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大佬,请问这是什么问题呢
SMILES:CC(C(OCCOP(OCC[N+](C)(C)C)([O-])=O)=O)([*])C[*],均聚, 聚合度10,名称:MAPC
Failed to run notebook: 3_create_Polymer_itp_top.ipynb
Return Code: 1
Standard Output:
Initial conformer count: 50
75 attempts, 5 duplicates, 21 failed filter.
0 0 0 0 0 0 0 0 0 0
0 0 0 0 2 2 0 0 0 0
2 7 0 11 4 1 0 1 5 0
2 11 0 8 4 1 0 1 5 0
2 11 0 8 3 1 0 1 5 0
2 11 0 8 0 1 3 1 9 0
2 11 2 8 0 1 3 1 9 0
2 11 1 8 0 2 3 1 9 0
2 11 1 8 0 2 3 1 2 0
2 11 1 8 1 2 4 1 9 2
2 11 1 8 1 2 4 1 9 1
2 11 2 8 1 2 4 1 9 1
2 11 2 8 1 2 3 1 9 1
2 11 2 8 1 2 0 1 9 1
0 11 2 8 2 2 0 1 9 1
0 11 2 8 1 2 0 2 9 1
0 11 2 8 2 2 0 2 9 1
2 11 2 8 2 2 1 2 9 1
0 8 2 8 2 2 1 2 9 1
0 1 2 8 4 2 1 2 9 1
1 6 2 3 4 2 3 2 9 0
1 6 2 3 4 2 3 1 9 0
2 6 2 3 4 2 3 1 9 0
2 6 2 8 4 2 3 1 9 0
2 6 0 8 0 2 3 1 9 0
2 6 0 8 0 1 3 1 2 0
2 6 0 8 0 1 1 1 2 0
2 6 2 1 1 2 4 1 9 1
2 6 2 1 2 2 0 2 9 1
2 6 2 1 2 2 0 1 9 1
2 6 2 1 2 2 0 1 9 2
2 6 2 1 2 2 2 1 9 2
2 6 2 1 2 2 3 0 9 0
2 6 1 1 2 2 3 0 9 0
2 6 1 1 2 2 3 0 2 1
2 6 1 1 2 2 2 0 9 2
2 6 1 1 2 2 2 2 4 2
2 6 1 1 2 2 1 2 4 2
2 6 2 1 2 2 3 0 4 0
2 3 2 1 2 2 3 0 4 0
2 3 1 1 2 2 3 0 4 0
2 3 1 1 2 2 3 0 4 2
1 3 1 1 2 2 3 0 4 0
1 3 1 0 2 2 3 2 4 0
1 3 1 0 2 2 3 1 4 0
2 3 1 0 2 2 3 1 4 0
2 3 1 5 2 2 3 1 4 0
2 3 1 0 1 2 3 2 4 0
2 8 1 0 1 2 3 2 11 0
2 3 1 0 1 0 3 2 11 2
=====> Starting conformers search with a Genetic Algorithm <=====
Perform elitist generation replacement with mutation only
Mutation probability: 0.2
Will stop after 25 generations without improvement.
