Tjh/add notebooks

.cmtbSettings

@@ -14,6 +14,8 @@ hpcSettings:
    hpcCores: 36
    hpcNodes: 1
 testName: ''
+hotStartFlag: false
+slack:
 logfileLoc: ./data/logs
 workingDirectory: ./data               # this is the directory where simulation files and QA/QC plots are made and existing architecture takes over
 netCDFdir: ./thredds_data             # this is the base directory where netCDF files are output

README.md

@@ -43,7 +43,7 @@ The test bed is established at the USACE CHL Field REsearch Facility in Duck, No
     - conda install <package>
 
       conda install -c conda-forge cartopy
-    * netCDF4, pyproj, utm, wavespectra, progressbar, opencv-python
+    * netCDF4, pyproj, utm (cf), wavespectra (cf), progressbar (cf), opencv (cf)
 
   - there's likely more, please add as you find!!  :-[]
 

frontback/frontBackNEW.py

@@ -59,7 +59,8 @@ def ww3simSetup(startTimeString, inputDict, allWind , allWL, allWave, wrr):
     print("Model Time Start : %s  Model Time End:  %s" % (startTime, endTime))
 
     # __________________Make Diretories_____________________________________________
-    fileHandling.makeCMTBfileStructure(pathPrefix)
+    fileHandling.makeCMTBfileStructure(wrr.workingDirectory)
+    print(wrr.workingDirectory)
 
     # ____________________________ begin model data gathering __________________________________________________________
     gdTB = getDataTestBed(startTime, endTime)        # initialize get data test bed (bathy)
@@ -69,7 +70,7 @@ def ww3simSetup(startTimeString, inputDict, allWind , allWL, allWave, wrr):
     assert rawspec is not None, "\n++++\nThere's No Wave data between %s and %s \n++++\n" % (startTime, endTime)
     # use generated time lists for these to provide accurate temporal values
     _, waveTimeList, wlTimeList, _, windTimeList = prepdata.createDifferentTimeLists(startTime, endTime, rawspec, rawWL,
-                                                                                     rawWind=rawwind)
+                                                                                     rawWind=rawwind,simTs=30*60)
     nFreq = np.size(rawspec['wavefreqbin'])
     # rotate and lower resolution of directional wave spectra
     wavepacket = prepdata.prep_spec(rawspec, version_prefix, datestr=dateString, plot=plotFlag, full=full, deltaangle=10,
@@ -221,9 +222,12 @@ class objects as listed below:
     if postProcessingDict['phaseResolved'] == True:
         spatialPostProcessed = postData.processNLwave(spatialData, wrr=wrr, ncFilesOnly=False)
         pointPostProcessed = None
+    elif postProcessingDict['phaseAveraged'] == True:
+        spatialPostProcessed = postData.processPAwave(spatialData, wrr=wrr, ncFilesOnly=False)
+        pointPostProcessed = postData.processPAStationWave(pointData, wrr=wrr, ncFilesOnly=False)
     else:
         spatialPostProcessed, pointPostProcessed = someFunctionPostProcesing(spatialData, pointData)
-    
+
     # __________________________2. make netCDF Files________________________________
     # __________________________2a. Spatial output _________________________________
 
@@ -255,21 +259,21 @@ class objects as listed below:
         elif postProcessingDict['phaseAveraged'] is True:
             variables = ncfile.variables.keys()
             for var in variables:
-                if var in ['waveHs', 'waveDm', 'waveTm'] and plotFlag is True:
+                if var in ['waveHs', 'waveMeanDirection', 'waveTm'] and plotFlag is True:
                     plotOutFname = 'test.png'
                     oP.unstructuredSpatialPlot(plotOutFname, fieldNc=ncfile, variable=var)
         else:
             raise NotImplementedError("other model plotting types haven't been implemented yet")
     # __________________________2b. point output _________________________________
     if pointPostProcessed is not None:
-        print(' post-processing point data is not developed yet')
+        print(' post-processing point data')
         fldrArch = os.path.join(model, version_prefix)
         varYaml_fname = f'yaml_files/waveModels/{fldrArch}/Station_var.yml'
         globalyaml_fname = f'yaml_files/waveModels/{fldrArch}/Station_globalmeta.yml'
         # frame work is shown below, post processing lays out nice nested dictionary for every save station
         for ss, station in enumerate(pointPostProcessed['stationList']):
             outFileName = fileHandling.makeTDSfileStructure(Thredds_Base, fldrArch, dateString, station)
-            p2nc.makenc_generic(outFileName, globalyaml_fname, varYaml_fname, pointPostProcessed[ss])
+            p2nc.makenc_generic(outFileName, globalyaml_fname, varYaml_fname, pointPostProcessed[station])
     # __________________________2bb. point plotting ________________________________
         print("is this necessary??")
 

