allegro
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20 hours ago •
mir-group
mir-group
AttributeError: 'numpy.int64' object has no attribute 'unsqueeze'
I'm trying to run a toy example of training using a toy dataset just to make sure I can get ase datasets working. I get this error when I try and run Nequip: AttributeError: 'numpy.int64' object has no attribute 'unsqueeze'
The dataset I'm using is this (taken from the discussion https://github.com/mir-group/allegro/discussions/74):
3
Lattice="1.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 3.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=-100 stress="0.0002 0.003 -0.004 0.003 -0.004 -0.005 -0.004 -0.005 -0.006" free_energy=-100 pbc="T T T"
H 14.80702000 9.47114000 14.83362000 0.05630700 0.18844700 0.12262800
C 14.40303000 9.58896000 4.81541000 0.28543000 -0.56192100 0.59003500
Al 0.15995000 9.61979000 9.87331000 -0.15746000 0.51516600 0.14365000
2
Lattice="1.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 3.0" Properties=species:S:1:pos:R:3:forces:R:3 energy=-100 stress="0.0002 0.003 -0.004 0.003 -0.004 -0.005 -0.004 -0.005 -0.006" free_energy=-100 pbc="T T T"
H 14.80702000 9.47114000 14.83362000 0.05630700 0.18844700 0.12262800
C 14.40303000 9.58896000 4.81541000 0.28543000 -0.56192100 0.59003500
Here is the data section of my .yaml:
dataset: ase
dataset_file_name: training.extxyz
ase_args:
format: extxyz
chemical_symbols:
- H
- C
- Al
Here is the full error output:
Processing dataset...
Traceback (most recent call last):
File "nequip/utils/auto_init.py", line 232, in instantiate
instance = builder(**positional_args, **final_optional_args)
File "nequip/data/dataset.py", line 880, in __init__
super().__init__(
File "nequip/data/dataset.py", line 166, in __init__
super().__init__(root=root, type_mapper=type_mapper)
File "nequip/data/dataset.py", line 50, in __init__
super().__init__(root=root, transform=type_mapper)
File "nequip/utils/torch_geometric/dataset.py", line 91, in __init__
self._process()
File "nequip/utils/torch_geometric/dataset.py", line 176, in _process
self.process()
File "nequip/data/dataset.py", line 218, in process
data = self.get_data()
File "nequip/data/dataset.py", line 971, in get_data
datas = reader(rank=0)
File "nequip/data/dataset.py", line 789, in _ase_dataset_reader
AtomicData.from_ase(atoms=atoms, **atomicdata_kwargs)
File "nequip/data/AtomicData.py", line 443, in from_ase
return cls.from_points(
File "nequip/data/AtomicData.py", line 330, in from_points
return cls(edge_index=edge_index, pos=torch.as_tensor(pos), **kwargs)
File "nequip/data/AtomicData.py", line 225, in __init__
_process_dict(kwargs)
File "nequip/data/AtomicData.py", line 155, in _process_dict
kwargs[k] = v.unsqueeze(-1)
AttributeError: 'numpy.int64' object has no attribute 'unsqueeze'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "nequip-train", line 8, in <module>
sys.exit(main())
File "nequip/scripts/train.py", line 72, in main
trainer = fresh_start(config)
