Adding test for DustGravity

plot_size.csv

+plots_cells,plots_size,plots_size_L0,plots_size_L1,plots_size_L2,caseID,caseDir
+4096,472612.0,461951.0,0.0,0.0,case12,plt_3d_00000
+8192,945273.0,923914.0,0.0,0.0,case12,plt_3d_00002
+12288,1.417935e6,1.385877e6,0.0,0.0,case12,plt_3d_00004
+16384,1.890595e6,1.84784e6,0.0,0.0,case12,plt_3d_00006
+20480,2.363255e6,2.309803e6,0.0,0.0,case12,plt_3d_00008
+24576,2.835917e6,2.771766e6,0.0,0.0,case12,plt_3d_00010

src/extractor/Amrex.jl

@@ -116,8 +116,8 @@ function _get_independent_variables(extractor::AbstractAmrex, parameters)::Dict{
     maxLevel = get(parameters, "amr.max_level", "")
     independentVariables["amr.max_level"] = maxLevel == "" ? 1 : parse(Int32, maxLevel)
 
-    regrid = prod(parse.(Int64, split(get(parameters, "amr.regrid_int", ["0"])))) 
-    independentVariables["amr.regrid_int"] = regrid == "" ? 1 : parse(Int64, regrid)
+    regrid = prod(parse.(Int64, split(get(parameters, "amr.regrid_int", ["0"]))))
+    independentVariables["amr.regrid_int"] = regrid
 
     return independentVariables
 

src/extractor/AmrexCastro.jl

@@ -92,7 +92,7 @@ function _get_linear_model_X(extractor::AmrexCastro)::DataFrames.DataFrame
         # get outputDir name
         independentVariables["caseID"] = helper_get_relative_path(outputDir)
 
-        if !isXInit
+        if isXInit == false
             X = DataFrames.DataFrame(independentVariables)
             isXInit = true
         else
@@ -141,7 +141,7 @@ function _run_linear_models_plots_size_step(extractor::AmrexCastro, X::DataFrame
     counter::Int32 = 1
     
     # extract ncells
-    ncells = X["amr.ncells"][index]
+    ncells = X[!,"amr.ncells"][index]
     
     # caseID
     caseID = helper_get_relative_path(outputDir)
@@ -199,63 +199,3 @@ function _run_linear_models_plots_size_step(extractor::AmrexCastro, X::DataFrame
   #readline()
 end
 
-
-# dead function
-function _run_linear_model_plots_size(extractor::AmrexCastro, X::DataFrames.DataFrame)
-
-    outputDirs = helper_get_prefix_directories(extractor.outputPrefix)
-
-    # single column DataFrame Y in the linear model
-    plotsSizesData = DataFrames.DataFrame(plots_sizes = Int64[])
-
-    for outputDir in outputDirs
-
-        # TODO refactor this later
-        inputFile::String = _get_input_file(extractor, outputDir)
-        parameters = _input_parser(extractor, inputFile)
-        rootPlotName = get(parameters, "amr.plot_file", "")
-
-        # find all directories with rootPlotName and get its size
-        plotFileDirs = helper_get_prefix_directories(string(outputDir, "/", rootPlotName))
-
-        plotsSize::Int64 = 0
-        for plotFileDir in plotFileDirs
-            sizeDir::Int64 = helper_get_directory_size(plotFileDir)
-            plotsSize += sizeDir
-        end
-
-        push!(plotsSizesData, [plotsSize])
-    end
-
-    println(plotsSizesData)
-
-    # Prepare the X independent variables in the linear model
-    XNames::Array{String} = extractor.outputs["plots_size"]
-
-    col1 = Symbol("amr.nplot_files")
-    col2 = Symbol("amr.ncells")
-
-    insert!(plotsSizesData, 2, X[!, col1] .* X[!, col2], :new_data)
-    #plotsSizesData[!,col1] = 
-
-    #for XName in XNames
-    #columnName = Symbol(XName)
-    # this syntax [!, symbol] does not make a copy, use [:, symbol] for copies
-    #plotsSizesData[!, columnName] = X[!, columnName]
-    #end
-
-    # formula from https://discourse.julialang.org/t/glm-jl-with-unknown-column-names/20692/5
-    response = Symbol(names(plotsSizesData)[1])
-    predictors = Symbol.(names(plotsSizesData)[2:end])
-
-    println(plotsSizesData)
-    f = @eval(GLM.@formula($response ~ (+)($(predictors...))))
-
-
-    ols = GLM.lm(f, plotsSizesData)
-    println("I/O linear model formula:")
-    println(ols)
-
-    #import Plots
-    #display(Plots.plot(X, Y))
-end

