Merge branch 'master' into wrf_partmc_for_partmc_merge

.github/workflows/mpi.yml

@@ -12,4 +12,4 @@ jobs:
     - name: Build the testing docker image
       run: docker build -f Dockerfile.mpi -t partmc-test . 
     - name: Run the tests in the docker container
-      run: docker run -t partmc-test bash -c 'cd /build; make test'
+      run: docker run -t partmc-test bash -c 'cd /build; CTEST_OUTPUT_ON_FAILURE=1 OMPI_MCA_rmaps_base_oversubscribe=false make test'

CMakeLists.txt

@@ -7,9 +7,9 @@ project(PARTMC Fortran C)
 
 set(PACKAGE_BUGREPORT "[email protected]")
 set(PACKAGE_NAME "PartMC")
-set(PACKAGE_STRING "PartMC 2.6.1")
+set(PACKAGE_STRING "PartMC 2.7.0")
 set(PACKAGE_TARNAME "partmc")
-set(PACKAGE_VERSION "2.6.1")
+set(PACKAGE_VERSION "2.7.0")
 
 ######################################################################
 # options

ChangeLog.md

@@ -1,3 +1,16 @@
+2.7.0 - 2023-08-11
+
+  * Add support for SUNDIALS 6+ (Alex Hirzel).
+
+  * Add wrapper around stop (Sylwester Arabas).
+
+  * Change timestepping structure in run_part (Jeff Curtis).
+
+  * Update kappa value of NaCl (Jeff Curtis).
+
+  * Remove optional communicator in photolysis.F90 (Jeff Curtis).
+
+  * Use relative tolerance for comparing water properties (Jeff Curtis).
 
 2.6.1 - 2022-02-18
 

README.md

@@ -5,14 +5,14 @@ PartMC: Particle-resolved Monte Carlo code for atmospheric aerosol simulation
 
 [![Latest version](https://img.shields.io/github/tag/compdyn/partmc.svg?label=version)](https://github.com/compdyn/partmc/blob/master/ChangeLog.md) [![Docker build status](https://img.shields.io/docker/automated/compdyn/partmc.svg)](https://hub.docker.com/r/compdyn/partmc/builds/) [![Github Actions Status](https://github.com/compdyn/partmc/workflows/CI/badge.svg?branch=master)](https://github.com/compdyn/partmc/actions/workflows/main.yml) [![License](https://img.shields.io/github/license/compdyn/partmc.svg)](https://github.com/compdyn/partmc/blob/master/COPYING) [![DOI](https://zenodo.org/badge/24058992.svg)](https://zenodo.org/badge/latestdoi/24058992)
 
-Version 2.6.1  
-Released 2022-02-18
+Version 2.7.0  
+Released 2023-08-11
 
 **Source:** <https://github.com/compdyn/partmc>
 
 **Homepage:** <http://lagrange.mechse.illinois.edu/partmc/>
 
-**Cite as:** M. West, N. Riemer, J. Curtis, M. Michelotti, and J. Tian (2022) PartMC, [![version](https://img.shields.io/github/release/compdyn/partmc.svg?label=version)](https://github.com/compdyn/partmc), [![DOI](https://zenodo.org/badge/24058992.svg)](https://zenodo.org/badge/latestdoi/24058992)
+**Cite as:** M. West, N. Riemer, J. Curtis, M. Michelotti, and J. Tian (2023) PartMC, [![version](https://img.shields.io/github/release/compdyn/partmc.svg?label=version)](https://github.com/compdyn/partmc), [![DOI](https://zenodo.org/badge/24058992.svg)](https://zenodo.org/badge/latestdoi/24058992)
 
 Copyright (C) 2005-2022 Nicole Riemer and Matthew West  
 Portions copyright (C) Andreas Bott, Richard Easter, Jeffrey Curtis,
@@ -184,12 +184,12 @@ Installation
 
 2. Unpack PartMC:
 
-        tar xzvf partmc-2.6.1.tar.gz
+        tar xzvf partmc-2.7.0.tar.gz
 
 3. Change into the main PartMC directory (where this README file is
    located):
 
-        cd partmc-2.6.1
+        cd partmc-2.7.0
 
 4. Make a directory called `build` and change into it:
 
@@ -273,3 +273,18 @@ particle-resolved runs) or binned data (from sectional or exact
 runs). The `extract_*` programs can read these per-timestep NetCDF
 files and output ASCII data (the `extract_sectional_*` programs are
 used for sectional and exact model output).
+
+Python bindings
+===============
+
+The [PyPartMC](https://github.com/open-atmos/PyPartMC) project offers
+pip-installable Python bindings to PartMC. Both source and binary
+packages are available and ship with all PartMC dependencies included.
+PyPartMC exposes internal components of PartMC (utility routines and 
+derived types) which then can serve as building blocks to develop PartMC 
+simulations in Python. Time stepping can be performed either using the
+internal PartMC time-stepper or externally within a Python loop. The
+latter allows to couple the simulation with external Python components
+in each timestep. PyPartMC features examples developed as Jupyter notebooks.
+Snippets of code provided in the README file depict how to use PyPartMC 
+from Julia (using PyCall.jl) and Matlab (using Matlab's built-in Python bridge).

