From e7a9da821ed033d709793146da87fafc788ec4c4 Mon Sep 17 00:00:00 2001
From: Corentin Prigent <corentin.prigent@u-bordeaux.fr>
Date: Tue, 16 Apr 2024 16:12:40 +0200
Subject: [PATCH 01/11] Introduced function PMMG_chkBdryTria

---
 src/analys_pmmg.c        |  4 ++--
 src/communicators_pmmg.c |  4 ++--
 src/hash_pmmg.c          | 49 ++++++++++++++++++++++++++++++++++++++++
 src/libparmmg.c          |  8 ++++---
 src/parmmg.h             |  5 ++--
 5 files changed, 61 insertions(+), 9 deletions(-)

diff --git a/src/analys_pmmg.c b/src/analys_pmmg.c
index 55726673..666cb59f 100644
--- a/src/analys_pmmg.c
+++ b/src/analys_pmmg.c
@@ -2327,7 +2327,7 @@ int PMMG_setdhd(PMMG_pParMesh parmesh,MMG5_pMesh mesh,MMG5_HGeom *pHash,MPI_Comm
  *
  * Check all boundary triangles.
  */
-int PMMG_analys_tria(PMMG_pParMesh parmesh,MMG5_pMesh mesh) {
+int PMMG_analys_tria(PMMG_pParMesh parmesh,MMG5_pMesh mesh, MMG5_int *permtria) {
   int       ier;
 
   /**--- stage 1: data structures for surface */
@@ -2362,7 +2362,7 @@ int PMMG_analys_tria(PMMG_pParMesh parmesh,MMG5_pMesh mesh) {
   }
 
   /* identify surface mesh */
-  if ( !MMG5_chkBdryTria(mesh) ) {
+  if ( !PMMG_chkBdryTria(mesh,permtria) ) {
     fprintf(stderr,"\n  ## Boundary problem. Exit program.\n");
     return 0;
   }
diff --git a/src/communicators_pmmg.c b/src/communicators_pmmg.c
index 0a8e3b46..0e47bd35 100644
--- a/src/communicators_pmmg.c
+++ b/src/communicators_pmmg.c
@@ -849,7 +849,7 @@ void PMMG_tria2elmFace_flags( PMMG_pParMesh parmesh ) {
  * - Store the index triplet in group communicator index 1,
  * - Tag corresponding triangle edges and nodes as PARBDY.
  */
-void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh ) {
+void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh, MMG5_int *permtria ) {
   PMMG_pGrp    grp;
   MMG5_pMesh   mesh;
   MMG5_pTria   ptt;
@@ -866,7 +866,7 @@ void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh ) {
   /* Process tria stored in index1 */
   for( i=0; i<grp->nitem_int_face_comm; i++ ) {
     kt    = grp->face2int_face_comm_index1[i];
-    ptt = &mesh->tria[kt];
+    ptt   = &mesh->tria[permtria[kt]];
     ie     = ptt->cc/4;
     ifac   = ptt->cc%4;
 
diff --git a/src/hash_pmmg.c b/src/hash_pmmg.c
index fc30f658..641f4675 100644
--- a/src/hash_pmmg.c
+++ b/src/hash_pmmg.c
@@ -275,6 +275,55 @@ int PMMG_bdryUpdate( MMG5_pMesh mesh )
   return PMMG_SUCCESS;
 }
 
+/**
+ * \param mesh pointer to the mesh structure.
+ * \return 1 if success, 0 otherwise.
+ *
+ * - Remove double triangles from tria array.
+ *
+ * - Remove triangles that do not belong to a boundary (non opnbdy mode) from
+ *   tria array.
+ *
+ * - Check the matching between actual and given number of faces in the mesh:
+ * Count the number of faces in mesh and compare this number to the number of
+ *   given triangles.
+ *
+ * - If the founded number exceed the given one, add the missing
+ *   boundary triangles (call to MMG5_bdryTria). Do nothing otherwise.
+ *
+ * - Fill the adjacency relationship between prisms and tetra (fill adjapr with
+ *   a negative value to mark this special faces).
+ *
+ * - Set to required the triangles at interface betwen prisms and tet.
+ *
+ */
+int PMMG_chkBdryTria(MMG5_pMesh mesh, MMG5_int* permtria) {
+  MMG5_int       ntmesh,ntpres;
+  int            ier;
+  MMG5_Hash      hashElt;
+
+  /** Step 1: scan the mesh and count the boundaries */
+  ier = MMG5_chkBdryTria_countBoundaries(mesh,&ntmesh,&ntpres);
+
+  /** Step 2: detect the extra boundaries (that will be ignored) provided by the
+   * user */
+  if ( mesh->nt ) {
+    ier = MMG5_chkBdryTria_hashBoundaries(mesh,ntmesh,&hashElt);
+    // Travel through the tria, flag those that are not in the hash tab or
+    // that are stored more that once.
+    ier = MMG5_chkBdryTria_flagExtraTriangles(mesh,&ntpres,&hashElt);
+    // Delete flagged triangles
+    ier = MMG5_chkBdryTria_deleteExtraTriangles(mesh, permtria);
+  }
+  ntmesh +=ntpres;
+
+  /** Step 3: add the missing boundary triangles or, if the mesh contains
+   * prisms, set to required the triangles at interface betwen prisms and tet */
+  ier = MMG5_chkBdryTria_addMissingTriangles(mesh,ntmesh,ntpres);
+
+  return 1;
+}
+
 /**
  * \param mesh pointer toward the mesh structure.
  * \param hash pointer toward the hash table of edges.
diff --git a/src/libparmmg.c b/src/libparmmg.c
index 4c6a3310..586bfdf1 100644
--- a/src/libparmmg.c
+++ b/src/libparmmg.c
@@ -243,6 +243,7 @@ int PMMG_preprocessMesh_distributed( PMMG_pParMesh parmesh )
   int8_t     tim;
   char       stim[32];
   mytime     ctim[TIMEMAX];
+  MMG5_int   *permtria;
   int ier = PMMG_SUCCESS;
 
