output_msh.cc

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/*!
 *
 * Copyright (C) 2015 Technical University of Liberec.  All rights reserved.
 * 
 * This program is free software; you can redistribute it and/or modify it under
 * the terms of the GNU General Public License version 3 as published by the
 * Free Software Foundation. (http://www.gnu.org/licenses/gpl-3.0.en.html)
 * 
 * This program is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
 *
 * 
 * @file    output_msh.cc
 * @brief   The functions for outputs to GMSH files.
 */
 
#include "output_msh.hh"
#include "output_mesh.hh"
#include "output_element.hh"
#include "mesh/mesh.h"
#include "element_data_cache_base.hh"
#include "input/factory.hh"
#include "tools/time_governor.hh"
 
 
FLOW123D_FORCE_LINK_IN_CHILD(gmsh)
 
 
using namespace Input::Type;
 
 
const Record & OutputMSH::get_input_type() {
    return Record("gmsh", "Parameters of gmsh output format.")
        // It is derived from abstract class
        .derive_from(OutputTime::get_input_format_type())
        .close();
}
 
const int OutputMSH::registrar = Input::register_class< OutputMSH >("gmsh") +
        OutputMSH::get_input_type().size();
 
 
OutputMSH::OutputMSH()
{
    this->enable_refinement_ = false;
    this->header_written = false;
 
    dummy_data_list_.resize(OutputTime::N_DISCRETE_SPACES);
 
 
}
 
OutputMSH::~OutputMSH()
{
    // Perform output of last time step
    this->write_time_frame();
 
    this->write_tail();
}
 
 
 
 
void OutputMSH::write_msh_header(void)
{
    ofstream &file = this->_base_file;
 
    // Write simple header
    file << "$MeshFormat" << endl;
    file << "2" << " 0 " << sizeof(double) << endl;
    file << "$EndMeshFormat" << endl;
}
 
void OutputMSH::write_msh_geometry(void)
{
    ofstream &file = this->_base_file;
 
    // Write information about nodes
    file << "$Nodes" << endl;
    file << this->nodes_->n_values() << endl;
    auto permutation_vec = output_mesh_->orig_mesh_->node_permutations();
    this->write_msh_ascii_data(this->node_ids_, this->nodes_, permutation_vec);
    file << "$EndNodes" << endl;
}
 
void OutputMSH::write_msh_topology(void)
{
    ofstream &file = this->_base_file;
    const static unsigned int gmsh_simplex_types_[4] = {0, 1, 2, 4};
    auto &id_elem_vec = *( this->elem_ids_->get_data().get() );
    auto &id_node_vec = *( this->node_ids_->get_data().get() );
    auto &connectivity_vec = *( this->connectivity_->get_data().get() );
    auto &offsets_vec = *( this->offsets_->get_data().get() );
    auto &regions_vec = *( this->region_ids_->get_data().get() );
    auto &partition_vec = *( this->partitions_->get_data().get() );
 
    unsigned int n_nodes, i_node=0;
 
    std::vector<unsigned int> gmsh_connectivity(4*id_elem_vec.size(), 0);
    for(unsigned int i_elm=0; i_elm < id_elem_vec.size(); ++i_elm) {
        n_nodes = offsets_vec[i_elm+1]-offsets_vec[i_elm];
        auto &new_to_old_node = output_mesh_->orig_mesh_->element_accessor(i_elm).orig_nodes_order();
        for(unsigned int i=0; i<n_nodes; i++, i_node++) {
            // permute element nodes to the order of the input mesh
            // works only for GMSH, serial output
            uint old_i = new_to_old_node[i];
            gmsh_connectivity[4*i_elm+old_i] = connectivity_vec[i_node];
        }
    }
 
