################
+## Setup Default namelist keys and values to update later ##
+############################################################
+
+KEYS[0]="config_time_integration"; VALUES[0]="'RK4'";
+KEYS[1]="config_run_duration"; VALUES[1]="'0200_00:00:00'";
+KEYS[2]="config_input_name"; VALUES[2]="'grid.nc'";
+KEYS[3]="config_output_name"; VALUES[3]="'output.nc'";
+KEYS[4]="config_restart_name"; VALUES[4]="'restart.nc'";
+KEYS[5]="config_output_interval"; VALUES[5]="'01_00:00:00'";
+KEYS[6]="config_do_restart"; VALUES[6]=".false.";
+KEYS[7]="config_vert_grid_type"; VALUES[7]="'zlevel'";
+KEYS[8]="config_rho0"; VALUES[8]="1000";
+KEYS[9]="config_bottom_drag_coeff"; VALUES[9]="1.0e-3";
+KEYS[10]="config_vert_visc_type"; VALUES[10]="'const'";
+KEYS[11]="config_vert_diff_type"; VALUES[11]="'const'";
+
+
#################################################
## Build perfect hex meshes using periodic_hex ##
#################################################
@@ -77,6 +95,24 @@
rm run_paths
fi
+########################################
+## Setup Template Namelist input file ##
+########################################
+if [ -a MPAS-namelist.input.repo ]; then
+ cp MPAS-namelist.input.repo MPAS-namelist.input.temporary
+else
+ cp MPAS-namelist.input.default MPAS-namelist.input.temporary
+fi
+
+i=1
+for ((i=0; i<${#KEYS[@]}; i++));
+do
+ cat MPAS-namelist.input.temporary | sed "s/${KEYS[$i]} .*/${KEYS[$i]} = ${VALUES[$i]}/g" > Temp
+ mv Temp MPAS-namelist.input.temporary
+done
+
+mv MPAS-namelist.input.temporary MPAS-namelist.input.template
+
touch run_paths
#################################################################
@@ -168,9 +204,14 @@
mv ${TCNAME}_${NAME}_${VERTLEV}levs_${AMPLITUDE}amp* ${NAME}_${VERTLEV}levs_${AMPLITUDE}amp/.
## Generate new namelist.input file for test case
- cat MPAS-namelist.input.template | sed "s/*VISC_H/${VISC_H}/g" \
- | sed "s/*VISC_V/${VISC_V}/g" | sed "s/*TIME_STEP/${TIME_STEP}/g" \
- | sed "s/*STATS/${STATS}/g" > ${NAME}_${VERTLEV}levs_${AMPLITUDE}amp/namelist.input
+ cat MPAS-namelist.input.template \
+ | sed "s/config_h_mom_eddy_visc2 .*/config_h_mom_eddy_visc2 = ${VISC_H}/g" \
+ | sed "s/config_h_tracer_eddy_diff2 .*/config_h_tracer_eddy_diff2 = ${VISC_H}/g" \
+ | sed "s/config_vert_visc .*/config_vert_visc = ${VISC_V}/g" \
+ | sed "s/config_vert_diff .*/config_vert_diff = ${VISC_V}/g" \
+ | sed "s/config_dt .*/config_dt = ${TIME_STEP}/g" \
+ | sed "s/config_stats_interval .*/config_stats_interval = ${STATS}/g" \
+ > ${NAME}_${VERTLEV}levs_${AMPLITUDE}amp/namelist.input
done
@@ -178,6 +219,7 @@
done
done
+rm MPAS-namelist.input.template
rm ${TCNAME}*
rm fort.*
Copied: branches/ocean_projects/ocean_test_cases_staging/ocean/lock_exchange/MPAS-namelist.input.default (from rev 1487, branches/ocean_projects/ocean_test_cases_staging/ocean/lock_exchange/MPAS-namelist.input.template)
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/lock_exchange/MPAS-namelist.input.default (rev 0)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/lock_exchange/MPAS-namelist.input.default 2012-02-08 21:59:30 UTC (rev 1488)
@@ -0,0 +1,90 @@
+&sw_model
+ config_test_case = 0
+ config_time_integration = 'split_explicit'
+ config_rk_filter_btr_mode = .false.
