Bearclaw Outline

Given below is a hierarchical diagram of the files used by bearclaw/astroBEAR. A similar diagram, but with all subroutines listed, maybe found here. Note: the latter does not at present include functions. Check the Definitions page for terminology.

Folders are bold. All text should link to relevant wikipages.

• dev
  • Makefile.inc, Makefile.LLE.inc, Makefile.nova.inc, Makefile.Pentium.inc, Makefile.RTC.inc, Makefile, Makefile.targets
  • doc
    • Change required in Environment variable documentation
    • Issue Log 2007-06-05: Compiling difficulties
    • Issue Log 2007-06-08: Single processor execution difficulties
    • Issue Log 2007-06-14: Single processor execution difficulties
    • Issue Log 2007-06-15: Single processor execution difficulties
    • Issue Log 2007-06-20: Multiprocessor success, single processor troubleshooting
    • Issue Log 2007-06-22: single-processor test run
    • Issue Log 2007-06-25: multi-processor test rum
    • Issue Log 2007-08-20: Compiling problem on Opteron processors
    • Issue Log 2007-09-04: Memory leak in AstroBEAR I/O
    • A note about commenting code
    • An overview of the BearCLAW data structures
    • Distributed computing in BearCLAW
    • instructions making HDF files into movies using VisIt
    • Problems with multiple writes to an HDF dataset.
    • Chombo formatting for HDF files.

• hdf
• images
• matlab
• opendx
• tests
• lib
  • bearez.f90, driver.f90
  • beario.f90
  • classicbear.f90, NodeInfoTypeClassicBEAR.f90
  • compactbear.f90, NodeInfoTypeCompactBEAR.f90
  • fastMP.f90, NodeInfoTypeFastMP.f90
  • fixup.f90
  • FuncParamTypeCommon.f90
  • InfoFieldUtils.f90
  • linsolve.f90
  • mpi_exec.f90, mpidriver.f90
  • MUSCLbear.f90, NodeInfoTypeMUSCLbear.f90
  • NodeInfoDef.f90
  • NodeInfoGlobal.f90
  • NodeInfoTypeCommon.f90
  • openmp_exec.f90, openmpdriver.f90
  • setbc.f90
  • treeops.f90
  • wavebear.f90, NodeInfoTypeWaveBEAR.f90
  • bearez.single_cpp.f90
  • bearez.mpi_cpp.f90
• contrib/astro
  • nodeinfodef.f90
  • globaldeclarations.f90
  • i_CT.f90
  • i_setprob.f90
  • i_qinit.f90
  • problem.f90
  • physics
    • i_physfluxMUSCL.f90
    • i_hydro_physfluxMUSCL.f90
    • i_MHD_physfluxMUSCL.f90
    • i_cosray.f90
    • i_protect.f90
    • i_src.f90
      • cool:
        • cool.f90
        • i_evolove.f90
    • tf.f90
    • i_i_ODEs.f90
    • vanderWaals
      • vanderWaals.f90
    • SESAME
      • SESAME.f90
      • interpolate.f90
  • clumps
  • disk
  • diskjet
  • envelope
  • jetwind
  • labjet
  • mhdtests
  • plugshock
  • rt
    • rt.betti.f90
    • rt.spectrum.parallelized.f90
  • sample_data_files
  • selfgravity
  • shock
  • template
  • tests
  • wind
  • SinkParticle
  • Bondi
  • JetLaunch
  • Outflow

---

Bearclaw Outline with Subroutines

Filenames are bold. NodeInfoType____.f90, ___driver.f90, and application module files are not included in this list.

