#741 obabel cyclization hang for large silicon cluster

[Jiahao Chen]

In converting the attached amorphous silicon cluster 3x3x3 supercell from XYZ to Mol2, obabel appears to hang while calculating the ring topology (the program did not finish in 22 hours). In contrast, the unit cell XYZ to Mol2 is successful and completes in five seconds. Please find attached a tarball, split into two chunks using gnu split, containing the structures and corresponding output logs, and the successful output for the single unit cell. In gdb, the backtrace is identical whenever I stop the execution except for lines #0 and #1. Shown is the backtrace after execution was stopped manually after 22 hrs.

This problem occurs with the head revision (r4519) on ubuntu-10.04 x86_64.

[Jiahao Chen]

tarball part 1

[Jiahao Chen]

tarball part 2