feat: Implement XAS (X-ray Absorption Spectroscopy) model, fitting, l…

deepmd/__about__.py

@@ -0,0 +1,3 @@
+# SPDX-License-Identifier: LGPL-3.0-or-later
+# Auto-generated stub for development use
+__version__ = "dev"

deepmd/dpmodel/model/model.py

@@ -104,13 +104,14 @@ def get_standard_model(data: dict) -> EnergyModel:
     else:
         raise RuntimeError(f"Unknown fitting type: {fitting_net_type}")
 
-    model = modelcls(
-        descriptor=descriptor,
-        fitting=fitting,
-        type_map=data["type_map"],
-        atom_exclude_types=atom_exclude_types,
-        pair_exclude_types=pair_exclude_types,
-    )
+    model_kwargs: dict = {
+        "descriptor": descriptor,
+        "fitting": fitting,
+        "type_map": data["type_map"],
+        "atom_exclude_types": atom_exclude_types,
+        "pair_exclude_types": pair_exclude_types,
+    }
+    model = modelcls(**model_kwargs)
     return model
 
 

deepmd/entrypoints/test.py

@@ -887,13 +887,19 @@ def test_property(
             high_prec=True,
         )
 
+    is_xas = var_name == "xas"
+
     if dp.get_dim_fparam() > 0:
         data.add(
             "fparam", dp.get_dim_fparam(), atomic=False, must=True, high_prec=False
         )
     if dp.get_dim_aparam() > 0:
         data.add("aparam", dp.get_dim_aparam(), atomic=True, must=True, high_prec=False)
 
+    # XAS requires sel_type.npy (per-frame absorbing element type index)
+    if is_xas:
+        data.add("sel_type", 1, atomic=False, must=True, high_prec=False)
+
     test_data = data.get_test()
     mixed_type = data.mixed_type
     natoms = len(test_data["type"][0])
@@ -918,21 +924,57 @@ def test_property(
     else:
         aparam = None
 
+    # XAS: per-atom outputs are needed to average over absorbing-element atoms
+    eval_atomic = has_atom_property or is_xas
     ret = dp.eval(
         coord,
         box,
         atype,
         fparam=fparam,
         aparam=aparam,
-        atomic=has_atom_property,
+        atomic=eval_atomic,
         mixed_type=mixed_type,
     )
 
-    property = ret[0]
+    if is_xas:
+        # ret[1]: per-atom property [numb_test, natoms, task_dim]
+        atom_prop = ret[1].reshape([numb_test, natoms, dp.task_dim])
+        if mixed_type:
+            atype_frames = atype  # [numb_test, natoms]
+        else:
+            atype_frames = np.tile(atype, (numb_test, 1))  # [numb_test, natoms]
+        sel_type_int = test_data["sel_type"][:numb_test, 0].astype(int)
+        property = np.zeros([numb_test, dp.task_dim], dtype=atom_prop.dtype)
+        for i in range(numb_test):
+            t = sel_type_int[i]
+            mask = atype_frames[i] == t  # [natoms]
+            count = max(mask.sum(), 1)
+            property[i] = atom_prop[i][mask].sum(axis=0) / count
+
+        # Add back the per-(type, edge) energy reference so output is in
+        # absolute eV (matching label format).  xas_e_ref is saved in the
+        # model checkpoint by XASLoss.compute_output_stats.
+        try:
+            xas_e_ref = dp.dp.model["Default"].atomic_model.xas_e_ref
+        except AttributeError:
+            xas_e_ref = None
+        if xas_e_ref is not None and fparam is not None:
+            import torch as _torch
+
+            edge_idx_all = (
+                _torch.tensor(fparam.reshape(numb_test, -1)).argmax(dim=-1).numpy()
+            )
+            e_ref_np = xas_e_ref.cpu().numpy()  # [ntypes, nfparam, 2]
+            for i in range(numb_test):
+                t = sel_type_int[i]
+                e = int(edge_idx_all[i])
+                property[i, :2] += e_ref_np[t, e]
+    else:
+        property = ret[0]
 
     property = property.reshape([numb_test, dp.task_dim])
 
-    if has_atom_property:
+    if has_atom_property and not is_xas:
         aproperty = ret[1]
         aproperty = aproperty.reshape([numb_test, natoms * dp.task_dim])
 

deepmd/pt/loss/__init__.py

@@ -21,6 +21,9 @@
 from .tensor import (
     TensorLoss,
 )
+from .xas import (
+    XASLoss,
+)
 
 __all__ = [
     "DOSLoss",
@@ -31,4 +34,5 @@
     "PropertyLoss",
     "TaskLoss",
     "TensorLoss",
+    "XASLoss",
 ]