doc/Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = PartMC
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 2.6.1
+PROJECT_NUMBER         = 2.7.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

doc/Makefile

@@ -1,5 +1,5 @@
 
-VERSION = 2.6.1
+VERSION = 2.7.0
 
 GRAPHVIZ_FILE = partmc_modules.gv
 GRAPHVIZ_PDF = $(patsubst %.gv,%.pdf,$(GRAPHVIZ_FILE))

src/aero_data.F90

@@ -918,6 +918,9 @@ subroutine aero_data_output_netcdf(aero_data, ncid)
     call pmc_nc_write_real_1d(ncid, aero_data%kappa, &
          "aero_kappa", (/ dimid_aero_species /), unit="1", &
          long_name="hygroscopicity parameters (kappas) of aerosol species")
+    call pmc_nc_write_integer(ncid, aero_data%i_water, &
+         "aero_i_water", long_name="Index of aerosol water or " &
+         // "0 if water does not exist.")
     call fractal_output_netcdf(aero_data%fractal, ncid)
 
   end subroutine aero_data_output_netcdf
@@ -1027,7 +1030,7 @@ subroutine aero_data_input_netcdf(aero_data, ncid)
     end do
     call assert(377166448, aero_weight_class_names == "")
 
-    call aero_data_set_water_index(aero_data)
+    call pmc_nc_read_integer(ncid, aero_data%i_water, "aero_i_water")
 
     call fractal_input_netcdf(aero_data%fractal, ncid)
 

src/camp_interface.F90

@@ -168,6 +168,10 @@ subroutine pmc_camp_interface_set_partmc_aerosol(aero_data, aero_state, &
     type(camp_state_t), intent(in) :: camp_state
 
     integer :: i_part, i_spec
+    real(kind=dp) :: reweight_num_conc(aero_state_n_part(aero_state))
+
+    call aero_state_num_conc_for_reweight(aero_state, aero_data, &
+         reweight_num_conc)
 
     associate (aero_rep => aero_data%aero_rep_ptr)
     select type (aero_rep)
@@ -190,6 +194,8 @@ subroutine pmc_camp_interface_set_partmc_aerosol(aero_data, aero_state, &
     end select
     end associate
 
+    call aero_state_reweight(aero_state, aero_data, reweight_num_conc)
+
   end subroutine pmc_camp_interface_set_partmc_aerosol
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

src/condense_solver.c

@@ -59,12 +59,14 @@ static int condense_check_flag(void *flagvalue, char *funcname, int opt);
 // solver block
 
 static int condense_solver_Solve(double t, N_Vector ycur, N_Vector fcur,
-				 N_Vector r, N_Vector b, double gamma, double delta, int lr, void *user_data);
+				 N_Vector r, N_Vector b, double gamma,
+                                 double delta, int lr, void *user_data);
 
 /*******************************************************/
 
 void condense_vf_f(int neq, realtype t, double *y_f, double *ydot_f);
-void condense_jac_solve_f(int neq, double t, double *ycur_f, double *fcur_f, double *b_f, double gamma);
+void condense_jac_solve_f(int neq, double t, double *ycur_f, double *fcur_f,
+                          double *b_f, double gamma);
 
 /** \brief Call the ODE solver.
  *
@@ -272,7 +274,8 @@ static int condense_check_flag(void *flagvalue, char *funcname, int opt)
 #pragma GCC diagnostic push
 #pragma GCC diagnostic ignored "-Wunused-parameter"
 static int condense_solver_Solve(double t, N_Vector ycur, N_Vector fcur,
-				 N_Vector b, N_Vector z, double gamma, double delta, int lr, void *user_data)
+				 N_Vector b, N_Vector z, double gamma,
+                                 double delta, int lr, void *user_data)
 {
 	realtype *b_data, *ycur_data, *fcur_data, *z_data;
 	int i, neq;

src/output.F90

@@ -82,7 +82,7 @@ module pmc_output
 #endif
 
   !> PartMC verson number.
-  character(len=100), parameter :: PARTMC_VERSION = "2.6.1"
+  character(len=100), parameter :: PARTMC_VERSION = "2.7.0"
 
   !> Type code for undefined or invalid output.
   integer, parameter :: OUTPUT_TYPE_INVALID = 0