File "nequip/scripts/train.py", line 148, in fresh_start
dataset = dataset_from_config(config, prefix="dataset")
File "nequip/data/_build.py", line 78, in dataset_from_config
instance, _ = instantiate(
File "nequip/utils/auto_init.py", line 234, in instantiate
raise RuntimeError(
RuntimeError: Failed to build object with prefix `dataset` using builder `ASEDataset`
I'm running it on a mac. Here are details of the environment:
# Name Version Build Channel
appdirs 1.4.4 pypi_0 pypi
ase 3.22.1 pypi_0 pypi
ca-certificates 2023.12.12 hca03da5_0
certifi 2024.2.2 pypi_0 pypi
cffi 1.16.0 py39h80987f9_0
charset-normalizer 3.3.2 pypi_0 pypi
click 8.1.7 pypi_0 pypi
contourpy 1.2.0 pypi_0 pypi
cycler 0.12.1 pypi_0 pypi
docker-pycreds 0.4.0 pypi_0 pypi
e3nn 0.5.1 pypi_0 pypi
fonttools 4.49.0 pypi_0 pypi
future 0.18.3 py39hca03da5_0
gitdb 4.0.11 pypi_0 pypi
gitpython 3.1.42 pypi_0 pypi
idna 3.6 pypi_0 pypi
importlib-resources 6.1.2 pypi_0 pypi
kiwisolver 1.4.5 pypi_0 pypi
libblas 3.9.0 16_osxarm64_openblas conda-forge
libcblas 3.9.0 16_osxarm64_openblas conda-forge
libcxx 14.0.6 h848a8c0_0
libffi 3.4.4 hca03da5_0
libgfortran 5.0.0 11_3_0_hca03da5_28
libgfortran5 11.3.0 h009349e_28
liblapack 3.9.0 16_osxarm64_openblas conda-forge
libopenblas 0.3.21 h269037a_0
llvm-openmp 14.0.6 hc6e5704_0
matplotlib 3.8.3 pypi_0 pypi
mir-allegro 0.2.0 pypi_0 pypi
mpmath 1.3.0 pypi_0 pypi
ncurses 6.4 h313beb8_0
nequip 0.5.6 pypi_0 pypi
ninja 1.10.2 hca03da5_5
ninja-base 1.10.2 h525c30c_5
npzviewer 0.2.0 pypi_0 pypi
numpy 1.26.4 pypi_0 pypi
openssl 3.0.13 h1a28f6b_0
opt-einsum 3.3.0 pypi_0 pypi
opt-einsum-fx 0.1.4 pypi_0 pypi
packaging 23.2 pypi_0 pypi
pillow 10.2.0 pypi_0 pypi
pip 23.3.1 py39hca03da5_0
protobuf 4.25.3 pypi_0 pypi
psutil 5.9.8 pypi_0 pypi
pycparser 2.21 pyhd3eb1b0_0
pyparsing 3.1.1 pypi_0 pypi
pyqt5 5.15.10 pypi_0 pypi
pyqt5-qt5 5.15.12 pypi_0 pypi
pyqt5-sip 12.13.0 pypi_0 pypi
python 3.9.18 hb885b13_0
python-dateutil 2.8.2 pypi_0 pypi
pytorch 1.10.2 cpu_py39h23cb94c_0
pyyaml 6.0.1 pypi_0 pypi
readline 8.2 h1a28f6b_0
requests 2.31.0 pypi_0 pypi
scipy 1.12.0 pypi_0 pypi
sentry-sdk 1.40.6 pypi_0 pypi
setproctitle 1.3.3 pypi_0 pypi
setuptools 68.2.2 py39hca03da5_0
six 1.16.0 pypi_0 pypi
smmap 5.0.1 pypi_0 pypi
sqlite 3.41.2 h80987f9_0
sympy 1.12 pypi_0 pypi
tk 8.6.12 hb8d0fd4_0
torch-ema 0.3 pypi_0 pypi
torch-runstats 0.2.0 pypi_0 pypi
tqdm 4.66.2 pypi_0 pypi
typing-extensions 4.9.0 py39hca03da5_1
typing_extensions 4.9.0 py39hca03da5_1
tzdata 2024a h04d1e81_0
urllib3 2.2.1 pypi_0 pypi
wandb 0.16.3 pypi_0 pypi
wheel 0.41.2 py39hca03da5_0
xz 5.4.5 h80987f9_0
zipp 3.17.0 pypi_0 pypi
zlib 1.2.13 h5a0b063_0
Thanks
Hi Jonathan,
The example is only for showing the format. The values are not physical as you can see the position coordinate is larger than the lattice vectors. Please use your own xyz file.
My mistake sorry; I wrongly assumed the error wasn't because of that, I thought I had the wrong version of some library or other. It works now thanks.