+ config_dt = *TIME_STEP
+ config_start_time = '0000-01-01_00:00:00'
+ config_run_duration = '0000_17:00:00'
+ config_stats_interval = 1
+/
+&io
+ config_input_name = 'grid.nc'
+ config_output_name = 'output.nc'
+ config_restart_name = 'restart.nc'
+ config_output_interval = '00_00:10:00'
+ config_frames_per_outfile = 1000000
+/
+&restart
+ config_do_restart = .false.
+ config_restart_interval = '120_00:00:00'
+/
+&grid
+ config_vert_grid_type = 'zlevel'
+ config_rho0 = 1000
+/
+&split_explicit_ts
+ config_n_ts_iter = 2
+ config_n_bcl_iter_beg = 1
+ config_n_bcl_iter_mid = 2
+ config_n_bcl_iter_end = 2
+ config_n_btr_subcycles = 10
+ config_n_btr_cor_iter = 2
+ config_u_correction = .true.
+ config_filter_btr_mode = .false.
+ config_btr_mom_eddy_visc2 = 0.0
+ config_btr_subcycle_loop_factor = 2
+ config_SSH_from = 'avg_flux'
+ config_new_btr_variables_from = 'btr_avg'
+ config_btr_gam1_uWt1 = 0.5
+ config_btr_gam2_SSHWt1 = 1.0
+ config_btr_gam3_uWt2 = 1.0
+ config_btr_solve_SSH2 = .false.
+/
+&hmix
+ config_h_mom_eddy_visc2 = *VISC_H
+ config_h_mom_eddy_visc4 = 0.0
+ config_visc_vorticity_term = .true.
+ config_h_tracer_eddy_diff2 = *VISC_H
+ config_h_tracer_eddy_diff4 = 0.0
+/
+&vmix
+ config_vert_visc_type = 'const'
+ config_vert_diff_type = 'const'
+ config_implicit_vertical_mix = .true.
+ config_convective_visc = 1.0
+ config_convective_diff = 1.0
+ config_bottom_drag_coeff = 1.0e-3
+/
+&vmix_const
+ config_vert_visc = *VISC_V
+ config_vert_diff = *VISC_V
+/
+&vmix_rich
+ config_bkrd_vert_visc = 1.0e-4
+ config_bkrd_vert_diff = 1.0e-4
+ config_rich_mix = 0.005
+/
+&vmix_tanh
+ config_max_visc_tanh = 2.5e-1
+ config_min_visc_tanh = 1.0e-4
+ config_max_diff_tanh = 2.5e-2
+ config_min_diff_tanh = 1.0e-5
+ config_zMid_tanh = -100
+ config_zWidth_tanh = 100
+/
+&eos
+ config_eos_type = 'linear'
+/
+&advection
+ config_vert_tracer_adv = 'spline'
+ config_vert_tracer_adv_order = 3
+ config_tracer_adv_order = 3
+ config_thickness_adv_order = 3
+ config_positive_definite = .false.
+ config_monotonic = .false.
+/
+&restore
+ config_restoreTS = .false.
+ config_restoreT_timescale = 30.0
+ config_restoreS_timescale = 30.0
+/
Deleted: branches/ocean_projects/ocean_test_cases_staging/ocean/lock_exchange/MPAS-namelist.input.template
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/lock_exchange/MPAS-namelist.input.template 2012-02-08 21:56:13 UTC (rev 1487)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/lock_exchange/MPAS-namelist.input.template 2012-02-08 21:59:30 UTC (rev 1488)
@@ -1,90 +0,0 @@
-&sw_model
- config_test_case = 0
- config_time_integration = 'split_explicit'
- config_rk_filter_btr_mode = .false.
