From 1257b0429b3b3ec2e8e5aa89c32e510b46dd9345 Mon Sep 17 00:00:00 2001
From: Abdullah Alperen <alperena@msu.edu>
Date: Thu, 22 Nov 2018 14:25:37 -0500
Subject: [PATCH] PuReMD: continue NT for Jacobi debugging
---
PuReMD/src/allocate.c | 6 +-
PuReMD/src/allocate.h | 2 +-
PuReMD/src/basic_comm.c | 57 ++++++++++++----
PuReMD/src/comm_tools.c | 17 +++--
PuReMD/src/forces.c | 132 +++++++++++++++++++++++++-----------
PuReMD/src/init_md.c | 2 +-
PuReMD/src/linear_solvers.c | 36 ++++++++--
PuReMD/src/reax_defs.h | 1 +
PuReMD/src/reax_types.h | 5 +-
9 files changed, 186 insertions(+), 72 deletions(-)
diff --git a/PuReMD/src/allocate.c b/PuReMD/src/allocate.c
index 862aa0e1..ffdd965b 100644
--- a/PuReMD/src/allocate.c
+++ b/PuReMD/src/allocate.c
@@ -708,7 +708,7 @@ void Deallocate_Grid( grid *g )
buffers are void*, type cast to the correct pointer type to access
the allocated buffers */
int Allocate_MPI_Buffers( mpi_datatypes *mpi_data, int est_recv,
- neighbor_proc *my_nbrs,
+ neighbor_proc *my_nbrs, neighbor_proc *my_nt_nbrs,
char *msg )
{
int i;
@@ -744,6 +744,7 @@ int Allocate_MPI_Buffers( mpi_datatypes *mpi_data, int est_recv,
mpi_data->in_nt_buffer[i] = (void*)
scalloc( my_nbrs[i].est_recv, sizeof(real), "mpibuf:in_nt_buffer", comm );
+ //TODO
mpi_buf = &( mpi_data->out_nt_buffers[i] );
/* allocate storage for the neighbor processor i */
mpi_buf->index = (int*)
@@ -1096,7 +1097,8 @@ void ReAllocate( reax_system *system, control_params *control,
/* reallocate mpi buffers */
Deallocate_MPI_Buffers( mpi_data );
ret = Allocate_MPI_Buffers( mpi_data, system->est_recv,
- system->my_nbrs, msg );
+ system->my_nbrs, system->my_nt_nbrs,
+ msg );
if ( ret != SUCCESS )
{
fprintf( stderr, "%s", msg );
diff --git a/PuReMD/src/allocate.h b/PuReMD/src/allocate.h
index 5458f29c..669861a2 100644
--- a/PuReMD/src/allocate.h
+++ b/PuReMD/src/allocate.h
@@ -36,7 +36,7 @@ void Allocate_Grid( reax_system*, MPI_Comm );
void Deallocate_Grid( grid* );
-int Allocate_MPI_Buffers( mpi_datatypes*, int, neighbor_proc*, char* );
+int Allocate_MPI_Buffers( mpi_datatypes*, int, neighbor_proc*, neighbor_proc*, char* );
int Allocate_Matrix( sparse_matrix**, int, int, int, MPI_Comm );
diff --git a/PuReMD/src/basic_comm.c b/PuReMD/src/basic_comm.c
index 834034ed..83f01e52 100644
--- a/PuReMD/src/basic_comm.c
+++ b/PuReMD/src/basic_comm.c
@@ -141,7 +141,6 @@ void Dist_NT( reax_system* system, mpi_datatypes *mpi_data,
neighbor_proc *nbr;
#if defined(DEBUG)
- fprintf( stderr, "p%d dist: entered\n", system->my_rank );
#endif
comm = mpi_data->comm_mesh3D;
out_bufs = mpi_data->out_nt_buffers;
