Improve folder structure of hdf5 / pouts / .dat

Examples/BinaryBH/BinaryBHLevel.cpp

@@ -178,9 +178,9 @@ void BinaryBHLevel::specificPostTimeStep()
             AMRReductions<VariableType::diagnostic> amr_reductions(m_gr_amr);
             double L2_Ham = amr_reductions.norm(c_Ham);
             double L2_Mom = amr_reductions.norm(Interval(c_Mom1, c_Mom3));
-            SmallDataIO constraints_file("constraint_norms", m_dt, m_time,
-                                         m_restart_time, SmallDataIO::APPEND,
-                                         first_step);
+            SmallDataIO constraints_file(m_p.data_path + "constraint_norms",
+                                         m_dt, m_time, m_restart_time,
+                                         SmallDataIO::APPEND, first_step);
             constraints_file.remove_duplicate_time_data();
             if (first_step)
             {

Examples/BinaryBH/Main_BinaryBH.cpp

@@ -55,7 +55,7 @@ int runGRChombo(int argc, char *argv[])
         int puncture_tracker_min_level = sim_params.max_level - 1;
         bh_amr.m_puncture_tracker.initial_setup(
             {sim_params.bh1_params.center, sim_params.bh2_params.center},
-            sim_params.checkpoint_prefix, puncture_tracker_min_level);
+            "punctures", sim_params.data_path, puncture_tracker_min_level);
     }
 
     // The line below selects the problem that is simulated

Examples/BinaryBH/SimulationParameters.hpp

@@ -34,9 +34,7 @@ class SimulationParameters : public SimulationParametersBase
     /// Read shared parameters
     void read_shared_params(GRParmParse &pp)
     {
-        // Do we want Weyl extraction, puncture tracking and constraint norm
-        // calculation?
-        pp.load("activate_extraction", activate_extraction, false);
+        // Do we want puncture tracking and constraint norm calculation?
         pp.load("track_punctures", track_punctures, false);
         pp.load("puncture_tracking_level", puncture_tracking_level, max_level);
         pp.load("calculate_constraint_norms", calculate_constraint_norms,
@@ -297,9 +295,9 @@ class SimulationParameters : public SimulationParametersBase
                         "must be between 0 and max_level (inclusive)");
     }
 
-    // Initial data
-    bool activate_extraction, track_punctures, calculate_constraint_norms;
+    bool track_punctures, calculate_constraint_norms;
     int puncture_tracking_level;
+
     // Collection of parameters necessary for initial conditions
     // Set these even in the case of TwoPunctures as they are used elsewhere
     // e.g. for puncture tracking/tagging

Examples/BinaryBH/params.txt

@@ -3,11 +3,56 @@
 # and a guide to this specific example at
 # https://github.com/GRChombo/GRChombo/wiki/Running-the-BBH-example
 
-# location / naming of output files (must give full path)
+#################################################
+# Filesystem parameters
+
 verbosity = 0
+
+# location / naming of output files
+# output_path = "" # Main path for all files. Must exist!
 chk_prefix = BinaryBHChk_
 plot_prefix = BinaryBHPlot_
-#restart_file = BinaryBHChk_000000.3d.hdf5
+# restart_file = BinaryBHChk_000000.3d.hdf5
+
+# HDF5files are written every dt = L/N*dt_multiplier*checkpoint_interval
+checkpoint_interval = 100
+# set to 0 to turn off plot files (except at t=0 and t=stop_time)
+# set to -1 to never ever print plotfiles
+plot_interval = 10
+num_plot_vars = 3
+plot_vars = chi Weyl4_Re Weyl4_Im
+
+# subpaths - specific directories for hdf5, pout, extraction data
+# (these are created at runtime)
+hdf5_subpath = "hdf5"
+pout_subpath = "pout"
+data_subpath = "data"
+
+# change the name of output files
+# pout_prefix = "pout"
+print_progress_only_to_rank_0 = 1
+
+# ignore_checkpoint_name_mismatch = 0
+# write_plot_ghosts = 0
+
+#################################################
+# Initial Data parameters
+
+# provide 'offset' or 'center'
+
+massA = 0.48847892320123
+massB = 0.48847892320123
+
+offsetA = 0.0 6.10679 0.0
+offsetB = 0.0 -6.10679 0.0
+# centerA = 256 232 256
+# centerB = 256 250 256
+
+momentumA = -0.0841746 -0.000510846 0.0
+momentumB =  0.0841746  0.000510846 0.0
+
+#################################################
+# Grid parameters
 
 # 'N' is the number of subdivisions in each direction of a cubic box
 # 'L' is the length of the longest side of the box, dx_coarsest = L/N
@@ -19,46 +64,29 @@ plot_prefix = BinaryBHPlot_
 N_full = 64
 L_full = 512
 
