Tools for generating non-global unstructured meshes

unst_msh_gen/regional/InterpolateBathymetry/AddBathyToMesh.py

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+
+#
+# Function for taking bathymetry field in a text file and replacing bathymetry
+# from a WW3 .msh files with the values from the file specified on the command
+# line:
+#
+# $python3 AddBathyToMesh.py MyBathy.txt 
+#
+# creates a new WW3 mesh with bathymetry from MyBathy.txt
+#
+#
+
+import FiniteElementMeshRoutines as FE
+import numpy as np
+import sys
+
+mshnm="HawaiiTest"
+mesh="meshes/"+mshnm+".msh"
+
+flin=sys.argv[1]
+flout=flin+".WW3.msh"
+
+x, y, z0, e, bnd = FE.loadWW3Mesh(mesh)
+
+zmin=1.
+nn=len(x)
+z=np.zeros(nn)
+f=open(flin, 'r')
+for k in range(nn):
+    line=f.readline()
+    #print(str(k)+" "+line)
+    z[k]=float(line.strip())
+    z[k]=-z[k]
+    z[k]=max(z[k],zmin)
+f.close
+FE.WriteWW3Mesh(flout,x,y,z,e,bnd)
+

unst_msh_gen/regional/InterpolateBathymetry/DivideMeshNodes.py

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+
+#
+# This script partitions the nodes in mshnm into NP parts and writes a script to
+# interpolate bathymetry data to the nodes in NP parallel parts
+# call:
+#
+# $ python3 DivideMeshNodes.py 100
+#
+# to create jobcard: jobcardInterpBathy2Mesh, which is then run: 
+#
+# $ sbatch jobcardInterpBathy2Mesh
+#
+# to interpolate the bathymetry in 100 parallel tasks
+#
+# This script should be run after the bathymetry data sets specified in 
+# InterpolateCRM.partscat.py are present
+#
+"""
+Ursa environment
+
+module purge
+module use /scratch3/NCEPDEV/climate/Keston.Smith/global-workflowA/sorc/ufs_model.fd/modulefiles
+module load ufs_ursa.intel
+module load py-scipy/1.14.1
+module load py-netcdf4/1.7.1.post2
+pip list
+"""
+
+import os
+import argparse
+import time
+import numpy as np
+import netCDF4 as nc
+import math
+import sys
+from scipy.interpolate import RegularGridInterpolator
+#import re
+import FiniteElementMeshRoutines as FE
+import random
+
+mshnm="HawaiiTest"
+mesh="meshes/"+mshnm+".msh"
+OutDir=mshnm+".files/"
+
+jobcard="jobcardInterpBathy2Mesh"
+
+
+def WriteInterpJobscript(fl,N, ComputeNodes):
+    with open(fl, 'w') as f:
+        #yi[k]=float(values[4])
+        f.write("#!/bin/bash \n")
+        f.write("#SBATCH --job-name=CRM_interp_masterscript \n")
+#        f.write("#SBATCH --ntasks="+str(N)+" \n")
+        f.write("#SBATCH --ntasks=1 \n") # ntasks per interpolation
+        f.write("#SBATCH --time=08:00:00 \n") 
+        f.write("#SBATCH --output=mpi_test_%j.log \n")
+        f.write("#SBATCH --error=%j.err \n")
+        f.write("#SBATCH --account=marine-cpu \n")
+        f.write("#SBATCH --nodes="+str(ComputeNodes)+" \n")
+        f.write("#SBATCH --ntasks-per-core=1"+" \n")
+        f.write("#SBATCH --array=0-"+str(N-1)+" \n")
+
+        f.write(" \n")
+
+        f.write("module purge \n")
+        f.write("module use /scratch3/NCEPDEV/climate/Keston.Smith/global-workflowA/sorc/ufs_model.fd/modulefiles \n")
+        f.write("module load ufs_ursa.intel \n")
+        f.write("module load py-scipy/1.14.1 \n")
+        f.write("module load py-netcdf4/1.7.1.post2 \n")
+        f.write("pip list \n")
+        f.write("srun python3  InterpolateCRM.partscat.py $SLURM_ARRAY_TASK_ID > InterpJob.$SLURM_ARRAY_TASK_ID.out \n")
+        f.write("wait \n")
+        f.write("## Run this after the full job array is compleate.\n")
+        f.write("## Patch randomly shuffled fields in orgigonal order.\n")
+
+        f.write("python3 KnitOutputBackTogether.py "+str(N)+" GMN\n")
+        f.write("python3 KnitOutputBackTogether.py "+str(N)+" GMU\n")
+        f.write("python3 KnitOutputBackTogether.py "+str(N)+" InvDist\n")
+        f.write("python3 KnitOutputBackTogether.py "+str(N)+" NDataPoints\n")
+        f.write("python3 KnitOutputBackTogether.py "+str(N)+" ClosestValue\n")
+        f.write("python3 KnitOutputBackTogether.py "+str(N)+" LengthScale\n")
+        f.write("python3 KnitOutputBackTogether.py "+str(N)+" GMU.std\n")
+        f.write("python3 KnitOutputBackTogether.py "+str(N)+" GMN.std\n")
+        #f.write("python3 KnitOutputBackTogether.py "+str(N)+" GMM\n")
+        #f.write("python3 KnitOutputBackTogether.py "+str(N)+" GM0\n")
+
+
+# Create the output directory------------------------------------------
+try:
+    os.mkdir(OutDir)
+    print(f"Directory '{OutDir}' created successfully.")
+except FileExistsError:
+    print(f"Directory '{OutDir}' already exists. Proceeding ...")
+except PermissionError:
+    print(f"Permission denied: Unable to create '{OutDir}'.")
+
+fl="meshes/"+mshnm+".msh"
+
+xi, yi, ei =FE.loadWW3MeshCoords(fl)
+
+#tmp
+lsE=FE.lengthscale(xi, yi, ei)
+areaE=FE.ElementArea(xi, yi, ei)
+lsN=FE.ComputeNodeLengthScale(lsE, areaE, ei)
+np.savetxt("LengthScaleNodes.txt",  lsN, fmt='%.6f', delimiter='\n')
+
+# randomly sort nodes for roughly equal jobs size
+# nodes within CRM envelope use far more compute than
+# open ocean nodes with fewer points used in interpolation
+
+nn=len(xi)
+Nodes = list(range( nn ))
+random.shuffle(Nodes) # randomize order of nodes for equitable job load
+
+Nparts=int(sys.argv[1])
+
+nn=xi.shape[0]
+NodesPerProc=math.ceil(nn/Nparts)
+print(str(NodesPerProc)+ " " + str(nn))
+a = range(nn)
+
+NodeList = [] 
+for i in range(0, len(a), NodesPerProc):  # Slice list in steps of n
+    NodeList.append(a[i:i + NodesPerProc])
+
+print("NodeList")
+print(NodeList)
+for k in range(Nparts):
+    flo=OutDir+'NodeList.'+str(k)+'.txt'
+    f=open(flo, 'w')
+    f.write("List of nodes for job "+str(k) + "\n")
+    List=NodeList[k]
+    n=len(List)
+    f.write(str(n) + "\n")
+    for j in range(n):
+        #f.write(str(List[j]) + '\n') # sequential order of nodes, output can be cat > back together
+        f.write(str(Nodes[List[j]]) + '\n') # random order of nodes
+    f.close
+
+#write jobcard to do interpolation
+WriteInterpJobscript(jobcard,Nparts,1)