@@ -157,10 +156,22 @@ void Dist_NT( reax_system* system, mpi_datatypes *mpi_data,
MPI_Irecv( buf + nbr->atoms_str * scale, nbr->atoms_cnt, type,
nbr->receive_rank, d, comm, &(req[d]) );
}
+
+ /*if(d==0)
+ {
+ fprintf( stdout, "p%d dist: entered and need to receive %d numbers from %d\n", system->my_rank, nbr->atoms_cnt, nbr->receive_rank );
+ fflush( stdout );
+ }*/
}
for( d = 0; d < 6; ++d)
{
+ nbr = &(system->my_nt_nbrs[d]);
+ if(d==0)
+ {
+ //fprintf( stdout, "p%d dist: entered and need to send %d numbers to %d\n", system->my_rank, out_bufs[d].cnt, nbr->rank );
+ //fflush( stdout );
+ }
/* send both messages in dimension d */
if ( out_bufs[d].cnt )
{
@@ -171,19 +182,34 @@ void Dist_NT( reax_system* system, mpi_datatypes *mpi_data,
}
/*
+ MPI_Barrier( MPI_COMM_WORLD );
+ fprintf( stdout, "p%d dist: MISSION COMPLETED\n", system->my_rank );
+ fflush( stdout );
+ */
+
for( d = 0; d < 6; ++d )
{
+ //fprintf( stdout, "p%d dist: direction %d\n", system->my_rank, d );
+ //fflush( stdout );
nbr = &(system->my_nbrs[d]);
if ( nbr->atoms_cnt )
{
MPI_Wait( &(req[d]), &(stat[d]) );
}
}
- */
- for( d = 0; d < count; ++d )
+
+
+ /*for( d = 0; d < count; ++d )
{
MPI_Waitany( REAX_MAX_NT_NBRS, req, &index, stat);
- }
+ }*/
+
+
+ /*
+ MPI_Barrier( MPI_COMM_WORLD );
+ fprintf( stdout, "p%d dist: MPI_Waitany is done\n", system->my_rank );
+ fflush( stdout );
+ */
#if defined(DEBUG)
@@ -317,47 +343,54 @@ void Coll_NT( reax_system* system, mpi_datatypes *mpi_data,
fprintf( stderr, "p%d coll: entered\n", system->my_rank );
#endif
comm = mpi_data->comm_mesh3D;
- out_bufs = mpi_data->out_buffers;
+ out_bufs = mpi_data->out_nt_buffers;
count = 0;
for ( d = 0; d < 6; ++d )
{
/* initiate recvs */
- nbr = &(system->my_nbrs[d]);
+ nbr = &(system->my_nt_nbrs[d]);
in[d] = mpi_data->in_nt_buffer[d];
if ( out_bufs[d].cnt )
{
count++;
MPI_Irecv(in[d], out_bufs[d].cnt, type, nbr->receive_rank, d, comm, &(req[d]));
+ //fprintf( stdout, "p%d coll: d = %d, receive_rank = %d, cnt = %d\n", system->my_rank, d, nbr->receive_rank, out_bufs[d].cnt );
}
}
for( d = 0; d < 6; ++d )
{
/* send both messages in direction d */
- nbr = &(system->my_nbrs[d]);
+ nbr = &(system->my_nt_nbrs[d]);
if ( nbr->atoms_cnt )
{
MPI_Send( buf + nbr->atoms_str * scale, nbr->atoms_cnt, type,
nbr->rank, d, comm );
+ //fprintf( stdout, "p%d coll: d = %d, send_rank = %d, cnt = %d\n", system->my_rank, d, nbr->rank, nbr->atoms_cnt );
}
}
-
- /*
+
for( d = 0; d < 6; ++d )
{
+ fprintf( stderr, "p%d coll: d = %d\n", system->my_rank, d );
+ fflush( stdout );
if ( out_bufs[d].cnt )
{
MPI_Wait( &(req[d]), &(stat[d]));
