diff --git a/PuReMD/Makefile.am b/PuReMD/Makefile.am
index 718c453fa84b45f83c4c3890eda1735fbb0b7f20..c657b37a7bde1349eaa877de14d82b8d8bf727cd 100644
--- a/PuReMD/Makefile.am
+++ b/PuReMD/Makefile.am
@@ -6,9 +6,8 @@ bin_puremd_SOURCES = src/allocate.c src/basic_comm.c src/ffield.c src/grid.c src
src/vector.c src/analyze.c src/box.c src/system_props.c src/control.c src/comm_tools.c \
src/geo_tools.c src/linear_solvers.c src/neighbors.c src/qEq.c src/bond_orders.c src/multi_body.c \
src/bonds.c src/valence_angles.c src/hydrogen_bonds.c src/torsion_angles.c src/nonbonded.c src/forces.c \
- src/integrate.c src/init_md.c src/parallelreax.c
-
-include_HEADERS = src/reax_defs.h src/reax_types.h \
+ src/integrate.c src/init_md.c src/parallelreax.c \
+ src/reax_defs.h src/reax_types.h \
src/allocate.h src/basic_comm.h src/ffield.h src/grid.h src/list.h src/lookup.h \
src/io_tools.h src/reset_tools.h src/restart.h src/random.h src/tool_box.h src/traj.h \
src/vector.h src/analyze.h src/box.h src/system_props.h src/control.h src/comm_tools.h \
@@ -16,5 +15,5 @@ include_HEADERS = src/reax_defs.h src/reax_types.h \
src/bonds.h src/valence_angles.h src/hydrogen_bonds.h src/torsion_angles.h src/nonbonded.h src/forces.h \
src/integrate.h src/init_md.h
-bin_puremd_CFLAGS = $(CFLAGS) $(MPI_CFLAGS)
-bin_puremd_LDADD = $(LDADD) $(MPI_LIBS)
+bin_puremd_CFLAGS = $(MPI_CFLAGS)
+bin_puremd_LDADD = $(MPI_LIBS)
diff --git a/PuReMD/configure.ac b/PuReMD/configure.ac
index 8833fc248a64e49a684106feeaeb4682c54bf715..6a1bb0a187736d4baf0207f537e2d224758a3901 100644
--- a/PuReMD/configure.ac
+++ b/PuReMD/configure.ac
@@ -74,7 +74,6 @@ fi
CONFIGURE_HEADLINE([ MPI compiler ])
ACX_MPI([], [AC_MSG_ERROR([could not find mpi library])])
AC_CHECK_PROG(MPIRUN, mpirun, mpirun)
-AC_SUBST(MPIRUN)
# try to find if we are using OpenMPI / MPICH by looking inside mpi.h
save_CC="${CC}"
diff --git a/PuReMD/src/basic_comm.c b/PuReMD/src/basic_comm.c
index 135abb6e49404c8305938ea510e5c0bb2aafd9c6..8d6277de6008da24a98e7ba22f1dfdcac8d8c21f 100644
--- a/PuReMD/src/basic_comm.c
+++ b/PuReMD/src/basic_comm.c
@@ -132,7 +132,7 @@ void Dist( reax_system* system, mpi_datatypes *mpi_data,
void Dist_NT( reax_system* system, mpi_datatypes *mpi_data,
void *buf, MPI_Datatype type, int scale, dist_packer pack )
{
- int d;
+ int d, count, index;
mpi_out_data *out_bufs;
MPI_Comm comm;
MPI_Request req[6];
@@ -145,12 +145,14 @@ void Dist_NT( reax_system* system, mpi_datatypes *mpi_data,
comm = mpi_data->comm_mesh3D;
out_bufs = mpi_data->out_nt_buffers;
+ count = 0;
/* initiate recvs */
for( d = 0; d < 6; ++d )
{
nbr = &(system->my_nt_nbrs[d]);
if ( nbr->atoms_cnt )
{
+ count++;
MPI_Irecv( buf + nbr->atoms_str * scale, nbr->atoms_cnt, type,
nbr->receive_rank, d, comm, &(req[d]) );
}
@@ -167,15 +169,21 @@ void Dist_NT( reax_system* system, mpi_datatypes *mpi_data,
}
}
+ /*
for( d = 0; d < 6; ++d )
{
nbr = &(system->my_nbrs[d]);
if ( nbr->atoms_cnt )
{
- // TODO: Wait(MPI_WAITANY)
MPI_Wait( &(req[d]), &(stat[d]) );
}
}
+ */
+ for( d = 0; d < count; ++d )
+ {
+ MPI_Waitany( MAX_NT_NBRS, req, &index, stat);
+ }
+
#if defined(DEBUG)
fprintf( stderr, "p%d dist: done\n", system->my_rank );
@@ -295,7 +303,7 @@ void Coll( reax_system* system, mpi_datatypes *mpi_data,
void Coll_NT( reax_system* system, mpi_datatypes *mpi_data,
void *buf, MPI_Datatype type, int scale, coll_unpacker unpack )
{
- int d;
+ int d, count, index;
void *in[6];
mpi_out_data *out_bufs;
MPI_Comm comm;
@@ -309,6 +317,7 @@ void Coll_NT( reax_system* system, mpi_datatypes *mpi_data,
comm = mpi_data->comm_mesh3D;
out_bufs = mpi_data->out_buffers;
+ count = 0;
for ( d = 0; d < 6; ++d )
{
/* initiate recvs */
@@ -316,6 +325,7 @@ void Coll_NT( reax_system* system, mpi_datatypes *mpi_data,
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]));
}
}
@@ -331,15 +341,21 @@ void Coll_NT( reax_system* system, mpi_datatypes *mpi_data,
}
}
+ /*
for( d = 0; d < 6; ++d )
{
if ( out_bufs[d].cnt )
{
- //TODO: WAITANY
MPI_Wait( &(req[d]), &(stat[d]));
unpack( in[d], buf, out_bufs + d );
}
}
+ */
+ for( d = 0; d < count; ++d )
+ {
+ MPI_Waitany( 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 9c2728f86ae1885b9abc8b4157c64cd207c5686c..28a41c5e2368ee9ca68872c9a6f28bb6ae57070c 100644
--- a/PuReMD/src/comm_tools.c
+++ b/PuReMD/src/comm_tools.c
@@ -46,8 +46,8 @@ void Setup_NT_Comm( reax_system* system, control_params* control,
{0, 0, -1}, // -z
{0, +1, 0}, // +y
{+1, +1, 0}, // +x+y
- {+1, 0, 0}, // -x
- {+1, -1, 0} // -x+y
+ {+1, 0, 0}, // +x
