From c8a2ee2eab04a080fd938d77e98a106c8bb12195 Mon Sep 17 00:00:00 2001 From: Michael Zingale Date: Thu, 17 Oct 2024 12:16:32 -0400 Subject: [PATCH 1/6] fix center for flame_wave in 1D (#2976) --- Exec/science/flame_wave/inputs.1d | 156 +++++++++++++++++++ Exec/science/flame_wave/problem_initialize.H | 4 + 2 files changed, 160 insertions(+) create mode 100644 Exec/science/flame_wave/inputs.1d diff --git a/Exec/science/flame_wave/inputs.1d b/Exec/science/flame_wave/inputs.1d new file mode 100644 index 0000000000..63e5a27caa --- /dev/null +++ b/Exec/science/flame_wave/inputs.1d @@ -0,0 +1,156 @@ +# ------------------ INPUTS TO MAIN PROGRAM ------------------- +max_step = 250000000 +stop_time = 3.0 + +# PROBLEM SIZE & GEOMETRY +geometry.is_periodic = 0 0 0 +geometry.prob_lo = 0 0 0 + +geometry.coord_sys = 0 # 0 => cart, 1 => RZ 2=>spherical + + geometry.prob_hi = 2.4576e4 + amr.n_cell = 192 + + # >>>>>>>>>>>>> BC FLAGS <<<<<<<<<<<<<<<< + # 0 = Interior 3 = Symmetry + # 1 = Inflow 4 = SlipWall + # 2 = Outflow 5 = NoSlipWall + # >>>>>>>>>>>>> BC FLAGS <<<<<<<<<<<<<<<< + castro.lo_bc = 3 + castro.hi_bc = 2 + + castro.fill_ambient_bc = 1 + castro.ambient_fill_dir = 0 + castro.ambient_outflow_vel = 1 + +#castro.allow_non_unit_aspect_zones = 1 + +castro.domain_is_plane_parallel = 1 + +# WHICH PHYSICS +castro.do_hydro = 1 +castro.do_react = 1 +castro.do_rotation = 0 +castro.do_grav = 1 +castro.do_sponge = 1 + +castro.small_temp = 1.e6 +castro.small_dens = 1.e-5 + +castro.ppm_type = 1 +castro.grav_source_type = 2 +castro.use_pslope = 1 +castro.pslope_cutoff_density = 1.e4 + +gravity.gravity_type = ConstantGrav +gravity.const_grav = -1.5e14 + +castro.rotational_period = 0.0 +castro.rotation_include_centrifugal = 0 + +castro.diffuse_temp = 0 +castro.diffuse_cutoff_density_hi = 5.e4 +castro.diffuse_cutoff_density = 2.e4 + +castro.diffuse_cond_scale_fac = 1.0 + +castro.react_rho_min = 1.e2 +castro.react_rho_max = 5.e6 + +castro.react_T_min = 6.e7 + +castro.sponge_upper_density = 1.e2 +castro.sponge_lower_density = 1.e0 +castro.sponge_timescale = 1.e-7 + +# GPU options +castro.hydro_memory_footprint_ratio = 3 + +# TIME STEP CONTROL +castro.cfl = 0.8 # cfl number for hyperbolic system +castro.init_shrink = 0.1 # scale back initial timestep +castro.change_max = 1.1 # max time step growth + +castro.use_retry = 1 +castro.max_subcycles = 16 + +castro.retry_small_density_cutoff = 10.0 + +castro.abundance_failure_tolerance = 0.1 +castro.abundance_failure_rho_cutoff = 1.0 + +# DIAGNOSTICS & VERBOSITY +castro.sum_interval = 10 # timesteps between computing mass +castro.v = 1 # verbosity in Castro.cpp +amr.v = 1 # verbosity in Amr.cpp + +# REFINEMENT / REGRIDDING +amr.max_level = 2 # maximum level number allowed +amr.ref_ratio = 4 2 2 2 # refinement ratio +amr.regrid_int = 0 # static grids ftw +amr.blocking_factor = 32 # block factor in grid generation +amr.max_grid_size = 128 +amr.n_error_buf = 2 2 2 2 # number of buffer cells in error est + +# CHECKPOINT FILES +amr.check_file = flame_wave_1000Hz_25cm_chk # root name of checkpoint file +#if AMREX_SPACEDIM == 3 +amr.check_int = 25 # number of timesteps between checkpoints +#elif AMREX_SPACEDIM == 2 +amr.check_int = 250 # number of timesteps between checkpoints +#endif + +amr.checkpoint_files_output = 1 + +# PLOTFILES +amr.plot_file = flame_wave_1000Hz_25cm_plt # root name of plotfile +amr.plot_per = 5.e-3 # number of seconds between plotfiles +amr.derive_plot_vars = ALL +amr.plot_files_output = 1 + +amr.small_plot_file = flame_wave_1000Hz_25cm_smallplt # root name of plotfile +amr.small_plot_per = 5.e-4 # number of seconds between plotfiles +amr.small_plot_vars = density Temp + +#if AMREX_SPACEDIM == 3 + amr.derive_small_plot_vars = abar magvel enuc +#elif AMREX_SPACEDIM == 2 + amr.derive_small_plot_vars = abar x_velocity y_velocity z_velocity enuc +#endif + +fab.format = NATIVE_32 + + +# problem initialization + +problem.dtemp = 1.2e9 +problem.x_half_max = 2.56e4 +problem.x_half_width = 2048.e0 + +problem.dens_base = 3.43e6 + +problem.T_star = 2.e8 +problem.T_hi = 2.e8 +problem.T_lo = 8.e6 + +problem.H_star = 2000.e0 +problem.atm_delta = 50.0 + +problem.fuel1_name = "helium-4" +problem.fuel1_frac = 1.0 + +problem.ash1_name = "nickel-56" +problem.ash1_frac = 1.0 + +problem.low_density_cutoff = 1.e-4 + +problem.tag_by_density = 0 +problem.refine_height = 3600.0 +problem.max_base_tagging_level = 3 + +# Microphysics + +integrator.rtol_spec = 1.e-6 +integrator.atol_spec = 1.e-6 + +network.use_tables = 1 diff --git a/Exec/science/flame_wave/problem_initialize.H b/Exec/science/flame_wave/problem_initialize.H index 61eb43808c..8c0d1fe5f8 100644 --- a/Exec/science/flame_wave/problem_initialize.H +++ b/Exec/science/flame_wave/problem_initialize.H @@ -190,6 +190,10 @@ void problem_initialize () problem::center[d] = 0.5_rt * (problo[d] + probhi[d]); } +#if AMREX_SPACEDIM == 1 + problem::center[0] = 0.0_rt; +#endif + #if AMREX_SPACEDIM == 2 // for axisymmetry, put the x-center on the x-axis // and the y-center at 0, so the height computation is okay From 713b6ab892575fc01da1c3e44dd667a48a173a38 Mon Sep 17 00:00:00 2001 From: Michael Zingale Date: Thu, 17 Oct 2024 15:06:32 -0400 Subject: [PATCH 2/6] add note about MHD still under development (#2977) --- Docs/source/mhd.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Docs/source/mhd.rst b/Docs/source/mhd.rst index 5ef47d31e0..caca15ec28 100644 --- a/Docs/source/mhd.rst +++ b/Docs/source/mhd.rst @@ -17,6 +17,9 @@ supported by MHD. .. note:: + The MHD solver is still under development and should not be used + for science simulations. See the issues in the github repo. + The MHD solver supports 3-d only. Currently the MHD solver is single-level only. AMR support is forthcoming. From 71b5b56ccf54e30aeb109e74e0c59b086134ba25 Mon Sep 17 00:00:00 2001 From: Michael Zingale Date: Thu, 17 Oct 2024 15:06:46 -0400 Subject: [PATCH 3/6] add an abort if we run true SDC with AMR (#2978) --- Source/driver/Castro.cpp | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/Source/driver/Castro.cpp b/Source/driver/Castro.cpp index 11d10c1b9d..8ea195e8d2 100644 --- a/Source/driver/Castro.cpp +++ b/Source/driver/Castro.cpp @@ -367,6 +367,14 @@ Castro::read_params () } #endif +#ifdef TRUE_SDC + int max_level; + ppa.query("max_level", max_level); + if (max_level > 0) { + amrex::Error("True SDC does not work with AMR."); + } +#endif + #ifndef TRUE_SDC if (time_integration_method == SpectralDeferredCorrections) { amrex::Error("True SDC currently requires USE_TRUE_SDC=TRUE when compiling."); From b6503500cdb1e31f0beff8d3e7f8b8418ebb2953 Mon Sep 17 00:00:00 2001 From: Michael Zingale Date: Tue, 22 Oct 2024 12:50:56 -0400 Subject: [PATCH 4/6] update the massive star plotting scripts (#2979) these reflect what was used in the paper --- .../analysis/massive_star_multi.py | 32 ++++-- .../analysis/massive_star_sequence.py | 17 ++- .../analysis/massive_star_slice.py | 105 ------------------ 3 files changed, 28 insertions(+), 126 deletions(-) delete mode 100755 Exec/science/massive_star/analysis/massive_star_slice.py diff --git a/Exec/science/massive_star/analysis/massive_star_multi.py b/Exec/science/massive_star/analysis/massive_star_multi.py index 4722093e33..0bf35f1684 100755 --- a/Exec/science/massive_star/analysis/massive_star_multi.py +++ b/Exec/science/massive_star/analysis/massive_star_multi.py @@ -13,7 +13,8 @@ matplotlib.use('agg') - +ANNOTATE_O16 = False +ANNOTATE_NSE = True def make_plot(plotfile, prefix="plot", width_frac=0.1, @@ -25,8 +26,8 @@ def make_plot(plotfile, prefix="plot", width_frac=0.1, t_drive = 0.0 if "[*] castro.drive_initial_convection_tmax" in ds.parameters: t_drive = ds.parameters["[*] castro.drive_initial_convection_tmax"] - elif "castro.drive_initial_convection_tmax" in ds.parameters: - t_drive = ds.parameters["castro.drive_initial_convection_tmax"] + elif "[*] castro.drive_initial_convection_tmax" in ds.parameters: + t_drive = ds.parameters["[*] castro.drive_initial_convection_tmax"] print(t_drive) xmin = ds.domain_left_edge[0] @@ -75,19 +76,26 @@ def make_plot(plotfile, prefix="plot", width_frac=0.1, sp.set_cmap(f, "magma") sp.set_zlim(f, 1.e-2, 5) - if f == "enuc": - # now do a contour of NSE - if ("boxlib", "in_nse") in ds.derived_field_list: - sp.annotate_contour("in_nse", ncont=1, clim=(0.5, 0.5), take_log=False, - plot_args={"colors": "k", "linewidths": 2}) + + # now do a contour of O + if ANNOTATE_O16: + sp.annotate_contour(("boxlib", "X(O16)"), ncont=1, clim=(0.5, 0.5), factor=32, take_log=False, + plot_args={"colors": "0.5", "linewidths": 2}) + + # now do a contour of NSE + if ANNOTATE_NSE: + if ("boxlib", "in_nse") in ds.derived_field_list: + sp.annotate_contour("in_nse", levels=1, clim=(0.5, 0.5), take_log=False, + plot_args={"colors": "k", "linewidths": 2}) + sp.set_axes_unit("cm") fig = sp.export_to_mpl_figure((layout[0], layout[1]), axes_pad=(1.0, 0.4), cbar_location=cbar_location, cbar_pad="2%") - fig.subplots_adjust(left=0.05, right=0.95, bottom=0.025, top=0.975) - fig.text(0.02, 0.02, f"$t - \\tau_\\mathrm{{drive}}$ = {float(ds.current_time) - t_drive:6.1f} s", + fig.subplots_adjust(left=0.05, right=0.95, bottom=0.035, top=0.975) + fig.text(0.02, 0.01, f"$t - \\tau_\\mathrm{{drive}}$ = {float(ds.current_time) - t_drive:6.1f} s", transform=fig.transFigure) fig.set_size_inches(size) fig.tight_layout() @@ -95,7 +103,7 @@ def make_plot(plotfile, prefix="plot", width_frac=0.1, if layout[0] >= layout[1]: extra = "_vertical" - fig.savefig(f"{prefix}_{os.path.basename(plotfile)}_w{width_frac:04.2f}{extra}.pdf", pad_inches=0.1, bbox_inches="tight") + fig.savefig(f"{prefix}_{os.path.basename(plotfile)}_w{width_frac:04.2f}{extra}.pdf", pad_inches=0.1) #, bbox_inches="tight") if __name__ == "__main__": @@ -112,7 +120,7 @@ def make_plot(plotfile, prefix="plot", width_frac=0.1, plotfile = args.plotfile[0] if args.vertical: - size = (7.5, 11.0) + size = (7.0, 10.0) layout = (2, 2) else: size = (19.2, 8.5) diff --git a/Exec/science/massive_star/analysis/massive_star_sequence.py b/Exec/science/massive_star/analysis/massive_star_sequence.py index 96b4218085..3d708158ec 100755 --- a/Exec/science/massive_star/analysis/massive_star_sequence.py +++ b/Exec/science/massive_star/analysis/massive_star_sequence.py @@ -15,7 +15,7 @@ matplotlib.use('agg') -times = [50, 100, 150, 200, 250] +times = [50, 100, 150, 200, 250, 300] def find_files(plist): @@ -60,8 +60,8 @@ def make_plot(field, pfiles, *, t_drive = 0.0 if "[*] castro.drive_initial_convection_tmax" in ds.parameters: t_drive = ds.parameters["[*] castro.drive_initial_convection_tmax"] - elif "castro.drive_initial_convection_tmax" in ds.parameters: - t_drive = ds.parameters["castro.drive_initial_convection_tmax"] + elif "[*] castro.drive_initial_convection_tmax" in ds.parameters: + t_drive = ds.parameters["[*] castro.drive_initial_convection_tmax"] print(t_drive) xmin = ds.domain_left_edge[0] @@ -127,11 +127,10 @@ def make_plot(field, pfiles, *, sp.set_cmap(f, "magma") sp.set_zlim(f, 1.e-2, 5) - if f == "enuc": - # now do a contour of NSE - if ("boxlib", "in_nse") in ds.derived_field_list: - sp.annotate_contour("in_nse", levels=1, clim=(0.5, 0.5), take_log=False, - plot_args={"colors": "k", "linewidths": 2}) + # now do a contour of NSE + if ("boxlib", "in_nse") in ds.derived_field_list: + sp.annotate_contour("in_nse", levels=1, clim=(0.5, 0.5), take_log=False, + plot_args={"colors": "k", "linewidths": 2}) sp.set_axes_unit("cm") @@ -168,7 +167,7 @@ def make_plot(field, pfiles, *, args = p.parse_args() if args.vertical: - size = (7.5, 8.5) + size = (7.0, 8.0) else: size = (19.2, 8.5) diff --git a/Exec/science/massive_star/analysis/massive_star_slice.py b/Exec/science/massive_star/analysis/massive_star_slice.py deleted file mode 100755 index 5980d8d04a..0000000000 --- a/Exec/science/massive_star/analysis/massive_star_slice.py +++ /dev/null @@ -1,105 +0,0 @@ -#!/usr/bin/env python3 - -import matplotlib -matplotlib.use('agg') - -import os -import sys -import yt -import matplotlib.pyplot as plt -import numpy as np -from functools import reduce - -from mpl_toolkits.axes_grid1 import ImageGrid - -# assume that our data is in CGS -from yt.units import cm, amu -from yt.frontends.boxlib.api import CastroDataset - -def make_plot(plotfile, fields, prefix="plot"): - - ds = CastroDataset(plotfile) - - xmin = ds.domain_left_edge[0] - xmax = ds.domain_right_edge[0] - - ymin = ds.domain_left_edge[1] - ymax = ds.domain_right_edge[1] - - xctr = 0.0 * xmin - L_x = xmax - xmin - - yctr = 0.5 * (ymin + ymax) - L_y = ymax - ymin - - - fig = plt.figure() - fig.set_size_inches(12.0, 