SEACAS: Test fixes and clang-format

packages/seacas/Jamfile

@@ -157,7 +157,9 @@ alias install-user-include : install-user-include0
                              install-user-include3
                              install-user-include4
                              install-user-include5
-                             install-user-include6 ;
+                             install-user-include6
+                             install-user-include7
+                             install-user-include8 ;
 
 # This rule copies all headers it finds in the include directory of the
 # source to the include directory of the install-root.
@@ -222,6 +224,21 @@ install install-user-include6
   : <location>$(install-root)/io_system/include
   ;
 
+
+explicit install-user-include7 ;
+install install-user-include7
+  : [ glob $(seacas-root)/libraries/aprepro_lib/*.h ]
+  : <location>$(install-root)/seacas/include
+  ;
+
+
+explicit install-user-include8 ;
+install install-user-include8
+  : [ glob $(seacas-root)/libraries/suplib_cpp/fmt/*.h ]
+  : <location>$(install-root)/io_system/include/fmt
+  ;
+
+
 explicit install-user-env ;
 alias install-user-env : install-user-jamfile
                           install-user-bin install-user-include install-user-lib ;

packages/seacas/applications/aprepro/CMakeLists.txt

@@ -87,13 +87,13 @@ TRIBITS_ADD_ADVANCED_TEST(
 TRIBITS_ADD_ADVANCED_TEST(
  aprepro_command_line_include_test
  TEST_0 EXEC aprepro
-	ARGS -q --info=test-vars.dump --include ${CMAKE_CURRENT_SOURCE_DIR}/test-include.i ${CMAKE_CURRENT_SOURCE_DIR}/test-dump.i
+	ARGS -q --info=test-include.dump --include ${CMAKE_CURRENT_SOURCE_DIR}/test-include.i ${CMAKE_CURRENT_SOURCE_DIR}/test-dump.i
 	test-include.out
   NOEXEPREFIX NOEXESUFFIX
   PASS_ANY
  TEST_1 CMND diff ARGS -w
 		       ${CMAKE_CURRENT_SOURCE_DIR}/test-dump.gold
-		       ${CMAKE_CURRENT_BINARY_DIR}/test-vars.dump
+		       ${CMAKE_CURRENT_BINARY_DIR}/test-include.dump
  COMM mpi serial
  OVERALL_NUM_MPI_PROCS 1
  FINAL_PASS_REGULAR_EXPRESSION

packages/seacas/applications/epu/epu.C

@@ -1961,7 +1961,7 @@ namespace {
       size_t max_nodes = glob_blocks[b].entity_count() * glob_blocks[b].nodesPerElement;
       linkage.resize(max_nodes);
       attributes.resize(static_cast<size_t>(glob_blocks[b].attributeCount) *
-			glob_blocks[b].entity_count());
+                        glob_blocks[b].entity_count());
 
       int error = 0;
       for (int p = 0; p < part_count; p++) {
@@ -2008,7 +2008,7 @@ namespace {
 
           // Get attributes list,  if it exists
           if (blocks[p][b].attributeCount > 0) {
-            size_t         max_attr = blocks[p][b].entity_count() * blocks[p][b].attributeCount;
+            size_t max_attr = blocks[p][b].entity_count() * blocks[p][b].attributeCount;
             local_attr.resize(max_attr);
 
             error = ex_get_attr(id, EX_ELEM_BLOCK, blocks[p][b].id, local_attr.data());
@@ -2039,8 +2039,8 @@ namespace {
       int id_out = ExodusFile::output(); // output file identifier
 
       if (!linkage.empty()) {
-        error = ex_put_conn(id_out, EX_ELEM_BLOCK, glob_blocks[b].id, linkage.data(), nullptr,
-                            nullptr);
+        error =
+            ex_put_conn(id_out, EX_ELEM_BLOCK, glob_blocks[b].id, linkage.data(), nullptr, nullptr);
         if (error < 0) {
           exodus_error(__LINE__);
         }
@@ -3635,8 +3635,8 @@ namespace {
 
               if (local_mesh[p]
                       .truthTable[static_cast<int>(vars.objectType)][input_truth_table_loc] > 0) {
-                int error = ex_get_var(id, time_step + 1, exodus_object_type(vars.objectType), i + 1,
-                                   local_sets[p][b].id, entity_count, values.data());
+                int error = ex_get_var(id, time_step + 1, exodus_object_type(vars.objectType),
+                                       i + 1, local_sets[p][b].id, entity_count, values.data());
                 if (error < 0) {
                   exodus_error(__LINE__);
                 }

packages/seacas/applications/nas2exo/N2EDataTypes.h

@@ -10,8 +10,8 @@
 #ifndef INCLUDE_N2EDATATYPES_H_
 #define INCLUDE_N2EDATATYPES_H_
 
