[FLASH-USERS] 3D Spherical errors (guard-cell variables zero)
Sean Couch
smc at flash.uchicago.edu
Mon Jul 7 20:41:21 EDT 2014
One quick suggestion I have is to add +pm4dev to you setup line. That brings in the most current grid package.
Sean
--------------------------------------------------------
Sean M. Couch
Hubble Fellow
Flash Center for Computational Science
Department of Astronomy & Astrophysics
The University of Chicago
5747 S Ellis Ave, Jo 315
Chicago, IL 60637
(773) 702-3899
www.flash.uchicago.edu/~smc
On Jul 7, 2014, at 9:30 AM, Luke Zoltan Kelley <lkelley at cfa.harvard.edu> wrote:
> Sure, I wasn't sure If flash-users allowed attachments so I've added the log contents:
>
>
> FLASH log file: 07-07-2014 10:26:23.961 Run number: 1
> ==============================================================================
> Number of MPI tasks: 1
> MPI version: 3
> MPI subversion: 0
> Dimensionality: 3
> Max Number of Blocks/Proc: 200
> Number x zones: 8
> Number y zones: 8
> Number z zones: 8
> Setup stamp: Mon Jul 7 10:25:52 2014
> Build stamp: Mon Jul 7 10:25:56 2014
> System info: Darwin daedalus.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 P
> Version: FLASH 4.2.2_release
> Build directory: /Users/lzkelley/Applications/flash/flash4.2.2/object_starwind
> Setup syntax: /Users/lzkelley/Applications/flash/flash4.2.2/bin/setup.py starwind -auto -objdir=object_starwind -3d +spherical -noclobber -debug
> f compiler flags: /opt/local//bin/mpif90 -ggdb -c -O0 -fdefault-real-8 -fdefault-double-8 -pedantic -Wall -Wextra -Waliasing -Wsurprising -Wconversion -Wunderflow -ffpe-trap=invalid,zero,overflow -fbounds-check -fimplicit-none -fstack-protector-all -ffree-line-length-0 -Wno-unused -Wno-unused-parameter -DMAXBLOCKS=200 -DNXB=8 -DNYB=8 -DNZB=8 -DN_DIM=3
> c compiler flags: /opt/local//bin/mpicc -I /opt/local//include -DH5_USE_16_API -ggdb -c -O0 -Wno-div-by-zero -Wundef -Wconversion -Wstrict-prototypes -Wunreachable-code -pedantic -Wall -Wextra -Winit-self -Wfloat-equal -Wunsafe-loop-optimizations -Wpadded -fstack-protector-all -DMAXBLOCKS=200 -DNXB=8 -DNYB=8 -DNZB=8 -DN_DIM=3 -DDarwin
> ==============================================================================
> Comment: FLASH 3 run
> ==============================================================================
> FLASH Units used:
> Driver/DriverMain/Split
> Grid/GridBoundaryConditions/OneRow
> Grid/GridMain/paramesh/interpolation/Paramesh4/prolong
> Grid/GridMain/paramesh/interpolation/prolong
> Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/headers
> Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/mpi_source
> Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/source
> Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/utilities/multigrid
> Grid/GridSolvers/Multipole_new
> Grid/localAPI
> IO/IOMain/hdf5/serial/PM
> IO/localAPI
> Multispecies/MultispeciesMain
> PhysicalConstants/PhysicalConstantsMain
> RuntimeParameters/RuntimeParametersMain
> Simulation/SimulationComposition/Burn
> Simulation/SimulationMain/starwind
> flashUtilities/contiguousConversion
> flashUtilities/general
> flashUtilities/interpolation/oneDim
> flashUtilities/nameValueLL
> flashUtilities/sorting/quicksort
> flashUtilities/system/memoryUsage/legacy
> monitors/Logfile/LogfileMain