9.0) - - width_frac = 0.1 - - grid = ImageGrid(fig, 111, nrows_ncols=(1, len(fields)), - axes_pad=1.0, label_mode="L", cbar_mode="each", cbar_pad=0) - - - for i, f in enumerate(fields): - - sp = yt.SlicePlot(ds, "theta", f, - center=[xmin + 0.5*width_frac*L_x, yctr, 0.0*cm], - width=[width_frac*L_x, width_frac*L_y, 0.0*cm], fontsize="12") - sp.set_buff_size((2400,2400)) - - if f == "Ye": - sp.set_zlim(f, 0.46, 0.5) - sp.set_log(f, False) - sp.set_cmap(f, "magma_r") - elif f == "abar": - sp.set_log(f, False) - sp.set_cmap(f, "viridis") - elif f == "enuc": - sp.set_log(f, True, linthresh=1.e12) - sp.set_zlim(f, -1.e20, 1.e20) - sp.set_cmap(f, "bwr") - elif f == "MachNumber": - sp.set_zlim(f, 1.e-4, 0.3) - sp.set_cmap(f, "plasma") - elif f == "magvel": - sp.set_zlim(f, 100.0, 2.e7) - sp.set_cmap(f, "viridis") - elif f == "magvort": - sp.set_cmap(f, "magma") - sp.set_zlim(f, 1.e-2, 5) - - if f == "enuc": - # now do a contour of density - sp.annotate_contour("in_nse", ncont=1, clim=(0.5, 0.5), take_log=False, - plot_args={"colors": "k", "linewidths": 2}) - - sp.set_axes_unit("cm") - - plot = sp.plots[f] - plot.figure = fig - plot.axes = grid[i].axes - plot.cax = grid.cbar_axes[i] - - sp._setup_plots() - - sp.plots[f].axes.xaxis.set_major_locator(plt.MaxNLocator(4)) - sp.plots[f].axes.ticklabel_format(axis="both", style="scientific", scilimits=(0,0)) - - fig.text(0.02, 0.02, "time = {:8.5f} s".format(float(ds.current_time)), transform=fig.transFigure) - - fig.set_size_inches(19.2, 10.8) - fig.tight_layout() - fig.savefig(f"{prefix}_{os.path.basename(plotfile)}_slice.png") - - -if __name__ == "__main__": - - plotfile = sys.argv[1] - - fields = ["Ye", "abar", "enuc"] - make_plot(plotfile, fields, prefix="comp") - - fields = ["MachNumber", "magvel", "magvort"] - make_plot(plotfile, fields, prefix="vel") From 1686df30aa9591e80d368858433ce58124912828 Mon Sep 17 00:00:00 2001 From: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Wed, 23 Oct 2024 14:54:34 -0400 Subject: [PATCH 5/6] update checks on bc for spherical2d (#2981) make sure we use symmetry boundary condition when theta is 0 and pi --- Source/driver/Castro.cpp | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/Source/driver/Castro.cpp b/Source/driver/Castro.cpp index 8ea195e8d2..6149e7f988 100644 --- a/Source/driver/Castro.cpp +++ b/Source/driver/Castro.cpp @@ -306,14 +306,26 @@ Castro::read_params () #elif (AMREX_SPACEDIM == 2) if ( dgeom.IsSPHERICAL() ) { + if ( (lo_bc[1] != amrex::PhysBCType::symmetry) && (dgeom.ProbLo(1) == 0.0) ) + { + std::cerr << "ERROR:Castro::read_params: must set theta=0 boundary condition to Symmetry for spherical\n"; + amrex::Error(); + } + + if ( (hi_bc[1] != amrex::PhysBCType::symmetry) && (std::abs(dgeom.ProbHi(1) - M_PI) <= 1.e-4_rt) ) + { + std::cerr << "ERROR:Castro::read_params: must set theta=pi boundary condition to Symmetry for spherical\n"; + amrex::Error(); + } + if ( (dgeom.ProbLo(1) < 0.0_rt) && (dgeom.ProbHi(1) > M_PI) ) { - amrex::Abort("Theta must be within [0, Pi] for spherical coordinate system in 2D"); + amrex::Abort("ERROR:Castro::read_params: Theta must be within [0, Pi] for spherical coordinate