Merge WRF-PartMC PartMC specific development to PartMC (#168)

* added aero_component to aero_particle

* added weight_class to aero_mode to note which weight class particles should be in

* added how to combine arrays of components for coagulation

* removed n_orig_part from aero_particle

* created a Makefile for building partmc for wrf

* added wrf_partmc variables to env_state and output

* added 3d and 4d array handling for netcdf files

* minor changes

* added 3d array handling with mpi

* edit makefile

* added ifdef to turn off dilution

* added PMC_USE_WRF flag

* added WRF CPP flag for special netcdf filenames

* fix error in 5d array pack subroutine

* added some useful debugging to aero_state.F90

* added debugging when sampling particles

* added chamber to Makefile

* added aero_component arrays to output

* modified aerosol input files to add weight classes

* removed left over debugging output

* cleaned up output.F90

* edit aero_dist files to add weight_class_name

* fixed nucleate source and weighting

* removed _SOURCE weighting options

* fixed netcdf array reading subroutines

* fixed env_state_input_netcdf to read WRF specific variables

* changed WRF-partmc output to entire column

* add cpp around wrf partmc output subroutine

* removed unused variables

* minor bug fixes for aero_components

* fixed missing weight class names in mpi functions

* changed gas_data and aero_data to not be arrays in output

* aero component fixes

* disabled per particle coagulation

* aero_id is now 64 bit

* fixed aero id in aero_state

* fixed remaining aero_ids to int64

* use mpi_integer8

* added error particle checking and removal from mosaic

* update env_state probablities to 4d arrays

* change rand_binomial to handle small values of p

* added a few netcdf subroutines

* improvements to aero_data input and output

* added netcdf int64 subroutines

* changes to partmc code for wrf partmc

* added sorting for real values

* changes to aero_state to not track removals in wrf-partmc

* added gsl to makefile

* add threshold for sampling

* fixed cutoff for low number concentration in sampling

* added size factor timescale for sampling

* added missing dependency in Makefile

* change large static character arrays in aero_data to allocatable to avoid compiler warning

* changed output of component array to avoid gcc compile warning

* change to netcdf4 to allow int64 type

* fixed missing weight_class_name for mixing_state test

* added missing weight_class_name to file in camp test

* reenable per particle coagulation

* remove two wrf partmc hacks

* moved particle_error debugging for mosaic to wrf partmc only

* changed aero_particle_zero to allocate component array of size 0 and adjusted coagulation copying of components

* increased maximum aero_component size

* add new way to determine aero_component array in coagulation

* remove component flag option in coagulation

* minor code format fix

* added note to makefile for WRF build and added camp_interface

* update to not require user specified weighting

* change weighting specification in test case inputs

* update inputs and spec files in scenarios for weighting changes

* remove leftover debugging output

* added tracking number of primary particles that make a particle

* change documentation to reflect change in order spec file for do_select_weighting

* clean up commented out code for sampling in aero_state

* fixed long code lines that were my fault

* added create_time to output and input. fixed typos for long line breaking.

* fix documentation for output of aero_state to include component features

* removed unused env_state variable

* remove hardcoded value for weighting

* added weighting testcase

* fix bug

* small bug fixes found after wrf-partmc compile

* update optical wavelengths

* added missing files in wrf-partmc makefile

* optical changes. added deaveraging and new mixing state metric by size

* bug fix and add cell_volume to env_state

* minor changes to optical code

* remove deaveraging

* fix to aero_state_input_netcdf

* add missing files to makefile

* move a few num_conc functions to aero_state

* update code to handle multiple wavelengths

* refactor mixing_state_metric_by_size

* fix spec files for parallel tests

* fix missing do_camp_chem in run_part_opt mpi calls

* clean up debugging code

* add comments about controlling the sampling range of normal distribution

* fix Makefile for wrf-partmc build

* add optical property functions for aerosol state

* set size of arrays in aero_state optical functions

* safeguard against copying aero_state with no particles

* fix dup_all_particles

* add write_real_4d

* fix repeated error codes that I introduced

* Apply formatting suggestions

Co-authored-by: Matthew West <[email protected]>

* move ifdef down a level in aero_state_total_particles_all_proc. fix bug in reading other particle ID

* fix comments. remove code that was no longer used

* improve weighting tests

* improve weighitng tests. add plotting

* remove num_weight_classes argument

* improve aero_state_num_concs_by_source to be weighted correctly

* fix comment in aero_particle_n_components

* rename Makefile to make it more obvious that it belongs only for wrf partmc

* move MAX_AERO_COMPONENT_SIZE to aero_particle.F90

* clean up unused variables

* rename abs and scat size-resolved functions

* improve by_size optical functions

* first pass at fixing n_component functionconfusion

* refactor size selecting code

* change binned analysis code to be more general

* revert to optical true

* change num_primary_parts to n_primary_parts. scale num_concs_by_source by primary parts and components

* randomly select aero_components when exceeding maximum

* allow partmc to get wavelengths of optical properties for multi-wavelength MOSAIC codes

* fix up wavelength in aero_data

* remove unneeded subroutine for wavelengths

* improve multiple wavelength build process

* rename variables regarding threshold sampling

* add comment regarding single wavelength optical subroutine

* improve bin_grid_contains

* fix double counting problem in bin_grid_contains

* handle possible problems in bin_grid_contains

* fix mpi calls for run_part_opt. add uuid comment to mosaic calls

* make camp happy

* fix typo

* fix mosaic aerosol_optical calls

* fix component scaling with sample_source_particle

* rename env_state variables. fix output bug for n_primary_parts

* add file input for column

* remove n_orig_part from output

* fix bin_grid_contains to be consistent with bin_grid_find

* move copy_weight outside of aero_state_sample_particles

* fix code for bin_grid_contains

---------

Co-authored-by: Matthew West <[email protected]>

.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