more robust version of atom exchange size

src/BODY/body_nparticle.cpp

@@ -44,6 +44,7 @@ BodyNparticle::BodyNparticle(LAMMPS *lmp, int narg, char **arg) :
 
   icp = new MyPoolChunk<int>(1,1);
   dcp = new MyPoolChunk<double>(3*nmin,3*nmax);
+  maxexchange = 1 + 3*nmax;        // icp max + dcp max
 
   memory->create(imflag,nmax,"body/nparticle:imflag");
   memory->create(imdata,nmax,4,"body/nparticle:imdata");

src/BODY/body_rounded_polygon.cpp

@@ -61,6 +61,7 @@ BodyRoundedPolygon::BodyRoundedPolygon(LAMMPS *lmp, int narg, char **arg) :
 
   icp = new MyPoolChunk<int>(1,1);
   dcp = new MyPoolChunk<double>(3*nmin+2*nmin+1+1,3*nmax+2*nmax+1+1);
+  maxexchange = 1 + 3*nmax+2*nmax+1+1;      // icp max + dcp max
 
   memory->create(imflag,nmax,"body/rounded/polygon:imflag");
   memory->create(imdata,nmax,7,"body/nparticle:imdata");

src/BODY/body_rounded_polyhedron.cpp

@@ -61,6 +61,7 @@ BodyRoundedPolyhedron::BodyRoundedPolyhedron(LAMMPS *lmp, int narg, char **arg)
   icp = new MyPoolChunk<int>(1,3);
   dcp = new MyPoolChunk<double>(3*nmin+2+1+1,
                                 3*nmax+2*nmax+MAX_FACE_SIZE*nmax+1+1);
+  maxexchange = 3 + 3*nmax+2*nmax+MAX_FACE_SIZE*nmax+1+1;  // icp max + dcp max
 
   memory->create(imflag,2*nmax,"body/rounded/polyhedron:imflag");
   memory->create(imdata,2*nmax,7,"body/polyhedron:imdata");

src/atom_vec.cpp

@@ -34,6 +34,8 @@ AtomVec::AtomVec(LAMMPS *lmp) : Pointers(lmp)
   mass_type = dipole_type = 0;
   forceclearflag = 0;
   size_data_bonus = 0;
+  maxexchange = 0;
+
   kokkosable = 0;
 
   nargcopy = 0;

src/atom_vec.h

@@ -39,6 +39,8 @@ class AtomVec : protected Pointers {
   int size_data_vel;                   // number of values in Velocity line
   int size_data_bonus;                 // number of values in Bonus line
   int xcol_data;                       // column (1-N) where x is in Atom line
+  int maxexchange;                     // max size of exchanged atom
+                                       // only needs to be set if size > BUFEXTRA
 
   class Molecule **onemols;            // list of molecules for style template
   int nset;                            // # of molecules in list

src/body.h

@@ -28,6 +28,8 @@ class Body : protected Pointers {
   char *style;
   int size_forward;           // max extra values packed for comm
   int size_border;            // max extra values packed for border comm
+  int maxexchange;            // max size of exchanged atom
+
   AtomVecBody *avec;          // ptr to class that stores body bonus info
 
   Body(class LAMMPS *, int, char **);

src/comm.cpp

@@ -39,7 +39,7 @@
 
 using namespace LAMMPS_NS;
 
-#define BUFMIN 1000             // also in comm styles
+#define BUFEXTRA 1024
 
 enum{ONELEVEL,TWOLEVEL,NUMA,CUSTOM};
 enum{CART,CARTREORDER,XYZ};
@@ -65,7 +65,10 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
   outfile = NULL;
   recv_from_partition = send_to_partition = -1;
   otherflag = 0;
-  maxexchange_atom = maxexchange_fix = 0;
+
+  maxexchange = maxexchange_atom = maxexchange_fix = 0;
+  maxexchange_fix_dynamic = 0;
+  bufextra = BUFEXTRA;
 
   grid2proc = NULL;
   xsplit = ysplit = zsplit = NULL;
@@ -225,6 +228,39 @@ void Comm::init()
 