   /* Chrono initialization */
@@ -342,8 +343,9 @@ int PMMG_preprocessMesh_distributed( PMMG_pParMesh parmesh )
 
   /** Mesh analysis I: Needed to create communicators
    *  Check triangles, create xtetras */
+  PMMG_CALLOC(parmesh,permtria,mesh->nt+1,MMG5_int,"permtria",return 0);
   if ( parmesh->myrank < parmesh->info.npartin ) {
-    if ( !PMMG_analys_tria(parmesh,mesh) ) {
+    if ( !PMMG_analys_tria(parmesh,mesh,permtria) ) {
       return PMMG_STRONGFAILURE;
     }
   }
@@ -358,7 +360,7 @@ int PMMG_preprocessMesh_distributed( PMMG_pParMesh parmesh )
        * each tria), and tag xtetra face as PARBDY before the tag is transmitted
        * to edges and nodes */
       if ( parmesh->myrank < parmesh->info.npartin ) {
-        PMMG_tria2elmFace_coords( parmesh );
+        PMMG_tria2elmFace_coords( parmesh, permtria );
       }
       /* 2) Build node communicators from face ones (here because the mesh needs
        *    to be unscaled) */
@@ -409,7 +411,7 @@ int PMMG_preprocessMesh_distributed( PMMG_pParMesh parmesh )
     /** Mesh analysis Ib : After LS discretization
      * Check triangles, create xtetras */
     if ( parmesh->myrank < parmesh->info.npartin ) {
-      if ( !PMMG_analys_tria(parmesh,mesh) ) {
+      if ( !PMMG_analys_tria(parmesh,mesh,permtria) ) {
         return PMMG_STRONGFAILURE;
       }
     }
diff --git a/src/parmmg.h b/src/parmmg.h
index 88941a4b..962d1330 100644
--- a/src/parmmg.h
+++ b/src/parmmg.h
@@ -445,7 +445,8 @@ void PMMG_Analys_Init_SurfNormIndex( MMG5_pTetra pt );
 int PMMG_Analys_Get_SurfNormalIndex( MMG5_pTetra pt,int ifac,int i );
 int PMMG_boulernm(PMMG_pParMesh parmesh,MMG5_pMesh mesh,MMG5_Hash *hash,int start,int ip,int *ng,int *nr);
 int PMMG_boulen(PMMG_pParMesh parmesh,MMG5_pMesh mesh,int start,int ip,int iface,double t[3]);
-int PMMG_analys_tria(PMMG_pParMesh parmesh,MMG5_pMesh mesh);
+int PMMG_analys_tria(PMMG_pParMesh parmesh,MMG5_pMesh mesh,MMG5_int *permtria);
+int PMMG_chkBdryTria(MMG5_pMesh mesh, MMG5_int* permtria);
 int PMMG_analys(PMMG_pParMesh parmesh,MMG5_pMesh mesh,MPI_Comm comm);
 int PMMG_update_analys(PMMG_pParMesh parmesh);
 int PMMG_hashPar( MMG5_pMesh mesh,MMG5_HGeom *pHash );
@@ -511,7 +512,7 @@ int PMMG_Compute_verticesGloNum( PMMG_pParMesh parmesh,MPI_Comm comm );
 int PMMG_Compute_trianglesGloNum( PMMG_pParMesh parmesh,MPI_Comm comm );
 int PMMG_color_commNodes( PMMG_pParMesh parmesh,MPI_Comm comm );
 void PMMG_tria2elmFace_flags( PMMG_pParMesh parmesh );
-void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh );
+void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh, MMG5_int *permtria );
 int PMMG_tria_highestcoord( MMG5_pMesh mesh, MMG5_int *v_t);
 int PMMG_build_nodeCommIndex( PMMG_pParMesh parmesh );
 int PMMG_build_faceCommIndex( PMMG_pParMesh parmesh );

From e347012b2df68db70523e5848a7f8c141744ec73 Mon Sep 17 00:00:00 2001
From: Corentin Prigent <corentin.prigent@u-bordeaux.fr>
Date: Thu, 18 Apr 2024 15:40:20 +0200
Subject: [PATCH 02/11] Take into account deletion of extra triangles when
 building internal communicators

---
 src/communicators_pmmg.c | 15 ++++++++++-----
 src/libparmmg.c          | 10 +++++++---
 src/parmmg.h             |  4 ++--
 3 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/src/communicators_pmmg.c b/src/communicators_pmmg.c
index 0e47bd35..49b62066 100644
--- a/src/communicators_pmmg.c
+++ b/src/communicators_pmmg.c
@@ -849,7 +849,7 @@ void PMMG_tria2elmFace_flags( PMMG_pParMesh parmesh ) {
  * - Store the index triplet in group communicator index 1,
  * - Tag corresponding triangle edges and nodes as PARBDY.
  */
-void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh, MMG5_int *permtria ) {
+void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh ) {
   PMMG_pGrp    grp;
   MMG5_pMesh   mesh;
   MMG5_pTria   ptt;
@@ -866,7 +866,7 @@ void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh, MMG5_int *permtria ) {
   /* Process tria stored in index1 */
   for( i=0; i<grp->nitem_int_face_comm; i++ ) {
     kt    = grp->face2int_face_comm_index1[i];
-    ptt   = &mesh->tria[permtria[kt]];
+    ptt    = &mesh->tria[kt];
     ie     = ptt->cc/4;
     ifac   = ptt->cc%4;
 
