Merge branch 'devel' into glads_gl

.github/workflows/build-macos-homebrew.yaml

@@ -86,6 +86,7 @@ jobs:
             -DCMAKE_Fortran_COMPILER=gfortran \
             -DCMAKE_INSTALL_PREFIX="${GITHUB_WORKSPACE}/usr" \
             -DBLA_VENDOR="OpenBLAS" \
+            -DUSE_MACOS_PACKAGE_MANAGER=OFF \
             -DCMAKE_PREFIX_PATH="$( [ "${{ matrix.openmp }}" == "with" ] && echo "${HOMEBREW_PREFIX}/opt/libomp;")${HOMEBREW_PREFIX}/opt/openblas;${HOMEBREW_PREFIX}/opt/qt;${HOMEBREW_PREFIX}/opt/qwt" \
             ${{ matrix.openmp == 'with'
               && '-DWITH_OpenMP=ON \

CMakeLists.txt

@@ -23,9 +23,12 @@ IF(APPLE)
   SET(CMAKE_MACOSX_RPATH 1)
 ENDIF()
 
+# Allow users to ignore package managers on macOS
+option(USE_MACOS_PACKAGE_MANAGER "Search for packages that are installed with Homebrew or MacPorts on macOS" ON)
+
 #shamelessly borrowed from FreeCAD project: https://github.com/FreeCAD/FreeCAD/blob/master/cMake/FreeCAD_Helpers/SetupPython.cmake
 # For building on OS X
-if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin" AND USE_MACOS_PACKAGE_MANAGER)
 
   # If the user doesn't tell us which package manager they're using
   if(NOT DEFINED MACPORTS_PREFIX AND NOT DEFINED HOMEBREW_PREFIX)

fem/src/Adaptive.F90

@@ -1085,7 +1085,8 @@ FUNCTION MMG_ReMesh( RefMesh, ErrorLimit, HValue, NodalError, &
     TYPE(Mesh_t), POINTER :: Mesh, TmpMesh, GatheredMesh
     INTEGER :: i,j,k,n,ierr
     REAL(KIND=dp) :: Lambda
-    CHARACTER(LEN=MAX_NAME_LEN) :: MeshCommand, Name, MeshInputFile
+    CHARACTER(LEN=MAX_NAME_LEN) :: MeshCommand, Name
+    CHARACTER(LEN=MAX_PATH_LEN) :: MeshInputFile
     LOGICAL :: Success, Rebalance, EnforceSerial
     REAL(KIND=dp) :: xmax, xmin, ymax, ymin, zmax, zmin, cscale
     LOGICAL :: ScaleCoord

fem/src/CMakeLists.txt

@@ -286,7 +286,8 @@ ENDIF()
 
 IF(WITH_AMGX)
   TARGET_LINK_LIBRARIES(elmersolver Elmer::MPI_C "${AMGX_LIBRARY};${CUDA_LIBRARIES}")
-ENDIF()  
+  TARGET_INCLUDE_DIRECTORIES(elmersolver PRIVATE "${CUDA_INCLUDE_DIRS}")
+ENDIF()
 
 IF(WITH_Trilinos)
   TARGET_LINK_LIBRARIES(elmersolver Elmer::MPI_CXX "${Trilinos_LIBRARIES};${ML_LIBRARIES};${Epetra_LIBRARIES};${Teuchos_LIBRARIES}")

fem/src/CRSMatrix.F90

@@ -3488,7 +3488,7 @@ FUNCTION CRS_IncompleteLU(A,ILUn) RESULT(Status)
     ELSE
       Values => A % Values
     END IF
-
+    
     IF ( .NOT. ASSOCIATED(A % ILUValues) ) THEN
 
        IF ( ILUn == 0 ) THEN
@@ -4987,10 +4987,7 @@ SUBROUTINE CRS_InspectMatrix( A )
     RowMax = MAXVAL( Rows )
     RowN = SIZE( Rows )
 
-    PRINT *,'Rows:'
-    PRINT *,'size:',RowN
-    PRINT *,'min:',RowMin
-    PRINT *,'max:',RowMax
+    PRINT *,'Rows (size '//I2S(RowN)//') range:',RowMin, RowMax
 
