git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8356 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/MANYBODY/fix_qeq_comb.cpp

@@ -130,9 +130,10 @@ void FixQEQComb::init()
   if (ngroup == 0) error->all(FLERR,"Fix qeq/comb group has no atoms");
 
   int irequest = neighbor->request(this);
+  neighbor->requests[irequest]->pair = 0;
+  neighbor->requests[irequest]->fix = 1;
   neighbor->requests[irequest]->half = 0;
   neighbor->requests[irequest]->full = 1;
-  neighbor->requests[irequest]->ghost = 1;
 }
 
 /* ---------------------------------------------------------------------- */

src/USER-REAXC/fix_qeq_reax.cpp

@@ -288,18 +288,12 @@ void FixQEqReax::init()
 {
   if (!atom->q_flag) error->all(FLERR,"Fix qeq/reax requires atom attribute q");
 	
-  // need a half neighbor list w/ Newton off
+  // need a half neighbor list w/ Newton off and ghost neighbors
   // built whenever re-neighboring occurs
 
   int irequest = neighbor->request(this);
   neighbor->requests[irequest]->pair = 0;
   neighbor->requests[irequest]->fix = 1;
-
-  // Ray
-  //neighbor->requests[irequest]->half = 0;
-  //neighbor->requests[irequest]->full = 1;
-  //neighbor->requests[irequest]->ghost = 2;	// 2 for newton off
-
   neighbor->requests[irequest]->newton = 2;
   neighbor->requests[irequest]->ghost = 1;
 

src/USER-REAXC/pair_reax_c.cpp

@@ -48,7 +48,6 @@
 #include "reaxc_traj.h"
 #include "reaxc_vector.h"
 #include "fix_reaxc_bonds.h"
-//#include "fix_reaxc_species.h"
 
 using namespace LAMMPS_NS;
 
@@ -288,6 +287,7 @@ void PairReaxC::coeff( int nargs, char **args )
 void PairReaxC::init_style( )
 {
   if (!atom->q_flag) error->all(FLERR,"Pair reax/c requires atom attribute q");
+
   // firstwarn = 1;
 
   int iqeq;
@@ -311,23 +311,7 @@ void PairReaxC::init_style( )
   if (force->newton_pair == 0)
     error->all(FLERR,"Pair style reax/c requires newton pair on");
 
-  // original
-  // need a half neighbor list w/ Newton off
-  // built whenever re-neighboring occurs
-
-  //int irequest = neighbor->request(this);
-  //neighbor->requests[irequest]->newton = 2;
-
-  // Ray
-  // need a full+ghost neighbor list w/ Newton off
-  // built whenever re-neighboring occurs
-
-  //int irequest = neighbor->request(this);
-  //neighbor->requests[irequest]->half = 0;
-  //neighbor->requests[irequest]->full = 1;
-  //neighbor->requests[irequest]->ghost = 2;	// 2 for newton off
-
-  // need a half neighbor list with ghosts w/ Newton off
+  // need a half neighbor list w/ Newton off and ghost neighbors
   // built whenever re-neighboring occurs
 
   int irequest = neighbor->request(this);

src/neighbor.cpp

@@ -475,7 +475,7 @@ void Neighbor::init()
     //   change this list to half_from_full and point at the full list
     //   parent could be copy list or pair or fix
     // fix/compute requests:
-    //   kind of request = half or full, occasional or not doesn't matter
+    //   whether request is occasional or not doesn't matter
     //   if request = half and non-skip pair half/respaouter exists,
     //     become copy of that list if cudable flag matches
     //   if request = full and non-skip pair full exists,
@@ -493,10 +493,8 @@ void Neighbor::init()
         lists[i]->listskip = lists[requests[i]->otherlist];
         lists[i]->copy_skip_info(requests[i]->iskip,requests[i]->ijskip);
 
-      } else if (requests[i]->half_from_full) {
+      } else if (requests[i]->half_from_full) 
         lists[i]->listfull = lists[i-1];
-        printf("AAA\n");
-      }
 
       else if (requests[i]->granhistory) {
         lists[i-1]->listgranhistory = lists[i];
@@ -522,7 +520,6 @@ void Neighbor::init()
           requests[i]->half = 0;
           requests[i]->half_from_full = 1;
           lists[i]->listfull = lists[j];
-          printf("BBB %d %d\n",nlist,j);
         }
 
       } else if (requests[i]->fix || requests[i]->compute) {
@@ -538,6 +535,7 @@ void Neighbor::init()
           j = nlist;
         if (j < nlist) {
           requests[i]->copy = 1;
+          requests[i]->otherlist = j;
           lists[i]->listcopy = lists[j];
         } else {
           for (j = 0; j < nlist; j++) {
@@ -550,7 +548,6 @@ void Neighbor::init()
             requests[i]->half = 0;
             requests[i]->half_from_full = 1;
             lists[i]->listfull = lists[j];
-            printf("CCC\n");
           }
         }
       }
@@ -985,12 +982,6 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
     }
   }
 
-  // general error check
-
-  //if (rq->ghost && !rq->full)
-  //  error->all(FLERR,
-  //             "Neighbors of ghost atoms only allowed for full neighbor lists");
-
   pair_build[index] = pb;
 }
 

src/read_dump.cpp

@@ -92,9 +92,9 @@ void ReadDump::command(int narg, char **arg)
   bigint nstep = ATOBIGINT(arg[1]);
 
   int nremain = narg - 2;
-  if (nremain) nremain = fields_and_keywords(narg-nremain,&arg[narg-nremain]);
+  if (nremain) nremain = fields_and_keywords(nremain,&arg[narg-nremain]);
   else nremain = fields_and_keywords(0,NULL);
-  if (nremain) setup_reader(narg-nremain,&arg[narg-nremain]);
+  if (nremain) setup_reader(nremain,&arg[narg-nremain]);
   else setup_reader(0,NULL);
 
   // find the snapshot and read/bcast/process header info

src/rerun.cpp

@@ -118,9 +118,9 @@ void Rerun::command(int narg, char **arg)
 
   rd->store_files(nfile,arg);
   if (nremain) 
-    nremain = rd->fields_and_keywords(narg-nremain,&arg[narg-nremain]);
+    nremain = rd->fields_and_keywords(nremain,&arg[narg-nremain]);
   else nremain = rd->fields_and_keywords(0,NULL);
-  if (nremain) rd->setup_reader(narg-nremain,&arg[narg-nremain]);
+  if (nremain) rd->setup_reader(nremain,&arg[narg-nremain]);
   else rd->setup_reader(0,NULL);
 
   // perform the psuedo run