diff --git a/PG-PuReMD/src/box.c b/PG-PuReMD/src/box.c
index 525f24e5cc43f1b50f7bcdaee912b634e2ecfc71..397d5e0daa3b896a8d273f933719747484482264 100644
--- a/PG-PuReMD/src/box.c
+++ b/PG-PuReMD/src/box.c
@@ -204,7 +204,7 @@ void Setup_My_Box( reax_system *system, control_params *control )
for ( d = 0; d < 3; ++d )
{
my_box->min[d] = big_box->box_norms[d] * system->my_coords[d] /
- control->procs_by_dim[d];
+ control->procs_by_dim[d];
my_box->box[d][d] = big_box->box_norms[d] / control->procs_by_dim[d];
//my_box->max[d] = big_box->box_norms[d] * (system->my_coords[d] + 1) /
//control->procs_by_dim[d];
diff --git a/PG-PuReMD/src/control.c b/PG-PuReMD/src/control.c
index 5cb8ce6f1099fde86343d81d8c7b147d41bc4864..4469443cdd8e5f626ee604c7a749f1a6831b8b9f 100644
--- a/PG-PuReMD/src/control.c
+++ b/PG-PuReMD/src/control.c
@@ -161,6 +161,12 @@ char Read_Control_File( char *control_file, control_params* control,
}
else if ( strcmp(tmp[0], "proc_by_dim") == 0 )
{
+ if ( c < 4 )
+ {
+ fprintf( stderr, "invalid number of control file parameters (procs_by_dim). terminating!\n" );
+ MPI_Abort( MPI_COMM_WORLD, INVALID_INPUT );
+ }
+
ival = atoi(tmp[1]);
control->procs_by_dim[0] = ival;
ival = atoi(tmp[2]);
diff --git a/PG-PuReMD/src/geo_tools.c b/PG-PuReMD/src/geo_tools.c
index dff292e74019a18c78daa34519bd15b5246d0224..6ac42e6be6afa355ae85d2431131d69e255d4f5c 100644
--- a/PG-PuReMD/src/geo_tools.c
+++ b/PG-PuReMD/src/geo_tools.c
@@ -162,10 +162,10 @@ char Read_Geo( char* geo_file, reax_system* system, control_params *control,
int Read_Box_Info( reax_system *system, FILE *geo, int geo_format )
{
char *cryst;
- char line[MAX_LINE + 1];
- char descriptor[9];
- char s_a[12], s_b[12], s_c[12], s_alpha[12], s_beta[12], s_gamma[12];
- char s_group[12], s_zValue[12];
+ char line[MAX_LINE + 1];
+ char descriptor[9];
+ char s_a[12], s_b[12], s_c[12], s_alpha[12], s_beta[12], s_gamma[12];
+ char s_group[12], s_zValue[12];
/* initialize variables */
fseek( geo, 0, SEEK_SET ); // set the pointer to the beginning of the file
@@ -181,23 +181,24 @@ int Read_Box_Info( reax_system *system, FILE *geo, int geo_format )
/* locate the cryst line in the geo file, read it and
initialize the big box */
- while ( !feof( geo ) )
+ while ( fgets( line, MAX_LINE, geo ) )
{
- fgets( line, MAX_LINE, geo );
-
if ( strncmp( line, cryst, 6 ) == 0 )
{
if ( geo_format == PDB )
+ {
sscanf( line, PDB_CRYST1_FORMAT,
&descriptor[0],
&s_a[0], &s_b[0], &s_c[0],
&s_alpha[0], &s_beta[0], &s_gamma[0],
&s_group[0], &s_zValue[0] );
+ }
/* compute full volume tensor from the angles */
Setup_Big_Box( atof(s_a), atof(s_b), atof(s_c),
- atof(s_alpha), atof(s_beta), atof(s_gamma),
- &(system->big_box) );
+ atof(s_alpha), atof(s_beta), atof(s_gamma),
+ &(system->big_box) );
+
return SUCCESS;
}
}
@@ -215,13 +216,13 @@ void Count_PDB_Atoms( FILE *geo, reax_system *system )