> monitors/Timers/TimersMain/MPINative
> physics/Eos/EosMain/Gamma
> physics/Eos/localAPI
> physics/Hydro/HydroMain/split/PPM/PPMKernel
> ==============================================================================
> RuntimeParameters:
>
> ==============================================================================
> bndpriorityone = 1
> bndprioritythree = 3
> bndprioritytwo = 2
> checkpointfileintervalstep = 0
> checkpointfilenumber = 0
> dr_abortpause = 2
> drift_break_inst = 0
> drift_trunc_mantissa = 2
> drift_verbose_inst = 0
> eos_entrelescalechoice = 6
> fileformatversion = 9
> forcedplotfilenumber = 0
> gr_lrefmaxtimevalue_1 = -1
> gr_lrefmaxtimevalue_10 = -1
> gr_lrefmaxtimevalue_11 = -1
> gr_lrefmaxtimevalue_12 = -1
> gr_lrefmaxtimevalue_13 = -1
> gr_lrefmaxtimevalue_14 = -1
> gr_lrefmaxtimevalue_15 = -1
> gr_lrefmaxtimevalue_16 = -1
> gr_lrefmaxtimevalue_17 = -1
> gr_lrefmaxtimevalue_18 = -1
> gr_lrefmaxtimevalue_19 = -1
> gr_lrefmaxtimevalue_2 = -1
> gr_lrefmaxtimevalue_20 = -1
> gr_lrefmaxtimevalue_3 = -1
> gr_lrefmaxtimevalue_4 = -1
> gr_lrefmaxtimevalue_5 = -1
> gr_lrefmaxtimevalue_6 = -1
> gr_lrefmaxtimevalue_7 = -1
> gr_lrefmaxtimevalue_8 = -1
> gr_lrefmaxtimevalue_9 = -1
> gr_pmrpdivergencefree = 1
> gr_pmrpifaceoff = 0
> gr_pmrpl2p5d = 0
> gr_pmrpmaxblocks = -1
> gr_pmrpmflags = 1
> gr_pmrpnboundaries = 6
> gr_pmrpndim = 3
> gr_pmrpnedgevar1 = -1
> gr_pmrpnfacevar = -1
> gr_pmrpnfielddivf = -1
> gr_pmrpnfluxvar = -1
> gr_pmrpnguard = -1
> gr_pmrpnguardwork = -1
> gr_pmrpnvar = -1
> gr_pmrpnvarwork = 1
> gr_pmrpnvarcorn = 0
> gr_pmrpnvaredge = 0
> gr_pmrpnxb = -1
> gr_pmrpnyb = -1
> gr_pmrpnzb = -1
> gr_restrictallmethod = 3
> gr_sanitizedatamode = 1
> gr_sanitizeverbosity = 5
> iprocs = 1
> igodu = 0
> interpol_order = 2
> iplm = 0
> irenorm = 0
> jprocs = 1
> kprocs = 1
> lrefine_del = 0
> lrefine_max = 4 [CHANGED]
> lrefine_min = 3 [CHANGED]
> lrefine_min_init = 1
> max_particles_per_blk = 100
> memory_stat_freq = 100000
> meshcopycount = 1
> min_particles_per_blk = 1
> mpole_innerzonesize = 16
> mpole_lmax = 8 [CHANGED]
> mpole_maxradialzones = 1
> nbegin = 1
> nblockx = 1
> nblocky = 1
> nblockz = 1
> nend = 1000000000 [CHANGED]
> nrefs = 2
> nriem = 10000 [CHANGED]
> nsteptotalsts = 5
> outputsplitnum = 1
> plotfileintervalstep = 0
> plotfilenumber = 0
> ppmeintcompfluxconstructionmeth = 0
> ppmeintfluxconstructionmeth = 0
> ppmenercompfluxconstructionmeth = 0
> ppmenerfluxconstructionmeth = 0
> refine_var_count = 4
> rolling_checkpoint = 10000
> sim_maxblocks = 40000
> sim_nsubzones = 4 [CHANGED]
> sweeporder = 123
> wr_integrals_freq = 1
> cfl = 0.800E+00
> checkpointfileintervaltime = 0.100E+06 [CHANGED]
> checkpointfileintervalz = 0.180+309
> cvisc = 0.100E+00
> derefine_cutoff_1 = 0.200E+00
> derefine_cutoff_2 = 0.200E+00
> derefine_cutoff_3 = 0.200E+00
> derefine_cutoff_4 = 0.200E+00
> dp_sh = 0.330E+00
> dp_sh_md = 0.330E+00
> dr_tstepslowstartfactor = 0.100E+00
> dtinit = 0.100E-03 [CHANGED]
> dtmax = 0.100E+09 [CHANGED]
> dtmin = 0.100E-09
> eintswitch = 0.100E-03 [CHANGED]
> eos_singlespeciesa = 0.100E+01
> eos_singlespeciesz = 0.100E+01
> epsiln = 0.330E+00
> gamma = 0.167E+01
> gr_lrefinemaxredlogbase = 0.100E+02
> gr_lrefinemaxredradiusfact = 0.000E+00
> gr_lrefinemaxredtref = 0.000E+00
> gr_lrefinemaxredtimescale = 0.100E+01
