Discontinuous galerkin

CMakeLists.txt

@@ -10,7 +10,7 @@ SET(Seacas_ENABLE_Zoltan_DEFAULT ON)
 SET(TRIBITS_HIDE_DEPRECATED_INCLUDE_DIRECTORIES_OVERRIDE TRUE)
 
 # Define the TriBITS minimum required CMake version
-SET(TRIBITS_CMAKE_MINIMUM_REQUIRED 3.17.0)
+SET(TRIBITS_CMAKE_MINIMUM_REQUIRED 3.22.0)
 
 # CMake requires this be in the top file and not in an include file :-(
 CMAKE_MINIMUM_REQUIRED(VERSION ${TRIBITS_CMAKE_MINIMUM_REQUIRED} FATAL_ERROR)

TPL/netcdf/runcmake.sh

@@ -67,6 +67,7 @@ cmake .. -DCMAKE_C_COMPILER:FILEPATH=${CC} \
          -DENABLE_MMAP:BOOL=ON \
          -DENABLE_DAP:BOOL=OFF \
          -DENABLE_BYTERANGE:BOOL=OFF \
+	 -DENABLE_NCZARR:BOOL=OFF \
          -DENABLE_V2_API:BOOL=OFF \
 	 -DENABLE_FILTER_TESTING:BOOL=OFF \
 	 -DENABLE_TESTS:BOOL=OFF \

packages/seacas/CMakeLists.txt

@@ -18,6 +18,7 @@ TRIBITS_ADD_OPTION_AND_DEFINE(
 set(${PROJECT_NAME}_C_Standard_DEFAULT c99)
 
 SET(${PROJECT_NAME}_CMAKE_CXX_STANDARD_DEFAULT 17)
+SET(CMAKE_CXX_STANDARD 17)
 SET(${PROJECT_NAME}_CMAKE_CXX_STANDARDS_ALLOWED "(14|17|20)")
 ADVANCED_SET(CMAKE_CXX_STANDARD ${${PROJECT_NAME}_CMAKE_CXX_STANDARD_DEFAULT}
   CACHE STRING

packages/seacas/README.md

@@ -13,4 +13,3 @@ Sandia National Laboratories,
 We appreciate feedback from users of this package.  Please send
 comments, suggestions, and bug reports to Greg Sjaardema
 <[email protected]>, <[email protected]>
-

packages/seacas/applications/blot/bl_version.f

@@ -1,4 +1,4 @@
-C Copyright(C) 1999-2020 National Technology & Engineering Solutions
+C Copyright(C) 1999-2020, 2024 National Technology & Engineering Solutions
 C of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
 C NTESS, the U.S. Government retains certain rights in this software.
 C
@@ -11,8 +11,8 @@ SUBROUTINE VERSION(QAINFO)
       CHARACTER*(MXQARC) QAINFO(6)
 
       QAINFO(1) = 'blot                            '
-      QAINFO(2) = '2021/03/31                      '
-      QAINFO(3) = ' 3.141                          '
+      QAINFO(2) = '2024/03/25                      '
+      QAINFO(3) = ' 3.1415                         '
       QAINFO(4) = '                                '
 
       RETURN

packages/seacas/applications/blot/matfac.f

@@ -1,4 +1,4 @@
-C Copyright(C) 1999-2020 National Technology & Engineering Solutions
+C Copyright(C) 1999-2020, 2024 National Technology & Engineering Solutions
 C of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
 C NTESS, the U.S. Government retains certain rights in this software.
 C
@@ -101,6 +101,6 @@ INTEGER FUNCTION MATFAC (LINKF1, MAXNPF, NPFS, iel, numnp, IERR)
 
   160 CONTINUE
       RETURN
-10000  FORMAT (' Poss. Contiguity Prob. at Hex ', I7,
-     *  ', Nodes ', 4(I7,1X), 10(I7,1X))
+10000  FORMAT (' Poss. Contiguity Prob. at Hex ', I11,
+     *  ', Nodes ', 4(I11,1X), 10(I11,1X))
       END

packages/seacas/applications/blot/scaprt.f

@@ -1,4 +1,4 @@
-C Copyright(C) 1999-2020 National Technology & Engineering Solutions
+C Copyright(C) 1999-2020, 2024 National Technology & Engineering Solutions
 C of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
 C NTESS, the U.S. Government retains certain rights in this software.
 C
@@ -94,7 +94,7 @@ SUBROUTINE SCAPRT (NAMECO, NAME, IVAR, TIMES,
      &            STIM(2)(:LTIM), NUMMAX, ISTMAX
 10000           FORMAT (4X, A7, 1X, A, 3X, 2 (1X, A),
      &            4X, A, 3X, A4, 3X, A4)
-10010           FORMAT (4X, A7, 1X, A, 3X, 2 (1X, A), 4X, A, I7, I7)
+10010           FORMAT (4X, A7, 1X, A, 3X, 2 (1X, A), 4X, A, I11, I11)
             ELSE
                WRITE (*, 10020) 'Range: ', SVAL(0)(:LVAL),
      &            SXYZ0(1)(:LX), SXYZ0(2)(:LY), SXYZ0(3)(:LZ),

