Bug summary
When the input STRU cell has a negative determinant, right_hand_rule() negates the cell and Cartesian coordinates. However, the SCF reader loads forces from running_scf.log without negating them.
The exported coordinates and forces therefore belong to inconsistent spatial representations. The trigger is cell handedness, not atom count.
dpdata Version
The same logic was also observed in GitHub master on September 20, 2026. The affected installation uses the older dpdata/abacus/ module path.
Input Files, Running Commands, Error Log, etc.
task.21.zip
calculation/
├── INPUT
├── STRU
└── OUT.ABACUS/running_scf.log
Read and export using:
import dpdata
system = dpdata.LabeledSystem("calculation", fmt="abacus/scf")
system.to_deepmd_npy("exported")
Observed values from an affected dataset:
eg:
Original Cartesian position ≈ [ 2.7337, 7.0893, 2.2321]
Exported coord.npy ≈ [-2.7337, -7.0891, -2.2320]
ABACUS TOTAL-FORCE = [-0.0020299593, 2.3578977033, 0.3664125131]
Exported force.npy ≈ [-0.002, 2.3579, 0.3664]
The coordinates are approximately negated, while the force signs remain unchanged. This is a silent data-consistency error rather than a parsing exception.
Steps to Reproduce
Prepare a converged ABACUS SCF calculation whose input STRU cell has det(cell) < 0 and whose output contains nonzero forces.
Read the calculation with dpdata.LabeledSystem(..., fmt="abacus/scf").
Compare the parsed cell and Cartesian coordinates with the original STRU.
Compare the parsed forces with the corresponding TOTAL-FORCE block.
Actual: Cell and coordinates are negated; forces retain their original signs.
Expected: If coordinates undergo spatial inversion, forces must also be negated. Energy, stress, and virial should remain unchanged under this inversion.
Further Information, Files, and Links
Relevant source code:
stru.py::right_hand_rule() negates only the cell and coordinates:
if np.linalg.det(cell) < 0:
cell = -cell
coord = -coord
get_frame_from_stru() calls this function without returning an inversion flag.
scf.py::get_force() reads forces without a spatial transformation.
scf.py::get_frame() combines the transformed structure with the untransformed forces.
Bug summary
When the input STRU cell has a negative determinant, right_hand_rule() negates the cell and Cartesian coordinates. However, the SCF reader loads forces from running_scf.log without negating them.
The exported coordinates and forces therefore belong to inconsistent spatial representations. The trigger is cell handedness, not atom count.
dpdata Version
The same logic was also observed in GitHub master on September 20, 2026. The affected installation uses the older dpdata/abacus/ module path.
Input Files, Running Commands, Error Log, etc.
task.21.zip
calculation/
├── INPUT
├── STRU
└── OUT.ABACUS/running_scf.log
Read and export using:
import dpdata
system = dpdata.LabeledSystem("calculation", fmt="abacus/scf")
system.to_deepmd_npy("exported")
Observed values from an affected dataset:
eg:
Original Cartesian position ≈ [ 2.7337, 7.0893, 2.2321]
Exported coord.npy ≈ [-2.7337, -7.0891, -2.2320]
ABACUS TOTAL-FORCE = [-0.0020299593, 2.3578977033, 0.3664125131]
Exported force.npy ≈ [-0.002, 2.3579, 0.3664]
The coordinates are approximately negated, while the force signs remain unchanged. This is a silent data-consistency error rather than a parsing exception.
Steps to Reproduce
Prepare a converged ABACUS SCF calculation whose input STRU cell has det(cell) < 0 and whose output contains nonzero forces.
Read the calculation with dpdata.LabeledSystem(..., fmt="abacus/scf").
Compare the parsed cell and Cartesian coordinates with the original STRU.
Compare the parsed forces with the corresponding TOTAL-FORCE block.
Actual: Cell and coordinates are negated; forces retain their original signs.
Expected: If coordinates undergo spatial inversion, forces must also be negated. Energy, stress, and virial should remain unchanged under this inversion.
Further Information, Files, and Links
Relevant source code:
stru.py::right_hand_rule() negates only the cell and coordinates:
if np.linalg.det(cell) < 0:
cell = -cell
coord = -coord
get_frame_from_stru() calls this function without returning an inversion flag.
scf.py::get_force() reads forces without a spatial transformation.
scf.py::get_frame() combines the transformed structure with the untransformed forces.