> gr_lrefmaxtime_1 = -0.100E+01
> gr_lrefmaxtime_10 = -0.100E+01
> gr_lrefmaxtime_11 = -0.100E+01
> gr_lrefmaxtime_12 = -0.100E+01
> gr_lrefmaxtime_13 = -0.100E+01
> gr_lrefmaxtime_14 = -0.100E+01
> gr_lrefmaxtime_15 = -0.100E+01
> gr_lrefmaxtime_16 = -0.100E+01
> gr_lrefmaxtime_17 = -0.100E+01
> gr_lrefmaxtime_18 = -0.100E+01
> gr_lrefmaxtime_19 = -0.100E+01
> gr_lrefmaxtime_2 = -0.100E+01
> gr_lrefmaxtime_20 = -0.100E+01
> gr_lrefmaxtime_3 = -0.100E+01
> gr_lrefmaxtime_4 = -0.100E+01
> gr_lrefmaxtime_5 = -0.100E+01
> gr_lrefmaxtime_6 = -0.100E+01
> gr_lrefmaxtime_7 = -0.100E+01
> gr_lrefmaxtime_8 = -0.100E+01
> gr_lrefmaxtime_9 = -0.100E+01
> larget = 0.100E+11
> mpole_innerzoneresolution = 0.100E+00
> mpole_zoneexponent_1 = 0.100E+01
> mpole_zoneexponent_2 = 0.100E+01
> mpole_zoneexponent_3 = 0.100E+01
> mpole_zoneexponent_4 = 0.100E+01
> mpole_zoneradiusfraction_1 = 0.100E+01
> mpole_zoneradiusfraction_2 = 0.100E+01
> mpole_zoneradiusfraction_3 = 0.100E+01
> mpole_zoneradiusfraction_4 = 0.100E+01
> mpole_zonescalar_1 = 0.100E+01
> mpole_zonescalar_2 = 0.100E+01
> mpole_zonescalar_3 = 0.100E+01
> mpole_zonescalar_4 = 0.100E+01
> nusts = 0.100E+00
> omg1 = 0.750E+00
> omg2 = 0.100E+02
> plotfileintervaltime = 0.100E-02 [CHANGED]
> plotfileintervalz = 0.180+309
> refine_cutoff_1 = 0.800E+00
> refine_cutoff_2 = 0.800E+00
> refine_cutoff_3 = 0.800E+00
> refine_cutoff_4 = 0.800E+00
> refine_filter_1 = 0.100E-01
> refine_filter_2 = 0.100E-01
> refine_filter_3 = 0.100E-01
> refine_filter_4 = 0.100E-01
> rieman_tol = 0.100E-13 [CHANGED]
> rss_limit = -0.100E+01
> sim_fluffdampcoeff = 0.950E+00
> sim_fluffdampcutoff = 0.100E-17 [CHANGED]
> sim_fluffrefinecutoff = 0.100E+02
> sim_fluidgamma = 0.167E+01 [CHANGED]
> sim_objcentdens = 0.165E+03 [CHANGED]
> sim_objcentpres = 0.246E+18 [CHANGED]
> sim_objmass = 0.999E+00 [CHANGED]
> sim_objpolyn = 0.300E+01
> sim_objradius = 0.102E+01 [CHANGED]
> sim_pambient = 0.100E-03
> sim_relaxrate = 0.900E+00 [CHANGED]
> sim_rhoambient = 0.100E-18 [CHANGED]
> sim_rotangle = 0.000E+00
> sim_rotfac = 0.000E+00
> sim_smallt = 0.100E+05
> sim_starptmass = 0.200E+34
> sim_tambient = 0.100E+01
> sim_trelax = 0.100E+05 [CHANGED]
> sim_tspinup = 0.000E+00
> sim_winddens = 0.100E-02 [CHANGED]
> sim_windduration = 0.250E+04 [CHANGED]
> sim_windpeak = 0.300E+05 [CHANGED]
> sim_windrampup = 0.300E+01
> sim_windtemp = 0.100E+05 [CHANGED]
> sim_windvel = 0.300E+08
> sim_xcenter = 0.100E+12 [CHANGED]
> sim_ycenter = 0.100E+12 [CHANGED]
> sim_zcenter = 0.100E+12 [CHANGED]
> small = 0.100E-14 [CHANGED]
> smalle = 0.100E+11 [CHANGED]
> smallp = 0.100E-03 [CHANGED]
> smallt = 0.100E-14 [CHANGED]
> smallu = 0.100E-14 [CHANGED]
> smallx = 0.100E-29 [CHANGED]
> smlrho = 0.100E-19 [CHANGED]
> tinitial = 0.000E+00
> tmax = 0.100E+01 [CHANGED]
> tstep_change_factor = 0.200E+01
> vgrid = 0.000E+00
> wall_clock_checkpoint = 0.432E+05
> wall_clock_time_limit = 0.605E+06
> x_refine_center = 0.000E+00
> xmax = 0.200E+12 [CHANGED]
> xmin = 0.000E+00
> y_refine_center = 0.000E+00
> ymax = 0.900E+02 [CHANGED]
> ymin = 0.000E+00
> zfinal = 0.000E+00
> zinitial = -0.100E+01
> z_refine_center = 0.000E+00
> zmax = 0.180E+03 [CHANGED]
> zmin = 0.000E+00
> unitsystem = none
> basenm = starwind_ [CHANGED]
> eosmode = dens_ie
