From cd9aaec0b6f772daaf52d0f2a6256a2e1948d3d5 Mon Sep 17 00:00:00 2001
From: Abdullah Alperen <alperena@msu.edu>
Date: Fri, 9 Nov 2018 11:07:25 -0500
Subject: [PATCH] PuReMD: add preprocessors for Neutral Territory
---
PuReMD/src/allocate.c | 19 +++++++++++---
PuReMD/src/basic_comm.c | 5 +++-
PuReMD/src/basic_comm.h | 4 +++
PuReMD/src/box.c | 2 ++
PuReMD/src/comm_tools.c | 12 ++++++++-
PuReMD/src/comm_tools.h | 4 +++
PuReMD/src/forces.c | 33 +++++++++++++++++++++++-
PuReMD/src/grid.c | 10 ++++++--
PuReMD/src/init_md.c | 8 ++++++
PuReMD/src/io_tools.c | 15 +++++++++--
PuReMD/src/linear_solvers.c | 50 +++++++++++++++++++++++++++++--------
PuReMD/src/neighbors.c | 4 +++
PuReMD/src/reax_types.h | 27 +++++++++++++++-----
13 files changed, 166 insertions(+), 27 deletions(-)
diff --git a/PuReMD/src/allocate.c b/PuReMD/src/allocate.c
index c91fae55..77b4164d 100644
--- a/PuReMD/src/allocate.c
+++ b/PuReMD/src/allocate.c
@@ -735,19 +735,24 @@ int Allocate_MPI_Buffers( mpi_datatypes *mpi_data, int est_recv,
comm );
}
- /* Note that in_nt_buffers are allocated in comm_tools.c */
-
+#if defined(NEUTRAL_TERRITORY)
/* Neutral Territory out buffers */
for ( i = 0; i < REAX_MAX_NT_NBRS; ++i )
{
+ //TODO: add an exact number
+ /* in buffers */
+ mpi_data->in_nt_buffer[i] = (void*)
+ scalloc( my_nbrs[i].est_recv, sizeof(real), "mpibuf:in_nt_buffer", comm );
+
mpi_buf = &( mpi_data->out_nt_buffers[i] );
/* allocate storage for the neighbor processor i */
mpi_buf->index = (int*)
scalloc( my_nbrs[i].est_send, sizeof(int), "mpibuf:nt_index", comm );
mpi_buf->out_atoms = (void*)
- scalloc( my_nbrs[i].est_send, sizeof(boundary_atom), "mpibuf:nt_out_atoms",
+ scalloc( my_nbrs[i].est_send, sizeof(real), "mpibuf:nt_out_atoms",
comm );
}
+#endif
return SUCCESS;
}
@@ -768,7 +773,7 @@ void Deallocate_MPI_Buffers( mpi_datatypes *mpi_data )
sfree( mpi_buf->out_atoms, "mpibuf:out_atoms" );
}
-
+#if defined(NEUTRAL_TERRITORY)
for ( i = 0; i < REAX_MAX_NT_NBRS; ++i )
{
sfree( mpi_data->in_nt_buffer[i], "in_nt_buffer" );
@@ -777,6 +782,7 @@ void Deallocate_MPI_Buffers( mpi_datatypes *mpi_data )
sfree( mpi_buf->index, "mpibuf:nt_index" );
sfree( mpi_buf->out_atoms, "mpibuf:nt_out_atoms" );
}
+#endif
}
@@ -1028,6 +1034,8 @@ void ReAllocate( reax_system *system, control_params *control,
break;
}
}
+
+#if defined(NEUTRAL_TERRITORY)
// also check individual outgoing Neutral Territory buffers
mpi_flag = 0;
for ( p = 0; p < REAX_MAX_NT_NBRS; ++p )
@@ -1041,6 +1049,7 @@ void ReAllocate( reax_system *system, control_params *control,
}
}
}
+#endif
if ( mpi_flag )
{
@@ -1065,12 +1074,14 @@ void ReAllocate( reax_system *system, control_params *control,
