compdyn · jtgasparik · Jul 8, 2024 · Jul 8, 2024 · Jul 13, 2024 · Jul 23, 2024
diff --git a/Dockerfile.camp b/Dockerfile.camp
@@ -10,6 +10,8 @@ RUN dnf -y update \
         sundials-devel \
         lapack-devel \
         openblas-devel \
+        git \
+        valgrind \
         gsl-devel \
         cmake \
     && dnf clean all
@@ -33,11 +35,14 @@ RUN curl -LO https://github.com/jacobwilliams/json-fortran/archive/6.1.0.tar.gz
     && make install \
     && cd ~
 
-RUN curl -LO https://github.com/open-atmos/camp/archive/refs/tags/v1.0.0-gamma.tar.gz \
-    && tar -zxvf v1.0.0-gamma.tar.gz
+#RUN git clone https://github.com/open-atmos/camp.git  
+RUN git clone https://github.com/jtgasparik/camp_.git \
+    && cd camp_ \
+    && git checkout SIMPOL_multiple_layers \
+    && cd ~
 
 # Install a modified version of CVODE
-RUN cd camp-1.0.0-gamma \
+RUN cd camp_ \
     && tar -zxvf cvode-3.4-alpha.tar.gz \
     && cd cvode-3.4-alpha \
     && mkdir build \
@@ -50,30 +55,31 @@ RUN cd camp-1.0.0-gamma \
     && make install \
     && cd ~
 
-ENV LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/lib:/usr/local/lib64:/usr/local/jsonfortran-gnu-6.1.0/lib"
+ENV LD_LIBRARY_PATH="${LD_LIBRARY_PATH:+$LD_LIBRARY_PATH:}/usr/local/lib:/usr/local/lib64:/usr/local/jsonfortran-gnu-6.1.0/lib"
+#ENV LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/lib:/usr/local/lib64:/usr/local/jsonfortran-gnu-6.1.0/lib"
 ENV PATH="${PATH}:/usr/local/jsonfortran-gnu-6.1.0/lib"
 
 # Build CAMP
-RUN  cd camp-1.0.0-gamma \
+RUN  cd camp_ \
     && mkdir build \
     && cd build \
     && export JSON_FORTRAN_HOME="/usr/local/jsonfortran-gnu-6.1.0" \
-    && cmake -D CMAKE_BUILD_TYPE=release \
-             -D CMAKE_C_FLAGS_DEBUG="-pg" \
-             -D CMAKE_Fortran_FLAGS_DEBUG="-pg" \
+    && cmake -D CMAKE_BUILD_TYPE=debug \
+             #-D CMAKE_C_FLAGS_DEBUG="-pg" \
+             #-D CMAKE_Fortran_FLAGS_DEBUG="-pg" \
              -D CMAKE_MODULE_LINKER_FLAGS="-pg" \
              -D ENABLE_GSL:BOOL=TRUE \
              .. \
     && make \
     && cd ~
 
 # NOTE: Modify .dockerignore to whitelist files/directories to copy.
-COPY . /partmc/
+COPY partmc_ /partmc/
 
 RUN mkdir /build \
     && cd /build \
-    && export CAMP_HOME="/camp-1.0.0-gamma/build/" \
-    && cmake -D CMAKE_BUILD_TYPE=release \
+    && export CAMP_HOME="/camp_/build/" \
+    && cmake -D CMAKE_BUILD_TYPE=debug \
              -D CMAKE_C_FLAGS_DEBUG="-g" \
              -D CMAKE_Fortran_FLAGS_DEBUG="-g" \
              -D CMAKE_C_FLAGS_RELEASE="-O2 -g -Werror -Wall -Wextra" \

