Merge pull request #38 from noaa-oar-arl/develop

Develop

.github/workflows/ci.yml

@@ -21,6 +21,10 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
+      - name: Install dependencies
+        run: |
+          sudo apt install libnetcdff-dev
+
       - name: Debug compile and run
         run: |
           make clean
@@ -38,3 +42,14 @@ jobs:
         env:
           DEBUG: 0
           FC: ${{ matrix.compiler }}
+
+      - name: Non-NetCDF comile and run
+        run: |
+          make clean
+          make
+          sed -e s/input_variables_2D.nc/input_variables.txt/g namelist.canopy > tmp && mv tmp namelist.canopy
+          ./canopy
+        env:
+          DEBUG: 0
+          FC: ${{ matrix.compiler }}
+          NETCDF: 0

.gitignore

@@ -1,6 +1,7 @@
 /canopy
 output*.txt
 test_*.txt
+test*.nc
 
 # Prerequisites
 *.d

Makefile

@@ -1,6 +1,7 @@
 #
-# Use `DEBUG=1 make` for a debug build
-#
+# Use `FC=<compiler> ... make` to select compiler
+# Use `DEBUG=1 ... make` for a debug build
+# Use `NETCDF=1 ... make` to build with NetCDF using `nf-config`
 
 # Compiler
 FC ?= gfortran
@@ -12,18 +13,37 @@ $(info FC setting: '$(FC)')
 # Default to non-debug build
 DEBUG ?= 0
 
+# Default to NetCDF build
+NETCDF ?= 1
+
 # Compile flags
+$(info DEBUG setting: '$(DEBUG)')
 ifeq ($(DEBUG), 1)
   FCFLAGS := -g -Wall -Wextra -Wconversion -Og -pedantic -fcheck=bounds -fmax-errors=5
 else ifeq ($(DEBUG), 0)
   FCFLAGS := -O3
 else
   $(error invalid setting for DEBUG, should be 0 or 1 but is '$(DEBUG)')
 endif
-$(info DEBUG setting: '$(DEBUG)')
 
-# Link flags
-FLFLAGS :=
+# NETCDF Settings here
+LIBS :=
+INC :=
+$(info NETCDF setting: '$(NETCDF)')
+ifeq ($(NETCDF), 1)
+  NETCDF_FLIBS := $(shell nf-config --flibs)
+  NETCDF_INC := -I$(shell nf-config --includedir)
+  #
+  LIBS += $(NETCDF_FLIBS)
+  INC += $(NETCDF_INC)
+  FCFLAGS += -DNETCDF
+else ifeq ($(NETCDF), 0)
+  #
+else
+  $(error invalid setting for NETCDF, should be 0 or 1 but is '$(NETCDF)')
+endif
+$(info LIBS: '$(LIBS)')
+$(info INC:  '$(INC)')
 
 # Source objects
 OBJS :=\
@@ -38,6 +58,8 @@ OBJS :=\
  canopy_alloc.o \
  canopy_init.o \
  canopy_txt_io_mod.o \
+ canopy_ncf_io_mod.o \
+ canopy_check_input.o \
  canopy_read_txt.o \
  canopy_dxcalc_mod.o \
  canopy_profile_mod.o \
@@ -50,18 +72,23 @@ OBJS :=\
  canopy_dealloc.o \
  canopy_app.o
 
+ifeq ($(NETCDF), 0)
+  _ncf_objs := canopy_check_input.o canopy_ncf_io_mod.o
+  OBJS := $(filter-out $(_ncf_objs),$(OBJS))
+endif
+
 # Program name
 PROGRAM := canopy
 
 # Targets
 .PHONY: all clean
 all: $(PROGRAM)
 
-$(PROGRAM): $(OBJS)
-	$(FC) $(FCFLAGS) $^ -o $@ $(FLFLAGS)
+$(PROGRAM): $(OBJS_APP) $(OBJS)
+	$(FC) $(FCFLAGS) $^ -o $@ $(LIBS) $(INC)
 
 %.o: %.F90
-	$(FC) $(FCFLAGS) -c $<
+	$(FC) $(FCFLAGS) $(INC) -c $<
 
 clean:
 	rm -f *.o *.mod $(PROGRAM)