+ {+1, -1, 0} // +x-y
};
my_box = &(system->my_box);
bndry_cut = system->bndry_cuts.ghost_cutoff;
diff --git a/PuReMD/src/forces.c b/PuReMD/src/forces.c
index dadb988eedf2d143d02fd26ec430aabc14b91dd5..76a38527d8702e4767d0b49bfc9bfa7a0d9b8bb4 100644
--- a/PuReMD/src/forces.c
+++ b/PuReMD/src/forces.c
@@ -346,11 +346,16 @@ void Init_Forces( reax_system *system, control_params *control,
int jhb_top;
int start_j, end_j;
int btop_j;
+ int total_cnt[6];
+ int bin[6];
+ int total_sum[6];
+ int nt_flag;
far_nbrs = lists[FAR_NBRS];
bonds = lists[BONDS];
hbonds = lists[HBONDS];
+
for ( i = 0; i < system->n; ++i )
workspace->bond_mark[i] = 0;
for ( i = system->n; i < system->N; ++i )
@@ -360,13 +365,47 @@ void Init_Forces( reax_system *system, control_params *control,
}
H = workspace->H;
- H->n = system->n;
+ H->n = system->N;
Htop = 0;
num_bonds = 0;
num_hbonds = 0;
btop_i = 0;
renbr = (data->step - data->prev_steps) % control->reneighbor == 0;
+ if( renbr )
+ {
+ for ( i = 0; i < 6; ++i )
+ {
+ total_cnt[i] = 0;
+ bin[i] = 0;
+ total_sum[i] = 0;
+ }
+ for ( i = system->n; i < system->N; ++i )
+ {
+ atom_i = &(system->my_atoms[i]);
+ if( atom_i->nt_dir != -1 )
+ {
+ total_cnt[ atom_i->nt_dir ]++;
+ }
+ }
+ total_sum[0] = system->n;
+ for ( i = 1; i < 6; ++i )
+ {
+ total_sum[i] = total_sum[i-1] + total_cnt[i-1];
+ }
+ for ( i = system->n; i < system->N; ++i )
+ {
+ atom_i = &(system->my_atoms[i]);
+ if( atom_i->nt_dir != -1 )
+ {
+ atom_i->pos = total_sum[ atom_i->nt_dir ] + bin[ atom_i->nt_dir ];
+ bin[ atom_i->nt_dir ]++;
+ }
+ }
+ H->NT = total_sum[6] + total_cnt[6];
+
+ }
+
for ( i = 0; i < system->N; ++i )
{
atom_i = &(system->my_atoms[i]);
@@ -385,12 +424,17 @@ void Init_Forces( reax_system *system, control_params *control,
}
sbp_i = &(system->reax_param.sbp[type_i]);
- //TODO: edit this part to include NT atoms
if ( i < system->n )
{
local = 1;
cutoff = control->nonb_cut;
}
+ else if( atom_i->nt_dir != -1 )
+ {
+ local = 2;
+ cutoff = control->nonb_cut;
+ nt_flag = 0;
+ }
else
{
local = 0;
@@ -399,7 +443,7 @@ void Init_Forces( reax_system *system, control_params *control,
ihb = -1;
ihb_top = -1;
- if ( local )
+ if ( local == 1 )
{
H->start[i] = Htop;
H->entries[Htop].j = i;
@@ -428,6 +472,14 @@ 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 )
@@ -465,18 +517,34 @@ void Init_Forces( reax_system *system, control_params *control,
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
- if ( local )
+ if ( local == 1 )
{
/* H matrix entry */
if ( (far_nbrs->format == HALF_LIST
&& (j < system->n || atom_i->orig_id < atom_j->orig_id))
|| far_nbrs->format == FULL_LIST )
{
- 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;
+ if( atom_j->nt_dir != -1 || j < system->n )
+ {
+ if( j < system->n )
+ {
+ H->entries[Htop].j = j;
+ }
+ else
+ {
+ H->entries[Htop].j = atom_i->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;
+ }
}
/* hydrogen bond lists */
@@ -506,6 +574,42 @@ 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
+ {
+ if( atom_j->nt_dir != -1 || j < system->n )
+ {
+ 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_i->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;
+ }
+ }
+
+ }
/* uncorrected bond orders */
if ( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
@@ -527,8 +631,17 @@ void Init_Forces( reax_system *system, control_params *control,
}
}
+ if ( local == 1 )
+ {
+ H->end[i] = Htop;
+ }
+ else if ( local == 2 )
+ {
+ H->end[atom_i->pos] = Htop;
+ }
+
Set_End_Index( i, btop_i, bonds );
- if ( local )
+ if ( local == 1 )
{
H->end[i] = Htop;
if ( ihb == 1 )
@@ -829,7 +942,7 @@ void Init_Forces_noQEq( reax_system *system, control_params *control,
void Estimate_Storages( reax_system *system, control_params *control,
reax_list **lists, int *Htop, int *hb_top,
- int *bond_top, int *num_3body, MPI_Comm comm )
+ int *bond_top, int *num_3body, MPI_Comm comm, int *matrix_dim )
{
int i, j, pj;
int start_i, end_i;
@@ -848,6 +961,7 @@ void Estimate_Storages( reax_system *system, control_params *control,
far_nbrs = lists[FAR_NBRS];
*Htop = 0;
+ *matrix_dim = 0;
memset( hb_top, 0, sizeof(int) * system->local_cap );
memset( bond_top, 0, sizeof(int) * system->total_cap );
*num_3body = 0;
@@ -865,8 +979,18 @@ void Estimate_Storages( reax_system *system, control_params *control,
local = 1;
cutoff = control->nonb_cut;
++(*Htop);
+ ++(*matrix_dim);
ihb = sbp_i->p_hbond;
}
+ else if ( atom_i->nt_dir != -1 )
+ {
+ local = 2;
+ cutoff = control->nonb_cut;
+ // TODO: Diag entries for NT atoms?