/* initialize variables */
fseek( geo, 0, SEEK_SET ); /* set the pointer to the beginning of the file */
- system->bigN = system->n = system->N = 0;
+ system->bigN = 0;
+ system->n = 0;
+ system->N = 0;
/* increment number of atoms for each line denoting an atom desc */
- while ( !feof( geo ) )
+ while ( fgets( line, MAX_LINE, geo ) )
{
- fgets( line, MAX_LINE, geo );
-
if ( strncmp( line, "ATOM", 4 ) == 0 ||
strncmp( line, "HETATM", 6 ) == 0 )
{
@@ -239,9 +240,13 @@ void Count_PDB_Atoms( FILE *geo, reax_system *system )
/* if the point is inside my_box, add it to my lists */
if ( is_Inside_Box(&(system->my_box), x) )
+ {
++system->n;
- //if( is_Inside_Box(&(system->my_ext_box), x) )
- // ++system->N;
+ }
+// if ( is_Inside_Box(&(system->my_ext_box), x) )
+// {
+// ++system->N;
+// }
}
}
@@ -307,18 +312,19 @@ char Read_PDB( char* pdb_file, reax_system* system, control_params *control,
fprintf( stderr, "p%d: starting to read the pdb file\n", system->my_rank );
#endif
fseek( pdb, 0, SEEK_SET );
- c = 0;
+ c = 0;
c1 = 0;
top = 0;
- while ( !feof( pdb ) )
+
+ s[0] = 0;
+ for ( i = 0; i < c1; ++i )
{
- /* clear previous input line */
- s[0] = 0;
- for ( i = 0; i < c1; ++i )
- tmp[i][0] = 0;
+ tmp[i][0] = 0;
+ }
+ while ( fgets( s, MAX_LINE, pdb ) )
+ {
/* read new line and tokenize it */
- fgets( s, MAX_LINE, pdb );
strncpy( s1, s, MAX_LINE - 1 );
c1 = Tokenize( s, &tmp );
@@ -400,7 +406,7 @@ char Read_PDB( char* pdb_file, reax_system* system, control_params *control,
Fit_to_Periodic_Box( &(system->big_box), &x );
- if ( is_Inside_Box( &(system->my_box), x ) )
+ if ( is_Inside_Box( &(system->my_box), x ) == TRUE )
{
/* store orig_id, type, name and coord info of the new atom */
atom = &(system->my_atoms[top]);
@@ -474,6 +480,13 @@ char Read_PDB( char* pdb_file, reax_system* system, control_params *control,
// fprintf( stderr, "\n" );
}
}
+
+ /* clear previous input line */
+ s[0] = 0;
+ for ( i = 0; i < c1; ++i )
+ {
+ tmp[i][0] = 0;
+ }
}
fclose( pdb );
diff --git a/PG-PuReMD/src/init_md.c b/PG-PuReMD/src/init_md.c
index d071f0dd3e5175ca55bc00d36a266344b41bd059..63e70dc40c5a3cd5f235fdcb502201a2a3a38335 100644
--- a/PG-PuReMD/src/init_md.c
+++ b/PG-PuReMD/src/init_md.c
@@ -427,7 +427,7 @@ void Init_Workspace( reax_system *system, control_params *control,
/************** setup communication data structures **************/
-int Init_MPI_Datatypes( reax_system *system, storage *workspace,
+void Init_MPI_Datatypes( reax_system *system, storage *workspace,
mpi_datatypes *mpi_data, char *msg )
{
int i, block[11];
@@ -442,12 +442,19 @@ int Init_MPI_Datatypes( reax_system *system, storage *workspace,
/* setup the world */
mpi_data->world = MPI_COMM_WORLD;
- /* mpi_atom - [orig_id, imprt_id, type, num_bonds, num_hbonds, name,
- x, v, f_old, s, t] */
