Merge pull request #464 from mark-petersen/ocean/coast_of_Maine into …

…ocean/develop

Adds Coast of Maine refined to COMPASS

testing_and_setup/compass/ocean/coastal/Maine/init/config_base_mesh.xml

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+<?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="mpas_model" source="testing_and_setup/compass/ocean/jigsaw_to_MPAS" dest="jigsaw_to_MPAS"/>
+	<add_link source_path="bathymetry_database" source="SRTM15_plus_earth_relief_15s.nc" dest="earth_relief_15s.nc"/>
+	<add_link source_path="script_test_dir" source="." dest="define_base_mesh"/>
+
+	<run_script name="run.py">
+		<step executable="python">
+			<argument flag="-m">jigsaw_to_MPAS.build_mesh</argument>
+		</step>
+	</run_script>
+
+</config>

testing_and_setup/compass/ocean/coastal/Maine/init/config_culled_mesh.xml

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+../../config_files/config_culled_mesh.xml

testing_and_setup/compass/ocean/coastal/Maine/init/config_driver.xml

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+../../config_files/config_driver_init.xml

testing_and_setup/compass/ocean/coastal/Maine/init/config_e3sm_coupling.xml

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+../../config_files/config_e3sm_coupling.xml

testing_and_setup/compass/ocean/coastal/Maine/init/config_initial_state.xml

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+../../config_files/config_initial_state.xml

testing_and_setup/compass/ocean/coastal/Maine/init/config_mesh_metrics.xml

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+../../config_files/config_mesh_metrics.xml