     IF( RowMin < 1 ) THEN
       PRINT *,'Outliers:'
@@ -5009,12 +5006,8 @@ SUBROUTINE CRS_InspectMatrix( A )
     ColMin = MINVAL( Cols )
     ColMax = MAXVAL( Cols )
     ColN = SIZE( Cols )
-
-    PRINT *,'Cols:'
-    PRINT *,'size:',ColN
-    PRINT *,'min:',ColMin
-    PRINT *,'max:',ColMax
-
+    PRINT *,'Cols (size '//I2S(ColN)//') range:',ColMin, ColMax
+
     IF( ColMin < 1 ) THEN
       PRINT *,'Outliers:'
       j = 0
@@ -5034,11 +5027,7 @@ SUBROUTINE CRS_InspectMatrix( A )
     ValN = SIZE( Values )
     TotalSum = SUM( Values )
 
-    PRINT *,'Values:'
-    PRINT *,'size:',ValN
-    PRINT *,'min:',ValMin
-    PRINT *,'max:',ValMax
-    PRINT *,'sum:',TotalSum
+    PRINT *,'Values (size '//I2S(ValN)//') range:',ValMin,ValMax,TotalSum
 
     IF( ColN /= RowMax - 1  ) THEN
       PRINT *,'Conflicting max row index :',n,RowMax-1

fem/src/DefUtils.F90

@@ -3613,6 +3613,7 @@ RECURSIVE SUBROUTINE DefaultStart( USolver )
          IF(SIZE(Solver % LocalSystem) < n ) DEALLOCATE(Solver % LocalSystem)
        END IF
        IF(.NOT. ASSOCIATED(Solver % LocalSystem ) ) THEN
+         CALL Info('DefaultStart','Allocating local storage of size: '//I2S(n),Level=7)
          ALLOCATE( Solver % LocalSystem(n) )
          Solver % LocalSystem(1:n) % eind = 0         
          ! If the stiffness matrix is constant the 1st element gives stiffness matrix for all!

fem/src/ElementDescription.F90

@@ -458,7 +458,7 @@ SUBROUTINE InitializeElementDescriptions()
 
       ! then the rest of them....
       !--------------------------
-      ALLOCATE(CHARACTER(MAX_STRING_LEN)::elmer_home)
+      ALLOCATE(CHARACTER(MAX_PATH_LEN)::elmer_home)
 
       tstr = 'ELMER_LIB'
       CALL envir( tstr,elmer_home,k ) 

fem/src/ElmerSolver.F90

@@ -99,8 +99,8 @@ SUBROUTINE ElmerSolver(initialize)
 
      TYPE(ParEnv_t), POINTER :: ParallelEnv
 
-     CHARACTER(LEN=MAX_NAME_LEN) :: ModelName, eq
-     CHARACTER(LEN=MAX_STRING_LEN) :: OptionString
+     CHARACTER(LEN=MAX_PATH_LEN) :: ModelName
+     CHARACTER(LEN=MAX_STRING_LEN) :: OptionString, eq
 
      CHARACTER(:), ALLOCATABLE :: str, PostFile, ExecCommand, OutputFile, RestartFile, &
           OutputName, PostName, When
@@ -125,7 +125,7 @@ SUBROUTINE ElmerSolver(initialize)
      INTEGER :: nr,ni,ExtMethod
      INTEGER, ALLOCATABLE :: ipar(:)
      REAL(KIND=dp), ALLOCATABLE :: rpar(:)
-     CHARACTER(LEN=MAX_NAME_LEN) :: MeshDir, MeshName
+     CHARACTER(LEN=MAX_PATH_LEN) :: MeshDir, MeshName
 
 #ifdef HAVE_TRILINOS
      INTERFACE
@@ -3760,7 +3760,7 @@ SUBROUTINE SaveToPost(CurrentStep)
     LOGICAL :: EigAnal = .FALSE., Found
     INTEGER :: i, j,k,l,n,q,CurrentStep,nlen,nlen2,timesteps,SavedEigenValues
     CHARACTER(LEN=MAX_NAME_LEN) :: Simul, SaveWhich
-    CHARACTER(MAX_NAME_LEN) :: OutputDirectory
+    CHARACTER(MAX_PATH_LEN) :: OutputDirectory
     TYPE(Solver_t), POINTER :: pSolver
 