+ //fprintf( stderr, "p%d coll: %d status complete\n", system->my_rank, d );
+ //fflush( stdout );
unpack( in[d], buf, out_bufs + d );
}
}
- */
- for( d = 0; d < count; ++d )
+ //fprintf( stderr, "p%d coll: entered\n", system->my_rank );
+ fflush( stdout );
+
+ /*for( d = 0; d < count; ++d )
{
MPI_Waitany( REAX_MAX_NT_NBRS, req, &index, stat);
unpack( in[index], buf, out_bufs + index );
- }
+ }*/
#if defined(DEBUG)
fprintf( stderr, "p%d coll: done\n", system->my_rank );
diff --git a/PuReMD/src/comm_tools.c b/PuReMD/src/comm_tools.c
index 5646b9cf..2162456c 100644
--- a/PuReMD/src/comm_tools.c
+++ b/PuReMD/src/comm_tools.c
@@ -33,7 +33,7 @@ void Setup_NT_Comm( reax_system* system, control_params* control,
real bndry_cut;
neighbor_proc *nbr_pr;
simulation_box *my_box;
- ivec nbr_coords;
+ ivec nbr_coords, nbr_recv_coords;
ivec r[12] = {
{0, 0, -1}, // -z
{0, 0, +1}, // +z
@@ -50,20 +50,18 @@ void Setup_NT_Comm( reax_system* system, control_params* control,
{+1, -1, 0} // +x-y
};
my_box = &(system->my_box);
- // TODO: verify this line
- //bndry_cut = system->bndry_cuts.ghost_cutoff;
- bndry_cut = control->vlist_cut;
+ bndry_cut = system->bndry_cuts.ghost_cutoff;
/* identify my neighbors */
system->num_nt_nbrs = REAX_MAX_NT_NBRS;
for ( i = 0; i < system->num_nt_nbrs; ++i )
{
- ivec_Sum( nbr_coords, system->my_coords, r[i] ); /* actual nbr coords */
nbr_pr = &(system->my_nt_nbrs[i]);
+ ivec_Sum( nbr_coords, system->my_coords, r[i] ); /* actual nbr coords */
MPI_Cart_rank( mpi_data->comm_mesh3D, nbr_coords, &(nbr_pr->rank) );
/* set the rank of the neighbor processor in the receiving direction */
- ivec_Sum( nbr_coords, system->my_coords, r[i + 6] ); /* actual nbr coords */
- MPI_Cart_rank( mpi_data->comm_mesh3D, nbr_coords, &(nbr_pr->receive_rank) );
+ ivec_Sum( nbr_recv_coords, system->my_coords, r[i + 6] ); /* actual nbr coords */
+ MPI_Cart_rank( mpi_data->comm_mesh3D, nbr_recv_coords, &(nbr_pr->receive_rank) );
for ( d = 0; d < 3; ++d )
{
@@ -164,7 +162,8 @@ void Init_Neutral_Territory( reax_system* system, mpi_datatypes *mpi_data )
if( mpi_data->in_nt_buffer[d] == NULL )
{
- mpi_data->in_nt_buffer[d] = (void *) smalloc( SAFER_ZONE * cnt * sizeof(real), "in", comm );
+ //TODO
+ mpi_data->in_nt_buffer[d] = (void *) smalloc( 100 * cnt * sizeof(real), "in", comm );
}
nbr = &(system->my_nt_nbrs[d]);
@@ -199,7 +198,7 @@ void Estimate_NT_Atoms( reax_system *system, mpi_datatypes *mpi_data )
out_bufs[d].out_atoms = (void*) calloc( nbr->est_send, sizeof(real) );
/* sort the atoms to their outgoing buffers */
- // TODO: ???
+ // TODO: to call or not to call?
