Merge branch 'master' of github.com:igfuw/libcloudphxx into sgs_tke

Author: pdziekan

.travis.yml

@@ -68,7 +68,7 @@ aliases:
 jobs:
     include:
       - <<: *precache_tests_mpi
-        env: TEST_SUITE=MPI_tests MPI=mvapich2
+        env: TEST_SUITE=tests MPI=mvapich2
         compiler: gcc
 #     clang MPI_tests disabled due to issues with manually built boost python libstdc++ / libc++ issues
 #      - <<: *precache_default
@@ -88,7 +88,7 @@ jobs:
           env: TEST_SUITE=cuda MPI=none
 
         - compiler: clang
-          env: TEST_SUITE=MPI_tests MPI=none
+          env: TEST_SUITE=tests MPI=mvapich2
 
         - compiler: clang
           env: TEST_SUITE=UWLCM_MT MPI=mvapich2
@@ -162,8 +162,10 @@ install:
     - if [[ $MPI != 'none'                              ]]; then . ./.travis_scripts/deps_install/boost.sh; fi
     - if [[ $MPI != 'none' && $TEST_SUITE == 'UWLCM_MT' ]]; then . ./.travis_scripts/deps_install/mpi_hdf5.sh; fi
 
-    - sudo pip3 install -U pytest --ignore-installed six
-    - sudo pip3 install -U scipy --ignore-installed six
+    - sudo -H pip3 install --upgrade pip
+    - sudo -H pip3 install -U pytest --ignore-installed six
+    - sudo -H pip3 install -U numpy==1.18.5 --ignore-installed six # newer versions require python >= 3.6
+    - sudo -H pip3 install -U scipy==1.4.1 six  # ditto
 
     - if [[ $TEST_SUITE == 'cuda'     ]]; then sudo apt-get install -y cuda-toolkit-8-0; fi
     - if [[ $TEST_SUITE == 'cuda'     ]]; then export CUDA_HOME=/usr/local/cuda; fi
@@ -178,7 +180,7 @@ install:
     - if [[ $MPI == 'none' && ($TEST_SUITE != 'tests' || $TEST_SUITE != 'KidA') ]]; then sudo ln -s /usr/lib/x86_64-linux-gnu/libboost_python-py35.so /usr/lib/x86_64-linux-gnu/libboost_python3.so; fi # different naming conventions for boost python with python 3
 
 # thrust
-    - git clone --depth=1 git://github.com/thrust/thrust.git;
+    - git clone --depth=1 git://github.com/thrust/thrust.git --branch 1.9.10-1;
     - sudo ln -s `pwd`/thrust/thrust /usr/local/include/thrust;
     - if [[ $TEST_SUITE == 'cuda' ]];  then  sudo ln -s `pwd`/thrust/thrust /usr/local/cuda/include/thrust; fi
 
@@ -200,6 +202,4 @@ script:
     - if [[ $TEST_SUITE == 'UWLCM_unit_smg' ]]; then . ./.travis_scripts/UWLCM.sh unit_smg; fi
     # KiD-A 1D
     - if [[ $TEST_SUITE == 'KidA' ]]; then . ./.travis_scripts/KidA.sh; fi
-    # unit tests and drops.py with MPI (drop drops here?)
-    - if [[ $TEST_SUITE == 'MPI_tests' ]]; then . ./.travis_scripts/tests.sh; fi
 

.travis_scripts/UWLCM.sh

@@ -29,9 +29,7 @@ sudo make install
 cd ../../..
 
 ## UWLCM
-# TEMP: use mpi branch from pdziekan
-git clone --depth=1 --branch=mpi_up_to_date git://github.com/pdziekan/UWLCM.git
-#git clone --depth=1 git://github.com/igfuw/UWLCM.git
+git clone --depth=1 git://github.com/igfuw/UWLCM.git
 cd UWLCM
 . .travis_scripts/$1.sh
 set +ex # see https://github.com/travis-ci/travis-ci/issues/6522

.travis_scripts/deps_install/boost.sh

@@ -19,7 +19,7 @@ DEPS_DIR="${TRAVIS_BUILD_DIR}/deps"
       cat $HOME/user-config.jam
       if [[ $COMPILER == 'g++' ]]; then
         ./bootstrap.sh --prefix=${DEPS_DIR}/boost/ --with-libraries=chrono,regex,serialization,mpi,atomic,thread,date_time,system,iostreams,timer,filesystem,program_options,python
-        ./b2 -d0 install
+        travis_wait 30 ./b2 -d0 install
       fi
       if [[ $COMPILER == 'clang++' ]]; then 
         #clang installation taken from https://gist.github.com/jimporter/10442880

CMakeLists.txt

@@ -13,7 +13,7 @@ project(libcloudph++ LANGUAGES CXX)
 #  cmake_policy(VERSION 3.0)
 #endif()
 