+ //++(*Htop);
+ //++(*matrix_dim);
+ ihb = -1;
+ }
else
{
local = 0;
@@ -890,13 +1014,16 @@ void Estimate_Storages( reax_system *system, control_params *control,
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
- if ( local )
+ if ( local == 1 )
{
if ( (far_nbrs->format == HALF_LIST
&& (j < system->n || atom_i->orig_id < atom_j->orig_id))
|| far_nbrs->format == FULL_LIST )
{
- ++(*Htop);
+ if( j < system->n || (system->my_atoms[j]).nt_dir != -1 )
+ {
+ ++(*Htop);
+ }
}
/* hydrogen bond lists */
@@ -917,6 +1044,20 @@ void Estimate_Storages( reax_system *system, control_params *control,
}
}
+ else if ( local == 2 )
+ {
+
+#if defined(HALF_LIST)
+ if ( j < system->n || atom_i->orig_id < atom_j->orig_id ) //tryQEq ||1
+#endif
+ {
+ if( j < system->n || (system->my_atoms[j]).nt_dir != -1 )
+ {
+ ++(*Htop);
+ }
+ }
+ }
+
/* uncorrected bond orders */
if ( nbr_pj->d <= control->bond_cut )
{
@@ -960,6 +1101,7 @@ void Estimate_Storages( reax_system *system, control_params *control,
}
*Htop = (int)(MAX( *Htop * SAFE_ZONE, MIN_CAP * MIN_HENTRIES ));
+ *matrix_dim = (int)(MAX( *matrix_dim * SAFE_ZONE, MIN_CAP ));
for ( i = 0; i < system->n; ++i )
hb_top[i] = (int)(MAX( hb_top[i] * SAFER_ZONE, MIN_HBONDS ));
@@ -1003,13 +1145,21 @@ void Compute_Forces( reax_system *system, control_params *control,
#elif defined(LAMMPS_REAX)
qeq_flag = 0;
#endif
-
+#if defined(NT_DEBUG)
+ fprintf( stdout, "forces.c before Init_Forces call\n");
+ fflush( stdout);
+#endif
if ( qeq_flag )
Init_Forces( system, control, data, workspace, lists, out_control, comm );
else
Init_Forces_noQEq( system, control, data, workspace,
lists, out_control, comm );
+#if defined(NT_DEBUG)
+ //MPI_Barrier(MPI_COMM_WORLD);
+ fprintf( stdout, "p%d, forces.c after Init_Forces call\n", system->my_rank);
+ fflush( stdout);
+#endif
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( mpi_data->world );
if ( system->my_rank == MASTER_NODE )
@@ -1020,6 +1170,11 @@ void Compute_Forces( reax_system *system, control_params *control,
/********* bonded interactions ************/
Compute_Bonded_Forces( system, control, data, workspace,
lists, out_control, mpi_data->world );
+#if defined(NT_DEBUG)
+ fprintf( stdout, "forces.c after Compute_Bonded_Forces call\n");
+ fflush( stdout);
+ MPI_Barrier( mpi_data->world );
+#endif
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( mpi_data->world );
@@ -1034,11 +1189,20 @@ void Compute_Forces( reax_system *system, control_params *control,
MPI_Barrier( mpi_data->world );
#endif
+#if defined(NT_DEBUG)
+ fprintf( stdout, "p%d, forces.c before QEq call\n", system->my_rank );
+ fflush( stdout);
+ MPI_Barrier( mpi_data->world );
+#endif
/**************** qeq ************************/
#if defined(PURE_REAX)
if ( qeq_flag )
QEq( system, control, data, workspace, out_control, mpi_data );
+#if defined(NT_DEBUG)
+ fprintf( stdout, "forces.c after QEq call\n");
+ fflush( stdout);
+#endif
#if defined(LOG_PERFORMANCE)
//MPI_Barrier( mpi_data->world );
diff --git a/PuReMD/src/forces.h b/PuReMD/src/forces.h
index 43d47cb46f66f45dc2b54d9415f8c92405a1d557..10b34395b3af6940a1779255fb8a3ebea7b45976 100644
--- a/PuReMD/src/forces.h
+++ b/PuReMD/src/forces.h
@@ -31,5 +31,5 @@ void Init_Force_Functions( control_params* );
void Compute_Forces( reax_system*, control_params*, simulation_data*,
storage*, reax_list**, output_controls*, mpi_datatypes* );
void Estimate_Storages( reax_system*, control_params*, reax_list**,
- int*, int*, int*, int*, MPI_Comm );
+ int*, int*, int*, int*, MPI_Comm, int* );
#endif
diff --git a/PuReMD/src/grid.c b/PuReMD/src/grid.c
index 0064f2201695b85625dcd15db75861fe7fcb80b9..1bd1b72a4fc98f9ee2b887e07b475d230c1e4cc4 100644
--- a/PuReMD/src/grid.c
+++ b/PuReMD/src/grid.c
@@ -30,11 +30,21 @@
/* determines the exchange boundaries with nbrs in terms of gcells */
void Mark_GCells( reax_system* system, grid *g, ivec procs, MPI_Comm comm )
{
- int x, y, z, d;
+ int i, x, y, z, d, len;
ivec r, nbr_coord, prdc;
ivec send_span, recv_span;
ivec str_send, end_send;
ivec str_recv, end_recv;
+ ivec nt_str, nt_end;
+
+ ivec dir[6] = {
+ {0, 0, +1}, // +z
+ {0, 0, -1}, // -z
+ {0, +1, 0}, // +y
+ {+1, +1, 0}, // +x+y
+ {+1, 0, 0}, // +x
