fix: skip empty frame properties when dumping deepmd format

When an ABACUS SCF run converges but computes no forces/stress (e.g.
cal_force/cal_stress disabled, as happens with some GPU/cusolver runs),
dpdata produces a LabeledSystem with size-0 forces. Dumping it to
deepmd/npy or deepmd/raw wrote a meaningless (nframes, 0) array, which
then failed to reload with 'cannot reshape array of size 0 into shape
(nframes, natoms, 3)'.

Skip empty optional frame properties on dump instead. A missing
force/virial file is already a supported state on load, so the
round-trip is now consistent.

Fixes deepmodeling#977

Author: Han Wang

dpdata/formats/deepmd/comp.py

@@ -152,6 +152,12 @@ def dump(folder, data, set_size=5000, comp_prec=np.float32, remove_sets=True):
                 f"Shape of {dtype.name} is not (nframes, ...), but {dtype.shape}. This type of data will not converted to deepmd/npy format."
             )
             continue
+        if nframes > 0 and np.asarray(data[dtype.name]).size == 0:
+            # an optional frame property (e.g. forces/virials when
+            # cal_force/cal_stress is disabled) may be empty while the
+            # system still has frames. Skip it instead of writing a
+            # meaningless (nframes, 0) array that cannot be reshaped on load.
+            continue
         ddata = np.reshape(data[dtype.name], [nframes, -1])
         if np.issubdtype(ddata.dtype, np.floating):
             ddata = ddata.astype(comp_prec)

dpdata/formats/deepmd/raw.py

@@ -136,5 +136,11 @@ def dump(folder, data):
                 f"Shape of {dtype.name} is not (nframes, ...), but {dtype.shape}. This type of data will not converted to deepmd/raw format."
             )
             continue
+        if nframes > 0 and np.asarray(data[dtype.name]).size == 0:
+            # an optional frame property (e.g. forces/virials when
+            # cal_force/cal_stress is disabled) may be empty while the
+            # system still has frames. Skip it instead of writing a
+            # meaningless (nframes, 0) array that cannot be reshaped on load.
+            continue
         ddata = np.reshape(data[dtype.name], [nframes, -1])
         np.savetxt(os.path.join(folder, f"{dtype.deepmd_name}.raw"), ddata)

tests/test_abacus_pw_scf.py

@@ -2,6 +2,7 @@
 
 import os
 import shutil
+import tempfile
 import unittest
 
 import numpy as np
@@ -163,6 +164,34 @@ def test_noforcestress_job(self):
         # test append self
         system_ch4.append(system_ch4)
 
+    def test_noforcestress_deepmd_roundtrip(self):
+        # a converged scf without force/stress should survive a
+        # round-trip through deepmd/npy without raising a reshape error
+        system_ch4 = dpdata.LabeledSystem("abacus.scf", fmt="abacus/scf")
+        tmp_dir = tempfile.mkdtemp()
+        try:
+            system_ch4.to("deepmd/npy", tmp_dir)
+            reloaded = dpdata.LabeledSystem(tmp_dir, fmt="deepmd/npy")
+            self.assertEqual(reloaded.get_nframes(), system_ch4.get_nframes())
+            # empty force/virial should not be written as bogus data
+            self.assertFalse(reloaded.data.get("forces", np.empty(0)).size)
+            self.assertTrue("virials" not in reloaded.data)
+        finally:
+            shutil.rmtree(tmp_dir)
+
+    def test_noforcestress_deepmd_raw_roundtrip(self):
+        # same as above but for the deepmd/raw format
+        system_ch4 = dpdata.LabeledSystem("abacus.scf", fmt="abacus/scf")
+        tmp_dir = tempfile.mkdtemp()
+        try:
+            system_ch4.to("deepmd/raw", tmp_dir)
+            reloaded = dpdata.LabeledSystem(tmp_dir, fmt="deepmd/raw")
+            self.assertEqual(reloaded.get_nframes(), system_ch4.get_nframes())
+            self.assertFalse(reloaded.data.get("forces", np.empty(0)).size)
+            self.assertTrue("virials" not in reloaded.data)
+        finally:
+            shutil.rmtree(tmp_dir)
+
 
 if __name__ == "__main__":
     unittest.main()