update to NCAR(upstream) master. README.md conflict resolved

.gitignore

@@ -26,3 +26,6 @@
 *.exe
 *.out
 *.app
+
+# other files
+*.local

README.md

@@ -1,3 +1,4 @@
+[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.56043.svg)](http://dx.doi.org/10.5281/zenodo.56043)
 # mizuRoute
 mizuRoute is a stand-alone, post-processor of runoff output from a hydrologic model to produce streamflow estimates in the river network. The tool was developed for the large scale river routing (e.g., river network over contiguous United States), but works for small-size headwater basin as well.
 

netcdf_test/Makefile

@@ -10,22 +10,23 @@
 CC=pgf90
 
 ifeq "$(CC)" "gfortran"
-NCDF_PATH=/opt/netcdf-4.3.0+gcc-4.7.2
+NCDF_PATH=/opt/netcdf4-gcc
 LIBNETCDF = -Wl,-rpath,$(NCDF_PATH)/lib \
             -L$(NCDF_PATH)/lib -lnetcdff -lnetcdf
 INCNETCDF = -I$(NCDF_PATH)/include
 endif
 
 ifeq "$(CC)" "ifort"
-NCDF_PATH = /usr/local/netcdf-4.3.0+ifort-12.1
+NCDF_PATH = /opt/netcdf4-intel
 LIBNETCDF = -Wl,-rpath,$(NCDF_PATH)/lib \
  	-L$(NCDF_PATH)/lib -lnetcdff -lnetcdf
 INCNETCDF = -I$(NCDF_PATH)/include
 endif
 
 ifeq "$(CC)" "pgf90"
- LIBNETCDF = -L/usr/local/netcdf-4.3.0+pgi-13.4/lib -lnetcdff -lnetcdf
- INCNETCDF = -I/usr/local/netcdf-4.3.0+pgi-13.4/include
+ NCDF_PATH = /opt/netcdf4-pgi
+ LIBNETCDF = -L$(NCDF_PATH)/lib -lnetcdff -lnetcdf
+ INCNETCDF = -I$(NCDF_PATH)/include
 endif
 
 # define flags
@@ -39,7 +40,8 @@ endif
 
 ifeq "$(CC)" "pgf90"
  FLAGS1 = -Bstatic -Mbackslash -g -Mchkptr -Mchkstk -Mpgicoff -Minform=inform -Ktrap=divz,inv -Mprof=lines,time
- FLAGS = -Bstatic -Mbackslash -g -Mchkptr -Mchkstk -Mpgicoff -Minform=inform -Ktrap=divz,inv
+ #FLAGS = -Bstatic -Mbackslash -g -Mchkptr -Mchkstk -Mpgicoff -Minform=inform -Ktrap=divz,inv
+ FLAGS = -Mbackslash -g -Mchkptr -Mchkstk -Mpgicoff -Minform=inform -Ktrap=divz,inv
 endif
 
 # define program

ntopo/build/Makefile

@@ -5,26 +5,65 @@
 #
 #
 #========================================================================
-# PART 0: Define directory paths
+# PART 0: User configure part 
 #========================================================================
+# Define fortran compiler - gfortran, ifort or pgf90
+FC  = COMPILERNAME
 
 # Define core directory below which everything resides
-F_MASTER = /home/mizukami/hydro_nm/nHRU_routing/ntopo.v1/
+# parent directory of the 'build' directory
+# do not put space at the end of path
+F_MASTER = PARENTDIRECTORY 
 
