PR: ML Potential Allegro fix

1. now your order of pseudo atoms will automatically match to the Allegro model's element list without sorting the order beforehand
2. some small update to the compilation file

NVC_COMPILE

@@ -6,7 +6,7 @@ CXX="nvc++"
 
 LINKFLAG="-L/opt/nvidia/hpc_sdk/Linux_x86_64/22.5/cuda/lib64 -L/usr/lib64/ -L/opt/local/lib/gcc11/"
 
-NVCFLAG="-O3 -std=c++20 -gpu=cc86 -Minline -fopenmp -cuda -stdpar=multicore"
+NVCFLAG="-O3 -std=c++20 -target=gpu -Minline -fopenmp -cuda -stdpar=multicore"
 
 $CXX $NVCFLAG $LINKFLAG -c axpy.cu
 

cppflow_NVC_COMPILE

@@ -6,7 +6,7 @@ CXX="nvc++"
 
 LINKFLAG="-ltensorflow -L/opt/nvidia/hpc_sdk/Linux_x86_64/22.5/cuda/lib64 -L/usr/lib64/ -L/opt/local/lib/gcc11/"
 
-NVCFLAG="-O3 -std=c++20 -gpu=cc86 -Minline -fopenmp -cuda -stdpar=multicore"
+NVCFLAG="-O3 -std=c++20 -target=gpu -Minline -fopenmp -cuda -stdpar=multicore"
 
 $CXX $NVCFLAG $LINKFLAG -c axpy.cu
 

libtorch-patch/Allegro/PATCH_ALLEGRO_main.cpp.txt

@@ -10,6 +10,8 @@ PATCH_ALLEGRO_MAIN_PREP
         printf("Setting up Allegro model\n");
         SystemComponents[a].DNN.ReadModel(SystemComponents[a].ModelName[0]);
         printf("DONE Reading the model, model name %s\n", SystemComponents[a].ModelName[0].c_str());
+        SystemComponents[a].DNN.Match_Element_PseudoAtom_with_model(SystemComponents[a].PseudoAtoms);
+
         SystemComponents[a].DNN.UCAtoms.resize(SystemComponents[a].NComponents.x);
         SystemComponents[a].DNN.ReplicaAtoms.resize(SystemComponents[a].NComponents.x);
 

libtorch_NVC_COMPILE

@@ -11,7 +11,7 @@ LINKFLAG="-D_GLIBCXX_USE_CXX11_ABI=1 -L${torchDir}/lib -I${torchDir}/include/ -I
 #LINKFLAG="-ltensorflow -L/opt/nvidia/hpc_sdk/Linux_x86_64/22.5/cuda/lib64 -L/usr/lib64/ -L/opt/local/lib/gcc11/"
 
 #NVCFLAG="-O3 -std=c++20 -gpu=cc86 -Minline -fopenmp -Minfo -DUSE_DOUBLE -cuda"
-NVCFLAG="-O3 -std=c++20 -gpu=cc86 -Minline -fopenmp -cuda -stdpar=multicore"
+NVCFLAG="-O3 -std=c++20 -target=gpu -Minline -fopenmp -cuda -stdpar=multicore"
 
 $CXX $NVCFLAG $LINKFLAG -c axpy.cu
 

src_clean/data_struct.h

@@ -774,18 +774,19 @@ struct FRAMEWORK_COMPONENT_LISTS
 struct PseudoAtomDefinitions //Always a host struct, never on the device
 {
   std::vector<std::string> Name;
-  std::vector<std::string> Symbol;
+  std::vector<std::string> Symbol; //Symbol name for each pseudo-atom
+  std::vector<std::string> UniqueSymbol; //all the unique Symbol list //
   std::vector<size_t> SymbolIndex; //It has the size of the number of pseudo atoms, it tells the ID of the symbol for the pseudo-atoms, e.g., CO2->C->2
   std::vector<double> oxidation;
   std::vector<double> mass;
   std::vector<double> charge;
   std::vector<double> polar; //polarizability
-  size_t MatchSymbolTypeFromSymbolName(std::string& SymbolName)
+  size_t MatchUniqueSymbolTypeFromSymbolName(std::string& SymbolName)
   {
-    size_t SymbolIdx = 0;
-    for(size_t i = 0; i < Symbol.size(); i++)
+    size_t SymbolIdx = UniqueSymbol.size();
+    for(size_t i = 0; i < UniqueSymbol.size(); i++)
     {
-      if(SymbolName == Symbol[i]) 
+      if(SymbolName == UniqueSymbol[i])
       {
         SymbolIdx = i; break;
       }

src_clean/read_data.cpp

@@ -1081,9 +1081,12 @@ void PseudoAtomParser(ForceField& FF, PseudoAtomDefinitions& PseudoAtom)
     {
       Split_Tab_Space(termsScannedLined, str);
       if(termsScannedLined[0] != PseudoAtom.Name[counter-3]) throw std::runtime_error("Order of pseudo-atom and force field definition don't match!");
-      PseudoAtom.Symbol.push_back(termsScannedLined[2]);
+
       //Match 1-to-1 list of pseudo_atom type and symbol type//
-      size_t SymbolIdx = PseudoAtom.MatchSymbolTypeFromSymbolName(termsScannedLined[2]);
+      PseudoAtom.Symbol.push_back(termsScannedLined[2]);
+      size_t SymbolIdx = PseudoAtom.MatchUniqueSymbolTypeFromSymbolName(termsScannedLined[2]);
+      if(SymbolIdx >= PseudoAtom.UniqueSymbol.size()) PseudoAtom.UniqueSymbol.push_back(termsScannedLined[2]);
+
       PseudoAtom.SymbolIndex.push_back(SymbolIdx);
       PseudoAtom.oxidation.push_back(std::stod(termsScannedLined[4]));
       PseudoAtom.mass.push_back(std::stod(termsScannedLined[5]));

