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Opened 11 months ago
Last modified 11 months ago
#16427 assigned defect
SEQCROW: problems reading ORCA output
| Reported by: | Owned by: | Tony Schaefer | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.11.5+bpo-amd64-x86_64-with-glibc2.36
ChimeraX Version: 1.9rc202411150349 (2024-11-15 03:49:13 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202411150349 (2024-11-15)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open STEOM2.out
Summary of feedback from opening STEOM2.out
---
error | unable to open STEOM2.out as a ORCA output file
warnings | WARNING AaronTools.fileIO.FileReader.read_orca_out
an error occured while reading the ORCA output file
WARNING AaronTools.fileIO.FileReader.read_orca_out
an error occured while reading the ORCA output file
WARNING AaronTools.fileIO.FileReader.read_orca_out
last line read: TDM done ( 125.0 sec)
WARNING AaronTools.fileIO.FileReader.read_orca_out
an error occured while reading the ORCA output file
WARNING AaronTools.fileIO.FileReader.read_orca_out
last line read: TDM done ( 125.0 sec)
WARNING AaronTools.fileIO.FileReader.read_orca_out
the following data has been read: error, charge, multiplicity, n_basis,
scf_energy, Mulliken Charges, Löwdin Charges, Mulliken gross atomic
population, Total nuclear charge, Mulliken gross atomic charge, Mayer's
total valence, Mayer's bonded valence, Mayer's free valence, energy, E(0),
E(SL-MP2), E(CORR)(strong-pairs), E(CORR)(weak-pairs), E(CORR)(corrected),
E(TOT), error_msg
WARNING AaronTools.fileIO.FileReader.read_orca_out
an error occured while reading the ORCA output file
WARNING AaronTools.fileIO.FileReader.read_orca_out
last line read: TDM done ( 125.0 sec)
WARNING AaronTools.fileIO.FileReader.read_orca_out
the following data has been read: error, charge, multiplicity, n_basis,
scf_energy, Mulliken Charges, Löwdin Charges, Mulliken gross atomic
population, Total nuclear charge, Mulliken gross atomic charge, Mayer's
total valence, Mayer's bonded valence, Mayer's free valence, energy, E(0),
E(SL-MP2), E(CORR)(strong-pairs), E(CORR)(weak-pairs), E(CORR)(corrected),
E(TOT), error_msg
WARNING AaronTools.fileIO.FileReader.read_orca_out
INPUT FILE
================================================================================
NAME =
/scratch/ochem/k360471/ORCA_scratch_k360471/orcajob__288438.lotte-p4Bw/STEOM2.inp
| 1> %pal
| 2> nprocs 8
| 3> end
| 4> %maxcore 5000
| 5>
| 6> !STEOM-DLPNO-CCSD def2-TZVPPD def2-TZVPPD/C RIJCOSX
| 7> !defgrid3
| 8> !SMD(HEXANE)
| 9> %MDCI
| 10> NROOTS 15
| 11> DOSOLV TRUE
| 12> END
| 13>
| 14> *XYZFILE 0 1 OPT2.001.xyz
| 15>
WARNING AaronTools.fileIO.FileReader.read_orca_out
an error occured while reading the ORCA output file
WARNING AaronTools.fileIO.FileReader.read_orca_out
last line read: TDM done ( 125.0 sec)
WARNING AaronTools.fileIO.FileReader.read_orca_out
the following data has been read: error, charge, multiplicity, n_basis,
scf_energy, Mulliken Charges, Löwdin Charges, Mulliken gross atomic
population, Total nuclear charge, Mulliken gross atomic charge, Mayer's
total valence, Mayer's bonded valence, Mayer's free valence, energy, E(0),
E(SL-MP2), E(CORR)(strong-pairs), E(CORR)(weak-pairs), E(CORR)(corrected),
E(TOT), error_msg
WARNING AaronTools.fileIO.FileReader.read_orca_out
INPUT FILE
================================================================================
NAME =
/scratch/ochem/k360471/ORCA_scratch_k360471/orcajob__288438.lotte-p4Bw/STEOM2.inp
| 1> %pal
| 2> nprocs 8
| 3> end
| 4> %maxcore 5000
| 5>
| 6> !STEOM-DLPNO-CCSD def2-TZVPPD def2-TZVPPD/C RIJCOSX
| 7> !defgrid3
| 8> !SMD(HEXANE)
| 9> %MDCI
| 10> NROOTS 15
| 11> DOSOLV TRUE
| 12> END
| 13>
| 14> *XYZFILE 0 1 OPT2.001.xyz
| 15>
WARNING AaronTools.fileIO.FileReader.read_orca_out
the following data has been read: error, charge, multiplicity, n_basis,
scf_energy, Mulliken Charges, Löwdin Charges, Mulliken gross atomic
