Troubleshooting

Installation

ModuleNotFoundError: No module named 'pydseams'

The package is not installed in the active interpreter.

python -c "import sys; print(sys.executable)"
python -m pip install pydseamslib

ImportError naming pip install 'pydseamslib[ase]'

ASE is not installed. The extra is optional:

pip install 'pydseamslib[ase]'

ImportError naming pip install 'pydseamslib[solvis]'

solvis-tools is not installed:

pip install 'pydseamslib[solvis]'

Loading frames

ValueError: ... has no atoms of type 1 or 2

Frame.from_file looks for LAMMPS type 2 (oxygen) then type 1. The dump has neither, or atom_type does not match the file. Pass atom_type explicitly, or use from_ase / from_arrays when the types are not 1/2.

ValueError: from_ase requires a cell periodic in all three directions

Set periodic boundary conditions on all three ASE cell directions. Partially periodic configurations do not define the three-dimensional periodic geometry required by the engine.

ValueError: from_ase cannot convert a singular cell

Supply a cell with nonzero volume. Orthorhombic and general triclinic cells are accepted when they are nonsingular and fully periodic.

ValueError: no atoms matched select=...

from_ase(..., select="O") found no oxygen. Pass the symbol or atomic number that is present, or select=None.

ValueError: bonded="hbond" requires a heavy-atom selection that excludes H

The ASE analysis selection contains hydrogen. Use select="O" (or another heavy species) for hydrogen-bond topology, or use bonded="cutoff" for an all-atom frame.

ValueError: Hydrogen-bond analysis needs hydrogens

bonded="hbond" (or "auto" when the constructor decided hbond) needs an H cloud. Pass ASE Atoms that include H, a LAMMPS dump with hydrogen, or set bonded="cutoff".

RuntimeError: chemfiles is not linked in this build of seams-core

.pdb / .gro / .dcd need a wheel that linked chemfiles. available_readers()["chemfiles"] is False on this build. Convert to LAMMPS or XYZ, or use a build with chemfiles.

RuntimeError: readcon-core is not linked

=.con~ needs a wheel that linked readcon-core. available_readers()["readcon"] reports the flag.

RuntimeError: this build has no readXYZ

=.xyz~ needs yoda.readXYZ. Check available_readers()["xyz"].

Classification

Cage score is all water on a mixed snapshot

That is the fixture result on tests/data/exampleTraj.lammpstrj: CHILL+ sees local ice, cages() finds no finished HC or DDC. See the classify-ice tutorial.

Counts differ from a documented dump

Confirm the path, the 1-indexed frame, cutoff (default 3.5 Angstroms), and atom_type. A different snapshot is a different histogram.

Common messages

Error	Cause	Action
No module named 'pydseams'	Wrong interpreter	python -m pip install pydseamslib
pip install 'pydseamslib[ase]'	ASE extra missing	install the extra
periodic in all three directions	Partial ASE periodicity	set all three PBC flags or use a compatible input geometry
cannot convert a singular cell	Zero-volume ASE cell	supply a nonsingular cell
Hydrogen-bond analysis needs hydrogens	No H cloud	bonded="cutoff" or pass H
chemfiles is not linked	Optional reader	check available_readers()

Getting help

1. FAQ

2. Python surface

3. PydSEAMSlib issues

Include the pydseams version, Python version, the file suffix, and the exact traceback.