diff --git a/scenarios/6_camp/aero_init_comp.dat b/scenarios/6_camp/aero_init_comp.dat
@@ -1,2 +1,4 @@
 #                      mass fractions
-organic_matter.POA  1.0
+one_layer.organic_matter.POA  0.4
+two_layer.organic_matter.POA  0.3
+three_layer.organic_matter.POA 0.3
diff --git a/scenarios/6_camp/aerosol_representation.json b/scenarios/6_camp/aerosol_representation.json
@@ -3,7 +3,42 @@
     {
       "name" : "PartMC single particle",
       "type" : "AERO_REP_SINGLE_PARTICLE",
-      "maximum computational particles" : 10500
+      "maximum computational particles" : 120,
+      "layers": [
+              {
+                      "name": "one_layer",
+                      "phases": [
+                              "dust",
+                              "sea_salt",
+                              "organic_matter",
+                              "black_carbon",
+                              "other_PM"
+                      ],
+                      "covers": "two_layer"
+              },
+              {
+                      "name": "two_layer",
+                      "phases": [
+                              "dust",
+                              "sea_salt",
+                              "organic_matter",
+                              "black_carbon",
+                              "other_PM"
+                      ],
+                      "covers": "three_layer"
+              },
+             {
+                      "name": "three_layer",
+                      "phases": [
+                              "dust",
+                              "sea_salt",
+                              "organic_matter",
+                              "black_carbon",
+                              "other_PM"
+                      ],
+                      "covers": "none"
+              }
+      ]
     }
   ]
 }
diff --git a/scenarios/6_camp/camp.spec b/scenarios/6_camp/camp.spec
@@ -1,7 +1,7 @@
 run_type particle               # particle-resolved run
 output_prefix out/camp   # prefix of output files
 n_repeat 1                      # number of Monte Carlo repeats
-n_part 10000                   # total number of particles
+n_part 100                     # 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)
 

diff --git a/scenarios/6_camp/plot_aero_species.py b/scenarios/6_camp/plot_aero_species.py
@@ -69,7 +69,7 @@ def major_formatter(x, pos):
     return f'{1e9*x:.1f}'
 
 pos = [0,0]
-mass_conc, mass_std = get_mass_conc(file, n_times,'organic_matter.ISOP-P1_aero',
+mass_conc, mass_std = get_mass_conc(file, n_times,'one_layer.organic_matter.ISOP-P1_aero',
      n_repeats=n_runs)
 axes[pos[0]][pos[1]].plot(times[partmc_ind_to_plot], mass_conc[partmc_ind_to_plot],
              color=colors[0], ls='', marker='%s'%(part_symbol), label="ISOP_P1_aero",
@@ -79,12 +79,12 @@ def major_formatter(x, pos):
 axes[pos[0]][pos[1]].grid(True,linestyle='--')
 axes[pos[0]][pos[1]].set_xlim([0,24*60])
 axes[pos[0]][pos[1]].xaxis.set_major_locator(ticker.FixedLocator([0,360,720,1080,1440]))
-axes[pos[0]][pos[1]].xaxis.set_major_formatter(time_formatter)
+#axes[pos[0]][pos[1]].xaxis.set_major_formatter(time_formatter)
 axes[pos[0]][pos[1]].set_ylim([0,3e-9])
-axes[pos[0]][pos[1]].yaxis.set_major_formatter(major_formatter)
+#axes[pos[0]][pos[1]].yaxis.set_major_formatter(major_formatter)
 axes[pos[0]][pos[1]].set_ylabel(r'Mass concentration ($\mu \rm g \, m^{-3}$)')
 pos = [1,0]
-mass_conc, mass_std = get_mass_conc(file, n_times,'organic_matter.ISOP-P2_aero',
+mass_conc, mass_std = get_mass_conc(file, n_times,'one_layer.organic_matter.ISOP-P2_aero',
      n_repeats=n_runs)
 axes[pos[0]][pos[1]].plot(times[partmc_ind_to_plot], mass_conc[partmc_ind_to_plot],
              color=colors[0], ls='', marker='%s'%(part_symbol), label="ISOP-P2_aero",
@@ -94,10 +94,10 @@ def major_formatter(x, pos):
 axes[pos[0]][pos[1]].set_xlabel('Simulation time (h)')
 axes[pos[0]][pos[1]].set_xlim([0,24*60])
 axes[pos[0]][pos[1]].xaxis.set_major_locator(ticker.FixedLocator([0,360,720,1080,1440]))
-axes[pos[0]][pos[1]].xaxis.set_major_formatter(time_formatter)
+#axes[pos[0]][pos[1]].xaxis.set_major_formatter(time_formatter)
 axes[pos[0]][pos[1]].set_ylabel(r'Mass concentration ($\mu \rm g \, m^{-3}$)')
 axes[pos[0]][pos[1]].set_ylim([0,3e-10])
-axes[pos[0]][pos[1]].yaxis.set_major_formatter(major_formatter)
+#axes[pos[0]][pos[1]].yaxis.set_major_formatter(major_formatter)
 out_filename = 'out/timeseries_aero.pdf'
 print("Writing %s" % out_filename)
 fig.savefig(out_filename)
diff --git a/scenarios/6_camp/plot_gas_species.py b/scenarios/6_camp/plot_gas_species.py
@@ -74,12 +74,12 @@ def time_formatter(x, pos):
 axes[pos[0]][pos[1]].grid(True,linestyle='--')
 axes[pos[0]][pos[1]].set_xlim([0,24*60])
 axes[pos[0]][pos[1]].xaxis.set_major_locator(ticker.FixedLocator([0,360,720,1080,1440]))
-axes[pos[0]][pos[1]].xaxis.set_major_formatter(time_formatter)
+#axes[pos[0]][pos[1]].xaxis.set_major_formatter(time_formatter)
 axes[pos[0]][pos[1]].set_ylabel("Mixing ratio (ppm)")
 axes[pos[0]][pos[1]].set_ylim([0,.14])
 positions = [0,.02,.04,.06,.08,.10,.12,.14]
 axes[pos[0]][pos[1]].yaxis.set_major_locator(ticker.FixedLocator(positions))
-axes[pos[0]][pos[1]].yaxis.set_major_formatter(major_formatter)
+#axes[pos[0]][pos[1]].yaxis.set_major_formatter(major_formatter)
 
