Fix memory issues revealed by cmake+GCC15 compile#1179

Merged

drroe merged 11 commits intoAmber-MD:masterfrom

Apr 14, 2026

Commits on Apr 14, 2026

Fix memory issue that manifests when compiling with gcc15 and cmake
Daniel R. Roe
committed
Fix issue where mask index could go 1 past end of the mask array
Daniel R. Roe
committed
Ensure all residue indices of atoms in residues after merged residues are updated
Daniel R. Roe
committed
After residues 1 and 2 are merged, the residue that was 3 should be 2
Daniel R. Roe
committed
Previously Andy was using the trick of &array[idx] and &array[idx+end] in std::copy to access array begin and end pointers. However, this fails if idx+end is equal to the actual end of the array wi…
Daniel R. Roe
committed
With gcc15+cmake, the array is referenced when empty causing a segfault. Protect against this.
Daniel R. Roe
committed
Protect against dereferencing past end of array
Daniel R. Roe
committed
keepframe needs to be allocated for the number of input frames.
Daniel R. Roe
committed
Looks like Dave sometimes used reserve when he meant resize
Daniel R. Roe
committed
Protect against empty coords
Daniel R. Roe
committed
Fix memory issues revealed by cmake + gcc15 compile.
Daniel R. Roe
committed