-#include <exodusII.h>
 #include <cstring>
+#include <exodusII.h>
 #include <string>
 #include <tuple>
 

packages/seacas/applications/nas2exo/N2EExoWriter.C

@@ -104,10 +104,10 @@ namespace ExoModules {
     bool result{true};
 
     // Now we write the nodes
-    size_t num_nodes = this->gridList.size();
-    double * x         = new double[num_nodes];
-    double * y         = new double[num_nodes];
-    double * z         = new double[num_nodes];
+    size_t  num_nodes = this->gridList.size();
+    double *x         = new double[num_nodes];
+    double *y         = new double[num_nodes];
+    double *z         = new double[num_nodes];
     for (size_t i = 0; i < num_nodes; i++) {
 
       N2EPoint3D crd = std::get<1>(this->gridList[i]);
@@ -162,7 +162,7 @@ namespace ExoModules {
       std::vector<elementType> thisBlock;
       int64_t                  block = (int)std::get<0>(sect);
 
-      int                    retvalue{0};
+      int retvalue{0};
 
       for (const elementType &elem : this->elementList) {
 
@@ -193,7 +193,7 @@ namespace ExoModules {
 
       for (const elementType &elem : thisBlock) {
 
-	const N2EModules::N2EGridPtList  &pts{std::get<3>(elem)};
+        const N2EModules::N2EGridPtList &pts{std::get<3>(elem)};
         std::copy(pts.v, pts.v + nodes_per_elem, elemCon.data() + numNodesCopied);
         numNodesCopied += nodes_per_elem;
       }

packages/seacas/applications/nem_slice/elb_loadbal.C

@@ -616,23 +616,23 @@ int generate_loadbal(Machine_Description *machine, Problem_Description *problem,
         }
       }
       else {
-        tmp_nv    = problem->num_vertices;
-	if (!graph->start.empty()) {
-	  tmp_start = &graph->start[0];
-	}
-	if (!graph->adj.empty()) {
-	  tmp_adj   = &graph->adj[0];
-	}
-	if (!weight->vertices.empty()) {
-	  tmp_vwgts = &weight->vertices[0];
-	}
-	if (!weight->edges.empty()) {
-	  tmp_ewgts = &weight->edges[0];
-	}
-        tmp_x     = x_ptr;
-        tmp_y     = y_ptr;
-        tmp_z     = z_ptr;
-        tmp_v2p   = lb->vertex2proc;
+        tmp_nv = problem->num_vertices;
+        if (!graph->start.empty()) {
+          tmp_start = &graph->start[0];
+        }
+        if (!graph->adj.empty()) {
+          tmp_adj = &graph->adj[0];
+        }
+        if (!weight->vertices.empty()) {
+          tmp_vwgts = &weight->vertices[0];
+        }
+        if (!weight->edges.empty()) {
+          tmp_ewgts = &weight->edges[0];
+        }
+        tmp_x   = x_ptr;
+        tmp_y   = y_ptr;
+        tmp_z   = z_ptr;
+        tmp_v2p = lb->vertex2proc;
 
         for (int cnt = 0; cnt < machine->num_dims; cnt++) {
           tmpdim[cnt] = machine->dim[cnt];

packages/seacas/applications/zellij/Cell.h

@@ -34,8 +34,8 @@ enum class Loc { C = 0, BL, B, BR, L, R, TL, T, TR };
 class Cell
 {
 public:
-  Cell() = default;
-  Cell(const Cell&) = default;
+  Cell()             = default;
+  Cell(const Cell &) = default;
 
   std::pair<double, double> get_coordinate_range(enum Axis) const;
   void                      initialize(size_t i, size_t j, std::shared_ptr<UnitCell> unit_cell);

packages/seacas/applications/zellij/Decompose.C

@@ -22,7 +22,6 @@
 
 extern unsigned int debug_level;
 