> eosmodeinit = dens_pres [CHANGED]
> geometry = spherical [CHANGED]
> gr_pmrpoutputdir = ./
> grav_boundary_type = isolated
> hy_eosmodeafter = dens_ie
> hy_fluxrepresentation = fluxes
> log_file = starwind.log [CHANGED]
> mpole_zonetype_1 = exponential
> mpole_zonetype_2 = exponential
> mpole_zonetype_3 = exponential
> mpole_zonetype_4 = logarithmic
> output_directory =
> pc_unitsbase = CGS
> plot_grid_var_1 = none
> plot_grid_var_10 = none
> plot_grid_var_11 = none
> plot_grid_var_12 = none
> plot_grid_var_2 = none
> plot_grid_var_3 = none
> plot_grid_var_4 = none
> plot_grid_var_5 = none
> plot_grid_var_6 = none
> plot_grid_var_7 = none
> plot_grid_var_8 = none
> plot_grid_var_9 = none
> plot_var_1 = dens [CHANGED]
> plot_var_10 = none
> plot_var_11 = none
> plot_var_12 = none
> plot_var_2 = temp [CHANGED]
> plot_var_3 = velx [CHANGED]
> plot_var_4 = vely [CHANGED]
> plot_var_5 = velz [CHANGED]
> plot_var_6 = none
> plot_var_7 = none
> plot_var_8 = none
> plot_var_9 = none
> prof_file = profile.dat
> refine_var_1 = dens [CHANGED]
> refine_var_2 = pres [CHANGED]
> refine_var_3 = none
> refine_var_4 = none
> run_comment = FLASH 3 run
> run_number = 1
> stats_file = flash.dat
> xl_boundary_type = reflecting [CHANGED]
> xr_boundary_type = diode [CHANGED]
> yl_boundary_type = periodic
> yr_boundary_type = periodic
> zl_boundary_type = outflow [CHANGED]
> zr_boundary_type = outflow [CHANGED]
> allowdtstsdominate = F
> alwayscomputeuservars = T
> alwaysrestrictcheckpoint = T
> bytepack = F
> charlimiting = T
> chkguardcellsinput = F
> chkguardcellsoutput = F
> converttoconsvdformeshcalls = F
> converttoconsvdinmeshinterp = T
> corners = F
> dr_printtsteploc = T
> dr_shortenlaststepbeforetmax = T [CHANGED]
> drift_tuples = F
> eachprocwritesownabortlog = F
> eachprocwritessummary = F
> earlyblockdistadjustment = T
> enablemaskedgcfill = F
> flux_correct = T
> geometryoverride = F
> gr_bcenableapplymixedgds = T
> gr_lrefinemaxbytime = F
> gr_lrefinemaxreddobylogr = F
> gr_lrefinemaxreddobytime = F
> gr_pmrpadvancealllevels = F
> gr_pmrpamrerrorchecking = F
> gr_pmrpcartesianpm = F
> gr_pmrpconserve = F
> gr_pmrpconsvfluxdensities = T
> gr_pmrpconsvfluxes = F
> gr_pmrpcurvilinear = F
> gr_pmrpcurvilinearconserve = F
> gr_pmrpcylindricalpm = F
> gr_pmrpdiagonals = T
> gr_pmrpedgevalue = T
> gr_pmrpedgevalueinteg = F
> gr_pmrpemptycells = F
> gr_pmrpforceconsistency = T
> gr_pmrplsingularline = F
> gr_pmrpnopermanentguardcells = F
> gr_pmrppolarpm = F
> gr_pmrppredcorr = F
> gr_pmrpsphericalpm = F
> gr_pmrptimingmpi = F
> gr_pmrptimingmpix = F
> gr_pmrpvardt = F
> hybrid_riemann = F
> ignoreforcedplot = F
> io_writemscalarintegrals = F
> leveque = F
> mpole_2dsymmetryplane = F
> mpole_3daxisymmetry = F
> mpole_dumpmoments = F
> mpole_ignoreinnerzone = F
> mpole_multithreading = F
> mpole_printradialinfo = F
> plotfilegridquantitydp = F
> plotfilemetadatadp = F
> ppm_modifystates = F
> reducegcellfills = F
> refine_on_particle_count = F
> restart = F
> summaryoutputonly = F
> threadblocklistbuild = F
> threaddelepblocklist = F
> threaddelepwithinblock = F
> threaddriverblocklist = F
> threaddriverwithinblock = F
> threadeoswithinblock = F
> threadhydroblocklist = F
> threadhydrowithinblock = F
> threadraytracebuild = F
> threadwithinblockbuild = F
> typematchedxfer = T