 
    // Write information about elements
    file << "$Elements" << endl;
    file << this->offsets_->n_values()-1 << endl;
    ElementAccessor<OutputElement::spacedim> elm;
    bool is_corner_output = (this->nodes_->n_values() != output_mesh_->orig_mesh_->node_permutations().size());
    unsigned int i_gmsh_elm, gmsh_id;
    auto permutation_vec = output_mesh_->orig_mesh_->element_permutations();
    for(unsigned int i_elm=0; i_elm < id_elem_vec.size(); ++i_elm) {
        i_gmsh_elm = permutation_vec[i_elm];
        if (is_corner_output) gmsh_id = id_elem_vec[i_elm];
        else gmsh_id = id_elem_vec[i_gmsh_elm];
 
        n_nodes = offsets_vec[i_gmsh_elm+1]-offsets_vec[i_gmsh_elm];
        // element_id element_type 3_other_tags material region partition
        file << gmsh_id
             << " " << gmsh_simplex_types_[ n_nodes-1 ]
             << " 3 " << regions_vec[i_gmsh_elm] << " " << regions_vec[i_gmsh_elm] << " " << partition_vec[i_gmsh_elm];
 
        for(unsigned int i=4*i_gmsh_elm; i<4*i_gmsh_elm+n_nodes; i++) {
            file << " " << id_node_vec[gmsh_connectivity[i]];
        }
        file << endl;
    }
    file << "$EndElements" << endl;
}
 
 
void OutputMSH::write_msh_ascii_data(std::shared_ptr<ElementDataCache<unsigned int>> id_cache, OutputDataPtr output_data,
        const std::vector<unsigned int> &permutations)
{
    unsigned int i_gmsh;
    unsigned int perm_idx;
    ofstream &file = this->_base_file;
    auto &id_vec = *( id_cache->get_data().get() );
 
    bool is_corner_output = (this->nodes_->n_values() != output_mesh_->orig_mesh_->node_permutations().size());
    bool permute_data = output_data->n_values() == permutations.size();
    for(unsigned int i=0; i < output_data->n_values(); ++i) {
 
        if (is_corner_output) i_gmsh = i;
        else i_gmsh = permutations[i];
 
        if (permute_data) perm_idx = permutations[i];
        else perm_idx = i;
 
        file << id_vec[i_gmsh] << " ";
        output_data->print_ascii(file, perm_idx);
        file << std::endl;
    }
}
 
 
void OutputMSH::write_node_data(OutputDataPtr output_data)
{
    ofstream &file = this->_base_file;
    double time_fixed = isfinite(this->registered_time_)?this->registered_time_:0;
    time_fixed /= this->time_unit_converter->get_coef();
 
    file << "$NodeData" << endl;
 
    file << "1" << endl;     // one string tag
    file << "\"" << output_data->field_input_name() <<"\"" << endl;
 
    file << "1" << endl;     // one real tag
    file << time_fixed << endl;    // first real tag = time
 
    file << "3" << endl;     // 3 integer tags
    file << this->current_step << endl;    // step number (start = 0)
    file << output_data->n_comp() << endl;   // number of components
    file << output_data->n_values() << endl;  // number of values
 
    auto permutation_vec = output_mesh_->orig_mesh_->node_permutations();
    this->write_msh_ascii_data(this->node_ids_, output_data, permutation_vec);
 
    file << "$EndNodeData" << endl;
}
 
 
void OutputMSH::write_corner_data(OutputDataPtr output_data)
{
    ofstream &file = this->_base_file;
    double time_fixed = isfinite(this->registered_time_)?this->registered_time_:0;
 
    file << "$ElementNodeData" << endl;
 
    file << "1" << endl;     // one string tag
    file << "\"" << output_data->field_input_name() <<"\"" << endl;
 
    file << "1" << endl;     // one real tag
    file << time_fixed << endl;    // first real tag = registered_time_
 
    file << "3" << endl;     // 3 integer tags
    file << this->current_step << endl;    // step number (start = 0)
    file << output_data->n_comp() << endl;   // number of components
    file << this->offsets_->n_values()-1 << endl; // number of values
 
