add molecule wrapping when reading restart file

RASPA-2/3, or the previous version of gRASPA, cannot handle atoms in the molecules being wrapped to two sides of the box.
Now, adding this new feature in gRASPA, each atom will be wrapped to the nearest image from the 1st atom in the molecule.

Author: Zhaoli2042

src_clean/main.cpp

@@ -225,7 +225,7 @@ int main(void)
     cudaMalloc(&Sims[a].d_a, sizeof(Atoms)*NComponents.x);
     if(RunSingleSim)
     {
-      if(a == SelectedSim && ReadRestart) {RestartFileParser(Sims[a], SystemComponents[a]); AlreadyHasFractionalMolecule = true;}
+      if(a == SelectedSim && ReadRestart) {RestartFileParser(Sims[a], Box[a], SystemComponents[a]); AlreadyHasFractionalMolecule = true;}
     }
     Copy_Atom_data_to_device((size_t) NComponents.x, device_System, SystemComponents[a].HostSystem);
     Prepare_TempSystem_On_Host(SystemComponents[a].TempSystem);

src_clean/read_data.cpp

@@ -2175,7 +2175,7 @@ void read_component_values_from_simulation_input(Components& SystemComponents, M
   std::cout << "-------------- END OF READING " << start_string << " (" << MolName << ")" << " --------------\n";
 }
 
-void RestartFileParser(Simulations& Sims, Components& SystemComponents)
+void RestartFileParser(Simulations& Sims, Boxsize& Box, Components& SystemComponents)
 {
   bool UseChargesFromCIFFile = true;  //Zhao's note: if not, use charge from pseudo atoms file, not implemented (if reading poscar, then self-defined charges probably need a separate file //
   std::string scannedLine; std::string str;
@@ -2320,6 +2320,21 @@ void RestartFileParser(Simulations& Sims, Components& SystemComponents)
         //printf("Reading Positions, atom: %zu, xyz: %.5f %.5f %.5f, Type: %zu, MolID: %zu\n", atom, pos[atom].x, pos[atom].y, pos[atom].z, Type[atom], MolID[atom]);
         //Zhao's note: adjust the MolID from absolute to relative to component//
         MolID[atom] -= PreviousCompNMol;
+        //Zhao's note, 051724, Consider adding a wrap/unwrap here//
+        //Calculate atom distance between atom A and the first atom in the molecule//
+        //I know, many code will consider using the oxygen atom as the reference for wrapping, no, this is not general enough//
+        //We will use the first atom//
+        double3 first_bead_pos;
+        if(atomid == 0)
+        {
+          first_bead_pos = pos[atom];
+        }
+        else if(atomid != 0)
+        {
+          double3 dist_vec = pos[atom] - first_bead_pos;
+          PBC(dist_vec, Box.Cell, Box.InverseCell, Box.Cubic);
+          pos[atom] = first_bead_pos + dist_vec;
+        }
       }
       //Read charge//
       if((counter >= start + interval * 3) && (counter < start + interval * 4))

src_clean/read_data.h

@@ -24,7 +24,7 @@ void MoleculeDefinitionParser(Atoms& Mol, Components& SystemComponents, std::str
 
 void read_component_values_from_simulation_input(Components& SystemComponents, Move_Statistics& MoveStats, size_t AdsorbateComponent, Atoms& Mol, PseudoAtomDefinitions PseudoAtom, size_t Allocate_space);
 
-void RestartFileParser(Simulations& Sims, Components& SystemComponents);
+void RestartFileParser(Simulations& Sims, Boxsize& Box, Components& SystemComponents);
 
 void read_Ewald_Parameters_from_input(double CutOffCoul, Boxsize& Box, double precision);