unst_msh_gen/regional/InterpolateBathymetry/DowloadBathyData.sh

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+#!/bin/bash 
+#############################################################################################################
+
+# Script to download global and regional bathymetry files:
+# You will need ~ 20 GB free space
+
+echo "Downloading bathymetry data"
+
+#############################################################################################################
+######################## Download main Coastal Relief Moesl (CRM) files #####################################
+#############################################################################################################
+# see: https://www.ncei.noaa.gov/products/coastal-relief-model
+#############################################################################################################
+#Northeast Atlantic
+wget --output-document crm_vol1_2023.nc https://www.ngdc.noaa.gov/thredds/fileServer/crm/cudem/crm_vol1_2023.nc
+#Southeast Atlantic
+wget --output-document crm_vol2_2023.nc https://www.ngdc.noaa.gov/thredds/fileServer/crm/cudem/crm_vol2_2023.nc
+# Florida and East Gulf of America
+wget --output-document crm_vol3_2023.nc https://www.ngdc.noaa.gov/thredds/fileServer/crm/cudem/crm_vol3_2023.nc
+# Central GOA
+wget --output-document crm_vol4_2023.nc https://www.ngdc.noaa.gov/thredds/fileServer/crm/cudem/crm_vol4_2023.nc
+# Western GOA
+wget --output-document crm_vol5_2023.nc https://www.ngdc.noaa.gov/thredds/fileServer/crm/cudem/crm_vol5_2023.nc
+#Central Pacific
+wget --output-document crm_vol7_2023.nc https://www.ngdc.noaa.gov/thredds/fileServer/crm/cudem/crm_vol7_2023.nc
+#Northwest Pacific
+wget --output-document crm_vol8_2023.nc https://www.ngdc.noaa.gov/thredds/fileServer/crm/cudem/crm_vol8_2023.nc
+#Puerto Rico
+wget --output-document crm_vol9_2023.nc https://www.ngdc.noaa.gov/thredds/fileServer/crm/cudem/crm_vol9_2023.nc
+#Hawaii
+wget --output-document crm_vol10_2023.nc https://www.ngdc.noaa.gov/thredds/fileServer/crm/cudem/crm_vol10_2023.nc
+#Other CRM files
+# Southern California
+wget --output-document crm_vol6.nc https://www.ngdc.noaa.gov/thredds/fileServer/crm/crm_vol6.nc
+# Southern Alaska
+wget --output-document crm_southak.nc https://www.ngdc.noaa.gov/thredds/fileServer/crm/crm_southak.nc
+#############################################################################################################
+
+echo "Done Coastal Relief Model (CRM) Download"
+
+#############################################################################################################
+######################## Download regional files in Pacific #################################################
+#############################################################################################################
+# see: https://pae-paha.pacioos.hawaii.edu/thredds/bathymetry.html
+#############################################################################################################
+# American Samoa
+wget --output-document ngdc_bathy_90m_amsamoa.nc https://pae-paha.pacioos.hawaii.edu/thredds/ncss/ngdc_bathy_90m_amsamoa?var=elev&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true
+# Mariana islands
+wget --output-document ngdc_bathy_180m_mariana.nc https://pae-paha.pacioos.hawaii.edu/thredds/ncss/ngdc_bathy_180m_mariana?var=elev&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true
+#North Western Hawiian islands
+wget --output-document hurl_bathy_60m_nwhi.nc https://pae-paha.pacioos.hawaii.edu/thredds/ncss/hurl_bathy_60m_nwhi?var=elev&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true
+#############################################################################################################
+
+echo "Done regional files in Pacific Download"
+
+#############################################################################################################
+######################## Download small scale bathymetry for US Minor outlying islands in Pacific ###########
+#############################################################################################################
+# see: https://pae-paha.pacioos.hawaii.edu/thredds/bathymetry.html