+# Define the NetCDF libraries and path to include files
+ifeq "$(FC)" "gfortran"
+  NCDF_PATH=/opt/netcdf4-gcc
+  LIBNETCDF = -Wl,-rpath,$(NCDF_PATH)/lib \
+  		-L$(NCDF_PATH)/lib -lnetcdff -lnetcdf
+  INCNETCDF = -I$(NCDF_PATH)/include
+endif
+ifeq "$(FC)" "ifort"
+ NCDF_PATH = /opt/netcdf4-intel
+ LIBNETCDF = -Wl,-rpath,$(NCDF_PATH)/lib \
+		-L$(NCDF_PATH)/lib -lnetcdff -lnetcdf
+ INCNETCDF = -I$(NCDF_PATH)/include
+endif
+ifeq "$(FC)" "pgf90"
+ NCDF_PATH = /opt/netcdf4-pgf90
+ LIBNETCDF = -L$(NCDF_PATH)/lib -lnetcdff -lnetcdf
+ INCNETCDF = -I$(NCDF_PATH)/include
+endif
+
+# Define flags
+ifeq "$(FC)" "gfortran"
+ FLAGS = -Wall -g -ffree-line-length-none
+endif
+ifeq "$(FC)" "ifort"
+ FLAGS1 = -warn all -noerror_limit -FR -O0 -auto -WB -traceback -g -fltconsistency
+# FLAGS = -static -debug -warn all -check all,noarg_temp_created -FR -O0 -auto -WB -traceback -g -fltconsistency -fpe0
+ FLAGS = -debug -warn all -check all,noarg_temp_created -FR -O0 -auto -WB -traceback -g -fltconsistency -fpe0
+endif
+ifeq "$(FC)" "pgf90"
+ FLAGS1 = -Bstatic -Mbackslash -g -Mchkptr -Mchkstk -Mpgicoff -Minform=inform -Ktrap=divz,inv -Mprof=lines,time
+ FLAGS = -Bstatic -Mbackslash -g -Mchkptr -Mchkstk -Mpgicoff -Minform=inform -Ktrap=divz,inv
+endif
+
+#========================================================================
+# PART 1: Define directory paths
+#========================================================================
 # Core directory that contains source code
-F_KORE_DIR = $(F_MASTER)build/
+F_KORE_DIR = $(F_MASTER)build/src/
 
 # Location of the compiled modules
 MOD_PATH = $(F_MASTER)build/
 
 # Define the directory for the executables
 EXE_PATH = $(F_MASTER)bin
-#
+
 #========================================================================
-# PART 1: Assemble all of the FUSE sub-routines
+# PART 1: Assemble all of the sub-routines
 #========================================================================
 # Define subroutines
-#
 # data types
 DATATYPES = \
 		nrtype.f90 \
@@ -50,47 +89,14 @@ QROUTE = \
 		network_topo.f90 \
 
 # concatanate model subroutines
-#TEMP_MODSUB = $(DATATYPES) $(UTILS) $(NUMREC) $(IO) $(QROUTE)
 TEMP_MODSUB = $(DATATYPES) $(UTILS) $(IO) $(QROUTE)
 
 # insert appropriate directory name
 MODSUB = $(patsubst %, $(F_KORE_DIR)%, $(TEMP_MODSUB))
 
 #========================================================================
-# PART 2: Define the libraries, driver programs, and executables
+# PART 2: Define driver programs, and executables
 #========================================================================
-
-# Define the Fortran Compiler
-FC  = ifort
-
-# Define the NetCDF libraries and path to include files
-ifeq "$(FC)" "gfortran"
-  HDF_PATH=/opt/hdf5
-  ZLIB=/opt/zlib
-  NCDF_PATH=/opt/netcdf-4.3.0+gcc-4.7.2
-  SZIP=/opt/szip
-  LIBNETCDF = -Wl,-rpath,$(HDF_PATH)/lib:$(ZLIB)/lib:$(NCDF_PATH)/lib:$(SZIP)/lib \
-  		-L$(NCDF_PATH)/lib -lnetcdff -lnetcdf \
-      -L$(HDF_PATH)/lib -lhdf5_hl -lhdf5 \
-      -L$(ZLIB) -L$(SZIP)-lsz -lz -lcurl
-  INCNETCDF = -I$(NCDF_PATH)/include -I/$(HDF_PATH)/include -I$(SZIP)/include -I$(ZLIB)/include
-endif
-ifeq "$(FC)" "ifort"
- HDF_PATH  = /usr/local/hdf5
- NCDF_PATH = /usr/local/netcdf-4.3.0+ifort-12.1
- LOCL_PATH = /usr/local
- SZIP = /opt/szip
- ZLIB = /opt/zlib
- XTRA_LIBS = -L$(LOCL_PATH) -L$(SZIP)/lib -L$(ZLIB)/lib -lsz -lz -lcurl
- LIBNETCDF = -Wl,-rpath,$(HDF_PATH)/lib:$(ZLIB)/lib:$(NCDF_PATH)/lib:$(SZIP)/lib \
-		-L$(NCDF_PATH)/lib -lnetcdff -lnetcdf -L$(HDF_PATH)/lib -lhdf5_hl -lhdf5 $(XTRA_LIBS)
- INCNETCDF = -I$(NCDF_PATH)/include -I/$(HDF_PATH)/include -I$(SZIP)/include -I$(ZLIB)/include
-endif
-ifeq "$(FC)" "pgf90"
- LIBNETCDF = -L/usr/local/netcdf4-pgi/lib -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lsz -lz
- INCNETCDF = -I/usr/local/netcdf4-pgi/include
-endif
-
 # Define the driver routine
 DRIVER = $(F_KORE_DIR)process_river_topology.f90
 
