void Generate_Initial_Velocities( reax_system *system, real T )
{
int i;
real m, scale, norm;
if( T <= 0.1 ) {
for( i = 0; i < system->n; i++ )
rvec_MakeZero( system->my_atoms[i].v );
}
else {
Randomize();
for( i = 0; i < system->n; i++ ) {
rvec_Random( system->my_atoms[i].v );
norm = rvec_Norm_Sqr( system->my_atoms[i].v );
m = system->reax_param.sbp[ system->my_atoms[i].type ].mass;
scale = sqrt( m * norm / (3.0 * K_B * T) );
rvec_Scale( system->my_atoms[i].v, 1./scale, system->my_atoms[i].v );
// fprintf( stderr, "v = %f %f %f\n",
// system->my_atoms[i].v[0],
// system->my_atoms[i].v[1],
// system->my_atoms[i].v[2] );
// fprintf( stderr, "scale = %f\n", scale );
// fprintf( stderr, "v = %f %f %f\n",
// system->my_atoms[i].v[0],
// system->my_atoms[i].v[1],
// system->my_atoms[i].v[2] );
}
}
}
void Calculate_Drift( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
FILE *fout )
{
int i, type;
int count[MAX_ATOM_TYPES];
real drift;
rvec driftvec;
real sum_sqr_drift[MAX_ATOM_TYPES], sum_drift[MAX_ATOM_TYPES];
for( i = 0; i < MAX_ATOM_TYPES; ++i )
{
count[i] = 0;
sum_sqr_drift[i] = sum_drift[i] = 0.0;
}
for( i = 0; i < system->N; ++i )
//if( control->restrict_type == -1 ||
// system->atoms[i].type == control->restrict_type )
if( workspace->x_old[i][0] > -system->box.box_norms[0] &&
workspace->x_old[i][1] > -system->box.box_norms[1] &&
workspace->x_old[i][2] > -system->box.box_norms[2] )
{
type = system->atoms[i].type;
++count[type];
Distance_on_T3_Gen( workspace->x_old[i], system->atoms[i].x,
&(system->box), driftvec );
if( fabs( driftvec[0] ) >= system->box.box_norms[0] / 2.0 - 2.0 ||
fabs( driftvec[0] ) >= system->box.box_norms[0] / 2.0 - 2.0 ||
fabs( driftvec[0] ) >= system->box.box_norms[0] / 2.0 - 2.0 ) {
/* the atom has moved almost half the box size.
exclude it from further drift computations as it might have an
improper contribution due to periodic boudnaries. */
workspace->x_old[i][0] = workspace->x_old[i][2] =
workspace->x_old[i][2] = -999999999999.0;
continue;
}
drift = rvec_Norm_Sqr( driftvec );
sum_sqr_drift[type] += drift;
sum_drift[type] += SQRT( drift );
}
fprintf( fout, "%7d oxy %6d %10.6f\n",
data->step, count[2], sum_sqr_drift[2] / count[2] );
fprintf( fout, "%7d hyd %6d %10.6f\n",
data->step, count[1], sum_sqr_drift[1] / count[1] );
fflush( fout );
}
void Init_Forces_noQEq( reax_system *system, control_params *control,
simulation_data *data, storage *workspace,
reax_list **lists, output_controls *out_control,
MPI_Comm comm ) {
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
int btop_i, btop_j, num_bonds, num_hbonds;
int ihb, jhb, ihb_top, jhb_top;
int local, flag, renbr;
double cutoff;
reax_list *far_nbrs, *bonds, *hbonds;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
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 ) {
workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance
}
num_bonds = 0;
num_hbonds = 0;
btop_i = btop_j = 0;
renbr = (data->step-data->prev_steps) % control->reneighbor == 0;
for( i = 0; i < system->N; ++i ) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
if (type_i < 0) continue;
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
btop_i = End_Index( i, bonds );
sbp_i = &(system->reax_param.sbp[type_i]);
if( i < system->n ) {
local = 1;
cutoff = MAX( control->hbond_cut, control->bond_cut );
}
else {
local = 0;
cutoff = control->bond_cut;
}
ihb = -1;
ihb_top = -1;
if( local && control->hbond_cut > 0 ) {
ihb = sbp_i->p_hbond;
if( ihb == 1 )
ihb_top = End_Index( atom_i->Hindex, hbonds );
else ihb_top = -1;
}
/* update i-j distance - check if j is within cutoff */
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
if( renbr ) {
