Issue 394 src rcv python

CMakeLists.txt

@@ -216,6 +216,7 @@ if (NOT HDF5_CXX_BUILD)
         mesh
         source_class
         receiver_class
+        yaml-cpp
         ${BOOST_LIBS}
         Kokkos::kokkos)
 else()
@@ -224,8 +225,9 @@ else()
         mesh
         source_class
         receiver_class
-
         Kokkos::kokkos
+        yaml-cpp
+        ${BOOST_LIBS}
         ${HDF5_LIBRARIES}
     )
 endif()

fortran/meshfem2d/CMakeLists.txt

@@ -207,12 +207,12 @@ add_custom_target(meshfem_mesh ALL
 )
 
 set( meshfem2D_PREPROCESSOR_OBJECTS
-  	decompose_mesh.mesh.o
+  decompose_mesh.mesh.o
 	metis_partitioning.mesh.o
 	part_unstruct.mesh.o
 	read_external_mesh_files.mesh.o
 	read_mesh_files.mesh.o
-  	scotch_partitioning.mesh.o
+  scotch_partitioning.mesh.o
 	meshfem2D.mesh.o
 )
 

include/IO/interface.hpp

@@ -7,6 +7,7 @@
 #include "source/interface.hpp"
 #include "specfem_mpi/interface.hpp"
 #include "specfem_setup.hpp"
+#include <yaml-cpp/yaml.h>
 
 namespace specfem {
 
@@ -24,10 +25,10 @@ specfem::mesh::mesh<specfem::dimension::type::dim2>
 read_mesh(const std::string filename, const specfem::MPI::MPI *mpi);
 
 /**
- * @brief Read receiver station file
+ * @brief Read station file
  *
  * Parse receiver stations file and create a vector of
- * specfem::source::source * object
+ * specfem::receiver::receiver * object
  *
  * @param stations_file Stations file describing receiver locations
  * @param angle Angle of the receivers
@@ -37,6 +38,29 @@ read_mesh(const std::string filename, const specfem::MPI::MPI *mpi);
 std::vector<std::shared_ptr<specfem::receivers::receiver> >
 read_receivers(const std::string stations_file, const type_real angle);
 
+/**
+ * @brief Read receivers from YAML Node
+ *
+ * Parse receiver stations file and create a vector of
+ * specfem::receiver::receiver * object
+ *
+ * The receivers are defined in the YAML file as
+ *
+ *     receivers:
+ *         stations-dict:
+ *             - network: "network_name"
+ *               station: "station_name"
+ *               x: x_coordinate
+ *               z: z_coordinate
+ *
+ * @param stations YAML node containing receiver locations
+ * @param angle Angle of the receivers
+ * @return std::vector<specfem::receivers::receiver *> vector of instantiated
+ * receiver objects
+ */
+std::vector<std::shared_ptr<specfem::receivers::receiver> >
+read_receivers(const YAML::Node &stations, const type_real angle);
+
 /**
  * @brief Read sources file written in .yml format
  *
@@ -53,5 +77,21 @@ read_sources(const std::string sources_file, const int nsteps,
              const type_real user_t0, const type_real dt,
              const specfem::simulation::type simulation_type);
 
+/**
+ * @brief Read sources file written in .yml format
+ *
+ * Parse source specification file written in yaml format and create a vector of
+ * specfem::source::source * object
+ *
+ * @param yaml YAML node containing source information
+ * @param mpi Pointer to specfem MPI object
+ * @return std::vector<specfem::sources::source *> vector of instantiated source
+ * objects
+ */
+std::tuple<std::vector<std::shared_ptr<specfem::sources::source> >, type_real>
+read_sources(const YAML::Node yaml, const int nsteps, const type_real user_t0,
+             const type_real dt,
+             const specfem::simulation::type simulation_type);
+
 } // namespace IO
 } // namespace specfem

include/parameter_parser/database_configuration.hpp

@@ -24,6 +24,14 @@ class database_configuration {
   database_configuration(std::string fortran_database,
                          std::string source_database)
       : fortran_database(fortran_database), source_database(source_database){};
+  /**
+   * @brief Construct a new database configuration object
+   *
+   * @param fortran_database location of fortran database
+   * @param source_node location of source file
+   */
+  database_configuration(std::string fortran_database, YAML::Node source_node)
+      : fortran_database(fortran_database), source_database(""){};
   /**
    * @brief Construct a new run setup object
    *

include/parameter_parser/receivers.hpp

@@ -14,48 +14,45 @@ namespace runtime_configuration {
  */
 class receivers {
 public:
-  receivers(const std::string stations_file, const int angle,
-            const int nstep_between_samples)
-      : stations_file(stations_file), angle(angle),
-        nstep_between_samples(nstep_between_samples){};
-
-  receivers(const YAML::Node &Node);
+  receivers(const YAML::Node &Node) : receivers_node(Node) {
+    assert(this->receivers_node["stations-file"].IsDefined());
+    assert(this->receivers_node["angle"].IsDefined());
+    assert(this->receivers_node["nstep_between_samples"].IsDefined());
+    assert(this->receivers_node["seismogram-type"].IsDefined());
+  };
 
