git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14528 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/neighbor.cpp

@@ -104,6 +104,11 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
   maxbin = 0;
   bins = NULL;
 
+  // SSA AIR binning
+
+  len_ssa_airnum = 0;
+  ssa_airnum = NULL;
+
   // pair exclusion list info
 
   includegroup = 0;
@@ -157,6 +162,7 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
   improperlist = NULL;
 
   copymode = 0;
+  last_binning_timestep = -1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -176,6 +182,8 @@ Neighbor::~Neighbor()
   memory->destroy(binhead);
   memory->destroy(bins);
 
+  memory->destroy(ssa_airnum);
+
   memory->destroy(ex1_type);
   memory->destroy(ex2_type);
   memory->destroy(ex_type);
@@ -1019,6 +1027,7 @@ int Neighbor::request(void *requestor, int instance)
    skip -> granular function if gran with granhistory,
            respa function if respaouter,
            skip_from function for everything else
+   ssa -> special case for USER-DPD pair styles
    half_from_full, half, full, gran, respaouter ->
      choose by newton and rq->newton and tri settings
      style NSQ options = newton off, newton on
@@ -1042,6 +1051,10 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
       else if (rq->respaouter) pb = &Neighbor::skip_from_respa;
       else pb = &Neighbor::skip_from;
 
+    } else if (rq->ssa) {
+      if (rq->half_from_full) pb = &Neighbor::half_from_full_newton_ssa;
+      else pb = &Neighbor::half_bin_newton_ssa;
+
     } else if (rq->half_from_full) {
       if (rq->newton == 0) {
         if (newton_pair == 0) pb = &Neighbor::half_from_full_no_newton;
@@ -1286,6 +1299,7 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
    determine which stencil_create function each neigh list needs
    based on settings of neigh request, only called if style != NSQ
    skip or copy or half_from_full -> no stencil
+   ssa = special case for USER-DPD pair styles
    half, gran, respaouter, full -> choose by newton and tri and dimension
    if none of these, ptr = NULL since this list needs no stencils
    use "else if" b/c skip,copy can be set in addition to half,full,etc
@@ -1297,7 +1311,11 @@ void Neighbor::choose_stencil(int index, NeighRequest *rq)
 
   if (rq->skip || rq->copy || rq->half_from_full) sc = NULL;
 
-  else if (rq->half || rq->gran || rq->respaouter) {
+  else if (rq->ssa) {
+    if (dimension == 2) sc = &Neighbor::stencil_half_bin_2d_ssa;
+    else if (dimension == 3) sc = &Neighbor::stencil_half_bin_3d_ssa;
+
+  } else if (rq->half || rq->gran || rq->respaouter) {
     if (style == BIN) {
       if (rq->newton == 0) {
         if (newton_pair == 0) {
@@ -1997,6 +2015,11 @@ void Neighbor::bin_atoms()
 {
   int i,ibin;
 
+  // NOTE: added for USER-DPD, why do we need this?
+
+  if (last_binning_timestep == update->ntimestep) return;
+  last_binning_timestep = update->ntimestep;
+
   for (i = 0; i < mbins; i++) binhead[i] = -1;
 
   // bin in reverse order so linked list will be in forward order
@@ -2152,6 +2175,8 @@ bigint Neighbor::memory_usage()
     bytes += memory->usage(binhead,maxhead);
   }
 
+  bytes += memory->usage(ssa_airnum,len_ssa_airnum);
+
   for (int i = 0; i < nrequest; i++)
     if (lists[i]) bytes += lists[i]->memory_usage();
 

src/neighbor.h

@@ -69,6 +69,14 @@ class Neighbor : protected Pointers {
   int nimproperlist;               // list of impropers to compute
   int **improperlist;
 
+  int cluster_check;               // 1 if check bond/angle/etc satisfies minimg
+
+  // USER-DPD package - better to make this private?
+
+  int *ssa_airnum;              // AIR number of each atom for SSA in USER-DPD
+
+  // methods
+
   Neighbor(class LAMMPS *);
   virtual ~Neighbor();
   virtual void init();
@@ -79,14 +87,13 @@ class Neighbor : protected Pointers {
   void setup_bins();                // setup bins based on box and cutoff
   virtual void build(int topoflag=1);  // create all neighbor lists (pair,bond)
   virtual void build_topology();    // create all topology neighbor lists
-  void build_one(class NeighList *list, int preflag=0);  // create a single neighbor list
+  void build_one(class NeighList *list,
+                 int preflag=0);    // create a single one-time neigh list
   void set(int, char **);           // set neighbor style and skin distance
   void modify_params(int, char**);  // modify parameters that control builds
   bigint memory_usage();
   int exclude_setting();
 
-  int cluster_check;               // 1 if check bond/angle/etc satisfies minimg
-
  protected:
   int me,nprocs;
 
@@ -114,6 +121,7 @@ class Neighbor : protected Pointers {
 
   int binatomflag;                 // bin atoms or not when build neigh list
                                    // turned off by build_one()
+  bigint last_binning_timestep;	   // last step neighbor binning was done
 
   int nbinx,nbiny,nbinz;           // # of global bins
   int *bins;                       // ptr to next atom in each bin
@@ -170,6 +178,12 @@ class Neighbor : protected Pointers {
   int *glist;                  // lists to grow atom arrays every reneigh
   int *slist;                  // lists to grow stencil arrays every reneigh
 
+  // USER-DPD package
+
+  int len_ssa_airnum;           // length of ssa_airnum array
+
+  // methods
+
   void bin_atoms();                     // bin all atoms
   double bin_distance(int, int, int);   // distance between binx
   int coord2bin(double *);              // mapping atom coord to a bin
@@ -304,6 +318,16 @@ class Neighbor : protected Pointers {
   void improper_template();           // improper list with templated bonds
   void improper_partial();            // exclude certain impropers
 
+  // SSA neighboring for USER-DPD
+
+  //int coord2ssa_airnum(double *);  // map atom coord to an AIR number
+  //void assign_ssa_airnums();       // set ssa_airnum values
+
+  void half_bin_newton_ssa(NeighList *) {}
+  void half_from_full_newton_ssa(class NeighList *) {}
+  void stencil_half_bin_2d_ssa(class NeighList *, int, int, int) {}
+  void stencil_half_bin_3d_ssa(class NeighList *, int, int, int) {}
+
   // find_special: determine if atom j is in special list of atom i
   // if it is not, return 0
   // if it is and special flag is 0 (both coeffs are 0.0), return -1