Generation #1 1.45357
Generation #2 1.5239
Generation #3 1.52817
Generation #4 1.56214
Generation #5 1.56214
Generation #6 1.56214
Generation #7 1.62632
Generation #8 1.62632
Generation #9 1.62632
Generation #10 1.62632
Generation #11 1.62632
Generation #12 1.62632
Generation #13 1.62632
Generation #14 1.62632
Generation #15 1.63665
Generation #16 1.63665
Generation #17 1.63665
Generation #18 1.64543
Generation #19 1.64543
Generation #20 1.64543
Generation #21 1.64543
Generation #22 1.64543
Generation #23 1.64543
Generation #24 1.64543
Generation #25 1.64543
Generation #26 1.64543
Generation #27 1.64543
Generation #28 1.64543
Generation #29 1.64543
Generation #30 1.64543
Generation #31 1.6512
Generation #32 1.6512
Generation #33 1.6512
Generation #34 1.6512
Generation #35 1.6512
Generation #36 1.6512
Generation #37 1.6512
Generation #38 1.6512
Generation #39 1.6512
Generation #40 1.65291
Generation #41 1.65291
Generation #42 1.65291
Generation #43 1.65291
Generation #44 1.65291
Generation #45 1.65291
Generation #46 1.65291
Generation #47 1.65291
Generation #48 1.65291
Generation #49 1.66003
Generation #50 1.66003
Generation #51 1.66003
Generation #52 1.66003
Generation #53 1.66003
Generation #54 1.66003
Generation #55 1.67593
Generation #56 1.67593
Generation #57 1.67593
Generation #58 1.67593
Generation #59 1.67593
Generation #60 1.67593
Generation #61 1.67593
Generation #62 1.67593
Generation #63 1.67593
Generation #64 1.67593
Generation #65 1.67593
Generation #66 1.67593
Generation #67 1.67593
Generation #68 1.67593
Generation #69 1.67593
Generation #70 1.67593
Generation #71 1.67593
Generation #72 1.67593
Generation #73 1.67593
Generation #74 1.67593
Generation #75 1.67593
Generation #76 1.67593
Generation #77 1.67593
Generation #78 1.67593
Generation #79 1.67593
Generation #80 1.67593
Generation #81 1.67593
0 11 2 1 0 0 1 0 9 2
1 2 1 11 2 0 4 0 11 2
2 7 0 4 4 2 4 0 9 2
1 2 0 5 0 2 3 1 10 1
2 0 2 5 0 2 3 1 2 0
1 3 1 0 2 0 4 2 9 2
2 11 0 3 1 0 4 0 9 2
2 7 0 4 1 2 4 2 9 2
1 2 2 11 3 0 3 0 4 0
1 0 2 5 0 2 3 1 2 0
2 6 2 7 2 0 4 2 4 0
2 6 0 1 2 2 0 0 5 0
2 6 0 1 2 0 0 0 5 0
1 6 1 3 0 2 3 1 2 2
0 11 0 3 0 2 3 0 9 1
2 11 0 4 1 2 4 2 9 2
0 6 0 1 2 2 0 0 9 1
1 11 0 2 0 2 3 0 11 0
2 11 0 4 1 2 4 0 9 2
1 11 1 5 0 2 3 1 2 0
0 6 0 1 3 1 0 2 5 1
0 9 0 11 2 2 0 2 5 1
2 9 2 3 1 2 4 1 3 2
0 11 1 3 0 2 3 0 2 1
1 11 0 5 0 1 3 1 2 1
1 11 1 5 3 2 3 0 2 0
0 5 0 1 0 1 1 2 3 1
1 11 0 2 0 2 1 1 2 2
0 11 0 5 3 2 3 0 2 0
2 6 2 2 2 2 0 2 3 0
1 11 2 8 3 2 3 0 9 0
0 11 0 1 2 0 0 0 5 0
1 6 2 3 0 2 3 1 2 2
1 6 2 3 0 0 0 0 11 1
0 6 2 1 2 2 1 0 5 2
0 11 0 5 0 2 3 1 2 1
1 11 2 5 0 1 3 1 2 1
0 11 2 1 0 2 1 0 9 1
2 1 2 8 2 1 4 2 4 0
2 2 1 3 2 2 4 2 4 2
0 9 2 6 1 0 4 2 0 2
1 11 2 8 3 1 3 1 9 0
0 5 1 5 0 2 3 1 2 0
0 9 2 3 1 2 4 0 3 2
1 11 1 5 0 1 3 1 5 0
0 11 2 1 2 2 1 0 5 0
0 11 0 5 4 1 3 1 2 1
0 5 2 4 0 2 3 0 1 1
1 9 2 11 2 2 3 2 4 0
2 6 1 2 2 2 0 2 3 0
GetConformers:
0 11 2 1 0 0 1 0 9 2
1 2 1 11 2 0 4 0 11 2
2 7 0 4 4 2 4 0 9 2
1 2 0 5 0 2 3 1 10 1
2 0 2 5 0 2 3 1 2 0
1 3 1 0 2 0 4 2 9 2
2 11 0 3 1 0 4 0 9 2
2 7 0 4 1 2 4 2 9 2
1 2 2 11 3 0 3 0 4 0
1 0 2 5 0 2 3 1 2 0
2 6 2 7 2 0 4 2 4 0
2 6 0 1 2 2 0 0 5 0
2 6 0 1 2 0 0 0 5 0