-
 namespace {
 #ifdef USE_ZOLTAN
 #define STRINGIFY(x) #x

packages/seacas/applications/zellij/UnitCell.h

@@ -24,8 +24,8 @@ struct GeneratedSideBlock
   //!
   //! Note that the `element_offset` is the 1-based index of the
   //! element within the element block that it is a member of
-  GeneratedSideBlock() = default;
-  GeneratedSideBlock(const GeneratedSideBlock&) = delete;
+  GeneratedSideBlock()                           = default;
+  GeneratedSideBlock(const GeneratedSideBlock &) = delete;
 
   std::map<std::string, std::vector<int64_t>> m_faces;
 

packages/seacas/applications/zellij/ZE_SystemInterface.C

@@ -177,7 +177,8 @@ void SystemInterface::enroll_options()
                   "\t\t  16 = Put exodus library into verbose mode.\n"
                   "\t\t  32 = Verbose decomposition information.\n"
                   "\t\t  64 = Verbose output database summary information.\n"
-                  "\t\t 128 = Verbose sideset generation information.", "0");
+                  "\t\t 128 = Verbose sideset generation information.",
+                  "0");
 
   options_.enroll("copyright", Ioss::GetLongOption::NoValue, "Show copyright and license data.",
                   nullptr);

packages/seacas/libraries/aprepro_lib/apr_aprepro.cc

@@ -24,10 +24,24 @@
 
 namespace {
   const unsigned int HASHSIZE       = 5939;
-  const char *       version_string = "5.27 (2021/07/20)";
+  const char *       version_string = "5.29 (2021/07/22";
 
   void output_copyright();
 
+  std::string get_value(const std::string &option, const std::string &optional_value)
+  {
+    size_t      index = option.find_first_of('=');
+    std::string value;
+
+    if (index != std::string::npos) {
+      value = option.substr(index + 1);
+    }
+    else {
+      value = optional_value;
+    }
+    return value;
+  }
+
   unsigned hash_symbol(const char *symbol)
   {
     unsigned hashval;
@@ -56,8 +70,8 @@ namespace SEAMS {
       outputStream.top()->flush();
     }
 
-    // May need to delete this if set via --info=file, but need a way to determine this.
-    // For now, flush so all data written and leave as is.
+    // May need to delete this if set via --info=filename command.
+    // May need a flag to determine this...
     infoStream->flush();
 
     if ((stringScanner != nullptr) && stringScanner != lexer) {
@@ -448,28 +462,17 @@ namespace SEAMS {
       ap_options.end_on_exit = true;
     }
     else if (option.find("--info") != std::string::npos) {
-      std::string value;
-
-      size_t index = option.find_first_of('=');
-      if (index != std::string::npos) {
-        value     = option.substr(index + 1);
-        auto info = open_file(value, "w");
-        if (info != nullptr) {
-          set_error_streams(nullptr, nullptr, info);
-        }
+      std::string value = get_value(option, optional_value);
+      ret_value         = value == optional_value ? 1 : 0;
+
+      auto info = open_file(value, "w");
+      if (info != nullptr) {
+        set_error_streams(nullptr, nullptr, info);
       }
     }
     else if (option.find("--include") != std::string::npos || (option[1] == 'I')) {
-      std::string value;
-
-      size_t index = option.find_first_of('=');
-      if (index != std::string::npos) {
-        value = option.substr(index + 1);
-      }
-      else {
-        value     = optional_value;
-        ret_value = 1;
-      }
+      std::string value = get_value(option, optional_value);
+      ret_value         = value == optional_value ? 1 : 0;
 
       if (is_directory(value)) {
         ap_options.include_path = value;
@@ -489,14 +492,8 @@ namespace SEAMS {
         comment = option.substr(2);
       }
       else {
-        size_t index = option.find_first_of('=');
-        if (index != std::string::npos) {
-          comment = option.substr(index + 1);
-        }
-        else {
-          comment   = optional_value;
-          ret_value = 1;
-        }
+        comment   = get_value(option, optional_value);
+        ret_value = comment == optional_value ? 1 : 0;
       }
       symrec *ptr = getsym("_C_");
       if (ptr != nullptr) {
@@ -516,7 +513,7 @@ namespace SEAMS {
              "encountered\n"
           << " --errors_and_warnings_fatal or -F: Exit program with nonzero status if "
              "warnings are encountered\n"
-          << "--require_defined or -R: Tread undefined variable warnings as fatal\n"
+          << "--require_defined or -R: Treat undefined variable warnings as fatal\n"
           << "--one_based_index or -1: Array indexing is one-based (default = zero-based)\n"
           << "    --interactive or -i: Interactive use, no buffering           \n"
           << "    --include=P or -I=P: Include file or include path            \n"
@@ -527,8 +524,9 @@ namespace SEAMS {
           << "        --exit_on or -e: End when 'Exit|EXIT|exit' entered       \n"
           << "           --help or -h: Print this list                         \n"
           << "        --message or -M: Print INFO messages                     \n"
+          << "            --info=file: Output INFO messages (e.g. DUMP() output) to file.\n"
           << "      --nowarning or -W: Do not print WARN messages              \n"
-          << "  --comment=char or -c=char: Change comment character to 'char'      \n"
+          << "  --comment=char or -c=char: Change comment character to 'char'  \n"
           << "      --copyright or -C: Print copyright message                 \n"
           << "   --keep_history or -k: Keep a history of aprepro substitutions.\n"
           << "                         (not for general interactive use)       \n"

