Merge pull request #21 from dreamer2368/ibm

Immersed boundary method
dreamer2368 · Dec 16, 2022 · 3f9aa79 · 3f9aa79
2 parents 90e35e1 + 34211d8
commit 3f9aa79
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Showing 78 changed files with 1,478 additions and 375 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -161,6 +161,7 @@ set(magudiObj_SOURCES
   ${PROJECT_SOURCE_DIR}/include/ReverseMigrator.f90
   ${PROJECT_SOURCE_DIR}/src/ReverseMigratorImpl.f90
   ${PROJECT_SOURCE_DIR}/include/MappingFunction.f90
+  ${PROJECT_SOURCE_DIR}/include/LevelsetFactory.f90
 
   # Extended types.
   ${PROJECT_SOURCE_DIR}/include/RK4Integrator.f90
@@ -211,6 +212,10 @@ set(magudiObj_SOURCES
   ${PROJECT_SOURCE_DIR}/src/ProbePatchImpl.f90
   ${PROJECT_SOURCE_DIR}/include/KolmogorovForcingPatch.f90
   ${PROJECT_SOURCE_DIR}/src/KolmogorovForcingPatchImpl.f90
+  ${PROJECT_SOURCE_DIR}/include/ImmersedBoundaryPatch.f90
+  ${PROJECT_SOURCE_DIR}/src/ImmersedBoundaryImpl.f90
+  ${PROJECT_SOURCE_DIR}/include/SinusoidalWallLevelset.f90
+  ${PROJECT_SOURCE_DIR}/src/SinusoidalWallLevelsetImpl.f90
 
   # C source files.
   ${PROJECT_SOURCE_DIR}/src/PLOT3DFormat.c

diff --git a/bin/Adjoint.f90 b/bin/Adjoint.f90
@@ -33,7 +33,6 @@ program adjoint
   type(t_Solver) :: solver
 
   ! << output variables >>
-  integer :: inputNumber, simulationNumber
   SCALAR_TYPE :: dummyValue = 0.0_wp
 
   ! Initialize MPI.

diff --git a/bin/CheckGradientAccuracy.f90 b/bin/CheckGradientAccuracy.f90
@@ -26,7 +26,6 @@ program gradient_accuracy
   integer, dimension(:,:), allocatable :: globalGridSizes
   type(t_Region) :: region
   type(t_Solver) :: solver
-  SCALAR_TYPE :: dummyValue
 
   ! Initialize MPI.
   call MPI_Init(ierror)

diff --git a/bin/Forward.f90 b/bin/Forward.f90
@@ -32,7 +32,6 @@ program forward
   type(t_Solver) :: solver
 
   ! << output variables >>
-  integer :: inputNumber, simulationNumber
   SCALAR_TYPE :: dummyValue = 0.0_wp
 
   ! Initialize MPI.

diff --git a/bin/Linearized_Forward.f90 b/bin/Linearized_Forward.f90
@@ -26,14 +26,12 @@ program linearized_forward
               inputFlag = .false., outputFlag = .false., saveMetricsFlag = .false.
   character(len = STRING_LENGTH) :: argument, inputFilename, outputFilename
   character(len = STRING_LENGTH) :: filename, outputPrefix, message
-  logical :: adjointRestart, fileExists, success
-  integer :: accumulatedNTimesteps
+  logical :: fileExists, success
   integer, dimension(:,:), allocatable :: globalGridSizes
-  type(t_Region) :: region, lineariedRegion
+  type(t_Region) :: region
   type(t_Solver) :: solver
 
   ! << output variables >>
-  integer :: inputNumber, simulationNumber
   SCALAR_TYPE :: dummyValue = 0.0_wp
 
   ! Initialize MPI.

diff --git a/bin/control_space_norm.f90 b/bin/control_space_norm.f90
@@ -20,17 +20,13 @@ program control_space_norm
   implicit none
 
   integer, parameter :: wp = SCALAR_KIND
-  integer :: i, stat, fileUnit, dictIndex, procRank, numProcs, ierror, STATUS
-  character(len = STRING_LENGTH) :: filename, resultFilename, outputPrefix, message
+  integer :: i, dictIndex, procRank, numProcs, ierror
+  character(len = STRING_LENGTH) :: filename, outputPrefix, message
   logical :: success
   integer, dimension(:,:), allocatable :: globalGridSizes
   type(t_Region) :: region
   type(t_Solver) :: solver
 
