Stable

CMake/catch.cmake

@@ -1,7 +1,7 @@
 # Captain! If catch2 alpine files do not exist, fetch content
-if( NOT EXISTS "usr/include/catch2/" OR 
-    NOT EXISTS "usr/lib/libCatch2Main.a" OR
-    NOT EXISTS "usr/lib/libCatch2.a" )
+if( NOT EXISTS "/usr/include/catch2/" OR 
+    NOT EXISTS "/usr/lib/libCatch2Main.a" OR
+    NOT EXISTS "/usr/lib/libCatch2.a" )
 
   message( "Ahoy! Not found in system locations - installing from source..." )
 

CMake/compile_time_options.cmake

@@ -6,7 +6,7 @@ set( CMAKE_BUILD_TYPE "Release" )
 
 # preprocessor definitions in source code are defined below:
 set( description "(no description added yet)" )
-set( GITR_USE_CUDA 1 CACHE STRING "${description}" FORCE )
+set( GITR_USE_CUDA 0 CACHE STRING "${description}" FORCE )
 set( GITR_USE_OPENMP 0 CACHE STRING "${description}" FORCE )
 set( GITR_USE_MPI 0 CACHE STRING "${description}" FORCE )
 set( GITR_USE_DOUBLE 1 CACHE STRING "${description}" FORCE )

CMake/crosslink_components.cmake

@@ -9,6 +9,7 @@ target_link_libraries( interp2d thrust )
 
 target_link_libraries( flags libconfig_cxx libconfig_c thrust )
 
+
 target_link_libraries( utils 
                        libconfig_cxx
                        libconfig_c
@@ -17,6 +18,10 @@ target_link_libraries( utils
                        netcdf_cxx
                        netcdf_c )
 
+target_link_libraries( config_interface 
+                       netcdf_cxx 
+                       netcdf_c )
+
 target_link_libraries( boris_data_broker 
                        boris 
                        flags 
@@ -163,6 +168,8 @@ target_link_libraries( file_io_tests
                        Catch2::Catch2WithMain
                        )
 
+target_link_libraries( interpolator_tests Catch2::Catch2WithMain )
+
 if( GITR_USE_MPI )
   target_link_libraries( GITR mpi )
   target_link_libraries( coulomb_tests mpi )

CMake/define_test_components.cmake

@@ -5,6 +5,10 @@ enable_testing()
 
 add_test(NAME sample_test COMMAND python3 ${CMAKE_CURRENT_SOURCE_DIR}/examples/sft_a/test.py WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/examples/sft_a )
 
+set( cpu_test_targets
+     interpolator_tests
+    )
+
 # gpu test targets first
 set( gpu_test_targets 
      boris_tests 
@@ -14,6 +18,16 @@ set( gpu_test_targets
      file_io_tests
      )
 
+foreach( component IN LISTS cpu_test_targets )
+
+  add_executable( ${component} test_src/${component}.cpp )
+
+  add_test( NAME ${component} COMMAND ${component} )
+
+  target_include_directories( ${component} PUBLIC include test_include )
+
+endforeach()
+
 # compile with nvcc
 if( GITR_USE_CUDA )
 

CMake/filepaths_default.cmake

@@ -38,30 +38,30 @@ else()
 set( NETCDF_C_HEADERS_DIR ${NETCDF_C_HEADERS_DIR} CACHE STRING "${description}" )
 endif()
 
-if( NOT DEFINED ${LIBCONFIG_CXX_LIB_DIR})
+if( NOT DEFINED LIBCONFIG_CXX_LIB_DIR)
 set( LIBCONFIG_CXX_LIB_DIR "/usr/lib/x86_64-linux-gnu" "/usr/lib"
      CACHE STRING "${description}" )
 else()
 set( LIBCONFIG_CXX_LIB_DIR ${LIBCONFIG_CXX_LIB_DIR}
      CACHE STRING "${description}" )
 endif()
 
-if( NOT DEFINED ${LIBCONFIG_C_LIB_DIR} )
+if( NOT DEFINED LIBCONFIG_C_LIB_DIR )
 set( LIBCONFIG_C_LIB_DIR "/usr/lib/x86_64-linux-gnu" "/usr/lib"
      CACHE STRING "${description}" )
 else()
 set( LIBCONFIG_C_LIB_DIR ${LIBCONFIG_C_LIB_DIR}
      CACHE STRING "${description}" )
 endif()
 
