284 lines
9.9 KiB
C
284 lines
9.9 KiB
C
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#ifndef IO_H
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#define IO_H
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#include <fstream>
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#include <vector>
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#if USE_HDF5
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#include "hdf5.h"
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#endif
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#include "tinyxml2.h"
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// to handle circular dependency
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#pragma once
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#include "grid.fwd.h"
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//#include "source.fwd.h"
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#include "io.fwd.h"
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#include "utils.h"
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#include "mpi_funcs.h"
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#include "grid.h"
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#include "config.h"
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#include "input_params.h"
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#include "eikonal_solver_2d.h"
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class IO_utils {
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public:
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IO_utils(InputParams&);
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~IO_utils();
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// initialize data output file
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void init_data_output_file();
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// finalize data/grid outpiut file (xdmf)
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void finalize_data_output_file();
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// change the output file name and xdmf objects
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void change_xdmf_obj(int);
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// output for updating xdmf file
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void update_xdmf_file();
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// change group name for source
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void reset_source_info(const int&, const std::string&);
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// change group name for model
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void change_group_name_for_model();
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// prepare grid for each inversion iteration
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void prepare_grid_inv_xdmf(int);
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// set id_sim
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void set_id_src(const int& id_src_){id_sim_src = id_src_;};
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// set source name
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void set_name_src(const std::string& name_src_){name_sim_src = name_src_;};
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//
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// write functions
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//
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// xdmf write out for grid data
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void write_xdmf_file_grid();
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// write grid data to output file
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void write_grid(Grid&);
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// general function for write out data in hdf5
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void write_data_h5(Grid&, std::string&, std::string&, CUSTOMREAL*, int, bool, bool for_tmp_db=false);
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// general function for write out data in hdf5 with merging subdomains
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void write_data_merged_h5(Grid&, std::string&, std::string&, std::string&, CUSTOMREAL*, bool, bool no_group=true);
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// general function for write out data in ascii
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void write_data_ascii(Grid&, std::string&, CUSTOMREAL*);
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// general function for write out data in ascii with merging subdomains
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void write_data_merged_ascii(Grid&, std::string&);
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// write true solution
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void write_true_solution(Grid&);
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// write velocity model
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void write_vel(Grid&, int);
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// write T0v
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void write_T0v(Grid&, int);
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// write u
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void write_u(Grid&);
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// write tau
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void write_tau(Grid&, int);
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// write temporal tau fields
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//void write_tmp_tau(Grid&, int);
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// write result timetable T
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void write_T(Grid&, int);
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// write temporal timetable T in a separated file
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void write_T_tmp(Grid&);
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// write residual (resudual = true_solution - result)
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void write_residual(Grid&);
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// write adjoint field
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void write_adjoint_field(Grid&, int);
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// write fun_loc
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void write_fun(Grid&, int);
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// write xi
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void write_xi(Grid&, int);
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// write eta
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void write_eta(Grid&, int);
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// write a
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void write_a(Grid&, int);
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// write b
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void write_b(Grid&, int);
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// write c
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void write_c(Grid&, int);
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// write f
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void write_f(Grid&, int);
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// Ks
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void write_Ks(Grid&, int);
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// Kxi
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void write_Kxi(Grid&, int);
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// Keta
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void write_Keta(Grid&, int);
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// Ks_density
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void write_Ks_density(Grid&, int);
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// Kxi_density
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void write_Kxi_density(Grid&, int);
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// Keta_density
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void write_Keta_density(Grid&, int);
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// Ks_over_Kden
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void write_Ks_over_Kden(Grid&, int);
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// Kxi_over_Kden
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void write_Kxi_over_Kden(Grid&, int);
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// Keta_over_Kden
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void write_Keta_over_Kden(Grid&, int);
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// Ks_update
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void write_Ks_update(Grid&, int);
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// Kxi_update
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void write_Kxi_update(Grid&, int);
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// Keta_update
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void write_Keta_update(Grid&, int);
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// Ks_density_update
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void write_Ks_density_update(Grid&, int);
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// Kxi_density_update
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void write_Kxi_density_update(Grid&, int);
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// Keta_density_update
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void write_Keta_density_update(Grid&, int);
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// Ks_descent_dir_loc
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void write_Ks_descent_dir(Grid&, int);
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// Kxi_descent_dir_loc
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void write_Kxi_descent_dir(Grid&, int);
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// Keta_descent_dir_loc
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void write_Keta_descent_dir(Grid&, int);
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// write all concerning parameters
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std::vector<CUSTOMREAL> get_grid_data(CUSTOMREAL * data);
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// void write_concerning_parameters(Grid&, int, InputParams&);
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// 2d traveltime field for teleseismic source
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void write_2d_travel_time_field(CUSTOMREAL*, CUSTOMREAL*, CUSTOMREAL*, int, int, CUSTOMREAL);
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void h5_create_and_write_dataset_2d(std::string&, int, int*, int, CUSTOMREAL*);
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void read_2d_travel_time_field(std::string&, CUSTOMREAL*, int, int);
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// 2d field for 1dinv
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void write_1dinv_field(CUSTOMREAL*, CUSTOMREAL*, CUSTOMREAL*, int, int, std::string&);
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// merged model
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void write_T_merged(Grid&, InputParams&, int);
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void write_merged_model(Grid&, InputParams&, std::string);
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bool node_of_this_subdomain(int*, const int&, const int&, const int&);
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//
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// read functions
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//
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// read model data
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void read_model(std::string&, const char*, CUSTOMREAL*, int, int, int);
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// read Travel time from file for earthquake relocation and common receiver double-difference
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void read_T(Grid&);
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// read Travel time from a temporal file for earthquake relocation and common receiver double-difference
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void read_T_tmp(Grid&);
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void read_data_ascii(Grid&, std::string&);
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//
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// delete functions
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//
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// Any deletion of data should be done on a created hdf5. Because the design of hdf5 is that
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// it is not possible to delete data from an existing hdf5 file. The only way to do so is to
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// create a new hdf5 file and copy the necessary data from the old one to the new one.
