Merge pull request #275 from trontrytel/new_names

New names

.travis_scripts/icicle.sh

@@ -34,7 +34,7 @@ cd ../../..
 
 ## icicle
 if [[ $TRAVIS_OS_NAME == 'linux' ]]; then sudo $apt_get_install libboost-program-options-dev; fi
-cd libcloudphxx/tests/paper_GMD_2015
+cd libcloudphxx/tests/2D_cloud
 mkdir -p build 
 cd build
 if [[ $TRAVIS_OS_NAME == 'osx' ]]; then cmake .. -DBOOST_ROOT=/usr/local; fi

tests/paper_GMD_2015/CMakeLists.txt → tests/2D_cloud/CMakeLists.txt

@@ -20,4 +20,5 @@ if (NOT libcloudphxx_LIBRARIES)
 endif()
 
 add_subdirectory(src) 
-add_subdirectory(tests)
+add_subdirectory(paper_GMD_2015)
+add_subdirectory(thesis_2017)

tests/paper_GMD_2015/tests/CMakeLists.txt → tests/2D_cloud/paper_GMD_2015/CMakeLists.txt

@@ -2,4 +2,3 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
 add_subdirectory(fig_a)
 add_subdirectory(fig_b)
 add_subdirectory(fig_c)
-add_subdirectory(chem_sandbox)

tests/paper_GMD_2015/tests/fig_a/plot_blk_1m.cpp → tests/2D_cloud/paper_GMD_2015/fig_a/plot_blk_1m.cpp

@@ -8,7 +8,7 @@ int main(int ac, char** av)
   if (ac != 2) error_macro("expecting 1 argument: CMAKE_BINARY_DIR")
 
   std::string 
-    dir = string(av[1]) + "/tests/fig_a/",
+    dir = string(av[1]) + "/paper_GMD_2015/fig_a/",
     h5  = dir + "out_blk_1m";
 
   auto n = h5n(h5);

tests/paper_GMD_2015/tests/fig_a/plot_blk_2m.cpp → tests/2D_cloud/paper_GMD_2015/fig_a/plot_blk_2m.cpp

@@ -8,7 +8,7 @@ int main(int ac, char** av)
   if (ac != 2) error_macro("expecting 1 argument: CMAKE_BINARY_DIR")
 
   std::string
-    dir = string(av[1]) + "/tests/fig_a/",
+    dir = string(av[1]) + "/paper_GMD_2015/fig_a/",
     h5  = dir + "out_blk_2m";
 
   auto n = h5n(h5);

tests/paper_GMD_2015/tests/fig_a/plot_lgrngn.cpp → tests/2D_cloud/paper_GMD_2015/fig_a/plot_lgrngn.cpp

@@ -8,7 +8,7 @@ int main(int ac, char** av)
   if (ac != 2) error_macro("expecting 1 argument: CMAKE_BINARY_DIR")
 
   std::string
-    dir = string(av[1]) + "/tests/fig_a/",
+    dir = string(av[1]) + "/paper_GMD_2015/fig_a/",
     h5  = dir + "out_lgrngn";
 
   auto n = h5n(h5);

tests/paper_GMD_2015/tests/fig_a/plot_lgrngn_spec.cpp → tests/2D_cloud/paper_GMD_2015/fig_a/plot_lgrngn_spec.cpp

@@ -10,7 +10,7 @@ int main(int ac, char** av)
   if (ac != 2) error_macro("expecting 1 argument: CMAKE_BINARY_DIR")
 
   std::string
-    dir = string(av[1]) + "/tests/fig_a/",
+    dir = string(av[1]) + "/paper_GMD_2015/fig_a/",
     h5  = dir + "out_lgrngn",
     svg = dir + "out_lgrngn_spec.svg";
 

tests/paper_GMD_2015/tests/fig_c/plot.cpp → tests/2D_cloud/paper_GMD_2015/fig_c/plot.cpp

@@ -6,7 +6,7 @@
 int main(int ac, char** av)
 {
   //read w_max, X and Z
-  std::string filename = string(av[1]) + "/tests/fig_a/out_lgrngn/const.h5";
+  std::string filename = string(av[1]) + "/paper_GMD_2015/fig_a/out_lgrngn/const.h5";
   H5::H5File h5f(filename, H5F_ACC_RDONLY);
   auto h5_group = h5f.openGroup("/");
   auto h5_data  = h5f.openDataSet("G");
@@ -25,7 +25,7 @@ int main(int ac, char** av)
   std::map<std::string, int> n({{"x", 15},{"z", 15}});
 