- config_dt = *TIME_STEP
- config_start_time = '0000-01-01_00:00:00'
- config_run_duration = '0000_17:00:00'
- config_stats_interval = 1
-/
-&io
- config_input_name = 'grid.nc'
- config_output_name = 'output.nc'
- config_restart_name = 'restart.nc'
- config_output_interval = '00_00:10:00'
- config_frames_per_outfile = 1000000
-/
-&restart
- config_do_restart = .false.
- config_restart_interval = '120_00:00:00'
-/
-&grid
- config_vert_grid_type = 'zlevel'
- config_rho0 = 1000
-/
-&split_explicit_ts
- config_n_ts_iter = 2
- config_n_bcl_iter_beg = 1
- config_n_bcl_iter_mid = 2
- config_n_bcl_iter_end = 2
- config_n_btr_subcycles = 10
- config_n_btr_cor_iter = 2
- config_u_correction = .true.
- config_filter_btr_mode = .false.
- config_btr_mom_eddy_visc2 = 0.0
- config_btr_subcycle_loop_factor = 2
- config_SSH_from = 'avg_flux'
- config_new_btr_variables_from = 'btr_avg'
- config_btr_gam1_uWt1 = 0.5
- config_btr_gam2_SSHWt1 = 1.0
- config_btr_gam3_uWt2 = 1.0
- config_btr_solve_SSH2 = .false.
-/
-&hmix
- config_h_mom_eddy_visc2 = *VISC_H
- config_h_mom_eddy_visc4 = 0.0
- config_visc_vorticity_term = .true.
- config_h_tracer_eddy_diff2 = *VISC_H
- config_h_tracer_eddy_diff4 = 0.0
-/
-&vmix
- config_vert_visc_type = 'const'
- config_vert_diff_type = 'const'
- config_implicit_vertical_mix = .true.
- config_convective_visc = 1.0
- config_convective_diff = 1.0
- config_bottom_drag_coeff = 1.0e-3
-/
-&vmix_const
- config_vert_visc = *VISC_V
- config_vert_diff = *VISC_V
-/
-&vmix_rich
- config_bkrd_vert_visc = 1.0e-4
- config_bkrd_vert_diff = 1.0e-4
- config_rich_mix = 0.005
-/
-&vmix_tanh
- config_max_visc_tanh = 2.5e-1
- config_min_visc_tanh = 1.0e-4
- config_max_diff_tanh = 2.5e-2
- config_min_diff_tanh = 1.0e-5
- config_zMid_tanh = -100
- config_zWidth_tanh = 100
-/
-&eos
- config_eos_type = 'linear'
-/
-&advection
- config_vert_tracer_adv = 'spline'
- config_vert_tracer_adv_order = 3
- config_tracer_adv_order = 3
- config_thickness_adv_order = 3
- config_positive_definite = .false.
- config_monotonic = .false.
-/
-&restore
- config_restoreTS = .false.
