From 7eede71b3a63307f3833378555141424da39f6aa Mon Sep 17 00:00:00 2001
From: "U-INTERNAL\\LROSLG" <LROSLG@CPNL070074.Internal.lr.org>
Date: Thu, 12 Sep 2013 10:25:07 +0200
Subject: [PATCH] Updated the CGNS read tp DMPlex function. Corrected loop
 counters and hexahedra cones. Also added counter to the
 coordinate reading for proper multi dimensional reads.

---
 src/dm/impls/plex/plexcgns.c |   35 ++++++++++++-----------------------
 1 files changed, 12 insertions(+), 23 deletions(-)

diff --git a/src/dm/impls/plex/plexcgns.c b/src/dm/impls/plex/plexcgns.c
index d2a2505..04c3bf6 100644
--- a/src/dm/impls/plex/plexcgns.c
+++ b/src/dm/impls/plex/plexcgns.c
@@ -101,7 +101,7 @@ PetscErrorCode DMPlexCreateCGNS(MPI_Comm comm, PetscInt cgid, PetscBool interpol
         ierr = cg_ElementDataSize(cgid, 1, z, 1, &elementDataSize);CHKERRQ(ierr);
         ierr = PetscMalloc(elementDataSize * sizeof(cgsize_t), &elements);CHKERRQ(ierr);
         ierr = cg_elements_read(cgid, 1, z, 1, elements, NULL);CHKERRQ(ierr);
-        for (c_loc = start, off = 0; c_loc < end; ++c_loc, ++c) {
+        for (c_loc = start, off = 0; c_loc <= end; ++c_loc, ++c) {
           switch (elements[off]) {
           case TRI_3:   numCorners = 3;break;
           case QUAD_4:  numCorners = 4;break;
@@ -121,7 +121,7 @@ PetscErrorCode DMPlexCreateCGNS(MPI_Comm comm, PetscInt cgid, PetscBool interpol
         case HEXA_8:  numCorners = 8;break;
         default: SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid cell type %d", (int) cellType);
         }
-        for (c_loc = start; c_loc < end; ++c_loc, ++c) {
+        for (c_loc = start; c_loc <= end; ++c_loc, ++c) {
           ierr = DMPlexSetConeSize(*dm, c, numCorners);CHKERRQ(ierr);
         }
       }
@@ -129,7 +129,7 @@ PetscErrorCode DMPlexCreateCGNS(MPI_Comm comm, PetscInt cgid, PetscBool interpol
     ierr = DMSetUp(*dm);CHKERRQ(ierr);
     for (z = 1, c = 0; z <= nzones; ++z) {
       ElementType_t cellType;
-      cgsize_t     *elements, elementDataSize, start, end;
+      cgsize_t     *elements, elementDataSize, start, end, subCellType;
       int           nbndry, parentFlag;
       PetscInt     *cone, numc, numCorners, maxCorners = 27;
 
@@ -141,8 +141,9 @@ PetscErrorCode DMPlexCreateCGNS(MPI_Comm comm, PetscInt cgid, PetscBool interpol
       ierr = cg_elements_read(cgid, 1, z, 1, elements, NULL);CHKERRQ(ierr);
       if (cellType == MIXED) {
         /* CGNS uses Fortran-based indexing, sieve uses C-style and numbers cell first then vertices. */
-        for (c_loc = 0, v = 0; c_loc < numc; ++c_loc, ++c) {
-          switch (elements[v]) {
+        for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) {
+          subCellType = elements[v];
+          switch (subCellType) {
           case TRI_3:   numCorners = 3;break;
           case QUAD_4:  numCorners = 4;break;
           case TETRA_4: numCorners = 4;break;
@@ -153,18 +154,12 @@ PetscErrorCode DMPlexCreateCGNS(MPI_Comm comm, PetscInt cgid, PetscBool interpol
           for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) {
             cone[v_loc] = elements[v]+numCells-1;
           }
-          /* Tetrahedra are inverted */
-          if (cellType == TETRA_4) {
+          /* Tetrahedra and hexahedra are inverted */
+          if (subCellType == TETRA_4 || subCellType == HEXA_8) {
             PetscInt tmp = cone[0];
             cone[0] = cone[1];
             cone[1] = tmp;
           }
-          /* Hexahedra are inverted */
-          if (cellType == HEXA_8) {
-            PetscInt tmp = cone[1];
-            cone[1] = cone[3];
-            cone[3] = tmp;
-          }
           ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr);
           ierr = DMPlexSetLabelValue(*dm, "zone", c, z);CHKERRQ(ierr);
         }
@@ -178,22 +173,16 @@ PetscErrorCode DMPlexCreateCGNS(MPI_Comm comm, PetscInt cgid, PetscBool interpol
         }
 
         /* CGNS uses Fortran-based indexing, sieve uses C-style and numbers cell first then vertices. */
-        for (c_loc = 0, v = 0; c_loc < numc; ++c_loc, ++c) {
+        for (c_loc = 0, v = 0; c_loc <= numc; ++c_loc, ++c) {
           for (v_loc = 0; v_loc < numCorners; ++v_loc, ++v) {
             cone[v_loc] = elements[v]+numCells-1;
           }
-          /* Tetrahedra are inverted */
-          if (cellType == TETRA_4) {
+          /* Tetrahedra and hexahedra are inverted */
+          if (cellType == TETRA_4 || cellType == HEXA_8) {
             PetscInt tmp = cone[0];
             cone[0] = cone[1];
             cone[1] = tmp;
           }
-          /* Hexahedra are inverted */
-          if (cellType == HEXA_8) {
-            PetscInt tmp = cone[1];
-            cone[1] = cone[3];
-            cone[3] = tmp;
-          }
           ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr);
           ierr = DMPlexSetLabelValue(*dm, "zone", c, z);CHKERRQ(ierr);
         }
@@ -255,7 +244,7 @@ PetscErrorCode DMPlexCreateCGNS(MPI_Comm comm, PetscInt cgid, PetscBool interpol
       ierr = cg_ncoords(cgid, 1, z, &ncoords);CHKERRQ(ierr);
       if (ncoords != dim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"CGNS file must have a coordinate array for each dimension, not %d\n",ncoords);
       for (d = 0; d < dim; ++d) {
-        ierr = cg_coord_info(cgid, 1, z, 1, &datatype, buffer);CHKERRQ(ierr);
+        ierr = cg_coord_info(cgid, 1, z, 1+d, &datatype, buffer);CHKERRQ(ierr);
         ierr = cg_coord_read(cgid, 1, z, buffer, RealSingle, range_min, range_max, x[d]);CHKERRQ(ierr);
       }
       if (dim > 0) {
-- 
1.7.9