@@ -100,23 +106,6 @@ EXE = process_river_topology.exe
 #========================================================================
 # PART 3: Compile the puppy
 #========================================================================
-
-# Define flags
-ifeq "$(FC)" "gfortran"
- FLAGS = -Wall -g -ffree-line-length-none
-endif
-ifeq "$(FC)" "ifort"
- FLAGS1 = -warn all -noerror_limit -FR -O0 -auto -WB -traceback -g -fltconsistency
-# FLAGS = -static -debug -warn all -check all,noarg_temp_created -FR -O0 -auto -WB -traceback -g -fltconsistency -fpe0
- FLAGS = -debug -warn all -check all,noarg_temp_created -FR -O0 -auto -WB -traceback -g -fltconsistency -fpe0
-endif
-ifeq "$(FC)" "pgf90"
- FLAGS1 = -Bstatic -Mbackslash -g -Mchkptr -Mchkstk -Mpgicoff -Minform=inform -Ktrap=divz,inv -Mprof=lines,time
- FLAGS = -Bstatic -Mbackslash -g -Mchkptr -Mchkstk -Mpgicoff -Minform=inform -Ktrap=divz,inv
-endif
-
-#FLAGS = -O3 -W -v
-
 #.SUFFIXES: .f .o .f90
 
 # tasks

route/build/Makefile

@@ -3,16 +3,55 @@
 #========================================================================
 #
 #
-# Define compiler
-FC  = ifort
 #
 #========================================================================
-# PART 1: Define directory paths and compiler
+# PART 0: User configure part 
 #========================================================================
+# Define fortran compiler - gfortran, ifort or pgf90
+FC  = COMPILERNAME
 
 # Define core directory below which everything resides
-F_MASTER = /home/mizukami/mizuRoute/route.v1/
+# parent directory of the 'build' directory
+# do not put space at the end of path
+F_MASTER = PARENTDIRECTORY 
 