1 6 1 3 0 2 3 1 2 2
0 11 0 3 0 2 3 0 9 1
2 11 0 4 1 2 4 2 9 2
0 6 0 1 2 2 0 0 9 1
1 11 0 2 0 2 3 0 11 0
2 11 0 4 1 2 4 0 9 2
1 11 1 5 0 2 3 1 2 0
0 6 0 1 3 1 0 2 5 1
0 9 0 11 2 2 0 2 5 1
2 9 2 3 1 2 4 1 3 2
0 11 1 3 0 2 3 0 2 1
1 11 0 5 0 1 3 1 2 1
1 11 1 5 3 2 3 0 2 0
0 5 0 1 0 1 1 2 3 1
1 11 0 2 0 2 1 1 2 2
0 11 0 5 3 2 3 0 2 0
2 6 2 2 2 2 0 2 3 0
1 11 2 8 3 2 3 0 9 0
0 11 0 1 2 0 0 0 5 0
1 6 2 3 0 2 3 1 2 2
1 6 2 3 0 0 0 0 11 1
0 6 2 1 2 2 1 0 5 2
0 11 0 5 0 2 3 1 2 1
1 11 2 5 0 1 3 1 2 1
0 11 2 1 0 2 1 0 9 1
2 1 2 8 2 1 4 2 4 0
2 2 1 3 2 2 4 2 4 2
0 9 2 6 1 0 4 2 0 2
1 11 2 8 3 1 3 1 9 0
0 5 1 5 0 2 3 1 2 0
0 9 2 3 1 2 4 0 3 2
1 11 1 5 0 1 3 1 5 0
0 11 2 1 2 2 1 0 5 0
0 11 0 5 4 1 3 1 2 1
0 5 2 4 0 2 3 0 1 1
1 9 2 11 2 2 3 2 4 0
2 6 1 2 2 2 0 2 3 0
Standard Error:
[NbConvertApp] Converting notebook /data/jupyternotebook_public/Project15_AI_ML_BMS_JZZ/cemp/media/Polymer/GeneratePolymer/20250828_103810_f737e6/3_create_Polymer_itp_top.ipynb to notebook
Traceback (most recent call last):
File "/data/jiazheju/anaconda3/envs/cemp_env/bin/jupyter-nbconvert", line 10, in
sys.exit(main())
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/jupyter_core/application.py", line 283, in launch_instance
super().launch_instance(argv=argv, **kwargs)
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/traitlets/config/application.py", line 1075, in launch_instance
app.start()
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/nbconvertapp.py", line 420, in start
self.convert_notebooks()
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/nbconvertapp.py", line 597, in convert_notebooks
self.convert_single_notebook(notebook_filename)
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/nbconvertapp.py", line 563, in convert_single_notebook
output, resources = self.export_single_notebook(
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/nbconvertapp.py", line 487, in export_single_notebook
output, resources = self.exporter.from_filename(
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/exporters/exporter.py", line 201, in from_filename
return self.from_file(f, resources=resources, **kw)
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/exporters/exporter.py", line 220, in from_file
return self.from_notebook_node(
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/exporters/notebook.py", line 36, in from_notebook_node
nb_copy, resources = super().from_notebook_node(nb, resources, **kw)
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/exporters/exporter.py", line 154, in from_notebook_node
nb_copy, resources = self._preprocess(nb_copy, resources)
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/exporters/exporter.py", line 353, in _preprocess
nbc, resc = preprocessor(nbc, resc)
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/preprocessors/base.py", line 48, in __call__
return self.preprocess(nb, resources)
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/preprocessors/execute.py", line 103, in preprocess
self.preprocess_cell(cell, resources, index)
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/preprocessors/execute.py", line 124, in preprocess_cell
