Merge WRF-PartMC PartMC specific development to PartMC

.gitignore

@@ -17,3 +17,5 @@ scenarios/3_condense/spec/
 scenarios/3_condense/temp/
 scenarios/3_condense/out/
 scenarios/4_chamber/out/
+*.o
+*.mod

CMakeLists.txt

@@ -76,8 +76,14 @@ if(ENABLE_MOSAIC)
     PATHS $ENV{MOSAIC_HOME} $ENV{MOSAIC_HOME}/lib)
   include_directories(${MOSAIC_INCLUDE_DIR})
   add_definitions(-DPMC_USE_MOSAIC)
+  option(ENABLE_OPT_MULTI_WAVELENGTH
+         "Enable MOSAIC multiple wavelength for optical calculations" OFF)
+  if(ENABLE_OPT_MULTI_WAVELENGTH)
+    add_definitions(-DPMC_USE_MOSAIC_MULTI_OPT)
+  endif()
 endif()
 
+
 ######################################################################
 # CAMP
 
@@ -169,6 +175,7 @@ add_library(partmclib src/aero_state.F90 src/integer_varray.F90
   src/netcdf.F90 src/aero_info.F90 src/aero_info_array.F90
   src/nucleate.F90 src/condense.F90 src/fractal.F90 src/chamber.F90
   src/camp_interface.F90 src/photolysis.F90 src/sys.F90
+  src/aero_component.F90
   ${SUNDIALS_SRC} ${GSL_SRC}
   ${C_SORT_SRC})
 

scenarios/1_urban_plume/urban_plume.spec

@@ -3,6 +3,7 @@ output_prefix out/urban_plume   # prefix of output files
 n_repeat 3                      # number of Monte Carlo repeats
 n_part 1000                     # total number of particles
 restart no                      # whether to restart from saved state (yes/no)
+do_select_weighting no          # whether to select weighting explicitly (yes/no)
 
 t_max 86400                     # total simulation time (s)
 del_t 60                        # timestep (s)
@@ -44,6 +45,5 @@ do_nucleation no                # whether to do nucleation (yes/no)
 rand_init 0                     # random initialization (0 to use time)
 allow_doubling yes              # whether to allow doubling (yes/no)
 allow_halving yes               # whether to allow halving (yes/no)
-do_select_weighting no          # whether to select weighting explicitly (yes/no)
 record_removals yes             # whether to record particle removals (yes/no)
 do_parallel no                  # whether to run in parallel (yes/no)

scenarios/2_urban_plume2/urban_plume2.spec

@@ -3,6 +3,7 @@ output_prefix out/urban_plume2  # prefix of output files
 n_repeat 1                      # number of Monte Carlo repeats
 n_part 1000                     # total number of particles
 restart no                      # whether to restart from saved state (yes/no)
+do_select_weighting no          # whether to select weighting explicitly (yes/no)
 
 t_max 172800                    # total simulation time (s)
 del_t 60                        # timestep (s)
@@ -44,6 +45,5 @@ do_nucleation no                # whether to do nucleation (yes/no)
 rand_init 0                     # random initialization (0 to use time)
 allow_doubling yes              # whether to allow doubling (yes/no)
 allow_halving yes               # whether to allow halving (yes/no)
-do_select_weighting no          # whether to select weighting explicitly (yes/no)
 record_removals yes             # whether to record particle removals (yes/no)
 do_parallel no                  # whether to run in parallel (yes/no)

scenarios/4_chamber/chamber.spec

@@ -3,6 +3,7 @@ output_prefix out/chamber       # prefix of output files
 n_repeat 10                     # number of Monte Carlo repeats
 n_part 10000                    # total number of particles
 restart no                      # whether to restart from saved state (yes/no)
+do_select_weighting no          # whether to select weighting explicitly (yes/no)
 
 t_max 20160                     # total simulation time (s)
 del_t 60                        # timestep (s)
@@ -51,6 +52,5 @@ do_nucleation no                # whether to do nucleation (yes/no)
 rand_init 7                     # random initialization (0 to auto-generate)
 allow_doubling yes              # whether to allow doubling (yes/no)
 allow_halving yes               # whether to allow halving (yes/no)
-do_select_weighting no          # whether to select weighting explicitly (yes/no)
 record_removals no              # whether to record particle removals (yes/no)
 do_parallel no                  # whether to run in parallel (yes/no)

scenarios/5_coag_brownian/example.spec

@@ -3,6 +3,7 @@ output_prefix out/example       # prefix of output files
 n_repeat 1                      # number of Monte Carlo repeats
 n_part 1000                     # total number of particles
 restart no                      # whether to restart from saved state (yes/no)
+do_select_weighting no          # whether to select weighting explicitly (yes/no)
 