     Simul = ListGetString( CurrentModel % Simulation,'Simulation Type' )

fem/src/MeshRemeshing.F90

@@ -1634,12 +1634,12 @@ SUBROUTINE RemeshMMG3D(Model, InMesh,OutMesh,EdgePairs,PairCount,&
     END IF
 
     IF(SaveMMGMeshes) THEN
-      WRITE(MeshName, '(A,i0,A)') TRIM(premmg_meshfile), time, '.mesh'
+      MeshName = TRIM(premmg_meshfile) // I2S(time) // '.mesh'
       CALL MMG3D_SaveMesh(mmgMesh,MeshName,LEN(TRIM(MeshName)),ierr)
     END IF
 
     IF(SaveMMGSols) THEN
-      WRITE(SolName, '(A,i0,A)') TRIM(premmg_solfile), time, '.sol'
+      SolName =  TRIM(premmg_solfile) // I2S(time) // '.sol'
       CALL MMG3D_SaveSol(mmgMesh, mmgSol,SolName,LEN(TRIM(SolName)),ierr)
     END IF
 
@@ -3072,7 +3072,7 @@ FUNCTION GET_MMG2D_MESH(MeshNumber,OutputFilename) RESULT(NewMesh)
     ! Initialize the new mesh stucture
     NewMesh => AllocateMesh(nt + nt0,na + na0,np + np0,ParEnv%PEs > 1)
     IF (MeshNumber > 0 ) THEN
-      WRITE(NewMesh % Name,'(A,A,I0)') TRIM(OutPutFileName),'_N',MeshNumber
+      NewMesh % Name = TRIM(OutPutFileName) // '_N' // I2S(MeshNumber)
     ELSE
       NewMesh % Name = TRIM(OutPutFileName)
     END IF

fem/src/ModelDescription.F90

@@ -72,7 +72,7 @@ FUNCTION GetProcAddr( str, Quiet, Abort ) RESULT( Proc )
 
     INTEGER(KIND=AddrInt) :: Proc
     INTEGER   :: i,j,slen,q,a
-    CHARACTER :: Libname(MAX_NAME_LEN),Procname(MAX_NAME_LEN)
+    CHARACTER :: Libname(MAX_PATH_LEN),Procname(MAX_NAME_LEN)
 !------------------------------------------------------------------------------
 
     DO slen=LEN(str),1,-1
@@ -279,7 +279,7 @@ FUNCTION ReloadInputFile( Model, RewindFile ) RESULT(got)
 
     INTEGER :: pos, posn
     INTEGER :: iostat
-    CHARACTER(LEN=MAX_NAME_LEN) :: MeshDir, MeshName
+    CHARACTER(LEN=MAX_PATH_LEN) :: MeshDir, MeshName
 
     IF( PRESENT( RewindFile ) ) THEN
       IF( RewindFile ) THEN
@@ -2543,7 +2543,7 @@ FUNCTION LoadModel( ModelName,BoundariesOnly,numprocs,mype,MeshIndex) RESULT( Mo
     INTEGER, TARGET :: Def_Dofs(10,6)
     REAL(KIND=dp) :: MeshPower
     REAL(KIND=dp), POINTER :: h(:)
-    CHARACTER(LEN=MAX_NAME_LEN) :: MeshDir,MeshName
+    CHARACTER(LEN=MAX_PATH_LEN) :: MeshDir,MeshName
     CHARACTER(:), ALLOCATABLE :: Name, ElementDef, str
     LOGICAL :: Parallel
     TYPE(valuelist_t), POINTER :: lst
@@ -3002,12 +3002,21 @@ FUNCTION LoadModel( ModelName,BoundariesOnly,numprocs,mype,MeshIndex) RESULT( Mo
       END IF
 
       i = i + 1
+      k = i
+      j = 0
+      DO WHILE( MeshName(i:i) /= CHAR(0) )
+        i = i + 1
+        j = j + 1
+      END DO
+
+      IF(ALLOCATED(Model % Meshes % Name)) DEALLOCATE(Model % Meshes % Name)
+      ALLOCATE(CHARACTER(j)::Model % Meshes % Name)
+      i = k
       k = 1
-      Model % Meshes % Name = ' '
       DO WHILE( MeshName(i:i) /= CHAR(0) )
         Model % Meshes % Name(k:k) = MeshName(i:i)
-        k = k + 1
         i = i + 1
+        k = k + 1
       END DO
 