cell = self.execute_cell(cell, index, store_history=True)
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
return loop.run_until_complete(inner)
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
return future.result()
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbclient/client.py", line 1062, in async_execute_cell
await self._check_raise_for_error(cell, cell_index, exec_reply)
File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbclient/client.py", line 918, in _check_raise_for_error
raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
# 创建使用原子名称{atom_type}_{name}代替索引与原子编号的copolymer的fake itp文件
generate_fake_itp_for_copolymer(df, polymer_node_list_path="polymer_node_list.json")
------------------
[0;31m---------------------------------------------------------------------------[0m
[0;31mFileNotFoundError[0m Traceback (most recent call last)
Cell [0;32mIn[21], line 2[0m
[1;32m 1[0m [38;5;66;03m# 创建使用原子名称{atom_type}_{name}代替索引与原子编号的copolymer的fake itp文件[39;00m
[0;32m----> 2[0m [43mgenerate_fake_itp_for_copolymer[49m[43m([49m[43mdf[49m[43m,[49m[43m [49m[43mpolymer_node_list_path[49m[38;5;241;43m=[39;49m[38;5;124;43m"[39;49m[38;5;124;43mpolymer_node_list.json[39;49m[38;5;124;43m"[39;49m[43m)[49m
Cell [0;32mIn[20], line 34[0m, in [0;36mgenerate_fake_itp_for_copolymer[0;34m(df, polymer_node_list_path)[0m
[1;32m 31[0m [38;5;28;01mraise[39;00m [38;5;167;01mValueError[39;00m([38;5;124m"[39m[38;5;124m第一条 copolymer_name 为空或无效。[39m[38;5;124m"[39m)
[1;32m 33[0m [38;5;66;03m# ========================= 1) 读取 atom_list =========================[39;00m
[0;32m---> 34[0m atom_list [38;5;241m=[39m [43mload_polymer_atom_list[49m[43m([49m[43mpolymer_node_list_path[49m[43m)[49m [38;5;66;03m# 中文注释:从 polymer_node_list_path 读取节点列表[39;00m
[1;32m 36[0m [38;5;66;03m# 将形如“{name}_{i}”的字符串统一裁剪为“{name}”;仅当末尾为“_纯数字”时才去掉[39;00m
[1;32m 37[0m [38;5;250m[39m[38;5;124;03m'''[39;00m
[1;32m 38[0m [38;5;124;03m由于atom_list = load_polymer_atom_list(polymer_node_list_path)的atom_list中的元素形如:“C0_test_C_C_20250821_1”,其结构为“{name}_{i}”,即[39;00m
[1;32m 39[0m [38;5;124;03mname为C0_test_C_C_20250821,也有可能是其他任何输入值,而{i}在这里为1,[39;00m
[1;32m 40[0m [38;5;124;03m现在我希望你在原来代码的基础上多补充代码,作用为:[39;00m
[1;32m 41[0m [38;5;124;03m将结构为“{name}_{i}”的元素全部转化为“{name}”,你不需要给出全部代码,只需要告诉我应该在哪里修改以及具体增补代码即可。[39;00m
[1;32m 42[0m [38;5;124;03m'''[39;00m
Cell [0;32mIn[10], line 16[0m, in [0;36mload_polymer_atom_list[0;34m(file_path)[0m
[1;32m 14[0m [38;5;66;03m# 中文注释:基本存在性检查,便于友好报错[39;00m
[1;32m 15[0m [38;5;28;01mif[39;00m [38;5;129;01mnot[39;00m os[38;5;241m.[39mpath[38;5;241m.[39misfile(file_path):
[0;32m---> 16[0m [38;5;28;01mraise[39;00m [38;5;167;01mFileNotFoundError[39;00m([38;5;124mf[39m[38;5;124m"[39m[38;5;124m未找到文件:[39m[38;5;132;01m{[39;00mfile_path[38;5;132;01m}[39;00m[38;5;124m"[39m)
[1;32m 18[0m [38;5;66;03m# 中文注释:读取JSON并解析为Python对象[39;00m
[1;32m 19[0m [38;5;28;01mwith[39;00m [38;5;28mopen[39m(file_path, [38;5;124m"[39m[38;5;124mr[39m[38;5;124m"[39m, encoding[38;5;241m=[39m[38;5;124m"[39m[38;5;124mutf-8[39m[38;5;124m"[39m) [38;5;28;01mas[39;00m f:
[0;31mFileNotFoundError[0m: 未找到文件:polymer_node_list.json |
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