- config_restoreT_timescale = 30.0
- config_restoreS_timescale = 30.0
-/
Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/lock_exchange/makeMeshes.sh
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/lock_exchange/makeMeshes.sh 2012-02-08 21:56:13 UTC (rev 1487)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/lock_exchange/makeMeshes.sh 2012-02-08 21:59:30 UTC (rev 1488)
@@ -17,7 +17,7 @@
REF_VISC_H="10.0"
REF_VISC_V="0.1"
REF_SPACING="500.0"
-TOTAL_TIME="1468800" # in seconds
+TOTAL_TIME="61200" # in seconds
echo "Building ${TCNAME} meshes"
@@ -31,6 +31,24 @@
Y_EXTENT="200000"
+############################################################
+## Setup Default namelist keys and values to update later ##
+############################################################
+
+KEYS[0]="config_time_integration"; VALUES[0]="'RK4'";
+KEYS[1]="config_run_duration"; VALUES[1]="'0000_16:00:00'";
+KEYS[2]="config_input_name"; VALUES[2]="'grid.nc'";
+KEYS[3]="config_output_name"; VALUES[3]="'output.nc'";
+KEYS[4]="config_restart_name"; VALUES[4]="'restart.nc'";
+KEYS[5]="config_output_interval"; VALUES[5]="'00_01:00:00'";
+KEYS[6]="config_do_restart"; VALUES[6]=".false.";
+KEYS[7]="config_vert_grid_type"; VALUES[7]="'zlevel'";
+KEYS[8]="config_rho0"; VALUES[8]="1000";
+KEYS[9]="config_bottom_drag_coeff"; VALUES[9]="1.0e-3";
+KEYS[10]="config_vert_visc_type"; VALUES[10]="'const'";
+KEYS[11]="config_vert_diff_type"; VALUES[11]="'const'";
+
+
#################################################
## Build perfect hex meshes using periodic_hex ##
#################################################
@@ -76,6 +94,24 @@
rm run_paths
fi
+########################################
+## Setup Template Namelist input file ##
+########################################
+if [ -a MPAS-namelist.input.repo ]; then
+ cp MPAS-namelist.input.repo MPAS-namelist.input.temporary
+else
+ cp MPAS-namelist.input.default MPAS-namelist.input.temporary
+fi
+
+i=1
+for ((i=0; i<${#KEYS[@]}; i++));
+do
+ cat MPAS-namelist.input.temporary | sed "s/${KEYS[$i]} .*/${KEYS[$i]} = ${VALUES[$i]}/g" > Temp
+ mv Temp MPAS-namelist.input.temporary
+done
+
+mv MPAS-namelist.input.temporary MPAS-namelist.input.template
+
touch run_paths
#################################################################
@@ -165,15 +201,21 @@
mv ${TCNAME}_${NAME}_${VERTLEV}levs* ${NAME}_${VERTLEV}levs/.
## Generate new namelist.input file for test case
- cat MPAS-namelist.input.template | sed "s/*VISC_H/${VISC_H}/g" \
- | sed "s/*VISC_V/${VISC_V}/g" | sed "s/*TIME_STEP/${TIME_STEP}/g" \
- | sed "s/*STATS/${STATS}/g" > ${NAME}_${VERTLEV}levs/namelist.input
+ cat MPAS-namelist.input.template \
+ | sed "s/config_h_mom_eddy_visc2 .*/config_h_mom_eddy_visc2 = ${VISC_H}/g" \
+ | sed "s/config_h_tracer_eddy_diff2 .*/config_h_tracer_eddy_diff2 = ${VISC_H}/g" \
+ | sed "s/config_vert_visc .*/config_vert_visc = ${VISC_V}/g" \
+ | sed "s/config_vert_diff .*/config_vert_diff = ${VISC_V}/g" \
+ | sed "s/config_dt .*/config_dt = ${TIME_STEP}/g" \
+ | sed "s/config_stats_interval .*/config_stats_interval = ${STATS}/g" \
+ > ${NAME}_${VERTLEV}levs/namelist.input
done
rm map
done
+rm MPAS-namelist.input.template
rm ${TCNAME}*
rm fort.*
Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/oceanTestCases.sh
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/oceanTestCases.sh 2012-02-08 21:56:13 UTC (rev 1487)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/oceanTestCases.sh 2012-02-08 21:59:30 UTC (rev 1488)