test/data/AmrexCastro/gravity_tests/DustCollapse/case12/chk_3d_00000/CPUtime

+0.10744606400000001
\ No newline at end of file

test/data/AmrexCastro/gravity_tests/DustCollapse/case12/chk_3d_00000/CastroHeader

+Checkpoint version: 7

test/data/AmrexCastro/gravity_tests/DustCollapse/case12/chk_3d_00000/FabArrayHeaders.txt

+Level_0/SD_0_New_MF
+Level_0/SD_1_New_MF
+Level_0/SD_3_New_MF

test/data/AmrexCastro/gravity_tests/DustCollapse/case12/chk_3d_00000/Header

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+)4
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+)-0.00036333937718578777
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+0
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+Level_0/SD_3_New_MF

test/data/AmrexCastro/gravity_tests/DustCollapse/case12/chk_3d_00000/Level_0/SD_0_New_MF_H

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+((0,8,0) (15,15,7) (0,0,0))
+((0,8,8) (15,15,15) (0,0,0))
+)
+4
+FabOnDisk: SD_0_New_MF_D_00000 0
+FabOnDisk: SD_0_New_MF_D_00002 0
+FabOnDisk: SD_0_New_MF_D_00001 0
+FabOnDisk: SD_0_New_MF_D_00003 0
+
+4,10
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+

test/data/AmrexCastro/gravity_tests/DustCollapse/case12/chk_3d_00000/Level_0/SD_1_New_MF_H

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+((0,8,8) (15,15,15) (0,0,0))
+)
+4
+FabOnDisk: SD_1_New_MF_D_00000 0
+FabOnDisk: SD_1_New_MF_D_00002 0
+FabOnDisk: SD_1_New_MF_D_00001 0
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test/data/AmrexCastro/gravity_tests/DustCollapse/case12/chk_3d_00000/Level_0/SD_3_New_MF_H