-# Spatial derivative order (only affects CCZ4 RHS)
-max_spatial_derivative_order = 4 # can be 4 or 6
-
-# Defaults to center of grid L/2
-# uncomment to change
-#center = 256.0 256.0 256.0
-
-# BH params, use puncture tracking to
-# ensure horizons resolved
-track_punctures = 1
-puncture_tracking_level = 5
-massA = 0.48847892320123
-offsetA = 0.0 6.10679 0.0
-momentumA = -0.0841746 -0.000510846 0.0
-massB = 0.48847892320123
-offsetB = 0.0 -6.10679 0.0
-momentumB =  0.0841746  0.000510846 0.0
+# Maximum number of times you can regrid above coarsest level
+max_level = 9 # There are (max_level+1) grids, so min is zero
 
-# regridding control, specify threshold (same on each level)
+# Frequency of regridding at each level and thresholds on the tagging
+# Need one for each level except the top one, ie max_level items
+# Generally you do not need to regrid frequently on every level
+# Level Regridding: 0   1   2   3   4   5   6   7   8
+regrid_interval =   0   0   0   64  64  64  64  64  64
 regrid_threshold = 0.05
-max_level = 9
-# need max_level entries for regrid interval
-regrid_interval = 0 0 0 64 64 64 64 64 64
 
 # Max and min box sizes
-max_grid_size = 16
-block_factor = 16
+max_box_size = 16
+min_box_size = 16
 
-# Set up time steps
-# dt will be dx*dt_multiplier on each grid level
-# HDF5files are written every dt = L/N*dt_multiplier*checkpoint_interval
-checkpoint_interval = 100
-# set to zero to turn off plot files, comps defined in BinaryBHLevel.cpp
-plot_interval = 10
-num_plot_vars = 3
-plot_vars = chi Weyl4_Re Weyl4_Im
-dt_multiplier = 0.25
-stop_time = 2200.0
+# tag_buffer_size = 3
+# grid_buffer_size = 8
+# fill_ratio = 0.7
+# num_ghosts = 3
+# center = 256.0 256.0 256.0 # defaults to center of the grid
+
+#################################################
+# Boundary Conditions parameters
 
-# boundaries and periodicity of grid
 # Periodic directions - 0 = false, 1 = true
 isPeriodic = 0 0 0
 # if not periodic, then specify the boundary type
@@ -86,34 +114,62 @@ num_nonzero_asymptotic_vars = 5
 nonzero_asymptotic_vars = chi h11 h22 h33 lapse
 nonzero_asymptotic_values = 1.0 1.0 1.0 1.0 1.0
 
+# if you are using extrapolating BC:
+# extrapolation_order = 1
+# num_extrapolating_vars = -1
+# extrapolating_vars =
+
+#################################################
+# Evolution parameters
+
+# dt will be dx*dt_multiplier on each grid level
+dt_multiplier = 0.25
+stop_time = 2200.0
+# max_steps = 100
+
+# Spatial derivative order (only affects CCZ4 RHS)
+max_spatial_derivative_order = 4 # can be 4 or 6
+
+nan_check = 1
+
 # Lapse evolution
 lapse_advec_coeff = 1.0
 lapse_coeff = 2.0
 lapse_power = 1.0
 
 # Shift evolution
-shift_advec_coeff = 0.0
+shift_advec_coeff = 0.0 # Usually no advection for beta
 shift_Gamma_coeff = 0.75
-eta = 1.0
+eta = 1.0 # eta of gamma driver, should be of order ~1/M_ADM of spacetime
 
 # CCZ4 parameters
+formulation = 0 # 1 for BSSN, 0 for CCZ4
 kappa1 = 0.1
-kappa2 = 0
-kappa3 = 1.0
+kappa2 = 0.
+kappa3 = 1.
 covariantZ4 = 1 # 0: keep kappa1; 1 [default]: replace kappa1 -> kappa1/lapse
 
 # coefficient for KO numerical dissipation
 sigma = 1.0
 
-# extraction params
-# default of extraction_center is center, uncomment to change
-#extraction_center = 256 256 256
+track_punctures = 1
+puncture_tracking_level = 5
+
+# calculate_constraint_norms = 0
+
+# min_chi = 1.e-4
+# min_lapse = 1.e-4
+
+#################################################
+# Extraction parameters
+
+# extraction_center = 256 256 256 # defaults to center
 activate_extraction = 1
 num_extraction_radii = 2
 extraction_radii = 50.0 100.0
 extraction_levels = 2 1
 num_points_phi = 24
-num_points_theta = 36
+num_points_theta = 37
 num_modes = 8
 modes = 2 0 # l m for spherical harmonics
         2 1
@@ -123,3 +179,12 @@ modes = 2 0 # l m for spherical harmonics
         4 2
         4 3
         4 4
+
+# integral_file_prefix = "Weyl4_mode_"
+
+# write_extraction = 0
+# extraction_subpath = "data/extraction" # directory for 'write_extraction = 1'
+# extraction_file_prefix = "Weyl4_extraction_"
+
+#################################################
+