population, Total nuclear charge, Mulliken gross atomic charge, Mayer's
total valence, Mayer's bonded valence, Mayer's free valence, energy, E(0),
E(SL-MP2), E(CORR)(strong-pairs), E(CORR)(weak-pairs), E(CORR)(corrected),
E(TOT), error_msg
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/__main__.py", line 1015, in init
commands.run(sess, "open %s" % StringArg.unparse(arg))
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 215, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 526, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 497, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/matthias/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/SEQCROW/__init__.py", line 596, in open
return open_aarontools(
^^^^^^^^^^^^^^^^
File "/home/matthias/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/SEQCROW/io.py", line 46, in open_aarontools
raise e
File "/home/matthias/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/SEQCROW/io.py", line 33, in open_aarontools
fr = FileReader(
^^^^^^^^^^^
File "/home/matthias/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/AaronTools/fileIO.py", line 1629, in __init__
self.read_orca_out(f, get_all, just_geom, log=None)
File "/home/matthias/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/AaronTools/fileIO.py", line 3189, in read_orca_out
raise e
File "/home/matthias/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/AaronTools/fileIO.py", line 3031, in read_orca_out
self.other["uv_vis"] = ValenceExcitations(s, orca_version=orca_version,
style="orca")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/matthias/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/AaronTools/spectra.py", line 1423, in __init__
super().__init__(*args, **kwargs)
File "/home/matthias/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/AaronTools/spectra.py", line 78, in __init__
self.parse_orca_lines(lines, *args, **kwargs)
File "/home/matthias/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/AaronTools/spectra.py", line 1595, in parse_orca_lines
oscillator_str.append(float(info[6]))
^^^^^^^^^^^^^^
ValueError: could not convert string to float: 'not'
ValueError: could not convert string to float: 'not'
File "/home/matthias/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/AaronTools/spectra.py", line 1595, in parse_orca_lines
oscillator_str.append(float(info[6]))
^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 24.2.4-1~bpo12+1
OpenGL renderer: Mesa Intel(R) HD Graphics 630 (KBL GT2)
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_GB.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb
XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: HP
Model: HP EliteDesk 800 G3 TWR
OS: Debian GNU/Linux 12
Architecture: 64bit ELF
Virtual Machine: none
CPU: 4 Intel(R) Core(TM) i5-7500 CPU @ 3.40GHz
Cache Size: 6144 KB
Memory:
total used free shared buff/cache available
Mem: 7.6Gi 6.2Gi 184Mi 1.5Gi 3.1Gi 1.4Gi
Swap: 164Gi 4.9Gi 159Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 630 [8086:5912] (rev 04)
DeviceName: Onboard IGD
Subsystem: Hewlett-Packard Company HD Graphics 630 [103c:8298]
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 2.4.1
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.7.1
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.7
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.7
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9rc202411150349
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.11
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.3.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.8
decorator: 5.1.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.1
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
Send2Trash: 1.8.3
SEQCROW: 1.8.16
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 11 months ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → SEQCROW: problems reading ORCA output |
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