@@ -42,6 +42,7 @@
setup_mpas () { #{{{
rm -f .run_info
rm -f run_paths
+ rm -f .mpas_namelist.input
touch .run_info
## Check out mpas from repository
@@ -71,6 +72,8 @@
## Create a header of a Makefile for use in compiling subcode with the same compiler.
echo "${COMPILE_SET}:" > .Makefile.front
echo -e "\t$MAKE_OPTS" >> .Makefile.front
+
+ cp mpas/namelist.input.ocean .mpas_namelist.input
} #}}}
## Setup test case
@@ -87,6 +90,7 @@
fi
cp .run_info run_info
+ cp .mpas_namelist.input ${CASE}/MPAS-namelist.input.repo
cd ${CASE}
## Call script to setup run directories, and meshes if needed
@@ -218,6 +222,7 @@
echo "Cleaning MPAS"
rm -rf mpas
rm -f .run_info .Makefile.front
+ rm -f .mpas_namelist.input
} #}}}
## Clean up test case directory
@@ -226,6 +231,7 @@
cd ${CASE}
rm -rf *m_*levs* submits
rm -f run_paths
+ rm -f MPAS-namelist.input.repo
cd ${CUR_DIR}
rm -f *${CASE}.sh
Copied: branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/MPAS-namelist.input.default (from rev 1487, branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/MPAS-namelist.input.template)
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/MPAS-namelist.input.default (rev 0)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/MPAS-namelist.input.default 2012-02-08 21:59:30 UTC (rev 1488)
@@ -0,0 +1,90 @@
+&sw_model
+ config_test_case = 0
+ config_time_integration = 'split_explicit'
+ config_rk_filter_btr_mode = .false.
+ config_dt = *TIME_STEP
+ config_start_time = '0000-01-01_00:00:00'
+ config_run_duration = '0000_06:00:00'
+ config_stats_interval = 1
+/
+&io
+ config_input_name = 'grid.nc'
+ config_output_name = 'output.nc'
+ config_restart_name = 'restart.nc'
+ config_output_interval = '00_00:00:30'
+ config_frames_per_outfile = 1000000
+/
+&restart
+ config_do_restart = .false.
+ config_restart_interval = '120_00:00:00'
+/
+&grid
+ config_vert_grid_type = 'zlevel'
+ config_rho0 = 1000
+/
+&split_explicit_ts
+ config_n_ts_iter = 2
+ config_n_bcl_iter_beg = 1
+ config_n_bcl_iter_mid = 2
+ config_n_bcl_iter_end = 2
+ config_n_btr_subcycles = 20
+ config_n_btr_cor_iter = 2
+ config_u_correction = .true.
+ config_filter_btr_mode = .false.
+ config_btr_mom_eddy_visc2 = 0.0
+ config_btr_subcycle_loop_factor = 2
+ config_SSH_from = 'avg_flux'
+ config_new_btr_variables_from = 'btr_avg'
+ config_btr_gam1_uWt1 = 0.5
+ config_btr_gam2_SSHWt1 = 1.0
+ config_btr_gam3_uWt2 = 1.0
+ config_btr_solve_SSH2 = .false.
+/
+&hmix
+ config_h_mom_eddy_visc2 = *VISC_H
+ config_h_mom_eddy_visc4 = 0.0
+ config_visc_vorticity_term = .true.
+ config_h_tracer_eddy_diff2 = *VISC_H
+ config_h_tracer_eddy_diff4 = 0.0
+/
+&vmix
+ config_vert_visc_type = 'const'
+ config_vert_diff_type = 'const'
+ config_implicit_vertical_mix = .true.
+ config_convective_visc = 1.0
+ config_convective_diff = 1.0
+ config_bottom_drag_coeff = 1.0e-3
+/
+&vmix_const
+ config_vert_visc = *VISC_V
+ config_vert_diff = *VISC_V
+/
+&vmix_rich
+ config_bkrd_vert_visc = 1.0e-4
+ config_bkrd_vert_diff = 1.0e-4
+ config_rich_mix = 0.005
+/
+&vmix_tanh
+ config_max_visc_tanh = 2.5e-1
+ config_min_visc_tanh = 1.0e-4
+ config_max_diff_tanh = 2.5e-2
+ config_min_diff_tanh = 1.0e-5
+ config_zMid_tanh = -100
+ config_zWidth_tanh = 100
+/
+&eos
+ config_eos_type = 'linear'
+/
+&advection
+ config_vert_tracer_adv = 'spline'
+ config_vert_tracer_adv_order = 3
+ config_tracer_adv_order = 3
+ config_thickness_adv_order = 3
+ config_positive_definite = .false.
