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 pydseams

ImportError naming pip install 'pydseams[ase]'#

ASE is not installed. The extra is optional:

pip install 'pydseams[ase]'

ImportError naming pip install 'pydseams[solvis]'#

solvis-tools is not installed:

pip install 'pydseams[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 needs an orthorhombic cell#

The engine box is three lengths. Make the Atoms cell orthorhombic, or build the frame with from_arrays from positions and [lx, ly, lz].

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: 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 Tutorial: 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 pydseams

pip install 'pydseams[ase]'

ASE extra missing

install the extra

orthorhombic cell

General ASE cell

three box lengths only

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. Frequently asked questions

  2. Python surface

  3. PydSEAMSlib issues

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