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Yeonghun1675 / ChatMOF

Predict and Inverse design for metal-organic framework with large-language models (llms)
https://www.nature.com/articles/s41467-024-48998-4
MIT License
50 stars 6 forks source link

Structure Generation Error #17

Open gokhanonderaksu opened 3 days ago

gokhanonderaksu commented 3 days ago

Hello! First of all, I would like to thank for bringing such a nice tool in the MOF literature. I assume I have done the exact steps with installation, but I have some problems with the generation part. Prediction or data search parts are working just fine. The error seems something like that:

########## Question ############################## Please enter the question below >> Can you generate the structures with the largest surface area?

Entering new ChatMOF chain...

Entering new AgentExecutor chain... The question is asking to generate a structure with the largest surface area. Action: generator Action Input: "Generate the structure with the largest surface area"

Entering new Generator chain...

[Generator] Thought: I need to generate a material with the largest surface area. [Generator] Objective: max [Generator] Predict Properties: accessible_surface_area load model : /home/lenovo/.local/lib/python3.10/site-packages/chatmof/database/load_model/accessible_surface_area/best.ckpt Predicting DataLoader 0: 100%|████████████████████████████████████████████████████████| 178/178 [00:41<00:00, 4.26it/s] load model : /home/lenovo/.local/lib/python3.10/site-packages/chatmof/database/load_model/accessible_surface_area/best.ckpt Predicting DataLoader 0: 1%|▎ | 1/163 [00:00<00:51, 3.16it/s]Error: Caught FileNotFoundError in DataLoader worker process 1. Original Traceback (most recent call last): File "/home/lenovo/.local/lib/python3.10/site-packages/torch/utils/data/_utils/worker.py", line 302, in _worker_loop data = fetcher.fetch(index) File "/home/lenovo/.local/lib/python3.10/site-packages/torch/utils/data/_utils/fetch.py", line 58, in fetch data = [self.dataset[idx] for idx in possibly_batched_index] File "/home/lenovo/.local/lib/python3.10/site-packages/torch/utils/data/_utils/fetch.py", line 58, in data = [self.dataset[idx] for idx in possibly_batched_index] File "/home/lenovo/.local/lib/python3.10/site-packages/moftransformer/datamodules/dataset.py", line 199, in getitem ret.update(self.get_grid_data(cif_id, draw_false_grid=self.draw_false_grid)) File "/home/lenovo/.local/lib/python3.10/site-packages/moftransformer/datamodules/dataset.py", line 123, in get_grid_data cell, volume, grid_data = self.get_raw_grid_data(cif_id) File "/home/lenovo/.local/lib/python3.10/site-packages/moftransformer/datamodules/dataset.py", line 107, in get_raw_grid_data with open(file_grid, "r") as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/lenovo/.local/lib/python3.10/site-packages/chatmof/database/structures/hMOF/dia+N562+E205.grid' . Continuing without this file.

Thanks for using CHATMOF! Predicting DataLoader 0: 1%|▎ | 1/163 [00:00<02:24, 1.12it/s]

It somehow searches for hMOF folder under database, but there is no folder either in the depository or loading scheme. How could I solve this issue?

Thanks in advance for your response.

Kind regards,

Yeonghun1675 commented 3 days ago

Hi @gokhanonderaksu,

Thank you for being so interested in my chatmof. We have checked the issue and found it to be an issue with the hMOF zip file during setup. I have uploaded a new hMOF.zip and changed the setup to receive the corrected hMOF. Please let me know if you run into any further issues.

gokhanonderaksu commented 1 day ago

Hello, thanks for your response!

I have uninstalled and installed everything using "chatmof setup", as it downloaded corecof, hmof, and load_model folders. chatmof folders But unfortunately I have still the same issue.