-  ! << output variables >>
-  integer :: inputNumber, simulationNumber
-  SCALAR_TYPE :: dummyValue = 0.0_wp
-
   ! Initialize MPI.
   call MPI_Init(ierror)
   call MPI_Comm_rank(MPI_COMM_WORLD, procRank, ierror)
@@ -169,8 +165,6 @@ subroutine collectControlSpaceNorm(this, region)
     class(t_TimeIntegrator), pointer :: timeIntegrator => null()
     class(t_Controller), pointer :: controller => null()
     class(t_Functional), pointer :: functional => null()
-    type(t_ReverseMigratorFactory) :: reverseMigratorFactory
-    class(t_ReverseMigrator), pointer :: reverseMigrator => null()
     integer :: i, j, timestep, startTimestep, timemarchDirection
     real(SCALAR_KIND) :: time, startTime, timeStepSize
 

diff --git a/bin/paste_control_forcing.f90 b/bin/paste_control_forcing.f90
@@ -86,13 +86,12 @@ subroutine pasteControlForcing(comm,ZFilename,XFilename,totalTimestep,startTimes
     integer, parameter :: wp = SCALAR_KIND
     integer :: i, procRank, numProcs, ierror, mpiFileHandle
     character(len = STRING_LENGTH) :: message
-    logical :: XFileExists, ZFileExists, success
-    integer(kind = MPI_OFFSET_KIND) :: XFileSize, ZFileSize, offset, globalOffset
+    logical :: XFileExists, ZFileExists
+    integer(kind = MPI_OFFSET_KIND) :: XFileSize, offset, globalOffset
 
     integer(kind = MPI_OFFSET_KIND) :: globalSize, patchSize, sliceSize, bufferSize, sendcnt, indexQuotient
     integer(kind = MPI_OFFSET_KIND), dimension(:), allocatable :: recvcnt, displc
     SCALAR_TYPE, dimension(:), allocatable :: XBuffer, ZBuffer
-    SCALAR_TYPE :: dummyValue
 
     ! Initialize MPI.
     call MPI_Comm_rank(comm, procRank, ierror)
@@ -230,87 +229,86 @@ subroutine pasteControlForcing(comm,ZFilename,XFilename,totalTimestep,startTimes
 
