可生成任意聚合度线形聚合物结构、拓扑以及电荷的在线程序 - 计算化学公社

应该写成CC，而非CC

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Your key is: gAAAAABoorXMMGdCiLetDoMgKUnbfh_gbipPL4fNmNxtncCuAJarECD3Jbq70IACyMceiB5uPMsagGO6eWPBRQfhyFSkfyv1RDT1abUIxt85BoZZLjH6COnNfXfZt6JF5g2tH9JYbiyRNCB51yW6tcluBIKknLnWHgiBpSb_9eufJOkuhC2e7sE_FxRtheLjqZ7TVMQYxHvk6FMiOlhL996USy9HEb3FeHeUWUF-I0GEU_tzBPVz1xTKYiFLo1jTw60g8al4PYmWLXaCR5nd3e6Tlx92YquSyle7XOugcbOSzBkqEV2CWkXviWH_p0gzA_PaCSvOD63QJ7b8eSyD5XGha2cKcEUvorI7Ruwi5ozexIxipjTqB-FhEbcDg8xRsLD9Mj5XACqTKeHqkunhlr2HrTtXX7Bhx60kjevJ4sVKUu2H7uchBlQ=

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Failed to run notebook: 1_Polymer_RESP_repeat_unit.ipynb
Return Code: 1
Standard Output:
Standard Error:
[NbConvertApp] Converting notebook /data/jupyternotebook_public/Project15_AI_ML_BMS_JZZ/cemp/media/Polymer/GeneratePolymer/20250818_131036_4e8d68/1_Polymer_RESP_repeat_unit.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:
------------------
# 创建成功和失败的文件夹
os.makedirs('Gaussian/RESPpolymer/success', exist_ok=True)
os.makedirs('Gaussian/RESPpolymer/failure', exist_ok=True)
# 定义Gaussian生成文件路径
base_dir = 'Gaussian/RESPpolymer'
success_dir = os.path.join(base_dir, 'success')
failure_dir = os.path.join(base_dir, 'failure')
# 设置opt+freq文件夹路径
Gaussian_path = "Gaussian/RESPpolymer/success"
#检查存储结构优化的文件Gaussian_database是否存在于当前账户上
gaussian_database_path, optfreq_gaussian_database_path, RESPpolymer_database_path = check_and_create_gaussian_database()
# 获取System.xlsx的dataframe，以及存储聚合物名称的列表
df, polymers = read_excel_and_create_lists('System_homopolymer.xlsx')
# 拷贝聚合物的文件，从数据库拷贝到当前目录下
not_found_polymers, found_polymers = copy_files_for_polymers(
RESPpolymer_database_path,
success_dir,
polymers
)
total_polymers = not_found_polymers + found_polymers
# 为未找到的聚合物重复单元创建Gaussian输入文件和电荷约束文件chgcons.txt
create_input_files_for_missing_polymers(df, not_found_polymers)
# 以下部分不能放在上面的循环中，否则会重复调用Gaussian进行计算
# 调用Gaussian对重复单元进行结构优化，同时进行静电势计算
calculate(success_dir, failure_dir, MAX_TASKS=1)
# 将结构优化成功的聚合物重复单元文件复制到Gaussian_database/RESPpolymer中
copy_newly_calculated_files(RESPpolymer_database_path, success_dir, not_found_polymers)
# 将当前目录下的chk文件转化为fchk文件
convert_chk_to_fchk(Gaussian_path)
# 创建断点文件 test1_pass.txt
with open("test1_pass.txt", "w") as f:
f.write("convert_chk_to_fchk completed successfully.\n")
# 对当前目录下所有聚合物，计算重复单元的RESP电荷
create_repeatunit_chg(total_polymers)
# 创建断点文件 test2_pass.txt
with open("test2_pass.txt", "w") as f:
f.write("create_repeatunit_chg completed successfully.\n")
------------------
----- stdout -----
Gaussian_database文件夹已存在于/data/Gaussian_database。
Found polymers: []
Polymers not found: ['12']
------------------
[0;31m---------------------------------------------------------------------------[0m
[0;31mIndexError[0m Traceback (most recent call last)
Cell [0;32mIn[18], line 29[0m
[1;32m 26[0m total_polymers [38;5;241m=[39m not_found_polymers [38;5;241m+[39m found_polymers
[1;32m 28[0m [38;5;66;03m# 为未找到的聚合物重复单元创建Gaussian输入文件和电荷约束文件chgcons.txt[39;00m
[0;32m---> 29[0m [43mcreate_input_files_for_missing_polymers[49m[43m([49m[43mdf[49m[43m,[49m[43m [49m[43mnot_found_polymers[49m[43m)[49m
[1;32m 31[0m [38;5;66;03m# 以下部分不能放在上面的循环中，否则会重复调用Gaussian进行计算 [39;00m
[1;32m 32[0m [38;5;66;03m# 调用Gaussian对重复单元进行结构优化，同时进行静电势计算[39;00m
[1;32m 33[0m calculate(success_dir, failure_dir, MAX_TASKS[38;5;241m=[39m[38;5;241m1[39m)
Cell [0;32mIn[16], line 4[0m, in [0;36mcreate_input_files_for_missing_polymers[0;34m(df, missing_polymers)[0m
[1;32m 2[0m [38;5;28;01mdef[39;00m [38;5;21mcreate_input_files_for_missing_polymers[39m(df, missing_polymers):
[1;32m 3[0m [38;5;28;01mfor[39;00m name [38;5;129;01min[39;00m missing_polymers:
[0;32m----> 4[0m smiles [38;5;241m=[39m [43mdf[49m[43m[[49m[43mdf[49m[43m[[49m[38;5;124;43m'[39;49m[38;5;124;43mName[39;49m[38;5;124;43m'[39;49m[43m][49m[43m [49m[38;5;241;43m==[39;49m[43m [49m[43mname[49m[43m][49m[43m[[49m[38;5;124;43m'[39;49m[38;5;124;43mSMILES[39;49m[38;5;124;43m'[39;49m[43m][49m[38;5;241;43m.[39;49m[43miloc[49m[43m[[49m[38;5;241;43m0[39;49m[43m][49m
[1;32m 5[0m [38;5;66;03m# 获取重复单元的端基索引，非端基索引和重复单元的电荷信息[39;00m
[1;32m 6[0m terminal_indices, non_terminal_indices, repeatunit_charge [38;5;241m=[39m create_repeatunit_Gaussian_inputfile(df, smiles, name)
File [0;32m/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/pandas/core/indexing.py:1191[0m, in [0;36m_LocationIndexer.__getitem__[0;34m(self, key)[0m
[1;32m 1189[0m maybe_callable [38;5;241m=[39m com[38;5;241m.[39mapply_if_callable(key, [38;5;28mself[39m[38;5;241m.[39mobj)
[1;32m 1190[0m maybe_callable [38;5;241m=[39m [38;5;28mself[39m[38;5;241m.[39m_check_deprecated_callable_usage(key, maybe_callable)
[0;32m-> 1191[0m [38;5;28;01mreturn[39;00m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_getitem_axis[49m[43m([49m[43mmaybe_callable[49m[43m,[49m[43m [49m[43maxis[49m[38;5;241;43m=[39;49m[43maxis[49m[43m)[49m
File [0;32m/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/pandas/core/indexing.py:1752[0m, in [0;36m_iLocIndexer._getitem_axis[0;34m(self, key, axis)[0m
[1;32m 1749[0m [38;5;28;01mraise[39;00m [38;5;167;01mTypeError[39;00m([38;5;124m"[39m[38;5;124mCannot index by location index with a non-integer key[39m[38;5;124m"[39m)
[1;32m 1751[0m [38;5;66;03m# validate the location[39;00m
[0;32m-> 1752[0m [38;5;28;43mself[39;49m[38;5;241;43m.[39;49m[43m_validate_integer[49m[43m([49m[43mkey[49m[43m,[49m[43m [49m[43maxis[49m[43m)[49m
[1;32m 1754[0m [38;5;28;01mreturn[39;00m [38;5;28mself[39m[38;5;241m.[39mobj[38;5;241m.[39m_ixs(key, axis[38;5;241m=[39maxis)
File [0;32m/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/pandas/core/indexing.py:1685[0m, in [0;36m_iLocIndexer._validate_integer[0;34m(self, key, axis)[0m
[1;32m 1683[0m len_axis [38;5;241m=[39m [38;5;28mlen[39m([38;5;28mself[39m[38;5;241m.[39mobj[38;5;241m.[39m_get_axis(axis))
[1;32m 1684[0m [38;5;28;01mif[39;00m key [38;5;241m>[39m[38;5;241m=[39m len_axis [38;5;129;01mor[39;00m key [38;5;241m<[39m [38;5;241m-[39mlen_axis:
[0;32m-> 1685[0m [38;5;28;01mraise[39;00m [38;5;167;01mIndexError[39;00m([38;5;124m"[39m[38;5;124msingle positional indexer is out-of-bounds[39m[38;5;124m"[39m)
[0;31mIndexError[0m: single positional indexer is out-of-bounds