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+

test/data/AmrexCastro/gravity_tests/DustCollapse/case12/chk_3d_00000/job_info

+==============================================================================
+ Castro Job Information
+==============================================================================
+job name: Castro
+
+inputs file: inputs_3d_fullstar
+
+number of MPI processes: 4
+
+hydro tile size:         (1024,16,16)
+
+CPU time used since start of simulation (CPU-hours): 2.64398e-05
+
+==============================================================================
+ Plotfile Information
+==============================================================================
+output date / time: Fri Sep 18 12:45:06 2020
+output dir:         /gpfs/alpine/csc310/proj-shared/wgodoy/amrex/Castro/Exec/gravity_tests/DustCollapse/case12
+I/O time (s):       0.0123682
+
+
+==============================================================================
+ Build Information
+==============================================================================
+build date:    2020-09-02 10:14:31.161672
+build machine: Linux login1 4.14.0-115.21.2.el7a.ppc64le #1 SMP Thu May 7 22:22:31 UTC 2020 ppc64le ppc64le ppc64le GNU/Linux
+build dir:     /gpfs/alpine/csc310/proj-shared/wgodoy/amrex/Castro/Exec/gravity_tests/DustCollapse
+AMReX dir:     ../../../external/amrex
+
+COMP:          gnu
+COMP version:  6.4.0
+
+C++ compiler:  mpicxx
+C++ flags:      -Werror=return-type -g -O3  -pthread  -DBL_USE_MPI -DAMREX_USE_MPI -DGPU_COMPATIBLE_PROBLEM -DAMREX_GIT_VERSION="20.06" -DBL_GCC_VERSION=6.4.0 -DBL_GCC_MAJOR_VERSION=6 -DBL_GCC_MINOR_VERSION=4 -DAMREX_LAUNCH= -DAMREX_DEVICE= -DAMREX_CUDA_FORT_GLOBAL= -DAMREX_CUDA_FORT_DEVICE= -DAMREX_CUDA_FORT_HOST= -DAMREX_CUDA_FORT_HOST_DEVICE= -DBL_SPACEDIM=3 -DAMREX_SPACEDIM=3 -DBL_FORT_USE_UNDERSCORE -DAMREX_FORT_USE_UNDERSCORE -DBL_Linux -DAMREX_Linux -DAMREX_DIMENSION_AGNOSTIC -DCRSEGRNDOMP -DSPONGE -DGRAVITY -DCASTRO_MLMG -DPROB_PARAMS -I. -I../../../external/amrex/Src/Base -I../../../external/amrex/Src/AmrCore -I../../../external/amrex/Src/Amr -I../../../external/amrex/Src/Boundary -I../../../external/amrex/Src/LinearSolvers/C_CellMG -I../../../external/amrex/Src/LinearSolvers/MLMG -I../../../external/Microphysics/util -I. -I../../../Source/driver -I../../../Source/hydro -I../../../Source/problems -I../../../Source/sources -I../../../Source/scf -I../../../Util/model_parser -I../../../Util/conservative_interpolate -I../../../Source/hydro -I../../../Source/gravity -I../../../external/Microphysics/EOS -I../../../external/Microphysics/EOS/gamma_law -I../../../external/Microphysics/networks/general_null -I../../../external/Microphysics/EOS -I../../../external/Microphysics/networks -I../../../external/Microphysics/interfaces -I../../../external/Microphysics/constants -Itmp_build_dir/castro_sources/3d.gnu.MPI.EXE -I../../../external/amrex/Tools/C_scripts
+
+Fortran comp:  mpif90
+Fortran flags:  -g -O3 -ffree-line-length-none -fno-range-check -fno-second-underscore -fimplicit-none  
+
+Link flags:    -L. -L/autofs/nccs-svm1_sw/summit/gcc/6.4.0/bin/../lib/gcc/powerpc64le-none-linux-gnu/6.4.0/../../../../lib64/
+Libraries:      -lmpi_ibm_mpifh -lmpi_ibm -lgfortran
+
+EOS: ../../../external/Microphysics/EOS/gamma_law
+NETWORK: ../../../external/Microphysics/networks/general_null
+
+Castro       git describe: 20.06-dirty
+AMReX        git describe: 20.06
+Microphysics git describe: 20.06
+
+
+==============================================================================
+ Grid Information
+==============================================================================
+ level: 0
+   number of boxes = 4
+   maximum zones   = 16 16 16 
+
+ Boundary conditions
+   -x: outflow
+   +x: outflow
+   -y: outflow
+   +y: outflow
+   -z: outflow
+   +z: outflow
+
+
+ Domain geometry info
+     center: 7.5e+08 , 7.5e+08 , 7.5e+08
+
+     geometry.is_periodic: 0 0 0 
+     geometry.coord_sys:   0
+     geometry.prob_lo:     0 0 0 
+     geometry.prob_hi:     1.5e+09 1.5e+09 1.5e+09 
+     amr.n_cell:           16 16 16 
+     amr.max_level:        0
+     amr.ref_ratio:        
+
+
+==============================================================================
+ Species Information
+==============================================================================
+ index                         name              A              Z
+------------------------------------------------------------------------------
+     0                          C12             12              6
+     1                          O16             16              8
+     2                         Mg24             24             12
+
+
+==============================================================================
+ Inputs File Parameters
+==============================================================================
+    castro.state_interp_order = 1
+    castro.lin_limit_state_interp = 0
+    castro.state_nghost = 0
+    castro.do_reflux = 1
+    castro.update_sources_after_reflux = 1
+    castro.apply_sources_consecutively = 0
+    castro.difmag = 0.1
+[*] castro.small_dens = 1e-06
+[*] castro.small_temp = 0.001
+[*] castro.small_pres = 1e-200
+[*] castro.small_ener = 1e-200
+[*] castro.do_hydro = 1
+    castro.time_integration_method = 0