@@ -1008,7 +1008,7 @@ int PMMG_build_nodeCommIndex( PMMG_pParMesh parmesh ) {
  * stored in the external face communicator.
  *
  */
-int PMMG_build_faceCommIndex( PMMG_pParMesh parmesh ) {
+int PMMG_build_faceCommIndex( PMMG_pParMesh parmesh, MMG5_int* permtria ) {
   PMMG_pGrp      grp;
   PMMG_pInt_comm int_face_comm;
   PMMG_pExt_comm ext_face_comm;
@@ -1038,7 +1038,12 @@ int PMMG_build_faceCommIndex( PMMG_pParMesh parmesh ) {
   for( iext_comm = 0; iext_comm < parmesh->next_face_comm; iext_comm++ ) {
     ext_face_comm = &parmesh->ext_face_comm[iext_comm];
     for( iext = 0; iext < ext_face_comm->nitem; iext++ ) {
-      grp->face2int_face_comm_index1[iint] = ext_face_comm->int_comm_index[iext];
+      if (permtria) {
+        grp->face2int_face_comm_index1[iint] = permtria[ext_face_comm->int_comm_index[iext]];
+      }
+      else {
+        grp->face2int_face_comm_index1[iint] = ext_face_comm->int_comm_index[iext];
+      }
       grp->face2int_face_comm_index2[iint] = iint;
       ext_face_comm->int_comm_index[iext] = iint++;
     }
@@ -1214,7 +1219,7 @@ int PMMG_build_faceCommFromNodes( PMMG_pParMesh parmesh,MPI_Comm comm ) {
   }
 
   /** 6) Set communicators indexing, convert tria index into iel face index */
-  ier = PMMG_build_faceCommIndex( parmesh );
+  ier = PMMG_build_faceCommIndex( parmesh, NULL );
   PMMG_tria2elmFace_flags( parmesh );
 
 
diff --git a/src/libparmmg.c b/src/libparmmg.c
index 586bfdf1..59df5c73 100644
--- a/src/libparmmg.c
+++ b/src/libparmmg.c
@@ -344,23 +344,26 @@ int PMMG_preprocessMesh_distributed( PMMG_pParMesh parmesh )
   /** Mesh analysis I: Needed to create communicators
    *  Check triangles, create xtetras */
   PMMG_CALLOC(parmesh,permtria,mesh->nt+1,MMG5_int,"permtria",return 0);
+  MMG5_int k;
+  for (k=0;k<=mesh->nt+1;k++) {
+    permtria[k] = k;
+  }
   if ( parmesh->myrank < parmesh->info.npartin ) {
     if ( !PMMG_analys_tria(parmesh,mesh,permtria) ) {
       return PMMG_STRONGFAILURE;
     }
   }
-
   /* For both API modes, build communicators indices and set xtetra as PARBDY */
   switch( parmesh->info.API_mode ) {
     case PMMG_APIDISTRIB_faces :
       /* 1) Set face communicators indexing */
-      if( !PMMG_build_faceCommIndex( parmesh ) ) return 0;
+      if( !PMMG_build_faceCommIndex( parmesh, permtria ) ) return 0;
 
       /* Convert tria index into iel face index (it needs a valid cc field in
        * each tria), and tag xtetra face as PARBDY before the tag is transmitted
        * to edges and nodes */
       if ( parmesh->myrank < parmesh->info.npartin ) {
-        PMMG_tria2elmFace_coords( parmesh, permtria );
+        PMMG_tria2elmFace_coords( parmesh );
       }
       /* 2) Build node communicators from face ones (here because the mesh needs
        *    to be unscaled) */
@@ -385,6 +388,7 @@ int PMMG_preprocessMesh_distributed( PMMG_pParMesh parmesh )
       if ( !PMMG_build_faceCommFromNodes(parmesh,parmesh->info.read_comm) ) return PMMG_STRONGFAILURE;
       break;
   }
+  MMG5_SAFE_FREE( permtria );
 
   /** Discretization of the isovalue  */
   if (mesh->info.iso) {
diff --git a/src/parmmg.h b/src/parmmg.h
index 962d1330..bdad2bc5 100644
--- a/src/parmmg.h
+++ b/src/parmmg.h
@@ -512,10 +512,10 @@ int PMMG_Compute_verticesGloNum( PMMG_pParMesh parmesh,MPI_Comm comm );
 int PMMG_Compute_trianglesGloNum( PMMG_pParMesh parmesh,MPI_Comm comm );
 int PMMG_color_commNodes( PMMG_pParMesh parmesh,MPI_Comm comm );
 void PMMG_tria2elmFace_flags( PMMG_pParMesh parmesh );
-void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh, MMG5_int *permtria );
+void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh );
 int PMMG_tria_highestcoord( MMG5_pMesh mesh, MMG5_int *v_t);
 int PMMG_build_nodeCommIndex( PMMG_pParMesh parmesh );
-int PMMG_build_faceCommIndex( PMMG_pParMesh parmesh );
+int PMMG_build_faceCommIndex( PMMG_pParMesh parmesh, MMG5_int* permtria );
 int PMMG_build_nodeCommFromFaces( PMMG_pParMesh parmesh, MPI_Comm comm );
 int PMMG_build_faceCommFromNodes( PMMG_pParMesh parmesh, MPI_Comm comm );
 int PMMG_build_simpleExtNodeComm( PMMG_pParMesh parmesh );

From d7c21d121487e0dd07cf0159b9167aac483a9613 Mon Sep 17 00:00:00 2001
From: Corentin Prigent <corentin.prigent@u-bordeaux.fr>
Date: Thu, 25 Apr 2024 11:26:14 +0200
Subject: [PATCH 03/11] modified GIT_TAG to suitable mmg commit

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3011a98d..8082dea4 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -252,7 +252,7 @@ IF ( DOWNLOAD_MMG )
 
   EXTERNALPROJECT_ADD ( Mmg
     GIT_REPOSITORY https://github.com/MmgTools/mmg.git
-    GIT_TAG 5788cf5b872d6f2e627b4279260ac39706d2a7f6
+    GIT_TAG e89f046ce10e969b5d46af9eb058ec6dc43af2d8
     INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
     CMAKE_ARGS ${MMG_ARGS} -DUSE_ELAS=OFF ${COMPILER_CFG} ${FLAGS_CFG}
     ${SCOTCH_CFG} ${VTK_CFG} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}

