Merge Pull Request #13376 from gsjaardema/Trilinos/SEACAS-Snapshot-20…

…24-08-20

Automatically Merged using Trilinos Pull Request AutoTester
PR Title: b'SEACAS: Snapshot 2024-08-20'
PR Author: gsjaardema

packages/seacas/applications/aprepro/aprepro.C

@@ -1,4 +1,4 @@
-// Copyright(C) 1999-2021, 2023 National Technology & Engineering Solutions
+// Copyright(C) 1999-2021, 2023, 2024, 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.
 //
@@ -14,6 +14,17 @@
 
 #include "aprepro.h"
 
+namespace {
+  bool is_double(const std::string &myString)
+  {
+    std::istringstream iss(myString);
+    double             f;
+    iss >> std::noskipws >> f; // noskipws considers leading whitespace invalid
+    // Check the entire string was consumed and if either failbit or badbit is set
+    return iss.eof() && !iss.fail();
+  }
+} // namespace
+
 int main(int argc, char *argv[])
 {
   SEAMS::Aprepro           aprepro;
@@ -42,7 +53,9 @@ int main(int argc, char *argv[])
         value = value.substr(1, value.length() - 2);
         aprepro.add_variable(var, value, true); // Make it immutable
       }
-      else {
+      // See if `value` contains any characters that are invalid for a number...
+
+      else if (is_double(value)) {
         try {
           double dval = std::stod(value);
           aprepro.add_variable(var, dval, true);
@@ -58,6 +71,9 @@ int main(int argc, char *argv[])
           }
         }
       }
+      else {
+        aprepro.add_variable(var, value, true); // Make it immutable
+      }
     }
     else {
       input_files.emplace_back(argv[ai]);

packages/seacas/applications/blot/linthc.blk

@@ -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
@@ -8,7 +8,7 @@ C    See packages/seacas/LICENSE for details
       REAL MSHBND, BLKBND, ELEBND
 C      --      Line thickness specification for lines appearing
 C      --      on mesh plots.  Specification is a real value in the
-C      --      range 0. - 1000., with 0. being the thinest line and
+C      --      range 0. - 1000., with 0. being the thinnest line and
 C      --      1000. being the thickest.
 C      -- MSHBND - Thickness of lines forming the mesh boundary.
 C      -- BLKBND - Thickness of lines forming element block boundaries.

packages/seacas/applications/cpup/CP_SystemInterface.C

@@ -64,8 +64,12 @@ void Cpup::SystemInterface::enroll_options()
   options_.enroll("steps", GetLongOption::MandatoryValue,
                   "Specify subset of timesteps to transfer to output file.\n"
                   "\t\tFormat is beg:end:step. 1:10:2 --> 1,3,5,7,9\n"
+                  "\t\tIf the 'beg' or 'end' is < 0, then it is the \"-Nth\" step...\n"
+                  "\t\t-1 is \"first last\" or last, -3 is \"third last\"\n"
+                  "\t\tTo copy just the last 3 steps, do: `-steps -3:-1`\n"
                   "\t\tEnter LAST for last step",
                   "1:", nullptr, true);
+
   options_.enroll("extension", GetLongOption::MandatoryValue,
                   "CGNS database extension for the input files", "cgns");
 
@@ -466,7 +470,11 @@ void Cpup::SystemInterface::parse_step_option(const char *tokens)
   //:    <li>":Y"                 -- 1 to Y by 1</li>
   //:    <li>"::Z"                -- 1 to oo by Z</li>
   //:  </ul>
-  //: The count and step must always be >= 0
+  //: The step must always be > 0
+  //: If the 'from' or 'to' is < 0, then it is the "-Nth" step...
+  //: -1 is "first last" or last
+  //: -4 is "fourth last step"
+  //: To copy just the last 3 steps, do: `-steps -3:-1`
 
   // Break into tokens separated by ":"
 
@@ -482,24 +490,24 @@ void Cpup::SystemInterface::parse_step_option(const char *tokens)
       for (auto &val : vals) {
         // Parse 'i'th field
         char tmp_str[128];
-        int  k = 0;
 