if( nbr_pj->d <= cutoff )
flag = 1;
else flag = 0;
}
else{
nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0];
nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1];
nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2];
nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec );
if( nbr_pj->d <= SQR(cutoff) ) {
nbr_pj->d = sqrt(nbr_pj->d);
flag = 1;
}
else {
flag = 0;
}
}
if( flag ) {
type_j = atom_j->type;
if (type_j < 0) continue;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
if( local ) {
/* hydrogen bond lists */
if( control->hbond_cut > 0 && (ihb==1 || ihb==2) &&
nbr_pj->d <= control->hbond_cut ) {
// fprintf( stderr, "%d %d\n", atom1, atom2 );
jhb = sbp_j->p_hbond;
if( ihb == 1 && jhb == 2 ) {
hbonds->select.hbond_list[ihb_top].nbr = j;
hbonds->select.hbond_list[ihb_top].scl = 1;
hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
++ihb_top;
++num_hbonds;
}
else if( j < system->n && ihb == 2 && jhb == 1 ) {
jhb_top = End_Index( atom_j->Hindex, hbonds );
hbonds->select.hbond_list[jhb_top].nbr = i;
hbonds->select.hbond_list[jhb_top].scl = -1;
hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
Set_End_Index( atom_j->Hindex, jhb_top+1, hbonds );
++num_hbonds;
}
}
}
if( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
nbr_pj->d <= control->bond_cut &&
BOp( workspace, bonds, control->bo_cut,
i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
num_bonds += 2;
++btop_i;
if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 ) {
workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
}
}
}
}
Set_End_Index( i, btop_i, bonds );
if( local && ihb == 1 )
Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
}
workspace->realloc.num_bonds = num_bonds;
workspace->realloc.num_hbonds = num_hbonds;
Validate_Lists( system, workspace, lists, data->step,
system->n, system->N, system->numH, comm );
}
void Init_Forces( reax_system *system, control_params *control,
simulation_data *data, storage *workspace, reax_list **lists,
output_controls *out_control, MPI_Comm comm ) {
int i, j, pj;
int start_i, end_i;
int type_i, type_j;
int Htop, btop_i, btop_j, num_bonds, num_hbonds;
int ihb, jhb, ihb_top, jhb_top;
int local, flag, renbr;
real r_ij, cutoff;
sparse_matrix *H;
reax_list *far_nbrs, *bonds, *hbonds;
single_body_parameters *sbp_i, *sbp_j;
two_body_parameters *twbp;
far_neighbor_data *nbr_pj;
reax_atom *atom_i, *atom_j;
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 ) {
workspace->bond_mark[i] = 1000; // put ghost atoms to an infinite distance
//workspace->done_after[i] = Start_Index( i, far_nbrs );
}
H = workspace->H;
H->n = system->n;
Htop = 0;
num_bonds = 0;
num_hbonds = 0;
btop_i = btop_j = 0;
renbr = (data->step-data->prev_steps) % control->reneighbor == 0;
for( i = 0; i < system->N; ++i ) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
start_i = Start_Index(i, far_nbrs);
end_i = End_Index(i, far_nbrs);
btop_i = End_Index( i, bonds );
sbp_i = &(system->reax_param.sbp[type_i]);
if( i < system->n ) {
local = 1;
cutoff = control->nonb_cut;
}
else {
local = 0;
cutoff = control->bond_cut;
}
ihb = -1;
ihb_top = -1;
if( local ) {
H->start[i] = Htop;
H->entries[Htop].j = i;
H->entries[Htop].val = sbp_i->eta;
++Htop;
if( control->hbond_cut > 0 ) {
ihb = sbp_i->p_hbond;
if( ihb == 1 )
ihb_top = End_Index( atom_i->Hindex, hbonds );
else ihb_top = -1;
}
}
/* update i-j distance - check if j is within cutoff */
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
atom_j = &(system->my_atoms[j]);
//fprintf( stderr, "%d%d i=%d x_i: %f %f %f,j=%d x_j: %f %f %f, d=%f\n",
// MIN(atom_i->orig_id, atom_j->orig_id),
// MAX(atom_i->orig_id, atom_j->orig_id),
// i, atom_i->x[0], atom_i->x[1], atom_i->x[2],