system in 2D"); } if ( dgeom.ProbLo(0) < static_cast(NUM_GROW) * dgeom.CellSize(0) ) { - amrex::Abort("R-min must be large enough so ghost cells doesn't extend to negative R"); + amrex::Abort("ERROR:Castro::read_params: R-min must be large enough so ghost cells doesn't extend to negative R"); } } #elif (AMREX_SPACEDIM == 3) From de4d8d91da97922ddc2cb1f2abe8f1fd9cc58f2b Mon Sep 17 00:00:00 2001 From: Zhi Chen <62574124+zhichen3@users.noreply.github.com> Date: Thu, 24 Oct 2024 13:55:38 -0400 Subject: [PATCH 6/6] fix divu in cylindrical coord (#2983) we should calculate vy as usual when i==0. This caused an issue where we have x-velocity emerging from the symmetry axis in cylindrical coord in a purely HSE setup. --- .../flame_wave/ci-benchmarks/grid_diag.out | 4 +- .../flame_wave/ci-benchmarks/species_diag.out | 4 +- .../ci-benchmarks/wdmerger_collision_2D.out | 46 +++++++++---------- Source/hydro/advection_util.cpp | 11 ++--- 4 files changed, 32 insertions(+), 33 deletions(-) diff --git a/Exec/science/flame_wave/ci-benchmarks/grid_diag.out b/Exec/science/flame_wave/ci-benchmarks/grid_diag.out index 3bfc78ca85..5cea0e9518 100644 --- a/Exec/science/flame_wave/ci-benchmarks/grid_diag.out +++ b/Exec/science/flame_wave/ci-benchmarks/grid_diag.out @@ -1,5 +1,5 @@ # COLUMN 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 # TIMESTEP TIME MASS XMOM YMOM ZMOM ANG. MOM. X ANG. MOM. Y ANG. MOM. Z KIN. ENERGY INT. ENERGY GAS ENERGY GRAV. ENERGY TOTAL ENERGY CENTER OF MASS X-LOC CENTER OF MASS Y-LOC CENTER OF MASS Z-LOC CENTER OF MASS X-VEL CENTER OF MASS Y-VEL CENTER OF MASS Z-VEL MAXIMUM TEMPERATURE MAXIMUM DENSITY MAXIMUM T_S / T_E 0 0.0000000000000000e+00 1.4700685690736437e+20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 2.9163021935541997e+37 2.9163021935541997e+37 0.0000000000000000e+00 2.9163021935541997e+37 2.7306641645125415e+04 6.8087525965685256e+02 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 1.3928678114307070e+09 3.0715027784567930e+07 0.0000000000000000e+00 - 1 5.9806047036494849e-08 1.4700700110495903e+20 3.3564221217849212e+23 7.2876252590226133e+23 1.2612378556916341e+20 3.1318391966955516e+23 -2.7141686347841742e+24 1.9066097493127676e+28 7.8605324800324878e+29 2.9163081863790706e+37 2.9163082649843738e+37 0.0000000000000000e+00 2.9163082649843738e+37 2.7306641717925955e+04 6.8087482283157317e+02 0.0000000000000000e+00 2.2831716153358752e+03 4.9573321027203638e+03 8.5794407491595881e-01 1.3929561431310942e+09 3.0715326643212341e+07 3.3873763041849706e-04 - 2 1.2559269877663918e-07 1.4700717750115462e+20 7.0484895445039834e+23 1.5304335700823335e+24 5.5619061962888426e+20 1.3810900989697918e+24 -1.1969287484132617e+25 4.0039912979259806e+28 3.0853275723280981e+30 2.9163145904135894e+37 2.9163148989463411e+37 0.0000000000000000e+00 2.9163148989463411e+37 2.7306641954244522e+04 6.8087461718998338e+02 0.0000000000000000e+00 4.7946567401095926e+03 1.0410604407871944e+04 3.7834249257966728e+00 1.3933944939675827e+09 3.0715562157563787e+07 3.3857586854903492e-04 + 1 5.9806047036494849e-08 1.4700700110495903e+20 3.3564221215590610e+23 7.2876252589700228e+23 1.2612378556594561e+20 