From 471025aabc3b335c96fd0b3a3212683a7befc154 Mon Sep 17 00:00:00 2001
From: Sebastian Schunert <snschune@ncsu.edu>
Date: Fri, 29 Nov 2019 20:41:54 -0700
Subject: [PATCH] Add a routine that checks timestamps (#367)

---
 include/userobjects/LAMMPSFileRunner.h |  3 ++-
 src/userobjects/LAMMPSFileRunner.C     | 21 ++++++++++++++++++---
 2 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/include/userobjects/LAMMPSFileRunner.h b/include/userobjects/LAMMPSFileRunner.h
index 8deda6cf..f67c64a6 100644
--- a/include/userobjects/LAMMPSFileRunner.h
+++ b/include/userobjects/LAMMPSFileRunner.h
@@ -45,6 +45,8 @@ class LAMMPSFileRunner : public MDRunBase
                                  std::pair<std::string, std::string> & filenames,
                                  std::pair<Real, Real> & timestamps);
 
+  bool isTimestamp(std::string ts_candidate) const;
+
   /// whether a sequence of input files or a single input file is read
   bool _time_sequence;
 
@@ -60,4 +62,3 @@ class LAMMPSFileRunner : public MDRunBase
   /// Conversion from FEM time to MD time_stamp
   const Function * _time_conversion;
 };
-
diff --git a/src/userobjects/LAMMPSFileRunner.C b/src/userobjects/LAMMPSFileRunner.C
index cd7cff0b..3fb7f663 100644
--- a/src/userobjects/LAMMPSFileRunner.C
+++ b/src/userobjects/LAMMPSFileRunner.C
@@ -10,6 +10,8 @@
 #include "MooseUtils.h"
 #include "Function.h"
 #include <sstream>
+#include <cstring>
+#include <cctype>
 
 registerMooseObject("MagpieApp", LAMMPSFileRunner);
 
@@ -136,9 +138,13 @@ LAMMPSFileRunner::findBracketingLAMMPSFiles(Real md_time,
                  " failed. LAMMPS filename must be base.<t>.xyz where <t> is the timestamp.");
     std::stringstream sstr(elements[1]);
 
-    if (sstr >> timestamp || sstr.eof())
-      if (sstr.fail())
-        continue;
+    if (!isTimestamp(elements[1]))
+      continue;
+    sstr >> timestamp;
+
+    // if (sstr >> timestamp || sstr.eof())
+    //  if (sstr.fail())
+    //    continue;
 
     // increase the counter & check if this file is a candidate for before/after
     ++lammps_files_found;
@@ -259,6 +265,15 @@ LAMMPSFileRunner::readLAMMPSFile(FileName filename)
   _md_particles.id.shrink_to_fit();
 }
 
+bool
+LAMMPSFileRunner::isTimestamp(std::string ts_candidate) const
+{
+  for (auto & s : ts_candidate)
+    if (!isdigit(s))
+      return false;
+  return true;
+}
+
 void
 LAMMPSFileRunner::readLAMMPSFileHistory(std::pair<FileName, FileName> filenames,
                                         std::pair<Real, Real> timestamps,