From c99ef0bbe8adf41fc84f381c1a7e776c99ea4ddc Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Fri, 28 Oct 2016 08:50:00 -0500
Subject: [PATCH] Fixed probable bug in memory allocation of bonds array
---
Configuration.cpp | 7 ++++++-
notes.org | 1 +
2 files changed, 7 insertions(+), 1 deletion(-)
diff --git a/Configuration.cpp b/Configuration.cpp
index b4fbcc9..5a818d2 100644
--- a/Configuration.cpp
+++ b/Configuration.cpp
@@ -1059,7 +1059,7 @@ void Configuration::readBonds() {
}
// If we don't have enough room in our bond array, we need to expand it.
- if (numBonds >= capacity) {
+ if (numBonds+1 >= capacity) { // "numBonds+1" because we are adding two bonds to array
// Temporary pointer to the old array
Bond* temp = bonds;
@@ -1087,6 +1087,11 @@ void Configuration::readBonds() {
continue;
}*/
+ if (ind1 < 0 || ind1 >= num || ind2 < 0 || ind2 >=num) {
+ printf("ERROR: Bond file line '%s' includes invalid index\n", line);
+ exit(1);
+ }
+
Bond* b = new Bond(op, ind1, ind2, file_name);
bonds[numBonds++] = *b;
b = new Bond(op, ind2, ind1, file_name);
diff --git a/notes.org b/notes.org
index c748a8d..a98f8d4 100644
--- a/notes.org
+++ b/notes.org
@@ -12,6 +12,7 @@
* TODO eventually
+** enable flag to disable physics-checking assertions in kernels (also write these assertions)
** split computation into multiple regions
*** simulate regions, also in overlap
**** atoms at edge of overlap can have DoF frozen
--
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