MPAS-Dev · xylar · Nov 9, 2020 · Apr 7, 2020 · Apr 7, 2020 · Apr 8, 2020
diff --git a/README_ocean.md b/README_ocean.md
@@ -0,0 +1,50 @@
+# Setting up COMPASS for ocean test case
+
+## COMPASS conda environment
+
+To set up and run ocean test cases from COMPASS, you will need a conda
+environment.  First, install Miniconda3 (if miniconda is not already
+installed), then create a new conda environment as follows:
+``` bash
+conda create -n compass_0.1.11 -c conda-forge -c e3sm python=3.7 compass=0.1.11
+```
+Each time you want to work with COMPASS, you will need to run:
+```
+conda activate compass_0.1.11
+```
+
+An appropriate conda environment is already available on Los Alamos National
+Laboratory's Institutional Computing (LANL IC) machines as well as Anvil, Compy
+and Cori.  In each case, you will run:
+```
+source <base_path>/load_latest_compass.sh
+```
+Values of `<base_path>` are:
+* grizzly and badger - `/usr/projects/climate/SHARED_CLIMATE/anaconda_envs`
+* anvil (blues) - `/lcrc/soft/climate/e3sm-unified/`
+* compy - `/share/apps/E3SM/conda_envs`
+* cori - `/global/cfs/cdirs/acme/software/anaconda_envs`
+
+## Setting config options
+
+The file `general.config.ocean` is a template containing a set of config
+options that the COMPASS user must set in order to set up ocean test cases.
+Make a copy of this file (e.g. `config.ocean`) and set the options as follows.
+In six places, replace `FULL_PATH_TO_MPAS_MODEL_REPO` with the path where you
+have checked out (and built) the branch of MPAS-Model you are planning to use.
+Five other paths are required, as explained below.
+
+### mesh\_database, initial\_condition\_database and bathymetry\_database
+
+These are directories for storing pre-generated mesh files, data sets for
+creating initial conditions, and bathymetry data. These can be empty directories, in which case
+meshes and other data sets will be downloaded as required during test-case
+setup.  (If a test case appears to hang during setup, it is most likely
+downloading mesh, initial-condition or bathymetry data.)
+
+On LANL IC, the shared data bases can be found at:
+```
+mesh_database = /usr/projects/regionalclimate/COMMON_MPAS/ocean/grids/mesh_database
+initial_condition_database = /usr/projects/regionalclimate/COMMON_MPAS/ocean/grids/initial_condition_database
+bathymetry_database = /usr/projects/regionalclimate/COMMON_MPAS/ocean/grids/bathymetry_database
+```
diff --git a/general.config.ocean b/general.config.ocean
@@ -9,31 +9,23 @@
 # init namelists in the default_inputs directory after a successful build of
 # the ocean model.
 [namelists]
-forward = FULL_PATH_TO_FORWARD_TEMPLATE_NAMELIST
-init = FULL_PATH_TO_INIT_TEMPLATE_NAMELIST
-
+forward = FULL_PATH_TO_MPAS_MODEL_REPO/namelist.ocean
+init    = FULL_PATH_TO_MPAS_MODEL_REPO/namelist.ocean
 
 # The streams section defines paths to template streams files that will be used
 # to generate specific streams files. Typically these will point to the forward and
 # init streams files in the default_inputs directory after a successful build of
 # the ocean model.
 [streams]
-forward = FULL_PATH_TO_FORWARD_TEMPLATE_STREAMS
-init = FULL_PATH_TO_INIT_TEMPLATE_STREAMS
-
+forward = FULL_PATH_TO_MPAS_MODEL_REPO/streams.ocean.forward
+init    = FULL_PATH_TO_MPAS_MODEL_REPO/streams.ocean.init
 
 # The executables section defines paths to required executables. These
 # executables are provided for use by specific test cases.
 # Full paths should be provided in order to access the executables from
 # anywhere on the machine.
 [executables]
-model = FULL_PATH_TO_MODEL
-mesh_converter = FULL_PATH_TO_MESH_CONVERTER
-cell_culler = FULL_PATH_TO_CELL_CULLER
-mask_creator = FULL_PATH_TO_MASK_CREATOR
-metis = FULL_PATH_TO_METIS
-mesh_generator = FULL_PATH_TO_EXECUTABLE_MESH_GENERATION_SCRIPT
-
+model = FULL_PATH_TO_MPAS_MODEL_REPO/ocean_model
 
 # The paths section describes paths that are used within the ocean core test
 # cases.
@@ -44,7 +36,15 @@ mesh_generator = FULL_PATH_TO_EXECUTABLE_MESH_GENERATION_SCRIPT
