update I/O format options to include hdf5
This commit is contained in:
James McClure
parent
b9d46f2865
commit
d926202d7f
@ -608,6 +608,9 @@ runAnalysis::runAnalysis( std::shared_ptr<Database> input_db, const RankInfoStru
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auto db = input_db->getDatabase( "Analysis" );
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auto vis_db = input_db->getDatabase( "Visualization" );
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/* set the I/O format */
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format = vis_db->getWithDefault<bool>( "format", "silo" );
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// Ids of work items to use for dependencies
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ThreadPool::thread_id_t d_wait_blobID;
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ThreadPool::thread_id_t d_wait_analysis;
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@ -645,8 +648,10 @@ runAnalysis::runAnalysis( std::shared_ptr<Database> input_db, const RankInfoStru
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d_rank = d_comm.getRank();
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writeIDMap( ID_map_struct(), 0, id_map_filename );
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// Initialize IO for silo
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IO::initialize( "", "silo", "false" );
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//std::string format = "silo";
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IO::initialize( "", format, "false" );
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// Create the MeshDataStruct
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d_meshData.resize( 1 );
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@ -786,7 +791,11 @@ runAnalysis::runAnalysis( ScaLBL_ColorModel &ColorModel)
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d_rank = d_comm.getRank();
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writeIDMap( ID_map_struct(), 0, id_map_filename );
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// Initialize IO for silo
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IO::initialize( "", "silo", "false" );
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//std::string format = "silo";
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format = vis_db->getWithDefault<bool>( "format", "silo" );
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IO::initialize( "", format, "false" );
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// Create the MeshDataStruct
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d_meshData.resize( 1 );
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@ -100,6 +100,8 @@ private:
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int d_subphase_analysis_interval;
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double d_beta;
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bool d_regular;
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std::string format; // IO format string "silo" or "hdf5"
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ThreadPool d_tpool;
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RankInfoStruct d_rank_info;
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IntArray d_Map;
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@ -754,7 +754,6 @@ double ScaLBL_ColorModel::Run(int returntime){
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timestep = INITIAL_TIMESTEP;
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TRIGGER_FORCE_RESCALE = true;
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if (rank == 0) printf(" Capillary number missed target value = %f (measured value was Ca = %f) \n ",capillary_number, Ca);
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}
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if (RESCALE_FORCE == true && SET_CAPILLARY_NUMBER == true && CURRENT_TIMESTEP > RESCALE_FORCE_AFTER_TIMESTEP){
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@ -925,198 +924,7 @@ void ScaLBL_ColorModel::Run(){
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if (analysis_db->keyExists( "analysis_interval" )){
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analysis_interval = analysis_db->getScalar<int>( "analysis_interval" );
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}
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/*
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int IMAGE_INDEX = 0;
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int IMAGE_COUNT = 0;
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std::vector<std::string> ImageList;
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bool SET_CAPILLARY_NUMBER = false;
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bool RESCALE_FORCE = false;
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bool MORPH_ADAPT = false;
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bool USE_MORPH = false;
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bool USE_SEED = false;
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bool USE_DIRECT = false;
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bool USE_MORPHOPEN_OIL = false;
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int MAX_MORPH_TIMESTEPS = 50000; // maximum number of LBM timesteps to spend in morphological adaptation routine
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int MIN_STEADY_TIMESTEPS = 100000;
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int MAX_STEADY_TIMESTEPS = 200000;
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int RESCALE_FORCE_AFTER_TIMESTEP = 0;
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int RAMP_TIMESTEPS = 0;//50000; // number of timesteps to run initially (to get a reasonable velocity field before other pieces kick in)
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int CURRENT_MORPH_TIMESTEPS=0; // counter for number of timesteps spent in morphological adaptation routine (reset each time)
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int CURRENT_STEADY_TIMESTEPS=0; // counter for number of timesteps spent in morphological adaptation routine (reset each time)
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int morph_interval = 100000;
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int morph_timesteps = 0;
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double morph_delta = 0.0;
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double seed_water = 0.0;
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double capillary_number = 0.0;
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double tolerance = 0.01;
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double Ca_previous = 0.f;
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double initial_volume = 0.0;
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double delta_volume = 0.0;
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double delta_volume_target = 0.0;
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double KRA_MORPH_FACTOR=0.5;
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double volA_prev = 0.0;
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double log_krA_prev = 1.0;
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double log_krA_target = 1.0;
