From 665dd3020da1a1d45a7631e25ed7433825d4966b Mon Sep 17 00:00:00 2001 From: Sharan Roongta Date: Fri, 4 Dec 2020 03:30:39 +0100 Subject: [PATCH 1/9] new gmsh version --- PRIVATE | 2 +- src/mesh/discretization_mesh.f90 | 14 ++++++++------ 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/PRIVATE b/PRIVATE index 68cde5229..113f44413 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit 68cde52291ebb683ca6f610879f2ae28372597a7 +Subproject commit 113f44413c88e9b577f3781012592ea9a4836458 diff --git a/src/mesh/discretization_mesh.f90 b/src/mesh/discretization_mesh.f90 index 7dbd05e46..d998c84db 100644 --- a/src/mesh/discretization_mesh.f90 +++ b/src/mesh/discretization_mesh.f90 @@ -69,7 +69,7 @@ subroutine discretization_mesh_init(restart) integer, allocatable, dimension(:) :: chunkPos integer :: dimPlex, & mesh_Nnodes, & !< total number of nodes in mesh - j, l, & + j, l, k, & debug_element, debug_ip PetscSF :: sf DM :: globalMesh @@ -96,7 +96,6 @@ subroutine discretization_mesh_init(restart) debug_element = config_debug%get_asInt('element',defaultVal=1) debug_ip = config_debug%get_asInt('integrationpoint',defaultVal=1) - call DMPlexCreateFromFile(PETSC_COMM_WORLD,interface_geomFile,PETSC_TRUE,globalMesh,ierr) CHKERRQ(ierr) call DMGetDimension(globalMesh,dimPlex,ierr) @@ -137,11 +136,14 @@ subroutine discretization_mesh_init(restart) l = l + 1 if (trim(fileContent(l)) == '$EndElements') exit chunkPos = IO_stringPos(fileContent(l)) - if (chunkPos(1) == 3+IO_intValue(fileContent(l),chunkPos,3)+dimPlex+1) then - call DMSetLabelValue(globalMesh,'material',j,IO_intValue(fileContent(l),chunkPos,4),ierr) - CHKERRQ(ierr) - j = j + 1 + if(IO_intValue(fileContent(l),chunkPos,1) == 3) then + do k = 1, IO_intValue(fileContent(l),chunkPos,4) + call DMSetLabelValue(globalMesh,'material',j,IO_intValue(fileContent(l),chunkPos,2),ierr) + CHKERRQ(ierr) + j = j + 1 + enddo endif + l = l + IO_intValue(fileContent(l),chunkPos,4) enddo exit endif From 579d2a91471d6b8735bf0ccc1b8a819989077042 Mon Sep 17 00:00:00 2001 From: Sharan Roongta Date: Fri, 4 Dec 2020 13:05:54 +0100 Subject: [PATCH 2/9] test file updated --- PRIVATE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PRIVATE b/PRIVATE index 113f44413..df8eb2621 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit 113f44413c88e9b577f3781012592ea9a4836458 +Subproject commit df8eb262174f2e07b3c5d6a8655022940c9fc5c9 From f563313ce97c61720d0daafe6f01498278e964fe Mon Sep 17 00:00:00 2001 From: Sharan Roongta Date: Sat, 5 Dec 2020 23:52:30 +0100 Subject: [PATCH 3/9] PETSc provides subroutine to read physical tags --- src/mesh/discretization_mesh.f90 | 47 ++++++++++---------------------- 1 file changed, 14 insertions(+), 33 deletions(-) diff --git a/src/mesh/discretization_mesh.f90 b/src/mesh/discretization_mesh.f90 index d998c84db..69c86798e 100644 --- a/src/mesh/discretization_mesh.f90 +++ b/src/mesh/discretization_mesh.f90 @@ -83,6 +83,7 @@ subroutine discretization_mesh_init(restart) class(tNode), pointer :: & num_mesh integer :: integrationOrder !