   end subroutine
 
-  subroutine createZeroControlForcing(comm,ZFilename,globalSize)
-
-    use MPI
-    use, intrinsic :: iso_fortran_env, only : output_unit
-
-    use InputHelper, only : parseInputFile, getOption, getRequiredOption
-    use ErrorHandler
-    use MPITimingsHelper, only : startTiming, endTiming, reportTimings, cleanupTimers
-
-    implicit none
-
-    ! <<< Arguments >>>
-    integer, intent(in) :: comm
-    integer(kind = MPI_OFFSET_KIND), intent(in) :: globalSize
-    character(len = *), intent(in) :: ZFilename
-
-    ! <<< Local variables >>>
-    integer, parameter :: wp = SCALAR_KIND
-    integer :: i, procRank, numProcs, ierror, mpiFileHandle
-    character(len = STRING_LENGTH) :: message
-    logical :: XFileExists, success
-    integer(kind = MPI_OFFSET_KIND) :: ZFileSize, offset, globalOffset
-
-    integer(kind = MPI_OFFSET_KIND) :: patchSize, sliceSize, bufferSize, sendcnt, indexQuotient
-    integer(kind = MPI_OFFSET_KIND), dimension(:), allocatable :: recvcnt, displc
-    SCALAR_TYPE, dimension(:), allocatable :: ZBuffer
-    SCALAR_TYPE :: dummyValue
-
-    ! Initialize MPI.
-    call MPI_Comm_rank(comm, procRank, ierror)
-    call MPI_Comm_size(comm, numProcs, ierror)
-
-    call startTiming("File name and size check")
-
-    write(message,'(3A)') "Creating zero ", trim(ZFilename), "... "
-    call writeAndFlush(comm, output_unit, message, advance = 'no')
-
-    call endTiming("File name and size check")
-    call startTiming("Buffer setup")
-
-    indexQuotient = MOD(globalSize,int(numProcs,MPI_OFFSET_KIND))
-    bufferSize = globalSize/int(numProcs,MPI_OFFSET_KIND)
-    allocate(recvcnt(0:numProcs-1))
-    allocate(displc(0:numProcs-1))
-    recvcnt(0:indexQuotient-1) = bufferSize+1
-    recvcnt(indexQuotient:numProcs-1) = bufferSize
-    displc = 0
-    do i=1,numProcs-1
-      displc(i) = SUM(recvcnt(0:i-1))
-    end do
-    offset = displc(procRank)*SIZEOF_SCALAR
-
-    if( procRank<indexQuotient ) then
-      sendcnt = bufferSize+1
-    else
-      sendcnt = bufferSize
-    end if
-    allocate(ZBuffer(sendcnt))
-    ZBuffer = 0.0_wp
-
-    call endTiming("Buffer setup")
-    call startTiming("Write file")
-
-    call MPI_Barrier(comm, ierror)
-
-    call MPI_File_open(comm, trim(ZFilename),                                 &
-                       MPI_MODE_WRONLY + MPI_MODE_CREATE, MPI_INFO_NULL,      &
-                       mpiFileHandle, ierror)
-    call MPI_FILE_SET_VIEW(mpiFileHandle,offset,MPI_DOUBLE,MPI_DOUBLE,        &
-                           'native',MPI_INFO_NULL,ierror)
-    call MPI_File_write_all(mpiFileHandle, ZBuffer, int(sendcnt),                   &
-                            SCALAR_TYPE_MPI, MPI_STATUS_IGNORE, ierror)
-    call MPI_File_close(mpiFileHandle, ierror)
-
-    call MPI_Barrier(comm, ierror)
-
-    call endTiming("Write file")
-
-    write(message, '(A)') " done!"
-    call writeAndFlush(comm, output_unit, message)
-
-  end subroutine
+  !NOTE: this subroutine is unused and thus commented out. Should be working.
+  ! subroutine createZeroControlForcing(comm,ZFilename,globalSize)
+  !
+  !   use MPI
+  !   use, intrinsic :: iso_fortran_env, only : output_unit
+  !
+  !   use InputHelper, only : parseInputFile, getOption, getRequiredOption
+  !   use ErrorHandler
+  !   use MPITimingsHelper, only : startTiming, endTiming, reportTimings, cleanupTimers
+  !
+  !   implicit none
+  !
+  !   ! <<< Arguments >>>
+  !   integer, intent(in) :: comm
+  !   integer(kind = MPI_OFFSET_KIND), intent(in) :: globalSize
+  !   character(len = *), intent(in) :: ZFilename
+  !
+  !   ! <<< Local variables >>>
+  !   integer, parameter :: wp = SCALAR_KIND
+  !   integer :: i, procRank, numProcs, ierror, mpiFileHandle
+  !   character(len = STRING_LENGTH) :: message
+  !   integer(kind = MPI_OFFSET_KIND) :: offset
+  !
+  !   integer(kind = MPI_OFFSET_KIND) :: bufferSize, sendcnt, indexQuotient
+  !   integer(kind = MPI_OFFSET_KIND), dimension(:), allocatable :: recvcnt, displc
+  !   SCALAR_TYPE, dimension(:), allocatable :: ZBuffer
+  !
+  !   ! Initialize MPI.
+  !   call MPI_Comm_rank(comm, procRank, ierror)
+  !   call MPI_Comm_size(comm, numProcs, ierror)
+  !
+  !   call startTiming("File name and size check")
+  !
+  !   write(message,'(3A)') "Creating zero ", trim(ZFilename), "... "
+  !   call writeAndFlush(comm, output_unit, message, advance = 'no')
+  !
+  !   call endTiming("File name and size check")
+  !   call startTiming("Buffer setup")
+  !
+  !   indexQuotient = MOD(globalSize,int(numProcs,MPI_OFFSET_KIND))
+  !   bufferSize = globalSize/int(numProcs,MPI_OFFSET_KIND)
+  !   allocate(recvcnt(0:numProcs-1))
+  !   allocate(displc(0:numProcs-1))
+  !   recvcnt(0:indexQuotient-1) = bufferSize+1
+  !   recvcnt(indexQuotient:numProcs-1) = bufferSize
+  !   displc = 0
+  !   do i=1,numProcs-1
+  !     displc(i) = SUM(recvcnt(0:i-1))
+  !   end do
+  !   offset = displc(procRank)*SIZEOF_SCALAR
+  !
+  !   if( procRank<indexQuotient ) then
+  !     sendcnt = bufferSize+1
+  !   else
+  !     sendcnt = bufferSize
+  !   end if
+  !   allocate(ZBuffer(sendcnt))
+  !   ZBuffer = 0.0_wp
+  !
+  !   call endTiming("Buffer setup")
+  !   call startTiming("Write file")
+  !
+  !   call MPI_Barrier(comm, ierror)
+  !
+  !   call MPI_File_open(comm, trim(ZFilename),                                 &
+  !                      MPI_MODE_WRONLY + MPI_MODE_CREATE, MPI_INFO_NULL,      &
+  !                      mpiFileHandle, ierror)
+  !   call MPI_FILE_SET_VIEW(mpiFileHandle,offset,MPI_DOUBLE,MPI_DOUBLE,        &
+  !                          'native',MPI_INFO_NULL,ierror)
+  !   call MPI_File_write_all(mpiFileHandle, ZBuffer, int(sendcnt),                   &
+  !                           SCALAR_TYPE_MPI, MPI_STATUS_IGNORE, ierror)
+  !   call MPI_File_close(mpiFileHandle, ierror)
+  !
+  !   call MPI_Barrier(comm, ierror)
+  ! 
+  !   call endTiming("Write file")
+  !
+  !   write(message, '(A)') " done!"
+  !   call writeAndFlush(comm, output_unit, message)
+  !
+  ! end subroutine
 