+    castro.limit_fourth_order = 1
+    castro.initialization_is_cell_average = 0
+    castro.use_reconstructed_gamma1 = 0
+    castro.add_ext_src = 0
+    castro.hybrid_hydro = 0
+    castro.ppm_type = 1
+    castro.ppm_temp_fix = 0
+    castro.plm_iorder = 2
+    castro.plm_limiter = 2
+    castro.hybrid_riemann = 0
+    castro.riemann_solver = 0
+    castro.cg_maxiter = 12
+    castro.cg_tol = 1e-05
+    castro.cg_blend = 2
+    castro.use_eos_in_riemann = 0
+    castro.use_flattening = 1
+    castro.transverse_use_eos = 0
+    castro.transverse_reset_density = 1
+    castro.transverse_reset_rhoe = 0
+    castro.dual_energy_eta1 = 1
+    castro.dual_energy_eta2 = 0.0001
+    castro.use_pslope = 1
+    castro.pslope_cutoff_density = -1e+20
+    castro.limit_fluxes_on_small_dens = 0
+    castro.limit_fluxes_on_large_vel = 0
+    castro.speed_limit = 2.99792e+10
+[*] castro.do_sponge = 1
+    castro.sponge_implicit = 1
+    castro.ext_src_implicit = 0
+    castro.source_term_predictor = 0
+    castro.first_order_hydro = 0
+    castro.xl_ext_bc_type = fillme
+    castro.xr_ext_bc_type = fillme
+    castro.yl_ext_bc_type = fillme
+    castro.yr_ext_bc_type = fillme
+    castro.zl_ext_bc_type = fillme
+    castro.zr_ext_bc_type = fillme
+    castro.hse_zero_vels = 0
+    castro.hse_interp_temp = 0
+    castro.hse_reflect_vels = 0
+    castro.fill_ambient_bc = 0
+    castro.ambient_fill_dir = -1
+    castro.ambient_outflow_vel = 0
+    castro.clamp_ambient_temp = 0
+    castro.ambient_safety_factor = 1.1
+    castro.sdc_order = 2
+    castro.sdc_quadrature = 0
+    castro.sdc_extra = 0
+    castro.sdc_solver = 1
+    castro.sdc_solver_tol_dens = 1e-06
+    castro.sdc_solver_tol_spec = 1e-06
+    castro.sdc_solver_tol_ener = 1e-06
+    castro.sdc_solver_atol = 1e-10
+    castro.sdc_solver_relax_factor = 1
+    castro.sdc_solve_for_rhoe = 1
+    castro.sdc_use_analytic_jac = 1
+    castro.fixed_dt = -1
+    castro.initial_dt = -1
+    castro.dt_cutoff = 1e-12
+    castro.max_dt = 1e+200
+[*] castro.cfl = 0.5
+[*] castro.init_shrink = 0.1
+[*] castro.change_max = 1.05
+    castro.plot_per_is_exact = 0
+    castro.small_plot_per_is_exact = 0
+    castro.use_retry = 1
+    castro.retry_subcycle_factor = 0.5
+    castro.use_post_step_regrid = 0
+    castro.max_subcycles = 10
+    castro.sdc_iters = 2
+    castro.dtnuc_e = 1e+200
+    castro.dtnuc_T = 1e+200
+    castro.dtnuc_X = 1e+200
+    castro.dtnuc_X_threshold = 0.001
+[*] castro.do_react = 0
+    castro.react_T_min = 0
+    castro.react_T_max = 1e+200
+    castro.react_rho_min = 0
+    castro.react_rho_max = 1e+200
+    castro.disable_shock_burning = 0
+    castro.T_guess = 1e+08
+    castro.reactions_max_solve_level = 100
+[*] castro.do_grav = 1
+    castro.moving_center = 0
+    castro.grav_source_type = 4
+    castro.do_rotation = -1
+    castro.do_acc = -1
+    castro.bndry_func_thread_safe = 1
+    castro.grown_factor = 1
+    castro.star_at_center = -1
+    castro.do_scf_initial_model = 0
+    castro.scf_maximum_density = -1e+06
+    castro.scf_equatorial_radius = -1e+09
+    castro.scf_polar_radius = -1e+09
+    castro.scf_relax_tol = 0.001
+    castro.scf_max_iterations = 30
+    castro.do_special_tagging = 0
+    castro.spherical_star = 0
+    castro.verbose = 0
+    castro.dump_old = 0
+    castro.domain_is_plane_parallel = 0
+    castro.print_fortran_warnings = 0
+    castro.print_update_diagnostics = 0
+    castro.track_grid_losses = 0
+[*] castro.sum_interval = 1
+    castro.sum_per = -1
+    castro.show_center_of_mass = 0
+    castro.job_name = Castro
+    castro.output_at_completion = 1
+    castro.reset_checkpoint_time = -1e+200
+    castro.reset_checkpoint_step = -1
+    castro.use_point_mass = 0
+    castro.point_mass = 0
+    castro.point_mass_fix_solution = 0
+[*] gravity.gravity_type = MonopoleGrav
+    gravity.const_grav = 0
+    gravity.direct_sum_bcs = 0
+[*] gravity.drdxfac = 4
+    gravity.lnum = 0
+    gravity.verbose = 0
+    gravity.no_sync = 0
+    gravity.no_composite = 0
+    gravity.do_composite_phi_correction = 1
+    gravity.max_solve_level = 14
+    gravity.get_g_from_phi = 0
+    gravity.mlmg_max_fmg_iter = 0
+    gravity.mlmg_agglomeration = 1
+    gravity.mlmg_consolidation = 1
+    gravity.mlmg_nsolve = 0
+ [*]                         eos_gamma =      1.666660000    
+                    eos_assume_neutral = T
+                               small_x =     0.1000000000E-29
+                            use_tables = F
+                    use_c12ag_deboer17 = F
+  
+ fortin parameters:
+                                 r_old =      650000000.0    
+                                 rho_0 =      1000000000.    
+ [*]                       rho_ambient =     0.1000000000E-04
+                                   r_0 =      650000000.0    
+ [*]                               p_0 =     0.1000000000E+16
+ [*]                      smooth_delta =      4000000.000    
+                              r_offset =      0.000000000    
+                   offset_smooth_delta =      1.000000000    
+ [*]                          center_x =      750000000.0    
+ [*]                          center_y =      750000000.0    
+ [*]                          center_z =      750000000.0    
+                                  nsub =          5

