something wrong happened when i run the example dump file

[pig-pig-man2020]

hi, i install reacnetgenerator by "conda install reacnetgenerator -c conda-forge" and something wrong happened with my dump file. so i download the example file you provide from https://bf.njzjz.win/reacnetgenerator/dump.reaxc and the same error still happened.

(base) E:\ChromeCoreDownloads>reacnetgenerator --type lammpsdumpfile -i dump.rea
xc -a C H O
�[32m2022-01-08 15:07:37,245�[0m - ReacNetGen 1.0.0 - �[1;30mINFO:�[0m ReacNetGe
nerator: an automatic reaction network generator for reactive
molecular dynamics simulation.

Plase 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 --dump -i dump.reaxc -a C H O
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 -i bonds.reaxc -a C H O

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

�[32m2022-01-08 15:07:37,251�[0m - ReacNetGen 1.0.0 - �[1;30mINFO:�[0m Version:
1.0.0 Creation date: 2018-03-11 Update date: 2019-10-07
Read bond information and Detect molecules: 401timestep [00:06, 84.23timestep/s]
Read bond information and Detect molecules: 702timestep [00:06, 167.52timestep/s
Read bond information and Detect molecules: 815timestep [00:07, 180.14timestep/s
Read bond information and Detect molecules: 1001timestep [00:07, 141.78timestep/
s]
Save molecules: 100%|███████████████| 2895/2895 [00:04<00:00, 624
.87molecule/s]
�[32m2022-01-08 15:07:50,323�[0m - ReacNetGen 1.0.0 - �[1;30mINFO:�[0m Step 1: D
one! Time consumed (s): 13.070 (Read bond information and Detect molecules)
HMM filter: 10%|██▏ | 301/2895 [00:04<00:30, 85.68molecule/
HMM filter: 21%|████▏ | 601/2895 [00:05<00:11, 192.96molecul
HMM filter: 31%|██████▏ | 901/2895 [00:05<00:06, 322.87molec
HMM filter: 41%|███████▉ | 1201/2895 [00:05<00:03, 491.64mole
HMM filter: 48%|█████████▏ | 1401/2895 [00:05<00:02, 616.61mo
HMM filter: 59%|███████████▏ | 1701/2895 [00:05<00:01, 831.51
HMM filter: 69%|████████████▍ | 2001/2895 [00:05<00:00, 1012.5
HMM filter: 83%|██████████████▉ | 2401/2895 [00:06<00:00, 1301
HMM filter: 97%|█████████████████▍| 2801/2895 [00:06<00:00, 1
HMM filter: 100%|███████████████████| 2895/2895 [00:06<00:00,
470.66molecule/s]
�[32m2022-01-08 15:07:57,238�[0m - ReacNetGen 1.0.0 - �[1;30mINFO:�[0m Step 2: D
one! Time consumed (s): 6.914 (HMM filter)
Indentify isomers: 1%|▏ | 1/102 [00:04<07:50, 4.66s/molecule]
Indentify isomers: 100%|███████████████| 102/102 [00:04<00:00, 21
.88molecule/s]
Analyze atoms: 100%|████████████████| 102/102 [00:00<00:00, 1133
3.25molecule/s]
Collect reaction paths: 100%|██████████████| 150/150 [00:04<00:00,
33.88atom/s]
Analyze reactions (A+B->C+D): 100%|█| 1000/1000 [00:04<00:00, 214.87timestep/s]