+# Define the NetCDF libraries and path to include files
+ifeq "$(FC)" "gfortran"
+  NCDF_PATH=/opt/netcdf4-gcc
+  LIBNETCDF = -Wl,-rpath,$(NCDF_PATH)/lib \
+  		-L$(NCDF_PATH)/lib -lnetcdff -lnetcdf
+  INCNETCDF = -I$(NCDF_PATH)/include
+endif
+ifeq "$(FC)" "ifort"
+ NCDF_PATH = /opt/netcdf4-intel
+ LIBNETCDF = -Wl,-rpath,$(NCDF_PATH)/lib \
+		-L$(NCDF_PATH)/lib -lnetcdff -lnetcdf
+ INCNETCDF = -I$(NCDF_PATH)/include
+endif
+ifeq "$(FC)" "pgf90"
+ NCDF_PATH = /opt/netcdf4-pgf90
+ LIBNETCDF = -L$(NCDF_PATH)/lib -lnetcdff -lnetcdf
+ INCNETCDF = -I$(NCDF_PATH)/include
+endif
+
+# Define flags
+ifeq "$(FC)" "gfortran"
+ FLAGS = -Wall -g -ffree-line-length-none
+endif
+ifeq "$(FC)" "ifort"
+ FLAGS1 = -warn all -noerror_limit -FR -O0 -auto -WB -traceback -g -fltconsistency
+# FLAGS = -static -debug -warn all -check all,noarg_temp_created -FR -O0 -auto -WB -traceback -g -fltconsistency -fpe0
+ FLAGS = -warn all -check all,noarg_temp_created -FR -O2 -auto -WB -traceback -g -fltconsistency -fpe0
+# FLAGS = -debug -warn all -check all,noarg_temp_created -FR -O0 -auto -WB -traceback -g -fltconsistency -fpe0
+endif
+ifeq "$(FC)" "pgf90"
+ FLAGS1 = -Bstatic -Mbackslash -g -Mchkptr -Mchkstk -Mpgicoff -Minform=inform -Ktrap=divz,inv -Mprof=lines,time
+ FLAGS = -Mbackslash -g -Mchkptr -Mchkstk -Mpgicoff -Minform=inform -Ktrap=divz,inv
+endif
+
+#========================================================================
+# PART 1: Define directory paths
+#========================================================================
 # Core directory that contains source code
 F_KORE_DIR = $(F_MASTER)build/src/
 
@@ -21,7 +60,7 @@ MOD_PATH = $(F_MASTER)build/
 
 # Define the directory for the executables
 EXE_PATH = $(F_MASTER)bin
-#
+
 #========================================================================
 # PART 2: Assemble all of the sub-routines
 #========================================================================
@@ -70,27 +109,8 @@ TEMP_MODSUB = $(DATATYPES) $(UTILS) $(NUMREC) $(IO) $(QROUTE)
 MODSUB = $(patsubst %, $(F_KORE_DIR)%, $(TEMP_MODSUB))
 
 #========================================================================
-# PART 3: Define the libraries, driver programs, and executables
+# PART 2: Define driver programs, and executables
 #========================================================================
-
-# Define the NetCDF libraries and path to include files
-ifeq "$(FC)" "gfortran"
-  NCDF_PATH=/opt/netcdf-4.3.0+gcc-4.7.2
-  LIBNETCDF = -Wl,-rpath,$(NCDF_PATH)/lib \
-  		-L$(NCDF_PATH)/lib -lnetcdff -lnetcdf
-  INCNETCDF = -I$(NCDF_PATH)/include
-endif
-ifeq "$(FC)" "ifort"
- NCDF_PATH = /usr/local/netcdf-4.3.0+ifort-12.1
- LIBNETCDF = -Wl,-rpath,$(NCDF_PATH)/lib \
-		-L$(NCDF_PATH)/lib -lnetcdff -lnetcdf
- INCNETCDF = -I$(NCDF_PATH)/include
-endif
-ifeq "$(FC)" "pgf90"
- LIBNETCDF = -L/usr/local/netcdf-4.3.0+pgi-13.4/lib -lnetcdff -lnetcdf
- INCNETCDF = -I/usr/local/netcdf-4.3.0+pgi-13.4/include
-endif
-
 # Define the driver routine
 DRIVER = $(F_KORE_DIR)route_runoff.f90
 