+#############################################################################################################
+wget --output-document ngdc_bathy_10m_wake.nc https://pae-paha.pacioos.hawaii.edu/thredds/ncss/ngdc_bathy_10m_wake?var=elev&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true
+
+wget --output-document pibhmc_bathy_20m_jarvis.nc https://pae-paha.pacioos.hawaii.edu/thredds/ncss/pibhmc_bathy_20m_jarvis?var=elev&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true
+
+wget --output-document pibhmc_bathy_20m_johnston.nc https://pae-paha.pacioos.hawaii.edu/thredds/ncss/pibhmc_bathy_20m_johnston?var=elev&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true
+
+wget --output-document pibhmc_bathy_20m_kingman.nc https://pae-paha.pacioos.hawaii.edu/thredds/ncss/pibhmc_bathy_20m_kingman?var=elev&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true
+
+wget --output-document pibhmc_bathy_40m_baker.nc https://pae-paha.pacioos.hawaii.edu/thredds/ncss/pibhmc_bathy_40m_baker?var=elev&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true
+
+wget --output-document pibhmc_bathy_40m_howland.nc https://pae-paha.pacioos.hawaii.edu/thredds/ncss/pibhmc_bathy_40m_howland?var=elev&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true
+
+wget --output-document pibhmc_bathy_40m_palmyra.nc https://pae-paha.pacioos.hawaii.edu/thredds/ncss/pibhmc_bathy_40m_palmyra?var=elev&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true
+
+wget --output-document pibhmc_bathy_40m_rose.nc https://pae-paha.pacioos.hawaii.edu/thredds/ncss/pibhmc_bathy_40m_rose?var=elev&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true
+
+wget --output-document pibhmc_bathy_40m_vailuluu.nc https://pae-paha.pacioos.hawaii.edu/thredds/ncss/pibhmc_bathy_40m_vailuluu?var=elev&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true
+
+wget --output-document pibhmc_bathy_40m_swains.nc https://pae-paha.pacioos.hawaii.edu/thredds/ncss/pibhmc_bathy_40m_swains?var=elev&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true
+
+wget --output-document pibhmc_bathy_5m_palmyra.nc https://pae-paha.pacioos.hawaii.edu/thredds/ncss/pibhmc_bathy_5m_palmyra?var=elev&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true
+
+wget --output-document sopac_bathy_50m_majuro_reef.nc https://pae-paha.pacioos.hawaii.edu/thredds/ncss/sopac_bathy_50m_majuro_reef?var=elev&disableLLSubset=on&disableProjSubset=on&horizStride=1&addLatLon=true
+#############################################################################################################
+
+echo "Done small scale bathymetry for US Minor outlying islands in Pacific download"
+
+#############################################################################################################
+######################## Global SDB [~0m to ~30m] depth from copernicus #####################################
+#############################################################################################################
+# see: https://data.marine.copernicus.eu/product/BATHYMETRY_GLO_PHY_COASTAL_L4_MY_016_001/files?subdataset=cmems_obs-sdb_glo_phy_comp_my_100m-l4-s2_static_202511
+#############################################################################################################
+wget --output-document cmems_obs-sdb_glo_phy-comp_my-oa-100m-l4-s2_static.nc https://s3.waw3-1.cloudferro.com/mdl-native-17/native/BATHYMETRY_GLO_PHY_COASTAL_L4_MY_016_001/cmems_obs-sdb_glo_phy_wk_my_100m-l4-s2_static_202511/cmems_obs-sdb_glo_phy-wk_my-oa-100m-l4-s2_static.nc
+#############################################################################################################
+
+echo "Done Global SDB download"
+
+#############################################################################################################
+######################## 60 second Global Bathymetry#########################################################
+wget https://github.com/dengwirda/dem/releases/download/v0.1.1/RTopo_2_0_4_GEBCO_v2024_60sec_pixel.zip
+#############################################################################################################
+
+echo "Done Global Bathymetry download"