 pos = [1,0]
 var = 'ISOP'
@@ -102,10 +102,10 @@ def time_formatter(x, pos):
 axes[pos[0]][pos[1]].grid(True,linestyle='--')
 axes[pos[0]][pos[1]].set_xlim([0,24*60])
 axes[pos[0]][pos[1]].xaxis.set_major_locator(ticker.FixedLocator([0,360,720,1080,1440]))
-axes[pos[0]][pos[1]].xaxis.set_major_formatter(time_formatter)
+#axes[pos[0]][pos[1]].xaxis.set_major_formatter(time_formatter)
 axes[pos[0]][pos[1]].set_ylabel("Mixing ratio (ppm)")
 axes[pos[0]][pos[1]].set_ylim([0,ymax[0]])
-axes[pos[0]][pos[1]].yaxis.set_major_formatter(major_formatter)
+#axes[pos[0]][pos[1]].yaxis.set_major_formatter(major_formatter)
 out_filename =  'out/camp_gases.pdf'
 print("Writing %s" % out_filename)
 fig.savefig(out_filename)
diff --git a/src/camp_interface.F90 b/src/camp_interface.F90
@@ -93,6 +93,7 @@ subroutine pmc_camp_interface_solve(camp_core, camp_state, &
 
     ! Update the PartMC gas-phase state
     call gas_state_get_camp_conc(gas_state, camp_state)
+    !call camp_core%print()
 
   end subroutine pmc_camp_interface_solve
 

diff --git a/test/camp/aero_init_comp.dat b/test/camp/aero_init_comp.dat
@@ -1,2 +1,2 @@
 #                      mass fractions
-organic_matter.POA  1.0
+one_layer.organic_matter.POA  1.0
diff --git a/test/camp/aerosol_representation.json b/test/camp/aerosol_representation.json
@@ -3,7 +3,16 @@
     {
       "name" : "PartMC single particle",
       "type" : "AERO_REP_SINGLE_PARTICLE",
-      "maximum computational particles" : 1050
+      "maximum computational particles" : 1050,
+      "layers": [
+              {
+                      "name": "one_layer",
+                      "phases": [
+                              "organic_matter"
+                      ],
+                      "covers": "none" 
+              }
+      ]
     }
   ]
 }