 t_max 86400                     # total simulation time (s)
 del_t 60                        # timestep (s)
@@ -43,6 +44,5 @@ do_nucleation no                # whether to do nucleation (yes/no)
 rand_init 66                    # random initialization (0 to use time)
 allow_doubling yes              # whether to allow doubling (yes/no)
 allow_halving yes               # whether to allow halving (yes/no)
-do_select_weighting no          # whether to select weighting explicitly (yes/no)
 record_removals yes             # whether to record particle removals (yes/no)
 do_parallel no                  # whether to run in parallel (yes/no)

scenarios/6_camp/camp.spec

@@ -3,6 +3,7 @@ output_prefix out/camp   # prefix of output files
 n_repeat 1                      # number of Monte Carlo repeats
 n_part 10000                   # total number of particles
 restart no                      # whether to restart from saved state (yes/no)
+do_select_weighting no          # whether to select weighting explicitly (yes/no)
 
 t_max 86400                    # total simulation time (s)
 del_t 120                        # timestep (s)
@@ -41,6 +42,5 @@ do_nucleation no                # whether to do nucleation (yes/no)
 rand_init 0                     # random initialization (0 to use time)
 allow_doubling no             # whether to allow doubling (yes/no)
 allow_halving no               # whether to allow halving (yes/no)
-do_select_weighting no          # whether to select weighting explicitly (yes/no)
 record_removals yes             # whether to record particle removals (yes/no)
 do_parallel no                  # whether to run in parallel (yes/no)