> unbiased_geometry = F
> updatehydrofluxes = T
> useburn = F
> usecollectivehdf5 = T
> useconductivity = F
> usecool = F
> usecosmology = F
> usedeleptonize = F
> usediffuse = F
> useenergydeposition = F
> useflame = F
> usegravity = F
> useheat = F
> useheatexchange = F
> usehydro = T
> useionize = F
> uselegacylabels = T
> usemagneticresistivity = F
> usemassdiffusivity = F
> useopacity = F
> useparticles = F
> usepolytrope = F
> useprimordialchemistry = F
> useradtrans = F
> usests = F
> usestsfordiffusion = F
> usestir = F
> usetreecol = F
> useturb = T
> useviscosity = F
> use_cma_advection = F
> use_cma_flattening = F
> use_cma_steepening = F
> use_steepening = T
> writestatsummary = T
>
> ==============================================================================
>
> Known units of measurement:
>
> Unit CGS Value Base Unit
> 1 cm 1.0000 cm
> 2 s 1.0000 s
> 3 g 1.0000 g
> 4 K 1.0000 K
> 5 esu 1.0000 esu
> 6 mol 1.0000 mol
> 7 m 100.00 cm
> 8 km 1.00000E+05 cm
> 9 pc 3.08568E+18 cm
> 10 kpc 3.08568E+21 cm
> 11 Mpc 3.08568E+24 cm
> 12 Gpc 3.08568E+27 cm
> 13 Rsun 6.96000E+10 cm
> 14 AU 1.49598E+13 cm
> 15 yr 3.15569E+07 s
> 16 Myr 3.15569E+13 s
> 17 Gyr 3.15569E+16 s
> 18 kg 1000.0 g
> 19 Msun 1.98892E+33 g
> 20 amu 1.66054E-24 g
> 21 eV 11605. K
> 22 C 2.99792E+09 esu
> 23 LFLY 3.08568E+24 cm
> 24 TFLY 2.05759E+17 s
> 25 MFLY 9.88470E+45 g
> 26 clLength 3.08568E+24 cm
> 27 clTime 3.15569E+16 s
> 28 clMass 1.98892E+48 g
> 29 clTemp 1.16044E+07 K
> -----------End of Units--------------------
>
> Known physical constants:
>
> Constant Name Constant Value cm s g K esu mol
> 1 Newton 6.67428E-08 3.0 -2.0 -1.0 0.0 0.0 0.0
> 2 speed of light 2.99792E+10 1.0 -1.0 0.0 0.0 0.0 0.0
> 3 Planck 6.62607E-27 2.0 -1.0 1.0 0.0 0.0 0.0
> 4 electron charge 4.80320E-10 0.0 0.0 0.0 0.0 1.0 0.0
> 5 electron mass 9.10938E-28 0.0 0.0 1.0 0.0 0.0 0.0
> 6 proton mass 1.67262E-24 0.0 0.0 1.0 0.0 0.0 0.0
> 7 fine-structure 7.29735E-03 0.0 0.0 0.0 0.0 0.0 0.0
> 8 Avogadro 6.02214E+23 0.0 0.0 0.0 0.0 0.0 -1.0
> 9 Boltzmann 1.38065E-16 2.0 -2.0 1.0 -1.0 0.0 0.0
> 10 ideal gas constant 8.31447E+07 2.0 -2.0 1.0 -1.0 0.0 -1.0
> 11 Wien 0.28978 1.0 0.0 0.0 1.0 0.0 0.0
> 12 Stefan-Boltzmann 5.67040E-05 0.0 -3.0 1.0 -4.0 0.0 0.0
> 13 Radiation Constant 7.56577E-15 -1.0 -2.0 1.0 -4.0 0.0 0.0
> 14 pi 3.1416 0.0 0.0 0.0 0.0 0.0 0.0
> 15 e 2.7183 0.0 0.0 0.0 0.0 0.0 0.0
> 16 Euler 0.57722 0.0 0.0 0.0 0.0 0.0 0.0
> ==============================================================================
>
> Multifluid database contents:
>
> Initially defined values of species:
> Name Index Total Positive Neutral Negative bind Ener Gamma eosType
>
> Name Index OpacityLowTemp Zmin Subtype ZFreeTableFile EnerTableFile PresTableFile
>
> Species Constituents
>
> ==============================================================================
> [ 07-07-2014 10:26:23.962 ] [amr_set_runtime_parameters] NOTE: Enabling curvilinear suppport because of the selected geometry
> [ 07-07-2014 10:26:23.999 ] [gr_initGeometry] checking BCs for idir: 1
> [ 07-07-2014 10:26:23.999 ] [gr_initGeometry] checking BCs for idir: 2
> [ 07-07-2014 10:26:23.999 ] [gr_initGeometry] checking BCs for idir: 3
> Object mass (m_sun): 9.98681760E-01
> Object radius: 7.08274944E+10
> Object central density: 1.65245400E+02
