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Commit 7508f9e3 authored by Pierre Cazenave's avatar Pierre Cazenave

Update the examples with those from the FVCOM v4.0 release.

parent 62f71657
Pipeline #723 skipped
...@@ -58,7 +58,8 @@ ...@@ -58,7 +58,8 @@
INSTALLDIR = $(TOPDIR)/libs/install INSTALLDIR = $(TOPDIR)/libs/install
#=========================================================================== #===========================================================================
# PREPROCESSOR OPTIONS FOR CPP # PREPROCESSOR OPTIONS FOR CPP
DEF_FLAGS = -P -C -traditional # DEF_FLAGS = -P -C -traditional
DEF_FLAGS = -P -traditional
#=========================================================================== #===========================================================================
# #
####################### MEDM ENVIRONMENT ##################################### ####################### MEDM ENVIRONMENT #####################################
...@@ -93,7 +94,8 @@ dashL= $(empty) -L ...@@ -93,7 +94,8 @@ dashL= $(empty) -L
# SET PATH TO LIBRARIES WITH IOLIBS # SET PATH TO LIBRARIES WITH IOLIBS
# SET PATH TO INCLUDE FILES (netcdf.mod) WITH IOINCS # SET PATH TO INCLUDE FILES (netcdf.mod) WITH IOINCS
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
IOLIBS = -lnetcdf #-L/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/lib -lnetcdf IOLIBS = -lnetcdff -lnetcdf #-lhdf5_hl -lhdf5 -lz -lcurl -lm
# IOLIBS = -lnetcdf #-L/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/lib -lnetcdf
IOINCS = #-I/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/include IOINCS = #-I/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/include
# IOLIBS = -L/usr/local/install/netcdf/gcc_ifort/3.6.2/lib -lnetcdf # IOLIBS = -L/usr/local/install/netcdf/gcc_ifort/3.6.2/lib -lnetcdf
# IOINCS = -I/usr/local/install/netcdf/gcc_ifort/3.6.2/include # IOINCS = -I/usr/local/install/netcdf/gcc_ifort/3.6.2/include
...@@ -245,7 +247,7 @@ dashL= $(empty) -L ...@@ -245,7 +247,7 @@ dashL= $(empty) -L
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# FLAG_11 = -DGOTM # FLAG_11 = -DGOTM
# GOTMLIB = -L../GOTM_source -lturbulence -lutil -lmeanflow # GOTMLIB = -L../GOTM_source -lturbulence -lutil #-lmeanflow
# GOTMINCS = -I../GOTM_source # GOTMINCS = -I../GOTM_source
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
...@@ -315,11 +317,24 @@ dashL= $(empty) -L ...@@ -315,11 +317,24 @@ dashL= $(empty) -L
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# SUSPENDED SEDIMENT MODEL: UNCOMMENT TO INCLUDE MODEL # SUSPENDED SEDIMENT MODEL: UNCOMMENT TO INCLUDE MODEL