src/Makefile.wrf_partmc

@@ -0,0 +1,208 @@
+# NOTE: This Makefile is only to be used when compiling PartMC in WRF
+
+LN      =       ln -sf
+MAKE    =       make -i -r
+RM      =       rm -f
+
+PMC_MODULES =                           \
+  aero_binned.o                 \
+  aero_component.o              \
+  aero_data.o                   \
+  aero_dist.o                   \
+  aero_info.o                   \
+  aero_info_array.o             \
+  aero_mode.o                   \
+  aero_particle.o               \
+  aero_particle_array.o         \
+  aero_state.o                  \
+  aero_sorted.o                 \
+  aero_weight.o                 \
+  aero_weight_array.o           \
+  bin_grid.o                    \
+  camp_interface.o              \
+  chamber.o                     \
+  coag_kernel.o                 \
+  coag_kernel_additive.o        \
+  coag_kernel_brown.o           \
+  coag_kernel_brown_cont.o      \
+  coag_kernel_brown_free.o      \
+  coag_kernel_constant.o        \
+  coag_kernel_sedi.o            \
+  coag_kernel_zero.o            \
+  coagulation.o                 \
+  coagulation_dist.o            \
+  condense.o                    \
+  constants.o                   \
+  env_state.o                   \
+  fractal.o                     \
+  gas_data.o                    \
+  gas_state.o                   \
+  integer_rmap.o                \
+  integer_rmap2.o               \
+  integer_varray.o              \
+  mosaic.o                      \
+  mpi.o                         \
+  netcdf.o                      \
+  nucleate.o                    \
+  output.o                      \
+  photolysis.o                  \
+  rand.o                        \
+  rand_gsl.o                    \
+  scenario.o                    \
+  spec_file.o                   \
+  spec_line.o                   \
+  stats.o                       \
+  util.o                        \
+  sort.o                        \
+  sys.o
+
+OBJS = \
+
+LIBTARGET    =  libpartmc.a
+TARGETDIR    =  ./
+$(LIBTARGET) :  $(MODULES) $(PMC_MODULES) $(OBJS)
+		$(AR) $(ARFLAGS) $(LIBTARGET) $(MODULES) $(PMC_MODULES) \
+		$(OBJS)
+		$(RANLIB) $(RANLIBFLAGS) $@
+
+include ../../WRFV3/configure.wrf
+
+all: pmc 
+
+pmc: $(PMC_MODULES)
+
+clean:
+	@ echo 'use the clean script'
+
+# DEPENDENCIES : only dependencies after this line (don't remove the word DEPENDENCIES)
+
+aero_binned.o: bin_grid.o aero_particle.o spec_file.o \
+     util.o aero_dist.o mpi.o aero_data.o
+
+aero_component.o: util.o mpi.o
+
+aero_data.o: spec_file.o mpi.o util.o fractal.o netcdf.o
+
+aero_dist.o: bin_grid.o util.o constants.o spec_file.o \
+     aero_data.o aero_mode.o mpi.o rand.o
+
+aero_info.o: util.o spec_file.o mpi.o
+
+aero_info_array.o: aero_info.o util.o spec_file.o mpi.o
+
+aero_mode.o: bin_grid.o util.o constants.o spec_file.o \
+     aero_data.o aero_weight.o mpi.o rand.o
+
+aero_particle.o: util.o aero_data.o spec_file.o env_state.o \
+     mpi.o aero_component.o
+
+aero_particle_array.o: aero_particle.o util.o spec_file.o mpi.o
+
+aero_sorted.o: integer_varray.o integer_rmap.o integer_rmap2.o \
+     aero_particle.o aero_particle_array.o bin_grid.o mpi.o
+
+aero_state.o: aero_particle_array.o aero_sorted.o integer_varray.o \
+     bin_grid.o aero_data.o aero_particle.o aero_dist.o \
+     util.o rand.o aero_binned.o mpi.o spec_file.o \
+     aero_info.o aero_info_array.o aero_weight.o \
+     aero_weight_array.o
+
+aero_weight.o: util.o constants.o rand.o spec_file.o \
+     aero_particle.o aero_data.o netcdf.o mpi.o
+
+aero_weight_array.o: util.o constants.o rand.o spec_file.o \
+     aero_particle.o netcdf.o mpi.o aero_weight.o aero_data.o
+
+bin_grid.o: constants.o util.o spec_file.o mpi.o netcdf.o
+
+camp_interface.o: aero_data.o aero_state.o aero_particle.o constants.o gas_data.o \
+     gas_state.o util.o
+
+chamber.o: aero_data.o constants.o env_state.o spec_file.o
+
+coag_kernel.o: env_state.o bin_grid.o aero_particle.o \
+     aero_data.o aero_weight.o aero_weight_array.o coag_kernel_sedi.o \
+     coag_kernel_additive.o coag_kernel_constant.o \
+     coag_kernel_brown.o coag_kernel_zero.o \
+     coag_kernel_brown_free.o coag_kernel_brown_cont.o
+
+coag_kernel_additive.o: bin_grid.o env_state.o util.o \
+     constants.o aero_binned.o aero_data.o aero_dist.o \
+     aero_particle.o
+
+coag_kernel_brown.o: env_state.o constants.o util.o \
+     aero_particle.o
+
+coag_kernel_brown_cont.o: env_state.o constants.o util.o \
+    aero_particle.o aero_data.o
+
+coag_kernel_brown_free.o: env_state.o constants.o util.o \
+    aero_particle.o aero_data.o
+
+coag_kernel_constant.o: env_state.o bin_grid.o util.o \
+     constants.o aero_binned.o aero_data.o aero_dist.o \
+     aero_data.o aero_particle.o
+
+coag_kernel_sedi.o: env_state.o constants.o aero_data.o \
+     aero_particle.o
+
+coag_kernel_zero.o: bin_grid.o env_state.o util.o aero_binned.o \
+     aero_dist.o aero_data.o aero_particle.o scenario.o
+
+coagulation.o: bin_grid.o aero_data.o util.o env_state.o \
+     aero_state.o aero_weight.o mpi.o coag_kernel.o stats.o \
+     aero_sorted.o
+
+coagulation_dist.o: bin_grid.o aero_data.o util.o env_state.o \
+     aero_state.o coagulation.o mpi.o
+
+condense.o: aero_state.o env_state.o aero_data.o util.o aero_particle.o constants.o
+
+constants.o:
+
+env_state.o: constants.o util.o spec_file.o mpi.o netcdf.o
+
+fractal.o: spec_file.o constants.o netcdf.o mpi.o
+
+gas_data.o: spec_file.o mpi.o util.o netcdf.o
+
+gas_state.o:util.o spec_file.o gas_data.o mpi.o netcdf.o env_state.o
+
+integer_rmap.o: integer_varray.o util.o mpi.o
+
+integer_rmap2.o: integer_varray.o util.o mpi.o
+
+integer_varray.o: util.o mpi.o
+
+mosaic.o: aero_data.o aero_state.o constants.o env_state.o \
+     gas_data.o gas_state.o output.o util.o
+
+mpi.o: util.o
+
+netcdf.o: util.o rand.o
+
+nucleate.o: env_state.o aero_state.o aero_data.o gas_data.o gas_state.o
+
+output.o: bin_grid.o aero_data.o aero_state.o aero_binned.o \
+     netcdf.o env_state.o util.o gas_data.o mpi.o
+
+photolysis.o: constants.o util.o
+
+rand.o: util.o constants.o mpi.o rand_gsl.o
+
+rand_gsl.o:
+
+scenario.o: gas_state.o aero_dist.o util.o env_state.o \
+     aero_state.o spec_file.o aero_data.o gas_data.o mpi.o chamber.o
+
+spec_file.o: spec_line.o util.o
+
+spec_line.o: util.o
+
+sort.o:
+
+stats.o:   util.o netcdf.o
+
+sys.o:
+
+util.o: constants.o sort.o sys.o