feat(pt): pass mapping from LAMMPS to PT

source/api_c/include/c_api.h

@@ -12,7 +12,7 @@ extern "C" {
 /** C API version. Bumped whenever the API is changed.
  * @since API version 22
  */
-#define DP_C_API_VERSION 24
+#define DP_C_API_VERSION 25
 
 /**
  * @brief Neighbor list.
@@ -31,7 +31,7 @@ extern DP_Nlist* DP_NewNlist(int inum_,
                              int* ilist_,
                              int* numneigh_,
                              int** firstneigh_);
-/*
+/**
  * @brief Create a new neighbor list with communication capabilities.
  * @details This function extends DP_NewNlist by adding support for parallel
  * communication, allowing the neighbor list to be used in distributed
@@ -68,7 +68,7 @@ extern DP_Nlist* DP_NewNlist_comm(int inum_,
                                   int* recvproc,
                                   void* world);
 
-/*
+/**
  * @brief Set mask for a neighbor list.
  *
  * @param nl Neighbor list.
@@ -78,6 +78,16 @@ extern DP_Nlist* DP_NewNlist_comm(int inum_,
  **/
 extern void DP_NlistSetMask(DP_Nlist* nl, int mask);
 
+/**
+ * @brief Set mapping for a neighbor list.
+ *
+ * @param nl Neighbor list.
+ * @param mapping mapping from all atoms to real atoms, in size nall.
+ * @since API version 25
+ *
+ **/
+extern void DP_NlistSetMapping(DP_Nlist* nl, int* mapping);
+
 /**
  * @brief Delete a neighbor list.
  *

source/api_c/include/deepmd.hpp

@@ -863,6 +863,11 @@ struct InputNlist {
    * @brief Set mask for this neighbor list.
    */
   void set_mask(int mask) { DP_NlistSetMask(nl, mask); };
+  /**
+   * @brief Set mapping for this neighbor list.
+   * @param mapping mapping from all atoms to real atoms, in size nall.
+   */
+  void set_mapping(int *mapping) { DP_NlistSetMapping(nl, mapping); };
 };
 
 /**

source/api_c/src/c_api.cc

@@ -43,6 +43,9 @@ DP_Nlist* DP_NewNlist_comm(int inum_,
   return new_nl;
 }
 void DP_NlistSetMask(DP_Nlist* nl, int mask) { nl->nl.set_mask(mask); }
+void DP_NlistSetMapping(DP_Nlist* nl, int* mapping) {
+  nl->nl.set_mapping(mapping);
+}
 void DP_DeleteNlist(DP_Nlist* nl) { delete nl; }
 
 // DP Base Model

source/api_cc/src/DeepPotPT.cc

@@ -203,6 +203,15 @@ void DeepPotPT::compute(ENERGYVTYPE& ener,
       comm_dict.insert("recv_num", recvnum_tensor);
       comm_dict.insert("communicator", communicator_tensor);
     }
+    if (lmp_list.mapping) {
+      std::vector<std::int64_t> mapping(nall_real);
+      for (size_t ii = 0; ii < nall_real; ii++) {
+        mapping[ii] = lmp_list.mapping[fwd_map[ii]];
+      }
+      mapping_tensor =
+          torch::from_blob(mapping.data(), {1, nall_real}, int_option)
+              .to(device);
+    }
   }
   at::Tensor firstneigh = createNlistTensor(nlist_data.jlist);
   firstneigh_tensor = firstneigh.to(torch::kInt64).to(device);

source/lib/include/neighbor_list.h

@@ -44,6 +44,8 @@ struct InputNlist {
   void* world;
   /// mask to the neighbor index
   int mask = 0xFFFFFFFF;
+  /// mapping from all atoms to real atoms, in the size of nall
+  int* mapping = nullptr;
   InputNlist()
       : inum(0),
         ilist(NULL),
@@ -99,6 +101,10 @@ struct InputNlist {
    * @brief Set mask for this neighbor list.
    */
   void set_mask(int mask_) { mask = mask_; };
+  /**
+   * @brief Set mapping for this neighbor list.
+   */
+  void set_mapping(int* mapping_) { mapping = mapping_; };
 };
 
 /**

source/lmp/fix_dplr.cpp

@@ -467,6 +467,14 @@ void FixDPLR::pre_force(int vflag) {
   int nghost = atom->nghost;
   int nall = nlocal + nghost;
 
+  // mapping (for DPA-2 JAX)
+  std::vector<int> mapping_vec(nall, -1);
+  if (comm->nprocs == 1 && atom->map_style != Atom::MAP_NONE) {
+    for (size_t ii = 0; ii < nall; ++ii) {
+      mapping_vec[ii] = atom->map(atom->tag[ii]);
+    }
+  }
+
   // if (eflag_atom) {
   //   error->all(FLERR,"atomic energy calculation is not supported by this
   //   fix\n");
@@ -499,6 +507,9 @@ void FixDPLR::pre_force(int vflag) {
   deepmd_compat::InputNlist lmp_list(list->inum, list->ilist, list->numneigh,
                                      list->firstneigh);
   lmp_list.set_mask(NEIGHMASK);
+  if (comm->nprocs == 1 && atom->map_style != Atom::MAP_NONE) {
+    lmp_list.set_mapping(mapping_vec.data());
+  }
   // declear output
   vector<FLOAT_PREC> tensor;
   // compute

source/lmp/pair_deepmd.cpp

@@ -155,6 +155,14 @@ void PairDeepMD::compute(int eflag, int vflag) {
     }
   }
 
+  // mapping (for DPA-2 JAX)
+  std::vector<int> mapping_vec(nall, -1);
+  if (comm->nprocs == 1 && atom->map_style != Atom::MAP_NONE) {
+    for (size_t ii = 0; ii < nall; ++ii) {
+      mapping_vec[ii] = atom->map(atom->tag[ii]);
+    }
+  }
+
   if (do_compute_aparam) {
     make_aparam_from_compute(daparam);
   } else if (aparam.size() > 0) {
@@ -198,6 +206,9 @@ void PairDeepMD::compute(int eflag, int vflag) {
         commdata_->firstrecv, commdata_->sendlist, commdata_->sendproc,
         commdata_->recvproc, &world);
     lmp_list.set_mask(NEIGHMASK);
+    if (comm->nprocs == 1 && atom->map_style != Atom::MAP_NONE) {
+      lmp_list.set_mapping(mapping_vec.data());
+    }
     deepmd_compat::InputNlist extend_lmp_list;
     if (single_model || multi_models_no_mod_devi) {
       // cvflag_atom is the right flag for the cvatom matrix