+ {+1, -1, 0} // +x-y
+ };
/* clear all gcell type info */
for ( x = 0; x < g->ncells[0]; x++ )
@@ -50,6 +60,39 @@ void Mark_GCells( reax_system* system, grid *g, ivec procs, MPI_Comm comm )
g->cells[x][y][z].type = NATIVE;
ivec_MakeZero( g->cells[x][y][z].rel_box );
}
+
+ /* mark NT cells */
+ for ( i = 0; i < 6; ++i )
+ {
+ for ( d = 0; d < 3; ++d )
+ {
+ if ( dir[i][d] > 0 )
+ {
+ nt_str[d] = MIN(g->native_end[d], g->ncells[d]);
+ nt_end[d] = MIN(g->native_end[d] + g->vlist_span[d], g->ncells[d]);
+ }
+ else if ( dir[i][d] < 0 )
+ {
+ nt_str[d] = MAX(0, g->native_str[d] - g->vlist_span[d] );
+ nt_end[d] = g->native_str[d];
+ }
+ else
+ {
+ nt_str[d] = g->native_str[d];
+ nt_end[d] = g->native_end[d];
+ }
+ }
+ for ( x = nt_str[0]; x < nt_end[0]; x++ )
+ {
+ for ( y = nt_str[1]; y < nt_end[1]; y++ )
+ {
+ for ( z = nt_str[2]; z < nt_end[2]; z++ )
+ {
+ g->cells[x][y][z].type = NT_NBRS + i;
+ }
+ }
+ }
+ }
/* loop over neighbors */
for ( r[0] = -1; r[0] <= 1; ++r[0])
@@ -137,7 +180,7 @@ void Find_Neighbor_GridCells( grid *g, control_params *control )
top = 0;
//fprintf( stderr, "grid1: %d %d %d:\n", ci[0], ci[1], ci[2] );
- if ( gc->type == NATIVE )
+ if ( gc->type == NATIVE || ( gc->type >= NT_NBRS && gc->type < NT_NBRS + 6 ) )
gc->cutoff = control->vlist_cut;
else gc->cutoff = control->bond_cut;
@@ -201,13 +244,13 @@ void Reorder_GridCells( grid *g )
fprintf( stderr, "reordered gcells:\n" );
for ( i = 0; i < top; ++i )
fprintf( stderr, "order%d: %d %d %d\n",
- i, g->order[i][0], g->order[i][1], g->order[i][2] );
+ i, g->order[i][0], g->order[i][1], g->order[i][2] );
#endif
}
void Setup_New_Grid( reax_system* system, control_params* control,
- MPI_Comm comm )
+ MPI_Comm comm )
{
int d, i, j, k;
grid *g;
@@ -242,13 +285,13 @@ void Setup_New_Grid( reax_system* system, control_params* control,
g->bond_span[d] = (int)ceil( control->bond_cut / g->cell_len[d] );
/* span of the ghost region in terms of gcells */
g->ghost_span[d] = (int)ceil(system->bndry_cuts.ghost_cutoff /
- g->cell_len[d]);
+ g->cell_len[d]);
g->ghost_nonb_span[d] = (int)ceil(system->bndry_cuts.ghost_nonb /
- g->cell_len[d]);
+ g->cell_len[d]);
g->ghost_hbond_span[d] = (int)ceil( system->bndry_cuts.ghost_hbond /
- g->cell_len[d] );
+ g->cell_len[d] );
g->ghost_bond_span[d] = (int)ceil( system->bndry_cuts.ghost_bond /
- g->cell_len[d] );
+ g->cell_len[d] );
}
/* total number of grid cells */
@@ -262,8 +305,8 @@ void Setup_New_Grid( reax_system* system, control_params* control,
/* upper bound on the number of gcells to be exchanged with a single nbr */
system->gcell_cap =
MAX3( g->native_cells[0] * g->native_cells[1] * g->ghost_span[2],
- g->native_cells[0] * g->native_cells[2] * g->ghost_span[1],
- g->native_cells[1] * g->native_cells[2] * g->ghost_span[0] ) + 1;
+ g->native_cells[0] * g->native_cells[2] * g->ghost_span[1],
+ g->native_cells[1] * g->native_cells[2] * g->ghost_span[0] ) + 1;
/* allocate grid space */
Allocate_Grid( system, comm );
@@ -331,9 +374,9 @@ void Update_Grid( reax_system* system, control_params* control, MPI_Comm comm )
ghost_span[d] = (int)ceil(system->bndry_cuts.ghost_cutoff / cell_len[d]);
ghost_nonb_span[d] = (int)ceil(system->bndry_cuts.ghost_nonb / cell_len[d]);
ghost_hbond_span[d] = (int)ceil( system->bndry_cuts.ghost_hbond /
- cell_len[d] );
+ cell_len[d] );
ghost_bond_span[d] = (int)ceil( system->bndry_cuts.ghost_bond /
- cell_len[d] );
+ cell_len[d] );
}
@@ -418,14 +461,14 @@ void Bin_My_Atoms( reax_system *system, reallocate_data *realloc )
if ( atoms[l].x[d] < my_box->min[d] || atoms[l].x[d] > my_box->max[d] )
{
fprintf( stderr, "p%d: local atom%d [%f %f %f] is out of my box!\n",
- system->my_rank, l,
- atoms[l].x[0], atoms[l].x[1], atoms[l].x[2] );
+ system->my_rank, l,
+ atoms[l].x[0], atoms[l].x[1], atoms[l].x[2] );
fprintf( stderr, "p%d: orig atom id is %d!\n",
- system->my_rank, atoms[l].orig_id);
+ system->my_rank, atoms[l].orig_id);
fprintf( stderr, "p%d: my_box=[%f-%f, %f-%f, %f-%f]\n",
- system->my_rank, my_box->min[0], my_box->max[0],
- my_box->min[1], my_box->max[1],
- my_box->min[2], my_box->max[2] );
+ system->my_rank, my_box->min[0], my_box->max[0],
+ my_box->min[1], my_box->max[1],
