feat: support data type dumped to a different name (#727)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **New Features**
- Introduced an optional `deepmd_name` parameter in the `DataType` class
for enhanced naming flexibility.
- Updated data type declarations in the `System` and `LabeledSystem`
classes for better integration with the DeepMD framework.

- **Bug Fixes**
- Removed handling of energy, force, and virial data to simplify data
processing and storage.

- **Documentation**
- Updated documentation for the `DataType` class to clarify the new
`deepmd_name` parameter.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

dpdata/data_type.py

@@ -46,6 +46,8 @@ class DataType:
         represents numbers
     required : bool, default=True
         whether this data is required
+    deepmd_name : str, optional
+        DeePMD-kit data type name. When not given, it is the same as `name`.
     """
 
     def __init__(
@@ -54,11 +56,13 @@ def __init__(
         dtype: type,
         shape: tuple[int | Axis, ...] | None = None,
         required: bool = True,
+        deepmd_name: str | None = None,
     ) -> None:
         self.name = name
         self.dtype = dtype
         self.shape = shape
         self.required = required
+        self.deepmd_name = name if deepmd_name is None else deepmd_name
 
     def real_shape(self, system: System) -> tuple[int]:
         """Returns expected real shape of a system."""

dpdata/deepmd/comp.py

@@ -26,10 +26,7 @@ def _load_set(folder, nopbc: bool):
         cells = np.zeros((coords.shape[0], 3, 3))
     else:
         cells = np.load(os.path.join(folder, "box.npy"))
-    eners = _cond_load_data(os.path.join(folder, "energy.npy"))
-    forces = _cond_load_data(os.path.join(folder, "force.npy"))
-    virs = _cond_load_data(os.path.join(folder, "virial.npy"))
-    return cells, coords, eners, forces, virs
+    return cells, coords
 