 end program paste_control_forcing
diff --git a/bin/patchup_qfile.f90 b/bin/patchup_qfile.f90
@@ -22,21 +22,17 @@ program patchup_qfile
   end type t_VectorInternal
 
   integer, parameter :: wp = SCALAR_KIND
-  integer :: i, j, stat, fileUnit, procRank, numProcs, ierror
+  integer :: i, j, procRank, numProcs, ierror
   integer :: kthArgument, numberOfArguments
   logical :: lookForInput = .false., inputFlag = .false.
   character(len = STRING_LENGTH) :: argument, inputFilename, mollifierFilename
   character(len = STRING_LENGTH) :: filename, outputPrefix, message,                                          &
-                                    Zfilename, Astr, Xfilename, Yfilename
+                                    Zfilename, Xfilename, Yfilename
   logical :: fileExists, zeroYfile = .false., success
   integer, dimension(:,:), allocatable :: globalGridSizes
   type(t_Region) :: region
   type(t_VectorInternal), allocatable :: X(:), Y(:), antiW(:)
 
-  ! << output variables >>
-  integer :: inputNumber, simulationNumber
-  SCALAR_TYPE :: A
-
   ! Initialize MPI.
   call MPI_Init(ierror)
   call MPI_Comm_rank(MPI_COMM_WORLD, procRank, ierror)

diff --git a/bin/qfile_zaxpy.f90 b/bin/qfile_zaxpy.f90
@@ -22,7 +22,7 @@ program qfile_zaxpy
   end type t_VectorInternal
 
   integer, parameter :: wp = SCALAR_KIND
-  integer :: i, j, stat, fileUnit, procRank, numProcs, ierror
+  integer :: i, j, procRank, numProcs, ierror
   integer :: kthArgument, numberOfArguments
   logical :: lookForInput = .false., lookForMollifier = .false.,                                              &
               inputFlag = .false., mollifierFlag = .false.
@@ -35,7 +35,6 @@ program qfile_zaxpy
   type(t_VectorInternal), allocatable :: X(:), Y(:)
 
   ! << output variables >>
-  integer :: inputNumber, simulationNumber
   SCALAR_TYPE :: A
 
   ! Initialize MPI.