From 483875d3a0111dd5e8e61ab9cebc15afebef047c Mon Sep 17 00:00:00 2001
From: Corentin Prigent <corentin.prigent@u-bordeaux.fr>
Date: Wed, 31 Jul 2024 16:58:05 +0200
Subject: [PATCH 04/11] deleted workflow

---
 .github/workflows/long-tests.yml | 30 ------------------------------
 1 file changed, 30 deletions(-)
 delete mode 100644 .github/workflows/long-tests.yml

diff --git a/.github/workflows/long-tests.yml b/.github/workflows/long-tests.yml
deleted file mode 100644
index be864006..00000000
--- a/.github/workflows/long-tests.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-name: Long tests
-
-on:
-  # run tests on push events
-  push:
-  # run tests on PR events
-  pull_request:
-    types: [opened, synchronize]
-
-  # run tests manually on a given branch (default is master)
-  workflow_dispatch:
-    # Inputs the workflow accepts.
-    inputs:
-      branch:
-        # branch to test
-        description: 'branch to test'
-        # Default value if no value is explicitly provided
-        default: 'master'
-        required: false
-
-# job
-jobs:
-  parmmg-debug:
-    uses: ./.github/workflows/main-job.yml
-    with:
-      cmake_build_type: RelWithAssert
-      add_cmake_cfg_args:
-      branch_name:  ${{github.event.inputs.branch}}
-      code_coverage: true
-    secrets: inherit

From b8c09599563d479b290f3ebf46fd4ad94c7d0ca3 Mon Sep 17 00:00:00 2001
From: Corentin Prigent <corentin.prigent@u-bordeaux.fr>
Date: Wed, 31 Jul 2024 16:59:22 +0200
Subject: [PATCH 05/11] copied workflow back

---
 .github/workflows/long-tests.yml | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 .github/workflows/long-tests.yml

diff --git a/.github/workflows/long-tests.yml b/.github/workflows/long-tests.yml
new file mode 100644
index 00000000..be864006
--- /dev/null
+++ b/.github/workflows/long-tests.yml
@@ -0,0 +1,30 @@
+name: Long tests
+
+on:
+  # run tests on push events
+  push:
+  # run tests on PR events
+  pull_request:
+    types: [opened, synchronize]
+
+  # run tests manually on a given branch (default is master)
+  workflow_dispatch:
+    # Inputs the workflow accepts.
+    inputs:
+      branch:
+        # branch to test
+        description: 'branch to test'
+        # Default value if no value is explicitly provided
+        default: 'master'
+        required: false
+
+# job
+jobs:
+  parmmg-debug:
+    uses: ./.github/workflows/main-job.yml
+    with:
+      cmake_build_type: RelWithAssert
+      add_cmake_cfg_args:
+      branch_name:  ${{github.event.inputs.branch}}
+      code_coverage: true
+    secrets: inherit

From 7a7994fb416256ebeb8f007dd60c3ec40d306ebe Mon Sep 17 00:00:00 2001
From: Corentin Prigent <corentin.prigent@u-bordeaux.fr>
Date: Tue, 16 Apr 2024 16:12:40 +0200
Subject: [PATCH 06/11] Introduced function PMMG_chkBdryTria

---
 src/analys_pmmg.c        |  4 ++--
 src/communicators_pmmg.c |  4 ++--
 src/hash_pmmg.c          | 49 ++++++++++++++++++++++++++++++++++++++++
 src/libparmmg.c          |  8 ++++---
 src/parmmg.h             |  5 ++--
 5 files changed, 61 insertions(+), 9 deletions(-)

diff --git a/src/analys_pmmg.c b/src/analys_pmmg.c
index 5e084eb0..2a56c56b 100644
--- a/src/analys_pmmg.c
+++ b/src/analys_pmmg.c
@@ -2403,7 +2403,7 @@ int PMMG_setdhd(PMMG_pParMesh parmesh,MMG5_pMesh mesh,MMG5_HGeom *pHash,MPI_Comm
  *
  * Check all boundary triangles.
  */
-int PMMG_analys_tria(PMMG_pParMesh parmesh,MMG5_pMesh mesh) {
+int PMMG_analys_tria(PMMG_pParMesh parmesh,MMG5_pMesh mesh, MMG5_int *permtria) {
   int       ier;
 
   /**--- stage 1: data structures for surface */
@@ -2438,7 +2438,7 @@ int PMMG_analys_tria(PMMG_pParMesh parmesh,MMG5_pMesh mesh) {
   }
 
   /* identify surface mesh */
-  if ( !MMG5_chkBdryTria(mesh) ) {
+  if ( !PMMG_chkBdryTria(mesh,permtria) ) {
     fprintf(stderr,"\n  ## Boundary problem. Exit program.\n");
     return 0;
   }
diff --git a/src/communicators_pmmg.c b/src/communicators_pmmg.c
index ad18fb13..8e3eec5e 100644
--- a/src/communicators_pmmg.c
+++ b/src/communicators_pmmg.c
@@ -849,7 +849,7 @@ void PMMG_tria2elmFace_flags( PMMG_pParMesh parmesh ) {
  * - Store the index triplet in group communicator index 1,
  * - Tag corresponding triangle edges and nodes as PARBDY.
  */
-void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh ) {
+void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh, MMG5_int *permtria ) {
   PMMG_pGrp    grp;
   MMG5_pMesh   mesh;
   MMG5_pTria   ptt;
@@ -866,7 +866,7 @@ void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh ) {
   /* Process tria stored in index1 */
   for( i=0; i<grp->nitem_int_face_comm; i++ ) {
     kt    = grp->face2int_face_comm_index1[i];
-    ptt = &mesh->tria[kt];
+    ptt   = &mesh->tria[permtria[kt]];
     ie     = ptt->cc/4;
     ifac   = ptt->cc%4;
 
diff --git a/src/hash_pmmg.c b/src/hash_pmmg.c
index fc30f658..641f4675 100644
--- a/src/hash_pmmg.c
+++ b/src/hash_pmmg.c
@@ -275,6 +275,55 @@ int PMMG_bdryUpdate( MMG5_pMesh mesh )
   return PMMG_SUCCESS;
 }
 
