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fix(pt): fix global bias stat with different natom #3944

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Merged
iProzd merged 1 commit into from
Jul 3, 2024
Merged

fix(pt): fix global bias stat with different natom #3944

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7 changes: 4 additions & 3 deletions deepmd/pt/utils/stat.py
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Original file line number Diff line number Diff line change
Expand Up @@ -313,7 +313,9 @@ def compute_output_stats(

model_pred_g = (
{
kk: [vv[idx] for idx in global_sampled_idx[kk]]
kk: [
np.sum(vv[idx], axis=1) for idx in global_sampled_idx[kk]
] # sum atomic dim
for kk, vv in model_pred.items()
}
if model_pred
Expand All @@ -328,7 +330,7 @@ def compute_output_stats(
else None
)

# concat all frames within those systmes
# concat all frames within those systems
model_pred_g = (
{
kk: np.concatenate(model_pred_g[kk])
Expand Down Expand Up @@ -460,7 +462,6 @@ def compute_output_stats_global(
else:
# subtract the model bias and output the delta bias

model_pred = {kk: np.sum(model_pred[kk], axis=1) for kk in keys}
stats_input = {
kk: merged_output[kk] - model_pred[kk] for kk in keys if kk in merged_output
}
Expand Down
31 changes: 31 additions & 0 deletions source/tests/pt/test_finetune.py
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Original file line number Diff line number Diff line change
Expand Up @@ -113,6 +113,22 @@ def test_finetune_change_out_bias(self):
data.dataloaders,
nbatches=1,
)
# make sampled of multiple frames with different atom numbs
numb_atom = sampled[0]["atype"].shape[1]
small_numb_atom = numb_atom // 2
small_atom_data = deepcopy(sampled[0])
atomic_key = ["coord", "atype"]
for kk in atomic_key:
small_atom_data[kk] = small_atom_data[kk][:, :small_numb_atom]
scale_pref = float(small_numb_atom / numb_atom)
small_atom_data[self.testkey] *= scale_pref
small_atom_data["natoms"][:, :2] = small_numb_atom
small_atom_data["natoms"][:, 2:] = torch.bincount(
small_atom_data["atype"][0],
minlength=small_atom_data["natoms"].shape[1] - 2,
)
sampled = [sampled[0], small_atom_data]

# get model
model = get_model(self.config["model"]).to(env.DEVICE)
atomic_model = model.atomic_model
Expand Down Expand Up @@ -144,12 +160,27 @@ def test_finetune_change_out_bias(self):
np.bincount(to_numpy_array(sampled[0]["atype"][0]))[idx_type_map],
(ntest, 1),
)
atom_nums_small = np.tile(
np.bincount(to_numpy_array(sampled[1]["atype"][0]))[idx_type_map],
(ntest, 1),
)
atom_nums = np.concatenate([atom_nums, atom_nums_small], axis=0)

energy = dp.eval(
to_numpy_array(sampled[0]["coord"][:ntest]),
to_numpy_array(sampled[0]["box"][:ntest]),
to_numpy_array(sampled[0]["atype"][0]),
)[0]
energy_small = dp.eval(
to_numpy_array(sampled[1]["coord"][:ntest]),
to_numpy_array(sampled[1]["box"][:ntest]),
to_numpy_array(sampled[1]["atype"][0]),
)[0]
energy_diff = to_numpy_array(sampled[0][self.testkey][:ntest]) - energy
energy_diff_small = (
to_numpy_array(sampled[1][self.testkey][:ntest]) - energy_small
)
energy_diff = np.concatenate([energy_diff, energy_diff_small], axis=0)
finetune_shift = (
energy_bias_after[idx_type_map] - energy_bias_before[idx_type_map]
).ravel()
Expand Down