Closed SamTov closed 2 years ago
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.
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.
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:
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.