remove unused code and update a readme

potentials/nep/readme.md

@@ -7,7 +7,7 @@
 | :-------------------- | :------------------ | :----------------------------------------------------------- |
 | Si_Fan_2021.txt       | [1] | This is a general-purpose potential for silicon, which should be applicable to most of the phases of silicon, but this is not guaranteed. Our tests show that the phonon dispersions of 2D silicene are not well described by this potential. |
 | Silicene_Fan_2021.txt | [1]         | The is a special potential for 2D silicene. The potential should be applicable to study elastic and thermal properties of 2D silicene (without defects and free edges) from 0 K to about 900 K and a biaxial strain from about -1% to about 1%. |
-| PbTe_Fan_2021.txt     | [1]         | The is a special potential for bulk PbTe. The potential should be applicable to study thermal properties of bulk PbTe (without defects and surfaces) from 0 K to about 900 K with a fixed lattice constant of about 6.57 A. |
+| PbTe_Fan_2021.txt     | [2]        | The is a special potential for bulk PbTe. The potential should be applicable to study thermal properties of bulk PbTe (without defects and surfaces) from 0 K to about 900 K with a fixed lattice constant of about 6.57 A. |
 
 
 

src/model/read_xyz.cu

@@ -176,7 +176,6 @@ void read_xyz_in_line_2(FILE* fid_xyz, Box& box)
 }
 
 void read_xyz_in_line_3(
-  char* input_dir,
   FILE* fid_xyz,
   const int N,
   const int has_velocity_in_xyz,
@@ -191,7 +190,7 @@ void read_xyz_in_line_3(
   cpu_mass.resize(N);
   cpu_position_per_atom.resize(N * 3);
   cpu_velocity_per_atom.resize(N * 3);
-  std::vector<int> types;
+  number_of_types = -1;
 
   for (int m = 0; m < group.size(); ++m) {
     group[m].cpu_label.resize(N);
@@ -203,8 +202,8 @@ void read_xyz_in_line_3(
     int count = fscanf(fid_xyz, "%d%lf%lf%lf%lf", &(cpu_type[n]), &x, &y, &z, &mass);
     PRINT_SCANF_ERROR(count, 5, "Reading error for xyz.in.");
 
-    if (cpu_type[n] < 0) {
-      PRINT_INPUT_ERROR("Atom type should >= 0.");
+    if (cpu_type[n] < 0 || cpu_type[n] >= N) {
+      PRINT_INPUT_ERROR("Atom type should >= 0 and < N.");
     }
 
     if (mass <= 0) {
@@ -216,14 +215,8 @@ void read_xyz_in_line_3(
     cpu_position_per_atom[n + N] = y;
     cpu_position_per_atom[n + N * 2] = z;
 
-    bool find_a_new_type = true;
-    for (int k = 0; k < types.size(); ++k) {
-      if (types[k] == cpu_type[n]) {
-        find_a_new_type = false;
-      }
-    }
-    if (find_a_new_type) {
-      types.emplace_back(cpu_type[n]);
+    if (cpu_type[n] > number_of_types) {
+      number_of_types = cpu_type[n];
     }
 
     if (has_velocity_in_xyz) {
@@ -253,37 +246,7 @@ void read_xyz_in_line_3(
     group[m].number++;
   }
 
-  number_of_types = types.size();
-
-  bool is_nep = true;
-  for (int k = 0; k < types.size(); ++k) {
-    if (types[k] == 0) {
-      is_nep = false;
-    }
-  }
-  if (is_nep) {
-    // generate a file that will be read by the NEP potential
-    char file_atomic_number[200];
-    strcpy(file_atomic_number, input_dir);
-    strcat(file_atomic_number, "/atomic_number.in");
-    FILE* fid_atomic_number = my_fopen(file_atomic_number, "w");
-    for (int n = 0; n < N; ++n) {
-      fprintf(fid_atomic_number, "%d\n", cpu_type[n]);
-    }
-    fclose(fid_atomic_number);
-
-    // to be consistent with other potentials, transform atomic numbers to types 0, 1, 2, ...
-    for (int n = 0; n < N; ++n) {
-      int index = 0;
-      for (int k = 0; k < types.size(); ++k) {
-        if (cpu_type[n] == types[k]) {
-          index = k;
-          break;
-        }
-      }
-      cpu_type[n] = index;
-    }
-  }
+  number_of_types++;
 }
 
 void find_type_size(
@@ -336,7 +299,7 @@ void initialize_position(
   read_xyz_in_line_2(fid_xyz, box);
 
   read_xyz_in_line_3(
-    input_dir, fid_xyz, N, has_velocity_in_xyz, number_of_types, atom.cpu_type, atom.cpu_mass,
+    fid_xyz, N, has_velocity_in_xyz, number_of_types, atom.cpu_type, atom.cpu_mass,
     atom.cpu_position_per_atom, atom.cpu_velocity_per_atom, group);
 
   fclose(fid_xyz);
@@ -394,4 +357,4 @@ void allocate_memory_gpu(
   atom.potential_per_atom.resize(N);
   atom.heat_per_atom.resize(N * 5);
   thermo.resize(6);
-}
+}