   if (force->newton == 0) maxreverse = 0;
   if (force->pair) maxreverse = MAX(maxreverse,force->pair->comm_reverse_off);
+
+  // maxexchange_atom = size of an exchanged atom, set by AtomVec
+  //   only needs to be set if size > BUFEXTRA
+  // maxexchange_fix_dynamic = 1 if any fix sets its maxexchange dynamically
+
+  maxexchange_atom = atom->avec->maxexchange;
+
+  int nfix = modify->nfix;
+  Fix **fix = modify->fix;
+
+  maxexchange_fix_dynamic = 0;
+  for (int i = 0; i < nfix; i++)
+    if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1;
+}
+
+/* ----------------------------------------------------------------------
+   set maxexchange based on AtomVec and fixes
+------------------------------------------------------------------------- */
+
+void Comm::init_exchange()
+{
+  int nfix = modify->nfix;
+  Fix **fix = modify->fix;
+
+  int onefix;
+  maxexchange_fix = 0;
+  for (int i = 0; i < nfix; i++) {
+    onefix = fix[i]->maxexchange;
+    maxexchange_fix = MAX(maxexchange_fix,onefix);
+  }
+
+  maxexchange = maxexchange_atom + maxexchange_fix;
+  bufextra = maxexchange + BUFEXTRA;
 }
 
 /* ----------------------------------------------------------------------

src/comm.h

@@ -38,9 +38,8 @@ class Comm : protected Pointers {
                                     // -1 if no recv or send
   int other_partition_style;        // 0 = recv layout dims must be multiple of
                                     //     my layout dims
-  int maxexchange_atom;             // max contribution to exchange from AtomVec
+
-  int maxexchange_fix;              // max contribution to exchange from Fixes
+  int nthreads;                // OpenMP threads per MPI process
-  int nthreads;                     // OpenMP threads per MPI process
 
   // public settings specific to layout = UNIFORM, NONUNIFORM
 
@@ -130,8 +129,13 @@ class Comm : protected Pointers {
   int size_reverse;                 // # of datums in reverse comm
   int size_border;                  // # of datums in forward border comm
 
-  int maxforward,maxreverse;        // max # of datums in forward/reverse comm
+  int maxforward,maxreverse;    // max # of datums in forward/reverse comm
-  int maxexchange;                  // max # of datums/atom in exchange comm
+  int maxexchange;              // max size of one exchanged atom
+  int maxexchange_atom;         // contribution to maxexchange from AtomVec
+  int maxexchange_fix;          // static contribution to maxexchange from Fixes
+  int maxexchange_fix_dynamic;  // 1 if a fix has a dynamic contribution
+  int bufextra;                 // augment size of send buf for an exchange atom
+
 
   int gridflag;                     // option for creating 3d grid
   int mapflag;                      // option for mapping procs to 3d grid
@@ -147,6 +151,7 @@ class Comm : protected Pointers {
   int coregrid[3];                  // 3d grid of cores within a node
   int user_coregrid[3];             // user request for cores in each dim
 
+  void init_exchange();
   int rendezvous_irregular(int, char *, int, int, int *,
                            int (*)(int, char *, int &, int *&, char *&, void *),
                            int, char *&, int, void *, int);

src/comm_brick.cpp

@@ -42,8 +42,7 @@
 using namespace LAMMPS_NS;
 
 #define BUFFACTOR 1.5
-#define BUFMIN 1000
+#define BUFMIN 1024
-#define BUFEXTRA 1000
 #define BIG 1.0e20
 
 /* ---------------------------------------------------------------------- */
@@ -110,14 +109,6 @@ void CommBrick::init_buffers()
   multilo = multihi = NULL;
   cutghostmulti = NULL;
 
-  // bufextra = max size of one exchanged atom
-  //          = allowed overflow of sendbuf in exchange()
-  // atomvec, fix reset these 2 maxexchange values if needed
-  // only necessary if their size > BUFEXTRA
-
-  maxexchange = maxexchange_atom + maxexchange_fix;
-  bufextra = maxexchange + BUFEXTRA;
-
   maxsend = BUFMIN;
   memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
   maxrecv = BUFMIN;
@@ -141,6 +132,10 @@ void CommBrick::init()
 {
   Comm::init();
 
