monthlyAggregateBFMData.py, script to postprocess the raw BFM output …

…for the paper on biogeochemistry
jalessandri · Apr 21, 2023 · 60b9dea · 60b9dea
1 parent 719eadd
commit 60b9dea
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Showing 3 changed files with 114 additions and 7 deletions.
diff --git a/acIndUtils/acIndUtils.py b/acIndUtils/acIndUtils.py
@@ -528,6 +528,17 @@ def generateDifferencDataset(projNcFileSpec,
 
 
 
+def addNavlonNavlatFields(ncFileSpec):
+    ds = netCDF4.Dataset(ncFileSpec.ncFileName, "r+")
+    x = ds.variables[ncFileSpec.xVarName][:]
+    y = ds.variables[ncFileSpec.yVarName][:]
+    lonmtx, latmtx = np.meshgrid(x, y)
+    nav_lon = ds.createVariable("nav_lon", 'f4', (ncFileSpec.yVarName, ncFileSpec.xVarName))
+    nav_lon[:] = lonmtx
+    nav_lat = ds.createVariable("nav_lat", 'f4', (ncFileSpec.yVarName, ncFileSpec.xVarName))
+    nav_lat[:] = latmtx
+    ds.close()
+
 
 
 

diff --git a/notebooksOther/monthlyAggregateBFMData.py b/notebooksOther/monthlyAggregateBFMData.py
@@ -5,11 +5,16 @@
 
 import acIndUtils, acIndAggregator
 
+cdo = "/g100/home/userexternal/lmentasc/usr/Miniconda3/bin/cdo"
+nccopy = "/g100/home/userexternal/lmentasc/usr/Miniconda3/bin/nccopy"
 
-bfmDataFlPattern = "/gss/gss_work/DRES_uBOC2/adriaClim/bfm/output/historical/test1997-1999/BFM_5d_*.nc"
-outFl = "/gss/gss_work/DRES_uBOC2/adriaClim/bfm/output/historical/test1997-1999/BFM_monthly.nc"
+outdir = "/gss/gss_work/DRES_uBOC2/adriaClim/bfm/output/historical/test1997-1999/"
+
+bfmDataFlPattern = os.path.join(outdir, "BFM_5d_*.nc")
 maskFilePath = "/g100/home/userexternal/lmentasc/src/git/projects/AdriaClim/configurationProjCineca/scenarios/mask_NEMO_AdriaClim_compressed.nc"
 
+os.system(f"cd {outdir}; rm BFM_1monclim*.nc BFM_monthly*.nc")
+
 inputNcFileSpec = acIndUtils.acNcFileSpec(
                                ncFileName = bfmDataFlPattern,
                                varName = "Chla",
@@ -20,10 +25,10 @@
                                )
 
 outputNcFileSpec = acIndUtils.acNcFileSpec(
-                               ncFileName = outFl,
-                               varName = "Chla",
-                               xVarName = "lon",
-                               yVarName = "lat",
+                               ncFileName = "",
+                               varName = "",
+                               xVarName = "x",
+                               yVarName = "y",
                                zVarName = "deptht",
                                tVarName = "time_counter"
                                )
@@ -37,9 +42,82 @@
                                tVarName = "time_counter"
                                )
 
-import pdb; pdb.set_trace()
+
+varName = "Chla"
+print("")
+print(f"elaborating {varName}")
+outFl = os.path.join(outdir, f"BFM_monthly_{varName}.nc")
+inputNcFileSpec.varName = varName
+outputNcFileSpec.varName = varName
+outputNcFileSpec.ncFileName = outFl
+acIndAggregator.collectMonthlyData(inputNcFileSpec,
+                                   outputNcFileSpec,
+                                   coordsNcFileSpec = coordsNcFileSpec,
+                                   fill_value = 0)
+
+
+varName = "O2o"
+print("")
+print(f"elaborating {varName}")
+outFl = os.path.join(outdir, f"BFM_monthly_{varName}.nc")
+inputNcFileSpec.varName = varName
+outputNcFileSpec.varName = varName
+outputNcFileSpec.ncFileName = outFl
+acIndAggregator.collectMonthlyData(inputNcFileSpec,
+                                   outputNcFileSpec,
+                                   coordsNcFileSpec = coordsNcFileSpec,
+                                   fill_value = 0)
+
+
+varName = "N1p"
+print("")
+print(f"elaborating {varName}")
+outFl = os.path.join(outdir, f"BFM_monthly_{varName}.nc")
+inputNcFileSpec.varName = varName
+outputNcFileSpec.varName = varName
+outputNcFileSpec.ncFileName = outFl
 acIndAggregator.collectMonthlyData(inputNcFileSpec,
                                    outputNcFileSpec,
                                    coordsNcFileSpec = coordsNcFileSpec,
                                    fill_value = 0)
 
+
+varName = "N3n"
+print("")
+print(f"elaborating {varName}")
+outFl = os.path.join(outdir, f"BFM_monthly_{varName}.nc")
+inputNcFileSpec.varName = varName
+outputNcFileSpec.varName = varName
+outputNcFileSpec.ncFileName = outFl
+acIndAggregator.collectMonthlyData(inputNcFileSpec,
+                                   outputNcFileSpec,
+                                   coordsNcFileSpec = coordsNcFileSpec,
+                                   fill_value = 0)
+
+
+varName = "N5s"
+print("")
+print(f"elaborating {varName}")
+outFl = os.path.join(outdir, f"BFM_monthly_{varName}.nc")
+inputNcFileSpec.varName = varName
+outputNcFileSpec.varName = varName
+outputNcFileSpec.ncFileName = outFl
+acIndAggregator.collectMonthlyData(inputNcFileSpec,
+                                   outputNcFileSpec,
+                                   coordsNcFileSpec = coordsNcFileSpec,
+                                   fill_value = 0)
+
+
+curdir = os.getcwd()
+os.chdir(outdir)
+print("merging ...")
+os.system(f"{cdo} merge BFM_monthly_*.nc BFM_monthly.nc")
+outputNcFileSpec.ncFileName = "BFM_monthly.nc"
+acIndUtils.addNavlonNavlatFields(outputNcFileSpec)
+print("creating monthly climatology ...")
+os.system(f"{cdo} ymonmean BFM_monthly.nc BFM_1monclim_uncompressed.nc")
+print("compressing ...")
+os.system(f"{nccopy} -d9 BFM_1monclim_uncompressed.nc BFM_1monclim.nc")
+os.chdir(curdir)
+
+
diff --git a/notebooksOther/monthlyAggregateBFMData.sh b/notebooksOther/monthlyAggregateBFMData.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --account=uBOC2_mentasc
+#SBATCH --partition=g100_all_serial
+##SBATCH --partition=g100_usr_prod
+##SBATCH --qos=noQOS
+#SBATCH --mem=30G
+#SBATCH --nodes 1
+#SBATCH --ntasks-per-node=1
+#SBATCH --time=4:00:00
+#SBATCH --job-name=monthlyAggregateBFMData
+#SBATCH --output=monthlyAggregateBFMData_%j.out
+#SBATCH --error=monthlyAggregateBFMData_%j.err
+#SBATCH --mail-user=lorenzo.mentaschi@unibo.it
+
+py=/g100/home/userexternal/lmentasc/usr/Miniconda3/bin/python3.9
+
+rm BFM_1monclim* BFM_monthly*
+$py monthlyAggregateBFMData.py