Thanks for the clarification, I managed to reproduce the fail. The problem comes from the fact that we do not generate code for a scalar reduction that is not detected as a scalar reduction with the variable connection$dim$1$lbound.
In the attached output from debug_loops (3) I selected the region of code containing both the original loops: loop_3 and loop_4 and the code generated by graphite with -fgraphite-identity: loop_22, loop_23. In loop_22 the computation on connection$dim$1$lbound disappears. I wonder what this variable stands for: it is not used elsewhere in the debug_loops (3) output of change_bond_length function, and I suspect that this is a global variable whose value is needed elsewhere outside the change_bond_length function. The bug is in the detection of scalar reductions. Sebastian
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