- block[0] = block[1] = block[2] = block[3] = block[4] = 1;
+ /* mpi_atom: orig_id, imprt_id, type, num_bonds, num_hbonds, name,
+ * x, v, f_old, s, t */
+ block[0] = 1;
+ block[1] = 1;
+ block[2] = 1;
+ block[3] = 1;
+ block[4] = 1;
block[5] = MAX_ATOM_NAME_LEN;
- block[6] = block[7] = block[8] = 3;
- block[9] = block[10] = 4;
+ block[6] = 3;
+ block[7] = 3;
+ block[8] = 3;
+ block[9] = 4;
+ block[10] = 4;
// MPI_Get_address( &sample, &base );
// MPI_Get_address( &(sample.orig_id), disp + 0 );
@@ -477,15 +484,27 @@ int Init_MPI_Datatypes( reax_system *system, storage *workspace,
disp[9] = offsetof( mpi_atom, s );
disp[10] = offsetof( mpi_atom, t );
- type[0] = type[1] = type[2] = type[3] = type[4] = MPI_INT;
+ type[0] = MPI_INT;
+ type[1] = MPI_INT;
+ type[2] = MPI_INT;
+ type[3] = MPI_INT;
+ type[4] = MPI_INT;
type[5] = MPI_CHAR;
- type[6] = type[7] = type[8] = type[9] = type[10] = MPI_DOUBLE;
+ type[6] = MPI_DOUBLE;
+ type[7] = MPI_DOUBLE;
+ type[8] = MPI_DOUBLE;
+ type[9] = MPI_DOUBLE;
+ type[10] = MPI_DOUBLE;
MPI_Type_create_struct( 11, block, disp, type, &(mpi_data->mpi_atom_type) );
MPI_Type_commit( &(mpi_data->mpi_atom_type) );
/* boundary_atom - [orig_id, imprt_id, type, num_bonds, num_hbonds, x] */
- block[0] = block[1] = block[2] = block[3] = block[4] = 1;
+ block[0] = 1;
+ block[1] = 1;
+ block[2] = 1;
+ block[3] = 1;
+ block[4] = 1;
block[5] = 3;
// MPI_Get_address( &b_sample, &base );
@@ -506,7 +525,11 @@ int Init_MPI_Datatypes( reax_system *system, storage *workspace,
disp[4] = offsetof( boundary_atom, num_hbonds );
disp[5] = offsetof( boundary_atom, x );
- type[0] = type[1] = type[2] = type[3] = type[4] = MPI_INT;
+ type[0] = MPI_INT;
+ type[1] = MPI_INT;
+ type[2] = MPI_INT;
+ type[3] = MPI_INT;
+ type[4] = MPI_INT;
type[5] = MPI_DOUBLE;
MPI_Type_create_struct( 6, block, disp, type, &(mpi_data->boundary_atom_type) );
@@ -545,9 +568,11 @@ int Init_MPI_Datatypes( reax_system *system, storage *workspace,
MPI_Type_commit( &(mpi_data->mpi_rvec2) );
/* restart_atom - [orig_id, type, name, x, v] */
- block[0] = block[1] = 1 ;
+ block[0] = 1;
+ block[1] = 1 ;
block[2] = MAX_ATOM_NAME_LEN;
- block[3] = block[4] = 3;
+ block[3] = 3;
+ block[4] = 3;
// MPI_Get_address( &r_sample, &base );
// MPI_Get_address( &(r_sample.orig_id), disp + 0 );
@@ -565,14 +590,14 @@ int Init_MPI_Datatypes( reax_system *system, storage *workspace,
disp[3] = offsetof( restart_atom, x );
disp[4] = offsetof( restart_atom, v );
- type[0] = type[1] = MPI_INT;
+ type[0] = MPI_INT;
+ type[1] = MPI_INT;
type[2] = MPI_CHAR;
- type[3] = type[4] = MPI_DOUBLE;
+ type[3] = MPI_DOUBLE;
+ type[4] = MPI_DOUBLE;
MPI_Type_create_struct( 5, block, disp, type, &(mpi_data->restart_atom_type) );
MPI_Type_commit( &(mpi_data->restart_atom_type) );
-
- return SUCCESS;
}
@@ -703,14 +728,7 @@ void Initialize( reax_system *system, control_params *control,
