Add per atom energies and stresses for batched LJ (#144)

* Add per atom energies and stresses for batched LJ

* update changelog for v0.2.0 (#147)

* update changelog for v0.2.0

* minor modification for PR template

* formatting fixes

* formatting and typos

* remove contributors bc they aren't linked

* Add tests

* simplify results

---------

Signed-off-by: Abhijeet Gangan <[email protected]>
Co-authored-by: Orion Cohen <[email protected]>

Author: abhijeetgangan

examples/scripts/1_Introduction/1.1_Lennard_Jones.py

@@ -10,6 +10,7 @@
 
 import torch
 
+from torch_sim.models.lennard_jones import LennardJonesModel
 from torch_sim.unbatched.models.lennard_jones import UnbatchedLennardJonesModel
 
 
@@ -69,6 +70,8 @@
     dtype=dtype,
     compute_forces=True,
     compute_stress=True,
+    per_atom_energies=True,
+    per_atom_stresses=True,
 )
 
 # Print system information
@@ -88,3 +91,37 @@
 print(f"Energy: {results['energy']}")
 print(f"Forces: {results['forces']}")
 print(f"Stress: {results['stress']}")
+print(f"Energies: {results['energies']}")
+print(f"Stresses: {results['stresses']}")
+
+# Batched model
+batched_model = LennardJonesModel(
+    use_neighbor_list=True,
+    cutoff=2.5 * 3.405,
+    sigma=3.405,
+    epsilon=0.0104,
+    device=device,
+    dtype=dtype,
+    compute_forces=True,
+    compute_stress=True,
+    per_atom_energies=True,
+    per_atom_stresses=True,
+)
+
+# Batched state
+state = dict(
+    positions=positions,
+    cell=cell.unsqueeze(0),
+    atomic_numbers=atomic_numbers,
+    pbc=True,
+)
+
+# Run the simulation and get results
+results = batched_model(state)
+
+# Print the results
+print(f"Energy: {results['energy']}")
+print(f"Forces: {results['forces']}")
+print(f"Stress: {results['stress']}")
+print(f"Energies: {results['energies']}")
+print(f"Stresses: {results['stresses']}")

tests/models/test_lennard_jones.py

@@ -155,6 +155,8 @@ def models(
         "dtype": torch.float64,
         "compute_forces": True,
         "compute_stress": True,
+        "per_atom_energies": True,
+        "per_atom_stresses": True,
     }
 
     cutoff = 2.5 * 3.405  # Standard LJ cutoff * sigma
@@ -178,6 +180,14 @@ def test_energy_match(
     assert torch.allclose(results_nl["energy"], results_direct["energy"], rtol=1e-10)
 
 
+def test_per_atom_energy_match(
+    models: tuple[dict[str, torch.Tensor], dict[str, torch.Tensor]],
+) -> None:
+    """Test that per-atom energy matches between neighbor list and direct calculations."""
+    results_nl, results_direct = models
+    assert torch.allclose(results_nl["energies"], results_direct["energies"], rtol=1e-10)
+
+
 def test_forces_match(
     models: tuple[dict[str, torch.Tensor], dict[str, torch.Tensor]],
 ) -> None:
@@ -194,6 +204,15 @@ def test_stress_match(
     assert torch.allclose(results_nl["stress"], results_direct["stress"], rtol=1e-10)
 
 
+def test_per_atom_stress_match(
+    models: tuple[dict[str, torch.Tensor], dict[str, torch.Tensor]],
+) -> None:
+    """Test that per-atom stress tensors match between neighbor list
+    and direct calculations."""
+    results_nl, results_direct = models
+    assert torch.allclose(results_nl["stresses"], results_direct["stresses"], rtol=1e-10)
+
+
 def test_force_conservation(
     models: tuple[dict[str, torch.Tensor], dict[str, torch.Tensor]],
 ) -> None:

torch_sim/models/lennard_jones.py

@@ -293,7 +293,10 @@ def forward(self, state: SimState | StateDict) -> dict[str, torch.Tensor]:
                     compute_forces=True)
                 - "stress": Stress tensor with shape [n_batches, 3, 3] (if
                     compute_stress=True)
-                - May include additional outputs based on configuration
+                - "energies": Per-atom energies with shape [n_atoms] (if
+                    per_atom_energies=True)
+                - "stresses": Per-atom stresses with shape [n_atoms, 3, 3] (if
+                    per_atom_stresses=True)
 
         Raises:
             ValueError: If batch cannot be inferred for multi-cell systems.
@@ -307,6 +310,8 @@ def forward(self, state: SimState | StateDict) -> dict[str, torch.Tensor]:
             energy = results["energy"]  # Shape: [n_batches]
             forces = results["forces"]  # Shape: [n_atoms, 3]
             stress = results["stress"]  # Shape: [n_batches, 3, 3]
+            energies = results["energies"]  # Shape: [n_atoms]
+            stresses = results["stresses"]  # Shape: [n_atoms, 3, 3]
         """
         if isinstance(state, dict):
             state = SimState(**state, masses=torch.ones_like(state["positions"]))
@@ -324,7 +329,7 @@ def forward(self, state: SimState | StateDict) -> dict[str, torch.Tensor]:
         for key in ("stress", "energy"):
             if key in properties:
                 results[key] = torch.stack([out[key] for out in outputs])
-        for key in ("forces",):
+        for key in ("forces", "energies", "stresses"):
             if key in properties:
                 results[key] = torch.cat([out[key] for out in outputs], dim=0)