Error when performing analysis

[GuokangOwO]

I successfully installed reacnetgenerator on my PC. However, when I attempted to use it for analyzing the lammpsbondfile generated by ReaxFF, an error occurred. I then tried running the same command on the HPC, but encountered the same error. The command and output are as follows:

reacnetgenerator -i A3.bonds -a H C Si --type bond --nohmm

2024-10-18 17:52:57,664 - ReacNetGenerator Unknown - INFO: ReacNetGenerator: an automatic reaction network generator for reactive
molecular dynamics simulation.

Please cite: ReacNetGenerator: an automatic reaction network generator
for reactive molecular dynamic simulations, Phys. Chem. Chem. Phys.,
2020, 22 (2): 683-691, doi: 10.1039/C9CP05091D

Jinzhe Zeng ([email protected]), Tong Zhu ([email protected])

==================
Features

• Processing of MD trajectory containing atomic coordinates or bond orders
• Hidden Markov Model (HMM) based noise filtering
• Isomers identifying accoarding to SMILES
• Generation of reaction network for visualization using force-directed
  algorithm
• Parallel computing

==================
Simple example

ReacNetGenerator can process any kind of trajectory files containing
atomic coordinates, e.g. a LAMMPS dump file prepared by running “dump 1
all custom 100 dump.reaxc id type x y z” in LAMMPS:
$ reacnetgenerator --type dump -i dump.reaxc -a C H O --nohmm
where C, H, and O are atomic names in the input file. Analysis report
will be generated automatically.

Also, ReacNetGenerator can process files containing bond information,
e.g. LAMMPS bond file:
$ reacnetgenerator --type bond -i bonds.reaxc -a C H O --nohmm

You can running the following script for help:
$ reacnetgenerator -h

2024-10-18 17:52:57,664 - ReacNetGenerator Unknown - INFO: Version: Unknown Creation date: 2018-03-11
Read bond information and Detect molecules: 0timestep [00:11, ?timestep/s]
2024-10-18 17:53:09,305 - ReacNetGenerator Unknown - ERROR: run_mp failed
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "D:\compute\conda\Lib\multiprocessing\pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^^^^^
File "D:\compute\conda\Lib\multiprocessing\pool.py", line 48, in mapstar
return list(map(*args))
^^^^^^^^^^^^^^^^
File "D:\compute\conda\Lib\site-packages\reacnetgenerator_detect.py", line 255, in _readstepfunc
molecules = self._connectmolecule(bond, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\compute\conda\Lib\site-packages\reacnetgenerator_detect.py", line 188, in _connectmolecule
mols, bondlists = dps(bond, level)
^^^^^^^^^^^^^^^^
File "dps.pyx", line 58, in reacnetgenerator.dps.dps
TypeError: object of type 'NoneType' has no len()
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "D:\compute\conda\Lib\site-packages\reacnetgenerator\utils.py", line 558, in run_mp
for item in results:
^^^^^^^
File "C:\Users\ol060\AppData\Roaming\Python\Python312\site-packages\tqdm\std.py", line 1181, in iter
for obj in iterable:
File "D:\compute\conda\Lib\multiprocessing\pool.py", line 451, in
return (item for chunk in result for item in chunk)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\compute\conda\Lib\multiprocessing\pool.py", line 873, in next
raise value
TypeError: object of type 'NoneType' has no len()
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "D:\compute\conda\Lib\multiprocessing\pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^^^^^
File "D:\compute\conda\Lib\multiprocessing\pool.py", line 48, in mapstar
return list(map(*args))
^^^^^^^^^^^^^^^^
File "D:\compute\conda\Lib\site-packages\reacnetgenerator_detect.py", line 255, in _readstepfunc
molecules = self._connectmolecule(bond, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\compute\conda\Lib\site-packages\reacnetgenerator_detect.py", line 188, in _connectmolecule
mols, bondlists = dps(bond, level)
^^^^^^^^^^^^^^^^
File "dps.pyx", line 58, in reacnetgenerator.dps.dps
TypeError: object of type 'NoneType' has no len()
"""
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "D:\compute\conda\Scripts\reacnetgenerator-script.py", line 10, in
sys.exit(_commandline())
^^^^^^^^^^^^^^
The above exception was the direct cause of the following exception:

).runanddraw()
).runanddraw()
  ^^^^^^^^^^^^
).runanddraw()
).runanddraw()
  ^^^^^^^^^^^^

File "D:\compute\conda\Lib\site-packages\reacnetgenerator\reacnetgen.py", line 269, in runanddraw ).runanddraw()
^^^^^^^^^^^^
File "D:\compute\conda\Lib\site-packages\reacnetgenerator\reacnetgen.py", line 269, in runanddraw ).runanddraw()
^^^^^^^^^^^^
File "D:\compute\conda\Lib\site-packages\reacnetgenerator\reacnetgen.py", line 269, in runanddraw ).runanddraw()
^^^^^^^^^^^^
File "D:\compute\conda\Lib\site-packages\reacnetgenerator\reacnetgen.py", line 269, in runanddraw ).runanddraw()
^^^^^^^^^^^^
File "D:\compute\conda\Lib\site-packages\reacnetgenerator\reacnetgen.py", line 269, in runanddraw ).runanddraw()
^^^^^^^^^^^^
File "D:\compute\conda\Lib\site-packages\reacnetgenerator\reacnetgen.py", line 269, in runanddraw self._readinputfile()
).runanddraw()
^^^^^^^^^^^^
File "D:\compute\conda\Lib\site-packages\reacnetgenerator\reacnetgen.py", line 269, in runanddra ).ru ).runanddraw()
^^^^^^^^^^^^
File "D:\compute\conda\Lib\site-packages\reacnetgenerator\reacnetgen.py", line 269, in runanddraw ).runanddraw()
^^^^^^^^^^^^
File "D:\compute\conda\Lib\site-packages\reacnetgenerator\reacnetgen.py", line 269, in runanddraw _Detect.gettype(self).detect()
).runanddraw()
).runanddraw()
^^^^^^^^^^^^
File "D:\compute\conda\Lib\site-packages\reacnetgenerator\reacnetgen.py", line 269, in runanddraw
self._process(processthing)
File "D:\compute\conda\Lib\site-packages\reacnetgenerator\reacnetgen.py", line 333, in _process
_Detect.gettype(self).detect()
File "D:\compute\conda\Lib\site-packages\reacnetgenerator_detect.py", line 132, in detect
self._readinputfile()
File "D:\compute\conda\Lib\site-packages\reacnetgenerator_detect.py", line 152, in _readinputfile
for molecules, (step, thetimestep) in results:
^^^^^^^
File "D:\compute\conda\Lib\site-packages\reacnetgenerator\utils.py", line 558, in run_mp
for item in results:
^^^^^^^
File "C:\Users\ol060\AppData\Roaming\Python\Python312\site-packages\tqdm\std.py", line 1181, in iter
for obj in iterable:
File "D:\compute\conda\Lib\multiprocessing\pool.py", line 451, in
return (item for chunk in result for item in chunk)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\compute\conda\Lib\multiprocessing\pool.py", line 873, in next
raise value
TypeError: object of type 'NoneType' has no len()

[njzjz]

Could you provide an example to reproduce the error?