//Sort_Neutral_Territory( system, d, out_bufs, 1 );
}
}
diff --git a/PuReMD/src/forces.c b/PuReMD/src/forces.c
index 7b66fa32..8178856d 100644
--- a/PuReMD/src/forces.c
+++ b/PuReMD/src/forces.c
@@ -412,6 +412,22 @@ void Init_Forces( reax_system *system, control_params *control,
}
#endif
+ //TODO: remove those variables
+ int local_to_local = 0;
+ //FILE *fp;
+#if defined(NEUTRAL_TERRITORY)
+ //TODO: remove those variables
+ int local_to_nt = 0;
+ int nt_to_local = 0;
+ int nt_to_nt = 0;
+ //fp = fopen( "NT_Pairs.txt", "w" );
+ int mark[6];
+ mark[0] = mark[1] = 1;
+ mark[2] = mark[3] = mark[4] = mark[5] = 2;
+#else
+ //fp = fopen( "Jacobi_Pairs.txt", "w" );
+#endif
+
for ( i = 0; i < system->N; ++i )
{
atom_i = &(system->my_atoms[i]);
@@ -451,12 +467,16 @@ void Init_Forces( reax_system *system, control_params *control,
ihb = -1;
ihb_top = -1;
+ //TODO: undo
if ( local == 1 )
{
H->start[i] = Htop;
H->entries[Htop].j = i;
H->entries[Htop].val = sbp_i->eta;
++Htop;
+ //TODO:
+ //fprintf( fp, "%d %d\n", atom_i->orig_id, atom_i->orig_id );
+ ++local_to_local;
if ( control->hbond_cut > 0 )
{
@@ -480,14 +500,6 @@ void Init_Forces( reax_system *system, control_params *control,
}
}
}
- // TODO: Diag entries for NT atoms?
- /*else if( local == 2 )
- {
- H->start[atom_i->pos] = Htop;
- H->entries[Htop].j = atom_i->pos;
- H->entries[Htop].val = sbp_i->eta;
- ++Htop;
- }*/
/* update i-j distance - check if j is within cutoff */
for ( pj = start_i; pj < end_i; ++pj )
@@ -533,14 +545,18 @@ void Init_Forces( reax_system *system, control_params *control,
|| far_nbrs->format == FULL_LIST )
{
#if defined(NEUTRAL_TERRITORY)
- if( atom_j->nt_dir != -1 || j < system->n )
+ if( atom_j->nt_dir > 0 || j < system->n )
{
+ //TODO
+ //fprintf( fp, "%d %d\n", atom_i->orig_id, atom_j->orig_id );
if( j < system->n )
{
+ ++local_to_local;
H->entries[Htop].j = j;
}
else
{
+ ++local_to_nt;
H->entries[Htop].j = atom_j->pos;
}
@@ -555,6 +571,10 @@ void Init_Forces( reax_system *system, control_params *control,
++Htop;
}
#else
+ //TODO
+ //fprintf( fp, "%d %d\n", atom_i->orig_id, atom_j->orig_id );
+ if( j < system->n )
+ ++local_to_local;
H->entries[Htop].j = j;
if ( control->tabulate == 0 )
{
@@ -599,38 +619,36 @@ void Init_Forces( reax_system *system, control_params *control,
else if ( local == 2 )
{
/* H matrix entry */
-#if defined(HALF_LIST)
- if ( j < system->n || atom_i->orig_id < atom_j->orig_id )
-#endif
+ //TODO
+ if( ( atom_j->nt_dir != -1 && mark[atom_i->nt_dir] != mark[atom_j->nt_dir] ) || ( j < system->n && atom_i->nt_dir != 0 ))
{
- if( atom_j->nt_dir != -1 || j < system->n )
+ //fprintf( fp, "%d %d\n", atom_i->orig_id, atom_j->orig_id );
+ if( !nt_flag )
{
- if( !nt_flag )
- {
- nt_flag = 1;
- H->start[atom_i->pos] = Htop;
- }
- if( j < system->n )
- {
- H->entries[Htop].j = j;
- }
- else
- {
- H->entries[Htop].j = atom_j->pos;
- }
+ nt_flag = 1;
+ H->start[atom_i->pos] = Htop;
+ }
+ if( j < system->n )
+ {
+ ++nt_to_local;
+ H->entries[Htop].j = j;
+ }
+ else
+ {
+ ++nt_to_nt;
+ H->entries[Htop].j = atom_j->pos;
+ }
- 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;
+ 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
@@ -664,7 +682,15 @@ void Init_Forces( reax_system *system, control_params *control,