total_send += nbr_pr->est_send;
}
+#if defined(NEUTRAL_TERRITORY)
for ( p = 0; p < REAX_MAX_NT_NBRS; ++p )
{
nbr_pr = &( system->my_nt_nbrs[p] );
nbr_data = &( mpi_data->out_nt_buffers[p] );
nbr_pr->est_send = MAX( nbr_data->cnt * SAFER_ZONE, MIN_SEND );
}
+#endif
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d: reallocating mpi_buf: recv=%d send=%d total=%dMB\n",
diff --git a/PuReMD/src/basic_comm.c b/PuReMD/src/basic_comm.c
index 35e04dc4..834034ed 100644
--- a/PuReMD/src/basic_comm.c
+++ b/PuReMD/src/basic_comm.c
@@ -129,6 +129,7 @@ void Dist( reax_system* system, mpi_datatypes *mpi_data,
}
+#if defined(NEUTRAL_TERRITORY)
void Dist_NT( reax_system* system, mpi_datatypes *mpi_data,
void *buf, MPI_Datatype type, int scale, dist_packer pack )
{
@@ -189,6 +190,7 @@ void Dist_NT( reax_system* system, mpi_datatypes *mpi_data,
fprintf( stderr, "p%d dist: done\n", system->my_rank );
#endif
}
+#endif
void real_unpacker( void *dummy_in, void *dummy_buf, mpi_out_data *out_buf )
@@ -299,7 +301,7 @@ void Coll( reax_system* system, mpi_datatypes *mpi_data,
#endif
}
-
+#if defined(NEUTRAL_TERRITORY)
void Coll_NT( reax_system* system, mpi_datatypes *mpi_data,
void *buf, MPI_Datatype type, int scale, coll_unpacker unpack )
{
@@ -361,6 +363,7 @@ void Coll_NT( reax_system* system, mpi_datatypes *mpi_data,
fprintf( stderr, "p%d coll: done\n", system->my_rank );
#endif
}
+#endif
#endif /*PURE_REAX*/
diff --git a/PuReMD/src/basic_comm.h b/PuReMD/src/basic_comm.h
index 31afb564..8c914973 100644
--- a/PuReMD/src/basic_comm.h
+++ b/PuReMD/src/basic_comm.h
@@ -29,13 +29,17 @@ void real_packer( void*, mpi_out_data* );
void rvec_packer( void*, mpi_out_data* );
void rvec2_packer( void*, mpi_out_data* );
void Dist(reax_system*, mpi_datatypes*, void*, MPI_Datatype, int, dist_packer);
+#if defined(NEUTRAL_TERRITORY)
void Dist_NT(reax_system*, mpi_datatypes*, void*, MPI_Datatype, int, dist_packer);
+#endif
void real_unpacker( void*, void*, mpi_out_data* );
void rvec_unpacker( void*, void*, mpi_out_data* );
void rvec2_unpacker( void*, void*, mpi_out_data* );
void Coll( reax_system*, mpi_datatypes*, void*, MPI_Datatype, int, coll_unpacker );
+#if defined(NEUTRAL_TERRITORY)
void Coll_NT( reax_system*, mpi_datatypes*, void*, MPI_Datatype, int, coll_unpacker );
+#endif
real Parallel_Norm( real*, int, MPI_Comm );
real Parallel_Dot( real*, real*, int, MPI_Comm );
diff --git a/PuReMD/src/box.c b/PuReMD/src/box.c
index 212d755a..d81a96db 100644
--- a/PuReMD/src/box.c
+++ b/PuReMD/src/box.c
@@ -285,7 +285,9 @@ void Setup_Environment( reax_system *system, control_params *control,
Setup_My_Box( system, control );