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double log_krA = 1.0;
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double slope_krA_volume = 0.0;
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if (color_db->keyExists( "vol_A_previous" )){
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volA_prev = color_db->getScalar<double>( "vol_A_previous" );
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}
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if (color_db->keyExists( "log_krA_previous" )){
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log_krA_prev = color_db->getScalar<double>( "log_krA_previous" );
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}
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if (color_db->keyExists( "krA_morph_factor" )){
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KRA_MORPH_FACTOR = color_db->getScalar<double>( "krA_morph_factor" );
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}
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if (color_db->keyExists( "capillary_number" )){
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capillary_number = color_db->getScalar<double>( "capillary_number" );
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SET_CAPILLARY_NUMBER=true;
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}
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if (color_db->keyExists( "rescale_force_after_timestep" )){
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RESCALE_FORCE_AFTER_TIMESTEP = color_db->getScalar<int>( "rescale_force_after_timestep" );
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RESCALE_FORCE = true;
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}
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if (color_db->keyExists( "timestep" )){
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timestep = color_db->getScalar<int>( "timestep" );
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}
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if (BoundaryCondition != 0 && BoundaryCondition != 5 && SET_CAPILLARY_NUMBER==true){
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if (rank == 0) printf("WARINING: capillary number target only supported for BC = 0 or 5 \n");
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SET_CAPILLARY_NUMBER=false;
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}
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if (analysis_db->keyExists( "seed_water" )){
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seed_water = analysis_db->getScalar<double>( "seed_water" );
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if (rank == 0) printf("Seed water in oil %f (seed_water) \n",seed_water);
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}
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if (analysis_db->keyExists( "morph_delta" )){
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morph_delta = analysis_db->getScalar<double>( "morph_delta" );
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if (rank == 0) printf("Target volume change %f (morph_delta) \n",morph_delta);
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}
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if (analysis_db->keyExists( "morph_interval" )){
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morph_interval = analysis_db->getScalar<int>( "morph_interval" );
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USE_MORPH = true;
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}
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if (analysis_db->keyExists( "use_morphopen_oil" )){
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USE_MORPHOPEN_OIL = analysis_db->getScalar<bool>( "use_morphopen_oil" );
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if (rank == 0 && USE_MORPHOPEN_OIL) printf("Volume change by morphological opening \n");
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USE_MORPH = true;
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}
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if (analysis_db->keyExists( "tolerance" )){
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tolerance = analysis_db->getScalar<double>( "tolerance" );
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}
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if (analysis_db->keyExists( "min_steady_timesteps" )){
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MIN_STEADY_TIMESTEPS = analysis_db->getScalar<int>( "min_steady_timesteps" );
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}
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if (analysis_db->keyExists( "max_steady_timesteps" )){
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MAX_STEADY_TIMESTEPS = analysis_db->getScalar<int>( "max_steady_timesteps" );
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}
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if (analysis_db->keyExists( "max_morph_timesteps" )){
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MAX_MORPH_TIMESTEPS = analysis_db->getScalar<int>( "max_morph_timesteps" );
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}
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auto protocol = color_db->getWithDefault<std::string>( "protocol", "none" );
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if (protocol == "image sequence"){
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// Get the list of images
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USE_DIRECT = true;
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ImageList = color_db->getVector<std::string>( "image_sequence");
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IMAGE_INDEX = color_db->getWithDefault<int>( "image_index", 0 );
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IMAGE_COUNT = ImageList.size();
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morph_interval = 10000;
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USE_MORPH = true;
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USE_SEED = false;
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}
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else if (protocol == "seed water"){
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morph_delta = -0.05;
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seed_water = 0.01;
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USE_SEED = true;
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USE_MORPH = true;
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}
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else if (protocol == "open connected oil"){
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morph_delta = -0.05;
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USE_SEED = false;
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USE_MORPH = true;
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USE_MORPHOPEN_OIL = true;
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}
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else if (protocol == "shell aggregation"){
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morph_delta = -0.05;
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USE_MORPH = true;
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USE_SEED = false;
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}