 # the same directory, or different directory. Additionally, if they are empty
 # some test cases might download data into them, which will then be reused if
 # the test case is run again later.
+mpas_model = FULL_PATH_TO_MPAS_MODEL_REPO
 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
-mesh_scripts = FULL_PATH_TO_LOCAL_CHECKOUT_OF_MESH_GENERATION_SCRIPTS
+bathymetry_database = FULL_PATH_TO_BATHYMETRY_DATABASE
+
+# The options in this section relate to configuring and running with a compass
+# conda environment
+[conda]
+
+# Whether a link to load_compass_env.sh should be included with each test case
+# (can also be specified with the --link_load_compass flag)
+link_load_compass = False
diff --git a/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/build_base_mesh.py b/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/build_base_mesh.py
@@ -0,0 +1,81 @@
+#!/usr/bin/env python
+import mpas_tools.ocean.coastal_tools as ct
+from mpas_tools.ocean import build_spherical_mesh
+
+
+def cellWidthVsLatLon():
+    """
+    This function specifies the resolution for a coastal refined mesh for
+    Delaware Bay.  It creates cell width array for this mesh on a regular
+    latitude-longitude grid.
+
+    It contains the following resolution regions:
+      1) a QU 120km global background resolution
+      2) 10km refinement region from the coast to past the shelf-break from
+         North Carolina to New Hampshire
+      3) 5km refinement region from the coast up to the shelf-break from
+         Virginia to past Long Island, New York
+      4) 2km refinement region inside Delaware Bay
+
+    Returns
+    -------
+       cellWidth : ndarray
+            m x n array, entries are desired cell width in km
+
+       lat : ndarray
+            latitude, vector of length m, with entries between -90 and 90,
+            degrees
+
+       lon : ndarray
+            longitude, vector of length n, with entries between -180 and 180,
+            degrees
+    """
+    # authors: Steven Brus, Phillip J. Wolfram
+    km = 1000.0
+
+    params = ct.default_params
+
+    print("****QU120 background mesh and 10km refinement from NC to NH****")
+    params["mesh_type"] = "QU"
+    params["dx_max_global"] = 120.0 * km
+    params["region_box"] = ct.Delaware_Bay
+    params["plot_box"] = ct.Western_Atlantic
+    params["dx_min_coastal"] = 10.0 * km
+    params["trans_width"] = 600.0 * km
+    params["trans_start"] = 400.0 * km
+
+    cell_width, lon, lat = ct.coastal_refined_mesh(params)
+
+    print("****5km refinement along coast from VA to NY****")
+    params["region_box"] = ct.Delaware_Region
+    params["plot_box"] = ct.Delaware
+    params["dx_min_coastal"] = 5.0 * km
+    params["trans_width"] = 175.0 * km
+    params["trans_start"] = 75.0 * km
+
+    cell_width, lon, lat = ct.coastal_refined_mesh(
+        params, cell_width, lon, lat)
+
+    print("****2km refinement inside Delaware Bay****")
+    params["region_box"] = ct.Delaware_Bay
+    params["plot_box"] = ct.Delaware
+    params["restrict_box"] = ct.Delaware_restrict
+    params["dx_min_coastal"] = 2.0 * km
+    params["trans_width"] = 100.0 * km
+    params["trans_start"] = 17.0 * km
+
+    cell_width, lon, lat = ct.coastal_refined_mesh(
+        params, cell_width, lon, lat)
+
+    return cell_width / 1000, lon, lat
+
+
+def main():
+    cellWidth, lon, lat = cellWidthVsLatLon()
+    build_spherical_mesh(cellWidth, lon, lat, out_filename='base_mesh.nc',
+                         do_inject_bathymetry=True, preserve_floodplain=True,
+                         floodplain_elevation=20.0)
+
+
+if __name__ == '__main__':
+    main()
diff --git a/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/config_base_mesh.xml b/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/config_base_mesh.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<config case="base_mesh">
+	<get_file dest_path="bathymetry_database" file_name="SRTM15_plus_earth_relief_15s.nc">
+		<mirror protocol="wget" url="https://web.lcrc.anl.gov/public/e3sm/mpas_standalonedata/mpas-ocean/bathymetry_database/"/>
+	</get_file>
+
+	<add_link source_path="script_test_dir" source="build_base_mesh.py" dest="build_base_mesh.py"/>
+	<add_link source_path="bathymetry_database" source="SRTM15_plus_earth_relief_15s.nc" dest="earth_relief_15s.nc"/>
+
+	<run_script name="run.py">
+		<step executable="./build_base_mesh.py">
+		</step>
+	</run_script>
+
+</config>