Setup_My_Ext_Box( system, control );
Setup_Comm( system, control, mpi_data );
+#if defined(NEUTRAL_TERRITORY)
Setup_NT_Comm( system, control, mpi_data );
+#endif
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d coord: %d %d %d\n",
diff --git a/PuReMD/src/comm_tools.c b/PuReMD/src/comm_tools.c
index 18fb2ded..5646b9cf 100644
--- a/PuReMD/src/comm_tools.c
+++ b/PuReMD/src/comm_tools.c
@@ -25,7 +25,7 @@
#include "tool_box.h"
#include "vector.h"
-
+#if defined(NEUTRAL_TERRITORY)
void Setup_NT_Comm( reax_system* system, control_params* control,
mpi_datatypes *mpi_data )
{
@@ -95,8 +95,10 @@ void Setup_NT_Comm( reax_system* system, control_params* control,
}
}
+#endif
+#if defined(NEUTRAL_TERRITORY)
int Sort_Neutral_Territory( reax_system *system, int dir, mpi_out_data *out_bufs, int write )
{
int i, cnt;
@@ -131,8 +133,10 @@ int Sort_Neutral_Territory( reax_system *system, int dir, mpi_out_data *out_bufs
return cnt;
}
+#endif
+#if defined(NEUTRAL_TERRITORY)
void Init_Neutral_Territory( reax_system* system, mpi_datatypes *mpi_data )
{
int d, end, cnt;
@@ -169,7 +173,10 @@ void Init_Neutral_Territory( reax_system* system, mpi_datatypes *mpi_data )
end += cnt;
}
}
+#endif
+
+#if defined(NEUTRAL_TERRITORY)
void Estimate_NT_Atoms( reax_system *system, mpi_datatypes *mpi_data )
{
int d;
@@ -196,6 +203,7 @@ void Estimate_NT_Atoms( reax_system *system, mpi_datatypes *mpi_data )
//Sort_Neutral_Territory( system, d, out_bufs, 1 );
}
}
+#endif
void Setup_Comm( reax_system* system, control_params* control,
@@ -822,7 +830,9 @@ void Comm_Atoms( reax_system *system, control_params *control,
Bin_Boundary_Atoms( system );
+#if defined(NEUTRAL_TERRITORY)
Init_Neutral_Territory( system, mpi_data );
+#endif
}
else
{
diff --git a/PuReMD/src/comm_tools.h b/PuReMD/src/comm_tools.h
index 787e120d..c333fa0c 100644
--- a/PuReMD/src/comm_tools.h
+++ b/PuReMD/src/comm_tools.h
@@ -25,12 +25,16 @@
#include "reax_types.h"
void Setup_Comm( reax_system*, control_params*, mpi_datatypes* );
+#if defined(NEUTRAL_TERRITORY)
void Setup_NT_Comm( reax_system*, control_params*, mpi_datatypes* );
+#endif
void Update_Comm( reax_system* );
void Sort_Boundary_Atoms( reax_system*, int, int, int, mpi_out_data* );
void Estimate_Boundary_Atoms( reax_system*, int, int, int, mpi_out_data* );
+#if defined(NEUTRAL_TERRITORY)
void Estimate_NT_Atoms( reax_system*, mpi_datatypes* );
+#endif
void Unpack_Exchange_Message( reax_system*, int, void*, int,
neighbor_proc*, int );
void Unpack_Estimate_Message( reax_system*, int, void*, int,
diff --git a/PuReMD/src/forces.c b/PuReMD/src/forces.c
index c710e2ae..7b66fa32 100644