+  int bufextra_old = bufextra;
+  init_exchange();
+  if (bufextra > bufextra_old) grow_send(maxsend+bufextra,0);
+
   // memory for multi-style communication
 
   if (mode == Comm::MULTI && multilo == NULL) {
@@ -603,15 +598,14 @@ void CommBrick::exchange()
   atom->nghost = 0;
   atom->avec->clear_bonus();
 
-  // insure send buf is large enough for single atom
+  // insure send buf has extra space for a single atom
-  // bufextra = max size of one atom = allowed overflow of sendbuf
+  // only need to reset if a fix can dynamically add to size of single atom
-  // fixes can change per-atom size requirement on-the-fly
 
-  int bufextra_old = bufextra;
+  if (maxexchange_fix_dynamic) {
-  maxexchange = maxexchange_atom + maxexchange_fix;
+    int bufextra_old = bufextra;
-  bufextra = maxexchange + BUFEXTRA;
+    init_exchange();
-  if (bufextra > bufextra_old)
+    if (bufextra > bufextra_old) grow_send(maxsend+bufextra,0);
-    grow_send(maxsend+bufextra,1);
+  }
 
   // subbox bounds for orthogonal or triclinic
 

src/comm_brick.h

@@ -74,7 +74,6 @@ class CommBrick : public Comm {
   double *buf_send;                 // send buffer for all comm
   double *buf_recv;                 // recv buffer for all comm
   int maxsend,maxrecv;              // current size of send/recv buffer
-  int bufextra;                     // extra space beyond maxsend in send buffer
   int smax,rmax;             // max size in atoms of single borders send/recv
 
   // NOTE: init_buffers is called from a constructor and must not be made virtual

src/comm_tiled.cpp

@@ -32,8 +32,7 @@ using namespace LAMMPS_NS;
 
 #define BUFFACTOR 1.5
 #define BUFFACTOR 1.5
-#define BUFMIN 1000
+#define BUFMIN 1024
-#define BUFEXTRA 1000
 #define EPSILON 1.0e-6
 
 #define DELTA_PROCS 16
@@ -80,14 +79,6 @@ CommTiled::~CommTiled()
 
 void CommTiled::init_buffers()
 {
-  // bufextra = max size of one exchanged atom
-  //          = allowed overflow of sendbuf in exchange()
-  // atomvec, fix reset these 2 maxexchange values if needed
-  // only necessary if their size > BUFEXTRA
-
-  maxexchange = maxexchange_atom + maxexchange_fix;
-  bufextra = maxexchange + BUFEXTRA;
-
   maxsend = BUFMIN;
   memory->create(buf_send,maxsend+bufextra,"comm:buf_send");
   maxrecv = BUFMIN;
@@ -108,6 +99,10 @@ void CommTiled::init()
 {
   Comm::init();
 
+  int bufextra_old = bufextra;
+  init_exchange();
+  if (bufextra > bufextra_old) grow_send(maxsend+bufextra,0);
+
   // temporary restrictions
 
   if (triclinic)
@@ -644,15 +639,14 @@ void CommTiled::exchange()
   atom->nghost = 0;
   atom->avec->clear_bonus();
 
-  // insure send buf is large enough for single atom
+  // insure send buf has extra space for a single atom
-  // bufextra = max size of one atom = allowed overflow of sendbuf
+  // only need to reset if a fix can dynamically add to size of single atom
-  // fixes can change per-atom size requirement on-the-fly
 
-  int bufextra_old = bufextra;
+  if (maxexchange_fix_dynamic) {
-  maxexchange = maxexchange_atom + maxexchange_fix;
+    int bufextra_old = bufextra;
-  bufextra = maxexchange + BUFEXTRA;
+    init_exchange();
-  if (bufextra > bufextra_old)
+    if (bufextra > bufextra_old) grow_send(maxsend+bufextra,1);
-    memory->grow(buf_send,maxsend+bufextra,"comm:buf_send");
+  }
 
