add support for sectional dry deposition

CMakeLists.txt

@@ -438,7 +438,7 @@ target_link_libraries(numeric_diff partmclib)
 add_executable(numeric_average src/numeric_average.F90)
 
 ######################################################################
-# scenarios/1_urban_plume/urban_plum_process
+# scenarios/1_urban_plume/urban_plume_process
 
 add_executable(urban_plume_process
   scenarios/1_urban_plume/urban_plume_process.F90)

scenarios/7_drydep/1_run_sect.sh

@@ -0,0 +1,12 @@
+#!/bin/sh
+
+# exit on error
+set -e
+# turn on command echoing
+set -v
+
+mkdir -p out
+
+../../build/partmc drydep_sect.spec
+
+# Now run ./2_process_sect.sh to process the data

scenarios/7_drydep/2_process_modal.sh

@@ -7,4 +7,4 @@ set -v
 
 # The data should have already been generated by ./1_run_modal.sh
 
-../../build/drydep_modal_process out/modal_dpg_00001000000000000000_sig_2_5_emerson_grass
+../../build/drydep_modal_process out/drydep_modal

scenarios/7_drydep/2_process_sect.sh

@@ -0,0 +1,12 @@
+#!/bin/sh
+
+# exit on error
+set -e
+# turn on command echoing
+set -v
+
+# The data should have already been generated by ./1_run_sect.sh
+
+../../build/extract_sectional_aero_time out/drydep_sect
+../../build/extract_sectional_aero_size --num out/drydep_sect
+../../build/extract_sectional_aero_size --mass out/drydep_sect

scenarios/7_drydep/README

@@ -0,0 +1,56 @@
+Dry deposition scenario
+=======================
+
+Demonstrates dry deposition of aerosol particles using both the
+modal and the sectional (binned) representations. Both are run
+with identical inputs so that their results can be compared directly.
+
+Running
+-------
+
+Modal:
+
+    ./1_run_modal.sh
+    ./2_process_modal.sh
+
+Sectional:
+
+    ./1_run_sect.sh
+    ./2_process_sect.sh
+
+Each simulates 8 hours with hourly output. The modal case is
+post-processed by drydep_modal_process, which writes total number and
+mass concentration time series to out/drydep_modal_process.nc. The
+sectional case uses the standard extract_sectional_* tools.
+
+Configuration
+-------------
+
+Both runs share:
+
+  aero_init_dist.dat   single log-normal mode, 3.2e9 m^-3, geometric
+                       mean diameter 100 nm, sigma (geom_std_dev)= 1.8
+  aero_data.dat        single species (SO4)
+  drydep_params.dat    deposition parameters (see below)
+  temp.dat, pres.dat, height.dat, gas_*.dat, aero_back*.dat,
+  aero_emit*.dat       meteorology, emissions and background
+
+Emissions and background rates are zero. Condensation and all
+other microphysical processes are disabled, so dry deposition is the
+only active process. The sectional case runs with the zero
+coagulation kernel. It also sets do_aero_dilution to no; the modal
+representation has no dilution treatment.
+
+Deposition parameters
+---------------------
+
+drydep_params.dat holds the coefficients of the size-resolved
+deposition scheme (Zhang et al. 2001; Emerson et al. 2020). The
+dry deposition velocity equation is
+
+    V_d = V_s + 1 / (R_a + R_s)
+
+following Slinn (1982), as used by both parameterizations. The
+land-use-dependent quantities (z_rough, A, alpha, gamma) and the
+scheme coefficients (C_B, C_IN, C_IM, nu, beta) are all read from
+this file.

scenarios/7_drydep/aero_init_dist.dat

@@ -3,5 +3,5 @@ mass_frac aero_init_comp.dat      # composition proportions of species
 diam_type geometric               # type of diameter specified
 mode_type log_normal              # type of distribution
 num_conc 3.2e9                    # particle number concentration (#/m^3)
-geom_mean_diam 1e-8               # geometric mean diameter (m)
-log10_geom_std_dev 0.041          # log_10 of geometric std dev of diameter
+geom_mean_diam 1e-7               # geometric mean diameter (m)
+log10_geom_std_dev 0.255          # log_10 of geometric std dev of diameter

scenarios/7_drydep/drydep_modal.spec

@@ -1,22 +1,22 @@
 run_type modal                         # modal run
-output_prefix out/modal_dpg_10_0_sig_2_5_emerson_broad
+output_prefix out/drydep_modal          # prefix of output files
 