--- a/PuReMD/src/forces.c
+++ b/PuReMD/src/forces.c
@@ -346,10 +346,12 @@ void Init_Forces( reax_system *system, control_params *control,
int jhb_top;
int start_j, end_j;
int btop_j;
+#if defined(NEUTRAL_TERRITORY)
int total_cnt[6];
int bin[6];
int total_sum[6];
int nt_flag;
+#endif
far_nbrs = lists[FAR_NBRS];
bonds = lists[BONDS];
@@ -371,8 +373,11 @@ void Init_Forces( reax_system *system, control_params *control,
num_hbonds = 0;
btop_i = 0;
renbr = (data->step - data->prev_steps) % control->reneighbor == 0;
+#if defined(NEUTRAL_TERRITORY)
nt_flag = 1;
+#endif
+#if defined(NEUTRAL_TERRITORY)
if( renbr )
{
for ( i = 0; i < 6; ++i )
@@ -405,6 +410,7 @@ void Init_Forces( reax_system *system, control_params *control,
}
H->NT = total_sum[5] + total_cnt[5];
}
+#endif
for ( i = 0; i < system->N; ++i )
{
@@ -429,12 +435,14 @@ void Init_Forces( reax_system *system, control_params *control,
local = 1;
cutoff = control->nonb_cut;
}
+#if defined(NEUTRAL_TERRITORY)
else if( atom_i->nt_dir != -1 )
{
local = 2;
cutoff = control->nonb_cut;
nt_flag = 0;
}
+#endif
else
{
local = 0;
@@ -524,6 +532,7 @@ void Init_Forces( reax_system *system, control_params *control,
&& (j < system->n || atom_i->orig_id < atom_j->orig_id))
|| far_nbrs->format == FULL_LIST )
{
+#if defined(NEUTRAL_TERRITORY)
if( atom_j->nt_dir != -1 || j < system->n )
{
if( j < system->n )
@@ -545,6 +554,18 @@ void Init_Forces( reax_system *system, control_params *control,
}
++Htop;
}
+#else
+ H->entries[Htop].j = j;
+ if ( control->tabulate == 0 )
+ {
+ H->entries[Htop].val = Compute_H(r_ij, twbp->gamma, workspace->Tap);
+ }
+ else
+ {
+ H->entries[Htop].val = Compute_tabH(r_ij, type_i, type_j);
+ }
+ ++Htop;
+#endif
}
/* hydrogen bond lists */
@@ -574,6 +595,7 @@ void Init_Forces( reax_system *system, control_params *control,
}
}
}
+#if defined(NEUTRAL_TERRITORY)
else if ( local == 2 )
{
/* H matrix entry */
@@ -610,6 +632,7 @@ void Init_Forces( reax_system *system, control_params *control,
}
}
+#endif
/* uncorrected bond orders */
if ( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
@@ -638,10 +661,12 @@ void Init_Forces( reax_system *system, control_params *control,
if ( ihb == 1 )
Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
}
+#if defined(NEUTRAL_TERRITORY)
else if ( local == 2 )
{
H->end[atom_i->pos] = Htop;
}
+#endif
}
if ( far_nbrs->format == FULL_LIST )
@@ -977,15 +1002,17 @@ void Estimate_Storages( reax_system *system, control_params *control,
++(*matrix_dim);
ihb = sbp_i->p_hbond;
}
+#if defined(NEUTRAL_TERRITORY)
else if ( atom_i->nt_dir != -1 )
{
local = 2;
cutoff = control->nonb_cut;
// TODO: Diag entries for NT atoms?
