=============== Troubleshooting =============== Installation ============ ``ModuleNotFoundError: No module named 'pydseams'`` --------------------------------------------------- The package is not installed in the active interpreter. .. code-block:: bash 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: .. code-block:: bash pip install 'pydseams[ase]' ``ImportError`` naming ``pip install 'pydseams[solvis]'`` --------------------------------------------------------- solvis-tools is not installed: .. code-block:: bash 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 :doc:`../tutorials/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. :doc:`faq` 2. :doc:`../reference/python` 3. `PydSEAMSlib `_ issues Include the ``pydseams`` version, Python version, the file suffix, and the exact traceback.