packages/seacas/libraries/aprepro_lib/apr_array.cc

@@ -18,18 +18,13 @@ namespace SEAMS {
      * (0.0 -> rows-1) (0.0 -> cols-1)
      */
 
-    if (aprepro->ap_options.one_based_index) {
-      row--;
-      col--;
-    }
+    int cols = arr->cols;
+    int rows = arr->rows;
 
     int irl = row;
-    int irh = irl + 1;
+    int irh = rows > 1 ? irl + 1 : irl;
     int icl = col;
-    int ich = icl + 1;
-
-    int cols = arr->cols;
-    int rows = arr->rows;
+    int ich = cols > 1 ? icl + 1 : icl;
 
     double value = 0.0;
 
@@ -38,8 +33,16 @@ namespace SEAMS {
       double v21 = arr->data[irh * cols + icl];
       double v12 = arr->data[irl * cols + ich];
       double v22 = arr->data[irh * cols + ich];
-      value      = v11 * (irh - row) * (ich - col) + v21 * (row - irl) * (ich - col) +
-              v12 * (irh - row) * (col - icl) + v22 * (row - irl) * (col - icl);
+      if (rows > 1 && cols > 1) {
+        value = (v11 * (irh - row) + v21 * (row - irl)) * (ich - col) +
+                (v12 * (irh - row) * v22 * (row - irl)) * (col - icl);
+      }
+      else if (rows > 1 && cols == 1) {
+        value = v11 * (irh - row) + v21 * (row - irl);
+      }
+      else if (cols > 1 && rows == 1) {
+        value = v11 * (ich - col) + v12 * (col - icl);
+      }
     }
     else {
       aprepro->error("Row or Column index out of range");

packages/seacas/libraries/exodus/src/ex_open.c

@@ -229,20 +229,19 @@ int ex_open_int(const char *path, int mode, int *comp_ws, int *io_ws, float *ver
 #endif
       }
       else if (type == 1) {
-	/* Possibly an issue with an older file created by a Java-based NetCDF library which wrote
-	 * corrupted data which is now being checked by newer releases of the NetCDF library...
-	 * SEE: https://github.com/Unidata/netcdf-c/issues/1115
-	 */
-      snprintf(errmsg, MAX_ERR_LENGTH,
-               "ERROR: failed to open '%s' of type %d for reading.\n"
-	       "\t\tIf this is an old file, it is possible that it has some internal corruption\n"
-	       "\t\tthat is now being checked by recent versions of the NetCDF library.\n"
-	       "\t\tTo fix, you can find an older version of `nccopy` (prior to 4.6.0)\n"
-               "\t\tthen try `nccopy bad_file.g fixed_file.g`.",
-               path, type);
-      ex_err(__func__, errmsg, status);
-      EX_FUNC_LEAVE(EX_FATAL);
-
+        /* Possibly an issue with an older file created by a Java-based NetCDF library which wrote
+         * corrupted data which is now being checked by newer releases of the NetCDF library...
+         * SEE: https://github.com/Unidata/netcdf-c/issues/1115
+         */
+        snprintf(errmsg, MAX_ERR_LENGTH,
+                 "ERROR: failed to open '%s' of type %d for reading.\n"
+                 "\t\tIf this is an old file, it is possible that it has some internal corruption\n"
+                 "\t\tthat is now being checked by recent versions of the NetCDF library.\n"
+                 "\t\tTo fix, you can find an older version of `nccopy` (prior to 4.6.0)\n"
+                 "\t\tthen try `nccopy bad_file.g fixed_file.g`.",
+                 path, type);
+        ex_err(__func__, errmsg, status);
+        EX_FUNC_LEAVE(EX_FATAL);
       }
       snprintf(errmsg, MAX_ERR_LENGTH,
                "ERROR: failed to open %s of type %d for reading. Either "