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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.
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:
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()
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-
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
algorithm
==================
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:
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()
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