-#cmake_policy(SET CMP0079 NEW)
+cmake_policy(SET CMP0079 NEW)
 
 # put out custom find scripts first
 list(INSERT CMAKE_MODULE_PATH 0 ${PROJECT_SOURCE_DIR}/cmake)
@@ -108,11 +108,11 @@ target_include_directories(cloudphxx_lgrngn
 )
 
 # enabling additional warnings
-target_compile_options(cloudphxx_lgrngn PRIVATE $<$<COMPILE_LANGUAGE:CXX>: -Wextra>)
+#target_compile_options(cloudphxx_lgrngn PRIVATE $<$<COMPILE_LANGUAGE:CXX>: -Wextra>)
 #set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wextra")
 
-# enabling c++11
-target_compile_features(cloudphxx_lgrngn PUBLIC cxx_std_11)
+# enabling c++14
+target_compile_features(cloudphxx_lgrngn PUBLIC cxx_std_14)
 # config-specific flags
 target_compile_options(cloudphxx_lgrngn PRIVATE $<$<AND:$<COMPILE_LANGUAGE:CXX>,$<CONFIG:DEBUG>>:         -g -Og -DTHRUST_DEBUG>)
 target_compile_options(cloudphxx_lgrngn PRIVATE $<$<AND:$<COMPILE_LANGUAGE:CXX>,$<CONFIG:RELWITHDEBINFO>>: -Ofast -march=native>)
@@ -332,7 +332,7 @@ file(WRITE "${tmpdir}/test.cpp" "
     chem_stepper.do_step(rhs(), v, 0, 1);
   }
 ")
-execute_process(COMMAND "${CMAKE_CXX_COMPILER}" "test.cpp" "-I${Boost_INCLUDE_DIR}" "-I${THRUST_INCLUDE_DIR}" WORKING_DIRECTORY ${tmpdir} RESULT_VARIABLE status ERROR_VARIABLE msg)
+execute_process(COMMAND "${CMAKE_CXX_COMPILER}" "-std=c++14" "test.cpp" "-I${Boost_INCLUDE_DIR}" "-I${THRUST_INCLUDE_DIR}" WORKING_DIRECTORY ${tmpdir} RESULT_VARIABLE status ERROR_VARIABLE msg)
 if (NOT status EQUAL 0) 
   message(FATAL_ERROR "${pfx}: c++ compiler failed\n ${msg}")
 endif()

include/libcloudph++/common/detail/toms748.hpp

@@ -295,6 +295,9 @@ T toms748_solve(F f, const T& ax, const T& bx, const T& fax, const T& fbx, Tol t
 
    a = ax;
    b = bx;
+   
+   fa = fax;
+   fb = fbx;
 
 #if !defined(NDEBUG)
    if(a >= b)
@@ -303,10 +306,6 @@ T toms748_solve(F f, const T& ax, const T& bx, const T& fax, const T& fbx, Tol t
      assert(0);
    }
 #endif
-   
-
-   fa = fax;
-   fb = fbx;
 
    if(tol(a, b) || (fa == 0) || (fb == 0))
    {

include/libcloudph++/common/kappa_koehler.hpp

@@ -34,7 +34,7 @@ namespace libcloudphxx
         quantity<si::dimensionless, real_t> RH
       )   
       {   
-        assert(RH > .05); // kappa-koehler assumes well dissolved matter
+        assert(RH > .03); // kappa-koehler assumes well dissolved matter
         assert(RH < 1.); // no equilibrium over RH=100%
         assert(kappa > 0); // pure-water case left out
         return rd3 * (1 - RH * (1 - kappa)) / (1 - RH);

include/libcloudph++/common/output.hpp

@@ -16,7 +16,8 @@ namespace libcloudphxx
       outS_VI = chem::S_VI,                        
       outH = chem::H,                          
       outliq_vol,
-      outdry_vol
+      outdry_vol,
+      outprtcl_num
     };
 
     const std::map<output_t, std::string> output_names
@@ -30,7 +31,8 @@ namespace libcloudphxx
       {outS_VI   , "S_VI"},                        
       {outH      , "H"},                          
       {outliq_vol, "liquid_volume"},
-      {outdry_vol, "dry_volume"}
+      {outdry_vol, "dry_volume"},
+      {outprtcl_num, "particle_number"}
     };
   };
 };

include/libcloudph++/lgrngn/opts_init.hpp

@@ -139,7 +139,9 @@ namespace libcloudphxx
 
       bool no_ccn_at_init; // if true, no ccn / SD are put at the start of the simulation
 
-      bool open_side_walls; // if true, side walls are "open", i.e. SD are removed at contact.
+      bool open_side_walls,       // if true, side walls are "open", i.e. SD are removed at contact. Periodic otherwise.
+           periodic_topbot_walls; // if true, top and bot walls are periodic. Open otherwise
+
 