 
 def to_system_data(folder, type_map=None, labels=True):
@@ -41,31 +38,13 @@ def to_system_data(folder, type_map=None, labels=True):
     sets = sorted(glob.glob(os.path.join(folder, "set.*")))
     all_cells = []
     all_coords = []
-    all_eners = []
-    all_forces = []
-    all_virs = []
     for ii in sets:
-        cells, coords, eners, forces, virs = _load_set(ii, data.get("nopbc", False))
+        cells, coords = _load_set(ii, data.get("nopbc", False))
         nframes = np.reshape(cells, [-1, 3, 3]).shape[0]
         all_cells.append(np.reshape(cells, [nframes, 3, 3]))
         all_coords.append(np.reshape(coords, [nframes, -1, 3]))
-        if eners is not None:
-            eners = np.reshape(eners, [nframes])
-        if labels:
-            if eners is not None and eners.size > 0:
-                all_eners.append(np.reshape(eners, [nframes]))
-            if forces is not None and forces.size > 0:
-                all_forces.append(np.reshape(forces, [nframes, -1, 3]))
-            if virs is not None and virs.size > 0:
-                all_virs.append(np.reshape(virs, [nframes, 3, 3]))
     data["cells"] = np.concatenate(all_cells, axis=0)
     data["coords"] = np.concatenate(all_coords, axis=0)
-    if len(all_eners) > 0:
-        data["energies"] = np.concatenate(all_eners, axis=0)
-    if len(all_forces) > 0:
-        data["forces"] = np.concatenate(all_forces, axis=0)
-    if len(all_virs) > 0:
-        data["virials"] = np.concatenate(all_virs, axis=0)
     # allow custom dtypes
     if labels:
         dtypes = dpdata.system.LabeledSystem.DTYPES
@@ -82,9 +61,6 @@ def to_system_data(folder, type_map=None, labels=True):
             "coords",
             "real_atom_names",
             "nopbc",
-            "energies",
-            "forces",
-            "virials",
         ):
             # skip as these data contains specific rules
             continue
@@ -93,13 +69,13 @@ def to_system_data(folder, type_map=None, labels=True):
                 f"Shape of {dtype.name} is not (nframes, ...), but {dtype.shape}. This type of data will not converted from deepmd/npy format."
             )
             continue
-        natoms = data["coords"].shape[1]
+        natoms = data["atom_types"].shape[0]
         shape = [
             natoms if xx == dpdata.system.Axis.NATOMS else xx for xx in dtype.shape[1:]
         ]
         all_data = []
         for ii in sets:
-            tmp = _cond_load_data(os.path.join(ii, dtype.name + ".npy"))
+            tmp = _cond_load_data(os.path.join(ii, dtype.deepmd_name + ".npy"))
             if tmp is not None:
                 all_data.append(np.reshape(tmp, [tmp.shape[0], *shape]))
         if len(all_data) > 0:
@@ -136,19 +112,6 @@ def dump(folder, data, set_size=5000, comp_prec=np.float32, remove_sets=True):
         np.savetxt(os.path.join(folder, "formal_charges.raw"), data["formal_charges"])
     # reshape frame properties and convert prec
     nframes = data["cells"].shape[0]
-    cells = np.reshape(data["cells"], [nframes, 9]).astype(comp_prec)
-    coords = np.reshape(data["coords"], [nframes, -1]).astype(comp_prec)
-    eners = None
-    forces = None
-    virials = None
-    if "energies" in data:
-        eners = np.reshape(data["energies"], [nframes]).astype(comp_prec)
-    if "forces" in data:
-        forces = np.reshape(data["forces"], [nframes, -1]).astype(comp_prec)
-    if "virials" in data:
-        virials = np.reshape(data["virials"], [nframes, 9]).astype(comp_prec)
-    if "atom_pref" in data:
-        atom_pref = np.reshape(data["atom_pref"], [nframes, -1]).astype(comp_prec)
     # dump frame properties: cell, coord, energy, force and virial
     nsets = nframes // set_size
     if set_size * nsets < nframes:
@@ -158,16 +121,6 @@ def dump(folder, data, set_size=5000, comp_prec=np.float32, remove_sets=True):
         set_end = (ii + 1) * set_size
         set_folder = os.path.join(folder, "set.%03d" % ii)
         os.makedirs(set_folder)
-        np.save(os.path.join(set_folder, "box"), cells[set_stt:set_end])
-        np.save(os.path.join(set_folder, "coord"), coords[set_stt:set_end])
-        if eners is not None:
-            np.save(os.path.join(set_folder, "energy"), eners[set_stt:set_end])
-        if forces is not None:
-            np.save(os.path.join(set_folder, "force"), forces[set_stt:set_end])
-        if virials is not None:
-            np.save(os.path.join(set_folder, "virial"), virials[set_stt:set_end])
-        if "atom_pref" in data:
-            np.save(os.path.join(set_folder, "atom_pref"), atom_pref[set_stt:set_end])
     try:
         os.remove(os.path.join(folder, "nopbc"))
     except OSError:
@@ -187,13 +140,8 @@ def dump(folder, data, set_size=5000, comp_prec=np.float32, remove_sets=True):
             "atom_names",
             "atom_types",
             "orig",
-            "cells",
-            "coords",
             "real_atom_names",
             "nopbc",
-            "energies",
-            "forces",
-            "virials",
         ):
             # skip as these data contains specific rules
             continue
@@ -211,4 +159,4 @@ def dump(folder, data, set_size=5000, comp_prec=np.float32, remove_sets=True):
             set_stt = ii * set_size
             set_end = (ii + 1) * set_size
             set_folder = os.path.join(folder, "set.%03d" % ii)
-            np.save(os.path.join(set_folder, dtype.name), ddata[set_stt:set_end])
+            np.save(os.path.join(set_folder, dtype.deepmd_name), ddata[set_stt:set_end])

dpdata/deepmd/hdf5.py

@@ -69,38 +69,7 @@ def to_system_data(
         data["nopbc"] = True
     sets = globfilter(g.keys(), "set.*")
 
-    data_types = {
-        "cells": {
-            "fn": "box",
-            "labeled": False,
-            "shape": (3, 3),
-            "required": "nopbc" not in data,
-        },
-        "coords": {
-            "fn": "coord",
-            "labeled": False,
-            "shape": (natoms, 3),
-            "required": True,
-        },
-        "energies": {
-            "fn": "energy",
-            "labeled": True,
-            "shape": tuple(),
-            "required": False,
-        },
-        "forces": {
-            "fn": "force",
-            "labeled": True,
-            "shape": (natoms, 3),
-            "required": False,
-        },
-        "virials": {
-            "fn": "virial",
-            "labeled": True,
-            "shape": (3, 3),
-            "required": False,
-        },
-    }
+    data_types = {}
     # allow custom dtypes
     if labels:
         dtypes = dpdata.system.LabeledSystem.DTYPES
@@ -112,14 +81,9 @@ def to_system_data(
             "atom_names",
             "atom_types",
             "orig",
-            "cells",
-            "coords",
             "real_atom_types",
             "real_atom_names",
             "nopbc",
-            "energies",
-            "forces",
-            "virials",
         ):
             # skip as these data contains specific rules
             continue
@@ -133,10 +97,10 @@ def to_system_data(
         ]
 