# ORIG : the sediment transport model developed by Geoffey Cowles in v3.1-v3.2
# CSTMS: Community Sediment Transport Modeling System with cohesive model
# DELFT: Sediment modeling system as Delft Flow (not included)
#
# note: only one model should be chosen for modeling.
#
# Utilities:
# OFFLINE_SEDIMENT : run sediment with offline hydrodynamic forcing
# FLUID_MUD : activate the 2-D fluid mud at bed-water interface
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# FLAG_21 = -DSEDIMENT # FLAG_21 = -DSEDIMENT
# FLAG_211 = -DORIG_SED
# FLAG_211 = -DCSTMS_SED
#
# FLAG_22 = -DOFFLINE_SEDIMENT # FLAG_22 = -DOFFLINE_SEDIMENT
# FLAG_43 = -DFLUID_MUD
#
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# KALMAN FILTERS # KALMAN FILTERS
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
...@@ -345,22 +360,31 @@ dashL= $(empty) -L ...@@ -345,22 +360,31 @@ dashL= $(empty) -L
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# GENERAL BIOLOGICAL MODEL: UNCOMMENT TO INCLUDE MODEL # GENERAL BIOLOGICAL MODEL: UNCOMMENT TO INCLUDE MODEL
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# FLAG_25 = -DBioGen # FLAG_25 = -DBioGen
# BIOLIB = -L$(TOPDIR)/BIO_source -lbiomodule # FLAG_251 = -DOFFLINE_BIOLOGY
# BIOINCS = -I$(TOPDIR)/BIO_source/ # BIOLIB = -L$(TOPDIR)/BIO_source -lbiomodule
# BIOINCS = -I$(TOPDIR)/BIO_source
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# Dynamic/Thermodynamic Ice # Dynamic/Thermodynamic Ice
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# NOTE: Must use -DSPHERICAL and -DHEAT_FLUX ----- only for old version v2.7 # NOTE: Must use -DSPHERICAL and -DHEAT_FLUX ----- this note only for old version v2.7
# ICE_EMBEDDING must with SEMI_IMPLICIT
# FLAG_26 = -DICE # FLAG_26 = -DICE
# FLAG_261 = -DICE_EMBEDDING
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# CALCULATE THE NET HEAT FLUX IN MODEL # CALCULATE THE NET HEAT FLUX IN MODEL (THREE CHOICES):
# 1. CALCULATE THE NET HEAT FLUX USING COARE26Z
# 2. CALCULATE THE NET HEAT FLUX USING COARE26Z for Great Lake
# 3. CALCULATE THE NET HEAT FLUX USING SOLAR HEATING MODULE
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# FLAG_27 = -DHEATING_CALCULATED # FLAG_27 = -DHEATING_CALCULATED
# FLAG_27 = -DHEATING_CALCULATED_GL
# FLAG_27 = -DHEATING_SOLAR
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# AIR_PRESSURE FROM SURFACE FORCING # AIR_PRESSURE FROM SURFACE FORCING
...@@ -432,7 +456,13 @@ dashL= $(empty) -L ...@@ -432,7 +456,13 @@ dashL= $(empty) -L
# PETSC Version # PETSC Version
# If your PETSc is 2.3.2 or older, uncomment this flag # If your PETSc is 2.3.2 or older, uncomment this flag
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
FLAG_41 = -DOLD_PETSC # FLAG_41 = -DOLD_PETSC
#--------------------------------------------------------------------------
# SPECIAL PARTITION
# This flag can make sure the identical repeat run for same amount of CPUs
#--------------------------------------------------------------------------
# FLAG_42 = -DPARTITION_SPECIAL
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# DEVELOPMENT FLAGS # DEVELOPMENT FLAGS
...@@ -507,7 +537,7 @@ dashL= $(empty) -L ...@@ -507,7 +537,7 @@ dashL= $(empty) -L
CXX = mpicxx CXX = mpicxx
CFLAGS = -O3 CFLAGS = -O3
FC = mpif90 FC = mpif90
# DEBFLGS = -check all # DEBFLGS = -check all -traceback
# Use 'OPT = -O0 -g' for fast compile to test the make # Use 'OPT = -O0 -g' for fast compile to test the make
# Use 'OPT = -xP' for fast run on em64t (Hydra and Guppy) # Use 'OPT = -xP' for fast run on em64t (Hydra and Guppy)
# Use 'OPT = -xN' for fast run on ia32 (Salmon and Minke) # Use 'OPT = -xN' for fast run on ia32 (Salmon and Minke)
...@@ -582,8 +612,9 @@ dashL= $(empty) -L ...@@ -582,8 +612,9 @@ dashL= $(empty) -L
$(FLAG_31) $(FLAG_32) $(FLAG_33) $(FLAG_34) \ $(FLAG_31) $(FLAG_32) $(FLAG_33) $(FLAG_34) \
$(FLAG_35) $(FLAG_36) $(FLAG_37) $(FLAG_38) \ $(FLAG_35) $(FLAG_36) $(FLAG_37) $(FLAG_38) \
$(FLAG_39) $(FLAG_40) $(FLAG_41) $(FLAG_42) \ $(FLAG_39) $(FLAG_40) $(FLAG_41) $(FLAG_42) \
$(FLAG_LAM)\ $(FLAG_43) $(FLAG_LAM)\
$(FLAG_101) $(FLAG_102) $(FLAG_103) $(FLAG_104) $(FLAG_105) $(FLAG_101) $(FLAG_102) $(FLAG_103) $(FLAG_104) $(FLAG_105)\
$(FLAG_211) $(FLAG_212) $(FLAG_213) $(FLAG_251) $(FLAG_261)
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# Libraries # Libraries
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
......