packages/seacas/applications/grepos/gp_mapvar.f

@@ -49,6 +49,7 @@ subroutine mapvar(nold, nnew, nvar, map, vars, scr)
 
       do 30 ivar = 1, nvar
         do 10 i = 1, nnew
+           write (*,*) i, map(i)
           scr(i) = vars(map(i) + nold * (ivar-1) )
  10     continue
 

packages/seacas/applications/nem_slice/elb.h

@@ -211,7 +211,7 @@ template <typename INT> struct Graph_Description
   std::vector<INT>              adj{};
   std::vector<INT>              start{};
   std::vector<std::vector<INT>> sur_elem;
-  Graph_Description<INT>() = default;
+  Graph_Description() = default;
 };
 
 /* Various constants */

packages/seacas/applications/slice/SL_Decompose.C

@@ -45,6 +45,24 @@ extern double seacas_timer();
 extern void   progress(const std::string &output);
 
 namespace {
+  char **get_name_array(size_t count, int size)
+  {
+    auto *names = new char *[count];
+    for (size_t i = 0; i < count; i++) {
+      names[i] = new char[size + 1];
+      std::memset(names[i], '\0', size + 1);
+    }
+    return names;
+  }
+
+  void delete_name_array(char **names, int count)
+  {
+    for (int i = 0; i < count; i++) {
+      delete[] names[i];
+    }
+    delete[] names;
+  }
+
   template <typename INT>
   void create_adjacency_list(const Ioss::Region &region, std::vector<idx_t> &pointer,
                              std::vector<idx_t> &adjacency, INT)
@@ -684,7 +702,7 @@ std::vector<int> decompose_elements(const Ioss::Region &region, SystemInterface
     if (map_count > 0) {
       int max_name_length = ex_inquire_int(exoid, EX_INQ_DB_MAX_USED_NAME_LENGTH);
       max_name_length     = max_name_length < 32 ? 32 : max_name_length;
-      char **names        = Ioss::Utils::get_name_array(map_count, max_name_length);
+      char **names        = get_name_array(map_count, max_name_length);
       int    error        = ex_get_names(exoid, EX_ELEM_MAP, names);
       if (error < 0) {
         exodus_error(__LINE__);
@@ -701,7 +719,7 @@ std::vector<int> decompose_elements(const Ioss::Region &region, SystemInterface
           break;
         }
       }
-      Ioss::Utils::delete_name_array(names, map_count);
+      delete_name_array(names, map_count);
     }
 
     if (!map_read) {

packages/seacas/cmake/Dependencies.cmake

@@ -4,7 +4,7 @@ TRIBITS_PACKAGE_DEFINE_DEPENDENCIES(
   Exodus_for  libraries/exodus_for    PT  OPTIONAL
   ExoIIv2for32 libraries/exoIIv2for32 PT  OPTIONAL
   Nemesis     libraries/nemesis       PT  OPTIONAL
-  Ioss        libraries/ioss          PT  REQUIRED
+  Ioss        libraries/ioss          PT  OPTIONAL
   Chaco       libraries/chaco         PT  OPTIONAL
   Aprepro_lib libraries/aprepro_lib   PT  OPTIONAL
   Supes       libraries/supes         PT  OPTIONAL

packages/seacas/libraries/exodus/CMakeLists.txt

@@ -35,6 +35,7 @@ TRIBITS_ADD_LIBRARY(
 )
 
 set_property(TARGET exodus PROPERTY C_STANDARD 99)
+set_property(TARGET exodus PROPERTY C_EXTENSIONS ON)
 
 if (SEACASExodus_ENABLE_SHARED)
    if (NOT BUILD_SHARED_LIBS)

packages/seacas/libraries/exodus/include/exodus-element-types.md

@@ -78,7 +78,7 @@ library, the IOSS library, nem_slice, and nem_spread.
  |       | 64  |  X   |    X  |           |    |
 
 Only the base topology name is required for the element type. For example, all
-elements of a `hex` toplogy can be referred to by the name `hex` no
+elements of a `hex` topology can be referred to by the name `hex` no
 matter how many nodes there are.  However, it is also correct to
 append the node count to the topology type for the element name.  For
 example, a 20-node hex could be named `hex20`.