         data_types[dtype.name] = {
-            "fn": dtype.name,
-            "labeled": True,
+            "fn": dtype.deepmd_name,
             "shape": shape,
-            "required": False,
+            "required": dtype.required
+            and not (dtype.name == "cells" and data.get("nopbc", False)),
         }
 
     for dt, prop in data_types.items():
@@ -206,13 +170,7 @@ def dump(
     nopbc = data.get("nopbc", False)
     reshaped_data = {}
 
-    data_types = {
-        "cells": {"fn": "box", "shape": (nframes, 9), "dump": not nopbc},
-        "coords": {"fn": "coord", "shape": (nframes, -1), "dump": True},
-        "energies": {"fn": "energy", "shape": (nframes,), "dump": True},
-        "forces": {"fn": "force", "shape": (nframes, -1), "dump": True},
-        "virials": {"fn": "virial", "shape": (nframes, 9), "dump": True},
-    }
+    data_types = {}
 
     labels = "energies" in data
     if labels:
@@ -226,14 +184,9 @@ def dump(
             "atom_names",
             "atom_types",
             "orig",
-            "cells",
-            "coords",
             "real_atom_types",
             "real_atom_names",
             "nopbc",
-            "energies",
-            "forces",
-            "virials",
         ):
             # skip as these data contains specific rules
             continue
@@ -244,9 +197,9 @@ def dump(
             continue
 
         data_types[dtype.name] = {
-            "fn": dtype.name,
+            "fn": dtype.deepmd_name,
             "shape": (nframes, -1),
-            "dump": True,
+            "dump": not (dtype.name == "cells" and nopbc),
         }
 
     for dt, prop in data_types.items():