README.md

@@ -5,6 +5,10 @@ Author(s):
 
 Patrick Campbell, Zachary Moon, and Wei-Ting Hung
 
+Build canopy model:
+
+Canopy-App requires NetCDF-Fortran Libraries (i.e., -lnetcdf -lnetcdff) for NetCDF I/O Option. See included Makefile for example.
+
 Compile, edit namelist, and run canopy model:
 - `make`
 - `namelist.canopy`
@@ -16,7 +20,7 @@ Canopy is parameterized by foliage distribution shape functions and parameters f
 
 Current Canopy-App components:
 
-1.  In-Canopy Winds and Wind Adjustment Factor (WAF) for wildland fire spread and air quality applications.
+1.  In-Canopy Winds and Wind Adjustment Factor (WAF) for wildfire spread and air quality applications.
 
     Namelist Option : `ifcanwind`
 
@@ -35,27 +39,34 @@ Current Canopy-App components:
 
     - `canopy_phot_mod.F90`
 
-    **Current Canopy-App Input:** Typical 1D/2D gridded atmospheric model input variables in 1st layer above canopy
+    **Current Canopy-App Input:** Typical 1D or 2D (time=1,lat,lon) gridded atmospheric model input variables in 1st layer above canopy
+
+    Namelist Option : `file_vars`  Full name of input file (Supports either text or NetCDF format with following formats:
+                                                            `.txt`, `.nc`, `.ncf`, or `.nc4`)
 
-    Namelist Option : `file_vars`  Name of input file (Currently only in txt format, e.g., `input_variables.txt`)
+- See example file inputs for variables and format (`input_variables.txt`, `input_variables_1D.nc`, or `input_variables_2D.nc`).
+- Canopy-App assumes the NetCDF input files are in CF-Convention; recommend using double or float for real variables.
+- Canopy-App can also be run with a single point of 1D input data in a text file (e.g. `input_variables_point.txt`).
 
-    **Current Canopy-App Output:** Outputs canopy winds/WAF, canopy vertical/eddy diffusivity values, and
-    canopy photolysis attenuation correction factors (currently only in txt format).
+    **Current Canopy-App Output:** Outputs 3D canopy winds, canopy vertical/eddy diffusivity values, and
+    canopy photolysis attenuation correction factors, and 2D Wind Adjustment Factor (WAF).
 
-    Namelist Option : `file_out`  Prefix of output file name (Currently only in txt format, e.g., `TESTRUN`)
+    Namelist Option : `file_out`  Prefix string (e.g., 'test') used for output file name (Currently in both 1D txt or 2D NetCDF format (only when 2D NCF input is used, i.e., infmt_opt=0).
 
 
-    **Table 1. Canopy-App input variables**
+    **Table 1. Canopy-App Required Input Variables**
 
     | Variable Name    | Variable Description and Units                    |
     | ---------------  | ------------------------------------------------- |  
     | LAT              | Latitude  (degrees)                               |
-    | LON              | Longitude (degrees)                               |
+    | LON              | Longitude (degrees; from 0-360)                   |
+    | TIME             | Timestamp (days since YYYY-N-D 0:0:0) (NetCDF Only) |
     | FH               | Forest canopy height (m)                          |
-    | WS               | Wind speed at reference height (m/s), e.g., 10 m  |
+    | HREF             | Reference height above canopy (m)                 |
+    | WS               | Wind speed at HREF (m/s), e.g., 10 m              |
     | CLU              | Forest clumping index (dimensionless)             |
     | LAI              | Leaf area index (m2/m2)                           |
-    | VTYPE            | Vegetation type (dimensionless), e.g., VIIRS      |
+    | VTYPE            | Vegetation type (dimensionless), VIIRS Only       |
     | FFRAC            | Forest fraction (dimensionless)                   |
     | UST              | Friction velocity (m/s)                           |
     | CSZ              | Cosine of the solar zenith angle (dimensionless)  |
@@ -67,15 +78,17 @@ Current Canopy-App components:
 
