cppp.x and atomic order

"The current version of QE, v 7.0, has a problem with the utility cppp.x, namely: cppp.x outputs atoms sorted by element, whether or not the input to cp.x was given in that order.

cp.x itself behaves properly with ATOMIC_POSITIONS entered in “molecule order”, i.e., reflecting the connectivity of atoms into successive molecules, as might be supplied by a classical MD simulation platform or molecule-building software. With such input, cp.x writes log entries to stdout that include snapshots of atomic positions in the same order as input.

However, it appears that the .pos and .for files saved by cp.x are sorted by atomic number, in the same order as atom types were given in ATOMIC_SPECIES. As written, cppp.x apparently outputs atoms in this sorted order. This is really awkward; in a better design, cppp.x would output atoms in the same order they were input." (noticed by Scott Milner, Penn State)