char msg[MAX_STR];
- if ( Init_MPI_Datatypes( system, workspace, mpi_data, msg ) == FAILURE )
- {
- fprintf( stderr, "p%d: init_mpi_datatypes: could not create datatypes\n",
- system->my_rank );
- fprintf( stderr, "p%d: mpi_data couldn't be initialized! terminating.\n",
- system->my_rank );
- MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
- }
+ Init_MPI_Datatypes( system, workspace, mpi_data, msg );
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized mpi datatypes\n", system->my_rank );
@@ -865,14 +883,7 @@ void Initialize( reax_system *system, control_params *control,
fprintf( stderr, "p%d: initialized workspace\n", system->my_rank );
#endif
- if ( Init_MPI_Datatypes( system, workspace, mpi_data, msg ) == FAILURE )
- {
- fprintf( stderr, "p%d: init_mpi_datatypes: could not create datatypes\n",
- system->my_rank );
- fprintf( stderr, "p%d: mpi_data couldn't be initialized! terminating.\n",
- system->my_rank );
- MPI_Abort( MPI_COMM_WORLD, CANNOT_INITIALIZE );
- }
+ Init_MPI_Datatypes( system, workspace, mpi_data, msg );
#if defined(DEBUG)
fprintf( stderr, "p%d: initialized mpi datatypes\n", system->my_rank );
diff --git a/PG-PuReMD/src/init_md.h b/PG-PuReMD/src/init_md.h
index c5222cbd3d2b2a4d2ddef5fe3b976e7d0644ffab..18ec71111056a5e4837680fca0ad03cdc247e622 100644
--- a/PG-PuReMD/src/init_md.h
+++ b/PG-PuReMD/src/init_md.h
@@ -31,7 +31,7 @@ extern "C" {
void Generate_Initial_Velocities( reax_system *, real );
-int Init_MPI_Datatypes( reax_system *, storage *, mpi_datatypes *, char * );
+void Init_MPI_Datatypes( reax_system *, storage *, mpi_datatypes *, char * );
void Initialize( reax_system*, control_params*, simulation_data*,
storage*, reax_list**, output_controls*, mpi_datatypes* );
diff --git a/PG-PuReMD/src/io_tools.c b/PG-PuReMD/src/io_tools.c
index 3cce1777cfea5efff1793db2aa1f7019471b9a04..77b222da1bbfba0d55cc147f4aa6d3ae5bbe7bca 100644
--- a/PG-PuReMD/src/io_tools.c
+++ b/PG-PuReMD/src/io_tools.c
@@ -58,7 +58,9 @@ int Init_Output_Files( reax_system *system, control_params *control,
{
ret = Init_Traj( system, control, out_control, mpi_data, msg );
if ( ret == FAILURE )
+ {
return ret;
+ }
}
if ( system->my_rank == MASTER_NODE )
@@ -470,30 +472,58 @@ int Init_Output_Files( reax_system *system, control_params *control,
/************************ close output files ************************/
-int Close_Output_Files( reax_system *system, control_params *control,
+void Close_Output_Files( reax_system *system, control_params *control,
output_controls *out_control, mpi_datatypes *mpi_data )
{
if ( out_control->write_steps > 0 )
+ {
End_Traj( system->my_rank, out_control );
+ }
if ( system->my_rank == MASTER_NODE )
{
if ( out_control->energy_update_freq > 0 )
{
- fclose( out_control->out );
- fclose( out_control->pot );
+ if ( out_control->out )