+        int k = 0;
         while (tokens[j] != '\0' && tokens[j] != ':') {
           tmp_str[k++] = tokens[j++];
         }
 
         tmp_str[k] = '\0';
         if (strlen(tmp_str) > 0) {
-          val = strtoul(tmp_str, nullptr, 0);
+          val = strtol(tmp_str, nullptr, 0);
         }
 
         if (tokens[j++] == '\0') {
           break; // Reached end of string
         }
       }
-      stepMin_      = abs(vals[0]);
-      stepMax_      = abs(vals[1]);
-      stepInterval_ = abs(vals[2]);
+      stepMin_      = vals[0];
+      stepMax_      = vals[1];
+      stepInterval_ = abs(vals[2]); // step is always positive...
     }
     else if (str_equal("LAST", tokens)) {
       stepMin_ = stepMax_ = -1;

packages/seacas/applications/cpup/CP_Version.h

@@ -1,5 +1,5 @@
 /*
- * Copyright(C) 1999-2023 National Technology & Engineering Solutions
+ * Copyright(C) 1999-2024 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.
  *
@@ -8,4 +8,4 @@
 #pragma once
 #include <array>
 #include <string>
-static const std::array<std::string, 3> qainfo{"cpup", "0.95 beta", "2023/04/25"};
+static const std::array<std::string, 3> qainfo{"cpup", "0.96 beta", "2024/08/06"};

packages/seacas/applications/cpup/cpup.C

@@ -1,4 +1,4 @@
-// Copyright(C) 1999-2023 National Technology & Engineering Solutions
+// Copyright(C) 1999-2024 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.
 //
@@ -406,9 +406,11 @@ template <typename INT> void cpup(Cpup::SystemInterface &interFace, INT /*dummy*
   int ts_max  = interFace.step_max();
   int ts_step = interFace.step_interval();
 
-  if (ts_min == -1 && ts_max == -1) {
-    ts_min = num_time_steps;
-    ts_max = num_time_steps;
+  if (ts_min < 0) {
+    ts_min = num_time_steps + 1 + ts_min;
+  }
+  if (ts_max < 0) {
+    ts_max = num_time_steps + 1 + ts_max;
   }
 
   // Time steps for output file

packages/seacas/applications/ejoin/EJ_SystemInterface.C

@@ -143,8 +143,11 @@ void SystemInterface::enroll_options()
   options_.enroll("steps", GetLongOption::MandatoryValue,
                   "Specify subset of timesteps to transfer to output file.\n"
                   "\t\tFormat is beg:end:step. 1:10:2 --> 1,3,5,7,9\n"
-                  "\t\tTo only transfer last step, use '-steps LAST'",
-                  "1:");
+                  "\t\tIf the 'beg' or 'end' is < 0, then it is the \"-Nth\" step...\n"
+                  "\t\t-1 is \"first last\" or last, -3 is \"third last\"\n"
+                  "\t\tTo copy just the last 3 steps, do: `-steps -3:-1`\n"
+                  "\t\tEnter LAST for last step",
+                  "1:", nullptr, true);
 
   options_.enroll("gvar", GetLongOption::MandatoryValue,
                   "Comma-separated list of global variables to be joined or ALL or NONE.", nullptr);
@@ -478,15 +481,17 @@ void SystemInterface::parse_step_option(const char *tokens)
   //: The defined formats for the count attribute are:<br>
   //:  <ul>
   //:    <li><missing> -- default -- 1 <= count <= oo  (all steps)</li>
-  //:    <li>"X"                  -- X <= count <= X  (just step X). If X == LAST, last step
-  // only</li>
+  //:    <li>"X"                  -- X <= count <= X  (just step X) LAST for last step.</li>
   //:    <li>"X:Y"                -- X to Y by 1</li>
   //:    <li>"X:"                 -- X to oo by 1</li>
   //:    <li>":Y"                 -- 1 to Y by 1</li>
   //:    <li>"::Z"                -- 1 to oo by Z</li>
-  //:    <li>"LAST"               -- last step only</li>
   //:  </ul>
-  //: The count and step must always be >= 0
+  //: The step must always be > 0
+  //: If the 'from' or 'to' is < 0, then it is the "-Nth" step...
+  //: -1 is "first last" or last
+  //: -4 is "fourth last step"
+  //: To copy just the last 3 steps, do: `-steps -3:-1`
 
   // Break into tokens separated by ":"
 
@@ -502,24 +507,24 @@ void SystemInterface::parse_step_option(const char *tokens)
       for (auto &val : vals) {
         // Parse 'i'th field
         char tmp_str[128];
-        int  k = 0;
 
+        int k = 0;
         while (tokens[j] != '\0' && tokens[j] != ':') {
           tmp_str[k++] = tokens[j++];
         }
 
         tmp_str[k] = '\0';
         if (strlen(tmp_str) > 0) {
-          val = strtoul(tmp_str, nullptr, 0);
+          val = strtol(tmp_str, nullptr, 0);
         }
 
         if (tokens[j++] == '\0') {
           break; // Reached end of string
         }
       }
-      stepMin_      = abs(vals[0]);
-      stepMax_      = abs(vals[1]);
-      stepInterval_ = abs(vals[2]);
+      stepMin_      = vals[0];
+      stepMax_      = vals[1];
+      stepInterval_ = abs(vals[2]); // step is always positive...
     }
     else if (str_equal("LAST", tokens)) {
       stepMin_ = stepMax_ = -1;

packages/seacas/applications/ejoin/EJ_Version.h

@@ -9,6 +9,6 @@
 
 static const std::array<std::string, 3> qainfo{
     "ejoin",
-    "2024/02/21",
-    "1.6.3",
+    "2024/08/06",
+    "1.6.4",
 };

packages/seacas/applications/ejoin/EJoin.C

@@ -528,9 +528,11 @@ double ejoin(SystemInterface &interFace, std::vector<Ioss::Region *> &part_mesh,
   int ts_step   = interFace.step_interval();
   int num_steps = static_cast<int>(global_times.size());
 