...@@ -214,7 +214,9 @@ ...@@ -214,7 +214,9 @@
ICE_AIR_TEMP = 0.0000000E+00, ICE_AIR_TEMP = 0.0000000E+00,
ICE_SPEC_HUMIDITY = 0.0000000E+00, ICE_SPEC_HUMIDITY = 0.0000000E+00,
ICE_SHORTWAVE = 0.0000000E+00, ICE_SHORTWAVE = 0.0000000E+00,
ICE_CLOUD_COVER = 0.0000000E+00 ICE_LONGWAVE_TYPE = 'PW',
ICE_CLOUD_COVER = 0.0000000E+00,
HIGH_LATITUDE_WAVE = F
/ /
&NML_PROBES &NML_PROBES
PROBES_ON = F, PROBES_ON = F,
......
...@@ -58,7 +58,8 @@ ...@@ -58,7 +58,8 @@
INSTALLDIR = $(TOPDIR)/libs/install INSTALLDIR = $(TOPDIR)/libs/install
#=========================================================================== #===========================================================================
# PREPROCESSOR OPTIONS FOR CPP # PREPROCESSOR OPTIONS FOR CPP
DEF_FLAGS = -P -C -traditional # DEF_FLAGS = -P -C -traditional
DEF_FLAGS = -P -traditional
#=========================================================================== #===========================================================================
# #
####################### MEDM ENVIRONMENT ##################################### ####################### MEDM ENVIRONMENT #####################################
...@@ -93,7 +94,8 @@ dashL= $(empty) -L ...@@ -93,7 +94,8 @@ dashL= $(empty) -L
# SET PATH TO LIBRARIES WITH IOLIBS # SET PATH TO LIBRARIES WITH IOLIBS
# SET PATH TO INCLUDE FILES (netcdf.mod) WITH IOINCS # SET PATH TO INCLUDE FILES (netcdf.mod) WITH IOINCS
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
IOLIBS = -lnetcdf #-L/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/lib -lnetcdf IOLIBS = -lnetcdff -lnetcdf #-lhdf5_hl -lhdf5 -lz -lcurl -lm
# IOLIBS = -lnetcdf #-L/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/lib -lnetcdf
IOINCS = #-I/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/include IOINCS = #-I/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/include
# IOLIBS = -L/usr/local/install/netcdf/gcc_ifort/3.6.2/lib -lnetcdf # IOLIBS = -L/usr/local/install/netcdf/gcc_ifort/3.6.2/lib -lnetcdf
# IOINCS = -I/usr/local/install/netcdf/gcc_ifort/3.6.2/include # IOINCS = -I/usr/local/install/netcdf/gcc_ifort/3.6.2/include
...@@ -245,7 +247,7 @@ dashL= $(empty) -L ...@@ -245,7 +247,7 @@ dashL= $(empty) -L
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# FLAG_11 = -DGOTM # FLAG_11 = -DGOTM
# GOTMLIB = -L../GOTM_source -lturbulence -lutil -lmeanflow # GOTMLIB = -L../GOTM_source -lturbulence -lutil #-lmeanflow
# GOTMINCS = -I../GOTM_source # GOTMINCS = -I../GOTM_source
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
...@@ -315,11 +317,24 @@ dashL= $(empty) -L ...@@ -315,11 +317,24 @@ dashL= $(empty) -L
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# SUSPENDED SEDIMENT MODEL: UNCOMMENT TO INCLUDE MODEL # SUSPENDED SEDIMENT MODEL: UNCOMMENT TO INCLUDE MODEL