+ {
+ fclose( out_control->out );
+ }
+ if ( out_control->pot )
+ {
+ fclose( out_control->pot );
+ }
+
#if defined(LOG_PERFORMANCE)
- fclose( out_control->log );
+ if ( out_control->log )
+ {
+ fclose( out_control->log );
+ }
#endif
}
if ( control->ensemble == NPT || control->ensemble == iNPT ||
control->ensemble == sNPT )
- fclose( out_control->prs );
+ {
+ if ( out_control->prs )
+ {
+ fclose( out_control->prs );
+ }
+ }
- if ( control->dipole_anal ) fclose( out_control->dpl );
- if ( control->diffusion_coef ) fclose( out_control->drft );
- if ( control->molecular_analysis ) fclose( out_control->mol );
+ if ( control->dipole_anal )
+ {
+ fclose( out_control->dpl );
+ }
+
+ if ( control->diffusion_coef )
+ {
+ fclose( out_control->drft );
+ }
+
+ if ( control->molecular_analysis )
+ {
+ fclose( out_control->mol );
+ }
}
#ifdef TEST_ENERGY
@@ -541,8 +571,6 @@ int Close_Output_Files( reax_system *system, control_params *control,
fclose( out_control->nlist );
#endif
#endif
-
- return SUCCESS;
}
@@ -673,8 +701,11 @@ void Print_GCell_Exchange_Bounds( int my_rank, neighbor_proc *my_nbrs )
/* loop over neighbor processes */
for ( r[0] = -1; r[0] <= 1; ++r[0])
+ {
for ( r[1] = -1; r[1] <= 1; ++r[1] )
+ {
for ( r[2] = -1; r[2] <= 1; ++r[2] )
+ {
if ( (nbr = Relative_Coord_Encoding( r )) != MYSELF )
{
nbr_pr = &(my_nbrs[nbr]);
@@ -696,8 +727,11 @@ void Print_GCell_Exchange_Bounds( int my_rank, neighbor_proc *my_nbrs )
nbr_pr->end_recv[0], nbr_pr->end_recv[1],
nbr_pr->end_recv[2] );
}
+ }
+ }
+ }
- fclose(f);
+ fclose( f );
}
@@ -719,7 +753,9 @@ void Print_Native_GCells( reax_system *system )
g = &(system->my_grid);
for ( i = g->native_str[0]; i < g->native_end[0]; i++ )
+ {
for ( j = g->native_str[1]; j < g->native_end[1]; j++ )
+ {
for ( k = g->native_str[2]; k < g->native_end[2]; k++ )
{
gc = &( g->cells[ index_grid_3d(i, j, k, g) ] );
@@ -733,20 +769,24 @@ void Print_Native_GCells( reax_system *system )
//for( l = gc->str; l < gc->end; ++l )
for ( l = g->str[index_grid_3d(i, j, k, g)]; l < g->end[index_grid_3d(i, j, k, g)]; ++l )
+ {
fprintf( f, "%5d", system->my_atoms[l].orig_id );
+ }
fprintf( f, "\n" );
}
+ }
+ }
- fclose(f);
+ fclose( f );
}
void Print_All_GCells( reax_system *system )
{
- int i, j, k, l;
- char fname[100];
- FILE *f;
- grid *g;
+ int i, j, k, l;
+ char fname[100];
+ FILE *f;
+ grid *g;
grid_cell *gc;
char gcell_type_text[10][12] =
{
@@ -759,7 +799,9 @@ void Print_All_GCells( reax_system *system )
g = &(system->my_grid);
for ( i = 0; i < g->ncells[0]; i++ )
+ {
for ( j = 0; j < g->ncells[1]; j++ )
+ {
for ( k = 0; k < g->ncells[2]; k++ )
{
gc = &( g->cells[ index_grid_3d(i, j, k, g) ] );
@@ -773,11 +815,15 @@ void Print_All_GCells( reax_system *system )
//for( l = gc->str; l < gc->end; ++l )
for ( l = g->str[index_grid_3d(i, j, k, g)]; l < g->end[index_grid_3d(i, j, k, g)]; ++l )