< order of quadrature rule required + print'(/,a)', ' <<<+- discretization_mesh init -+>>>' @@ -96,12 +97,16 @@ subroutine discretization_mesh_init(restart) debug_element = config_debug%get_asInt('element',defaultVal=1) debug_ip = config_debug%get_asInt('integrationpoint',defaultVal=1) + ! vol_tag = 10 call DMPlexCreateFromFile(PETSC_COMM_WORLD,interface_geomFile,PETSC_TRUE,globalMesh,ierr) CHKERRQ(ierr) call DMGetDimension(globalMesh,dimPlex,ierr) CHKERRQ(ierr) call DMGetStratumSize(globalMesh,'depth',dimPlex,mesh_NcpElemsGlobal,ierr) CHKERRQ(ierr) + call DMView(globalMesh, PETSC_VIEWER_STDOUT_WORLD,ierr) + CHKERRQ(ierr) + ! get number of IDs in face sets (for boundary conditions?) call DMGetLabelSize(globalMesh,'Face Sets',mesh_Nboundaries,ierr) CHKERRQ(ierr) @@ -109,6 +114,14 @@ subroutine discretization_mesh_init(restart) call MPI_Bcast(mesh_NcpElemsGlobal,1,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr) call MPI_Bcast(dimPlex,1,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr) + if (worldrank == 0) then + call DMClone(globalMesh,geomMesh,ierr) + CHKERRQ(ierr) + else + call DMPlexDistribute(globalMesh,0,sf,geomMesh,ierr) + CHKERRQ(ierr) + endif + allocate(mesh_boundaries(mesh_Nboundaries), source = 0) call DMGetLabelSize(globalMesh,'Face Sets',nFaceSets,ierr) CHKERRQ(ierr) @@ -123,38 +136,6 @@ subroutine discretization_mesh_init(restart) endif call MPI_Bcast(mesh_boundaries,mesh_Nboundaries,MPI_INTEGER,0,PETSC_COMM_WORLD,ierr) - if (worldrank == 0) then - fileContent = IO_readlines(interface_geomFile) - l = 0 - do - l = l + 1 - if (IO_isBlank(fileContent(l))) cycle ! need also to ignore C and C++ style comments? - if (trim(fileContent(l)) == '$Elements') then - j = 0 - l = l + 1 - do - l = l + 1 - if (trim(fileContent(l)) == '$EndElements') exit - chunkPos = IO_stringPos(fileContent(l)) - if(IO_intValue(fileContent(l),chunkPos,1) == 3) then - do k = 1, IO_intValue(fileContent(l),chunkPos,4) - call DMSetLabelValue(globalMesh,'material',j,IO_intValue(fileContent(l),chunkPos,2),ierr) - CHKERRQ(ierr) - j = j + 1 - enddo - endif - l = l + IO_intValue(fileContent(l),chunkPos,4) - enddo - exit - endif - enddo - call DMClone(globalMesh,geomMesh,ierr) - CHKERRQ(ierr) - else - call DMPlexDistribute(globalMesh,0,sf,geomMesh,ierr) - CHKERRQ(ierr) - endif - call DMDestroy(globalMesh,ierr); CHKERRQ(ierr) call DMGetStratumSize(geomMesh,'depth',dimPlex,mesh_NcpElems,ierr) @@ -169,7 +150,7 @@ subroutine discretization_mesh_init(restart) allocate(materialAt(mesh_NcpElems)) do j = 1, mesh_NcpElems - call DMGetLabelValue(geomMesh,'material',j-1,materialAt(j),ierr) + call DMGetLabelValue(geomMesh,'Cell Sets',j-1,materialAt(j),ierr) CHKERRQ(ierr) end do From 21faee4eaa9f5dddfa11f68a6795906eff55e9f5 Mon Sep 17 00:00:00 2001 From: Sharan Roongta Date: Mon, 7 Dec 2020 13:03:18 +0100 Subject: [PATCH 4/9] '0' based indexing --- PRIVATE | 2 +- src/mesh/discretization_mesh.f90 | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/PRIVATE b/PRIVATE index df8eb2621..899f0ae9e 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit df8eb262174f2e07b3c5d6a8655022940c9fc5c9 +Subproject commit 899f0ae9e25ddad62530ec8a9381cf520aad083b diff --git a/src/mesh/discretization_mesh.f90 b/src/mesh/discretization_mesh.f90 index 69c86798e..0a9c5adaa 100644 --- a/src/mesh/discretization_mesh.f90 +++ b/src/mesh/discretization_mesh.f90 @@ -97,7 +97,6 @@ subroutine discretization_mesh_init(restart) debug_element = config_debug%get_asInt('element',defaultVal=1) debug_ip = config_debug%get_asInt('integrationpoint',defaultVal=1) - ! vol_tag = 10 call DMPlexCreateFromFile(PETSC_COMM_WORLD,interface_geomFile,PETSC_TRUE,globalMesh,ierr) CHKERRQ(ierr) call DMGetDimension(globalMesh,dimPlex,ierr) @@ -153,6 +152,7 @@ subroutine discretization_mesh_init(restart) call DMGetLabelValue(geomMesh,'Cell Sets',j-1,materialAt(j),ierr) CHKERRQ(ierr) end do + materialAt(:) = materialAt(:) + 1 if (debug_element < 1 .or. debug_element > mesh_NcpElems) call IO_error(602,ext_msg='element') if (debug_ip < 1 .or. debug_ip > mesh_maxNips) call IO_error(602,ext_msg='IP') From 7ac8fa307818d14c8cc56473f0991ad45feae669 Mon Sep 17 00:00:00 2001 From: Sharan Roongta Date: Thu, 7 Jan 2021 16:37:28 +0100 Subject: [PATCH 5/9] updated PRIVATE --- PRIVATE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PRIVATE b/PRIVATE index 899f0ae9e..76f383c4e 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit 899f0ae9e25ddad62530ec8a9381cf520aad083b +Subproject commit 76f383c4e57cb41b55de9aad4d9baf209a91633d From 52aaf2fa5e73d205703925e9645cd5d4301bd943 Mon Sep 17 00:00:00 2001 From: Sharan Roongta Date: Thu, 7 Jan 2021 17:04:30 +0100 Subject: [PATCH 6/9] not needed --- src/mesh/discretization_mesh.f90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/mesh/discretization_mesh.f90 b/src/mesh/discretization_mesh.f90 index 67b061fa4..1320d2609 100644 --- a/src/mesh/discretization_mesh.f90 +++ b/src/mesh/discretization_mesh.f90 @@ -68,7 +68,7 @@ subroutine discretization_mesh_init(restart) integer, allocatable, dimension(:) :: chunkPos integer :: dimPlex, & mesh_Nnodes, & !< total number of nodes in mesh - j, l, k, & + j, l, & debug_element, debug_ip PetscSF :: sf DM :: globalMesh From 0d291235b0242b6f751e71c0d1aa3a4a73429c66 Mon Sep 17 00:00:00 2001 From: Sharan Roongta Date: Fri, 8 Jan 2021 18:14:36 +0100 Subject: [PATCH 7/9] updated PRIVATE --- PRIVATE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PRIVATE b/PRIVATE index 76f383c4e..9282365fd 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit 76f383c4e57cb41b55de9aad4d9baf209a91633d +Subproject commit 9282365fd54ccff1e8e57f4ea38967d733a4adc0 From dc55aa002a05c48ded960260e933d3cfe05f961d Mon Sep 17 00:00:00 2001 From: Sharan Roongta Date: Tue, 12 Jan 2021 14:13:26 +0100 Subject: [PATCH 8/9] updated test repo --- PRIVATE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PRIVATE b/PRIVATE index 9282365fd..f6fd3227e 160000 --- a/PRIVATE +++ b/PRIVATE @@ -1 +1 @@ -Subproject commit 9282365fd54ccff1e8e57f4ea38967d733a4adc0 +Subproject commit f6fd3227ec0f9c03fbf991bf7f8732b22ae96530 From c01fbe79bec51716ed92dfb3749a88fa0398c01f Mon Sep 17 00:00:00 2001 From: Test User Date: Wed, 13 Jan 2021 19:31:03 +0100 Subject: [PATCH 9/9] [skip ci] updated version information after successful test of v3.0.0-alpha2-279-g8182c9c54 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 364cb0e13..6e2dff56f 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v3.0.0-alpha2-258-g715504ee5 +v3.0.0-alpha2-279-g8182c9c54