src_clean/torch_allegro.h

@@ -6,6 +6,8 @@ struct Allegro
   Boxsize ReplicaBox;
   std::vector<Atoms> UCAtoms;
   std::vector<Atoms> ReplicaAtoms;
+  std::vector<std::string> ElementSymbolUsed;
+  std::vector<int>Match_AllegroElement_PseudoAtom_order; //length = # of PseudoAtoms, value stored = order in the Allegro Model//
   double Cutoff = 6.0;
   double Cutoffsq = 0.0;
   NeighList NL;
@@ -15,6 +17,22 @@ struct Allegro
 
   size_t nstep = 0;
 
+  void Match_Element_PseudoAtom_with_model(PseudoAtomDefinitions& PseudoAtoms)
+  {
+    printf("------- MATCHING ALLEGRO ELEMENTS WITH PSEUDO ATOM ELEMENT SYMBOLS -------\n");
+    Match_AllegroElement_PseudoAtom_order.resize(PseudoAtoms.Symbol.size(), -1);
+    for(size_t i = 0; i < PseudoAtoms.Symbol.size(); i++)
+    {
+      for(size_t j = 0; j < ElementSymbolUsed.size(); j++)
+        if(PseudoAtoms.Symbol[i] == ElementSymbolUsed[j])
+        {
+          Match_AllegroElement_PseudoAtom_order[i] = j;
+          printf("PseudoAtom Symbol[%zu]: %s, Allegro Symbol[%zu]: %s, MATCHED\n", i, PseudoAtoms.Symbol[i].c_str(), j, ElementSymbolUsed[j].c_str());
+          break;
+        }
+    }
+  }
+
   void GetSQ_From_Cutoff()
   {
     Cutoffsq = Cutoff * Cutoff;
@@ -190,9 +208,9 @@ struct Allegro
       if(comp != 0)
         if(!ConsiderThisAdsorbateAtom[i]) continue;
       UCAtoms[comp].pos[update_i]  = HostAtoms.pos[i];
-      size_t SymbolIdx = PseudoAtoms.GetSymbolIdxFromPseudoAtomTypeIdx(HostAtoms.Type[i]);
+      size_t SymbolIdx = Match_AllegroElement_PseudoAtom_order[HostAtoms.Type[i]];
       UCAtoms[comp].Type[update_i] = SymbolIdx;
-      //printf("Component %zu, Atom %zu, xyz %f %f %f, Type %zu, SymbolIndex %zu\n", comp, i, UCAtoms[comp].pos[i].x, UCAtoms[comp].pos[i].y, UCAtoms[comp].pos[i].z, HostAtoms.Type[i], UCAtoms[comp].Type[i]);
+      if(i < 5 || i > (NAtoms - 5)) printf("Component %zu, Atom %zu, xyz %f %f %f, Type %zu, SymbolIndex %zu\n", comp, i, UCAtoms[comp].pos[i].x, UCAtoms[comp].pos[i].y, UCAtoms[comp].pos[i].z, HostAtoms.Type[i], UCAtoms[comp].Type[i]);
       update_i ++;
     }
   }
@@ -239,6 +257,15 @@ struct Allegro
     Model.eval();
     //Freeze the model
     Model = torch::jit::freeze(Model);
+    std::cout << "MODEL TYPE NAMES " << metadata["type_names"] << "\n";
+    std::cout << "MODEL SPECIES "    << metadata["n_species"] << "\n";
+    //std::string name = std::to_string(metadata["type_names"]);
+    std::string name = metadata["type_names"];
+    std::vector<std::string> termsScannedLined{};
+    Split_Tab_Space(termsScannedLined, name);
+    ElementSymbolUsed = termsScannedLined;
+    printf("First element of type: %s, first: %s\n", name.c_str(), ElementSymbolUsed[0].c_str());
+    //printf("Model");
     //ReadCutOffFromModel(ModelName);
   }
 
@@ -265,7 +292,7 @@ struct Allegro
       pos[counter][2] = ReplicaAtoms[comp].pos[i].z;
       ij2type[counter]= ReplicaAtoms[comp].Type[i];
       //if(comp != 0)
-      //  printf("comp %zu, counter %zu, ij2type %zu\n", comp, counter, ij2type[counter]);
+      //printf("comp %zu, counter %zu, ij2type %zu\n", comp, counter, ij2type[counter]);
       counter ++;
     }
     size_t N_Replica_FrameworkAtoms = 0; size_t NFrameworkAtoms = 0;
@@ -551,6 +578,7 @@ struct Allegro
     WrapSuperCellAtomIntoUCBox(comp);
     GenerateReplicaCells(Initialize);
     Get_Neighbor_List_Replica(Initialize);
+    //printf("Doing Neighbor list\n");
     double DNN_E = Predict();
     //This generates the unit of eV, convert to 10J/mol.
     //https://www.weizmann.ac.il/oc/martin/tools/hartree.html