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add pbc and unit cell to input data files section in readme
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thorben-frank committed Aug 21, 2024
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12 changes: 8 additions & 4 deletions README.md
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Expand Up @@ -130,9 +130,13 @@ assumes the following relations between property and key
```
{
atomic_position: R, # shape: (n_data, n, 3)
atomic_type: z, # shape: (n_data, n) or (n)
energy: E, # shape: (n_data, 1)
force: F # shape: (n_data, n, 3)
atomic_type: z, # shape: (n_data, n) or (n)
energy: E, # shape: (n_data, 1)
force: F # shape: (n_data, n, 3)
# in case mic should be applied (via --mic keyword)
unit_cell: unit_cell # shape: (n_data, 3, 3) # lattice vectors are row-wise
pbc: pbc # shape: (n_data, 3)
}
```
If you have an `*.npz` file which uses a different convention, you can specify the keys customizing the property keys
Expand All @@ -155,7 +159,7 @@ train_so3krates --ckpt_dir dha_module --train_file dha.npz --n_train 1000 --n_va
Note the character strings for the units, which are necessary in the course of internal processing. This will internally
rescale the energy and the forces to `eV` and `eV/Ang`.
### Minimal Image Convention
In [3] `So3krates` was used to calculate EOS and heat flux in solids, such that it must be capable of
In [3] `SO3krates` was used to calculate EOS and heat flux in solids, such that it must be capable of
handling periodic boundary conditions. If you want to apply the minimal image convention, you can specify this by
adding the corresponding flag to the training command
```
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