+/**
+ * \param mesh pointer to the mesh structure.
+ * \return 1 if success, 0 otherwise.
+ *
+ * - Remove double triangles from tria array.
+ *
+ * - Remove triangles that do not belong to a boundary (non opnbdy mode) from
+ *   tria array.
+ *
+ * - Check the matching between actual and given number of faces in the mesh:
+ * Count the number of faces in mesh and compare this number to the number of
+ *   given triangles.
+ *
+ * - If the founded number exceed the given one, add the missing
+ *   boundary triangles (call to MMG5_bdryTria). Do nothing otherwise.
+ *
+ * - Fill the adjacency relationship between prisms and tetra (fill adjapr with
+ *   a negative value to mark this special faces).
+ *
+ * - Set to required the triangles at interface betwen prisms and tet.
+ *
+ */
+int PMMG_chkBdryTria(MMG5_pMesh mesh, MMG5_int* permtria) {
+  MMG5_int       ntmesh,ntpres;
+  int            ier;
+  MMG5_Hash      hashElt;
+
+  /** Step 1: scan the mesh and count the boundaries */
+  ier = MMG5_chkBdryTria_countBoundaries(mesh,&ntmesh,&ntpres);
+
+  /** Step 2: detect the extra boundaries (that will be ignored) provided by the
+   * user */
+  if ( mesh->nt ) {
+    ier = MMG5_chkBdryTria_hashBoundaries(mesh,ntmesh,&hashElt);
+    // Travel through the tria, flag those that are not in the hash tab or
+    // that are stored more that once.
+    ier = MMG5_chkBdryTria_flagExtraTriangles(mesh,&ntpres,&hashElt);
+    // Delete flagged triangles
+    ier = MMG5_chkBdryTria_deleteExtraTriangles(mesh, permtria);
+  }
+  ntmesh +=ntpres;
+
+  /** Step 3: add the missing boundary triangles or, if the mesh contains
+   * prisms, set to required the triangles at interface betwen prisms and tet */
+  ier = MMG5_chkBdryTria_addMissingTriangles(mesh,ntmesh,ntpres);
+
+  return 1;
+}
+
 /**
  * \param mesh pointer toward the mesh structure.
  * \param hash pointer toward the hash table of edges.
diff --git a/src/libparmmg.c b/src/libparmmg.c
index 4c6a3310..586bfdf1 100644
--- a/src/libparmmg.c
+++ b/src/libparmmg.c
@@ -243,6 +243,7 @@ int PMMG_preprocessMesh_distributed( PMMG_pParMesh parmesh )
   int8_t     tim;
   char       stim[32];
   mytime     ctim[TIMEMAX];
+  MMG5_int   *permtria;
   int ier = PMMG_SUCCESS;
 
   /* Chrono initialization */
@@ -342,8 +343,9 @@ int PMMG_preprocessMesh_distributed( PMMG_pParMesh parmesh )
 
   /** Mesh analysis I: Needed to create communicators
    *  Check triangles, create xtetras */
+  PMMG_CALLOC(parmesh,permtria,mesh->nt+1,MMG5_int,"permtria",return 0);
   if ( parmesh->myrank < parmesh->info.npartin ) {
-    if ( !PMMG_analys_tria(parmesh,mesh) ) {
+    if ( !PMMG_analys_tria(parmesh,mesh,permtria) ) {
       return PMMG_STRONGFAILURE;
     }
   }
@@ -358,7 +360,7 @@ int PMMG_preprocessMesh_distributed( PMMG_pParMesh parmesh )
        * each tria), and tag xtetra face as PARBDY before the tag is transmitted
        * to edges and nodes */
       if ( parmesh->myrank < parmesh->info.npartin ) {
-        PMMG_tria2elmFace_coords( parmesh );
+        PMMG_tria2elmFace_coords( parmesh, permtria );
       }
       /* 2) Build node communicators from face ones (here because the mesh needs
        *    to be unscaled) */
@@ -409,7 +411,7 @@ int PMMG_preprocessMesh_distributed( PMMG_pParMesh parmesh )
     /** Mesh analysis Ib : After LS discretization
      * Check triangles, create xtetras */
     if ( parmesh->myrank < parmesh->info.npartin ) {
-      if ( !PMMG_analys_tria(parmesh,mesh) ) {
+      if ( !PMMG_analys_tria(parmesh,mesh,permtria) ) {
         return PMMG_STRONGFAILURE;
       }
     }
diff --git a/src/parmmg.h b/src/parmmg.h
index 57c6dd39..f058070f 100644
--- a/src/parmmg.h
+++ b/src/parmmg.h
@@ -447,7 +447,8 @@ void PMMG_Analys_Init_SurfNormIndex( MMG5_pTetra pt );
 int PMMG_Analys_Get_SurfNormalIndex( MMG5_pTetra pt,int ifac,int i );
 int PMMG_boulernm(PMMG_pParMesh parmesh,MMG5_pMesh mesh,MMG5_Hash *hash,int start,int ip,int *ng,int *nr);
 int PMMG_boulen(PMMG_pParMesh parmesh,MMG5_pMesh mesh,int start,int ip,int iface,double t[3]);
-int PMMG_analys_tria(PMMG_pParMesh parmesh,MMG5_pMesh mesh);
+int PMMG_analys_tria(PMMG_pParMesh parmesh,MMG5_pMesh mesh,MMG5_int *permtria);
+int PMMG_chkBdryTria(MMG5_pMesh mesh, MMG5_int* permtria);
 int PMMG_analys(PMMG_pParMesh parmesh,MMG5_pMesh mesh,MPI_Comm comm);
 int PMMG_update_analys(PMMG_pParMesh parmesh);
 int PMMG_hashPar( MMG5_pMesh mesh,MMG5_HGeom *pHash );
@@ -513,7 +514,7 @@ int PMMG_Compute_verticesGloNum( PMMG_pParMesh parmesh,MPI_Comm comm );
 int PMMG_Compute_trianglesGloNum( PMMG_pParMesh parmesh,MPI_Comm comm );
 int PMMG_color_commNodes( PMMG_pParMesh parmesh,MPI_Comm comm );
 void PMMG_tria2elmFace_flags( PMMG_pParMesh parmesh );
-void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh );
+void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh, MMG5_int *permtria );
 int PMMG_tria_highestcoord( MMG5_pMesh mesh, MMG5_int *v_t);
 int PMMG_build_nodeCommIndex( PMMG_pParMesh parmesh );
 int PMMG_build_faceCommIndex( PMMG_pParMesh parmesh );