   // domain properties used in exchange method and methods it calls
   // subbox bounds for orthogonal or triclinic

src/comm_tiled.h

@@ -87,7 +87,6 @@ class CommTiled : public Comm {
   double *buf_send;             // send buffer for all comm
   double *buf_recv;             // recv buffer for all comm
   int maxsend,maxrecv;          // current size of send/recv buffer
-  int bufextra;                 // extra space beyond maxsend in send buffer
   int smaxone,rmaxone;          // max size in atoms of single borders send/recv
   int smaxall,rmaxall;          // max size in atoms of any borders send/recv
                                 //   for comm to all procs in one swap

src/fix.cpp

@@ -78,6 +78,8 @@ Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) :
   enforce2d_flag = 0;
   respa_level_support = 0;
   respa_level = -1;
+  maxexchange = 0;
+  maxexchange_dynamic = 0;
 
   scalar_flag = vector_flag = array_flag = 0;
   peratom_flag = local_flag = 0;

src/fix.h

@@ -56,6 +56,8 @@ class Fix : protected Pointers {
   int enforce2d_flag;            // 1 if has enforce2d method
   int respa_level_support;       // 1 if fix supports fix_modify respa
   int respa_level;               // which respa level to apply fix (1-Nrespa)
+  int maxexchange;               // max # of per-atom values for Comm::exchange()
+  int maxexchange_dynamic;       // 1 if fix sets maxexchange dynamically  
 
   int scalar_flag;               // 0/1 if compute_scalar() function exists
   int vector_flag;               // 0/1 if compute_vector() function exists

src/fix_neigh_history.cpp

@@ -42,6 +42,7 @@ FixNeighHistory::FixNeighHistory(LAMMPS *lmp, int narg, char **arg) :
 
   restart_peratom = 1;
   create_attribute = 1;
+  maxexchange_dynamic = 1;
 
   newton_pair = force->newton_pair;
 
@@ -296,11 +297,11 @@ void FixNeighHistory::pre_exchange_onesided()
   }
 
   // set maxpartner = max # of partners of any owned atom
-  // bump up comm->maxexchange_fix if necessary
+  // maxexchange = max # of values for any Comm::exchange() atom
 
   maxpartner = 0;
   for (i = 0; i < nlocal_neigh; i++) maxpartner = MAX(maxpartner,npartner[i]);
-  comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
+  maxexchange = (dnum+1)*maxpartner + 1;
 
   // zero npartner values from previous nlocal_neigh to current nlocal
 
@@ -424,11 +425,11 @@ void FixNeighHistory::pre_exchange_newton()
   comm->reverse_comm_fix_variable(this);
 
   // set maxpartner = max # of partners of any owned atom
-  // bump up comm->maxexchange_fix if necessary
+  // maxexchange = max # of values for any Comm::exchange() atom
 
   maxpartner = 0;
   for (i = 0; i < nlocal_neigh; i++) maxpartner = MAX(maxpartner,npartner[i]);
-  comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
+  maxexchange = (dnum+1)*maxpartner + 1;
 
   // zero npartner values from previous nlocal_neigh to current nlocal
 
@@ -531,11 +532,11 @@ void FixNeighHistory::pre_exchange_no_newton()
   }
 
   // set maxpartner = max # of partners of any owned atom
-  // bump up comm->maxexchange_fix if necessary
+  // maxexchange = max # of values for any Comm::exchange() atom
 
   maxpartner = 0;
   for (i = 0; i < nlocal_neigh; i++) maxpartner = MAX(maxpartner,npartner[i]);
-  comm->maxexchange_fix = MAX(comm->maxexchange_fix,(dnum+1)*maxpartner+1);
+  maxexchange = (dnum+1)*maxpartner + 1;
 
   // zero npartner values from previous nlocal_neigh to current nlocal
 
@@ -796,9 +797,6 @@ void FixNeighHistory::unpack_reverse_comm(int n, int *list, double *buf)
 
 int FixNeighHistory::pack_exchange(int i, double *buf)
 {
-  // NOTE: how do I know comm buf is big enough if extreme # of touching neighs
-  // Comm::BUFEXTRA may need to be increased
-
   int m = 0;
   buf[m++] = npartner[i];
   for (int n = 0; n < npartner[i]; n++) {

src/fix_store.cpp

@@ -106,6 +106,7 @@ vstore(NULL), astore(NULL), rbuf(NULL)
       for (int i = 0; i < nlocal; i++)
         for (int j = 0; j < nvalues; j++)
           astore[i][j] = 0.0;
+    maxexchange = nvalues;
   }
 }