dpdata/deepmd/raw.py

@@ -49,16 +49,6 @@ def to_system_data(folder, type_map=None, labels=True):
             data["cells"] = np.loadtxt(os.path.join(folder, "box.raw"), ndmin=2)
         data["cells"] = np.reshape(data["cells"], [nframes, 3, 3])
         data["coords"] = np.reshape(data["coords"], [nframes, -1, 3])
-        if labels:
-            if os.path.exists(os.path.join(folder, "energy.raw")):
-                data["energies"] = np.loadtxt(os.path.join(folder, "energy.raw"))
-                data["energies"] = np.reshape(data["energies"], [nframes])
-            if os.path.exists(os.path.join(folder, "force.raw")):
-                data["forces"] = np.loadtxt(os.path.join(folder, "force.raw"))
-                data["forces"] = np.reshape(data["forces"], [nframes, -1, 3])
-            if os.path.exists(os.path.join(folder, "virial.raw")):
-                data["virials"] = np.loadtxt(os.path.join(folder, "virial.raw"))
-                data["virials"] = np.reshape(data["virials"], [nframes, 3, 3])
         if os.path.isfile(os.path.join(folder, "nopbc")):
             data["nopbc"] = True
         # allow custom dtypes
@@ -77,9 +67,6 @@ def to_system_data(folder, type_map=None, labels=True):
                 "real_atom_types",
                 "real_atom_names",
                 "nopbc",
-                "energies",
-                "forces",
-                "virials",
             ):
                 # skip as these data contains specific rules
                 continue
@@ -88,14 +75,14 @@ def to_system_data(folder, type_map=None, labels=True):
                     f"Shape of {dtype.name} is not (nframes, ...), but {dtype.shape}. This type of data will not converted from deepmd/raw format."
                 )
                 continue
-            natoms = data["coords"].shape[1]
+            natoms = data["atom_types"].shape[0]
             shape = [
                 natoms if xx == dpdata.system.Axis.NATOMS else xx
                 for xx in dtype.shape[1:]
             ]
-            if os.path.exists(os.path.join(folder, f"{dtype.name}.raw")):
+            if os.path.exists(os.path.join(folder, f"{dtype.deepmd_name}.raw")):
                 data[dtype.name] = np.reshape(
-                    np.loadtxt(os.path.join(folder, f"{dtype.name}.raw")),
+                    np.loadtxt(os.path.join(folder, f"{dtype.deepmd_name}.raw")),
                     [nframes, *shape],
                 )
         return data
@@ -108,10 +95,6 @@ def dump(folder, data):
     nframes = data["cells"].shape[0]
     np.savetxt(os.path.join(folder, "type.raw"), data["atom_types"], fmt="%d")
     np.savetxt(os.path.join(folder, "type_map.raw"), data["atom_names"], fmt="%s")
-    np.savetxt(os.path.join(folder, "box.raw"), np.reshape(data["cells"], [nframes, 9]))
-    np.savetxt(
-        os.path.join(folder, "coord.raw"), np.reshape(data["coords"], [nframes, -1])
-    )
     # BondOrder System
     if "bonds" in data:
         np.savetxt(
@@ -121,21 +104,6 @@ def dump(folder, data):
         )
     if "formal_charges" in data:
         np.savetxt(os.path.join(folder, "formal_charges.raw"), data["formal_charges"])
-    # Labeled System
-    if "energies" in data:
-        np.savetxt(
-            os.path.join(folder, "energy.raw"),
-            np.reshape(data["energies"], [nframes, 1]),
-        )
-    if "forces" in data:
-        np.savetxt(
-            os.path.join(folder, "force.raw"), np.reshape(data["forces"], [nframes, -1])
-        )
-    if "virials" in data:
-        np.savetxt(
-            os.path.join(folder, "virial.raw"),
-            np.reshape(data["virials"], [nframes, 9]),
-        )
     try:
         os.remove(os.path.join(folder, "nopbc"))
     except OSError:
@@ -155,14 +123,9 @@ def dump(folder, data):
             "atom_names",
             "atom_types",
             "orig",
-            "cells",
-            "coords",
             "real_atom_types",
             "real_atom_names",
             "nopbc",
-            "energies",
-            "forces",
-            "virials",
         ):
             # skip as these data contains specific rules
             continue
@@ -174,4 +137,4 @@ def dump(folder, data):
             )
             continue
         ddata = np.reshape(data[dtype.name], [nframes, -1])
-        np.savetxt(os.path.join(folder, f"{dtype.name}.raw"), ddata)
+        np.savetxt(os.path.join(folder, f"{dtype.deepmd_name}.raw"), ddata)

dpdata/system.py

@@ -91,8 +91,10 @@ class System:
         DataType("atom_names", list, (Axis.NTYPES,)),
         DataType("atom_types", np.ndarray, (Axis.NATOMS,)),
         DataType("orig", np.ndarray, (3,)),
-        DataType("cells", np.ndarray, (Axis.NFRAMES, 3, 3)),
-        DataType("coords", np.ndarray, (Axis.NFRAMES, Axis.NATOMS, 3)),
+        DataType("cells", np.ndarray, (Axis.NFRAMES, 3, 3), deepmd_name="box"),
+        DataType(
+            "coords", np.ndarray, (Axis.NFRAMES, Axis.NATOMS, 3), deepmd_name="coord"
+        ),
         DataType(
             "real_atom_types", np.ndarray, (Axis.NFRAMES, Axis.NATOMS), required=False
         ),
@@ -1204,9 +1206,17 @@ class LabeledSystem(System):
     """
 
     DTYPES: tuple[DataType, ...] = System.DTYPES + (
-        DataType("energies", np.ndarray, (Axis.NFRAMES,)),
-        DataType("forces", np.ndarray, (Axis.NFRAMES, Axis.NATOMS, 3)),
-        DataType("virials", np.ndarray, (Axis.NFRAMES, 3, 3), required=False),
+        DataType("energies", np.ndarray, (Axis.NFRAMES,), deepmd_name="energy"),
+        DataType(
+            "forces", np.ndarray, (Axis.NFRAMES, Axis.NATOMS, 3), deepmd_name="force"
+        ),
+        DataType(
+            "virials",
+            np.ndarray,
+            (Axis.NFRAMES, 3, 3),
+            required=False,
+            deepmd_name="virial",
+        ),
         DataType("atom_pref", np.ndarray, (Axis.NFRAMES, Axis.NATOMS), required=False),
     )