     | Namelist Option  | Namelist Description and Units                                                       |
     | ---------------  | ---------------------------------------------------------------------------------- |
-    | nlat             | number of latitude cells (must match # of LAT in `file_vars` above )               |
-    | nlon             | number of longitude cells (must match # of LON in `file_vars`above )               |
+    | infmt_opt        | integer for choosing 1D or 2D input file format (default = 0, 2D)                  |
+    | nlat             | number of latitude cells (must match # of LAT in `file_vars` above)                |
+    | nlon             | number of longitude cells (must match # of LON in `file_vars`above)                |
     | modlays          | number of model (below and above canopy) layers                                    |
     | modres           | above and below canopy model vertical resolution (m)                               |
     | ifcanwind        | logical canopy wind option (default = .FALSE.)                                     |
     | ifcanwaf         | logical canopy WAF option (default = .FALSE.)**                                    |
     | ifcaneddy        | logical canopy eddy Kz option (default = .FALSE.)                                  |
     | ifcanphot        | logical canopy photolysis option (default = .FALSE.)                               |
-    | href             | real value of reference height above canopy associated with input wind speed (m)   |
+    | href_opt         | integer for using href_set in namelist (= 0) or array from file (= 1); default = 0 |
+    | href_set         | user set real value of reference height above canopy associated with input wind speed (m) (only used if href_opt = 0)  |
     | z0ghc            | ratio of ground roughness length to canopy top height (Massman et al., 2017)       |
     | lamdars          | Value representing influence of roughness sublayer (Massman et al., 2017)          |
     | dx_opt           | 0=Calculation of dx resolution/distance from lon; 1=user set dx grid resolution    |

canopy_alloc.F90

@@ -17,51 +17,56 @@ SUBROUTINE canopy_alloc
 !-------------------------------------------------------------------------------
 ! Allocate canopy input variables
 !-------------------------------------------------------------------------------
-!   TODO:  If txt or 1D ncf...
-    if(.not.allocated(variables))  allocate(variables(nlat*nlon))
-!   TODO:  If 2D ncf...
-!   if(.not.allocated(variables))  allocate(variables(nlat,nlon))
+
+    if(.not.allocated(variables))     allocate(variables(nlat*nlon))
+    if(.not.allocated(variables_2d))  allocate(variables_2d(nlat,nlon))
 
 !-------------------------------------------------------------------------------
-! Allocate arrays for Canopy Distribution
+! Allocate arrays for Internal Canopy Distribution Variables
 !-------------------------------------------------------------------------------
 
     if(.not.allocated(zhc))        allocate(zhc(modlays))
     if(.not.allocated(fafraczInt)) allocate(fafraczInt(modlays))
 
 !-------------------------------------------------------------------------------
-! Allocate arrays for Canopy Wind
+! Allocate arrays for Canopy Wind Outputs
 !-------------------------------------------------------------------------------
 
     if (ifcanwind .or. ifcanwaf) then
         write(*,*)  'Canopy wind and/or WAF option selected'
         write(*,*)  '-------------------------------'
-        if(.not.allocated(canBOT))     allocate(canBOT(modlays))
-        if(.not.allocated(canTOP))     allocate(canTOP(modlays))
-        if(.not.allocated(canWIND))    allocate(canWIND(modlays,nlat*nlon))
-        if(.not.allocated(dx))         allocate(dx(nlat*nlon))
-        if(.not.allocated(waf))        allocate(waf(nlat*nlon))
+        if(.not.allocated(canBOT))        allocate(canBOT(modlays))
+        if(.not.allocated(canTOP))        allocate(canTOP(modlays))
+        if(.not.allocated(canWIND))       allocate(canWIND(nlat*nlon,modlays))
+        if(.not.allocated(canWIND_3d))    allocate(canWIND_3d(nlat,nlon,modlays))
+        if(.not.allocated(dx))            allocate(dx(nlat*nlon))
+        if(.not.allocated(dx_2d))         allocate(dx_2d(nlat,nlon))
+        if(.not.allocated(waf))           allocate(waf(nlat*nlon))
+        if(.not.allocated(waf_2d))        allocate(waf_2d(nlat,nlon))
+
     end if
 
