Merge PR MPAS-Dev#49 'ocean/remove_landlocked_cells_script' into ocea…

…n/develop This is needed to create a V3 mesh with COMPASS. It has a matching PR in MPAS-Tools. NON-BFB MATCH for ocean nightly regression suite for global (QU240) cases when tested against previous commit. The QU240 will have a different number of cells. In order for new scripts to work, this version of MPAS-Model must be run with this commit of MPAS-Tools or later: f825edf Merge PR MPAS-Dev#220 'ocean/remove_landlocked_cells' into master
matthewhoffman · Jun 11, 2018 · 0b984bd · 0b984bd
2 parents 2007545 + 81c1b4f
commit 0b984bd
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Showing 29 changed files with 92 additions and 16 deletions.
diff --git a/testing_and_setup/compass/general.config.ocean b/testing_and_setup/compass/general.config.ocean
@@ -34,7 +34,6 @@ mask_creator = FULL_PATH_TO_MASK_CREATOR
 metis = FULL_PATH_TO_METIS
 mesh_generator = FULL_PATH_TO_EXECUTABLE_MESH_GENERATION_SCRIPT
 
-
 # The paths section describes paths that are used within the ocean core test
 # cases.
 [paths]
@@ -47,4 +46,5 @@ mesh_generator = FULL_PATH_TO_EXECUTABLE_MESH_GENERATION_SCRIPT
 mesh_database = FULL_PATH_TO_LOCAL_MESH_DATABASE
 initial_condition_database = FULL_PATH_TO_LOCAL_INITIAL_CONDITION_DATABASE
 geometric_features = FULL_PATH_TO_LOCAL_CHECKOUT_OF_GEOMETRIC_FEATURES_DATABASE
+mpas_tools = FULL_PATH_TO_MPAS_TOOLS_REPO
 mesh_scripts = FULL_PATH_TO_LOCAL_CHECKOUT_OF_MESH_GENERATION_SCRIPTS
diff --git a/testing_and_setup/compass/ocean/global_ocean/EC120to60/default/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/EC120to60/default/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.EC.120-60km.160115.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/EC120to60/spin_up/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/EC120to60/spin_up/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.EC.120-60km.160115.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/EC60to30/default/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/EC60to30/default/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.EC.60-30km.160115.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/EC60to30/five_cell/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/EC60to30/five_cell/config_init1.xml
@@ -10,6 +10,8 @@
 
 	<add_link source_path="mesh_database" source="mesh.EC.60-30km.160115.nc" dest="base_mesh.nc"/>
 	<add_link source_path="compass" source="ocean/global_ocean/EC60to30/five_cell/land_coverage_5_cell.geojson" dest="land_coverage_5_cell.geojson"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./MpasMaskCreator.x">

diff --git a/testing_and_setup/compass/ocean/global_ocean/EC60to30/single_cell/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/EC60to30/single_cell/config_init1.xml
@@ -10,6 +10,8 @@
 
 	<add_link source_path="mesh_database" source="mesh.EC.60-30km.160115.nc" dest="base_mesh.nc"/>
 	<add_link source_path="compass" source="ocean/global_ocean/EC60to30/single_cell/land_coverage_1_cell.geojson" dest="land_coverage_1_cell.geojson"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./MpasMaskCreator.x">

diff --git a/testing_and_setup/compass/ocean/global_ocean/EC60to30/spin_up/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/EC60to30/spin_up/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.EC.60-30km.160115.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/EC60to30/with_land_ice/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/EC60to30/with_land_ice/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.EC.60-30km.160115.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/QU120/default/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/QU120/default/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.QU.120km.151026.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/QU120/ecosys_60_layer/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/QU120/ecosys_60_layer/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.QU.120km.151026.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/QU120/with_land_ice/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/QU120/with_land_ice/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.QU.120km.151026.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/QU240/analysis_test/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/QU240/analysis_test/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.QU.10242.151022.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/QU240/default/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/QU240/default/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.QU.10242.151022.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/QU240/performance_test/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/QU240/performance_test/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.QU.10242.151022.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/QU240/restart_test/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/QU240/restart_test/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.QU.10242.151022.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/QU240/rk4_blocks_test/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/QU240/rk4_blocks_test/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.QU.10242.151022.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/QU240/se_blocks_test/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/QU240/se_blocks_test/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.QU.10242.151022.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/QU240/with_land_ice/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/QU240/with_land_ice/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.QU.10242.151022.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/QU240/with_land_ice_no_iter/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/QU240/with_land_ice_no_iter/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.QU.10242.151022.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/QU240/zstar_128_layers/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/QU240/zstar_128_layers/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.QU.10242.151022.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/QU480/default/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/QU480/default/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.QU.480km.151026.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/RRS15to5/default/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/RRS15to5/default/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.RRS.15-5km.160214.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/RRS15to5/spin_up/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/RRS15to5/spin_up/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.RRS.15-5km.160214.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/RRS18to6/default/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/RRS18to6/default/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.RRS.18-6km.160828.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/RRS18to6/spin_up/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/RRS18to6/spin_up/config_init1.xml
@@ -11,6 +11,8 @@
 	<add_link source_path="mesh_database" source="mesh.RRS.18-6km.160828.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">

diff --git a/testing_and_setup/compass/ocean/global_ocean/RRS30to10/default/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/RRS30to10/default/config_init1.xml
@@ -11,10 +11,13 @@
 	<add_link source_path="mesh_database" source="mesh.RRS.30-10km.160214.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">
 			<argument flag="-p">geometric_features</argument>
+			<argument flag="--with_critical_passages"></argument>
 		</step>
 	</run_script>
 </config>
diff --git a/testing_and_setup/compass/ocean/global_ocean/RRS30to10/spin_up/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/RRS30to10/spin_up/config_init1.xml
@@ -11,10 +11,13 @@
 	<add_link source_path="mesh_database" source="mesh.RRS.30-10km.160214.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">
 			<argument flag="-p">geometric_features</argument>
+			<argument flag="--with_critical_passages"></argument>
 		</step>
 	</run_script>
 </config>
diff --git a/testing_and_setup/compass/ocean/global_ocean/RRS30to10/with_land_ice/config_init1.xml b/testing_and_setup/compass/ocean/global_ocean/RRS30to10/with_land_ice/config_init1.xml
@@ -11,11 +11,14 @@
 	<add_link source_path="mesh_database" source="mesh.RRS.30-10km.160214.nc" dest="base_mesh.nc"/>
 	<add_link source_path="geometric_features" source="." dest="geometric_features"/>
 	<add_link source_path="script_configuration_dir" source="init_step1.py" dest="init_step1.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/add_land_locked_cells_to_mask.py" dest="add_land_locked_cells_to_mask.py"/>
+	<add_link source_path="mpas_tools" source="ocean/coastline_alteration/widen_transect_edge_masks.py" dest="widen_transect_edge_masks.py"/>
 
 	<run_script name="run.py">
 		<step executable="./init_step1.py">
 			<argument flag="-p">geometric_features</argument>
 			<argument flag="--with_cavities"></argument>
+			<argument flag="--with_critical_passages"></argument>
 		</step>
 	</run_script>
 </config>