+ my_box->min[2], my_box->max[2] );
MPI_Abort( MPI_COMM_WORLD, -1 );
}
@@ -437,10 +480,10 @@ void Bin_My_Atoms( reax_system *system, reallocate_data *realloc )
}
#if defined(DEBUG)
fprintf( stderr, "p%d bin_my_atoms: l:%d - atom%d @ %.5f %.5f %.5f"\
- "--> cell: %d %d %d\n",
- system->my_rank, l, atoms[l].orig_id,
- atoms[l].x[0], atoms[l].x[1], atoms[l].x[2],
- c[0], c[1], c[2] );
+ "--> cell: %d %d %d\n",
+ system->my_rank, l, atoms[l].orig_id,
+ atoms[l].x[0], atoms[l].x[1], atoms[l].x[2],
+ c[0], c[1], c[2] );
#endif
gc = &( g->cells[c[0]][c[1]][c[2]] );
gc->atoms[ gc->top++ ] = l;
@@ -460,13 +503,13 @@ void Bin_My_Atoms( reax_system *system, reallocate_data *realloc )
max_atoms = gc->top;
#if defined(DEBUG)
fprintf( stderr, "p%d gc[%d,%d,%d]->top=%d\n",
- system->my_rank, i, j, k, gc->top );
+ system->my_rank, i, j, k, gc->top );
#endif
}
#if defined(DEBUG)
fprintf( stderr, "p%d max_atoms=%d, g->max_atoms=%d\n",
- system->my_rank, max_atoms, g->max_atoms );
+ system->my_rank, max_atoms, g->max_atoms );
#endif
/* check if current gcell->max_atoms is safe */
if ( max_atoms >= g->max_atoms * DANGER_ZONE )
@@ -524,7 +567,7 @@ void Reorder_My_Atoms( reax_system *system, storage *workspace )
void Get_Boundary_GCell( grid *g, rvec base, rvec x, grid_cell **gc,
- rvec *cur_min, rvec *cur_max )
+ rvec *cur_min, rvec *cur_max )
{
int d;
ivec c;
@@ -540,7 +583,7 @@ void Get_Boundary_GCell( grid *g, rvec base, rvec x, grid_cell **gc,
}
#if defined(DEBUG)
fprintf( stderr, "get_bndry_gc: base=[%f %f %f] x=[%f %f %f] c=[%d %d %d]\n",
- base[0], base[1], base[2], x[0], x[1], x[2], c[0], c[1], c[2] );
+ base[0], base[1], base[2], x[0], x[1], x[2], c[0], c[1], c[2] );
#endif
*gc = &( g->cells[c[0]][c[1]][c[2]] );
@@ -548,11 +591,11 @@ void Get_Boundary_GCell( grid *g, rvec base, rvec x, grid_cell **gc,
rvec_Sum( *cur_max, (*gc)->max, loosen );
#if defined(DEBUG)
fprintf( stderr, "get_bndry_gc: gcmin=[%f %f %f] gcmax=[%f %f %f]\n",
- (*gc)->min[0], (*gc)->min[1], (*gc)->min[2],
- (*gc)->max[0], (*gc)->max[1], (*gc)->max[2] );
+ (*gc)->min[0], (*gc)->min[1], (*gc)->min[2],
+ (*gc)->max[0], (*gc)->max[1], (*gc)->max[2] );
fprintf( stderr, "get_bndry_gc: curmin=[%f %f %f] curmax=[%f %f %f]\n",
- (*cur_min)[0], (*cur_min)[1], (*cur_min)[2],
- (*cur_max)[0], (*cur_max)[1], (*cur_max)[2] );
+ (*cur_min)[0], (*cur_min)[1], (*cur_min)[2],
+ (*cur_max)[0], (*cur_max)[1], (*cur_max)[2] );
#endif
}
@@ -599,8 +642,8 @@ void Bin_Boundary_Atoms( reax_system *system )
if ( !is_Within_GCell( atoms[start].x, ext_box->min, ext_box->max ) )
{
fprintf( stderr, "p%d: ghost atom%d [%f %f %f] is out of my box!\n",
- system->my_rank, start,
- atoms[start].x[0], atoms[start].x[1], atoms[start].x[2] );
+ system->my_rank, start,
+ atoms[start].x[0], atoms[start].x[1], atoms[start].x[2] );
MPI_Abort( MPI_COMM_WORLD, -1 );
}
@@ -613,8 +656,8 @@ void Bin_Boundary_Atoms( reax_system *system )
if ( !is_Within_GCell( atoms[i].x, ext_box->min, ext_box->max ) )
{
fprintf( stderr, "p%d: ghost atom%d [%f %f %f] is out of my box!\n",
- system->my_rank, i,
- atoms[i].x[0], atoms[i].x[1], atoms[i].x[2] );
+ system->my_rank, i,
+ atoms[i].x[0], atoms[i].x[1], atoms[i].x[2] );
MPI_Abort( MPI_COMM_WORLD, -1 );
}
@@ -628,11 +671,11 @@ void Bin_Boundary_Atoms( reax_system *system )
if ( gc->top != 0 )
{
fprintf( stderr, "p%d bin_boundary_atoms: atom%d map was unexpected! ",
- system->my_rank, i );
+ system->my_rank, i );
fprintf( stderr, "[%f %f %f] --> [%f %f %f] to [%f %f %f]\n",
- atoms[i].x[0], atoms[i].x[1], atoms[i].x[2],
- gc->min[0], gc->min[1], gc->min[2],
- gc->max[0], gc->max[1], gc->max[2] );
+ atoms[i].x[0], atoms[i].x[1], atoms[i].x[2],
+ gc->min[0], gc->min[1], gc->min[2],
+ gc->max[0], gc->max[1], gc->max[2] );
MPI_Abort( MPI_COMM_WORLD, INVALID_INPUT );
}
gc->str = i;
@@ -646,4 +689,4 @@ void Bin_Boundary_Atoms( reax_system *system )
#if defined(DEBUG)
fprintf( stderr, "p%d bin_boundary_atoms: done\n", system->my_rank );
#endif
-}
+ }
diff --git a/PuReMD/src/init_md.c b/PuReMD/src/init_md.c
index 4fac0f1d08a9ab918e29906bc76b13c4c9f83c3c..45cdc2e999a55fb3243058f78620a7cf5f4790f6 100644
--- a/PuReMD/src/init_md.c
+++ b/PuReMD/src/init_md.c