• dev:
  • Makefile.inc, Makefile.LLE.inc, Makefile.nova.inc, Makefile.Pentium.inc, Makefile.RTC.inc, Makefile, Makefile.targets
  • doc:
  • hdf:
  • images:
  • matlab:
  • opendx:
  • tests:
  • lib:
    • bearez.f90
      • ReadLine
      • BEAR
      • GetTreeFileName
      • ReleaseFields
      • MarkNode
      • MarkNodeToBeDeleted
      • RootDecompose
      • RootInit
      • RestartRootInit
      • Initialq
      • SetRestartFlags
      • SetAuxFields
      • AllocateStartInfos
      • BEARStep
      • ReSetGrids
      • AMR
      • SetFinestLevel
      • SetGhost
      • SetStep
      • FindTimeStep
      • GhostOverlap
      • PeriodicPairs
      • PeriodicOverlap
      • TransferPeriodicOverlap
      • TransferOverlap
      • TransferValues
      • EstimateLevelErrors
      • EstimateErrors
      • EstimateErrorsWorkers
      • SetTrueTimeStepFlag
      • TimeStepLevel
      • ReGridTime
      • SetRegridFlag
      • PhysicalBC
      • PeriodicBC
      • TransferBC
      • GridAdapt
      • Transferq
      • UserInit
      • ProblemInit
      • SynchLevels
      • CheckErrCode
      • MemoryCheck
      • FindCFLMax
    • beario.f90
      • Writeq
      • ReadInfos
      • Readq
      • Inputq
      • Outputq
      • ReadRestartInfos
      • MakeChomboFile
      • Add_Chombo_Attribute_Int
      • Add_Chombo_Attribute_Float
      • Add_Chombo_Attribute_String
      • Add_Chombo_Attribute_IntVector
      • Add_Chombo_Attribute_FloatVector
      • Add_Chombo_Attribute_Box
      • GetMinimumXlowers
      • GetMaximumXuppers
      • ReadFromChomboFile
      • Add_Chombo_Dataset_Float
      • Read_Chombo_Dataset_Float
    • classicbear.f90
    • compactbear.f90
    • fastMP.f90
    • fixup.f90
      • UpdateFixups
      • CoarseFine1D
      • CoarseFineFlux
    • FuncParamTypeCommon.f90
    • InfoFieldUtils.f90
      • After_Advance_Recv
      • After_Advance_Send
      • AllocFields
      • ApplyAfterfixupMaster
      • ApplyAfterfixupWorker
      • Before_Advance_Recv
      • Before_Advance_Send

• CalcSignatures
• CoarseInit
• CoarseStep
• DeAllocFields
• ErrFlag
• FixUpParent
• FormFixUpMask
• FormParentFixUpMask
• GetWorkerInfos
• GridFlagRatio
• InitFields
• NewGrid
• NewSubGrids
• NullifyPointers
• Overlap_Recv_Pointers
• Overlap_Send_Pointers
• OverlapAuxCopy
• ParentUpdate_Recv
• ParentUpdate_Send
• qFields_Pointers_Recv
• qFields_Pointers_Send
• qold_Recv
• qold_Send
• RestrictFields
• TakeTimeStep
• TimeStep
• TimeStepMaster
• TimeStepWorkers
• UpdateLevel
• UpdateParent

• linsolve.f90
  • linsolve
  • MultiGridLinSolveEZ
  • RestrictResidualEZ
  • ProlongCorrectionEZ
  • StoreCornerDeltaq
  • RestoreCornerDeltaq
  • AccumulateCorrections
  • AddCorrection
  • DbgPrint
  • MultiGridLinSolve
  • MGstencils
  • RestrictResidual
  • ProlongCorrection
  • ComputeRHS
  • TransferMGVars
  • SmoothCorrection
  • LinSystemResidual
  • ComputeResidual
  • ApplyOperator
  • ApplyOperatorAtCell
  • OpLaplace
  • OpLaplaceCurv
  • OpVarCoefElliptic
  • OpVarCoefEllipticCurv
  • OpCrankNicolson
  • OpCrankNicolsonCurv
  • OpCrankNicolsonVarCoef
  • OpCrankNicolsonVarCoefCurv
  • HessianCurv
  • GradAuxCurv
  • ComputeMetric
  • DivMetricCorr
• mpi_exec.f90
  • MPI_Initialize
  • Initalq_Workers
  • InitialTests
  • MPI_Worker
  • TestInfoTypeSendRecv
  • TestInfoSendRecv
  • TestW2WInfoSendRecv
  • SendFields
  • RecvFields
  • TransferInfo
  • TransferFields
  • Print2Info
  • PrintCompareInfo
  • CompareInfo
  • CompareInfoFields
  • MPI_Restart_Distribute
  • MPI_MoveGrids
  • MPI_Dispatch
  • MPI_Dispatch_Finalize
  • MPI_Distribute
  • ComputeCurrentLoad
  • BalanceLoads
  • MPI_WorkerPing
  • MPI_TransferOverlap
  • MPI_TransferAuxOverlap
  • MPI_CopyFieldsToMaster
  • MPI_RemoveFieldsCopy
  • MPI_Worker_afterfixup
  • MP_UpdateInfo
  • AllocateParentUpdateBuffer
  • UpdateParentWithChildData
  • AccumulateFixups
  • AccumulateUpdates
  • Worker_InitTimeStepFixUp
  • Worker_ParentChildSignature
  • Worker_FixupInit
  • GetInfoPointer
  • RemoveInfoFromWorker
  • CreateInfoOnWorker
• MUSCLbear.f90
  • step
  • Diffusion
  • LOF
  • numflux
  • updateq
  • extract1D
  • Extract2Dslab
  • Extract3Dslab
  • Extract4Dslab
  • AllocateSchemeFields
  • DeAllocSchemeFields
  • NullifySchemeFields
  • ReadSchemeRootData
• NodeInfoDef.f90
  • ReadRootData
  • NodeInfoInit
  • AllocUserFields
  • DeAllocUserFields
  • NullifyUserFields
  • NodeInfoKill
  • ReadNodeInfo
  • WriteNodeInfo
• NodeInfoGlobal.f90
• NodeInfoTypeCommon.f90
• openmp_exec.f90
• setbc.f90
  • SetBC1
  • SetBC2
  • SetBC3
  • SetBC4
• treeops.f90
  • InitForest
  • KillForest
  • ReadForest
  • ReadNode
  • WriteForest
  • AddRootLevelNode
  • AddRootLevelNodeOrig
  • CreateChild
  • KillNode
  • OpenMPApplyOnLevel
  • ApplyOnLevel
  • ApplyOnLevelTarget
  • ApplyOnLevelPairs
  • ApplyOnChildren
  • ApplyOnForest
  • ApplyOnLevels
  • ApplyOnLeaves
  • TrueCond
  • LevelCond
  • LeafCond
  • ForestTraversal
  • TreeTraversal
  • ExistLevel
  • PushForest
  • PopForest
  • GetLevel
  • GetNrOfChildren
  • GetSiblingIndex
  • GetNodeInfo
  • GetYoungestOnLevel
  • GetNeighbor
  • GetNrOfNodes
  • GetForestNodeCount
  • MapNodeInfoPtr
• wavebear.f90