+ config_monotonic = .false.
+/
+&restore
+ config_restoreTS = .false.
+ config_restoreT_timescale = 30.0
+ config_restoreS_timescale = 30.0
+/
Deleted: branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/MPAS-namelist.input.template
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/MPAS-namelist.input.template 2012-02-08 21:56:13 UTC (rev 1487)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/MPAS-namelist.input.template 2012-02-08 21:59:30 UTC (rev 1488)
@@ -1,90 +0,0 @@
-&sw_model
- config_test_case = 0
- config_time_integration = 'split_explicit'
- config_rk_filter_btr_mode = .false.
- config_dt = *TIME_STEP
- config_start_time = '0000-01-01_00:00:00'
- config_run_duration = '0000_06:00:00'
- config_stats_interval = 1
-/
-&io
- config_input_name = 'grid.nc'
- config_output_name = 'output.nc'
- config_restart_name = 'restart.nc'
- config_output_interval = '00_00:00:30'
- config_frames_per_outfile = 1000000
-/
-&restart
- config_do_restart = .false.
- config_restart_interval = '120_00:00:00'
-/
-&grid
- config_vert_grid_type = 'zlevel'
- config_rho0 = 1000
-/
-&split_explicit_ts
- config_n_ts_iter = 2
- config_n_bcl_iter_beg = 1
- config_n_bcl_iter_mid = 2
- config_n_bcl_iter_end = 2
- config_n_btr_subcycles = 20
- config_n_btr_cor_iter = 2
- config_u_correction = .true.
- config_filter_btr_mode = .false.
- config_btr_mom_eddy_visc2 = 0.0
- config_btr_subcycle_loop_factor = 2
- config_SSH_from = 'avg_flux'
- config_new_btr_variables_from = 'btr_avg'
- config_btr_gam1_uWt1 = 0.5
- config_btr_gam2_SSHWt1 = 1.0
- config_btr_gam3_uWt2 = 1.0
- config_btr_solve_SSH2 = .false.
-/
-&hmix
- config_h_mom_eddy_visc2 = *VISC_H
- config_h_mom_eddy_visc4 = 0.0
- config_visc_vorticity_term = .true.
- config_h_tracer_eddy_diff2 = *VISC_H
- config_h_tracer_eddy_diff4 = 0.0
-/
-&vmix
- config_vert_visc_type = 'const'
- config_vert_diff_type = 'const'
- config_implicit_vertical_mix = .true.
- config_convective_visc = 1.0
- config_convective_diff = 1.0
- config_bottom_drag_coeff = 1.0e-3
-/
-&vmix_const
- config_vert_visc = *VISC_V
- config_vert_diff = *VISC_V
-/
-&vmix_rich
- config_bkrd_vert_visc = 1.0e-4
- config_bkrd_vert_diff = 1.0e-4
- config_rich_mix = 0.005
-/
-&vmix_tanh
- config_max_visc_tanh = 2.5e-1
- config_min_visc_tanh = 1.0e-4
- config_max_diff_tanh = 2.5e-2
- config_min_diff_tanh = 1.0e-5
- config_zMid_tanh = -100
- config_zWidth_tanh = 100
-/
-&eos
- config_eos_type = 'linear'
-/
-&advection
- config_vert_tracer_adv = 'spline'
- config_vert_tracer_adv_order = 3
- config_tracer_adv_order = 3
- config_thickness_adv_order = 3
- config_positive_definite = .false.
- config_monotonic = .false.