@@ -568,7 +568,7 @@ int Init_Lists( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
mpi_datatypes *mpi_data, char *msg )
{
- int i, num_nbrs, far_nbr_list_format, cm_format;
+ int i, num_nbrs, far_nbr_list_format, cm_format, matrix_dim;
int total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;
MPI_Comm comm;
@@ -631,21 +631,13 @@ int Init_Lists( reax_system *system, control_params *control,
hb_top = (int*) calloc( system->local_cap, sizeof(int) );
//bond_top = (int*) malloc( system->total_cap * sizeof(int) );
//hb_top = (int*) malloc( system->local_cap * sizeof(int) );
+
Estimate_Storages( system, control, lists,
- &Htop, hb_top, bond_top, &num_3body, comm );
+ &Htop, hb_top, bond_top, &num_3body, comm, &matrix_dim );
- Allocate_Matrix( &(workspace->H), system->local_cap, Htop,
- cm_format, comm );
+ Allocate_Matrix( &(workspace->H), matrix_dim, Htop, cm_format, comm );
workspace->L = NULL;
workspace->U = NULL;
-
- //TODO: uncomment for SAI
-// Allocate_Matrix2( &(workspace->H_spar_patt), workspace->H->n, system->local_cap,
-// workspace->H->m, SYM_HALF_MATRIX, comm );
-// Allocate_Matrix( &(workspace->H_spar_patt_full), workspace->H->n,
-// 2 * workspace->H->m - workspace->H->n, SYM_FULL_MATRIX, comm );
-// Allocate_Matrix2( &(workspace->H_app_inv), workspace->H->n, system->local_cap,
-// workspace->H->m, SYM_FULL_MATRIX, comm );
workspace->H_spar_patt = NULL;
workspace->H_app_inv = NULL;
@@ -749,7 +741,7 @@ int Init_Lists( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
mpi_datatypes *mpi_data, char *msg )
{
- int i, num_nbrs;
+ int i, num_nbrs, matrix_dim;
int total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop;
int *hb_top, *bond_top;
int nrecv[MAX_NBRS];
@@ -760,7 +752,7 @@ int Init_Lists( reax_system *system, control_params *control,
bond_top = (int*) calloc( system->total_cap, sizeof(int) );
hb_top = (int*) calloc( system->local_cap, sizeof(int) );
Estimate_Storages( system, control, lists,
- &Htop, hb_top, bond_top, &num_3body, comm );
+ &Htop, hb_top, bond_top, &num_3body, comm, &matrix_dim );
if ( control->hbond_cut > 0 )
{
diff --git a/PuReMD/src/linear_solvers.c b/PuReMD/src/linear_solvers.c
index 98bc9b2923baf2259db4dc3062801b2202e3bcd1..fd068c99f7023b58b37c5c62f4f5f71ee469b03c 100644
--- a/PuReMD/src/linear_solvers.c
+++ b/PuReMD/src/linear_solvers.c
@@ -717,9 +717,6 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
}
}
- //fprintf(stderr, "After dist call, p%d\n", system->my_rank );
- //fflush(stderr);
-
X = (int *) malloc( sizeof(int) * (system->bigN + 1) );
pos_x = (int *) malloc( sizeof(int) * (system->bigN + 1) );
@@ -741,7 +738,7 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
++N;
/* for each of those indices
- * * search through the row of full A of that index */
+ * search through the row of full A of that index */
/* the case where the local matrix has that index's row */
if( j_temp < A->n )
@@ -838,7 +835,7 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
}
/* create the right hand side of the linear equation
- * * that is the full column of the identity matrix */
+ * that is the full column of the identity matrix */
e_j = (real *) malloc( sizeof(real) * M );
for ( k = 0; k < M; ++k )
@@ -928,7 +925,7 @@ void dual_Sparse_MatVec( sparse_matrix *A, rvec2 *x, rvec2 *b, int N )
}
}
}
- else if ( A->format == SYM_FULL_MATRIX )
+ else if ( A->format == SYM_FULL_MATRIX || A->format == FULL_MATRIX )
{
/* perform multiplication */
for ( i = 0; i < A->n; ++i )
@@ -1168,7 +1165,7 @@ void Sparse_MatVec( sparse_matrix *A, real *x, real *b, int N )
}
}
}
- else if ( A->format == SYM_FULL_MATRIX )
+ else if ( A->format == SYM_FULL_MATRIX || A->format == FULL_MATRIX )
{
for ( i = 0; i < A->n; ++i )
{
@@ -1205,16 +1202,19 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
t_start = Get_Time( );
scale = sizeof(real) / sizeof(void);
Dist( system, mpi_data, x, MPI_DOUBLE, scale, real_packer );
+// Dist_NT( system, mpi_data, x, MPI_DOUBLE, scale, real_packer );
t_comm += Get_Timing_Info( t_start );
t_start = Get_Time( );
- Sparse_MatVec( H, x, workspace->q, system->N );
+ //Sparse_MatVec( H, x, workspace->q, system->N );
+ Sparse_MatVec( H, x, workspace->q, H->NT );
t_spmv += Get_Timing_Info( t_start );