   /**
    * @brief Get the path of stations file
    *
    * @return std::string describing the locations of stations file
    */
-  std::string get_stations_file() const { return this->stations_file; }
+  YAML::Node get_stations() const { return this->receivers_node; }
   /**
    * @brief Get the angle of the receiver
    *
    * @return type_real describing the angle of the receiver
    */
-  type_real get_angle() const { return this->angle; };
+  type_real get_angle() const {
+    return this->receivers_node["angle"].as<type_real>();
+  };
   /**
    * @brief Get the number of time steps between seismogram sampling
    *
    * @return int descibing seismogram sampling frequency
    */
-  int get_nstep_between_samples() const { return this->nstep_between_samples; }
+  int get_nstep_between_samples() const {
+    return this->receivers_node["nstep_between_samples"].as<int>();
+  }
+
   /**
    * @brief Get the types of seismogram requested
    *
    * @return std::vector<specfem::seismogram::type> vector seismogram types
    */
-  std::vector<specfem::enums::seismogram::type> get_seismogram_types() const {
-    return stypes;
-  }
+  std::vector<specfem::enums::seismogram::type> get_seismogram_types() const;
 
 private:
-  std::string stations_file; ///< path to stations file
-  type_real angle;           ///< Angle of the receiver
-  int nstep_between_samples; ///< Seismogram sampling frequency
-  std::vector<specfem::enums::seismogram::type> stypes; ///< std::vector
-                                                        ///< containing type of
-                                                        ///< seismograms to be
-                                                        ///< written
+  YAML::Node receivers_node; /// Node that contains receiver information
 };
 } // namespace runtime_configuration
 } // namespace specfem

include/parameter_parser/setup.hpp

@@ -1,13 +1,14 @@
 #ifndef _PARAMETER_SETUP_HPP
 #define _PARAMETER_SETUP_HPP
 
+#include "IO/reader.hpp"
 #include "database_configuration.hpp"
 #include "header.hpp"
 #include "parameter_parser/solver/interface.hpp"
 #include "quadrature.hpp"
-#include "IO/reader.hpp"
 #include "receivers.hpp"
 #include "run_setup.hpp"
+#include "sources.hpp"
 #include "specfem_setup.hpp"
 #include "time_scheme/interface.hpp"
 #include "writer/kernel.hpp"
@@ -105,14 +106,19 @@ class setup {
     return databases->get_databases();
   }
 
+  /**
+   * @brief Get the sources YAML object
+   *
+   * @return YAML::Node YAML node describing the sources
+   */
+  YAML::Node get_sources() const { return this->sources->get_sources(); }
+
   /**
    * @brief Get the path to stations file
    *
    * @return std::string path to stations file
    */
-  std::string get_stations_file() const {
-    return this->receivers->get_stations_file();
-  }
+  YAML::Node get_stations() const { return this->receivers->get_stations(); }
 
   /**
    * @brief Get the angle of receivers
@@ -140,8 +146,7 @@ class setup {
    * @return specfem::IO::writer* Pointer to an instantiated writer
    object
    */
-  std::shared_ptr<specfem::IO::writer>
-  instantiate_seismogram_writer() const {
+  std::shared_ptr<specfem::IO::writer> instantiate_seismogram_writer() const {
     if (this->seismogram) {
       return this->seismogram->instantiate_seismogram_writer(
           this->time_scheme->get_dt(), this->time_scheme->get_t0(),
@@ -151,17 +156,15 @@ class setup {
     }
   }
 
-  std::shared_ptr<specfem::IO::writer>
-  instantiate_wavefield_writer() const {
+  std::shared_ptr<specfem::IO::writer> instantiate_wavefield_writer() const {
     if (this->wavefield) {
       return this->wavefield->instantiate_wavefield_writer();
     } else {
       return nullptr;
     }
   }
 
-  std::shared_ptr<specfem::IO::reader>
-  instantiate_wavefield_reader() const {
+  std::shared_ptr<specfem::IO::reader> instantiate_wavefield_reader() const {
     if (this->wavefield) {
       return this->wavefield->instantiate_wavefield_reader();
     } else {
@@ -234,6 +237,11 @@ class setup {
                   ///< quadrature object
   std::unique_ptr<specfem::runtime_configuration::receivers>
       receivers; ///< Pointer to receivers object
+  std::unique_ptr<specfem::runtime_configuration::sources>
+      sources; ///< Pointer
+               ///< to
+               ///< receivers
+               ///< object
   std::unique_ptr<specfem::runtime_configuration::seismogram>
       seismogram; ///< Pointer to
                   ///< seismogram object

include/parameter_parser/sources.hpp

@@ -0,0 +1,32 @@
+#pragma once
+
+#include "enumerations/specfem_enums.hpp"
+#include "yaml-cpp/yaml.h"
+#include <string>
+
+namespace specfem {
+namespace runtime_configuration {
+/**
+ * @brief class to read source information
+ *
+ */
+class sources {
+public:
+  sources(const std::string sources_file) {
+    source_node = YAML::LoadFile(sources_file);
+  };
+
+  sources(const YAML::Node &Node) { source_node = Node; };
+
+  /**
+   * @brief Get the sources
+   *
+   * @return YAML::Node describing the sources
+   */
+  YAML::Node get_sources() const { return source_node; }
+
+protected:
+  YAML::Node source_node; /// Node that contains sources information
+};
+} // namespace runtime_configuration
+} // namespace specfem

include/source/moment_tensor_source.hpp

@@ -30,6 +30,26 @@ class moment_tensor : public source {
    *
    */
   moment_tensor(){};
+
+  /**
+   * @brief Get the Mxx component of the moment tensor
+   *
+   * @return type_real x-coordinate
+   */
+  type_real get_Mxx() const { return Mxx; }
+  /**
+   * @brief Get the Mxz component of the moment tensor
+   *
+   * @return type_real z-coordinate
+   */
+  type_real get_Mxz() const { return Mxz; }
+  /**
+   * @brief Get the Mzz component of the moment tensor
+   *
+   * @return type_real z-coordinate
+   */
+  type_real get_Mzz() const { return Mzz; }
+
   /**
    * @brief Construct a new moment tensor force object
    *