c: change the required shape of electric field to nloc * 3 (#3237)

[A segfault](https://github.com/deepmodeling/deepmd-kit/actions/runs/7782245372/job/21218255452) sometimes appears in the tests after #3223. The reason is that the required shape of the electric field is set to nall * 3 in the C interface, but a vector of nloc * 3 is given in the tests and lammps and used in the C++ interface. It was not caught before, as the program didn't write to these addresses (only reading it usually won't cause a segfault, unless the address is invalid). Perhaps fix #2895. --------- Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit e281a8c)
deepmodeling · Apr 6, 2024 · 5d9e627 · 5d9e627
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diff --git a/source/api_c/include/c_api.h b/source/api_c/include/c_api.h
@@ -1134,20 +1134,20 @@ extern void DP_DeleteDipoleChargeModifier(DP_DipoleChargeModifier* dcm);
  *modifier with the neighbor list. (double version)
  * @param[in] dcm The dipole charge modifier to use.
  * @param[in] natoms The number of atoms.
- * @param[in] coord The coordinates of atoms. The array should be of size natoms
+ * @param[in] coord The coordinates of atoms. The array should be of size nall
  *x 3.
- * @param[in] atype The atom types. The array should contain natoms ints.
+ * @param[in] atype The atom types. The array should contain nall ints.
  * @param[in] cell The cell of the region. The array should be of size 9. Pass
  *NULL if pbc is not used.
  * @param[in] pairs The pairs of atoms. The list should contain npairs pairs of
  *ints.
  * @param[in] npairs The number of pairs.
  * @param[in] delef_ The electric field on each atom. The array should be of
- *size nframes x natoms x 3.
+ *size nframes x nloc x 3.
  * @param[in] nghost The number of ghost atoms.
  * @param[in] nlist The neighbor list.
  * @param[out] dfcorr_ Output force correction. The array should be of size
- *natoms x 3.
+ *nall x 3.
  * @param[out] dvcorr_ Output virial correction. The array should be of size 9.
  * @warning The output arrays should be allocated before calling this function.
  *Pass NULL if not required.

diff --git a/source/api_c/include/deepmd.hpp b/source/api_c/include/deepmd.hpp
@@ -1965,13 +1965,13 @@ class DipoleChargeModifier {
    * @param[out] dfcorr_ The force correction on each atom.
    * @param[out] dvcorr_ The virial correction.
    * @param[in] dcoord_ The coordinates of atoms. The array should be of size
-   *natoms x 3.
-   * @param[in] datype_ The atom types. The list should contain natoms ints.
+   *nall x 3.
+   * @param[in] datype_ The atom types. The list should contain nall ints.
    * @param[in] dbox The cell of the region. The array should be of size 9.
    * @param[in] pairs The pairs of atoms. The list should contain npairs pairs
    *of ints.
    * @param[in] delef_ The electric field on each atom. The array should be of
-   *size natoms x 3.
+   *size nghost x 3.
    * @param[in] nghost The number of ghost atoms.
    * @param[in] lmp_list The neighbor list.
    **/

diff --git a/source/api_c/src/c_api.cc b/source/api_c/src/c_api.cc
@@ -785,7 +785,7 @@ inline void DP_DipoleChargeModifierComputeNList_variant(
   for (int i = 0; i < npairs; i++) {
     pairs_.push_back(std::make_pair(pairs[i * 2], pairs[i * 2 + 1]));
   }
-  std::vector<VALUETYPE> delef_(delef, delef + natoms * 3);
+  std::vector<VALUETYPE> delef_(delef, delef + (natoms - nghost) * 3);
   std::vector<VALUETYPE> df, dv;
 
   DP_REQUIRES_OK(dcm, dcm->dcm.compute(df, dv, coord_, atype_, cell_, pairs_,

diff --git a/source/api_cc/include/DataModifier.h b/source/api_cc/include/DataModifier.h
@@ -127,13 +127,13 @@ class DipoleChargeModifier {
    * @param[out] dfcorr_ The force correction on each atom.
    * @param[out] dvcorr_ The virial correction.
    * @param[in] dcoord_ The coordinates of atoms. The array should be of size
-   *natoms x 3.
-   * @param[in] datype_ The atom types. The list should contain natoms ints.
+   *nall x 3.
+   * @param[in] datype_ The atom types. The list should contain nall ints.
    * @param[in] dbox The cell of the region. The array should be of size 9.
    * @param[in] pairs The pairs of atoms. The list should contain npairs pairs
    *of ints.
    * @param[in] delef_ The electric field on each atom. The array should be of
-   *size natoms x 3.
+   *size nloc x 3.
    * @param[in] nghost The number of ghost atoms.
    * @param[in] lmp_list The neighbor list.
    **/

diff --git a/source/api_cc/include/DataModifierTF.h b/source/api_cc/include/DataModifierTF.h
@@ -41,13 +41,13 @@ class DipoleChargeModifierTF : public DipoleChargeModifierBase {
    * @param[out] dfcorr_ The force correction on each atom.
    * @param[out] dvcorr_ The virial correction.
    * @param[in] dcoord_ The coordinates of atoms. The array should be of size
-   *natoms x 3.
-   * @param[in] datype_ The atom types. The list should contain natoms ints.
+   *nall x 3.
+   * @param[in] datype_ The atom types. The list should contain nall ints.
    * @param[in] dbox The cell of the region. The array should be of size 9.
    * @param[in] pairs The pairs of atoms. The list should contain npairs pairs
    *of ints.
    * @param[in] delef_ The electric field on each atom. The array should be of
-   *size natoms x 3.
+   *size nloc x 3.
    * @param[in] nghost The number of ghost atoms.
    * @param[in] lmp_list The neighbor list.
    **/