diff --git a/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/config_culled_mesh.xml b/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/config_culled_mesh.xml
@@ -0,0 +1,28 @@
+<?xml version="1.0"?>
+<config case="culled_mesh">
+	<get_file dest_path="bathymetry_database" file_name="SRTM15_plus_earth_relief_15s.nc">
+		<mirror protocol="wget" url="https://web.lcrc.anl.gov/public/e3sm/mpas_standalonedata/mpas-ocean/bathymetry_database/"/>
+	</get_file>
+
+	<add_link source="../base_mesh/base_mesh.nc" dest="base_mesh.nc"/>
+	<add_link source_path="script_core_dir" source="global_ocean/scripts/cull_mesh.py" dest="cull_mesh.py"/>
+	<add_link source_path="bathymetry_database" source="SRTM15_plus_earth_relief_15s.nc" dest="earth_relief_15s.nc"/>
+
+	<run_script name="run.py">
+		<step executable="./cull_mesh.py">
+			<argument flag="--with_critical_passages"></argument>
+			<argument flag="--preserve_floodplain"></argument>
+		</step>
+		<step executable="inject_bathymetry">
+			<argument flag="">culled_mesh.nc</argument>
+		</step>
+		<step executable="paraview_vtk_field_extractor.py">
+			<argument flag="">--ignore_time</argument>
+			<argument flag="">-l</argument>
+			<argument flag="-d">maxEdges=0</argument>
+			<argument flag="-v">allOnCells</argument>
+			<argument flag="-f">culled_mesh.nc</argument>
+			<argument flag="-o">culled_mesh_vtk</argument>
+		</step>
+	</run_script>
+</config>
diff --git a/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/config_driver_init.xml b/ocean/Gaussian_hump/USDEQU120cr10rr2/build_mesh/config_driver_init.xml
@@ -0,0 +1,8 @@
+<driver_script name="run.py">
+	<case name="base_mesh">
+		<step executable="./run.py" quiet="true" pre_message=" * Creating 2D global base mesh with jigsaw..." post_message="     complete!  Created file:  base_mesh/base_mesh.nc"/>
+	</case>
+	<case name="culled_mesh">
+		<step executable="./run.py" quiet="true" pre_message=" * Culling land cells from 2D global mesh..." post_message="     complete!  Created file:  culled_mesh/culled_mesh.nc"/>
+	</case>
+</driver_script>
diff --git a/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_analysis.xml b/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_analysis.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<config case="analysis">
+	<add_link source="../forward/output.nc" dest="output.nc"/>
+
+	<run_script name="run.py">
+		<step executable="paraview_vtk_field_extractor.py">
+			<argument flag="-f">output.nc</argument>
+			<argument flag="-o">vtk_output</argument>
+			<argument flag="-v">allOnCells</argument>
+			<argument flag="-d">maxEdges=0</argument>
+			<argument flag="">nVertLevels=0:10</argument>
+			<argument flag="--combine"></argument>
+		</step>
+	</run_script>
+</config>
diff --git a/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_driver.xml b/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_driver.xml
@@ -0,0 +1,8 @@
+<driver_script name="run_test.py">
+	<case name="init">
+		<step executable="./run.py" quiet="true" pre_message=" * Running init" post_message="     Complete"/>
+	</case>
+	<case name="forward">
+		<step executable="./run.py" quiet="true" pre_message=" * Running forward" post_message="     Complete"/>
+	</case>
+</driver_script>
diff --git a/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_forward.xml b/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_forward.xml
@@ -0,0 +1,60 @@
+<?xml version="1.0"?>
+<config case="forward">
+	<add_link source="../init/ocean.nc" dest="input.nc"/>
+	<add_link source="../init/graph.info" dest="graph.info"/>
+
+	<namelist name="namelist.ocean" mode="forward">
+		<option name="config_start_time">'0001-01-01_00:00:00'</option>
+		<option name="config_run_duration">'00_18:00:00'</option>
+
+<!--
+		<option name="config_time_integrator">'split_explicit'</option>
+		<option name="config_dt">'00:00:30'</option>
+		<option name="config_btr_dt">'0000_00:00:03'</option>
+-->
+		<option name="config_dt">'00:00:10'</option>
+		<option name="config_time_integrator">'RK4'</option>
+		<option name="config_hmix_scaleWithMesh">.true.</option>
+		<option name="config_mom_del4">4.0e8</option>
+		<option name="config_use_mom_del4">.true.</option>
+		<option name="config_vert_coord_movement">'uniform_stretching'</option>
+		<option name="config_ALE_thickness_proportionality">'weights_only'</option>
+		<option name="config_use_bulk_wind_stress">.true.</option>