   Gnuplot gp;
-  init(gp, "./plot.svg", 1, 1, n);
+  init(gp, string(av[1]) + "/paper_GMD_2015/fig_c/plot.svg", 1, 1, n);
 
   float dx = X / (n["x"]-1), dz = Z / (n["z"]-1);
 

tests/2D_cloud/thesis_2017/CMakeLists.txt

@@ -0,0 +1,2 @@
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+add_subdirectory(thesis_chap_6)

tests/2D_cloud/thesis_2017/common.hpp

@@ -0,0 +1,40 @@
+#pragma once
+
+#include <iostream>
+#include <iomanip>
+#include <set>
+#include <string>
+#include <sstream>
+#include <vector>
+
+using std::set;
+using std::string;
+using std::ostringstream;
+using std::cerr;
+using std::endl;
+using std::exception;
+using std::vector;
+
+#include <boost/units/systems/si.hpp>
+namespace si = boost::units::si;
+using boost::units::quantity;
+
+
+// error reporting
+#define error_macro(msg) \
+{ \
+  cerr << "error: " << msg << endl; \
+  throw exception(); \
+}
+
+#define notice_macro(msg) \
+{ \
+  cerr << " info: " << msg << endl; \
+}
+
+string zeropad(int n, int w=3)
+{
+  std::ostringstream tmp;
+  tmp << std::setw(w) << std::setfill('0') << n;
+  return tmp.str();
+}

tests/paper_GMD_2015/tests/chem_sandbox/CMakeLists.txt → tests/2D_cloud/thesis_2017/thesis_chap_6/CMakeLists.txt

@@ -1,12 +1,12 @@
 add_executable(calc_chem calc_chem.cpp)
-add_test(calc_chem calc_chem ${CMAKE_BINARY_DIR})
+#add_test(calc_chem calc_chem ${CMAKE_BINARY_DIR})
 
 find_package(HDF5 COMPONENTS CXX REQUIRED QUIET)
 find_package(Boost COMPONENTS iostreams system filesystem REQUIRED)
 
-foreach(case lgrngn_ch lgrngn_ch_spec lgrngn_ch_chem lgrngn_ch_spec_chem)
+foreach(case lgrngn_ch lgrngn_ch_chem)
   add_executable(plot_${case} plot_${case}.cpp)
-  add_test(plot_${case} plot_${case} ${CMAKE_BINARY_DIR})
+  #add_test(plot_${case} plot_${case} ${CMAKE_BINARY_DIR})
   target_link_libraries(plot_${case} ${HDF5_LIBRARIES})
   target_include_directories(plot_${case} PUBLIC ${HDF5_INCLUDE_DIRS})
   target_link_libraries(plot_${case} ${Boost_LIBRARIES})

tests/paper_GMD_2015/tests/chem_sandbox/chem_plots/how_effective.py → tests/2D_cloud/thesis_2017/thesis_chap_6/chem_plots/how_effective.py

@@ -15,7 +15,7 @@
 from libcloudphxx import common as cm
 
 # path to build directory with data
-dir_path = '../../../build/tests/chem_sandbox/'
+dir_path = '../../../build/thesis_2017/thesis_chap_6/'
 
 for case in ['case_base', 'case3', 'case4', 'case5', 'case6']:
 

tests/paper_GMD_2015/tests/chem_sandbox/chem_plots/ph_plot.py → tests/2D_cloud/thesis_2017/thesis_chap_6/chem_plots/ph_plot.py

@@ -21,7 +21,7 @@
 
 for case in ('case_base', 'case1a', 'case3', 'case4', 'case5', 'case6'):
     # path to build directory with data and plots
-    dir_path = '../../../build/tests/chem_sandbox/'
+    dir_path = '../../../build/thesis_2017/thesis_chap_6/'
 
     # read in the data
     data = h5.File(dir_path + 'out_' + case + '/timestep0000011800.h5', 'r')

tests/paper_GMD_2015/tests/chem_sandbox/chem_plots/rain_histograms_all.py → tests/2D_cloud/thesis_2017/thesis_chap_6/chem_plots/rain_histograms_all.py

@@ -6,7 +6,7 @@
 import os
 
 # path to build directory with data
-dir_path = '../../../build/tests/chem_sandbox/'
+dir_path = '../../../build/thesis_2017/thesis_chap_6/'
 
 # all the collision kernels
 kernels = { "hall_pinsky_stratocumulus",

tests/paper_GMD_2015/tests/chem_sandbox/chem_plots/rain_histograms_single.py → tests/2D_cloud/thesis_2017/thesis_chap_6/chem_plots/rain_histograms_single.py

@@ -26,7 +26,7 @@
 num_wet   = wet_edges.size - 1
 
 # path to directory with data
-dir_path = '../../../build/tests/chem_sandbox/'
+dir_path = '../../../build/thesis_2017/thesis_chap_6/'
 