> Ambient CFL timestep: 6.12372436E+01
> Fluff CFL timestep: 1.93649167E+01
> Obj. radius: 7.08274944E+10
> [ 07-07-2014 10:26:24.007 ] [GRID amr_refine_derefine]: initiating refinement
> [ 07-07-2014 10:26:24.007 ] [GRID amr_refine_derefine]: redist. phase. tot blks requested: 9
> [GRID amr_refine_derefine] min blks 9 max blks 9 tot blks 9
> [GRID amr_refine_derefine] min leaf blks 8 max leaf blks 8 tot leaf blks 8
> [ 07-07-2014 10:26:24.008 ] [GRID amr_refine_derefine]: refinement complete
> [ 07-07-2014 10:26:24.010 ] [GRID gr_expandDomain]: iteration=1, create level=3
> INFO: Grid_fillGuardCells is ignoring masking.
> [ 07-07-2014 10:26:24.097 ] [mpi_amr_comm_setup]: buffer_dim_send=1, buffer_dim_recv=1
> [ 07-07-2014 10:26:24.139 ] WARNING after gc filling: min. unk(DENS_VAR)=0.000000000000000000000 PE=0 block=1 type=2
> [ 07-07-2014 10:26:24.140 ] WARNING after gc filling: min. unk(ENER_VAR)=0.000000000000000 PE=0 block=1 type=2
> [ 07-07-2014 10:26:24.140 ] WARNING after gc filling: min. unk(EINT_VAR)=0.000000000000000 PE=0 block=1 type=2
> [ 07-07-2014 10:26:24.141 ] WARNING after gc filling: min. unk(DENS_VAR)=0.000000000000000000000 PE=0 block=2 type=1
> [ 07-07-2014 10:26:24.141 ] WARNING after gc filling: min. unk(ENER_VAR)=0.000000000000000 PE=0 block=2 type=1
> [ 07-07-2014 10:26:24.142 ] WARNING after gc filling: min. unk(EINT_VAR)=0.000000000000000 PE=0 block=2 type=1
> [ 07-07-2014 10:26:24.142 ] WARNING after gc filling: min. unk(DENS_VAR)=0.000000000000000000000 PE=0 block=3 type=1
> [ 07-07-2014 10:26:24.142 ] WARNING after gc filling: min. unk(ENER_VAR)=0.000000000000000 PE=0 block=3 type=1
> [ 07-07-2014 10:26:24.143 ] WARNING after gc filling: min. unk(EINT_VAR)=0.000000000000000 PE=0 block=3 type=1
> [ 07-07-2014 10:26:24.143 ] WARNING after gc filling: min. unk(DENS_VAR)=0.000000000000000000000 PE=0 block=4 type=1
> [ 07-07-2014 10:26:24.143 ] WARNING after gc filling: min. unk(ENER_VAR)=0.000000000000000 PE=0 block=4 type=1
> [ 07-07-2014 10:26:24.144 ] WARNING after gc filling: min. unk(EINT_VAR)=0.000000000000000 PE=0 block=4 type=1
> [ 07-07-2014 10:26:24.144 ] WARNING after gc filling: min. unk(DENS_VAR)=0.000000000000000000000 PE=0 block=5 type=1
> [ 07-07-2014 10:26:24.145 ] WARNING after gc filling: min. unk(ENER_VAR)=0.000000000000000 PE=0 block=5 type=1
> [ 07-07-2014 10:26:24.145 ] WARNING after gc filling: min. unk(EINT_VAR)=0.000000000000000 PE=0 block=5 type=1
> [ 07-07-2014 10:26:24.145 ] WARNING after gc filling: min. unk(DENS_VAR)=0.000000000000000000000 PE=0 block=6 type=1
> [ 07-07-2014 10:26:24.146 ] WARNING after gc filling: min. unk(ENER_VAR)=0.000000000000000 PE=0 block=6 type=1
> [ 07-07-2014 10:26:24.146 ] WARNING after gc filling: min. unk(EINT_VAR)=0.000000000000000 PE=0 block=6 type=1
> [ 07-07-2014 10:26:24.146 ] WARNING after gc filling: min. unk(DENS_VAR)=0.000000000000000000000 PE=0 block=7 type=1
> [ 07-07-2014 10:26:24.146 ] WARNING after gc filling: min. unk(ENER_VAR)=0.000000000000000 PE=0 block=7 type=1
> [ 07-07-2014 10:26:24.147 ] WARNING after gc filling: min. unk(EINT_VAR)=0.000000000000000 PE=0 block=7 type=1
> [ 07-07-2014 10:26:24.147 ] WARNING after gc filling: min. unk(DENS_VAR)=0.000000000000000000000 PE=0 block=8 type=1