       ! Ok, give name also to the parent meshes as they might be saved too
@@ -3245,9 +3254,18 @@ FUNCTION LoadModel( ModelName,BoundariesOnly,numprocs,mype,MeshIndex) RESULT( Mo
 
         IF ( OneMeshName ) i = 0
 
-        k = 1
         i = i + 1
-        Solver % Mesh % Name = ' '
+        k = i
+        j = 0
+        DO WHILE( MeshName(i:i) /= CHAR(0) )
+          j = j + 1
+          i = i + 1
+        END DO
+
+        IF(ALLOCATED(Solver % Mesh % Name)) DEALLOCATE(Solver % Mesh % Name)
+        ALLOCATE(CHARACTER(j)::Solver % Mesh % Name)
+        i = k
+        k = 1
         DO WHILE( MeshName(i:i) /= CHAR(0) )
           Solver % Mesh % Name(k:k) = MeshName(i:i)
           k = k + 1
@@ -3269,7 +3287,7 @@ FUNCTION LoadModel( ModelName,BoundariesOnly,numprocs,mype,MeshIndex) RESULT( Mo
     CALL SetCoordinateSystem( Model )
 
     IF ( OutputPath == ' ' ) THEN
-      DO i=1,MAX_NAME_LEN
+      DO i=1,MAX_PATH_LEN
         IF ( MeshDir(i:i) == CHAR(0) ) EXIT
         OutputPath(i:i) = MeshDir(i:i)
       END DO

fem/src/SOLVER.KEYWORDS

@@ -1087,6 +1087,7 @@ Solver:Logical:     'Convect'
 Solver:Logical:     'Convective'
 Solver:Logical:     'Coupled Solver'
 Solver:Logical:     'Cumulative Displacements'
+Solver:Logical:     'Darwin Model'
 Solver:Logical:     'Discontinuous Galerkin'
 Solver:Logical:     'Displace Mesh'
 Solver:Logical:     'Displaced Shape'
@@ -1734,7 +1735,6 @@ bc:logical:          '1d fluid coupling'
 bc:logical:          '1d structure coupling'
 body:logical:        'gap down mask'
 body:logical:        'gap up mask'
-material:real:       'elecric conductivity'
 simulation:integer:  'max output partition'
 simulation:integer:  'max output thread'
 simulation:logical:  'additive namespaces'

fem/src/SaveUtils.F90

@@ -936,7 +936,7 @@ SUBROUTINE SaveGmshOutput( Model,Solver,dt,Transient )
 
     INTEGER, PARAMETER :: LENGTH = 1024
     CHARACTER(LEN=LENGTH) :: Txt, FieldName, CompName
-    CHARACTER(MAX_NAME_LEN) :: OutputFile
+    CHARACTER(MAX_PATH_LEN) :: OutputFile
     CHARACTER(:), ALLOCATABLE :: OutputDirectory
     INTEGER :: GmshUnit
     CHARACTER(*), PARAMETER :: Caller = 'SaveGmshOutput'

fem/src/SolverUtils.F90

@@ -15245,21 +15245,21 @@ END SUBROUTINE AMGXSolve
           DO i=1,ParEnV % PEs
             IF(i-1==me .OR. .NOT. ParEnv % IsNeighbour(i)) CYCLE
 
-            CALL MPI_BSEND(SendTo(i),1,MPI_INTEGER,i-1,1200,ELMER_COMM_WORLD,status, ierr)
+            CALL MPI_BSEND(SendTo(i),1,MPI_INTEGER,i-1,1200,ELMER_COMM_WORLD, ierr)
             IF(Sendto(i)==0) CYCLE
 