 # loop for case with and without aqueous chemistry
 for case in ['case1', 'case_base', 'case3', 'case4', 'case5', 'case6']:

tests/paper_GMD_2015/tests/chem_sandbox/chem_plots/test_mole_const.py → tests/2D_cloud/thesis_2017/thesis_chap_6/chem_plots/test_mole_const.py

@@ -11,7 +11,7 @@
 from libcloudphxx import common as cm
 
 # path to directory with data
-dir_path = '../../../build/tests/chem_sandbox/'
+dir_path = '../../../build/thesis_2017/thesis_chap_6/'
 
 for case in ['case_base', 'case3', 'case4', 'case5', 'case6']:
 

tests/paper_GMD_2015/tests/chem_sandbox/plot_lgrngn_ch.cpp → tests/2D_cloud/thesis_2017/thesis_chap_6/plot_lgrngn_ch.cpp

@@ -12,7 +12,7 @@ int main(int ac, char** av)
 {
   if (ac != 2) error_macro("expecting 1 argument: CMAKE_BINARY_DIR")
 
-  std::string dir = string(av[1]) + "/tests/chem_sandbox/";
+  std::string dir = string(av[1]) + "/thesis_2017/thesis_chap_6/";
 
   for (const std::string sim_run :
            {

tests/paper_GMD_2015/tests/chem_sandbox/plot_lgrngn_ch_chem.cpp → tests/2D_cloud/thesis_2017/thesis_chap_6/plot_lgrngn_ch_chem.cpp

@@ -12,7 +12,7 @@ int main(int ac, char** av)
 {
   if (ac != 2) error_macro("expecting 1 argument: CMAKE_BINARY_DIR")
 
-  std::string dir = string(av[1]) + "/tests/chem_sandbox/";
+  std::string dir = string(av[1]) + "/thesis_2017/thesis_chap_6/";
 
   for (const std::string sim_run :
            {

tests/2D_cloud/thesis_2017/thesis_chap_6/thesis_script.sh

@@ -0,0 +1,62 @@
+#!/bin/bash
+
+# Runs all the simulations and plots the results from chapter 6 of PhD thesis of Jaruga.
+# The simulations take up to 12 hours (on cuda-k-2 server using CUDA and one thread)
+# It might be useful to run them in the background: nohup ./thesis_script.sh &
+
+cd ../../build/thesis_2017/thesis_chap_6
+
+export OMP_NUM_THREADS=1
+
+# run all the thesis test cases
+./calc_chem ../../
+
+ plot the quicklook plots
+./plot_lgrngn_ch ../../
+./plot_lgrngn_ch_chem ../../
+
+# plot the python scripts for pH and size distributions
+python ../../../thesis_2017/thesis_chap_6/chem_plots/ph_plot.py
+python ../../../thesis_2017/thesis_chap_6/chem_plots/rain_histograms_single.py
+python ../../../thesis_2017/thesis_chap_6/chem_plots/rain_histograms_all.py
+
+# check how much H2SO4 mass was created and what is the error
+python ../../../thesis_2017/thesis_chap_6/chem_plots/how_effective.py
+python ../../../thesis_2017/thesis_chap_6/chem_plots/test_mole_const.py
+
+# thesis_plots folder will contain all plots included in thesis
+mkdir -p thesis_plots
+
+ copy quicklook plots from case1 and case4
+for sim_run in case1 case4; do
+  for el in nc na ef rd rr sd_conc; do
+    dir_name=out_${sim_run}.plot/${el}/;
+    mkdir -p thesis_plots/${dir_name};
+    for sim_time in 10000 11800; do
+      cp ${dir_name}/${sim_time}.svg thesis_plots/${dir_name}/${sim_time}.svg;
+    done
+  done
+done
+
+# copy quicklook plots from the base case
+for el in nc na ef rd rr sd_conc SO2g O3g H2O2g S_VI_aq H2O2_aq O3_aq; do
+  dir_name=out_case_base.plot/${el}/;
+  mkdir -p thesis_plots/${dir_name};
+  for sim_time in 10000 11800; do
+    cp ${dir_name}/${sim_time}.svg thesis_plots/${dir_name}/${sim_time}.svg;
+  done
+done
+
+# copy quicklook plots from case2
+for kernel in hall hall_davis_no_waals hall_pinsky_stratocumulus onishi_hall onishi_hall_davis_no_waals vohl_davis_no_waals; do
+  dir_name=out_case2_${kernel}_42.plot/rr/;
+  mkdir -p thesis_plots/${dir_name};
+  cp ${dir_name}/11800.svg thesis_plots/${dir_name}/11800.svg;
+done
+
+# copy pH and size distribution plots
+cp -r plots_of_pH/ thesis_plots/.
+cp -r plots_of_size_distr/ thesis_plots/.
+
+# pack all plots included in thesis
+tar -cvf thesis_plots.tar thesis_plots