3.1318391966786556e+23 -2.7141686347838510e+24 1.9066097493139366e+28 7.8605324800584047e+29 2.9163081863790706e+37 2.9163082649843738e+37 0.0000000000000000e+00 2.9163082649843738e+37 2.7306641717925955e+04 6.8087482283158556e+02 0.0000000000000000e+00 2.2831716151822361e+03 4.9573321026845897e+03 8.5794407489407010e-01 1.3929529135508094e+09 3.0715326539046615e+07 3.3873763041849706e-04 + 2 1.2559269877663918e-07 1.4700717750115462e+20 7.0484895413073359e+23 1.5304335700221490e+24 5.5619061951241526e+20 1.3810900989051759e+24 -1.1969287484120623e+25 4.0039912979436722e+28 3.0853275724059276e+30 2.9163145904135894e+37 2.9163148989463416e+37 0.0000000000000000e+00 2.9163148989463416e+37 2.7306641954244522e+04 6.8087461719003727e+02 0.0000000000000000e+00 4.7946567379351090e+03 1.0410604407462544e+04 3.7834249250044056e+00 1.3933796339641171e+09 3.0715561813912578e+07 3.3857586854903492e-04 diff --git a/Exec/science/flame_wave/ci-benchmarks/species_diag.out b/Exec/science/flame_wave/ci-benchmarks/species_diag.out index f3c2dcfe7a..f2e2da45d1 100644 --- a/Exec/science/flame_wave/ci-benchmarks/species_diag.out +++ b/Exec/science/flame_wave/ci-benchmarks/species_diag.out @@ -1,5 +1,5 @@ # COLUMN 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 # TIMESTEP TIME Mass He4 Mass C12 Mass O16 Mass Ne20 Mass Mg24 Mass Si28 Mass S32 Mass Ar36 Mass Ca40 Mass Ti44 Mass Cr48 Mass Fe52 Mass Ni56 0 0.0000000000000000e+00 2.8142378112400895e-15 7.3932235330395157e-24 7.3932235330395157e-24 7.3932235330395157e-24 7.3932235330395157e-24 7.3932235330395157e-24 7.3932235330395157e-24 7.3932235330395157e-24 7.3932235330395157e-24 7.3932235330395157e-24 7.3932235330395157e-24 7.3932235330395157e-24 7.1117997526547418e-14 - 1 5.9806047036494849e-08 2.8142323856670446e-15 5.4329394398418374e-21 7.4194443455948811e-24 7.3934514829832856e-24 7.3935541949306949e-24 7.3933935989353088e-24 7.3932321468740865e-24 7.3932312019180345e-24 7.3932308328287333e-24 7.3932307869392985e-24 7.3932307850741519e-24 7.3932307849933044e-24 7.1118070045957103e-14 - 2 1.2559269877663918e-07 2.8142264165381050e-15 1.1401993450709496e-20 7.4929528148974785e-24 7.3944694290388374e-24 7.3939305042586412e-24 7.3935838894001731e-24 7.3932425308122493e-24 7.3932405326301655e-24 7.3932397568503098e-24 7.3932396603620498e-24 7.3932396564405566e-24 7.3932396562705492e-24 7.1118158758588142e-14 + 1 5.9806047036494849e-08 2.8142323856670446e-15 5.4329394398523593e-21 7.4194443428333686e-24 7.3934514828234477e-24 7.3935541949253214e-24 7.3933935989348298e-24 7.3932321468740835e-24 7.3932312019180345e-24 7.3932308328287333e-24 7.3932307869392985e-24 7.3932307850741519e-24 7.3932307849933044e-24 7.1118070045957103e-14 + 2 1.2559269877663918e-07 2.8142264165381050e-15 1.1401993450700379e-20 7.4929526498089992e-24 7.3944694218302123e-24 7.3939305039811099e-24 7.3935838893792728e-24 7.3932425308121303e-24 7.3932405326301640e-24 7.3932397568503098e-24 7.3932396603620498e-24 7.3932396564405580e-24 7.3932396562705492e-24 7.1118158758588142e-14 diff --git a/Exec/science/wdmerger/ci-benchmarks/wdmerger_collision_2D.out b/Exec/science/wdmerger/ci-benchmarks/wdmerger_collision_2D.out