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// Therefore, the deletion of data is not implemented in this class.
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// Reference : https://stackoverflow.com/questions/1124994/removing-data-from-a-hdf5-file
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private:
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// member variables
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std::string h5_output_grid_fname = "out_data_grid.h5"; // output file name
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std::string h5_output_fname = "out_data.h5"; // output file name
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std::string h5_output_fname_tmp = "out_data_tmp.h5"; // output file name
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std::string xdmf_output_fname = "out_data.xmf"; // output file name
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std::string h5_group_name_grid = "Mesh"; // group name for grid data
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std::string h5_group_name_event = "Event"; // group name for event data
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std::string h5_group_name_data = "Data"; // group name for event data
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std::string h5_dset_name_node_coords_x = "node_coords_x"; // dataset name for node coordinates
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std::string h5_dset_name_node_coords_y = "node_coords_y"; // dataset name for node coordinates
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std::string h5_dset_name_node_coords_z = "node_coords_z"; // dataset name for node coordinates
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std::string h5_dset_name_node_coords_p = "node_coords_p"; // dataset name for node coordinates
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std::string h5_dset_name_node_coords_t = "node_coords_t"; // dataset name for node coordinates
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std::string h5_dset_name_node_coords_r = "node_coords_r"; // dataset name for node coordinates
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std::string h5_dset_name_elem_conn = "elem_conn"; // dataset name for element connectivity
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std::string h5_dset_name_procid = "procid"; // dataset name for my_procs
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std::string h5_file_and_group = h5_output_grid_fname + ":/" + h5_group_name_grid;
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std::string h5_whole_name_conn = h5_file_and_group + "/" + h5_dset_name_elem_conn;
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std::string h5_whole_name_x = h5_file_and_group + "/" + h5_dset_name_node_coords_x;
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std::string h5_whole_name_y = h5_file_and_group + "/" + h5_dset_name_node_coords_y;
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std::string h5_whole_name_z = h5_file_and_group + "/" + h5_dset_name_node_coords_z;
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std::string h5_whole_name_proc = h5_file_and_group + "/" + h5_dset_name_procid;
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// index of current simulation used for naming output files and datasets
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int id_sim_src;
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// name of current simulation used for naming output files and datasets
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std::string name_sim_src;
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int nnodes_glob = 0;
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int nelms_glob = 0;
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int array_rank_default = 2; // default array rank
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int custom_real_flag; // custom real type
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// custom data type for real
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std::string type_name = "Float";
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std::string type_size = "4";
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// helper for xdmf/xml file io
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tinyxml2::XMLDocument* doc;
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tinyxml2::XMLNode* xdmf, *domain, *grid;
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tinyxml2::XMLNode* inversions, *inv_grid;
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void init_xdmf_file();
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void write_xdmf_file();
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void finalize_xdmf_file();
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void insert_data_xdmf(std::string&, std::string&, std::string&);
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#ifdef USE_HDF5
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// h5 variables
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hid_t file_id;
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hid_t group_id;
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hid_t space_id;
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hid_t dset_id;
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hid_t plist_id, plist_id_dset;
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hid_t file_dspace_id, mem_dspace_id;
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herr_t status;
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hid_t plist_id_2d;
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hid_t file_id_2d;
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// h5 low level utilities
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void h5_create_file_by_group_main(std::string&);
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void h5_open_file_by_group_main(std::string&);
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void h5_open_file_collective(std::string&);
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void h5_open_file_collective_input(std::string&);
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void h5_close_file_by_group_main();
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void h5_close_file_collective();
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void h5_create_group_by_group_main(std::string& );
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void h5_open_group_by_group_main(std::string& );
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void h5_open_group_collective(std::string& );
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void h5_close_group_by_group_main();
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void h5_close_group_collective();
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void h5_create_dataset(std::string&, int, int*, int, bool no_group = false);
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void h5_open_dataset(std::string&);
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void h5_open_dataset_no_group(std::string&);
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void h5_close_dataset();
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template <typename T>
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void h5_write_array(std::string&, int, int*, T*, int offset_one, int offset_two=0, int offset_three=0, bool no_group=false);
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template <typename T>
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void h5_read_array(std::string&, int, int*, T*, int*, bool);
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template <typename T>
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void h5_read_array_simple(std::string&, T*);
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void read_data_h5(Grid&, CUSTOMREAL*, std::string, std::string);
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#endif // HDF_HDF5
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// utilities
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std::string create_fname_ascii(std::string&);
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std::string create_fname_ascii_model(std::string&);
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// flag for data type
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const bool model_data = true;
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const bool src_data = false;
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};
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#endif // IO_H
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