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else if (protocol == "fractional flow"){
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USE_MORPH = false;
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USE_SEED = false;
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}
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else if (protocol == "centrifuge"){
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USE_MORPH = false;
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USE_SEED = false;
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}
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else if (protocol == "core flooding"){
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USE_MORPH = false;
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USE_SEED = false;
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if (SET_CAPILLARY_NUMBER){
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double MuB = rhoB*(tauB - 0.5)/3.0;
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double IFT = 6.0*alpha;
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double CrossSectionalArea = (double) (nprocx*(Nx-2)*nprocy*(Ny-2));
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flux = Dm->Porosity()*CrossSectionalArea*IFT*capillary_number/MuB;
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}
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} if (rank==0){
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printf("********************************************************\n");
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if (protocol == "image sequence"){
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printf(" using protocol = image sequence \n");
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printf(" min_steady_timesteps = %i \n",MIN_STEADY_TIMESTEPS);
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printf(" max_steady_timesteps = %i \n",MAX_STEADY_TIMESTEPS);
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printf(" tolerance = %f \n",tolerance);
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std::string first_image = ImageList[IMAGE_INDEX];
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printf(" first image in sequence: %s ***\n", first_image.c_str());
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}
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else if (protocol == "seed water"){
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printf(" using protocol = seed water \n");
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printf(" min_steady_timesteps = %i \n",MIN_STEADY_TIMESTEPS);
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printf(" max_steady_timesteps = %i \n",MAX_STEADY_TIMESTEPS);
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printf(" tolerance = %f \n",tolerance);
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printf(" morph_delta = %f \n",morph_delta);
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printf(" seed_water = %f \n",seed_water);
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}
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else if (protocol == "open connected oil"){
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printf(" using protocol = open connected oil \n");
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printf(" min_steady_timesteps = %i \n",MIN_STEADY_TIMESTEPS);
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printf(" max_steady_timesteps = %i \n",MAX_STEADY_TIMESTEPS);
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printf(" tolerance = %f \n",tolerance);
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printf(" morph_delta = %f \n",morph_delta);
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}
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else if (protocol == "shell aggregation"){
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printf(" using protocol = shell aggregation \n");
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printf(" min_steady_timesteps = %i \n",MIN_STEADY_TIMESTEPS);
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printf(" max_steady_timesteps = %i \n",MAX_STEADY_TIMESTEPS);
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printf(" tolerance = %f \n",tolerance);
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printf(" morph_delta = %f \n",morph_delta);
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}
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else if (protocol == "fractional flow"){
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printf(" using protocol = fractional flow \n");
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printf(" min_steady_timesteps = %i \n",MIN_STEADY_TIMESTEPS);
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printf(" max_steady_timesteps = %i \n",MAX_STEADY_TIMESTEPS);
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printf(" tolerance = %f \n",tolerance);
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}
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else if (protocol == "centrifuge"){
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printf(" using protocol = centrifuge \n");
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printf(" driving force = %f \n",Fz);
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if (Fz < 0){
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printf(" Component B displacing component A \n");
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}
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else if (Fz > 0){
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printf(" Component A displacing component B \n");
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}
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}
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else if (protocol == "core flooding"){
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printf(" using protocol = core flooding \n");
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printf(" capillary number = %f \n", capillary_number);
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}
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printf("No. of timesteps: %i \n", timestepMax);
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fflush(stdout);
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}
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*/
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//************ MAIN ITERATION LOOP ***************************************/
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comm.barrier();
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PROFILE_START("Loop");
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@ -1293,26 +1101,5 @@ void ScaLBL_ColorModel::WriteDebug(){
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fwrite(PhaseField.data(),8,N,VELZ_FILE);
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fclose(VELZ_FILE);
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/* ScaLBL_Comm->RegularLayout(Map,&ColorGrad[0],PhaseField);
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FILE *CGX_FILE;
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sprintf(LocalRankFilename,"Gradient_X.%05i.raw",rank);
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CGX_FILE = fopen(LocalRankFilename,"wb");