genericWorkFlow.py

@@ -31,6 +31,8 @@ def Master_workFlow(inputDict):
     pbsFlag = inputDict['pbsFlag']
     analyzeFlag = inputDict['analyzeFlag']
     plotFlag = inputDict['plotFlag']
+    hotStartFlag = inputDict['hotStartFlag']
+    hotStartDirectory = inputDict.get('hotStartDirectory',None)
     modelName = inputDict['modelSettings'].get('modelName', None)
     log = inputDict.get('logging', True)
     updateBathy = inputDict.get('updateBathy', None)
@@ -44,6 +46,7 @@ def Master_workFlow(inputDict):
         workingDirectory = os.path.join(cmtbRootDir,workingDir[2:],modelName.lower(), version_prefix)
     else:
         workingDirectory = os.path.join(workingDir, modelName.lower(), version_prefix)
+    print(workingDirectory)
     inputDict['netCDFdir'] = os.path.join(inputDict['netCDFdir'], 'waveModels')
     inputDict['path_prefix'] = workingDirectory
     # ______________________ Logging/FileHandling ____________________________
@@ -94,9 +97,8 @@ def Master_workFlow(inputDict):
             if modelName in ['ww3']:
                 wrr = wrrClass.ww3io(workingDirectory=workingDirectory,testName=testName, versionPrefix=version_prefix,
                                      startTime=DT.datetime.strptime(time, '%Y-%m-%dT%H:%M:%SZ'),
-                                     endTime=DT.datetime.strptime(time, '%Y-%m-%dT%H:%M:%SZ') + DT.timedelta(
-                                     hours=inputDict['simulationDuration']), runFlag=runFlag,
-                                     generateFlag=generateFlag, readFlag=analyzeFlag, pbsFlag=pbsFlag)
+                                     endTime=DT.datetime.strptime(endTime, '%Y-%m-%dT%H:%M:%SZ'), runFlag=runFlag,
+                                     generateFlag=generateFlag, readFlag=analyzeFlag, pbsFlag=pbsFlag, hotStartFlag=hotStartFlag)
 
                 if generateFlag is True:
                     wavePacket, windPacket, wlPacket, bathyPacket, gridFname, wrr = frontBackNEW.ww3simSetup(time,
@@ -156,25 +158,24 @@ def Master_workFlow(inputDict):
                     print("windPacket has keys: {}".format(windPacket.keys()))
                 except AttributeError:
                     pass
-
-                if pbsFlag is True:
-                    wrr.hpcCores = inputDict['hpcSettings']['hpcCores']
-                    wrr.hpcNodes = inputDict['hpcSettings']['hpcNodes']
+                print(updateBathy)                
                 # write simulation files (if assigned)
                 wrr.writeAllFiles(wavePacket=wavePacket, windPacket=windPacket, wlPacket=wlPacket,
                                   bathyPacket=bathyPacket, gridfname=gridFname,
-                                  ctdPacket=ctdPacket, updateBathy=updateBathy)
+                                  ctdPacket=ctdPacket, updateBathy=updateBathy,hotStartDirectory=hotStartDirectory)
 
             # run simulation (as appropriate)
             if runFlag is True:
-                wrr.runSimulation(modelExecutable=inputDict['modelExecutable'])
+                if pbsFlag is True:
+                    wrr.hpcCores = inputDict['hpcSettings']['hpcCores']
+                    wrr.hpcNodes = inputDict['hpcSettings']['hpcNodes']
+                wrr.runSimulation(modelExecutable=inputDict['modelExecutable'],hotStartDirectory=hotStartDirectory)
 
             # post process (as appropriate)
             if analyzeFlag == True:
                 spatialData, savePointData = wrr.readAllFiles()
                 frontBackNEW.genericPostProcess(time, inputDict, spatialData=spatialData, pointData=savePointData,
                                                 wrr=wrr)
-
             # if it's a live run, move the plots to the output directory
             if plotFlag is True and DT.date.today() == projectEnd or inputDict['slack'] is not None:
                 from testbedutils import cmtbSlack

grids/ww3/unww3_Irene_REFACTORED.inbnd

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