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Your request has been submitted successfully.
Your key is: gAAAAABootoetREtaqqQhgnqsAyzvSv9UzhWYRbqf6DmXn1GobNqb49VAAUusLWCtInWRLVL8-yzp-lXWJfp12wZ90c50hE4N4j-VttlTmPjDO7XTeeOQFl915SCtzD9Kuw_vIppL_uNaLDFGfGbqyTjYjcQmGWBwWFiKacdG3nbdVvX7d09hjlNBS4mggUlvdFYOfO4is0P4nCvbY6_tGDaToOrsCVpl9Pf-otnudvJM8TKKhLtZUIyKz-BiU1O7MrsA8upyoTe_z0i_0H3NqqivkhkNouect9MKCKEx31U5ADDW6U-LD-WU0fRlhfbIEF_KvB9KUK5eCxyJY8T-izyZCWzpQUQy1yJjJXHiUaOK-G6nceWDSTQSeOytvpXlc29tS77edoTYNLSz2Zk6y5LDndUjOJsnlpc4p-NUXj4_fT6D4eQN58=

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Task failed. Please review the error details below:

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<blockquote>Your request has been submitted successfully.

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Task Details:
- Task Type: Generate_random_copolymer
- Submission Time: 2025-08-19 01:47:56
- Completion Time: 2025-08-19 01:57:05
- Task Status: Success

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