# ORIG : the sediment transport model developed by Geoffey Cowles in v3.1-v3.2
# CSTMS: Community Sediment Transport Modeling System with cohesive model
# DELFT: Sediment modeling system as Delft Flow (not included)
#
# note: only one model should be chosen for modeling.
#
# Utilities:
# OFFLINE_SEDIMENT : run sediment with offline hydrodynamic forcing
# FLUID_MUD : activate the 2-D fluid mud at bed-water interface
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
FLAG_21 = -DSEDIMENT # FLAG_21 = -DSEDIMENT
# FLAG_211 = -DORIG_SED
# FLAG_211 = -DCSTMS_SED
#
# FLAG_22 = -DOFFLINE_SEDIMENT # FLAG_22 = -DOFFLINE_SEDIMENT
# FLAG_43 = -DFLUID_MUD
#
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# KALMAN FILTERS # KALMAN FILTERS
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
...@@ -345,22 +360,31 @@ dashL= $(empty) -L ...@@ -345,22 +360,31 @@ dashL= $(empty) -L
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# GENERAL BIOLOGICAL MODEL: UNCOMMENT TO INCLUDE MODEL # GENERAL BIOLOGICAL MODEL: UNCOMMENT TO INCLUDE MODEL
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# FLAG_25 = -DBioGen # FLAG_25 = -DBioGen
# BIOLIB = -L$(TOPDIR)/BIO_source -lbiomodule # FLAG_251 = -DOFFLINE_BIOLOGY
# BIOINCS = -I$(TOPDIR)/BIO_source/ # BIOLIB = -L$(TOPDIR)/BIO_source -lbiomodule
# BIOINCS = -I$(TOPDIR)/BIO_source
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# Dynamic/Thermodynamic Ice # Dynamic/Thermodynamic Ice
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# NOTE: Must use -DSPHERICAL and -DHEAT_FLUX ----- only for old version v2.7 # NOTE: Must use -DSPHERICAL and -DHEAT_FLUX ----- this note only for old version v2.7
# ICE_EMBEDDING must with SEMI_IMPLICIT
# FLAG_26 = -DICE # FLAG_26 = -DICE
# FLAG_261 = -DICE_EMBEDDING
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# CALCULATE THE NET HEAT FLUX IN MODEL # CALCULATE THE NET HEAT FLUX IN MODEL (THREE CHOICES):
# 1. CALCULATE THE NET HEAT FLUX USING COARE26Z
# 2. CALCULATE THE NET HEAT FLUX USING COARE26Z for Great Lake
# 3. CALCULATE THE NET HEAT FLUX USING SOLAR HEATING MODULE
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# FLAG_27 = -DHEATING_CALCULATED # FLAG_27 = -DHEATING_CALCULATED
# FLAG_27 = -DHEATING_CALCULATED_GL
# FLAG_27 = -DHEATING_SOLAR
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# AIR_PRESSURE FROM SURFACE FORCING # AIR_PRESSURE FROM SURFACE FORCING
...@@ -432,7 +456,13 @@ dashL= $(empty) -L ...@@ -432,7 +456,13 @@ dashL= $(empty) -L
# PETSC Version # PETSC Version
# If your PETSc is 2.3.2 or older, uncomment this flag # If your PETSc is 2.3.2 or older, uncomment this flag
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
FLAG_41 = -DOLD_PETSC # FLAG_41 = -DOLD_PETSC
#--------------------------------------------------------------------------
# SPECIAL PARTITION
# This flag can make sure the identical repeat run for same amount of CPUs
#--------------------------------------------------------------------------
# FLAG_42 = -DPARTITION_SPECIAL
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# DEVELOPMENT FLAGS # DEVELOPMENT FLAGS
...@@ -507,7 +537,7 @@ dashL= $(empty) -L ...@@ -507,7 +537,7 @@ dashL= $(empty) -L
CXX = mpicxx CXX = mpicxx
CFLAGS = -O3 CFLAGS = -O3
FC = mpif90 FC = mpif90
# DEBFLGS = -check all # DEBFLGS = -check all -traceback
# Use 'OPT = -O0 -g' for fast compile to test the make # Use 'OPT = -O0 -g' for fast compile to test the make
# Use 'OPT = -xP' for fast run on em64t (Hydra and Guppy) # Use 'OPT = -xP' for fast run on em64t (Hydra and Guppy)
# Use 'OPT = -xN' for fast run on ia32 (Salmon and Minke) # Use 'OPT = -xN' for fast run on ia32 (Salmon and Minke)
...@@ -582,8 +612,9 @@ dashL= $(empty) -L ...@@ -582,8 +612,9 @@ dashL= $(empty) -L
$(FLAG_31) $(FLAG_32) $(FLAG_33) $(FLAG_34) \ $(FLAG_31) $(FLAG_32) $(FLAG_33) $(FLAG_34) \
$(FLAG_35) $(FLAG_36) $(FLAG_37) $(FLAG_38) \ $(FLAG_35) $(FLAG_36) $(FLAG_37) $(FLAG_38) \
$(FLAG_39) $(FLAG_40) $(FLAG_41) $(FLAG_42) \ $(FLAG_39) $(FLAG_40) $(FLAG_41) $(FLAG_42) \
$(FLAG_LAM)\ $(FLAG_43) $(FLAG_LAM)\
$(FLAG_101) $(FLAG_102) $(FLAG_103) $(FLAG_104) $(FLAG_105) $(FLAG_101) $(FLAG_102) $(FLAG_103) $(FLAG_104) $(FLAG_105)\
$(FLAG_211) $(FLAG_212) $(FLAG_213) $(FLAG_251) $(FLAG_261)
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# Libraries # Libraries
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
......