//++(*Htop);
- //++(*matrix_dim);
+ ++(*matrix_dim);
ihb = -1;
}
+#endif
else
{
local = 0;
@@ -1015,7 +1042,9 @@ void Estimate_Storages( reax_system *system, control_params *control,
&& (j < system->n || atom_i->orig_id < atom_j->orig_id))
|| far_nbrs->format == FULL_LIST )
{
+#if defined(NEUTRAL_TERRITORY)
if( j < system->n || (system->my_atoms[j]).nt_dir != -1 )
+#endif
{
++(*Htop);
}
@@ -1039,6 +1068,7 @@ void Estimate_Storages( reax_system *system, control_params *control,
}
}
+#if defined(NEUTRAL_TERRITORY)
else if ( local == 2 )
{
@@ -1052,6 +1082,7 @@ void Estimate_Storages( reax_system *system, control_params *control,
}
}
}
+#endif
/* uncorrected bond orders */
if ( nbr_pj->d <= control->bond_cut )
diff --git a/PuReMD/src/grid.c b/PuReMD/src/grid.c
index 1bd1b72a..ce251430 100644
--- a/PuReMD/src/grid.c
+++ b/PuReMD/src/grid.c
@@ -35,8 +35,8 @@ void Mark_GCells( reax_system* system, grid *g, ivec procs, MPI_Comm comm )
ivec send_span, recv_span;
ivec str_send, end_send;
ivec str_recv, end_recv;
+#if defined(NEUTRAL_TERRITORY)
ivec nt_str, nt_end;
-
ivec dir[6] = {
{0, 0, +1}, // +z
{0, 0, -1}, // -z
@@ -45,6 +45,7 @@ void Mark_GCells( reax_system* system, grid *g, ivec procs, MPI_Comm comm )
{+1, 0, 0}, // +x
{+1, -1, 0} // +x-y
};
+#endif
/* clear all gcell type info */
for ( x = 0; x < g->ncells[0]; x++ )
@@ -61,6 +62,7 @@ void Mark_GCells( reax_system* system, grid *g, ivec procs, MPI_Comm comm )
ivec_MakeZero( g->cells[x][y][z].rel_box );
}
+#if defined(NEUTRAL_TERRITORY)
/* mark NT cells */
for ( i = 0; i < 6; ++i )
{
@@ -93,6 +95,7 @@ void Mark_GCells( reax_system* system, grid *g, ivec procs, MPI_Comm comm )
}
}
}
+#endif
/* loop over neighbors */
for ( r[0] = -1; r[0] <= 1; ++r[0])
@@ -179,8 +182,11 @@ void Find_Neighbor_GridCells( grid *g, control_params *control )
gc = &(g->cells[ci[0]][ci[1]][ci[2]]);
top = 0;
//fprintf( stderr, "grid1: %d %d %d:\n", ci[0], ci[1], ci[2] );
-
+#if defined(NEUTRAL_TERRITORY)
if ( gc->type == NATIVE || ( gc->type >= NT_NBRS && gc->type < NT_NBRS + 6 ) )
+#else
+ if ( gc->type == NATIVE )
+#endif
gc->cutoff = control->vlist_cut;
else gc->cutoff = control->bond_cut;
diff --git a/PuReMD/src/init_md.c b/PuReMD/src/init_md.c
index a6058ec3..b8115820 100644
--- a/PuReMD/src/init_md.c
+++ b/PuReMD/src/init_md.c
@@ -155,7 +155,9 @@ int Init_System( reax_system *system, control_params *control,
Estimate_Boundary_Atoms, Unpack_Estimate_Message, 1 );
system->total_cap = MAX( (int)(system->N * SAFE_ZONE), MIN_CAP );
Bin_Boundary_Atoms( system );
+#if defined(NEUTRAL_TERRITORY)
Estimate_NT_Atoms( system, mpi_data );
+#endif
//fprintf( stderr, "p%d SEND RECV SEND!\n", system->my_rank );
//MPI_Barrier( mpi_data->world );
@@ -469,10 +471,12 @@ int Init_MPI_Datatypes( reax_system *system, storage *workspace,
/* init mpi buffers */
mpi_data->in1_buffer = NULL;
mpi_data->in2_buffer = NULL;
+#if defined(NEUTRAL_TERRITORY)
for ( i = 0; i < REAX_MAX_NT_NBRS; ++i )
{
mpi_data->in_nt_buffer[i] = NULL;