-  if (ts_min == -1 && ts_max == -1) {
-    ts_min = num_steps;
-    ts_max = num_steps;
+  if (ts_min < 0) {
+    ts_min = num_steps + 1 + ts_min;
+  }
+  if (ts_max < 0) {
+    ts_max = num_steps + 1 + ts_max;
   }
   ts_max = ts_max < num_steps ? ts_max : num_steps;
 

packages/seacas/applications/epu/EP_SystemInterface.C

@@ -175,6 +175,9 @@ void Excn::SystemInterface::enroll_options()
   options_.enroll("steps", GetLongOption::MandatoryValue,
                   "Specify subset of timesteps to transfer to output file.\n"
                   "\t\tFormat is beg:end:step. 1:10:2 --> 1,3,5,7,9\n"
+                  "\t\tIf the 'beg' or 'end' is < 0, then it is the \"-Nth\" step...\n"
+                  "\t\t-1 is \"first last\" or last, -3 is \"third last\"\n"
+                  "\t\tTo copy just the last 3 steps, do: `-steps -3:-1`\n"
                   "\t\tEnter LAST for last step",
                   "1:", nullptr, true);
 
@@ -545,7 +548,11 @@ void Excn::SystemInterface::parse_step_option(const char *tokens)
   //:    <li>":Y"                 -- 1 to Y by 1</li>
   //:    <li>"::Z"                -- 1 to oo by Z</li>
   //:  </ul>
-  //: The count and step must always be >= 0
+  //: The step must always be > 0
+  //: If the 'from' or 'to' is < 0, then it is the "-Nth" step...
+  //: -1 is "first last" or last
+  //: -4 is "fourth last step"
+  //: To copy just the last 3 steps, do: `-steps -3:-1`
 
   // Break into tokens separated by ":"
 
@@ -555,34 +562,30 @@ void Excn::SystemInterface::parse_step_option(const char *tokens)
     if (strchr(tokens, ':') != nullptr) {
       // The string contains a separator
 
-      int vals[3];
-      vals[0] = stepMin_;
-      vals[1] = stepMax_;
-      vals[2] = stepInterval_;
+      std::array<int, 3> vals{stepMin_, stepMax_, stepInterval_};
 
       int j = 0;
       for (auto &val : vals) {
         // Parse 'i'th field
         char tmp_str[128];
-        ;
-        int k = 0;
 
+        int k = 0;
         while (tokens[j] != '\0' && tokens[j] != ':') {
           tmp_str[k++] = tokens[j++];
         }
 
         tmp_str[k] = '\0';
         if (strlen(tmp_str) > 0) {
-          val = strtoul(tmp_str, nullptr, 0);
+          val = strtol(tmp_str, nullptr, 0);
         }
 
         if (tokens[j++] == '\0') {
           break; // Reached end of string
         }
       }
-      stepMin_      = abs(vals[0]);
-      stepMax_      = abs(vals[1]);
-      stepInterval_ = abs(vals[2]);
+      stepMin_      = vals[0];
+      stepMax_      = vals[1];
+      stepInterval_ = abs(vals[2]); // step is always positive...
     }
     else if (str_equal("LAST", tokens)) {
       stepMin_ = stepMax_ = -1;

packages/seacas/applications/epu/EP_Version.h

@@ -11,6 +11,6 @@
 
 static const std::array<std::string, 3> qainfo{
     "epu --  E Pluribus Unum",
-    "6.09",
-    "2024/04/18",
+    "6.10",
+    "2024/08/06",
 };

packages/seacas/applications/epu/epu.C

@@ -1325,9 +1325,11 @@ int epu(SystemInterface &interFace, int start_part, int part_count, int cycle, T
   int ts_max  = interFace.step_max();
   int ts_step = interFace.step_interval();
 
-  if (ts_min == -1 && ts_max == -1) {
-    ts_min = num_time_steps;
-    ts_max = num_time_steps;
+  if (ts_min < 0) {
+    ts_min = num_time_steps + 1 + ts_min;
+  }
+  if (ts_max < 0) {
+    ts_max = num_time_steps + 1 + ts_max;
   }
 
   // Time steps for output file