From 95683ec7e0b4934fabcfbc0f45a1f39e192029d9 Mon Sep 17 00:00:00 2001
From: Corentin Prigent <corentin.prigent@u-bordeaux.fr>
Date: Thu, 18 Apr 2024 15:40:20 +0200
Subject: [PATCH 07/11] Take into account deletion of extra triangles when
 building internal communicators

---
 src/communicators_pmmg.c | 15 ++++++++++-----
 src/libparmmg.c          | 10 +++++++---
 src/parmmg.h             |  4 ++--
 3 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/src/communicators_pmmg.c b/src/communicators_pmmg.c
index 8e3eec5e..94b9518c 100644
--- a/src/communicators_pmmg.c
+++ b/src/communicators_pmmg.c
@@ -849,7 +849,7 @@ void PMMG_tria2elmFace_flags( PMMG_pParMesh parmesh ) {
  * - Store the index triplet in group communicator index 1,
  * - Tag corresponding triangle edges and nodes as PARBDY.
  */
-void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh, MMG5_int *permtria ) {
+void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh ) {
   PMMG_pGrp    grp;
   MMG5_pMesh   mesh;
   MMG5_pTria   ptt;
@@ -866,7 +866,7 @@ void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh, MMG5_int *permtria ) {
   /* Process tria stored in index1 */
   for( i=0; i<grp->nitem_int_face_comm; i++ ) {
     kt    = grp->face2int_face_comm_index1[i];
-    ptt   = &mesh->tria[permtria[kt]];
+    ptt    = &mesh->tria[kt];
     ie     = ptt->cc/4;
     ifac   = ptt->cc%4;
 
@@ -1008,7 +1008,7 @@ int PMMG_build_nodeCommIndex( PMMG_pParMesh parmesh ) {
  * stored in the external face communicator.
  *
  */
-int PMMG_build_faceCommIndex( PMMG_pParMesh parmesh ) {
+int PMMG_build_faceCommIndex( PMMG_pParMesh parmesh, MMG5_int* permtria ) {
   PMMG_pGrp      grp;
   PMMG_pInt_comm int_face_comm;
   PMMG_pExt_comm ext_face_comm;
@@ -1038,7 +1038,12 @@ int PMMG_build_faceCommIndex( PMMG_pParMesh parmesh ) {
   for( iext_comm = 0; iext_comm < parmesh->next_face_comm; iext_comm++ ) {
     ext_face_comm = &parmesh->ext_face_comm[iext_comm];
     for( iext = 0; iext < ext_face_comm->nitem; iext++ ) {
-      grp->face2int_face_comm_index1[iint] = ext_face_comm->int_comm_index[iext];
+      if (permtria) {
+        grp->face2int_face_comm_index1[iint] = permtria[ext_face_comm->int_comm_index[iext]];
+      }
+      else {
+        grp->face2int_face_comm_index1[iint] = ext_face_comm->int_comm_index[iext];
+      }
       grp->face2int_face_comm_index2[iint] = iint;
       ext_face_comm->int_comm_index[iext] = iint++;
     }
@@ -1214,7 +1219,7 @@ int PMMG_build_faceCommFromNodes( PMMG_pParMesh parmesh,MPI_Comm comm ) {
   }
 
   /** 6) Set communicators indexing, convert tria index into iel face index */
-  ier = PMMG_build_faceCommIndex( parmesh );
+  ier = PMMG_build_faceCommIndex( parmesh, NULL );
   PMMG_tria2elmFace_flags( parmesh );
 
 
diff --git a/src/libparmmg.c b/src/libparmmg.c
index 586bfdf1..59df5c73 100644
--- a/src/libparmmg.c
+++ b/src/libparmmg.c
@@ -344,23 +344,26 @@ int PMMG_preprocessMesh_distributed( PMMG_pParMesh parmesh )
   /** Mesh analysis I: Needed to create communicators
    *  Check triangles, create xtetras */
   PMMG_CALLOC(parmesh,permtria,mesh->nt+1,MMG5_int,"permtria",return 0);
+  MMG5_int k;
+  for (k=0;k<=mesh->nt+1;k++) {
+    permtria[k] = k;
+  }
   if ( parmesh->myrank < parmesh->info.npartin ) {
     if ( !PMMG_analys_tria(parmesh,mesh,permtria) ) {
       return PMMG_STRONGFAILURE;
     }
   }
-
   /* For both API modes, build communicators indices and set xtetra as PARBDY */
   switch( parmesh->info.API_mode ) {
     case PMMG_APIDISTRIB_faces :
       /* 1) Set face communicators indexing */
-      if( !PMMG_build_faceCommIndex( parmesh ) ) return 0;
+      if( !PMMG_build_faceCommIndex( parmesh, permtria ) ) return 0;
 