}
+#endif
/* mpi_atom - [orig_id, imprt_id, type, num_bonds, num_hbonds, name,
x, v, f_old, s, t] */
@@ -640,7 +644,11 @@ int Init_Lists( reax_system *system, control_params *control,
Estimate_Storages( system, control, lists,
&Htop, hb_top, bond_top, &num_3body, comm, &matrix_dim );
+#if defined(NEUTRAL_TERRITORY)
Allocate_Matrix( &(workspace->H), matrix_dim, Htop, cm_format, comm );
+#else
+ Allocate_Matrix( &(workspace->H), system->local_cap, Htop, comm );
+#endif
workspace->L = NULL;
workspace->U = NULL;
workspace->H_spar_patt = NULL;
diff --git a/PuReMD/src/io_tools.c b/PuReMD/src/io_tools.c
index b22ef6bf..1abf9753 100644
--- a/PuReMD/src/io_tools.c
+++ b/PuReMD/src/io_tools.c
@@ -851,8 +851,18 @@ void Print_HBonds( reax_system *system, reax_list **lists,
FILE *fout;
reax_list *hbonds = lists[HBONDS];
- sprintf( fname, "%s.hbonds.%d.%d", control->sim_name, step, system->my_rank );
- fout = sfopen( fname, "w", "Print_HBonds" );
+ snprintf( fname, MAX_STR, "hbonds.%d.%d", step, system->my_rank );
+
+ fprintf( stdout, "p%d, Round 1, Printing H bonds, numH = %d\n", system->my_rank, system->numH );
+ fflush( stdout );
+ MPI_Barrier( MPI_COMM_WORLD );
+
+ //fout = sfopen( fname, "w", "Print_HBonds" );
+ fout = fopen( fname, "w" );
+
+ fprintf( stdout, "p%d, Round 2, Printing H bonds, numH = %d\n", system->my_rank, system->numH );
+ fflush( stdout );
+ MPI_Barrier( MPI_COMM_WORLD );
for ( i = 0; i < system->numH; ++i )
{
@@ -867,6 +877,7 @@ void Print_HBonds( reax_system *system, reax_list **lists,
}
}
+
sfclose( fout, "Print_HBonds" );
}
diff --git a/PuReMD/src/linear_solvers.c b/PuReMD/src/linear_solvers.c
index fd068c99..36a6b15e 100644
--- a/PuReMD/src/linear_solvers.c
+++ b/PuReMD/src/linear_solvers.c
@@ -1201,20 +1201,29 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
t_start = Get_Time( );
scale = sizeof(real) / sizeof(void);
+#if defined(NEUTRAL_TERRITORY)
+ Dist_NT( system, mpi_data, x, MPI_DOUBLE, scale, real_packer );
+#else
Dist( system, mpi_data, x, MPI_DOUBLE, scale, real_packer );
-// Dist_NT( system, mpi_data, x, MPI_DOUBLE, scale, real_packer );
+#endif
t_comm += Get_Timing_Info( t_start );
t_start = Get_Time( );
- //Sparse_MatVec( H, x, workspace->q, system->N );
+#if defined(NEUTRAL_TERRITORY)
Sparse_MatVec( H, x, workspace->q, H->NT );
+#else
+ Sparse_MatVec( H, x, workspace->q, system->N );
+#endif
t_spmv += Get_Timing_Info( t_start );
if ( H->format == SYM_HALF_MATRIX )
{
t_start = Get_Time( );
+#if defined(NEUTRAL_TERRITORY)
+ Coll_NT( system, mpi_data, workspace->q, MPI_DOUBLE, scale, real_unpacker );
+#else
Coll( system, mpi_data, workspace->q, MPI_DOUBLE, scale, real_unpacker );
-// Coll_NT( system, mpi_data, workspace->q, MPI_DOUBLE, scale, real_unpacker );
+#endif
t_comm += Get_Timing_Info( t_start );
}
@@ -1226,13 +1235,19 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
if( control->cm_solver_pre_comp_type == SAI_PC )
{
t_start = Get_Time( );
+#if defined(NEUTRAL_TERRITORY)