diff --git a/bin/slice_control_forcing.f90 b/bin/slice_control_forcing.f90
@@ -72,13 +72,12 @@ subroutine sliceControlForcing(comm,ZFilename,XFilename,totalTimestep,startTimes
     integer, parameter :: wp = SCALAR_KIND
     integer :: i, procRank, numProcs, ierror, mpiFileHandle
     character(len = STRING_LENGTH) :: message
-    logical :: XFileExists, success
-    integer(kind = MPI_OFFSET_KIND) :: XFileSize, ZFileSize, offset, globalOffset
+    logical :: XFileExists
+    integer(kind = MPI_OFFSET_KIND) :: XFileSize, offset, globalOffset
 
     integer(kind = MPI_OFFSET_KIND) :: globalSize, patchSize, sliceSize, bufferSize, sendcnt, indexQuotient
     integer(kind = MPI_OFFSET_KIND), dimension(:), allocatable :: recvcnt, displc
     SCALAR_TYPE, dimension(:), allocatable :: XBuffer
-    SCALAR_TYPE :: dummyValue
 
     ! Initialize MPI.
     call MPI_Comm_rank(comm, procRank, ierror)

diff --git a/bin/spatial_inner_product.f90 b/bin/spatial_inner_product.f90
@@ -35,7 +35,6 @@ program spatial_inner_product
   type(t_VectorInternal), allocatable :: temp(:)
 
   ! << output variables >>
-  integer :: inputNumber, simulationNumber
   SCALAR_TYPE :: dummyValue = 0.0_wp
 
   ! Initialize MPI.

diff --git a/bin/terminal_objective.f90 b/bin/terminal_objective.f90
@@ -29,14 +29,12 @@ program terminal_objective
   integer :: mode
   character(len = STRING_LENGTH) :: argument, inputFilename, outputFilename
   character(len = STRING_LENGTH) :: filename, outputPrefix, message
-  logical :: adjointRestart, fileExists, success
-  integer :: accumulatedNTimesteps
+  logical :: fileExists, success
   integer, dimension(:,:), allocatable :: globalGridSizes
   type(t_Region) :: region
   type(t_Solver) :: solver
 
   ! << output variables >>
-  integer :: inputNumber, simulationNumber
   SCALAR_TYPE :: dummyValue = 0.0_wp
 
   ! Initialize MPI.
@@ -221,10 +219,9 @@ function runTerminalObjective(this, region, mode) result(instantaneousCostFuncti
     character(len = STRING_LENGTH) :: filename, message
     class(t_Functional), pointer :: functional => null()
     class(t_Patch), pointer :: patch => null()
-    integer :: i, j, timestep, startTimestep
-    real(wp) :: time, startTime, timeStepSize
-    logical :: controllerSwitch = .false., solutionCrashes = .false.,           &
-                nonzeroAdjointInitialCondition = .false.
+    integer :: i, j, startTimestep
+    real(wp) :: startTime
+    logical :: nonzeroAdjointInitialCondition = .false.
 
     call startTiming("runTerminalObjective")
 

diff --git a/bin/zXdotY.f90 b/bin/zXdotY.f90
@@ -13,7 +13,7 @@ program run_zXdotY
   implicit none
 
   integer, parameter :: wp = SCALAR_KIND
-  character(len = STRING_LENGTH) :: zFilename, WFilename, XFilename, YFilename, normFilename, message
+  character(len = STRING_LENGTH) :: zFilename, XFilename, YFilename, normFilename, message
   SCALAR_TYPE :: z
   integer :: stat, fileUnit, procRank, ierror
 

diff --git a/examples/DeformingWall2D/.gitignore b/examples/DeformingWall2D/.gitignore
@@ -0,0 +1,2 @@
+*.q
+*.f
diff --git a/examples/DeformingWall2D/bc.dat b/examples/DeformingWall2D/bc.dat
@@ -0,0 +1,10 @@
+# Name                 Type                  Grid normDir iMin iMax jMin jMax kMin kMax
+# ==================== ===================== ==== ======= ==== ==== ==== ==== ==== ====
+  farField.N           SAT_FAR_FIELD            1      -2    1   -1   -1   -1    1   -1
+  inflow.W             SAT_FAR_FIELD            1       1    1    1    1   -1    1   -1
+  outflow.E            SAT_FAR_FIELD            1      -1   -1   -1    1   -1    1   -1
+  immersed1            IMMERSED_BOUNDARY        1       0    1   -1    1  171    1   -1
+  sponge.N             SPONGE                   1      -2    1   -1  -15   -1    1   -1
+  sponge.W             SPONGE                   1       1    1   15    1   -1    1   -1
+  sponge.E             SPONGE                   1      -1  -15   -1    1   -1    1   -1
+#  targetRegion         COST_TARGET              1       2    1   -1    1    1    1   -1