    //this->write_msh_ascii_data(this->elem_ids_, output_data, true);
    auto &id_vec = *( this->elem_ids_->get_data().get() );
    auto &offsets_vec = *( this->offsets_->get_data().get() );
    unsigned int n_nodes, i_corner;
    auto permutation_vec = output_mesh_->orig_mesh_->element_permutations();
    for(unsigned int i=0; i < id_vec.size(); ++i) {
        unsigned int i_gmsh_elm = permutation_vec[i];
        n_nodes = offsets_vec[i_gmsh_elm+1]-offsets_vec[i_gmsh_elm];
        i_corner = offsets_vec[i_gmsh_elm];
        file << id_vec[i] << " " << n_nodes << " ";
        for (unsigned int j=0; j<n_nodes; j++)
            output_data->print_ascii(file, i_corner++);
        file << std::endl;
    }
 
    file << "$EndElementNodeData" << endl;
}
 
void OutputMSH::write_elem_data(OutputDataPtr output_data)
{
    ofstream &file = this->_base_file;
    double time_fixed = isfinite(this->registered_time_)?this->registered_time_:0;
 
    file << "$ElementData" << endl;
 
    file << "1" << endl;     // one string tag
    file << "\"" << output_data->field_input_name() <<"\"" << endl;
 
    file << "1" << endl;     // one real tag
    file << time_fixed << endl;    // first real tag = registered_time_
 
    file << "3" << endl;     // 3 integer tags
    file << this->current_step << endl;    // step number (start = 0)
    file << output_data->n_comp() << endl;   // number of components
    file << output_data->n_values() << endl;  // number of values
 
    auto permutation_vec = output_mesh_->orig_mesh_->element_permutations();
    this->write_msh_ascii_data(this->elem_ids_, output_data, permutation_vec);
 
    file << "$EndElementData" << endl;
}
 
int OutputMSH::write_head(void)
{
    LogOut() << __func__ << ": Writing output file " << this->_base_filename << " ... ";
 
    this->write_msh_header();
 
    this->write_msh_geometry();
 
    this->write_msh_topology();
 
    LogOut() << "O.K.";
 
    return 1;
}
 
int OutputMSH::write_data(void)
{
    /* Output of serial format is implemented only in the first process */
    if (this->rank_ != 0) {
        return 0;
    }
 
    // Write header with mesh, when it hasn't been written to output file yet
    if(this->header_written == false) {
        this->fix_main_file_extension(".msh");
        try {
            this->_base_filename.open_stream( this->_base_file );
            this->set_stream_precision(this->_base_file);
        } INPUT_CATCH(FilePath::ExcFileOpen, FilePath::EI_Address_String, input_record_)
 
        this->write_head();
        this->header_written = true;
    }
 
    LogOut() << __func__ << ": Writing output file " << this->_base_filename << " ... ";
 
 
    auto &node_data_list = this->output_data_vec_[NODE_DATA];
    for(auto data_it = node_data_list.begin(); data_it != node_data_list.end(); ++data_it) {
        write_node_data(*data_it);
    }
    auto &corner_data_list = this->output_data_vec_[CORNER_DATA];
    for(auto data_it = corner_data_list.begin(); data_it != corner_data_list.end(); ++data_it) {
        write_corner_data(*data_it);
    }
    auto &elem_data_list = this->output_data_vec_[ELEM_DATA];
    for(auto data_it = elem_data_list.begin(); data_it != elem_data_list.end(); ++data_it) {
        write_elem_data(*data_it);
    }
 
    // Flush stream to be sure everything is in the file now
    this->_base_file.flush();
 
    LogOut() << "O.K.";
 
    return 1;
}
 
 
 
int OutputMSH::write_tail(void)
{
    return 1;
}
 
 
void OutputMSH::set_output_data_caches(std::shared_ptr<OutputMeshBase> mesh_ptr) {
    OutputTime::set_output_data_caches(mesh_ptr);
 
    mesh_ptr->get_master_mesh()->create_id_caches();
    this->node_ids_ = mesh_ptr->get_master_mesh()->node_ids_;
    this->elem_ids_ = mesh_ptr->get_master_mesh()->elem_ids_;
    this->region_ids_ = mesh_ptr->get_master_mesh()->region_ids_;
    this->partitions_ = mesh_ptr->get_master_mesh()->partitions_;
}