             CALL MPI_BSEND(APerm(SendStuff(i) % Rows),SendTo(i),MPI_INTEGER,i-1, &
-                          1201,ELMER_COMM_WORLD,status,ierr )
+                          1201,ELMER_COMM_WORLD,ierr )
 
             CALL MPI_BSEND( SendStuff(i) % Size,SendTo(i),MPI_INTEGER,i-1, &
-                          1202,ELMER_COMM_WORLD,status,ierr )
+                          1202,ELMER_COMM_WORLD,ierr )
             DO j=1,SendTo(i)
               k = SendStuff(i) % Rows(j)
               CALL MPI_BSEND(APerm(A % Cols(A % Rows(k):A % Rows(k+1)-1)),SendStuff(i) % Size(j), &
-                         MPI_INTEGER,i-1, 1203,ELMER_COMM_WORLD, status, ierr )
+                         MPI_INTEGER,i-1, 1203,ELMER_COMM_WORLD, ierr )
 
               CALL MPI_BSEND(A % Values(A % Rows(k):A % Rows(k+1)-1),SendStuff(i) % Size(j), &
-                      MPI_DOUBLE_PRECISION,i-1,1204,ELMER_COMM_WORLD, status, ierr )
+                      MPI_DOUBLE_PRECISION,i-1,1204,ELMER_COMM_WORLD, ierr )
             END DO
           END DO
 

fem/src/Types.F90

@@ -54,7 +54,7 @@ MODULE Types
    USE Lua
    IMPLICIT NONE
 
-   INTEGER, PARAMETER :: MAX_NAME_LEN = 128, MAX_STRING_LEN=2048
+   INTEGER, PARAMETER :: MAX_NAME_LEN = 128, MAX_STRING_LEN=2048, MAX_PATH_LEN=4096
    ! Parameter for internal blocking
    INTEGER, PARAMETER :: VECTOR_BLOCK_LENGTH = 128
    ! Parameter for internally avoiding calls to BLAS
@@ -799,7 +799,7 @@ MODULE Types
    END TYPE FactorsStore_t 
 
    TYPE Mesh_t
-     CHARACTER(MAX_NAME_LEN) :: Name
+     CHARACTER(:), ALLOCATABLE :: Name
      TYPE(Mesh_t), POINTER   :: Next => NULL(), Parent => NULL(), Child => NULL()
 
      TYPE(Projector_t), POINTER :: Projector => NULL()

fem/src/modules/Isosurface.F90

@@ -363,14 +363,14 @@ SUBROUTINE IsosurfaceSolver( Model,Solver,dt,Transient )
   NoEdges = 0
   CALL Info('IsosurfaceSolver','Creating mesh edges',Level=9)
   IF (.NOT.ASSOCIATED(Mesh % Edges)) THEN
+    NoOrigBoundaryElements = Mesh % NumberOfBoundaryElements
+    Mesh % NumberOfBoundaryElements = 0
     IF( dim == 2 ) THEN
-      NoOrigBoundaryElements = Mesh % NumberOfBoundaryElements
-      Mesh % NumberOfBoundaryElements = 0
       CALL FindMeshEdges2D(Mesh)
-      Mesh % NumberOfBoundaryElements = NoOrigBoundaryElements
     ELSE
       CALL FindMeshEdges3D(Mesh)
     END IF
+    Mesh % NumberOfBoundaryElements = NoOrigBoundaryElements
   END IF
   NoEdges = Mesh % NumberOfEdges
 

fem/src/modules/MagnetoDynamics/WhitneyAVSolver.F90

@@ -367,7 +367,7 @@ SUBROUTINE WhitneyAVSolver( Model,Solver,dt,Transient )
   CHARACTER(LEN=MAX_NAME_LEN):: CoilCurrentName
   TYPE(Variable_t), POINTER :: CoilCurrentVar
   REAL(KIND=dp) :: CurrAmp
-  LOGICAL :: UseCoilCurrent, ElemCurrent, ElectroDynamics, EigenSystem
+  LOGICAL :: UseCoilCurrent, ElemCurrent, ElectroDynamics, Darwin, EigenSystem
 