       /* Convert tria index into iel face index (it needs a valid cc field in
        * each tria), and tag xtetra face as PARBDY before the tag is transmitted
        * to edges and nodes */
       if ( parmesh->myrank < parmesh->info.npartin ) {
-        PMMG_tria2elmFace_coords( parmesh, permtria );
+        PMMG_tria2elmFace_coords( parmesh );
       }
       /* 2) Build node communicators from face ones (here because the mesh needs
        *    to be unscaled) */
@@ -385,6 +388,7 @@ int PMMG_preprocessMesh_distributed( PMMG_pParMesh parmesh )
       if ( !PMMG_build_faceCommFromNodes(parmesh,parmesh->info.read_comm) ) return PMMG_STRONGFAILURE;
       break;
   }
+  MMG5_SAFE_FREE( permtria );
 
   /** Discretization of the isovalue  */
   if (mesh->info.iso) {
diff --git a/src/parmmg.h b/src/parmmg.h
index f058070f..49573519 100644
--- a/src/parmmg.h
+++ b/src/parmmg.h
@@ -514,10 +514,10 @@ int PMMG_Compute_verticesGloNum( PMMG_pParMesh parmesh,MPI_Comm comm );
 int PMMG_Compute_trianglesGloNum( PMMG_pParMesh parmesh,MPI_Comm comm );
 int PMMG_color_commNodes( PMMG_pParMesh parmesh,MPI_Comm comm );
 void PMMG_tria2elmFace_flags( PMMG_pParMesh parmesh );
-void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh, MMG5_int *permtria );
+void PMMG_tria2elmFace_coords( PMMG_pParMesh parmesh );
 int PMMG_tria_highestcoord( MMG5_pMesh mesh, MMG5_int *v_t);
 int PMMG_build_nodeCommIndex( PMMG_pParMesh parmesh );
-int PMMG_build_faceCommIndex( PMMG_pParMesh parmesh );
+int PMMG_build_faceCommIndex( PMMG_pParMesh parmesh, MMG5_int* permtria );
 int PMMG_build_nodeCommFromFaces( PMMG_pParMesh parmesh, MPI_Comm comm );
 int PMMG_build_faceCommFromNodes( PMMG_pParMesh parmesh, MPI_Comm comm );
 int PMMG_build_simpleExtNodeComm( PMMG_pParMesh parmesh );

From 70c60773f55f1fd0a44ef8250360d49404210b0e Mon Sep 17 00:00:00 2001
From: Corentin Prigent <corentin.prigent@u-bordeaux.fr>
Date: Mon, 2 Sep 2024 15:28:25 +0200
Subject: [PATCH 08/11] Fixed wrong index range

---
 src/libparmmg.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/libparmmg.c b/src/libparmmg.c
index 59df5c73..a54ec25b 100644
--- a/src/libparmmg.c
+++ b/src/libparmmg.c
@@ -345,7 +345,7 @@ int PMMG_preprocessMesh_distributed( PMMG_pParMesh parmesh )
    *  Check triangles, create xtetras */
   PMMG_CALLOC(parmesh,permtria,mesh->nt+1,MMG5_int,"permtria",return 0);
   MMG5_int k;
-  for (k=0;k<=mesh->nt+1;k++) {
+  for (k=0;k<=mesh->nt;k++) {
     permtria[k] = k;
   }
   if ( parmesh->myrank < parmesh->info.npartin ) {

From b69a7870a1e776f390068fba122f275129b6f987 Mon Sep 17 00:00:00 2001
From: Corentin Prigent <corentin.prigent@u-bordeaux.fr>
Date: Tue, 3 Sep 2024 15:15:36 +0200
Subject: [PATCH 09/11] Added CI test for validating PR

---
 cmake/testing/pmmg_tests.cmake | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/cmake/testing/pmmg_tests.cmake b/cmake/testing/pmmg_tests.cmake
index 08e73f60..5798c845 100644
--- a/cmake/testing/pmmg_tests.cmake
+++ b/cmake/testing/pmmg_tests.cmake
@@ -434,6 +434,13 @@ IF( BUILD_TESTING )
       ${CI_DIR}/LevelSet/2p_toygeom/cube-distributed-faces-nomat-1edge.mesh -v 10 -hsiz 0.1
       -out ${CI_DIR_RESULTS}/update-ref-tag.o.mesh)
 
+    # Test to check that when not using -opnbdy option, internal triangles are correctly removed.
+    # See ParMmg PR#110
+    add_test( NAME extrainternaltriangles
+      COMMAND ${MPIEXEC} ${MPI_ARGS} ${MPIEXEC_NUMPROC_FLAG} 3 $<TARGET_FILE:${PROJECT_NAME}>
+      ${CI_DIR}/Cube/internaltriangles-P3.mesh -v 10
+      -out ${CI_DIR_RESULTS}/internaltriangles-P3.o.mesh)
+
     ###############################################################################
     #####
     #####        Test isovalue mode - ls discretization

From 48862c0720e552ff32b79ba33b7824e1f3a0f2b3 Mon Sep 17 00:00:00 2001
From: Corentin Prigent <corentin.prigent@u-bordeaux.fr>
Date: Tue, 3 Sep 2024 16:27:56 +0200
Subject: [PATCH 10/11] Modified commit tag of testparmmg

---
 cmake/testing/pmmg_tests.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/testing/pmmg_tests.cmake b/cmake/testing/pmmg_tests.cmake
index 5798c845..da85754f 100644
--- a/cmake/testing/pmmg_tests.cmake
+++ b/cmake/testing/pmmg_tests.cmake
@@ -21,7 +21,7 @@ IF( BUILD_TESTING )
       ENDIF()
       EXECUTE_PROCESS(
         COMMAND ${GIT_EXECUTABLE} -C ${CI_DIR} fetch
-        COMMAND ${GIT_EXECUTABLE} -C ${CI_DIR} checkout 0b1fce5e92fd42514fd75e8542ff67adeb6d77f8
+        COMMAND ${GIT_EXECUTABLE} -C ${CI_DIR} checkout a8b02c1196945bab072664f4f30f053dabb2639c
         TIMEOUT 20
         WORKING_DIRECTORY ${CI_DIR}
         #COMMAND_ECHO STDOUT