packages/seacas/libraries/exodus/include/exodusII.h

@@ -47,6 +47,9 @@
 #include <stdint.h>
 #include <stdlib.h>
 
+/** Maximum length of name permitted by NetCDF */
+#define EX_MAX_NAME NC_MAX_NAME
+
 #ifndef NC_INT64
 #error "NetCDF version 4.1.2 or later is required."
 #endif
@@ -282,6 +285,98 @@ enum ex_entity_type {
 };
 typedef enum ex_entity_type ex_entity_type;
 
+enum ex_field_type {
+  EX_FIELD_TYPE_INVALID = 0,
+  EX_FIELD_TYPE_USER_DEFINED,
+  EX_FIELD_TYPE_SEQUENCE,
+  EX_BASIS,
+  EX_QUADRATURE,
+  EX_SCALAR,
+  EX_VECTOR_1D,
+  EX_VECTOR_2D,
+  EX_VECTOR_3D,
+  EX_QUATERNION_2D,
+  EX_QUATERNION_3D,
+  EX_FULL_TENSOR_36,
+  EX_FULL_TENSOR_32,
+  EX_FULL_TENSOR_22,
+  EX_FULL_TENSOR_16,
+  EX_FULL_TENSOR_12,
+  EX_SYM_TENSOR_33,
+  EX_SYM_TENSOR_31,
+  EX_SYM_TENSOR_21,
+  EX_SYM_TENSOR_13,
+  EX_SYM_TENSOR_11,
+  EX_SYM_TENSOR_10,
+  EX_ASYM_TENSOR_03,
+  EX_ASYM_TENSOR_02,
+  EX_ASYM_TENSOR_01,
+  EX_MATRIX_2X2,
+  EX_MATRIX_3X3
+};
+typedef enum ex_field_type ex_field_type;
+
+#define EX_MAX_FIELD_NESTING 2
+typedef struct ex_field
+{
+  ex_entity_type entity_type;
+  int64_t        entity_id;
+  char           name[EX_MAX_NAME + 1]; /* Name of the field */
+  /*
+   * For basis, user, quadrature -- what is name of the subtype. This
+   * is a comma-separated list of `nesting` names Use two consecutive
+   * commas for an empty type_name. Leave empty if no type_names
+   */
+  int           nesting; /* Number of composite fields (vector at each quadrature point = 2) */
+  char          type_name[EX_MAX_NAME + 1];
+  ex_field_type type[EX_MAX_FIELD_NESTING];                /* ex_field_type of each nested field */
+  int           cardinality[EX_MAX_FIELD_NESTING];         /* 0 to calculate based on type */
+  char          component_separator[EX_MAX_FIELD_NESTING]; /* empty defaults to '_'; */
+  char          suffices[EX_MAX_NAME + 1]; /* Optional comma-separated list of suffices if type is
+                                              EX_FIELD_TYPE_USER_DEFINED */
+} ex_field;
+
+typedef struct ex_basis
+{
+  /*
+   clang-format off
+   *
+   * subc_dim: dimension of the subcell associated with the specified DoF ordinal 
+   *      -- 0 node, 1 edge, 2 face, 3 volume [Range: 0..3]
+   * subc_ordinal: ordinal of the subcell relative to its parent cell
+   *      -- 0..n for each ordinal with the same subc dim [Range: <= DoF ordinal] 
+   * subc_dof_ordinal: ordinal of the DoF relative to the subcell 
+   * subc_num_dof: cardinality of the DoF set associated with this subcell. 
+   * xi, eta, mu (ξ, η, ζ): Parametric coordinate location of the DoF 
+   *      -- (Only first ndim values are valid)
+   *
+   clang-format on
+   */
+
+  char    name[EX_MAX_NAME + 1];
+  int     cardinality; /* number of `basis` points == dimension of non-null subc_*, xi, eta, mu */
+  int    *subc_dim;
+  int    *subc_ordinal;
+  int    *subc_dof_ordinal;
+  int    *subc_num_dof;
+  double *xi;
+  double *eta;
+  double *zeta;
+} ex_basis;
+
+typedef struct ex_quadrature
+{
+  char    name[EX_MAX_NAME + 1];
+  int     cardinality; /* Number of quadrature points */
+  int     dimension;   /* 1,2,3 -- spatial dimension of points */
+  double *xi;          /* xi  (x) coordinate of points; dimension = cardinality  or NULL */
+  double *
+      eta; /* eta (y) coordinate of points; dimension = cardinality if dimension = 2 or 3 or NULL */
+  double
+      *zeta; /* zeta (z) coordinate of points; dimension = cardinality if dimension == 3. or NULL */
+  double *weight; /* weights for each point; dimension = cardinality or NULL */
+} ex_quadrature;
+
 /*!
  * ex_opts() function codes - codes are OR'ed into exopts
  */
@@ -305,9 +400,6 @@ typedef enum ex_options ex_options;
  * @{
  */
 
