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Bug #3214

Out-of-bounds, overflow and incorrect outputs in gmx spatial

Added by Shun Sakuraba 10 months ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
analysis tools
Target version:
-
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

While using gmx spatial I encountered multiple problems. After reading the source I also found multiple problems that corrupts the results of the analysis (especially the wrong number of grid counts and incorrect coordinates are problematic ones).

  1. Out-of-bound memory writes
  2. Confusing error message when the coordinate is exactly on the boundary (happens with .xtc files)
  3. Norm may become negative due to overflow
  4. Having negative iIGNOREOUTER (default -1) led to incorrect number of grid points
  5. The coordinates of the grid points were incorrect especially when iIGNOREOUTER is non-zero
  6. Norm calculation was incorrect

Attached patches should solve the problems.

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