 t_max 28800                            # total simulation time (s)
 del_t 60                               # timestep (s)
 t_output 3600                          # output interval (0 disables) (s)
 t_progress 0                           # progress printing interval (0 disables) (s)
 
 n_bin 1000                             # number of bins (for processing purposes)
-d_min 4e-8                             # minimum diameter (m)
-d_max 2.5e-3                           # maximum diameter (m)
+d_min 1e-10                            # minimum diameter (m)
+d_max 1e-3                             # maximum diameter (m)
 
 do_camp_chem no                        # whether to use CAMP for chemistry (yes/no)
 do_tchem no                            # whether to use TChem for chemistry (yes/no)
 
 gas_data gas_data.dat                  # file containing gas data
 aerosol_data aero_data.dat             # file containing aerosol data
 do_fractal no                          # whether to do fractal treatment (yes/no)
-aerosol_init aero_init_run.dat
+aerosol_init aero_init_dist.dat        # aerosol initial condition file
 
 temp_profile temp.dat                  # temperature profile file
 pressure_profile pres.dat              # pressure profile file
@@ -26,7 +26,7 @@ gas_background gas_back.dat            # background gas concentrations file
 aero_emissions aero_emit.dat           # aerosol emissions file
 aero_background aero_back.dat          # aerosol background file
 loss_function drydep                   # loss function specification
-drydep_params drydep_broad_emerson.dat
+drydep_params drydep_params.dat        # dry deposition parameters
 
 rel_humidity 0.95                      # initial relative humidity (1)
 latitude 0                             # latitude (degrees, -90 to 90)

scenarios/7_drydep/drydep_sect.spec

@@ -0,0 +1,45 @@
+run_type sectional                     # sectional (binned) run
+output_prefix out/drydep_sect          # prefix of output files
+
+t_max 28800                            # total simulation time (s)
+del_t 60                               # timestep (s)
+t_output 3600                          # output interval (0 disables) (s)
+t_progress 0                           # progress printing interval (0 disables) (s)
+
+n_bin 1000                             # number of bins
+d_min 1e-10                            # minimum diameter (m)
+d_max 1e-3                             # maximum diameter (m)
+
+do_camp_chem no                        # whether to use CAMP for chemistry (yes/no)
+do_tchem no                            # whether to use TChem for chemistry (yes/no)
+
+gas_data gas_data.dat                  # file containing gas data
+aerosol_data aero_data.dat             # file containing aerosol data
+do_fractal no                          # whether to do fractal treatment (yes/no)
+aerosol_init aero_init_dist.dat        # aerosol initial condition file
+
+temp_profile temp.dat                  # temperature profile file
+pressure_profile pres.dat              # pressure profile file
+height_profile height.dat              # height profile file
+gas_emissions gas_emit.dat             # gas emissions file
+gas_background gas_back.dat            # background gas concentrations file
+aero_emissions aero_emit.dat           # aerosol emissions file
+aero_background aero_back.dat          # aerosol background file
+loss_function drydep                   # loss function specification
+drydep_params drydep_params.dat        # dry deposition parameters
+
+rel_humidity 0.95                      # initial relative humidity (1)
+latitude 0                             # latitude (degrees, -90 to 90)
+longitude 0                            # longitude (degrees, -180 to 180)
+altitude 0                             # altitude (m)
+start_time 21600                       # start time (s since 00:00 UTC)
+start_day 200                          # start day of year (UTC)
+
+do_aero_dilution no                    # whether to do aerosol dilution (yes/no)
+do_coagulation yes                     # whether to do coagulation (yes/no)
+coag_kernel zero                       # coagulation kernel (zero = no coagulation)
+do_condensation no                     # whether to do condensation (yes/no)
+do_mosaic no                           # whether to do MOSAIC (yes/no)
+do_optical no                          # whether to compute optical props (yes/no)
+do_nucleation no                       # whether to do nucleation (yes/no)
+do_immersion_freezing no               # whether to do freezing (yes/no)

src/output.F90

@@ -662,7 +662,7 @@ end subroutine input_n_files
 
   !> Write the current sectional data.
   subroutine output_sectional(prefix, bin_grid, aero_data, aero_binned, &
-       gas_data, gas_state, env_state, index, time, del_t, uuid)
+       gas_data, gas_state, env_state, scenario, index, time, del_t, uuid)
 