index 50abd61af7..54c364e26e 100644 --- a/Exec/science/wdmerger/ci-benchmarks/wdmerger_collision_2D.out +++ b/Exec/science/wdmerger/ci-benchmarks/wdmerger_collision_2D.out @@ -1,29 +1,29 @@ plotfile = plt00086 time = 1.25 variables minimum value maximum value - density 8.6936468335e-05 19568007.309 - xmom -5.4959005475e+14 1.3559838981e+14 - ymom -2.5540206053e+15 2.5540214496e+15 + density 8.6940338039e-05 19441641.375 + xmom -5.4953770416e+14 1.3594264808e+14 + ymom -2.4933243003e+15 2.4933250525e+15 zmom 0 0 - rho_E 7.4987846833e+11 5.0676543192e+24 - rho_e 7.1083104678e+11 5.0648015049e+24 - Temp 242292.44287 1409581841.1 - rho_He4 8.6936468335e-17 3.5973411848 - rho_C12 3.4774587333e-05 7826946.398 - rho_O16 5.2161881e-05 11740633.889 - rho_Ne20 8.6936468335e-17 181819.49413 - rho_Mg24 8.6936468335e-17 1190.7712386 - rho_Si28 8.6936468335e-17 6.6817951193 - rho_S32 8.6936468335e-17 0.00019451843176 - rho_Ar36 8.6936468335e-17 1.9568007618e-05 - rho_Ca40 8.6936468335e-17 1.9568007341e-05 - rho_Ti44 8.6936468335e-17 1.9568007318e-05 - rho_Cr48 8.6936468335e-17 1.9568007318e-05 - rho_Fe52 8.6936468335e-17 1.9568007318e-05 - rho_Ni56 8.6936468335e-17 1.9568007318e-05 - phiGrav -5.8709462562e+17 -2.3375498549e+16 - grav_x -685026429.13 -51428.265677 - grav_y -739654246.49 739654206.24 + rho_E 7.4973602186e+11 5.0768248379e+24 + rho_e 7.1068648973e+11 5.0744783673e+24 + Temp 242282.60874 1404450633.1 + rho_He4 8.6940338039e-17 3.398107373 + rho_C12 3.4776135215e-05 7775850.9371 + rho_O16 5.2164202823e-05 11664450.012 + rho_Ne20 8.6940338039e-17 172485.537 + rho_Mg24 8.6940338039e-17 1043.054267 + rho_Si28 8.6940338039e-17 5.9869391361 + rho_S32 8.6940338039e-17 0.00016459247232 + rho_Ar36 8.6940338039e-17 1.9441643669e-05 + rho_Ca40 8.6940338039e-17 1.9441641397e-05 + rho_Ti44 8.6940338039e-17 1.9441641384e-05 + rho_Cr48 8.6940338039e-17 1.9441641384e-05 + rho_Fe52 8.6940338039e-17 1.9441641384e-05 + rho_Ni56 8.6940338039e-17 1.9441641384e-05 + phiGrav -5.870743119e+17 -2.337549858e+16 + grav_x -685044085.4 -51428.268861 + grav_y -739591083.78 739591039.26 grav_z 0 0 - rho_enuc -4.7815621457e+12 7.6360058391e+23 + rho_enuc -7.5385126121e+12 7.1503781318e+23 diff --git a/Source/hydro/advection_util.cpp b/Source/hydro/advection_util.cpp index 27d3befa3c..515778c4d1 100644 --- a/Source/hydro/advection_util.cpp +++ b/Source/hydro/advection_util.cpp @@ -270,7 +270,6 @@ Castro::divu(const Box& bx, if (i == 0) { ux = 0.0_rt; - vy = 0.0_rt; // is this part correct? } else { Real rl = (i - 0.5_rt) * dx[0] + problo[0]; Real rr = (i + 0.5_rt) * dx[0] + problo[0]; @@ -282,13 +281,13 @@ Castro::divu(const Box& bx, // Take 1/r d/dr(r*u) ux = (rr * ur - rl * ul) * dxinv / rc; + } - // These are transverse averages in the x-direction - Real vb = 0.5_rt * (q_arr(i,j-1,k,QV) + q_arr(i-1,j-1,k,QV)); - Real vt = 0.5_rt * (q_arr(i,j,k,QV) + q_arr(i-1,j,k,QV)); + // These are transverse averages in the x-direction + Real vb = 0.5_rt * (q_arr(i,j-1,k,QV) + q_arr(i-1,j-1,k,QV)); + Real vt = 0.5_rt * (q_arr(i,j,k,QV) + q_arr(i-1,j,k,QV)); - vy = (vt - vb) * dyinv; - } + vy = (vt - vb) * dyinv; } else {