• contrib/astro:
  • nodeinfodef.f90
    • ReadRootData
    • NodeInfoInit
    • AllocUserFields
    • DeAllocUSerFields
    • NullifyUserFields
    • NodeInfoKill
    • ReadNodeInfo
    • WriteNodeInfo
  • globaldeclarations.f90
  • i_CT.f90
    • Field_Update2D
    • Field_Update3D
    • Compute_EMF2D
    • Compute_EMF3D
    • afterfixupMHD
  • i_setprob.f90
    • setprob
    • InitializeRun
    • ReadDomain
    • ReadPhysics
    • CalcGlobalScale
    • PrintSytem
  • i_qinit.f90
    • qinit
    • PlaceBackPlate
    • PlaceSidePlate
  • problem.f90
    • GetVisc
    • problemBC
    • scaleplot
    • problemIO
    • setaux
    • b4step
    • afterstep
    • afterfixup
    • b4stepMHD
    • problemBadCFL
    • SetFlags
    • problemErrFlag
    • Restrict
    • problemInitFields
    • ProlongationFixup
    • ProlongationFixup3D
    • ProblemNodeInfoInit
  • physics:
    • i_physfluxMUSCL.f90
    • i_hydro_physfluxMUSCL.f90
    • i_MHD_physfluxMUSCL.f90
    • i_cosray.f90
    • i_protect.f90
    • i_src.f90
      • src
      • Stiff
      • LUDecompose
      • LUBackSubst
    • cool:
      • cool.f90
        • initneqCool
        • EOS_vars
        • nparticle
        • InitDMCool
      • i_evolove.f90
        • Cool_Derivatives
        • Cool_Jacobian
        • evolve
    • tf.f90
    • i_i_ODEs.f90
      • Derivatives2D
      • Jacobian2D
      • eightwavesD
      • Cyl2D
      • Cyl2DMHD
      • Gravity
      • UniformGravity
      • DMCool
      • NEQPhysics
      • eightwavesJ
      • Cyl2DJac
      • Cyl2DJacMHD
      • GravityJac
      • UniformGravityJac
      • DMCoolJac
      • NEQPhysicsJac
      • Derivatives3D
      • Jacobian3D
      • InitCool
    • vanderWaals.f90
  • clumps
  • disk
  • diskjet
  • envelope
  • jetwind
  • labjet
  • mhdtests
  • plugshock
  • rt
  • sample_data_files
  • selfgravity
  • shock
  • template
  • tests
  • wind