�[32m2022-01-08 15:08:13,234�[0m - ReacNetGen 1.0.0 - �[1;30mINFO:�[0m Step 3: D
one! Time consumed (s): 15.995 (Indentify isomers and collect reaction paths)
F:\anaconda3\Scripts\reacnetgenerator-script.py:10: DeprecationWarning: np.int
is a deprecated alias for the builtin int. To silence this warning, use int
by itself. Doing this will not modify any behavior and is safe. When replacing
np.int, you may wish to use e.g. np.int64 or np.int32 to specify the preci
sion. If you wish to review your current use, check the release note link for ad
ditional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdo
cs/release/1.20.0-notes.html#deprecations
sys.exit(_commandline())
�[32m2022-01-08 15:08:13,520�[0m - ReacNetGen 1.0.0 - �[1;30mINFO:�[0m Step 4: D
one! Time consumed (s): 0.286 (Reaction matrix generation)
�[32m2022-01-08 15:08:13,776�[0m - ReacNetGen 1.0.0 - �[1;30mINFO:�[0m Species a
re:
�[32m2022-01-08 15:08:13,777�[0m - ReacNetGen 1.0.0 - �[1;30mINFO:�[0m 1 [HH]
�[32m2022-01-08 15:08:13,777�[0m - ReacNetGen 1.0.0 - �[1;30mINFO:�[0m 2 [H]C
�[32m2022-01-08 15:08:13,778�[0m - ReacNetGen 1.0.0 - �[1;30mINFO:�[0m 3 C#C
�[32m2022-01-08 15:08:13,791�[0m - ReacNetGen 1.0.0 - �[1;30mERROR:�[0m �[31mErr
or: cannot draw images. Details: random_state_index is incorrect�[0m
File "reacnetgenerator_draw.py", line 71, in reacnetgenerator._draw._DrawNetw
ork._draw
File "F:\anaconda3\lib\site-packages\decorator.py", line 231, in fun
return caller(func, *(extras + args), **kw)
File "F:\anaconda3\lib\site-packages\networkx\utils\decorators.py", line 400,
in _random_state
raise nx.NetworkXError("random_state_index is incorrect") from e
�[32m2022-01-08 15:08:13,882�[0m - ReacNetGen 1.0.0 - �[1;30mINFO:�[0m Step 5: D
one! Time consumed (s): 0.362 (Draw reaction network)
3it [00:05, 1.81s/it]
Traceback (most recent call last):
File "F:\anaconda3\Scripts\reacnetgenerator-script.py", line 10, in
sys.exit(_commandline())
File "reacnetgenerator\commandline.py", line 59, in reacnetgenerator.commandli
ne._commandline
File "reacnetgenerator\reacnetgen.py", line 131, in reacnetgenerator.reacnetge
n.ReacNetGenerator.runanddraw
File "reacnetgenerator\reacnetgen.py", line 188, in reacnetgenerator.reacnetge
n.ReacNetGenerator._process
File "reacnetgenerator_reachtml.py", line 45, in reacnetgenerator.reachtml.
HTMLResult.report
File "reacnetgenerator_reachtml.py", line 137, in reacnetgenerator._reachtml.
_HTMLResult._generateresult
File "reacnetgenerator_reachtml.py", line 157, in reacnetgenerator._reachtml.
_HTMLResult._generatenetwork
FileNotFoundError: [Errno 2] No such file or directory: 'dump.reaxc.svg'

(base) E:\ChromeCoreDownloads>

[njzjz]

This is a known issue of NetworkX (networkx/networkx#4718). The issue should have been fixed in a newer version.

[njzjz]

You need to check the version of networkx.

[pig-pig-man2020]

thank you very much
i update NetworkX=2.6.3 and got what i want with the example dump file and a small dump file of mine
but when i run with a larger dump file of mine ( which is just more md steps than the small dump file i mentioned above ) , something wrong happened

(base) PS F:> reacnetgenerator --type lammpsdumpfile -i .\H_O.dump -a H O
�[32m2022-01-08 18:19:02,558�[0m - ReacNetGen 1.0.0 - �[1;30mINFO:�[0m ReacNetGe
nerator: an automatic reaction network generator for reactive
molecular dynamics simulation.

Plase 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 --dump -i dump.reaxc -a C H O
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 -i bonds.reaxc -a C H O

