Fix NPT Nose-Hoover things

tests/test_integrators.py

@@ -339,7 +339,7 @@ def test_nvt_nose_hoover(ar_double_sim_state: ts.SimState, lj_model: LennardJone
     temperatures_list = [t.tolist() for t in temperatures_tensor.T]
     assert torch.allclose(
         temperatures_tensor[-1],
-        torch.tensor([300.0096, 299.7024], dtype=dtype),
+        torch.tensor([290.3553, 289.9699], dtype=dtype),
     )
 
     energies_tensor = torch.stack(energies)
@@ -728,7 +728,7 @@ def test_npt_nose_hoover(ar_double_sim_state: ts.SimState, lj_model: LennardJone
     temperatures_list = [t.tolist() for t in temperatures_tensor.T]
     assert torch.allclose(
         temperatures_tensor[-1],
-        torch.tensor([298.2752, 297.9444], dtype=dtype),
+        torch.tensor([287.5729, 287.1330], dtype=dtype),
     )
 
     energies_tensor = torch.stack(energies)

torch_sim/integrators/md.py

@@ -409,7 +409,7 @@ def init_fn(
 
         Q = (
             kT_batched.unsqueeze(-1)
-            * torch.square(tau_batched).unsqueeze(-1) ** 2
+            * torch.square(tau_batched).unsqueeze(-1)
             * torch.ones((n_systems, chain_length), dtype=dtype, device=device)
         )
         Q[:, 0] *= degrees_of_freedom

torch_sim/integrators/npt.py

@@ -1179,9 +1179,9 @@ def _npt_nose_hoover_compute_cell_force(
         internal_pressure = torch.trace(stress).unsqueeze(0).expand(n_systems)
 
     # Compute force on cell coordinate per system
-    # F = alpha * KE - dU/dV - P*V*d
+    # F = alpha * (2 * KE) - dU/dV - P*V*d
     return (
-        (alpha * KE_per_system)
+        (alpha * 2 * KE_per_system)
         - (internal_pressure * volume)
         - (external_pressure * volume * dim)
     )
@@ -1226,21 +1226,18 @@ def _npt_nose_hoover_inner_step(
     volume, volume_to_cell = _npt_nose_hoover_cell_info(state)
     cell = volume_to_cell(volume)
 
-    # Get model output
-    state.cell = cell
-    model_output = model(state)
-
     # First half step: Update momenta
-    n_atoms_per_system = torch.bincount(state.system_idx, minlength=state.n_systems)
-    alpha = 1 + 1 / n_atoms_per_system  # [n_systems]
+    # alpha = 1 + dim / degrees_of_freedom (3 * natoms - 3)
+    alpha = 1 + 3 / state.get_number_of_degrees_of_freedom()  # [n_systems]
 
+    # Reuse stress from previous step since positions and cell unchanged
     cell_force_val = _npt_nose_hoover_compute_cell_force(
         alpha=alpha,
         volume=volume,
         positions=positions,
         momenta=momenta,
         masses=masses,
-        stress=model_output["stress"],
+        stress=state.stress,
         external_pressure=external_pressure,
         system_idx=state.system_idx,
     )
@@ -1406,7 +1403,8 @@ def npt_nose_hoover_init(
         )
 
     # Compute total DOF for thermostat initialization and a zero KE placeholder
-    dof_per_system = torch.bincount(state.system_idx, minlength=n_systems) * dim
+    dof_per_system = state.get_number_of_degrees_of_freedom() - 3
+
     KE_thermostat = ts.calc_kinetic_energy(
         masses=state.masses, momenta=momenta, system_idx=state.system_idx
     )
@@ -1612,13 +1610,12 @@ def npt_nose_hoover_invariant(
     )
 
     # Calculate degrees of freedom per system
-    n_atoms_per_system = torch.bincount(state.system_idx, minlength=state.n_systems)
-    dof_per_system = n_atoms_per_system * state.positions.shape[-1]  # n_atoms * n_dim
+    dof_per_system = state.get_number_of_degrees_of_freedom()
 
     # Initialize total energy with PE + KE
     e_tot = e_pot + e_kin_per_system
 
-    # Add thermostat chain contributions (batched per system, DOF = n_atoms * 3)
+    # Add thermostat chain contributions (batched per system, DOF = 3 * n_atoms - 3)
     e_tot += _compute_chain_energy(state.thermostat, kT, e_tot, dof_per_system)
 
     # Add barostat chain contributions (batched per system, DOF = 1)

torch_sim/integrators/nvt.py

@@ -314,11 +314,9 @@ def nvt_nose_hoover_init(
         masses=state.masses, momenta=momenta, system_idx=state.system_idx
     )
 
-    # Calculate degrees of freedom per system
-    n_atoms_per_system = torch.bincount(state.system_idx)
-    dof_per_system = (
-        n_atoms_per_system * state.positions.shape[-1]
-    )  # n_atoms * n_dimensions
+    # Calculate degrees of freedom per system (subtract 3 for COM motion,
+    # matching LAMMPS compute_temp which uses dof = 3N - 3)
+    dof_per_system = state.get_number_of_degrees_of_freedom() - 3
 
     # Initialize state
     return NVTNoseHooverState.from_state(
@@ -431,9 +429,8 @@ def nvt_nose_hoover_invariant(
         masses=state.masses, momenta=state.momenta, system_idx=state.system_idx
     )
 
-    # Get system degrees of freedom per system
-    n_atoms_per_system = torch.bincount(state.system_idx)
-    dof = n_atoms_per_system * state.positions.shape[-1]  # n_atoms * n_dimensions
+    # Get system degrees of freedom per system (3N - 3 for COM correction)
+    dof = state.get_number_of_degrees_of_freedom()
 
     # Start with system energy
     e_tot = e_pot + e_kin