From 492a404d7b2522311bea7963bb6a65f0aae0fa15 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Feb 2026 14:50:14 +0000
Subject: [PATCH 1/4] Initial plan


From 8678f4b55933311dd70307eb4574868efe0b6048 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Feb 2026 14:52:21 +0000
Subject: [PATCH 2/4] Fix checkpoint restart file check to match Run() logic

Co-authored-by: The9Cat <25960766+The9Cat@users.noreply.github.com>
---
 src/OutHDF5.cc | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/OutHDF5.cc b/src/OutHDF5.cc
index 3d3e9a74a..7259adcaa 100644
--- a/src/OutHDF5.cc
+++ b/src/OutHDF5.cc
@@ -193,13 +193,15 @@ void OutHDF5::initialize()
       else {
 	std::ostringstream fname;
 
-	if (chkpt)
+	if (chkpt) {
 	  fname << outdir
-		<<  "checkpoint_" << runtag << ".1";
-	else
+		<<  "checkpoint_" << runtag;
+	  if (numprocs>1) fname << ".1";
+	} else {
 	  fname << outdir
 		<<  filename << "_" << setw(5) << setfill('0') << nbeg
 		<< ".1";
+	}
 
 	std::filesystem::path file_path = fname.str();
 

From 71c9bb30bae20bfff3379b6b4a9a6355fc076c57 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Feb 2026 14:53:16 +0000
Subject: [PATCH 3/4] Complete checkpoint restart fix

Co-authored-by: The9Cat <25960766+The9Cat@users.noreply.github.com>
---
 _codeql_detected_source_root | 1 +
 1 file changed, 1 insertion(+)
 create mode 120000 _codeql_detected_source_root

diff --git a/_codeql_detected_source_root b/_codeql_detected_source_root
new file mode 120000
index 000000000..945c9b46d
--- /dev/null
+++ b/_codeql_detected_source_root
@@ -0,0 +1 @@
+.
\ No newline at end of file

From a8d1f57575984dfd05ae0bbacaccd0517c6f6646 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Feb 2026 14:53:32 +0000
Subject: [PATCH 4/4] Remove CodeQL artifact and update gitignore

Co-authored-by: The9Cat <25960766+The9Cat@users.noreply.github.com>
---
 .gitignore                   | 1 +
 _codeql_detected_source_root | 1 -
 2 files changed, 1 insertion(+), 1 deletion(-)
 delete mode 120000 _codeql_detected_source_root

diff --git a/.gitignore b/.gitignore
index 319d66928..9f36e853c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -25,3 +25,4 @@ src/exp
 src/user/CylindricalDisk.cc
 src/user/EllipsoidForce.cc
 src/user/SLSphere.cc
+_codeql_detected_source_root
diff --git a/_codeql_detected_source_root b/_codeql_detected_source_root
deleted file mode 120000
index 945c9b46d..000000000
--- a/_codeql_detected_source_root
+++ /dev/null
@@ -1 +0,0 @@
-.
\ No newline at end of file