+ {
fprintf( f, "%5d", system->my_atoms[l].orig_id );
+ }
fprintf( f, "\n" );
}
+ }
+ }
- fclose(f);
+ fclose( f );
}
@@ -798,12 +844,14 @@ void Print_My_Atoms( reax_system *system )
// system->my_rank, system->n );
for ( i = 0; i < system->n; ++i )
+ {
fprintf( fh, "p%-2d %-5d %2d %24.15e%24.15e%24.15e\n",
system->my_rank,
system->my_atoms[i].orig_id, system->my_atoms[i].type,
system->my_atoms[i].x[0],
system->my_atoms[i].x[1],
system->my_atoms[i].x[2] );
+ }
fclose( fh );
}
@@ -826,12 +874,14 @@ void Print_My_Ext_Atoms( reax_system *system )
// system->my_rank, system->n );
for ( i = 0; i < system->N; ++i )
+ {
fprintf( fh, "p%-2d %-5d imprt%-5d %2d %24.15e%24.15e%24.15e\n",
system->my_rank, system->my_atoms[i].orig_id,
system->my_atoms[i].imprt_id, system->my_atoms[i].type,
system->my_atoms[i].x[0],
system->my_atoms[i].x[1],
system->my_atoms[i].x[2] );
+ }
fclose( fh );
}
@@ -840,13 +890,13 @@ void Print_My_Ext_Atoms( reax_system *system )
void Print_Far_Neighbors( reax_system *system, reax_list **lists,
control_params *control )
{
- char fname[100];
- int i, j, id_i, id_j, nbr, natoms;
+ char fname[100];
+ int i, j, id_i, id_j, nbr, natoms;
FILE *fout;
reax_list *far_nbrs;
sprintf( fname, "%s.far_nbrs.%d", control->sim_name, system->my_rank );
- fout = fopen( fname, "w" );
+ fout = fopen( fname, "w" );
far_nbrs = (*lists) + FAR_NBRS;
natoms = system->N;
@@ -996,14 +1046,16 @@ void Print_LinSys_Soln( reax_system *system, real *x, real *b_prm, real *b )
{
int i;
char fname[100];
- FILE *fout;
+ FILE *fout;
sprintf( fname, "qeq.%d.out", system->my_rank );
fout = fopen( fname, "w" );
for ( i = 0; i < system->n; ++i )
+ {
fprintf( fout, "%6d%10.4f%10.4f%10.4f\n",
system->my_atoms[i].orig_id, x[i], b_prm[i], b[i] );
+ }
fclose( fout );
}
@@ -1011,19 +1063,21 @@ void Print_LinSys_Soln( reax_system *system, real *x, real *b_prm, real *b )
void Print_Charges( reax_system *system )
{
- int i;
- char fname[100];
- FILE *fout;
+ int i;
+ char fname[100];
+ FILE *fout;
sprintf( fname, "q.%d.out", system->my_rank );
fout = fopen( fname, "w" );
for ( i = 0; i < system->n; ++i )
+ {
fprintf( fout, "%6d %10.7f %10.7f %10.7f\n",
system->my_atoms[i].orig_id,
system->my_atoms[i].s[0],
system->my_atoms[i].t[0],
system->my_atoms[i].q );
+ }
fclose( fout );
}
@@ -1134,12 +1188,16 @@ void Print_Bond_List2( reax_system *system, reax_list *bonds, char *fname )
nbr = bonds->select.bond_list[pj].nbr;
id_j = system->my_atoms[nbr].orig_id;
if ( id_i < id_j )
+ {
temp[num++] = id_j;
+ }
}
- qsort(&temp, num, sizeof(int), fn_qsort_intcmp);
- for (j = 0; j < num; j++)
+ qsort( &temp, num, sizeof(int), fn_qsort_intcmp );
+ for ( j = 0; j < num; j++ )
+ {
fprintf(f, "%6d", temp[j] );
+ }
fprintf(f, "\n");
}
}
@@ -1255,7 +1313,7 @@ void Output_Results( reax_system *system, control_params *control,