if ( H->format == SYM_HALF_MATRIX )
{
t_start = Get_Time( );
Coll( system, mpi_data, workspace->q, MPI_DOUBLE, scale, real_unpacker );
+// Coll_NT( system, mpi_data, workspace->q, MPI_DOUBLE, scale, real_unpacker );
t_comm += Get_Timing_Info( t_start );
}
@@ -1227,10 +1227,12 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
{
t_start = Get_Time( );
Dist( system, mpi_data, workspace->r, MPI_DOUBLE, scale, real_packer );
+// Dist_NT( system, mpi_data, workspace->r, MPI_DOUBLE, scale, real_packer );
t_comm += Get_Timing_Info( t_start );
t_start = Get_Time( );
- Sparse_MatVec( workspace->H_app_inv, workspace->r, workspace->d, system->n );
+ //Sparse_MatVec( workspace->H_app_inv, workspace->r, workspace->d, system->n );
+ Sparse_MatVec( workspace->H_app_inv, workspace->r, workspace->d, H->NT );
t_pa += Get_Timing_Info( t_start );
}
@@ -1253,16 +1255,19 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
{
t_start = Get_Time( );
Dist( system, mpi_data, workspace->d, MPI_DOUBLE, scale, real_packer );
+// Dist_NT( system, mpi_data, workspace->d, MPI_DOUBLE, scale, real_packer );
t_comm += Get_Timing_Info( t_start );
t_start = Get_Time( );
- Sparse_MatVec( H, workspace->d, workspace->q, system->N );
+ //Sparse_MatVec( H, workspace->d, workspace->q, system->N );
+ Sparse_MatVec( H, workspace->d, workspace->q, H->NT );
t_spmv += Get_Timing_Info( t_start );
if ( H->format == SYM_HALF_MATRIX )
{
t_start = Get_Time( );
Coll(system, mpi_data, workspace->q, MPI_DOUBLE, scale, real_unpacker);
+// Coll_NT(system, mpi_data, workspace->q, MPI_DOUBLE, scale, real_unpacker);
t_comm += Get_Timing_Info( t_start );
}
@@ -1281,10 +1286,12 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
{
t_start = Get_Time( );
Dist( system, mpi_data, workspace->r, MPI_DOUBLE, scale, real_packer );
+// Dist_NT( system, mpi_data, workspace->r, MPI_DOUBLE, scale, real_packer );
t_comm += Get_Timing_Info( t_start );
t_start = Get_Time( );
- Sparse_MatVec( workspace->H_app_inv, workspace->r, workspace->p, system->n );
+ //Sparse_MatVec( workspace->H_app_inv, workspace->r, workspace->p, system->n );
+ Sparse_MatVec( workspace->H_app_inv, workspace->r, workspace->p, H->NT );
t_pa += Get_Timing_Info( t_start );
}
diff --git a/PuReMD/src/neighbors.c b/PuReMD/src/neighbors.c
index 96800433bbdb63fa939448e4a4481c34d9e36804..c62af733a8147c5b8704fa4171a10883c8c94b73 100644
--- a/PuReMD/src/neighbors.c
+++ b/PuReMD/src/neighbors.c
@@ -104,6 +104,14 @@ void Generate_Neighbor_Lists( reax_system *system, simulation_data *data,
for (l = gci->str; l < gci->end; ++l )
{
atom1 = &(system->my_atoms[l]);
+ if( gci->type >= NT_NBRS && gci->type < NT_NBRS + 6 )
+ {
+ atom1->nt_dir = gci->type - NT_NBRS;
+ }
+ else
+ {
+ atom1->nt_dir = -1;
+ }
Set_Start_Index( l, num_far, far_nbrs );
//fprintf( stderr, "\tatom %d\n", atom1 );
@@ -205,6 +213,14 @@ int Estimate_NumNeighbors( reax_system *system, reax_list **lists,
for ( l = gci->str; l < gci->end; ++l )
{
atom1 = &(system->my_atoms[l]);
+ if( gci->type >= NT_NBRS && gci->type < NT_NBRS + 6 )
+ {
+ atom1->nt_dir = gci->type - NT_NBRS;
+ }
+ else
+ {
+ atom1->nt_dir = -1;
+ }
//fprintf( stderr, "\tatom %d: ", l );
//tmp = num_far; tested = 0;
itr = 0;
diff --git a/PuReMD/src/parallelreax.c b/PuReMD/src/parallelreax.c
index 894d7fde02ea631ec37a01cc5cbf8c775b5b8e13..660d254e1c00064518ea7383fd0e0bef0b010a82 100644
--- a/PuReMD/src/parallelreax.c
+++ b/PuReMD/src/parallelreax.c
@@ -115,6 +115,11 @@ static void usage(char* argv[])
int main( int argc, char* argv[] )
{
+#if defined(NT_DEBUG)
+ fprintf( stdout, "main beginning\n");
+ fflush( stdout);
+#endif
+
reax_system *system;
control_params *control;
simulation_data *data;
@@ -163,6 +168,10 @@ int main( int argc, char* argv[] )
lists[i]->far_nbr_list = NULL;
lists[i]->hbond_list = NULL;
}
+#if defined(NT_DEBUG)
+ fprintf( stdout, "main reax lists allocated\n");
+ fflush( stdout);
+#endif
out_control = (output_controls *)
smalloc( sizeof(output_controls), "out_control", MPI_COMM_WORLD );
mpi_data = (mpi_datatypes *)
@@ -183,6 +192,10 @@ int main( int argc, char* argv[] )
fprintf( stderr, "p%d: read simulation info\n", system->my_rank );
MPI_Barrier( MPI_COMM_WORLD );