+ Dist_NT( system, mpi_data, workspace->r, MPI_DOUBLE, scale, real_packer );
+#else
Dist( system, mpi_data, workspace->r, MPI_DOUBLE, scale, real_packer );
-// Dist_NT( system, mpi_data, workspace->r, MPI_DOUBLE, scale, real_packer );
+#endif
t_comm += Get_Timing_Info( t_start );
t_start = Get_Time( );
- //Sparse_MatVec( workspace->H_app_inv, workspace->r, workspace->d, system->n );
+#if defined(NEUTRAL_TERRITORY)
Sparse_MatVec( workspace->H_app_inv, workspace->r, workspace->d, H->NT );
+#else
+ Sparse_MatVec( workspace->H_app_inv, workspace->r, workspace->d, system->n );
+#endif
t_pa += Get_Timing_Info( t_start );
}
@@ -1254,20 +1269,29 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
for ( i = 0; i < control->cm_solver_max_iters && sqrt(sig_new) / b_norm > tol; ++i )
{
t_start = Get_Time( );
+#if defined(NEUTRAL_TERRITORY)
+ Dist_NT( system, mpi_data, workspace->d, MPI_DOUBLE, scale, real_packer );
+#else
Dist( system, mpi_data, workspace->d, MPI_DOUBLE, scale, real_packer );
-// Dist_NT( system, mpi_data, workspace->d, MPI_DOUBLE, scale, real_packer );
+#endif
t_comm += Get_Timing_Info( t_start );
t_start = Get_Time( );
- //Sparse_MatVec( H, workspace->d, workspace->q, system->N );
+#if defined(NEUTRAL_TERRITORY)
Sparse_MatVec( H, workspace->d, workspace->q, H->NT );
+#else
+ Sparse_MatVec( H, workspace->d, workspace->q, system->N );
+#endif
t_spmv += Get_Timing_Info( t_start );
if ( H->format == SYM_HALF_MATRIX )
{
t_start = Get_Time( );
+#if defined(NEUTRAL_TERRITORY)
+ Coll_NT(system, mpi_data, workspace->q, MPI_DOUBLE, scale, real_unpacker);
+#else
Coll(system, mpi_data, workspace->q, MPI_DOUBLE, scale, real_unpacker);
-// Coll_NT(system, mpi_data, workspace->q, MPI_DOUBLE, scale, real_unpacker);
+#endif
t_comm += Get_Timing_Info( t_start );
}
@@ -1285,13 +1309,19 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
if( control->cm_solver_pre_comp_type == SAI_PC )
{
t_start = Get_Time( );
+#if defined(NEUTRAL_TERRITORY)
+ Dist_NT( system, mpi_data, workspace->r, MPI_DOUBLE, scale, real_packer );
+#else
Dist( system, mpi_data, workspace->r, MPI_DOUBLE, scale, real_packer );
-// Dist_NT( system, mpi_data, workspace->r, MPI_DOUBLE, scale, real_packer );
+#endif
t_comm += Get_Timing_Info( t_start );
t_start = Get_Time( );
- //Sparse_MatVec( workspace->H_app_inv, workspace->r, workspace->p, system->n );
+#if defined(NEUTRAL_TERRITORY)
Sparse_MatVec( workspace->H_app_inv, workspace->r, workspace->p, H->NT );
+#else
+ Sparse_MatVec( workspace->H_app_inv, workspace->r, workspace->p, system->n );
+#endif
t_pa += Get_Timing_Info( t_start );
}
diff --git a/PuReMD/src/neighbors.c b/PuReMD/src/neighbors.c
index c62af733..69f8c653 100644
--- a/PuReMD/src/neighbors.c
+++ b/PuReMD/src/neighbors.c
@@ -104,6 +104,7 @@ void Generate_Neighbor_Lists( reax_system *system, simulation_data *data,
for (l = gci->str; l < gci->end; ++l )
{
atom1 = &(system->my_atoms[l]);
+#if defined(NEUTRAL_TERRITORY)
if( gci->type >= NT_NBRS && gci->type < NT_NBRS + 6 )