data->tot_press[0], data->tot_press[1], data->tot_press[2],
system->big_box.V );
- fflush( out_control->prs);
+ fflush( out_control->prs );
}
fflush( out_control->out );
diff --git a/PG-PuReMD/src/io_tools.h b/PG-PuReMD/src/io_tools.h
index f83c9686400a03a70e35a06f777b1a9965e0f02e..cb69ad0501a020bccf6bdd21f4f5f8c1c0054c94 100644
--- a/PG-PuReMD/src/io_tools.h
+++ b/PG-PuReMD/src/io_tools.h
@@ -32,7 +32,7 @@ extern "C" {
int Init_Output_Files( reax_system*, control_params*,
output_controls*, mpi_datatypes*, char* );
-int Close_Output_Files( reax_system*, control_params*,
+void Close_Output_Files( reax_system*, control_params*,
output_controls*, mpi_datatypes* );
void Print_Box( simulation_box*, char*, FILE* );
diff --git a/PG-PuReMD/src/parallelreax.c b/PG-PuReMD/src/parallelreax.c
index da9074127fec719403a9ea0e892961314c7a7b29..3b3757f186b619540d9cd18cc117ffca0738d028 100644
--- a/PG-PuReMD/src/parallelreax.c
+++ b/PG-PuReMD/src/parallelreax.c
@@ -183,10 +183,12 @@ int main( int argc, char* argv[] )
real t_begin, t_end;
#endif
+ MPI_Init( &argc, &argv );
+
if ( argc != 4 )
{
usage( argv );
- exit( INVALID_INPUT );
+ MPI_Abort( MPI_COMM_WORLD, INVALID_INPUT );
}
#ifdef HAVE_CUDA
@@ -228,7 +230,6 @@ int main( int argc, char* argv[] )
}
/* setup MPI environment */
- MPI_Init( &argc, &argv );
MPI_Comm_size( MPI_COMM_WORLD, &(control->nprocs) );
MPI_Comm_rank( MPI_COMM_WORLD, &(system->my_rank) );
@@ -443,7 +444,6 @@ int main( int argc, char* argv[] )
}
/* setup MPI environment */
- MPI_Init( &argc, &argv );
MPI_Comm_size( MPI_COMM_WORLD, &(control->nprocs) );
MPI_Comm_rank( MPI_COMM_WORLD, &(system->my_rank) );
@@ -561,17 +561,6 @@ int main( int argc, char* argv[] )
// Write_PDB( &system, &(lists[BOND]), &out_control );
Close_Output_Files( system, control, out_control, mpi_data );
- MPI_Finalize( );
-
- /* deallocate data structures */
- sfree( system, "main::system" );
- sfree( control, "main::control" );
- sfree( data, "main::data" );
- sfree( workspace, "main::workspace" );
- sfree( lists, "main::lists" );
- sfree( out_control, "main::out_control" );
- sfree( mpi_data, "main::mpi_data" );
-
#if defined(TEST_ENERGY) || defined(TEST_FORCES)
// Integrate_Results(control);
#endif
@@ -580,5 +569,24 @@ int main( int argc, char* argv[] )
fprintf( stderr, "p%d has reached the END\n", system->my_rank );
#endif
+ MPI_Finalized( &ret );
+ if ( !ret )
+ {
+ MPI_Finalize( );
+ }
+
+ /* deallocate data structures */
+ sfree( mpi_data, "main::mpi_data" );
+ sfree( out_control, "main::out_control" );
+ for ( i = 0; i < LIST_N; ++i )
+ {
+ sfree( lists[i], "main::lists[i]" );
+ }
+ sfree( lists, "main::lists" );
+ sfree( workspace, "main::workspace" );
+ sfree( data, "main::data" );
+ sfree( control, "main::control" );
+ sfree( system, "main::system" );
+
return 0;
}