Troubleshooting

This page lists common setup failures and the input file area to check first.

Existing Output Files

PQ does not overwrite output files by default. If setup stops with File already exists - filename = ..., either remove the previous output files, change file_prefix, or set:

overwrite_output = true;

Missing Setup Files

Errors such as Cannot open start file, Cannot open topology file or Cannot open parameter file mean that the path in the input file cannot be opened from the current working directory. Run examples from their own directory, or use explicit paths for the corresponding setup-file key.

Some setup files are only required for specific modes:

topology_file is required when force-field is set to bonded or on, or when shake is set to on or shake.

parameter_file is required when force-field is set to bonded or on.

mshake_file is required when shake = mshake is selected.

dftb_file is required for direct DFTB+ calculations.

Unknown Job Type

If setup reports an invalid jobtype, use one of the supported job types:

mm-md

qm-md

qm-rpmd

mm-opt

ASE and Slater-Koster Files

Built-in Slater-Koster sets for ase-dftbplus require ASE support at build time. If PQ was built without ASE support and the input requests slakos = 3ob or slakos = matsci, rebuild with:

$ cmake .. -DCMAKE_BUILD_TYPE=Release -DBUILD_WITH_ASE=On

For custom Slater-Koster files, set slakos = custom and provide slakos_path.

Kokkos Fallbacks

When PQ is built with Kokkos support, the accelerated MM path is only used for supported non-Coulombic and Coulomb settings. If another combination is requested, PQ prints a warning and falls back to serial execution.

Constraint Setup

For shake = shake or shake = mshake, check that:

topology_file is set when SHAKE bond constraints are needed.

mshake_file is set for M-SHAKE.

atom names in the M-SHAKE reference match the referenced molecule type.

atom indices in topology files refer to the current structure.