Skip to content
GitLab
Projects Groups Topics Snippets
  • /
  • Help
    • Help
    • Support
    • Community forum
    • Submit feedback
    • Contribute to GitLab
  • Sign in
  • nomad-FAIR nomad-FAIR
  • Project information
    • Project information
    • Activity
    • Labels
    • Members
  • Repository
    • Repository
    • Files
    • Commits
    • Branches
    • Tags
    • Contributor statistics
    • Graph
    • Compare revisions
  • Issues 243
    • Issues 243
    • List
    • Boards
    • Service Desk
    • Milestones
  • Merge requests 45
    • Merge requests 45
  • CI/CD
    • CI/CD
    • Pipelines
    • Jobs
    • Schedules
  • Deployments
    • Deployments
    • Environments
    • Releases
  • Packages and registries
    • Packages and registries
    • Package Registry
    • Container Registry
    • Infrastructure Registry
  • Monitor
    • Monitor
    • Incidents
  • Analytics
    • Analytics
    • Value stream
    • CI/CD
    • Repository
  • Snippets
    • Snippets
  • Activity
  • Graph
  • Create a new issue
  • Jobs
  • Commits
  • Issue Boards
Collapse sidebar
  • nomad-labnomad-lab
  • nomad-FAIRnomad-FAIR
  • Issues
  • #556
Closed
Open
Issue created Jun 08, 2021 by Markus Scheidgen@mscheidgOwner

CP2K Exceptions

These are the entries (not published):

https://nomad-lab.eu/prod/rae/gui/entry/id/sa6kfegYRumPwIR2ZEptlQ/x6ggFOMoG3EZUXlZgGvOyn7LlpSa/logs

https://nomad-lab.eu/prod/rae/gui/entry/id/sa6kfegYRumPwIR2ZEptlQ/14mjscjcq8Yy7N1c64neFlOV-uBV/logs

These are the exceptions:

Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1425, in parse
    self.parse_configurations_quickstep()
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1137, in parse_configurations_quickstep
    parse_calculations(md_steps)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1113, in parse_calculations
    sec_system = self.parse_system(atomic_coord)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1004, in parse_system
    lattice_vectors = self.get_lattice_vectors(trajectory._frame)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 852, in get_lattice_vectors
    cell.get('ABC').split(), dtype=float), units).to('angstrom').magnitude
ValueError: could not convert string to float: '${LBOX}'
Traceback (most recent call last):
  File "/app/nomad/processing/data.py", line 460, in parsing
    self._parser_results, logger=logger)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1425, in parse
    self.parse_configurations_quickstep()
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1137, in parse_configurations_quickstep
    parse_calculations(md_steps)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1107, in parse_calculations
    parse_md_step(calculation)
  File "/usr/local/lib/python3.7/site-packages/cp2kparser/cp2k_parser.py", line 1080, in parse_md_step
    val = val.to('joule').magnitude
AttributeError: 'numpy.ndarray' object has no attribute 'to'

There are other errors: "Error reading trajectory", "Error reading MD energies".

Assignee
Assign to
Time tracking