Failed to create dataset from extxyz

[tawe141]

This is the error message I'm seeing:

Traceback (most recent call last):
  File "/home/etaw/miniconda3/envs/nequip/lib/python3.10/site-packages/nequip/utils/auto_init.py", line 232, in instantiate
    instance = builder(**positional_args, **final_optional_args)
  File "/home/etaw/miniconda3/envs/nequip/lib/python3.10/site-packages/nequip/data/dataset.py", line 800, in __init__
    super().__init__(
  File "/home/etaw/miniconda3/envs/nequip/lib/python3.10/site-packages/nequip/data/dataset.py", line 123, in __init__
    super().__init__(root=root, transform=type_mapper)
  File "/home/etaw/miniconda3/envs/nequip/lib/python3.10/site-packages/nequip/utils/torch_geometric/dataset.py", line 90, in __init__
    self._process()
  File "/home/etaw/miniconda3/envs/nequip/lib/python3.10/site-packages/nequip/utils/torch_geometric/dataset.py", line 175, in _process
    self.process()
  File "/home/etaw/miniconda3/envs/nequip/lib/python3.10/site-packages/nequip/data/dataset.py", line 279, in process
    data = Batch.from_data_list(data_list, exclude_keys=fixed_fields.keys())
  File "/home/etaw/miniconda3/envs/nequip/lib/python3.10/site-packages/nequip/utils/torch_geometric/batch.py", line 145, in from_data_list
    batch[key] = torch.cat(items, cat_dim)
TypeError: expected Tensor as element 270 in argument 0, but got NoneType

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

Traceback (most recent call last):
  File "/home/etaw/miniconda3/envs/nequip/bin/nequip-train", line 8, in <module>
    sys.exit(main())
  File "/home/etaw/miniconda3/envs/nequip/lib/python3.10/site-packages/nequip/scripts/train.py", line 74, in main
    trainer = fresh_start(config)
  File "/home/etaw/miniconda3/envs/nequip/lib/python3.10/site-packages/nequip/scripts/train.py", line 177, in fresh_start
    dataset = dataset_from_config(config, prefix="dataset")
  File "/home/etaw/miniconda3/envs/nequip/lib/python3.10/site-packages/nequip/data/_build.py", line 78, in dataset_from_config
    instance, _ = instantiate(
  File "/home/etaw/miniconda3/envs/nequip/lib/python3.10/site-packages/nequip/utils/auto_init.py", line 234, in instantiate
    raise RuntimeError(
RuntimeError: Failed to build object with prefix `dataset` using builder `ASEDataset`

The relevant part of the yaml file is as follows:

dataset: ase
dataset_file_name: all_outputs.extxyz
ase_args:
        format: extxyz
chemical_symbols:
  - H
  - C
  - O
  - N

The extxyz file comes directly from ase.io.write, so it should be in the right format.

All unit tests pass, so I'm sure it's just me doing something silly. What could be going wrong here?

[Linux-cpp-lisp]

Hi @tawe141 ,

We've generally seen this error before when one or more frames in your dataset are missing something, such as forces or the energy. Please check your data, such as by loading it using ase.io.read, to find which frame(s) are incomplete.

[tawe141]

Great, found a few that were problematic and now it works beautifully. Thanks!

[KellekKan]

May I know how can you solve this issue, coz I am also facing this issue.

Indeed, I am using the full.yaml file provided, I change the url to http://quantum-machine.org/gdml/data/xyz/ethanol_ccsd_t.zip for downloading the xyz format of ethanol to check how can actually start the learning process using extxyz file.

But i am not possible to do so, after using the nequip-train command, the downloading process is not even started, then i decided to idle the dataset_url keyword, then I downloaded and unzipped the .zip to get the ethanol.xyz and took only 10 points for training, the resulting extxyz file is shown below,

leading to the error that you shown.

May I know what does it mean (as by loading it using ase.io.read) ?

[Linux-cpp-lisp]

@KellekKan what exact error do you get from this file?

[DQM520]

Great, found a few that were problematic and now it works beautifully. Thanks!
May I ask how do you get the formal extxyz file using ase.io.write? I am new to nequip and I use lammps dump command 1 all custom ${DUMP_FREQ} methane.lammpstrj id type x y z to get the xyz file. I don't know how to convert it into extxyz file contains force and energy. Could you give me some advice? My questions attached #463