training with VASP data

[nisargjoshi10]

Hi!

I am using nequip to train a model with VASP data. I have some vasp simulations for water system and when I try to run the training, I'm getting the following error:

Torch device: cuda
Traceback (most recent call last):
  File "/gscratch/pfaendtner/nisargj/codes/miniconda/envs/nequip/lib/python3.9/site-packages/nequip/utils/auto_init.py", line 232, in instantiate
    instance = builder(**positional_args, **final_optional_args)
  File "/gscratch/pfaendtner/nisargj/codes/miniconda/envs/nequip/lib/python3.9/site-packages/nequip/data/transforms.py", line 80, in __init__
    raise ValueError(
ValueError: None of chemical_symbols, chemical_symbol_to_type, nor type_names was provided; exactly one is required

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

Traceback (most recent call last):
  File "/gscratch/pfaendtner/nisargj/codes/miniconda/envs/nequip/bin/nequip-train", line 8, in <module>
    sys.exit(main())
  File "/gscratch/pfaendtner/nisargj/codes/miniconda/envs/nequip/lib/python3.9/site-packages/nequip/scripts/train.py", line 65, in main
    trainer = fresh_start(config)
  File "/gscratch/pfaendtner/nisargj/codes/miniconda/envs/nequip/lib/python3.9/site-packages/nequip/scripts/train.py", line 163, in fresh_start
    dataset = dataset_from_config(config, prefix="dataset")
  File "/gscratch/pfaendtner/nisargj/codes/miniconda/envs/nequip/lib/python3.9/site-packages/nequip/data/_build.py", line 72, in dataset_from_config
    type_mapper, _ = instantiate(TypeMapper, prefix=prefix, optional_args=config)
  File "/gscratch/pfaendtner/nisargj/codes/miniconda/envs/nequip/lib/python3.9/site-packages/nequip/utils/auto_init.py", line 234, in instantiate
    raise RuntimeError(
RuntimeError: Failed to build object with prefix `dataset` using builder `TypeMapper`

I also attached my training script. Going through the documentation, I see you suggest to use extxyz data format, but was wondering if I am missing something for VASP.
water_train.txt

Following to that, I had another question about converting data to extxyz. Do you suggest any other steps other than using ase.io.read(file) and then ase.io.write(file.extxyz, format=extxyz)? I have been only getting output as a single frame and I can work on figuring that out later but if you have any suggestions that'd be great.

Thanks for the help!

Nisarg

[Linux-cpp-lisp]

The error says exactly what the problem is:

ValueError: None of chemical_symbols, chemical_symbol_to_type, nor type_names was provided; exactly one is required

You must specify the species present in your system using one of these schemes of options in your config. Please see example.yaml.

[nisargjoshi10]

aah I'm sorry to bother you with that. I totally missed that

[Linux-cpp-lisp]

Re your second question, you just need to pass a list of ase.Atoms to ase.io.write to get a single file containing multiple frames.