@@ -100,26 +120,6 @@ EXE = route_runoff.exe
 #========================================================================
 # PART 4: Compile the puppy
 #========================================================================
-
-# Define flags
-ifeq "$(FC)" "gfortran"
- FLAGS = -Wall -g -ffree-line-length-none
-endif
-ifeq "$(FC)" "ifort"
- FLAGS1 = -warn all -noerror_limit -FR -O0 -auto -WB -traceback -g -fltconsistency
-# FLAGS = -static -debug -warn all -check all,noarg_temp_created -FR -O0 -auto -WB -traceback -g -fltconsistency -fpe0
- FLAGS = -warn all -check all,noarg_temp_created -FR -O2 -auto -WB -traceback -g -fltconsistency -fpe0
-# FLAGS = -debug -warn all -check all,noarg_temp_created -FR -O0 -auto -WB -traceback -g -fltconsistency -fpe0
-endif
-ifeq "$(FC)" "pgf90"
- FLAGS1 = -Bstatic -Mbackslash -g -Mchkptr -Mchkstk -Mpgicoff -Minform=inform -Ktrap=divz,inv -Mprof=lines,time
- FLAGS = -Mbackslash -g -Mchkptr -Mchkstk -Mpgicoff -Minform=inform -Ktrap=divz,inv
-endif
-
-#FLAGS = -O3 -W -v
-
-#.SUFFIXES: .f .o .f90
-
 # tasks
 all: compile install clean
 

scripts/Calc_hru_wgtavg_nc.py

@@ -18,6 +18,17 @@
 import math 
 import netCDF4 as nc4
 
+############################################ 
+#         hardcoded variables              #
+############################################
+# Name of netCDF variable for polygon ID in input data
+IDNM='hru_id'               
+# Name of netCDF variable for weight in weight data
+WGTNM='weight'
+OVRPLYNM='overlapPolyId'
+LATNM='latitude'
+LONNM='longitude'
+OVRNM='overlaps'
 ############################################ 
 #              Class                       #
 ############################################
@@ -29,11 +40,11 @@ def __init__(self,ncName):
 
     def getWgtHru(self,hru):
         """For given hru id, get weight of the intersected polygons and associated ID and lat/lon"""
-        wgtAll        = getNetCDFData(self.ncName, 'weight') 
-        overlapsIdAll = getNetCDFData(self.ncName, 'overlapPolyId') 
-        latAll        = getNetCDFData(self.ncName, 'latitude')
-        lonAll        = getNetCDFData(self.ncName, 'longitude')
-        overlapsAll   = getNetCDFData(self.ncName, 'overlaps')
+        wgtAll        = getNetCDFData(self.ncName, WGTNM) 
+        overlapsIdAll = getNetCDFData(self.ncName, OVRPLYNM) 
+        latAll        = getNetCDFData(self.ncName, LATNM)
+        lonAll        = getNetCDFData(self.ncName, LONNM)
+        overlapsAll   = getNetCDFData(self.ncName, OVRNM)
 
         self.hruList = self.getHruID()            # get hru id list
         idx=self.hruList.index(hru)               # get indix in array corresponding hru
@@ -46,7 +57,8 @@ def getWgtHru(self,hru):
         return (self.wgt, self.overlapsId, self.lat, self.lon, self.overlaps)
 
     def getHruIdName(self):
-        """ get Name of hru ID """
+        """ get Name of hru ID 
+            it must be the 1st dimension """
         f = nc4.Dataset(self.ncName,'r')
         self.dim = f.dimensions
         self.dimName = self.dim.keys()
@@ -109,7 +121,7 @@ def compAvgVal(nc_wgt,nc_in,varname):
 
   dataVal  = getNetCDFData(nc_in,varname) # Get data value 
   FillVal  = getNetCDFAtt(nc_in,varname,'_FillValue') # Get data value 
-  IdVal    = getNetCDFData(nc_in,'hru_id') 
+  IdVal    = getNetCDFData(nc_in,IDNM) 
   dim1size = dataVal.shape[0]
 
   #Initialize wgtVal[ntime,nhru] 
@@ -146,7 +158,6 @@ def compAvgVal(nc_wgt,nc_in,varname):
     Val2 = np.zeros((dim1size))
     if np.nansum(wgtArray) > 0.0:
     #  print (np.nansum(wgtArray) > 0.0)
-    #  print (overlaps != 0.0)
       # Adjust weight value if valid weight value (> 0) exist in list
       newWgtArray = [x/np.nansum(wgtArray) for x in wgtArray]
     #  print "%d invalid polygons out of %d polygons" %(numvoid,overlaps)