+		<option name="config_use_time_varying_atmospheric_forcing">.false.</option>
+		<option name="config_check_ssh_consistency">.false.</option>
+		<option name="config_use_wetting_drying">.true.</option>
+		<option name="config_prevent_drying">.true.</option>
+		<option name="config_drying_min_cell_height">0.1</option>
+		<option name="config_verify_not_dry">.true.</option>
+		<option name="config_zero_drying_velocity">.true.</option>
+		<option name="config_thickness_flux_type">'upwind'</option>
+	</namelist>
+
+	<streams name="streams.ocean" keep="immutable" mode="forward">
+		<stream name="mesh">
+			<attribute name="filename_template">input.nc</attribute>
+		</stream>
+		<stream name="input">
+			<attribute name="filename_template">input.nc</attribute>
+		</stream>
+		<template file="minimal_output.xml" path_base="script_core_dir" path="templates/streams"/>
+		<stream name="output">
+			<attribute name="output_interval">01:00:00</attribute>
+			<add_contents>
+				<member name="ssh" type="var"/>
+				<member name="kineticEnergyCell" type="var"/>
+			</add_contents>
+			<remove_contents>
+				<member name="tracers"/>
+					<member name="normalVelocity"/>
+			</remove_contents>
+		</stream>
+	</streams>
+
+	<run_script name="run.py">
+		<step executable="gpmetis">
+			<argument flag="graph.info">360</argument>
+		</step>
+		<model_run procs="360" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
+	</run_script>
+</config>
diff --git a/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_init.xml b/ocean/Gaussian_hump/USDEQU120cr10rr2/delaware/config_init.xml
@@ -0,0 +1,66 @@
+<?xml version="1.0"?>
+<config case="init">
+	<add_link source="../../build_mesh/culled_mesh/culled_mesh.nc" dest="mesh.nc"/>
+	<add_link source="../../build_mesh/culled_mesh/culled_graph.info" dest="graph.info"/>
+
+	<namelist name="namelist.ocean" mode="init">
+		<option name="config_init_configuration">'hurricane'</option>
+		<option name="config_vert_levels">-1</option>
+		<option name="config_ocean_run_mode">'init'</option>
+		<option name="config_write_cull_cell_mask">.false.</option>
+		<option name="config_realistic_coriolis_parameter">.true.</option>
+		<option name="config_vertical_grid">'60layerPHC'</option>
+		<option name="config_hurricane_vert_levels">60</option>
+		<option name="config_hurricane_min_depth">-30.0</option>
+		<option name="config_hurricane_max_depth">2000.0</option>
+		<option name="config_hurricane_use_gaussian_hump">.true.</option>
+		<option name="config_hurricane_gaussian_hump_amplitude">4.0</option>
+		<option name="config_hurricane_gaussian_width">0.25</option>
+		<option name="config_use_wetting_drying">.true.</option>
+		<option name="config_drying_min_cell_height">0.10001</option>
+	</namelist>
+
+	<streams name="streams.ocean" keep="immutable" mode="init">
+		<stream name="input_init">
+			<attribute name="filename_template">mesh.nc</attribute>
+		</stream>
+		<stream name="bathymetry">
+			<attribute name="filename_template">mesh.nc</attribute>
+	                <attribute name="type">input</attribute>
+	                <attribute name="input_interval">initial_only</attribute>
+			<add_contents>
+				<member name="bottomDepthObserved" type="var"/>
+			</add_contents>                
+		</stream>
+		<stream name="output_init">
+			<attribute name="type">output</attribute>
+			<attribute name="output_interval">0000_00:00:01</attribute>
+			<attribute name="clobber_mode">truncate</attribute>
+			<attribute name="filename_template">ocean.nc</attribute>
+			<add_contents>
+				<member name="input_init" type="stream"/>
+				<member name="tracers" type="var_struct"/>
+				<member name="refZMid" type="var"/>
+				<member name="normalVelocity" type="var"/>
+				<member name="layerThickness" type="var"/>
+				<member name="restingThickness" type="var"/>
+				<member name="refBottomDepth" type="var"/>
+				<member name="bottomDepth" type="var"/>
+				<member name="bottomDepthObserved" type="var"/>
+				<member name="maxLevelCell" type="var"/>
+				<member name="vertCoordMovementWeights" type="var"/>
+				<member name="ssh" type="var"/>
+			</add_contents>
+		</stream>
+	</streams>
+
+	<run_script name="run.py">
+<!--
+		<step executable="gpmetis">
+		        <argument flag="graph.info">6</argument>
+		</step>
+-->
+		<model_run procs="1" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
+	</run_script>
+
+</config>
diff --git a/ocean/README.md b/ocean/README.md
@@ -0,0 +1 @@
+../README_ocean.md