Opening ORCA file: could not broadcast input array from shape

[mhvg1994@…]

The following bug report has been submitted:
Platform:        macOS-13.2.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Tried to open an Orca output file.

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/matthewgraneri/Documents/Homework/PhD/calculations/p2/complexes/ma.h2s/c1/orca/ccsdt/orca-5.0.2/final/ma.h2s-opt-
> freq-ccsdt-tz-mo2.out

Summary of feedback from opening
/Users/matthewgraneri/Documents/Homework/PhD/calculations/p2/complexes/ma.h2s/c1/orca/ccsdt/orca-5.0.2/final/ma.h2s-opt-
freq-ccsdt-tz-mo2.out  
---  
error | unable to open ma.h2s-opt-freq-ccsdt-tz-mo2.out  
  
Traceback (most recent call last):  
File
"/Applications/Chimera/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/Chimera/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/Chimera/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/Chimera/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/Chimera/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/Chimera/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/Chimera/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File
"/Applications/Chimera/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/__init__.py", line 431, in open  
return open_aarontools(  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/io.py", line 44, in open_aarontools  
raise e  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/SEQCROW/io.py", line 36, in open_aarontools  
fr = FileReader(  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/fileIO.py", line 1177, in __init__  
self.read_orca_out(f, get_all, just_geom)  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/fileIO.py", line 1888, in read_orca_out  
gradient[i] = np.array([float(x) for x in info[3:]])  
ValueError: could not broadcast input array from shape (0,) into shape (3,)  
  
ValueError: could not broadcast input array from shape (0,) into shape (3,)  
  
File "/Users/matthewgraneri/Library/Application Support/ChimeraX/1.5/site-
packages/AaronTools/fileIO.py", line 1888, in read_orca_out  
gradient[i] = np.array([float(x) for x in info[3:]])  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: Z14X000EVX/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 64 GB
      System Firmware Version: 8419.80.7
      OS Loader Version: 8419.80.7

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 11 minutes, 23 seconds

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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    ChimeraX-AddH: 2.2.1
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    ChimeraX-CellPack: 1.0
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File attachment: ma.h2s-opt-freq-ccsdt-tz-mo2.out

ma.h2s-opt-freq-ccsdt-tz-mo2.out​

[mhvg1994@…]

Added by email2trac

[pett]

Reported by "Matthew"

[Tony Schaefer]

Thanks for reporting this. It looks like our ORCA file parser is getting
tripped up when reading the energy gradient. ORCA usually prints a blank
line before the gradient, but that is not present in this file. I suspect
this is because this is a numerical gradient, but I'll have to investigate.
Either way, I should have a fix for this soon.

Tony

On Tue, Feb 14, 2023 at 9:17 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[mhvg1994@…]

HI Tony,

That was my initial thought too - not many methods in Orca that don’t have analytic first derivatives (at least, not many methods that people would use to optimise geometries), so wouldn’t surprise me if no one had come across it before. I just tested another CCSD(T) example I had and the same error popped up.

I also tested another method which had analytical first derivatives but numerical second derivatives and that opened without issue. So you’re probably right about the gradient being the issue.

Thanks for looking into this!

Regards,

Matthew

[Tony Schaefer]

Matthew,

Numerical gradients were indeed the issue. This should be fixed in SEQCROW
1.6. You can update through the toolshed (on the ChimeraX menu, Tools ->
More Tools... -> SEQCROW page -> update).

Best,

Tony

On Wed, Feb 15, 2023 at 12:14 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote: