From 5844756696b6dcb78fec27df7de7642207b8b062 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 28 Jan 2026 15:59:23 +0000
Subject: [PATCH 1/3] Initial plan


From 8dde3062431387216184b6ad50a4f0717c13e512 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 28 Jan 2026 16:00:37 +0000
Subject: [PATCH 2/3] Fix inline comments to clarify sqrt_eps_ij usage in
 vdw_rules.h

Co-authored-by: David-Araripe <79095854+David-Araripe@users.noreply.github.com>
---
 src/core/vdw_rules.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/core/vdw_rules.h b/src/core/vdw_rules.h
index 1b17b003..74776517 100644
--- a/src/core/vdw_rules.h
+++ b/src/core/vdw_rules.h
@@ -45,8 +45,8 @@ __device__ __host__ inline void calc_vdw_arithmetic(
     double R2 = Rstar_ij * Rstar_ij;
     double R6 = R2 * R2 * R2;
 
-    *V_a = sqrt_eps_ij * R6 * R6 * r6 * r6;  // eps * R^12 * r^-12
-    *V_b = 2.0 * sqrt_eps_ij * R6 * r6;       // 2 * eps * R^6 * r^-6
+    *V_a = sqrt_eps_ij * R6 * R6 * r6 * r6;  // sqrt(eps_i * eps_j) * R^12 * r^-12
+    *V_b = 2.0 * sqrt_eps_ij * R6 * r6;       // 2 * sqrt(eps_i * eps_j) * R^6 * r^-6
 }
 
 #endif /* __VDW_RULES_H__ */

From 3a32af7af1c626f5163a938bad1ac8005cd5140a Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 28 Jan 2026 16:01:21 +0000
Subject: [PATCH 3/3] Complete PR: addressed feedback on inline comments

Co-authored-by: David-Araripe <79095854+David-Araripe@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 00000000..945c9b46
--- /dev/null
+++ b/_codeql_detected_source_root
@@ -0,0 +1 @@
+.
\ No newline at end of file