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Add an option to run PBC in single system mode #795

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merged 5 commits into from
Aug 6, 2024
Merged

Add an option to run PBC in single system mode #795

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7b52be2
do pbc per system
misko May 30, 2024
ed635ad
add option to use single system pbc
misko May 31, 2024
bee4b41
remove comments
misko Aug 5, 2024
ae57bae
Merge branch 'main' into pbc_single_option
misko Aug 5, 2024
0252178
integrate use_pbc_single to all the models in repo; add test
misko Aug 6, 2024
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48 changes: 42 additions & 6 deletions src/fairchem/core/models/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@ def generate_graph(
use_pbc=None,
otf_graph=None,
enforce_max_neighbors_strictly=None,
use_pbc_single=False,
):
cutoff = cutoff or self.cutoff
max_neighbors = max_neighbors or self.max_neighbors
Expand Down Expand Up @@ -84,12 +85,47 @@ def generate_graph(

if use_pbc:
if otf_graph:
edge_index, cell_offsets, neighbors = radius_graph_pbc(
data,
cutoff,
max_neighbors,
enforce_max_neighbors_strictly,
)
if use_pbc_single:
(
edge_index_per_system,
cell_offsets_per_system,
neighbors_per_system,
) = list(
zip(
*[
radius_graph_pbc(
data[idx],
cutoff,
max_neighbors,
enforce_max_neighbors_strictly,
)
for idx in range(len(data))
]
)
)

# atom indexs in the edge_index need to be offset
atom_index_offset = data.natoms.cumsum(dim=0).roll(1)
atom_index_offset[0] = 0
edge_index = torch.hstack(
[
edge_index_per_system[idx] + atom_index_offset[idx]
for idx in range(len(data))
]
)
cell_offsets = torch.vstack(cell_offsets_per_system)
neighbors = torch.hstack(neighbors_per_system)
else:
## TODO this is the original call, but blows up with memory
## using two different samples
## sid='mp-675045-mp-675045-0-7' (MPTRAJ)
## sid='75396' (OC22)
edge_index, cell_offsets, neighbors = radius_graph_pbc(
data,
cutoff,
max_neighbors,
enforce_max_neighbors_strictly,
)

out = get_pbc_distances(
data.pos,
Expand Down