> [ 07-07-2014 10:26:24.147 ] WARNING after gc filling: min. unk(ENER_VAR)=0.000000000000000 PE=0 block=8 type=1
> [ 07-07-2014 10:26:24.148 ] WARNING after gc filling: min. unk(EINT_VAR)=0.000000000000000 PE=0 block=8 type=1
> [ 07-07-2014 10:26:24.148 ] WARNING after gc filling: min. unk(DENS_VAR)=0.000000000000000000000 PE=0 block=9 type=1
> [ 07-07-2014 10:26:24.148 ] WARNING after gc filling: min. unk(ENER_VAR)=0.000000000000000 PE=0 block=9 type=1
> [ 07-07-2014 10:26:24.148 ] WARNING after gc filling: min. unk(EINT_VAR)=0.000000000000000 PE=0 block=9 type=1
>
>
>
>
>
>
> On Jul 7, 2014, at 10:17 AM, Sean Couch <smc at flash.uchicago.edu> wrote:
>
>> Hi Luke,
>>
>> Could you send along your log file so that we can see exactly what setup and runtime parameters you’re using?
>>
>> Cheers,
>> Sean
>>
>> --------------------------------------------------------
>> Sean M. Couch
>> Hubble Fellow
>> Flash Center for Computational Science
>> Department of Astronomy & Astrophysics
>> The University of Chicago
>> 5747 S Ellis Ave, Jo 315
>> Chicago, IL 60637
>> (773) 702-3899
>> www.flash.uchicago.edu/~smc
>>
>>
>>
>>
>> On Jul 6, 2014, at 11:06 AM, Luke Zoltan Kelley <lkelley at cfa.harvard.edu> wrote:
>>
>>> Hello flash-users!
>>>
>>> I'm new to FLASH and trying to convert a simulation from cartesian to (3D) spherical, but I'm running into some errors. If anyone has had recent success using 3D spherical, I would be very appreciative of any tips they had, or issues they overcame. In particular, I'm getting a warning from source/Grid/GridMain/paramesh/paramesh4/gr_sanitizeDataAfterInterp.F90 that my guard-cells aren't being set correctly:
>>>
>>>
>>> WARNING after gc filling: min. unk(DENS_VAR)=0.000000000000000000000 PE=0 block=1 type=2
>>> 16 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
>>> 15 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
>>> 14 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
>>> 13 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
>>> 12 0.10E-18 0.63E-01 0.63E-01 0.62E-01 0.62E-01 0.63E-01 0.63E-01 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18
>>> 11 0.10E-18 0.63E-01 0.62E-01 0.63E-01 0.63E-01 0.62E-01 0.63E-01 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18
>>> 10 0.10E-18 0.62E-01 0.62E-01 0.63E-01 0.63E-01 0.62E-01 0.62E-01 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18
>>> 9 0.10E-18 0.63E-01 0.63E-01 0.62E-01 0.62E-01 0.63E-01 0.63E-01 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18
>>> 8 0.10E-18 0.62E-01 0.63E-01 0.63E-01 0.63E-01 0.63E-01 0.62E-01 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18
>>> 7 0.10E-18 0.63E-01 0.62E-01 0.62E-01 0.62E-01 0.62E-01 0.63E-01 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18
>>> 6 0.10E-18 0.62E-01 0.63E-01 0.62E-01 0.62E-01 0.63E-01 0.62E-01 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18
>>> 5 0.10E-18 0.62E-01 0.63E-01 0.63E-01 0.63E-01 0.63E-01 0.62E-01 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18 0.10E-18
>>> 4 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
>>> 3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
>>> 2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
>>> 1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
>>>
>>>
>>> These warnings are given for DENS_VAR, ENER_VAR, EINT_VAR and all blocks.
