From 361b8c25c43716b6ac462c002e23fbad562e1a40 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 30 Jul 2024 00:34:12 -0400
Subject: [PATCH] use c++11 function to convert strings to numbers

---
 src/variable.cpp                     | 42 ++++++++++++++++------------
 unittest/commands/test_variables.cpp | 13 ++++++++-
 2 files changed, 36 insertions(+), 19 deletions(-)

diff --git a/src/variable.cpp b/src/variable.cpp
index f308ed6efc..b1aa57732d 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -799,8 +799,8 @@ int Variable::next(int narg, char **arg)
         fclose(fp);
 
         if (strlen(buf) > 0) {
-           nextindex = atoi(buf);
-           break;
+          nextindex = std::stoi(buf);
+          break;
         }
         delay = (int) (1000000*random->uniform());
         platform::usleep(delay);
@@ -1115,7 +1115,11 @@ double Variable::compute_equal(int ivar)
     if (ifunc < 0)
       print_var_error(FLERR,fmt::format("cannot find python function {}",data[ivar][0]),ivar);
     python->invoke_function(ifunc,data[ivar][1]);
-    value = atof(data[ivar][1]);
+    try {
+      value = std::stod(data[ivar][1]);
+    } catch (std::exception &e) {
+      print_var_error(FLERR,"has an invalid value", ivar);
+    }
   }
 
   eval_in_progress[ivar] = 0;
@@ -3555,7 +3559,7 @@ tagint Variable::int_between_brackets(char *&ptr, int varallow)
   } else {
     varflag = 0;
     while (*ptr && *ptr != ']') {
-      if (!isdigit(*ptr))
+      if (!(isdigit(*ptr) || (*ptr == '-') || (*ptr == '+') || (*ptr == '*') || (*ptr == '/')))
         error->all(FLERR,"Non digit character between brackets in variable");
       ptr++;
     }
@@ -3566,21 +3570,23 @@ tagint Variable::int_between_brackets(char *&ptr, int varallow)
 
   *ptr = '\0';
 
-  // evaluate index as floating point variable or as tagint via ATOTAGINT()
-
-  if (varflag) {
-    char *id = start+2;
-    int ivar = find(id);
-    if (ivar < 0)
-      error->all(FLERR,"Invalid variable name {} in variable formula", id);
-
-    char *var = retrieve(id);
-    if (var == nullptr)
-      error->all(FLERR,"Invalid variable evaluation for variable {} in variable formula", id);
-    index = static_cast<tagint> (atof(var));
-
-  } else index = ATOTAGINT(start);
+  // evaluate index as floating point variable or as tagint via strtoll()
+  
+  try {
+    if (varflag) {
+      char *id = start+2;
+      int ivar = find(id);
+      if (ivar < 0)
+        error->all(FLERR,"Invalid variable name {} in variable formula", id);
 
+      char *var = retrieve(id);
+      if (var == nullptr)
+        error->all(FLERR,"Invalid variable evaluation for variable {} in variable formula", id);
+      index = static_cast<tagint>(std::stod(var));
+    } else index = static_cast<tagint>(std::stoll(start));
+  } catch (std::exception &e) {
+    error->all(FLERR,"Illegal value in brackets: {}({})", e.what(), start);
+  }
   *ptr = ']';
 
   if (index <= 0)
diff --git a/unittest/commands/test_variables.cpp b/unittest/commands/test_variables.cpp
index 8f2f4ba9d9..2390b1b675 100644
--- a/unittest/commands/test_variables.cpp
+++ b/unittest/commands/test_variables.cpp
@@ -287,6 +287,7 @@ TEST_F(VariableTest, AtomicSystem)
     ASSERT_DOUBLE_EQ(variable->compute_equal("f_press[1]"), 0.0);
     ASSERT_DOUBLE_EQ(variable->compute_equal("c_press"), 0.0);
     ASSERT_DOUBLE_EQ(variable->compute_equal("c_press[2]"), 0.0);
+    ASSERT_DOUBLE_EQ(variable->compute_equal("c_press[1+1]"), 0.0);
     ASSERT_DOUBLE_EQ(variable->compute_equal("1.5+3.25"), 4.75);
     ASSERT_DOUBLE_EQ(variable->compute_equal("-2.5*1.5"), -3.75);
 
@@ -302,8 +303,18 @@ TEST_F(VariableTest, AtomicSystem)
                  variable->compute_equal("v_self"););
     TEST_FAILURE(".*ERROR: Variable sum2: Inconsistent lengths in vector-style variable.*",
                  variable->compute_equal("max(v_sum2)"););
-    TEST_FAILURE("ERROR: Mismatched fix in variable formula.*",
+    TEST_FAILURE(".*ERROR: Mismatched fix in variable formula.*",
                  variable->compute_equal("f_press"););
+    TEST_FAILURE(".*ERROR .*Variable formula compute vector is accessed out-of-range.*",
+                 variable->compute_equal("c_press[10]"););
+    TEST_FAILURE(".*ERROR: Non digit character between brackets in variable.*",
+                 variable->compute_equal("c_press[axy]"););
+    TEST_FAILURE(".*ERROR: Illegal value in brackets: stoll.*",
+                 variable->compute_equal("c_press[73786976294838206464]"););
+    TEST_FAILURE(".*ERROR: Index between variable brackets must be positive.*",
+                 variable->compute_equal("c_press[-2]"););
+    TEST_FAILURE(".*ERROR: Index between variable brackets must be positive.*",
+                 variable->compute_equal("c_press[0]"););
 }
 
 TEST_F(VariableTest, Expressions)