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Difficulty with PBC #605
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Your definition of the periodic system is incorrect. This must pass (3, 3) matrix of cell vectors to |
Samuel: the current implementation of PBC in TorchANI is not 'batched', you
can not do a batch of crystals.
…On Fri, Dec 10, 2021 at 11:53 AM Olexandr Isayev ***@***.***> wrote:
Your definition of the periodic system is incorrect. This must pass (3, 3)
matrix of cell vectors to cell variable and boolean vector of size 3 to
pbc if you want to have periodicity in all 3 dimensions.
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Perfect, thank you for the feedback. |
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Hello, I am trying to train some torchANI models for periodic systems but struggling to get the PBC to work well. The tensors I give it for cell and pbc are of the form:
I have this for each configuration of atoms (ase Atoms objects). My pass to the network looks like this:
where in this case cell and condition are of the shape (n_configurations, 3, 3) for the cell and (n_configurations, 3) for condition.
When I run this I find an error like this:
num_repeats = torch.where(pbc, num_repeats, num_repeats.new_zeros(())) RuntimeError: The size of tensor a (3) must match the size of tensor b (64) at non-singleton dimension 1
I have tried to play around with the shape of the data but struggle to get anything meaningful from it. Any suggestions would be greatly appreciated.
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