>>> (presumably) for this reason I'm getting arithmetic exceptions when source/physics/Eos/EosMain/Gamma/eos_idealGamma.F90 tries to divide by the (zero) densities, the backtrace I get is:
>>>
>>>
>>> Program received signal EXC_ARITHMETIC, Arithmetic exception.
>>> 0x000000010024cf6e in eos_idealgamma_ (mode=103, veclen=8, eosdata=(), vecbegin=Cannot access memory at address 0x0
>>> ) at eos_idealGamma.F90:341
>>> 341 eosData(dens+ilo:dens+ihi)
>>> (gdb) bt
>>> #0 0x000000010024cf6e in eos_idealgamma_ (mode=103, veclen=8, eosdata=(), vecbegin=Cannot access memory at address 0x0
>>> ) at eos_idealGamma.F90:341
>>> #1 0x000000010001149b in eos_ (mode=103, veclen=8, eosdata=(), massfrac=(), mask=(.FALSE., .FALSE., .FALSE., .FALSE., .FALSE., .FALSE., .FALSE., .FALSE., .FALSE., .FALSE., .FALSE., .FALSE., .FALSE.), vecbegin=Cannot access memory at address 0x0
>>> ) at Eos.F90:265
>>> #2 0x000000010001edea in eos_wrapped_ (mode=103, range=(( 5, 12) ( 1, 4) ( 1, 1) ), blockid=1, griddatastruct=Cannot access memory at address 0x0
>>> ) at Eos_wrapped.F90:220
>>> #3 0x0000000100019b15 in complexskipping.1886 () at Eos_guardCells.F90:43
>>> #4 0x000000010001afd8 in eos_guardcells_ (corners=.TRUE., layers=(4, 4, 4), skipsrl=.TRUE.) at Eos_guardCells.F90:120
>>> #5 0x00000001000322d7 in grid_fillguardcells_ (griddatastruct=380, idir=-1, minlayers=Cannot access memory at address 0x0
>>> ) at Grid_fillGuardCells.F90:482
>>> #6 0x000000010006340e in grid_markrefinederefine_ () at Grid_markRefineDerefine.F90:98
>>> #7 0x000000010029eec2 in gr_expanddomain_ (particlesinitialized=.FALSE.) at gr_expandDomain.F90:212
>>> #8 0x0000000100061385 in grid_initdomain_ (restart=.FALSE., particlesinitialized=.FALSE.) at Grid_initDomain.F90:98
>>> #9 0x000000010000d405 in driver_initflash_ () at Driver_initFlash.F90:156
>>> #10 0x000000010001f19c in flash () at Flash.F90:49
>>> #11 0x000000010001f20e in main (argc=1, argv=0x7fff5fbff870 '/Users/lzkelley/Applications/flash/flash4.2.2/object_starwind/flash4\000') at Flash.F90:43
>>>
>>>
>>> In my Simulation_initBlock.F90, I am looping over the guard-cells and setting all densities to non-zero values --- if I print out the densities during the initialization loop I get the appropriate densities from i,j,k = {1,1,1} up to {16,16,16} --- so it seems like the guard-cells are being overwritten to zero...
>>> This does not occur in 3D cartesian, and also does *not* occur when I run SodSpherical (which seems to work properly, strangely enough).
>>>
>>> I believe I've also found a bug in source/physics/Hydro/HydroMain/split/PPM/PPMKernel/avisco.F90:416, when sweeping along "y" (theta) in 3D spherical the denominator [ 'sin(xl(i))' ] is allowed to be zero and causes arithmetic exceptions.
>>>
>>> Any help on this particular problem, or on getting spherical running in general would be greatly appreciated!
>>> Thanks,
>>> Luke
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://flash.rochester.edu/pipermail/flash-users/attachments/20140707/abc1b44b/attachment.htm>
More information about the flash-users
mailing list