Yeonghun1675 commented 3 hours ago

The hMOF download link changed during the process of uploading a new database. Please update ChatMOF to version 0.2.2 and proceed with the setup again. If not, you can get it from the following link: https://figshare.com/articles/dataset/Database_for_ChatMOF/24287731

gokhanonderaksu commented 27 minutes ago

Hello again,

Yes, this time, generator works; however, there are some missing linker files that give such errors: [Generator] Generate Structures: >>> [Errno 2] No such file or directory: '/home/lenovo/.local/lib/python3.10/site-packages/pormake/database/topologies/pcu.pickle' Traceback (most recent call last): File "/home/lenovo/.local/lib/python3.10/site-packages/pormake/database.py", line 81, in get_topology with pickle_path.open("rb") as f: File "/usr/lib/python3.10/pathlib.py", line 1119, in open return self._accessor.open(self, mode, buffering, encoding, errors, FileNotFoundError: [Errno 2] No such file or directory: '/home/lenovo/.local/lib/python3.10/site-packages/pormake/database/topologies/pcu.pickle' pcu: 0%| | 0/99 [00:00<?, ?it/s]WARNING:jax._src.xla_bridge:An NVIDIA GPU may be present on this machine, but a CUDA-enabled jaxlib is not installed. Falling back to cpu. pcu: 100%|██████████████████████████████████████████████████████| 99/99 [00:51<00:00, 1.91it/s]

[Errno 2] No such file or directory: '/home/lenovo/.local/lib/python3.10/site-packages/pormake/database/topologies/dia.pickle' Traceback (most recent call last): File "/home/lenovo/.local/lib/python3.10/site-packages/pormake/database.py", line 81, in get_topology with pickle_path.open("rb") as f: File "/usr/lib/python3.10/pathlib.py", line 1119, in open return self._accessor.open(self, mode, buffering, encoding, errors, FileNotFoundError: [Errno 2] No such file or directory: '/home/lenovo/.local/lib/python3.10/site-packages/pormake/database/topologies/dia.pickle' dia: 9%|█████▏ | 9/96 [00:07<01:03, 1.37it/s]>>> BuildingBlock loading is failed: [Errno 2] No such file or directory: '/home/lenovo/.local/lib/python3.10/site-packages/pormake/database/bbs/E310.xyz'. ERROR:generate_mof.log:BuildingBlock loading is failed: [Errno 2] No such file or directory: '/home/lenovo/.local/lib/python3.10/site-packages/pormake/database/bbs/E310.xyz'. BuildingBlock loading is failed: [Errno 2] No such file or directory: '/home/lenovo/.local/lib/python3.10/site-packages/pormake/database/bbs/E649.xyz'. ERROR:generate_mof.log:BuildingBlock loading is failed: [Errno 2] No such file or directory: '/home/lenovo/.local/lib/python3.10/site-packages/pormake/database/bbs/E649.xyz'. BuildingBlock loading is failed: [Errno 2] No such file or directory: '/home/lenovo/.local/lib/python3.10/site-packages/pormake/database/bbs/E515.xyz'. ERROR:generate_mof.log:BuildingBlock loading is failed: [Errno 2] No such file or directory: '/home/lenovo/.local/lib/python3.10/site-packages/pormake/database/bbs/E515.xyz'. BuildingBlock loading is failed: [Errno 2] No such file or directory: '/home/lenovo/.local/lib/python3.10/site-packages/pormake/database/bbs/E267.xyz'. ERROR:generate_mof.log:BuildingBlock loading is failed: [Errno 2] No such file or directory: '/home/lenovo/.local/lib/python3.10/site-packages/pormake/database/bbs/E267.xyz'. BuildingBlock loading is failed: [Errno 2] No such file or directory: '/home/lenovo/.local/lib/python3.10/site-packages/pormake/database/bbs/E515.xyz'. ERROR:generate_mof.log:BuildingBlock loading is failed: [Errno 2] No such file or directory: '/home/lenovo/.local/lib/python3.10/site-packages/pormake/database/bbs/E515.xyz'.

I checked folders both for topologies and linkers. For topologies, probably there is a print error regarding "pormake". For linkers, yes, they are missing. Could you also provide an update for the linker files, or how to download them and integrate them to corresponding folders?

Thank you so much once again!