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

�[32m2022-01-08 18:19:02,560�[0m - ReacNetGen 1.0.0 - �[1;30mINFO:�[0m Version:
1.0.0 Creation date: 2018-03-11 Update date: 2019-10-07
Read bond information and Detect molecules: 101timestep [00:13, 10.23timestep/s]
Read bond information and Detect molecules: 201timestep [00:14, 23.03timestep/s]
Read bond information and Detect molecules: 301timestep [00:15, 37.32timestep/s]
Read bond information and Detect molecules: 401timestep [00:22, 22.62timestep/s]
Read bond information and Detect molecules: 501timestep [00:23, 30.54timestep/s]
Read bond information and Detect molecules: 601timestep [00:23, 45.15timestep/s]
Read bond information and Detect molecules: 701timestep [00:25, 44.91timestep/s]
Read bond information and Detect molecules: 801timestep [00:30, 31.96timestep/s]
Read bond information and Detect molecules: 901timestep [00:32, 37.35timestep/s]
Read bond information and Detect molecules: 1001timestep [00:32, 51.84timestep/s
Read bond information and Detect molecules: 1101timestep [00:35, 47.40timestep/s
Read bond information and Detect molecules: 1201timestep [00:39, 35.28timestep/s
Read bond information and Detect molecules: 1301timestep [00:41, 39.74timestep/s
Read bond information and Detect molecules: 1401timestep [00:43, 40.72timestep/s
Read bond information and Detect molecules: 1501timestep [00:44, 51.10timestep/s
Read bond information and Detect molecules: 1601timestep [00:48, 38.30timestep/s
Read bond information and Detect molecules: 1701timestep [00:52, 35.98timestep/s
Read bond information and Detect molecules: 1801timestep [00:53, 41.04timestep/s
Read bond information and Detect molecules: 1901timestep [00:54, 53.93timestep/s
Read bond information and Detect molecules: 2001timestep [00:57, 42.82timestep/s
Read bond information and Detect molecules: 2101timestep [01:01, 35.47timestep/s
Read bond information and Detect molecules: 2195timestep [01:01, 49.02timestep/s
Read bond information and Detect molecules: 2228timestep [01:02, 45.59timestep/s
Read bond information and Detect molecules: 2301timestep [01:03, 50.87timestep/s
Read bond information and Detect molecules: 2401timestep [01:06, 45.35timestep/s
Read bond information and Detect molecules: 2500timestep [01:07, 36.98timestep/s
]
�[32m2022-01-08 18:20:10,388�[0m - ReacNetGen 1.0.0 - �[1;30mERROR:�[0m �[31mrun
_mp failed�[0m
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "F:\anaconda3\lib\multiprocessing\pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "F:\anaconda3\lib\multiprocessing\pool.py", line 48, in mapstar
return list(map(*args))
File "reacnetgenerator_detect.py", line 281, in reacnetgenerator._detect._Det
ectLAMMPSdump._readstepfunc
UnboundLocalError: local variable 'linecontent' referenced before assignment
"""

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

Traceback (most recent call last):
File "reacnetgenerator\utils.py", line 214, in reacnetgenerator.utils.run_mp
File "F:\anaconda3\lib\site-packages\tqdm\std.py", line 1178, in iter
for obj in iterable:
File "F:\anaconda3\lib\multiprocessing\pool.py", line 448, in
return (item for chunk in result for item in chunk)
File "F:\anaconda3\lib\multiprocessing\pool.py", line 868, in next
raise value
UnboundLocalError: local variable 'linecontent' referenced before assignment
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "F:\anaconda3\lib\multiprocessing\pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "F:\anaconda3\lib\multiprocessing\pool.py", line 48, in mapstar
return list(map(*args))
File "reacnetgenerator_detect.py", line 281, in reacnetgenerator._detect._Det
ectLAMMPSdump._readstepfunc
UnboundLocalError: local variable 'linecontent' referenced before assignment
"""

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

Traceback (most recent call last):
File "F:\anaconda3\Scripts\reacnetgenerator-script.py", line 10, in
sys.exit(_commandline())
File "reacnetgenerator\commandline.py", line 59, in reacnetgenerator.commandli
ne._commandline
File "reacnetgenerator\reacnetgen.py", line 131, in reacnetgenerator.reacnetge
n.ReacNetGenerator.runanddraw
File "reacnetgenerator\reacnetgen.py", line 178, in reacnetgenerator.reacnetge
n.ReacNetGenerator._process
File "reacnetgenerator_detect.py", line 74, in reacnetgenerator._detect._Dete
ct.detect
File "reacnetgenerator_detect.py", line 82, in reacnetgenerator._detect._Dete
ct._readinputfile
File "reacnetgenerator_detect.py", line 85, in reacnetgenerator._detect._Dete
ct._readinputfile
File "reacnetgenerator\utils.py", line 220, in run_mp
File "reacnetgenerator\utils.py", line 214, in reacnetgenerator.utils.run_mp
File "F:\anaconda3\lib\site-packages\tqdm\std.py", line 1178, in iter
for obj in iterable:
File "F:\anaconda3\lib\multiprocessing\pool.py", line 448, in
return (item for chunk in result for item in chunk)
File "F:\anaconda3\lib\multiprocessing\pool.py", line 868, in next
raise value
UnboundLocalError: local variable 'linecontent' referenced before assignment
(base) PS F:>

[njzjz]

Please check if your file is correct and complete, especially the last frame.

[pig-pig-man2020]

thank you very much 大神
i checked my largest dump file and found it really lost some lines compare to other file with less md steps
thank you very much again

[pig-pig-man2020]

i lost 2 atoms during the laregst md stimulation and add "thermo_modify lost ignore" to the input file of lammps
so the dump file is "incomplete"
write down here for anyone who have the same question in the future