...@@ -222,7 +222,8 @@ ...@@ -222,7 +222,8 @@
SEDIMENT_PARAMETER_TYPE = 'constant' , SEDIMENT_PARAMETER_TYPE = 'constant' ,
BEDFLAG_TYPE = 'constant' , BEDFLAG_TYPE = 'constant' ,
ICE_MODEL = F, ICE_MODEL = F,
ICING_MODEL =F ICING_MODEL =F,
HIGH_LATITUDE_WAVE = F
/ /
&NML_PROBES &NML_PROBES
...@@ -287,3 +288,15 @@ NCNEST_NODE_FILES= 'testnodes.dat' ...@@ -287,3 +288,15 @@ NCNEST_NODE_FILES= 'testnodes.dat'
NESTING_BLOCKSIZE_WAVE = -1, NESTING_BLOCKSIZE_WAVE = -1,
NESTING_FILE_NAME_WAVE = inlet_nesting_wave.nc NESTING_FILE_NAME_WAVE = inlet_nesting_wave.nc
/ /
&NML_WAVE_SPARSE_TIMESERIES
OUT_WAVE_SPARSE_TIMESERIES_ON = F,
SPARSE_DISTANCE = 1000.000 ,
OUT_WIND_VELOCITY_SPARSE = F,
OUT_SIG_WAVE_HEIGHT_SPARSE = F,
OUT_REL_PEAK_PERIOD_SPARSE = F,
OUT_WAVE_DIRECTION_SPARSE = F,
OUT_ENERGY_SPECTRUM_SPARSE = F,
OUT_WAVE_PARTITION_SPARSE = F,
OUT_INTERVAL_SPARSE = 'seconds=3600.0'
/
...@@ -58,7 +58,8 @@ ...@@ -58,7 +58,8 @@
INSTALLDIR = $(TOPDIR)/libs/install INSTALLDIR = $(TOPDIR)/libs/install
#=========================================================================== #===========================================================================
# PREPROCESSOR OPTIONS FOR CPP # PREPROCESSOR OPTIONS FOR CPP
DEF_FLAGS = -P -C -traditional # DEF_FLAGS = -P -C -traditional
DEF_FLAGS = -P -traditional
#=========================================================================== #===========================================================================
# #
####################### MEDM ENVIRONMENT ##################################### ####################### MEDM ENVIRONMENT #####################################
...@@ -93,7 +94,8 @@ dashL= $(empty) -L ...@@ -93,7 +94,8 @@ dashL= $(empty) -L
# SET PATH TO LIBRARIES WITH IOLIBS # SET PATH TO LIBRARIES WITH IOLIBS
# SET PATH TO INCLUDE FILES (netcdf.mod) WITH IOINCS # SET PATH TO INCLUDE FILES (netcdf.mod) WITH IOINCS
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
IOLIBS = -lnetcdf #-L/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/lib -lnetcdf IOLIBS = -lnetcdff -lnetcdf #-lhdf5_hl -lhdf5 -lz -lcurl -lm
# IOLIBS = -lnetcdf #-L/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/lib -lnetcdf
IOINCS = #-I/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/include IOINCS = #-I/hosts/mao/usr/medm/install/netcdf/3.6.3/em64t/include
# IOLIBS = -L/usr/local/install/netcdf/gcc_ifort/3.6.2/lib -lnetcdf # IOLIBS = -L/usr/local/install/netcdf/gcc_ifort/3.6.2/lib -lnetcdf
# IOINCS = -I/usr/local/install/netcdf/gcc_ifort/3.6.2/include # IOINCS = -I/usr/local/install/netcdf/gcc_ifort/3.6.2/include
...@@ -245,7 +247,7 @@ dashL= $(empty) -L ...@@ -245,7 +247,7 @@ dashL= $(empty) -L
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# FLAG_11 = -DGOTM # FLAG_11 = -DGOTM
# GOTMLIB = -L../GOTM_source -lturbulence -lutil -lmeanflow # GOTMLIB = -L../GOTM_source -lturbulence -lutil #-lmeanflow
# GOTMINCS = -I../GOTM_source # GOTMINCS = -I../GOTM_source
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