#if defined(NEUTRAL_TERRITORY)
else if ( local == 2 )
{
- H->end[atom_i->pos] = Htop;
+ if( nt_flag )
+ {
+ H->end[atom_i->pos] = Htop;
+ }
+ else
+ {
+ H->start[atom_i->pos] = 0;
+ H->end[atom_i->pos] = 0;
+ }
}
#endif
}
@@ -700,6 +726,30 @@ void Init_Forces( reax_system *system, control_params *control,
}
}
+ int Htot, localtot;
+
+ MPI_Allreduce(&Htop, &Htot, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
+ MPI_Allreduce(&local_to_local, &localtot, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
+
+#if defined(NEUTRAL_TERRITORY)
+ int tot2, tot3, tot4;
+ MPI_Allreduce(&local_to_nt, &tot2, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
+ MPI_Allreduce(&nt_to_local, &tot3, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
+ MPI_Allreduce(&nt_to_nt, &tot4, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
+#endif
+
+ if(system->my_rank == MASTER_NODE )
+ {
+ fprintf( stdout, "total number of entries across all matrices: %d\n", Htot );
+ fprintf( stdout, "total number of local to local entries across all matrices: %d\n", localtot );
+#if defined(NEUTRAL_TERRITORY)
+ fprintf( stdout, "total number of local to nt entries across all matrices: %d\n", tot2 );
+ fprintf( stdout, "total number of nt to local entries across all matrices: %d\n", tot3 );
+ fprintf( stdout, "total number of nt to nt entries across all matrices: %d\n", tot4 );
+#endif
+ fflush( stdout );
+ }
+
workspace->realloc.Htop = Htop;
workspace->realloc.num_bonds = num_bonds;
workspace->realloc.num_hbonds = num_hbonds;
@@ -725,6 +775,8 @@ void Init_Forces( reax_system *system, control_params *control,
Validate_Lists( system, workspace, lists, data->step,
system->n, system->N, system->numH, comm );
+
+ //fclose( fp );
}
@@ -1109,10 +1161,6 @@ void Estimate_Storages( reax_system *system, control_params *control,
BO_pi2 = exp( C56 );
}
else BO_pi2 = C56 = 0.0;
-
- /* Initially BO values are the uncorrected ones, page 1 */
- BO = BO_s + BO_pi + BO_pi2;
-
if ( BO >= control->bo_cut )
{
++bond_top[i];
@@ -1230,6 +1278,8 @@ void Compute_Forces( reax_system *system, control_params *control,
//MPI_Barrier( mpi_data->world );
if ( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.nonb) );
+#endif
+ Update_Timing_Info( &t_start, &(data->timing.nonb) );
#endif
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: nonbonded forces completed\n",
diff --git a/PuReMD/src/init_md.c b/PuReMD/src/init_md.c
index 4e3000b5..9ea85cca 100644
--- a/PuReMD/src/init_md.c
+++ b/PuReMD/src/init_md.c
@@ -589,7 +589,7 @@ int Init_Lists( reax_system *system, control_params *control,
comm = mpi_data->world;
- if ( control->cm_solver_pre_comp_type == SAI_PC )
+ if ( control->cm_solver_pre_comp_type == SAI_PC || 1 )
{
far_nbr_list_format = FULL_LIST;
cm_format = SYM_FULL_MATRIX;
diff --git a/PuReMD/src/linear_solvers.c b/PuReMD/src/linear_solvers.c
index 36a6b15e..3606d90d 100644
--- a/PuReMD/src/linear_solvers.c
+++ b/PuReMD/src/linear_solvers.c
@@ -1137,7 +1137,7 @@ void dual_Sparse_MatVec( sparse_matrix *A, rvec2 *x, rvec2 *b, int N )
void Sparse_MatVec( sparse_matrix *A, real *x, real *b, int N )
{
- int i, j, k, si;
+ int i, j, k, si, dim;
real val;
for ( i = 0; i < N; ++i )
@@ -1145,9 +1145,14 @@ void Sparse_MatVec( sparse_matrix *A, real *x, real *b, int N )