 !-------------------------------------------------------------------------------
-! Allocate arrays for Canopy Diffusivity Profile
+! Allocate arrays for Canopy Diffusivity Profile Outputs
 !-------------------------------------------------------------------------------
 
     if (ifcaneddy) then
         write(*,*)  'Canopy eddy Kz option selected'
         write(*,*)  '-------------------------------'
-        if(.not.allocated(Kz))         allocate(Kz(modlays,nlat*nlon))
+        if(.not.allocated(Kz))            allocate(Kz(nlat*nlon,modlays))
+        if(.not.allocated(Kz_3d))         allocate(Kz_3d(nlat,nlon,modlays))
     end if
 
 
 !-------------------------------------------------------------------------------
-! Allocate arrays for Canopy Photolysis Correction Factor
+! Allocate arrays for Canopy Photolysis Correction Factor Outputs
 !-------------------------------------------------------------------------------
 
     if (ifcanphot) then
         write(*,*)  'Canopy photolysis option selected'
         write(*,*)  '-------------------------------'
-        if(.not.allocated(rjcf))         allocate(rjcf(modlays,nlat*nlon))
+        if(.not.allocated(rjcf))            allocate(rjcf(nlat*nlon,modlays))
+        if(.not.allocated(rjcf_3d))         allocate(rjcf_3d(nlat,nlon,modlays))
     end if
 
 

canopy_app.F90

@@ -6,7 +6,10 @@ program canopy_app
 !    Prototype: Patrick C. Campbell, 06/2022
 !    Revised  : PCC (10/2022)
 !-------------------------------------------------------------
-    use canopy_files_mod   !main canopy input files
+    use canopy_files_mod  ! main canopy input files
+#ifdef NETCDF
+    use canopy_ncf_io_mod
+#endif
 
     implicit none
 
@@ -28,25 +31,15 @@ program canopy_app
 
     call canopy_init
 
-!    TODO :: Add a separate intialize routine for gridded ncdf canopy variables
-!            to fit ncf file, e.g.,, call canout_ncf_init
-
 !-------------------------------------------------------------------------------
-! Read met/sfc gridded model input file (currently text or 1D or 2D ncf).
+! Read met/sfc gridded model input file (currently 1D TXT or 1D/2D NETCDF).
 !-------------------------------------------------------------------------------
 
-! ... TODO:  NL condition for data read from txt or netcdf 1D or 2D
-
+#ifdef NETCDF
+    call canopy_check_input(file_vars(1))
+#else
     call canopy_read_txt(file_vars(1))
-
-! ... TODO:  add option to read met/sfc input variables from 1D ncf file
-    !e.g., call canopy_read_ncf_1D(file_vars(1))
-
-! ... TODO:  add option to read met/sfc input variables from 2D ncf file
-    !e.g., call canopy_read_ncf_2D(file_vars(1))
-
-! ... TODO:  Set nlat = nlat_user (if txt) or nlat = nlat_file (if ncf)
-! ... TODO:  Set nlon = nlat_user (if txt) or nlon = nlon_file (if ncf)
+#endif
 
 !-------------------------------------------------------------------------------
 ! Main canopy model calculations.
@@ -55,13 +48,25 @@ program canopy_app
     call canopy_calcs
 
 !-------------------------------------------------------------------------------
-! Write model output of canopy model calculations.
+! Allocate and initialize 2D/3D NetCDF output data structures
 !-------------------------------------------------------------------------------
 
-! ... TODO:  NL condition for data write to txt or netcdf 1D or 2D
+#ifdef NETCDF
+    call canopy_outncf_alloc
+
+    call canopy_outncf_init
+#endif
+
+!-------------------------------------------------------------------------------
+! Write model output of canopy model calculations.
+!-------------------------------------------------------------------------------
 
     call canopy_write_txt(file_out(1))
 
+#ifdef NETCDF
+    call canopy_write_ncf(file_out(1)) !only output if 2D input NCF is used
+#endif
+
 !-------------------------------------------------------------------------------
 ! Dellocate necessary variables.
 !-------------------------------------------------------------------------------