   TYPE(ValueHandle_t), SAVE :: mu_h 
   TYPE(Solver_t), POINTER :: pSolver
@@ -395,6 +395,7 @@ SUBROUTINE WhitneyAVSolver( Model,Solver,dt,Transient )
   pSolver => Solver
 
   ElectroDynamics = ListGetLogical( SolverParams, 'Electrodynamics model', Found )
+  Darwin = ListGetLogical( SolverParams, 'Darwin model', Found )
   EigenSystem = ListGetLogical( SolverParams, 'Eigen Analysis', Found )
 
   CALL EdgeElementStyle(SolverParams, PiolaVersion, SecondOrder )
@@ -2154,7 +2155,7 @@ SUBROUTINE LocalMatrix( MASS, DAMP, STIFF, FORCE, JFixFORCE, JFixVec, LOAD, &
          ! All terms that are added here depend on the electrical conductivity or permittivity,
          ! so they have an effect on a conductor only.
          ! --------------------------------------------------------
-         CONDUCTOR: IF ( SUM(ABS(C)) > AEPS .OR. ElectroDynamics ) THEN
+         CONDUCTOR: IF ( SUM(ABS(C)) > AEPS .OR. ElectroDynamics .OR. Darwin) THEN
            IF ( Transient.OR.EigenSystem ) THEN
              DO p=1,np
                DO q=1,np
@@ -2167,6 +2168,9 @@ SUBROUTINE LocalMatrix( MASS, DAMP, STIFF, FORCE, JFixFORCE, JFixVec, LOAD, &
                  IF(ElectroDynamics) THEN
                    DAMP(p,q) = DAMP(p,q) + P_ip*SUM( dBasisdx(q,:)*dBasisdx(p,:) )*detJ*IP % s(t)
                  END IF
+                 IF (Darwin) THEN
+                   MASS(p,q) = MASS(p,q) + P_ip*SUM( dBasisdx(q,:)*dBasisdx(p,:) )*detJ*IP % s(t)
+                 END IF
                END DO
                DO j=1,nd-np
                  q = j+np
@@ -2188,6 +2192,9 @@ SUBROUTINE LocalMatrix( MASS, DAMP, STIFF, FORCE, JFixFORCE, JFixVec, LOAD, &
                  IF(ElectroDynamics) THEN
                    DAMP(q,p) = DAMP(q,p) + P_ip*SUM( dBasisdx(p,:)*WBasis(j,:) )*detJ*IP % s(t)
                  END IF
+                 IF (Darwin) THEN
+                   MASS(q,p) = MASS(q,p) + P_ip*SUM( dBasisdx(p,:)*WBasis(j,:) )*detJ*IP % s(t)
+                 END IF
                END DO
              END DO
 

fem/src/modules/ShellSolver.F90

@@ -942,7 +942,7 @@ SUBROUTINE ReadSurfaceDirector(MeshName, NumberOfNodes, SolverPars, Director, &
 !------------------------------------------------------------------------------
     IMPLICIT NONE
 
-    CHARACTER(LEN=MAX_NAME_LEN), INTENT(IN) :: MeshName
+    CHARACTER(LEN=*), INTENT(IN) :: MeshName
     INTEGER, INTENT(IN) :: NumberOfNodes
     TYPE(ValueList_t), POINTER, INTENT(IN) :: SolverPars
     TYPE(Variable_t), POINTER, INTENT(IN) :: Director
@@ -954,7 +954,8 @@ SUBROUTINE ReadSurfaceDirector(MeshName, NumberOfNodes, SolverPars, Director, &
     REAL(KIND=dp), POINTER :: NodalDirector(:,:)  
     REAL(KIND=dp), POINTER :: DirectorValues(:)
     REAL(KIND=dp) :: ElementDirectors(3*MaxBGElementNodes)
-    CHARACTER(LEN=MAX_NAME_LEN) :: DirectorFile, FormatString
+    CHARACTER(LEN=MAX_PATH_LEN) :: DirectorFile
+    CHARACTER(LEN=MAX_NAME_LEN) :: FormatString
     !------------------------------------------------------------------------------
     ReadNodalDirectors = .FALSE.