b[i] = 0;
}
+#if defined(NEUTRAL_TERRITORY)
+ dim = A->NT;
+#else
+ dim = A->n;
+#endif
if ( A->format == SYM_HALF_MATRIX )
{
- for ( i = 0; i < A->n; ++i )
+ for ( i = 0; i < dim; ++i )
{
si = A->start[i];
@@ -1167,7 +1172,7 @@ void Sparse_MatVec( sparse_matrix *A, real *x, real *b, int N )
}
else if ( A->format == SYM_FULL_MATRIX || A->format == FULL_MATRIX )
{
- for ( i = 0; i < A->n; ++i )
+ for ( i = 0; i < dim; ++i )
{
si = A->start[i];
@@ -1187,6 +1192,9 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
storage *workspace, sparse_matrix *H, real *b,
real tol, real *x, mpi_datatypes* mpi_data, FILE *fout, int nprocs )
{
+ fprintf(stdout, "%d %d\n", H->n, H->NT);
+ fflush(stdout);
+
int i, j, scale;
real tmp, alpha, beta, b_norm;
real sig_old, sig_new;
@@ -1227,6 +1235,18 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
t_comm += Get_Timing_Info( t_start );
}
+ else
+ {
+#if defined(NEUTRAL_TERRITORY)
+ fprintf(stdout,"BEFORE COLL\n");
+ fflush( stdout );
+
+ Coll_NT( system, mpi_data, workspace->q, MPI_DOUBLE, scale, real_unpacker );
+ fprintf(stdout,"AFTER COLL\n");
+ fflush( stdout );
+#endif
+ }
+
t_start = Get_Time( );
Vector_Sum( workspace->r , 1., b, -1., workspace->q, system->n );
t_vops += Get_Timing_Info( t_start );
@@ -1268,6 +1288,8 @@ 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 )
{
+ fprintf( stdout, "p%d, i = %d, res = %.6f\n", system->my_rank, i, sqrt(sig_new) / b_norm );
+ fflush( stdout );
t_start = Get_Time( );
#if defined(NEUTRAL_TERRITORY)
Dist_NT( system, mpi_data, workspace->d, MPI_DOUBLE, scale, real_packer );
@@ -1294,6 +1316,12 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
#endif
t_comm += Get_Timing_Info( t_start );
}
+ else
+ {
+#if defined(NEUTRAL_TERRITORY)
+ Coll_NT( system, mpi_data, workspace->q, MPI_DOUBLE, scale, real_unpacker );
+#endif
+ }
t_start = Get_Time( );
tmp = Parallel_Dot(workspace->d, workspace->q, system->n, mpi_data->world);
@@ -1336,7 +1364,7 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
}
t_start = Get_Time( );
- sig_old = sig_new;
+ //sig_new = Parallel_Dot(workspace->r, workspace->p, H->NT, mpi_data->world);
sig_new = Parallel_Dot(workspace->r, workspace->p, system->n, mpi_data->world);
t_allreduce += Get_Timing_Info( t_start );
diff --git a/PuReMD/src/reax_defs.h b/PuReMD/src/reax_defs.h
index 0f3b9089..daa3f283 100644
--- a/PuReMD/src/reax_defs.h
+++ b/PuReMD/src/reax_defs.h
@@ -133,6 +133,7 @@ enum gcell_types { NO_NBRS = 0, NEAR_ONLY = 1, HBOND_ONLY = 2, FAR_ONLY = 4,
NEAR_HBOND = 3, NEAR_FAR = 5, HBOND_FAR = 6, FULL_NBRS = 7,
NATIVE = 8, NT_NBRS = 9 // 9 through 14
};
+enum nt_atom_type { TOWER = 1, PLATE = 2 };
enum atoms { C_ATOM = 0, H_ATOM = 1, O_ATOM = 2, N_ATOM = 3,
S_ATOM = 4, SI_ATOM = 5, GE_ATOM = 6, X_ATOM = 7
diff --git a/PuReMD/src/reax_types.h b/PuReMD/src/reax_types.h
index 464bfb3a..8a08c5ad 100644
--- a/PuReMD/src/reax_types.h
+++ b/PuReMD/src/reax_types.h
@@ -978,9 +978,10 @@ typedef struct
/* matrix storage format */
int format;
int cap, n, m;
-#if defined(NEUTRAL_TERRITORY)
+ //TODO: uncomment
+//#if defined(NEUTRAL_TERRITORY)
int NT;
-#endif
+//#endif
int *start, *end;
sparse_matrix_entry *entries;
} sparse_matrix;
--
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