testing_and_setup/compass/ocean/coastal/Maine/init/define_base_mesh.py

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+#!/usr/bin/env python
+from __future__ import absolute_import, division, print_function, \
+    unicode_literals
+
+import numpy as np
+import jigsaw_to_MPAS.coastal_tools as ct
+
+
+def cellWidthVsLatLon():
+
+    km = 1000.0
+
+    params = ct.default_params
+
+    # Use 1.0 degree for fast scoping, and 0.1 for the final creation:
+    params["ddeg"] = 0.2
+    #params["ddeg"] = 1.0
+    #params["ddeg"] = 0.5
+
+    params["dx_min_coastal"] = 12.0*km
+    params["trans_start"] = 400.0*km
+    params["trans_width"] = 600.0*km
+    params["n_longest"] = 20
+    params["mesh_type"] = "EC"
+
+    params["plot_box"] = ct.Entire_Globe
+    params["plot_option"] = False
+
+    print("***Gulf Coast***")
+    params["region_box"] = ct.US_Gulf_Coast
+    params["restrict_box"] = ct.Gulf_restrict
+    params["trans_start"] = 400.0*km
+    params["trans_width"] = 600.0*km
+    cell_width, lon, lat = ct.coastal_refined_mesh(params)
+
+    print("***East Coast***")
+    params["region_box"] = ct.US_East_Coast
+    params["restrict_box"] = ct.East_Coast_restrict
+    params["trans_start"] = 400.0*km
+    params["trans_width"] = 600.0*km
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print("***Gulf Stream extension***")
+    params["restrict_box"] = ct.Empty
+    params["trans_width"] = 600.0*km
+    params["region_box"] = {"include":[np.array([-78,-70,40,42])],
+                            "exclude":[]}
+    params["trans_start"] = 700.0*km
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+    params["region_box"] = {"include":[np.array([-74,-50,42,55])],
+                            "exclude":[]}
+    params["trans_start"] = 1100.0*km
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print("***Gulf Coast spot***")
+    params["restrict_box"] = ct.Empty
+    params["trans_width"] = 100.0*km
+    params["region_box"] = {"include":[np.array([-98,-94,28,30])],
+                            "exclude":[]}
+    params["trans_start"] = 400.0*km
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print("***Greenland***")
+    params["region_box"] = ct.Greenland
+    params["restrict_box"] = ct.Empty
+    params["trans_width"] = 600.0*km
+    params["trans_start"] = 275.0*km
+    cell_width, lon, lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print("***Greenland-Iceland smooth kink***")
+    params["region_box"] = {"include":[np.array([-45,-40,59,62])],
+                            "exclude":[]}
+    params["trans_start"] = 700.0*km
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print( "***Hudson Bay***")
+    params["region_box"] = {"include":[np.array([-100,-70,50,65])],
+                            "exclude":[]}
+    params["restrict_box"] = {"include":[np.array([-100,-70,50,65])],
+                            "exclude":[]}
+    params["trans_start"] = 600.0*km
+    params["trans_width"] = 100.0*km
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print( "***Northern Canada***")
+    params["region_box"] = {"include":[np.array([-168,-59,67,85])],
+                            "exclude":[]}
+    params["restrict_box"] = ct.Empty
+    params["trans_start"] = 275.0*km
+    params["trans_width"] = 600.0*km
+    params["n_longest"] = 20
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print("***Alaska***")
+    params["region_box"] = ct.Alaska
+    params["trans_start"] = 400.0*km
+    params["trans_width"] = 600.0*km
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print( "***Crook at Alaska/Canada***")
+    params["region_box"] = {"include":[np.array([-144,-127,68.5,71])],
+                            "exclude":[]}
+    params["restrict_box"] = ct.Empty
+    params["trans_start"] = 550.0*km
+    params["trans_width"] = 600.0*km
+    params["n_longest"] = 20
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print("***Caribbean***")
+    params["region_box"] = ct.Caribbean
+    params["restrict_box"] = ct.Caribbean_restrict
+    params["trans_width"] = 400.0*km
+    params["trans_start"] = 300.0*km
+    params["n_longest"] = 50
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print("***West Coast***")
+    params["region_box"] = ct.US_West_Coast
+    params["restrict_box"] = ct.Empty
+    params["trans_width"] = 600.0*km
+    params["trans_start"] = 400.0*km
+    params["n_longest"] = 10
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print("***Aleutian Islands (West)***")
+    params["region_box"] = ct.Aleutian_Islands_W
+    params["n_longest"] = 100
+    params["trans_start"] = 200.0*km
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print("****Aleutian Islands (East)***")
+    params["region_box"] = ct.Aleutian_Islands_E
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print("***Bering Sea (East)****")
+    params["region_box"] = ct.Bering_Sea_E
+    params["trans_start"] = 400.0*km
+    params["trans_width"] = 600.0*km
+    params["n_longest"] = 10
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print("***Bering Sea (West)***")
+    params["region_box"] = ct.Bering_Sea_W
+    params["restrict_box"] = ct.Bering_Sea_restrict
+    params["trans_start"] = 450.0*km
+    params["trans_width"] = 600.0*km
+    params["n_longest"] = 10
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print("***Newfoundland***")
+    Newfoundland = {"include":[np.array([-65.0,-50.0,44.0,60.0]),
+                               np.array([-65.5,-64.5,61.0,62.0])],
+                    "exclude":[]}
+    params["region_box"] = Newfoundland
+    params["restrict_box"] = ct.Empty
+    params["trans_width"] = 600.0*km
+    params["trans_start"] = 400.0*km
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print("***Labrador Sea***")
+    params["region_box"] = ct.Empty
+    params["restrict_box"] = ct.Empty
+    params["point_list"] = [np.array([-50.0,55.0])]
+    params["trans_width"] = 600.0*km
+    params["trans_start"] = 400.0*km
+    cell_width, lon, lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    print("***Central America (West Coast)***")
+    Central_America = {"include":[np.array([[-110.26,20.69],
+                                            [-87.84, 8.94 ],
+                                            [-84.55, 12.03],
+                                            [-104.26,23.11]]),
+                                  np.array([[-88.02, 10.47],
+                                            [-81.53, 6.14],
+                                            [-81.45, 8.07],
+                                            [-84.80, 11.51]]),
+                                  np.array([[-81.92, 7.76],
+                                            [-76.84, 4.51],
+                                            [-77.41, 8.22],
+                                            [-79.23, 9.28]])],
+                       "exclude":[]}
+    params["region_box"] = Central_America
+    params["restrict_box"] = ct.Empty
+    params["point_list"] = None
+    params["trans_width"] = 600.0*km
+    params["trans_start"] = 400.0*km
+    cell_width, lon, lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    # coast of Maine
+    params["dx_min_coastal"] = 6.0*km
+    params["trans_start"] = 500.0*km
+    params["trans_width"] = 300.0*km
+    params["n_longest"] = 20
+    params["region_box"] = {"include":[np.array([-70,-68,43,45])],
+                            "exclude":[]}
+    params["restrict_box"] = {"include":[],
+                            "exclude":[np.array([-73,-60,46,50])]}
+    params["point_list"] = [[-68.8,43.8]]
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    # coast of Maine
+    params["dx_min_coastal"] = 2.0*km
+    params["trans_start"] = 150.0*km
+    params["trans_width"] = 300.0*km
+    params["n_longest"] = 20
+    params["region_box"] = {"include":[np.array([-70,-68,43,45])],
+                            "exclude":[]}
+    params["restrict_box"] = {"include":[],
+                            "exclude":[np.array([-73,-50,46,50])]}
+    params["point_list"] = [[-68.8,43.8]]
+    cell_width,lon,lat = ct.coastal_refined_mesh(params,cell_width,lon,lat)
+
+    return cell_width / km, lon, lat

testing_and_setup/compass/ocean/coastal/Maine/template_forward.xml

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+<template>
+	<namelist>
+		<option name="config_dt">'00:12:00'</option>
+		<option name="config_btr_dt">'00:00:30'</option>
+		<option name="config_pio_num_iotasks"