-/** Maximum length of name permitted by NetCDF */
-#define EX_MAX_NAME NC_MAX_NAME
-
 /** Maximum length of QA record, element type name */
 #define MAX_STR_LENGTH 32L
 /** Default maximum length of an entity name, attribute name, variable name.
@@ -368,10 +460,10 @@ typedef enum ex_type ex_type;
 typedef struct ex_attribute
 {
   ex_entity_type entity_type;
-  ex_entity_id   entity_id;
-  char           name[NC_MAX_NAME + 1];
+  int64_t        entity_id;
+  char           name[EX_MAX_NAME + 1];
   ex_type        type; /* int, double, text */
-  size_t         value_count;
+  int            value_count;
   void          *values; /* not accessed if NULL */
 } ex_attribute;
 
@@ -953,6 +1045,20 @@ EXODUS_EXPORT int ex_get_blob(int exoid, struct ex_blob *blob);
 EXODUS_EXPORT int ex_put_blobs(int exoid, size_t count, const struct ex_blob *blobs);
 EXODUS_EXPORT int ex_get_blobs(int exoid, struct ex_blob *blobs);
 
+EXODUS_EXPORT int ex_put_field_metadata(int exoid, const ex_field field);
+EXODUS_EXPORT int ex_put_field_suffices(int exoid, const ex_field field, const char *suffices);
+EXODUS_EXPORT int ex_get_field_metadata(int exoid, ex_field *field);
+EXODUS_EXPORT int ex_get_field_metadata_count(int exoid, ex_entity_type obj_type, ex_entity_id id);
+EXODUS_EXPORT int ex_get_field_suffices(int exoid, const ex_field field, char *suffices);
+
+EXODUS_EXPORT int ex_get_basis_count(int exoid);
+EXODUS_EXPORT int ex_get_basis(int exoid, ex_basis **pbasis, int *num_basis);
+EXODUS_EXPORT int ex_put_basis(int exoid, const ex_basis basis);
+
+EXODUS_EXPORT int ex_get_quadrature_count(int exoid);
+EXODUS_EXPORT int ex_get_quadrature(int exoid, ex_quadrature **pquad, int *num_quad);
+EXODUS_EXPORT int ex_put_quadrature(int exoid, const ex_quadrature quad);
+
 /*  Write arbitrary integer, double, or text attributes on an entity */
 EXODUS_EXPORT int ex_put_attribute(int exoid, const ex_attribute attributes);
 EXODUS_EXPORT int ex_put_attributes(int exoid, size_t attr_count, const ex_attribute *attributes);
@@ -1202,6 +1308,17 @@ EXODUS_EXPORT int ex_put_elem_cmap(int             exoid,    /**< NetCDF/Exodus
                                    int             processor /**< This processor ID */
 );
 
+EXODUS_EXPORT int ex_initialize_basis_struct(ex_basis *basis, size_t num_basis, int mode);
+EXODUS_EXPORT int ex_initialize_quadrature_struct(ex_quadrature *quad, size_t num_quad, int mode);
+
+EXODUS_EXPORT const char *ex_component_field_name(ex_field *field,
+                                                  int       component[EX_MAX_FIELD_NESTING]);
+EXODUS_EXPORT const char *ex_field_component_suffix(ex_field *field, int nest_level, int component);
+EXODUS_EXPORT int         ex_field_cardinality(const ex_field_type field_type);
+EXODUS_EXPORT const char *ex_field_type_name(const ex_field_type field_type);
+EXODUS_EXPORT ex_field_type ex_string_to_field_type_enum(const char *field_name);
+EXODUS_EXPORT const char   *ex_field_type_enum_to_string(const ex_field_type field_type);
+
 /*! @} */
 
 /* Deprecated Code Handling Options:

packages/seacas/libraries/exodus/include/exodusII_int.h

@@ -1,6 +1,6 @@
 /*
 
- * Copyright(C) 1999-2020, 2022, 2023 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2020, 2022, 2023, 2024 National Technology & Engineering Solutions
  * of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
  * NTESS, the U.S. Government retains certain rights in this software.
  *
@@ -88,6 +88,9 @@ extern "C" {
 #define EX_FILE_ID_MASK (0xffff0000) /**< Must match FILE_ID_MASK in NetCDF nc4internal.h */
 #define EX_GRP_ID_MASK  (0x0000ffff) /**< Must match GRP_ID_MASK in NetCDF nc4internal.h */
 
+/* Utility function to find variable to store entity attribute on */
+int exi_get_varid(int exoid, ex_entity_type obj_type, ex_entity_id id);
+
 void exi_reset_error_status(void);
 
 #if defined(EXODUS_THREADSAFE)