test/data/AmrexCastro/gravity_tests/DustCollapse/case12/chk_3d_00000/state_names.txt

+density
+xmom
+ymom
+zmom
+rho_E
+rho_e
+Temp
+rho_C12
+rho_O16
+rho_Mg24

test/data/AmrexCastro/gravity_tests/DustCollapse/case12/chk_3d_00005/CPUtime

+0.58346280799999994
\ No newline at end of file

test/data/AmrexCastro/gravity_tests/DustCollapse/case12/chk_3d_00005/CastroHeader

+Checkpoint version: 7

test/data/AmrexCastro/gravity_tests/DustCollapse/case12/chk_3d_00005/FabArrayHeaders.txt

+Level_0/SD_0_New_MF
+Level_0/SD_1_New_MF
+Level_0/SD_3_New_MF

test/data/AmrexCastro/gravity_tests/DustCollapse/case12/chk_3d_00005/Header

+CheckPointVersion_1.0
+3
+0.0011463584437322346
+0
+0
+(0 (0,0,0)(93750000,93750000,93750000) 1)
+(RealBox 0 1500000000 0 1500000000 0 1500000000 )((0,0,0) (15,15,15) (0,0,0))P(0,0,0) 
+
+0.00021030537325734882 
+0.00021030537325734882 
+1 
+5 
+5 
+0
+(0 (0,0,0)(93750000,93750000,93750000) 1)