...@@ -315,11 +317,24 @@ dashL= $(empty) -L ...@@ -315,11 +317,24 @@ dashL= $(empty) -L
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# SUSPENDED SEDIMENT MODEL: UNCOMMENT TO INCLUDE MODEL # SUSPENDED SEDIMENT MODEL: UNCOMMENT TO INCLUDE MODEL
# ORIG : the sediment transport model developed by Geoffey Cowles in v3.1-v3.2
# CSTMS: Community Sediment Transport Modeling System with cohesive model
# DELFT: Sediment modeling system as Delft Flow (not included)
#
# note: only one model should be chosen for modeling.
#
# Utilities:
# OFFLINE_SEDIMENT : run sediment with offline hydrodynamic forcing
# FLUID_MUD : activate the 2-D fluid mud at bed-water interface
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# FLAG_21 = -DSEDIMENT # FLAG_21 = -DSEDIMENT
# FLAG_211 = -DORIG_SED
# FLAG_211 = -DCSTMS_SED
#
# FLAG_22 = -DOFFLINE_SEDIMENT # FLAG_22 = -DOFFLINE_SEDIMENT
# FLAG_43 = -DFLUID_MUD
#
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# KALMAN FILTERS # KALMAN FILTERS
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
...@@ -345,22 +360,31 @@ dashL= $(empty) -L ...@@ -345,22 +360,31 @@ dashL= $(empty) -L
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# GENERAL BIOLOGICAL MODEL: UNCOMMENT TO INCLUDE MODEL # GENERAL BIOLOGICAL MODEL: UNCOMMENT TO INCLUDE MODEL
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# FLAG_25 = -DBioGen # FLAG_25 = -DBioGen
# BIOLIB = -L$(TOPDIR)/BIO_source -lbiomodule # FLAG_251 = -DOFFLINE_BIOLOGY
# BIOINCS = -I$(TOPDIR)/BIO_source/ # BIOLIB = -L$(TOPDIR)/BIO_source -lbiomodule
# BIOINCS = -I$(TOPDIR)/BIO_source
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# Dynamic/Thermodynamic Ice # Dynamic/Thermodynamic Ice
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# NOTE: Must use -DSPHERICAL and -DHEAT_FLUX ----- only for old version v2.7 # NOTE: Must use -DSPHERICAL and -DHEAT_FLUX ----- this note only for old version v2.7
# ICE_EMBEDDING must with SEMI_IMPLICIT
# FLAG_26 = -DICE # FLAG_26 = -DICE
# FLAG_261 = -DICE_EMBEDDING
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# CALCULATE THE NET HEAT FLUX IN MODEL # CALCULATE THE NET HEAT FLUX IN MODEL (THREE CHOICES):
# 1. CALCULATE THE NET HEAT FLUX USING COARE26Z
# 2. CALCULATE THE NET HEAT FLUX USING COARE26Z for Great Lake
# 3. CALCULATE THE NET HEAT FLUX USING SOLAR HEATING MODULE
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# FLAG_27 = -DHEATING_CALCULATED # FLAG_27 = -DHEATING_CALCULATED
# FLAG_27 = -DHEATING_CALCULATED_GL
# FLAG_27 = -DHEATING_SOLAR
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# AIR_PRESSURE FROM SURFACE FORCING # AIR_PRESSURE FROM SURFACE FORCING
...@@ -432,7 +456,13 @@ dashL= $(empty) -L ...@@ -432,7 +456,13 @@ dashL= $(empty) -L
# PETSC Version # PETSC Version
# If your PETSc is 2.3.2 or older, uncomment this flag # If your PETSc is 2.3.2 or older, uncomment this flag
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