From 8668151935afcf8f1443964f64ab70539c4c9b84 Mon Sep 17 00:00:00 2001
From: Algiane Froehly <algiane.froehly@inria.fr>
Date: Thu, 12 Sep 2024 15:12:11 +0200
Subject: [PATCH 11/11] Remove ununsed function

In a first place, Luca, that implemented the // analysis, guessed that some part of the analysis (such as the analysis of non-manifold situations)  were not
possible at the beginning of the process and have to be updated after interface migration. Finally, the non-manifold analysis is done during the pre-processing step and the 'update_nmgeom' function is not called anymore and can be removed.
---
 src/analys_pmmg.c | 109 ----------------------------------------------
 1 file changed, 109 deletions(-)

diff --git a/src/analys_pmmg.c b/src/analys_pmmg.c
index 5e084eb0..003b6b93 100644
--- a/src/analys_pmmg.c
+++ b/src/analys_pmmg.c
@@ -1477,115 +1477,6 @@ int PMMG_hashNorver( PMMG_pParMesh parmesh,MMG5_pMesh mesh,MMG5_HGeom *hash,
   return 1;
 }
 
-/**
- * \param parmesh pointer to the parmesh structure
- * \param mesh pointer to the mesh structure
- *
- * \return 1 if success, 0 if failure.
- *
- * Compute continuous geometric support (normal and tangent vectors) on
- * non-manifold MG_OLDPARBDY points.
- *
- * \remark Analogous to the MMG3D_nmgeom function, but it only travels on
- * old parallel points.
- * \remark Normal and tangent vectors on these points are overwritten.
- *
- */
-int PMMG_update_nmgeom(PMMG_pParMesh parmesh,MMG5_pMesh mesh){
-  MMG5_pTetra     pt;
-  MMG5_pPoint     p0;
-  MMG5_pxPoint    pxp;
-  int             k,base;
-  int             *adja;
-  double          n[3],t[3];
-  int             ip;
-  int8_t          i,j,ier;
-
-  for( ip = 1; ip <= mesh->np; ip++ ) {
-    mesh->point[ip].flag = mesh->base;
-  }
-
-  base = ++mesh->base;
-  for (k=1; k<=mesh->ne; k++) {
-    pt   = &mesh->tetra[k];
-    if( !MG_EOK(pt) ) continue;
-    adja = &mesh->adja[4*(k-1)+1];
-    for (i=0; i<4; i++) {
-      if ( adja[i] ) continue;
-      for (j=0; j<3; j++) {
-        ip = MMG5_idir[i][j];
-        p0 = &mesh->point[pt->v[ip]];
-        if ( p0->flag == base )  continue;
-        else if ( !(p0->tag & MG_OLDPARBDY) ) continue;
-        else if ( !(p0->tag & MG_NOM) )  continue;
-
-        p0->flag = base;
-        ier = MMG5_boulenm(mesh,k,ip,i,n,t);
-
-        if ( ier < 0 )
-          return 0;
-        else if ( !ier ) {
-          p0->tag |= MG_REQ;
-          p0->tag &= ~MG_NOSURF;
-        }
-        else {
-          if ( !p0->xp ) {
-            ++mesh->xp;
-            if(mesh->xp > mesh->xpmax){
-              MMG5_TAB_RECALLOC(mesh,mesh->xpoint,mesh->xpmax,MMG5_GAP,MMG5_xPoint,
-                                 "larger xpoint table",
-                                 mesh->xp--;
-                                 fprintf(stderr,"  Exit program.\n");return 0;);
-            }
-            p0->xp = mesh->xp;
-          }
-          pxp = &mesh->xpoint[p0->xp];
-          memcpy(pxp->n1,n,3*sizeof(double));
-          memcpy(p0->n,t,3*sizeof(double));
-        }
-      }
-    }
-  }
-  /* Deal with the non-manifold points that do not belong to a surface
-   * tetra (a tetra that has a face without adjacent)*/
-  for (k=1; k<=mesh->ne; k++) {
-    pt   = &mesh->tetra[k];
-    if( !MG_EOK(pt) ) continue;
-    
-    for (i=0; i<4; i++) {
-      p0 = &mesh->point[pt->v[i]];
-      if ( !(p0->tag & MG_OLDPARBDY) ) continue;
-      else if ( p0->tag & MG_PARBDY || p0->tag & MG_REQ || !(p0->tag & MG_NOM) || p0->xp ) continue;
-      ier = MMG5_boulenmInt(mesh,k,i,t);
-      if ( ier ) {
-        ++mesh->xp;
-        if(mesh->xp > mesh->xpmax){
-          MMG5_TAB_RECALLOC(mesh,mesh->xpoint,mesh->xpmax,MMG5_GAP,MMG5_xPoint,
-                            "larger xpoint table",
-                            mesh->xp--;
-                            fprintf(stderr,"  Exit program.\n");return 0;);
-        }
-        p0->xp = mesh->xp;
-        pxp = &mesh->xpoint[p0->xp];
-        memcpy(p0->n,t,3*sizeof(double));
-      }
-      else {
-        p0->tag |= MG_REQ;
-        p0->tag &= ~MG_NOSURF;
-      }
-    }
-  }
-
-  /*for (k=1; k<=mesh->np; k++) {
-    p0 = &mesh->point[k];
-    if ( !(p0->tag & MG_NOM) || p0->xp ) continue;
-    p0->tag |= MG_REQ;
-    p0->tag &= ~MG_NOSURF;
-  }*/
-  
-  return 1;
-}
-
 static inline
 int MMG5_skip_nonOldParBdy ( int8_t tag ) {
   return !(tag & MG_OLDPARBDY);