-/
-&restore
- config_restoreTS = .false.
- config_restoreT_timescale = 30.0
- config_restoreS_timescale = 30.0
-/
Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/makeMeshes.sh
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/makeMeshes.sh 2012-02-08 21:56:13 UTC (rev 1487)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/overflow/makeMeshes.sh 2012-02-08 21:59:30 UTC (rev 1488)
@@ -32,6 +32,24 @@
Y_EXTENT="200000"
+############################################################
+## Setup Default namelist keys and values to update later ##
+############################################################
+
+KEYS[0]="config_time_integration"; VALUES[0]="'RK4'";
+KEYS[1]="config_run_duration"; VALUES[1]="'0000_06:00:00'";
+KEYS[2]="config_input_name"; VALUES[2]="'grid.nc'";
+KEYS[3]="config_output_name"; VALUES[3]="'output.nc'";
+KEYS[4]="config_restart_name"; VALUES[4]="'restart.nc'";
+KEYS[5]="config_output_interval"; VALUES[5]="'00_00:30:00'";
+KEYS[6]="config_do_restart"; VALUES[6]=".false.";
+KEYS[7]="config_vert_grid_type"; VALUES[7]="'zlevel'";
+KEYS[8]="config_rho0"; VALUES[8]="1000";
+KEYS[9]="config_bottom_drag_coeff"; VALUES[9]="1.0e-3";
+KEYS[10]="config_vert_visc_type"; VALUES[10]="'const'";
+KEYS[11]="config_vert_diff_type"; VALUES[11]="'const'";
+
+
#################################################
## Build perfect hex meshes using periodic_hex ##
#################################################
@@ -77,6 +95,24 @@
rm run_paths
fi
+########################################
+## Setup Template Namelist input file ##
+########################################
+if [ -a MPAS-namelist.input.repo ]; then
+ cp MPAS-namelist.input.repo MPAS-namelist.input.temporary
+else
+ cp MPAS-namelist.input.default MPAS-namelist.input.temporary
+fi
+
+i=1
+for ((i=0; i<${#KEYS[@]}; i++));
+do
+ cat MPAS-namelist.input.temporary | sed "s/${KEYS[$i]} .*/${KEYS[$i]} = ${VALUES[$i]}/g" > Temp
+ mv Temp MPAS-namelist.input.temporary
+done
+
+mv MPAS-namelist.input.temporary MPAS-namelist.input.template
+
touch run_paths
#################################################################
@@ -166,15 +202,22 @@
mv ${TCNAME}_${NAME}_${VERTLEV}levs* ${NAME}_${VERTLEV}levs/.
## Generate new namelist.input file for test case
- cat MPAS-namelist.input.template | sed "s/*VISC_H/${VISC_H}/g" \
- | sed "s/*VISC_V/${VISC_V}/g" | sed "s/*TIME_STEP/${TIME_STEP}/g" \
- | sed "s/*STATS/${STATS}/g" > ${NAME}_${VERTLEV}levs/namelist.input
+ cat MPAS-namelist.input.template \
+ | sed "s/config_h_mom_eddy_visc2 .*/config_h_mom_eddy_visc2 = ${VISC_H}/g" \
+ | sed "s/config_h_tracer_eddy_diff2 .*/config_h_tracer_eddy_diff2 = ${VISC_H}/g" \
+ | sed "s/config_vert_visc .*/config_vert_visc = ${VISC_V}/g" \
+ | sed "s/config_vert_diff .*/config_vert_diff = ${VISC_V}/g" \
+ | sed "s/config_dt .*/config_dt = ${TIME_STEP}/g" \
+ | sed "s/config_stats_interval .*/config_stats_interval = ${STATS}/g" \
+ > ${NAME}_${VERTLEV}levs/namelist.input
+
done
rm map
done
+rm MPAS-namelist.input.template
rm ${TCNAME}*
rm fort.*
</font>
</pre>