FLAG_41 = -DOLD_PETSC # FLAG_41 = -DOLD_PETSC
#--------------------------------------------------------------------------
# SPECIAL PARTITION
# This flag can make sure the identical repeat run for same amount of CPUs
#--------------------------------------------------------------------------
# FLAG_42 = -DPARTITION_SPECIAL
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# DEVELOPMENT FLAGS # DEVELOPMENT FLAGS
...@@ -507,7 +537,7 @@ dashL= $(empty) -L ...@@ -507,7 +537,7 @@ dashL= $(empty) -L
CXX = mpicxx CXX = mpicxx
CFLAGS = -O3 CFLAGS = -O3
FC = mpif90 FC = mpif90
# DEBFLGS = -check all # DEBFLGS = -check all -traceback
# Use 'OPT = -O0 -g' for fast compile to test the make # Use 'OPT = -O0 -g' for fast compile to test the make
# Use 'OPT = -xP' for fast run on em64t (Hydra and Guppy) # Use 'OPT = -xP' for fast run on em64t (Hydra and Guppy)
# Use 'OPT = -xN' for fast run on ia32 (Salmon and Minke) # Use 'OPT = -xN' for fast run on ia32 (Salmon and Minke)
...@@ -582,8 +612,9 @@ dashL= $(empty) -L ...@@ -582,8 +612,9 @@ dashL= $(empty) -L
$(FLAG_31) $(FLAG_32) $(FLAG_33) $(FLAG_34) \ $(FLAG_31) $(FLAG_32) $(FLAG_33) $(FLAG_34) \
$(FLAG_35) $(FLAG_36) $(FLAG_37) $(FLAG_38) \ $(FLAG_35) $(FLAG_36) $(FLAG_37) $(FLAG_38) \
$(FLAG_39) $(FLAG_40) $(FLAG_41) $(FLAG_42) \ $(FLAG_39) $(FLAG_40) $(FLAG_41) $(FLAG_42) \
$(FLAG_LAM)\ $(FLAG_43) $(FLAG_LAM)\
$(FLAG_101) $(FLAG_102) $(FLAG_103) $(FLAG_104) $(FLAG_105) $(FLAG_101) $(FLAG_102) $(FLAG_103) $(FLAG_104) $(FLAG_105)\
$(FLAG_211) $(FLAG_212) $(FLAG_213) $(FLAG_251) $(FLAG_261)
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
# Libraries # Libraries
#-------------------------------------------------------------------------- #--------------------------------------------------------------------------
......
...@@ -214,7 +214,9 @@ ...@@ -214,7 +214,9 @@
ICE_AIR_TEMP = 0.0000000E+00, ICE_AIR_TEMP = 0.0000000E+00,
ICE_SPEC_HUMIDITY = 0.0000000E+00, ICE_SPEC_HUMIDITY = 0.0000000E+00,
ICE_SHORTWAVE = 0.0000000E+00, ICE_SHORTWAVE = 0.0000000E+00,
ICE_CLOUD_COVER = 0.0000000E+00 ICE_LONGWAVE_TYPE = 'PW',
ICE_CLOUD_COVER = 0.0000000E+00,
HIGH_LATITUDE_WAVE = F
/ /
&NML_PROBES &NML_PROBES
PROBES_ON = F, PROBES_ON = F,
......
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1. This cohesive bed case is consisted of four classes of cohesive suspended sediment (mud_1, mud_2, mud_3 and mud_4), and cohesive bed process.
2. The CSTMS_SED and OFFLINE_SEDIMENT flags should be activated when compiling the FVCOM source code.
3. All sediment parameters are included in the fvcom_sediment_inlet_test.inp.
4. The descriptions for the sediment parameters could be found at the end of input file.
5. The model details could be refered to:
!=======================================================================
! Harris and Wiberg (1997): !
! -Approaches to quantifying long-term continental shelf sediment transport
! -with an example from the northern California STRESS mid-shelf site!