     !> Prefix of filename to write
     character(len=*), intent(in) :: prefix
@@ -678,6 +678,8 @@ subroutine output_sectional(prefix, bin_grid, aero_data, aero_binned, &
     type(gas_state_t), intent(in) :: gas_state
     !> Environment state.
     type(env_state_t), intent(in) :: env_state
+    !> Scenario data.
+    type(scenario_t), intent(in) :: scenario
     !> Filename index.
     integer, intent(in) :: index
     !> Current time (s).
@@ -705,6 +707,10 @@ subroutine output_sectional(prefix, bin_grid, aero_data, aero_binned, &
     call aero_binned_output_netcdf(aero_binned, ncid, bin_grid, &
          aero_data)
 
+    if (scenario%loss_function_type == SCENARIO_LOSS_FUNCTION_DRYDEP) then
+       call drydep_params_output_netcdf(scenario%drydep, ncid)
+    end if
+
     call pmc_nc_check(nf90_close(ncid))
 
   end subroutine output_sectional
@@ -713,7 +719,7 @@ end subroutine output_sectional
 
   !> Input sectional data.
   subroutine input_sectional(filename, index, time, del_t, uuid, bin_grid, &
-       aero_data, aero_binned, gas_data, gas_state, env_state)
+       aero_data, aero_binned, gas_data, gas_state, env_state, scenario)
 
     !> Filename to read.
     character(len=*), intent(in) :: filename
@@ -737,6 +743,8 @@ subroutine input_sectional(filename, index, time, del_t, uuid, bin_grid, &
     type(gas_state_t), optional, intent(inout) :: gas_state
     !> Environment state.
     type(env_state_t), optional, intent(inout) :: env_state
+    !> Scenario data.
+    type(scenario_t), optional, intent(inout) :: scenario
 
     integer :: ncid
 
@@ -779,6 +787,10 @@ subroutine input_sectional(filename, index, time, del_t, uuid, bin_grid, &
        call env_state_input_netcdf(env_state, ncid)
     end if
 
+    if (present(scenario)) then
+       call drydep_params_input_netcdf(scenario%drydep, ncid)
+    end if
+
     call pmc_nc_close(ncid)
 
   end subroutine input_sectional
@@ -834,7 +846,10 @@ subroutine output_modal(prefix, aero_binned, aero_dist, aero_data, &
     call gas_state_output_netcdf(gas_state, ncid, gas_data)
     call aero_data_output_netcdf(aero_data, ncid)
     call bin_grid_output_netcdf(bin_grid, ncid, "diam", unit="m")
-    call drydep_params_output_netcdf(scenario%drydep, ncid)
+
+    if (scenario%loss_function_type == SCENARIO_LOSS_FUNCTION_DRYDEP) then
+       call drydep_params_output_netcdf(scenario%drydep, ncid)
+    end if
 
     call pmc_nc_check(nf90_close(ncid))
 

src/partmc.F90

@@ -732,6 +732,11 @@ subroutine partmc_sect(file)
     !!   format should be \subpage input_format_aero_dist
     !! - \subpage input_format_scenario
     !! - \subpage input_format_env_state
+    !! - \b do_aero_dilution (logical): whether to apply aerosol
+    !!   dilution. If \c no, both the background-exchange dilution and
+    !!   the mixing-layer-growth correction are skipped, which allows
+    !!   other processes (for example dry deposition) to be studied in
+    !!   isolation.
     !! - \b do_coagulation (logical): whether to perform particle
     !!   coagulation.  If \c do_coagulation is \c yes, then the
     !!   following parameters must also be provided:
@@ -771,6 +776,7 @@ subroutine partmc_sect(file)
     !! start_time 0                    # start time (s since 00:00 UTC)
     !! start_day 1                     # start day of year (UTC)
     !!
+    !! do_aero_dilution yes            # whether to do dilution (yes/no)
     !! do_coagulation yes              # whether to do coagulation (yes/no)
     !! kernel brown                    # coagulation kernel
     !! </pre>

src/run_exact.F90

@@ -78,8 +78,8 @@ subroutine run_exact(bin_grid, scenario, env_state, aero_data, &
             run_exact_opt%coag_kernel_type, aero_dist_init, scenario, &
             env_state, time, aero_binned)
        call output_sectional(run_exact_opt%prefix, bin_grid, aero_data, &
-            aero_binned, gas_data, gas_state, env_state, i_time + 1, &
-            time, run_exact_opt%t_output, run_exact_opt%uuid)
+            aero_binned, gas_data, gas_state, env_state, scenario, &
+            i_time + 1, time, run_exact_opt%t_output, run_exact_opt%uuid)
     end do
 
   end subroutine run_exact