       // ctor with defaults (C++03 compliant) ...
       opts_init_t() : 
@@ -183,7 +185,8 @@ namespace libcloudphxx
         rd_min(0.),
         diag_incloud_time(false),
         no_ccn_at_init(false),
-        open_side_walls(false)
+        open_side_walls(false),
+        periodic_topbot_walls(false)
       {}
 
       // dtor (just to silence -Winline warnings)

models/kinematic_2D/tests/paper_GMD_2015/fig_a/CMakeLists.txt

@@ -59,7 +59,7 @@ add_test(travis_2D_kin_cloud_dims_blk bash -c "
 add_test(travis_2D_kin_cloud_diff_blk_1m bash -c "
   for dir in travis_out_blk_1m; do
     echo 'comparing const.h5'                                                                                                &&
-    h5diff --delta=2e-7  -v2 $dir/const.h5           ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/const.h5                       &&
+    h5diff --delta=3e-7  -v2 $dir/const.h5           ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/const.h5                       &&
     echo 'comparing timestep0000000000.h5'                                                                                   &&
     h5diff --delta=2e-5  -v2 $dir/timestep0000000000.h5 ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/timestep0000000000.h5  /rv  &&
     h5diff --delta=2e-5  -v2 $dir/timestep0000000000.h5 ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/timestep0000000000.h5  /rr  &&
@@ -76,7 +76,7 @@ add_test(travis_2D_kin_cloud_diff_blk_1m bash -c "
 add_test(travis_2D_kin_cloud_diff_blk_2m bash -c "
   for dir in travis_out_blk_2m; do
     echo 'comparing const.h5'
-    h5diff --delta=2e-7     -v2 $dir/const.h5              ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/const.h5                    &&
+    h5diff --delta=3e-7     -v2 $dir/const.h5              ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/const.h5                    &&
     echo 'comparing timestep0000000000.h5'                                                                                     &&
     h5diff --relative=1e-9  -v2 $dir/timestep0000000000.h5 ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/timestep0000000000.h5  /rv  &&
     h5diff --relative=1e-9  -v2 $dir/timestep0000000000.h5 ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/timestep0000000000.h5  /rr  &&
@@ -106,14 +106,14 @@ add_test(travis_2D_kin_cloud_dims_lgrngn bash -c "
 add_test(travis_2D_kin_cloud_diff_lgrngn bash -c "
   for dir in travis_out_lgrngn; do
     echo 'comparing const.h5'
-    h5diff --delta=1e-6     -v2 $dir/const.h5                ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/travis_const.h5                       &&
+    h5diff --delta=1e-6      -v2 $dir/const.h5                ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/travis_const.h5                       &&
     echo 'comparing timestep0000000000.h5'                                                                                                  &&
-    h5diff --relative=1e-9  -v2 $dir/timestep0000000000.h5   ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/travis_timestep0000000000.h5 /th      &&
-    h5diff --relative=1e-9  -v2 $dir/timestep0000000000.h5   ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/travis_timestep0000000000.h5 /rv      &&
-    h5diff --relative=1e-9  -v2 $dir/timestep0000000000.h5   ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/travis_timestep0000000000.h5 /sd_conc &&
+    h5diff --relative=1e-9   -v2 $dir/timestep0000000000.h5   ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/travis_timestep0000000000.h5 /th      &&
+    h5diff --relative=1e-9   -v2 $dir/timestep0000000000.h5   ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/travis_timestep0000000000.h5 /rv      &&
+    h5diff --relative=1e-9   -v2 $dir/timestep0000000000.h5   ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/travis_timestep0000000000.h5 /sd_conc &&
     echo 'comparing timestep0000000020.h5'                                                                                                  &&
-    h5diff --relative=0.001 -v2 $dir/timestep0000000020.h5   ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/travis_timestep0000000020.h5 /th      &&
-    h5diff --relative=0.002 -v2 $dir/timestep0000000020.h5   ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/travis_timestep0000000020.h5 /rv      &&
-    h5diff --delta=1        -v2 $dir/timestep0000000020.h5   ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/travis_timestep0000000020.h5 /sd_conc || exit 1;
+    h5diff --relative=0.001  -v2 $dir/timestep0000000020.h5   ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/travis_timestep0000000020.h5 /th      &&
+    h5diff --relative=0.0021 -v2 $dir/timestep0000000020.h5   ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/travis_timestep0000000020.h5 /rv      &&
+    h5diff --delta=1         -v2 $dir/timestep0000000020.h5   ${CMAKE_CURRENT_SOURCE_DIR}/refdata/$dir/travis_timestep0000000020.h5 /sd_conc || exit 1;
   done  
 ")

src/detail/config.hpp

@@ -28,6 +28,8 @@ namespace libcloudphxx
         // range of beard77fast bins:
         const real_t vt0_ln_r_min, vt0_ln_r_max;
 
+        const real_t bcond_tolerance = 2e-4; // [m]; error tolerance for position near bcond after distmem copy  
+
         // ctor
         config():
           vt0_ln_r_min(log(5e-7)),