! [Continental Shelf REsearch, 17, 1389-1418] !
! !
! Meyer-Peter, E. and R. Muller, 1948: Formulas for bedload transport !
! In: Report on the 2nd Meeting International Association Hydraulic !
! Research, Stockholm, Sweden, pp 39-64. !
! !
! Soulsby, R.L. and J.S. Damgaard, 2005: Bedload sediment transport !
! in coastal waters, Coastal Engineering, 52 (8), 673-689. !
! !
! Warner, J.C., C.R. Sherwood, R.P. Signell, C.K. Harris, and H.G. !
! Arango, 2008: Development of a three-dimensional, regional, !
! coupled wave, current, and sediment-transport model, Computers !
! & Geosciences, 34, 1284-1306. !
! !
! Colella, P. and P. Woodward, 1984: The piecewise parabolic method !
! (PPM) for gas-dynamical simulations, J. Comp. Phys., 54, 174-201. !
! !
! Liu, X.D., S. Osher, and T. Chan, 1994: Weighted essentially !
! nonoscillatory shemes, J. Comp. Phys., 115, 200-212. !
! !
! Verney, R., Lafite, R., Claude Brun-Cottan, J., & Le Hir, P. (2011).!
! Behaviour of a floc population during a tidal cycle: laboratory !
! experiments and numerical modelling. Continental Shelf Research, !
! 31(10), S64-S83. !
!=======================================================================
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!==============================================================================!
! INPUT FILE FOR PARAMETERS CONTROLLING FVCOM SEDIMENT MODEL !
! FORMAT: !
! 1.) VARIABLE = VALUE (EQUAL SIGN MUST BE USED) !
! 2.) FLOATING POINT VARIABLES MUST CONTAIN A PERIOD "." EX: 1.3, 2.,etc !
! 3.) BLANK LINES ARE IGNORED AS ARE LINES BEGINNING WITH ! (F90 COMMENT)!
! 4.) COMMENTS CAN FOLLOW VALUES IF MARKED BY ! !
! 5.) ORDER OF VARIABLES IS NOT IMPORTANT !
! 6.) FOR MULTIPLE VALUE VARIABLES FIRST ENTRY IS NUMBER OF VARIABLES !
! TO FOLLOW (OR 0 IF NONE) !
! 7.) DO NOT USE COMMAS TO SEPARATE VARIABLES !
! 8.) DO NOT EXCEED EIGHTY CHARACTERS PER LINE !
! 9.) TRUE = T, FALSE = F !
! !
! THE PREVIOUS FORMAT OF "VARIABLE: VALUE" IS NO LONGER VALID !
! THE MORE ATTRACTIVE " = " FORMAT WAS SUGGESTED BY Hernan G. Arango !
! !
!------------------------------------------------------------------------------!
! Sediment Module Dynamics Parameters
! BEDLOAD: True of bedload is to be considered
! SUSLOAD: True of suspended load is to be considered
!------------------------------------------------------------------------------!
SED_ONED = F
SED_NUDGE = F
SED_ALPHA = 0.5
SED_RAMP = 1
SED_START = 0
BEDLOAD = F
SUSLOAD = T
SED_PTSOURCE = T
SED_HOT_START = F
!------------------------------------------------------------------------------!
! Morphodynamics (unstable - will not be activated)
! MORPHO_MODEL: F => no bathy change, T => bathy changes to follow bottom
! MORPHO_FACTOR: amount bathy is changed relative to calculated accre/depo
! = 0, no change, = 1, follows bottom exactly
! Caution, even if MORPHO_MODEL is F, MORPHO_FACTOR will still be active
! and affect the rate of sediment dep/ero and bedload flux
! MORPHO_INCR: Update the bathymetry only every morpho_incr iterations of
! internal time steps. MORPHO_INCR > 10 can allow flow to adjust
! a bit before morphing.
!------------------------------------------------------------------------------!
MORPHO_MODEL = F
MORPHO_FACTOR = 10.0
MORPHO_INCR = 1
MORPHO_STRT = 0
!------------------------------------------------------------------------------!
! Sediment Settling Parameters
! SETTLE_CFL: set the CFL number for the settling scheme [>0, 1]
! SETTLE_LIMITER: set the limiter type for the settling advection eq.