{
atom1->nt_dir = gci->type - NT_NBRS;
@@ -112,6 +113,7 @@ void Generate_Neighbor_Lists( reax_system *system, simulation_data *data,
{
atom1->nt_dir = -1;
}
+#endif
Set_Start_Index( l, num_far, far_nbrs );
//fprintf( stderr, "\tatom %d\n", atom1 );
@@ -213,6 +215,7 @@ int Estimate_NumNeighbors( reax_system *system, reax_list **lists,
for ( l = gci->str; l < gci->end; ++l )
{
atom1 = &(system->my_atoms[l]);
+#if defined(NEUTRAL_TERRITORY)
if( gci->type >= NT_NBRS && gci->type < NT_NBRS + 6 )
{
atom1->nt_dir = gci->type - NT_NBRS;
@@ -221,6 +224,7 @@ int Estimate_NumNeighbors( reax_system *system, reax_list **lists,
{
atom1->nt_dir = -1;
}
+#endif
//fprintf( stderr, "\tatom %d: ", l );
//tmp = num_far; tested = 0;
itr = 0;
diff --git a/PuReMD/src/reax_types.h b/PuReMD/src/reax_types.h
index b42dcd22..9957f148 100644
--- a/PuReMD/src/reax_types.h
+++ b/PuReMD/src/reax_types.h
@@ -217,12 +217,15 @@ typedef struct
MPI_Datatype bond_view;
MPI_Datatype angle_line;
MPI_Datatype angle_view;
+ mpi_out_data out_buffers[REAX_MAX_NBRS];
- mpi_out_data out_buffers[REAX_MAX_NT_NBRS];
- mpi_out_data out_nt_buffers[REAX_MAX_NT_NBRS];
void *in1_buffer;
void *in2_buffer;
+
+#if defined(NEUTRAL_TERRITORY)
+ mpi_out_data out_nt_buffers[REAX_MAX_NT_NBRS];
void *in_nt_buffer[REAX_MAX_NT_NBRS];
+#endif
} mpi_datatypes;
@@ -435,8 +438,10 @@ typedef struct
int num_bonds;
int num_hbonds;
int renumber;
+#if defined(NEUTRAL_TERRITORY)
int nt_dir;
int pos;
+#endif
} reax_atom;
@@ -544,16 +549,20 @@ typedef struct
int n, N, bigN, numH;
int local_cap, total_cap, gcell_cap, Hcap;
int est_recv, est_trans, max_recved;
- int wsize, my_rank, num_nbrs, num_nt_nbrs;
+ int wsize, my_rank, num_nbrs;
ivec my_coords;
neighbor_proc my_nbrs[REAX_MAX_NBRS];
- neighbor_proc my_nt_nbrs[REAX_MAX_NT_NBRS];
int *global_offset;
simulation_box big_box, my_box, my_ext_box;
grid my_grid;
boundary_cutoff bndry_cuts;
reax_atom *my_atoms;
+
+#if defined(NEUTRAL_TERRITORY)
+ int num_nt_nbrs;
+ neighbor_proc my_nt_nbrs[REAX_MAX_NT_NBRS];
+#endif
} reax_system;
@@ -887,6 +896,7 @@ typedef struct
} far_neighbor_data;
+#if defined(NEUTRAL_TERRITORY)
typedef struct
{
int nbr;
@@ -894,6 +904,7 @@ typedef struct
real d;
rvec dvec;
} nt_neighbor_data;
+#endif
typedef struct
@@ -966,7 +977,10 @@ typedef struct
{
/* matrix storage format */
int format;
- int cap, n, m, NT;
+ int cap, n, m;
+#if defined(NEUTRAL_TERRITORY)
+ int NT;
+#endif
int *start, *end;
sparse_matrix_entry *entries;
} sparse_matrix;
@@ -1080,7 +1094,6 @@ typedef union
//dbond_data *dbo_list;
//dDelta_data *dDelta_list;
//far_neighbor_data *far_nbr_list;
- //nt_neighbor_data *nt_nbr_list;
//hbond_data *hbond_list;
} list_type;
@@ -1107,7 +1120,9 @@ typedef struct
dbond_data *dbo_list;
dDelta_data *dDelta_list;
far_neighbor_data *far_nbr_list;
+#if defined(NEUTRAL_TERRITORY)
nt_neighbor_data *nt_nbr_list;
+#endif
hbond_data *hbond_list;
} reax_list;
--
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