#endif
+#if defined(NT_DEBUG)
+ fprintf( stdout, "main simulatin info read\n");
+ fflush( stdout);
+#endif
/* measure total simulation time after input is read */
if ( system->my_rank == MASTER_NODE )
@@ -190,6 +203,10 @@ int main( int argc, char* argv[] )
/* initialize datastructures */
Initialize( system, control, data, workspace, lists, out_control, mpi_data );
+#if defined(NT_DEBUG)
+ fprintf( stdout, "main data structures initialized\n");
+ fflush( stdout);
+#endif
#if defined(DEBUG)
fprintf( stderr, "p%d: initializated data structures\n", system->my_rank );
@@ -198,12 +215,32 @@ int main( int argc, char* argv[] )
/* compute f_0 */
Comm_Atoms( system, control, data, workspace, lists, mpi_data, 1 );
+#if defined(NT_DEBUG)
+ fprintf( stdout, "main after calling Comm_Atoms\n");
+ fflush( stdout);
+#endif
Reset( system, control, data, workspace, lists, MPI_COMM_WORLD );
+#if defined(NT_DEBUG)
+ fprintf( stdout, "main system is reset\n");
+ fflush( stdout);
+#endif
Generate_Neighbor_Lists( system, data, workspace, lists );
+#if defined(NT_DEBUG)
+ fprintf( stdout, "main neighbor lists are generated\n");
+ fflush( stdout);
+#endif
Compute_Forces( system, control, data, workspace,
lists, out_control, mpi_data );
+#if defined(NT_DEBUG)
+ fprintf( stdout, "main forces are computed\n");
+ fflush( stdout);
+#endif
Compute_Kinetic_Energy( system, data, mpi_data->comm_mesh3D );
Output_Results( system, control, data, lists, out_control, mpi_data );
+#if defined(NT_DEBUG)
+ fprintf( stdout, "main results are written\n");
+ fflush( stdout);
+#endif
#if defined(DEBUG)
fprintf( stderr, "p%d: computed forces at t0\n", system->my_rank );
diff --git a/PuReMD/src/reax_defs.h b/PuReMD/src/reax_defs.h
index 310a46f769ba98f67f6ee4ce22d9fba6b1e30944..0f3b9089aefa559dec4ae4f3c17c340633ef0e98 100644
--- a/PuReMD/src/reax_defs.h
+++ b/PuReMD/src/reax_defs.h
@@ -131,7 +131,7 @@ enum exchanges { NONE = 0, NEAR_EXCH = 1, FULL_EXCH = 2 };
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
+ NATIVE = 8, NT_NBRS = 9 // 9 through 14
};
enum atoms { C_ATOM = 0, H_ATOM = 1, O_ATOM = 2, N_ATOM = 3,
diff --git a/PuReMD/src/reax_types.h b/PuReMD/src/reax_types.h
index 2b08d03e15726c1893cf236dbe22685b1313edea..b42dcd22c5e77ce8506d3c4b43dfa66a75223631 100644
--- a/PuReMD/src/reax_types.h
+++ b/PuReMD/src/reax_types.h
@@ -40,6 +40,7 @@
/************* SOME DEFS - crucial for reax_types.h *********/
#define PURE_REAX
+//#define NT_DEBUG
//#define LAMMPS_REAX
//#define DEBUG
//#define DEBUG_FOCUS
@@ -217,14 +218,7 @@ typedef struct
MPI_Datatype angle_line;
MPI_Datatype angle_view;
- //MPI_Request send_req1[REAX_MAX_NBRS];
- //MPI_Request send_req2[REAX_MAX_NBRS];
- //MPI_Status send_stat1[REAX_MAX_NBRS];
- //MPI_Status send_stat2[REAX_MAX_NBRS];
- //MPI_Status recv_stat1[REAX_MAX_NBRS];
- //MPI_Status recv_stat2[REAX_MAX_NBRS];
-
- 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;
@@ -441,6 +435,8 @@ typedef struct
int num_bonds;
int num_hbonds;
int renumber;
+ int nt_dir;
+ int pos;
} reax_atom;
@@ -891,6 +887,15 @@ typedef struct
} far_neighbor_data;
+typedef struct
+{
+ int nbr;
+ ivec rel_box;
+ real d;
+ rvec dvec;
+} nt_neighbor_data;
+
+
typedef struct
{
int nbr;
@@ -961,7 +966,7 @@ typedef struct
{
/* matrix storage format */
int format;
- int cap, n, m;
+ int cap, n, m, NT;
int *start, *end;
sparse_matrix_entry *entries;
} sparse_matrix;
@@ -1075,6 +1080,7 @@ 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;
@@ -1101,6 +1107,7 @@ typedef struct
dbond_data *dbo_list;
dDelta_data *dDelta_list;
far_neighbor_data *far_nbr_list;
+ nt_neighbor_data *nt_nbr_list;
hbond_data *hbond_list;
} reax_list;
diff --git a/configure.ac b/configure.ac
index 95a0443651267cfed80e6c99245af81a209f7925..830a2ce26a6b8bce71fccc7c059593fa2b7aafb2 100644
--- a/configure.ac
+++ b/configure.ac
@@ -84,9 +84,7 @@ if test "x${DEBUG}" = "xyes"
then
# #TODO: fix exporting to subdirs
# # See: http://stackoverflow.com/questions/34124337/changing-flags-in-configure-ac-vs-caching-with-subprojects
-# CFLAGS="-g3 -O0 -D_GLIBCXX_DEBUG ${CFLAGS}"
- export BUILD_DEBUG="true"
- export DEBUG_FLAGS="-g2 -O0 -D_GLIBCXX_DEBUG"
+ export BUILD_DEBUG="yes"
fi
# gprof flags.