-if( NOT DEFINED ${LIBCONFIG_CXX_HEADERS_DIR} )
+if( NOT DEFINED LIBCONFIG_CXX_HEADERS_DIR )
 set( LIBCONFIG_CXX_HEADERS_DIR "/usr/lib/x86_64-linux-gnu" "/usr/lib"
      CACHE STRING "${description}" )
 else()
 set( LIBCONFIG_CXX_HEADERS_DIR ${LIBCONFIG_CXX_HEADERS_DIR}
      CACHE STRING "${description}" )
 endif()
-if( NOT DEFINED ${LIBCONFIG_C_HEADERS_DIR} )
+if( NOT DEFINED LIBCONFIG_C_HEADERS_DIR )
 set( LIBCONFIG_C_HEADERS_DIR "/usr/lib/x86_64-linux-gnu" "/usr/lib"
      CACHE STRING "${description}" )
 else()

containers/Dockerfile_alpine

@@ -8,6 +8,8 @@ run apk add --update netcdf-dev
 run apk add --update netcdf-cxx4-dev
 run apk add --update catch2-3 --repository http://dl-cdn.alpinelinux.org/alpine/edge/testing
 run apk add --update libconfig-dev
+run apk add --update gdb
+run apk add --update ninja
 #cli11
 #I think that's it... and we need GITR itself too... should we just install it now...
 

containers/build_alpine.sh

@@ -1,4 +1,4 @@
 #DOCKER_BUILDKIT=1 \
 docker build \
---file GITR/containers/Dockerfile_alpine \
+--file containers/Dockerfile_alpine \
 --tag alpine_interactive_image .

examples/sft_a/generate_inputs.py

@@ -104,9 +104,12 @@ def generate():
     Ti =np.zeros(nZ);
     Ti = TD0+dT_ds*z;
     Ti2D = np.matlib.repmat(Ti,nR,1);
+
 
     vz2D = np.transpose(vz2D)
     Ti2D = np.transpose(Ti2D)
+
+    # Captain! Ti2D is nZ rows and nR columns
 
     # Write 2D plasma profiles to netcdf
     rootgrp = netCDF4.Dataset("input/profiles.nc", "w", format="NETCDF4")

examples/sft_a/input/gitrInput.cfg

@@ -128,7 +128,8 @@ backgroundPlasmaProfiles =
 timeStep = 
 {
   dt = 1E-8;
-  nT = 4000000;
+  # Captain! Changed from 4e6 to 4e4 for a faster test
+  nT = 40000;
 }
 
 surfaces = 

include/background_plasma.h

@@ -0,0 +1,103 @@
+#pragma once
+#include "config_interface.h"
+#include "array.h"
+#include <cstdlib>
+
+class temperature_grid_type
+{
+  public:
+
+  temperature_grid_type( libconfig_string_query const &query_metadata, 
+                         std::string parent_module_name )
+    :
+    full_module_path( parent_module_name + "." + module_name + "." )
+  {
+    // metadata keys (put in a namespace later?)
+    std::string raw_input_file_key = "fileString";
+
+    // meta keys have values that serve as keys to a final value
+    std::string r_grid_size_meta_key = "gridNrString";
+    std::string y_grid_size_meta_key = "gridNyString";
+    std::string z_grid_size_meta_key = "gridNzString";
+
+    std::string r_grid_meta_key = "gridRString";
+    std::string y_grid_meta_key = "gridYString";
+    std::string z_grid_meta_key = "gridZString";
+
+    std::string ion_temp_data_meta_key = "IonTempString";
+    std::string electron_temp_data_meta_key = "ElectronTempString";
+    std::string ion_temp_data_key;
+    std::string electron_temp_data_key;
+
+    // create netcdf file reader object:
+    std::string raw_input_file_path;
+
+    query_metadata( full_module_path + raw_input_file_key, raw_input_file_path );
+
+    // step 0: meta_key --> key
+    std::string r_grid_size_key;
+    std::string z_grid_size_key;
+    query_metadata( full_module_path + r_grid_size_meta_key, r_grid_size_key );
+    query_metadata( full_module_path + z_grid_size_meta_key, z_grid_size_key );
+
+    query_metadata( full_module_path + ion_temp_data_meta_key, ion_temp_data_key );
+    query_metadata( full_module_path + electron_temp_data_meta_key, electron_temp_data_key );
+
+    // query query_raw_input using the keys and values above
+    netcdf_string_query const query_raw_input( "input/" + raw_input_file_path );
+
+    int r_grid_size = -1;
+    int z_grid_size = -1;
+    query_raw_input( r_grid_size_key, r_grid_size );
+    query_raw_input( z_grid_size_key, z_grid_size );
+
+    // check grid sizes here:
+    if( r_grid_size == -1 ) std::cout << "error: r_grid_size is -1";
+    if( z_grid_size == -1 ) std::cout << "error: z_grid_size is -1";
+
+    ti.resize( r_grid_size * z_grid_size );
+    te.resize( r_grid_size * z_grid_size );
+
+    query_raw_input( ion_temp_data_key, ti.data() );
+    query_raw_input( electron_temp_data_key, te.data() );
+  }
+
+  // members:
+  sim::Array< double > ti;
+  sim::Array< double > te;
+
+  // include these as sim::array initially and then pass to tensor class
+  // ti data
+  // te data
+
+  /*
+     Temperature =
+     {
+      #ti = 10.0;
+      #te = 10.0;
+      fileString = "profiles.nc";
+      gridNrString = "nR";
+      gridNzString = "nZ";
+      gridRString = "gridR";
+      gridZString = "gridZ";
+      IonTempString = "ti";
+      ElectronTempString = "te";
+      }
+   */
+  std::string const module_name = "Temperature";
+  std::string const full_module_path;
+};
+
+class background_plasma
+{
+  public:
+
+  std::string const module_name = "backgroundPlasmaProfiles";
+
+  temperature_grid_type temperature_grid;
+
+  background_plasma( libconfig_string_query const &query_metadata )
+    :
+    temperature_grid( query_metadata, module_name )
+  { }
+};