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fwrite(PhaseField.data(),8,N,CGX_FILE);
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fclose(CGX_FILE);
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ScaLBL_Comm->RegularLayout(Map,&ColorGrad[Np],PhaseField);
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FILE *CGY_FILE;
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sprintf(LocalRankFilename,"Gradient_Y.%05i.raw",rank);
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CGY_FILE = fopen(LocalRankFilename,"wb");
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fwrite(PhaseField.data(),8,N,CGY_FILE);
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fclose(CGY_FILE);
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ScaLBL_Comm->RegularLayout(Map,&ColorGrad[2*Np],PhaseField);
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FILE *CGZ_FILE;
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sprintf(LocalRankFilename,"Gradient_Z.%05i.raw",rank);
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CGZ_FILE = fopen(LocalRankFilename,"wb");
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fwrite(PhaseField.data(),8,N,CGZ_FILE);
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fclose(CGZ_FILE);
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*/
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}
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@ -20,6 +20,7 @@ void ScaLBL_MRTModel::ReadParams(string filename){
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db = std::make_shared<Database>( filename );
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domain_db = db->getDatabase( "Domain" );
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mrt_db = db->getDatabase( "MRT" );
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vis_db = db->getDatabase( "Visualization" );
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tau = 1.0;
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timestepMax = 100000;
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@ -371,50 +372,7 @@ void ScaLBL_MRTModel::Run(){
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void ScaLBL_MRTModel::VelocityField(){
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/* Minkowski Morphology(Mask);
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int SIZE=Np*sizeof(double);
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ScaLBL_D3Q19_Momentum(fq,Velocity, Np);
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ScaLBL_DeviceBarrier(); comm.barrier();
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ScaLBL_CopyToHost(&VELOCITY[0],&Velocity[0],3*SIZE);
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memcpy(Morphology.SDn.data(), Distance.data(), Nx*Ny*Nz*sizeof(double));
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Morphology.Initialize();
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Morphology.UpdateMeshValues();
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Morphology.ComputeLocal();
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Morphology.Reduce();
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double count_loc=0;
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double count;
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double vax,vay,vaz;
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double vax_loc,vay_loc,vaz_loc;
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vax_loc = vay_loc = vaz_loc = 0.f;
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for (int n=0; n<ScaLBL_Comm->LastExterior(); n++){
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vax_loc += VELOCITY[n];
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vay_loc += VELOCITY[Np+n];
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vaz_loc += VELOCITY[2*Np+n];
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count_loc+=1.0;
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}
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for (int n=ScaLBL_Comm->FirstInterior(); n<ScaLBL_Comm->LastInterior(); n++){
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vax_loc += VELOCITY[n];
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vay_loc += VELOCITY[Np+n];
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vaz_loc += VELOCITY[2*Np+n];
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count_loc+=1.0;
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}
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MPI_Allreduce(&vax_loc,&vax,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
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MPI_Allreduce(&vay_loc,&vay,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
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MPI_Allreduce(&vaz_loc,&vaz,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
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MPI_Allreduce(&count_loc,&count,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
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vax /= count;
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vay /= count;
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vaz /= count;
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double mu = (tau-0.5)/3.f;
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if (rank==0) printf("Fx Fy Fz mu Vs As Js Xs vx vy vz\n");
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if (rank==0) printf("%.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g\n",Fx, Fy, Fz, mu,
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Morphology.V(),Morphology.A(),Morphology.J(),Morphology.X(),vax,vay,vaz);
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*/
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auto format = vis_db->getWithDefault<string>( "format", "silo" );
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std::vector<IO::MeshDataStruct> visData;
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fillHalo<double> fillData(Dm->Comm,Dm->rank_info,{Dm->Nx-2,Dm->Ny-2,Dm->Nz-2},{1,1,1},0,1);
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@ -424,7 +382,7 @@ void ScaLBL_MRTModel::VelocityField(){
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auto VzVar = std::make_shared<IO::Variable>();
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auto SignDistVar = std::make_shared<IO::Variable>();
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IO::initialize("","silo","false");
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IO::initialize("",format,"false");
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// Create the MeshDataStruct
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visData.resize(1);
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visData[0].meshName = "domain";
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@ -49,6 +49,7 @@ public:
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std::shared_ptr<Database> db;
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std::shared_ptr<Database> domain_db;
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std::shared_ptr<Database> mrt_db;
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std::shared_ptr<Database> vis_db;
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IntArray Map;
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DoubleArray Distance;
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