include/config_interface.h

@@ -1,3 +1,4 @@
+#pragma once
 #include <iostream>
 #include <string>
 #include <memory>
@@ -7,9 +8,59 @@
 #include <cassert>
 #include <typeinfo>
 
-#include "config_interface_exceptions.h"
+#include "netcdf.h"
+#include "ncFile.h"
+#include "ncVar.h"
+#include "ncDim.h"
 #include "libconfig.h++"
 
+class netcdf_string_query
+{
+  public:
+
+  netcdf_string_query( std::string netcdf_file_init = "" );
+
+  ~netcdf_string_query();
+
+  template< typename T >
+  void operator()( std::string const &query_key, T &query_value ) const;
+
+  template< typename T >
+  void operator()( std::string const &query_key, T* query_value ) const;
+
+  std::string netcdf_file_name = "empty";
+
+  netCDF::NcFile nc;
+};
+
+template< typename T >
+void netcdf_string_query::operator()( std::string const &query_key, T* query_value ) const
+{
+  std::cout << "Ahoy, Captain! Correct overload called for " << query_key << std::endl;
+
+  netCDF::NcVar ncvar;
+
+  ncvar = nc.getVar( query_key );
+
+  if( ncvar.isNull() )
+  {
+    std::cout << "error: could not find " << query_key << std::endl;
+  }
+
+  else ncvar.getVar( query_value );
+}
+
+template< typename T >
+void netcdf_string_query::operator()( std::string const &query_key, T &query_value ) const
+{
+  netCDF::NcDim nc_nx(nc.getDim(query_key));
+
+  int n_x = nc_nx.getSize();
+
+  query_value = n_x;
+}
+
+
 /* This class wraps the libconfig object and inserts
    a key-string mapping in between. This creates an
    internal separation between the internal representation
@@ -42,7 +93,7 @@ void libconfig_string_query::operator()( std::string const query_key,
 
   if( cfg.exists( query_key.c_str() ) == false )
   {
-    throw invalid_key( query_key );
+    throw 0;
   }
 
   auto const &setting = cfg.getRoot().lookup( query_key );
@@ -76,7 +127,9 @@ void libconfig_string_query::operator()( std::string const query_key, T &query_v
 {
   if( cfg.exists( query_key.c_str() ) == false )
   {
-    throw invalid_key( query_key );
+    //throw invalid_key( query_key );
+    std::cout << "libconfig could not find" << query_key << std::endl;
+    throw 0;
   }
 
   auto const &setting = cfg.getRoot().lookup( query_key );
@@ -94,7 +147,9 @@ void libconfig_string_query::operator()( std::string const query_key, T &query_v
 
     if( success == false ) 
     {
-      throw lookup_failed( query_key );
+      //throw lookup_failed( query_key );
+      std::cout << "libconfig " << query_key << " lookup failed!" << std::endl;
+      throw 0;
     }
   }
 }