// j, atom_j->x[0], atom_j->x[1], atom_j->x[2], nbr_pj->d );
if( renbr ) {
if(nbr_pj->d <= cutoff)
flag = 1;
else flag = 0;
}
else{
nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0];
nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1];
nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2];
nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec );
if( nbr_pj->d <= SQR(cutoff) ) {
nbr_pj->d = sqrt(nbr_pj->d);
flag = 1;
}
else {
flag = 0;
}
}
if( flag ){
type_j = atom_j->type;
r_ij = nbr_pj->d;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
if( local ) {
/* H matrix entry */
if( j < system->n || atom_i->orig_id < atom_j->orig_id ) {//tryQEq||1
H->entries[Htop].j = j;
//fprintf( stdout, "%d%d %d %d\n",
// MIN(atom_i->orig_id, atom_j->orig_id),
// MAX(atom_i->orig_id, atom_j->orig_id),
// MIN(atom_i->orig_id, atom_j->orig_id),
// MAX(atom_i->orig_id, atom_j->orig_id) );
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 */
if( control->hbond_cut > 0 && (ihb==1 || ihb==2) &&
nbr_pj->d <= control->hbond_cut ) {
// fprintf( stderr, "%d %d\n", atom1, atom2 );
jhb = sbp_j->p_hbond;
if( ihb == 1 && jhb == 2 ) {
hbonds->select.hbond_list[ihb_top].nbr = j;
hbonds->select.hbond_list[ihb_top].scl = 1;
hbonds->select.hbond_list[ihb_top].ptr = nbr_pj;
++ihb_top;
++num_hbonds;
}
else if( j < system->n && ihb == 2 && jhb == 1 ) {
jhb_top = End_Index( atom_j->Hindex, hbonds );
hbonds->select.hbond_list[jhb_top].nbr = i;
hbonds->select.hbond_list[jhb_top].scl = -1;
hbonds->select.hbond_list[jhb_top].ptr = nbr_pj;
Set_End_Index( atom_j->Hindex, jhb_top+1, hbonds );
++num_hbonds;
}
}
}
/* uncorrected bond orders */
if( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) &&
nbr_pj->d <= control->bond_cut &&
BOp( workspace, bonds, control->bo_cut,
i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
num_bonds += 2;
++btop_i;
if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 ) {
workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
//if( workspace->bond_mark[i] == 1000 )
// workspace->done_after[i] = pj;
}
//fprintf( stdout, "%d%d - %d(%d) %d(%d)\n",
// i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
}
}
}
Set_End_Index( i, btop_i, bonds );
if( local ) {
H->end[i] = Htop;
if( ihb == 1 )
Set_End_Index( atom_i->Hindex, ihb_top, hbonds );
}
}
//fprintf( stderr, "after the first init loop\n" );
/*for( i = system->n; i < system->N; ++i )
if( workspace->bond_mark[i] > 3 ) {
start_i = Start_Index(i, bonds);
end_i = End_Index(i, bonds);
num_bonds -= (end_i - start_i);
Set_End_Index(i, start_i, bonds );
}*/
/*for( i = system->n; i < system->N; ++i ) {
start_i = Start_Index(i, far_nbrs);
end_i = workspace->done_after[i];
if( workspace->bond_mark[i] >= 2 && start_i < end_i ) {
atom_i = &(system->my_atoms[i]);
type_i = atom_i->type;
btop_i = End_Index( i, bonds );
sbp_i = &(system->reax_param.sbp[type_i]);
for( pj = start_i; pj < end_i; ++pj ) {
nbr_pj = &( far_nbrs->select.far_nbr_list[pj] );
j = nbr_pj->nbr;
if( workspace->bond_mark[j] >= 2 && nbr_pj->d <= control->bond_cut ) {
atom_j = &(system->my_atoms[j]);
type_j = atom_j->type;
sbp_j = &(system->reax_param.sbp[type_j]);
twbp = &(system->reax_param.tbp[type_i][type_j]);
if( BOp( workspace, bonds, control->bo_cut,
i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) {
num_bonds += 2;
++btop_i;
if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 )
workspace->bond_mark[j] = workspace->bond_mark[i] + 1;
else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 )
workspace->bond_mark[i] = workspace->bond_mark[j] + 1;
//fprintf( stdout, "%d%d - %d(%d) %d(%d) new\n",
// i , j, i, workspace->bond_mark[i], j, workspace->bond_mark[j] );
}
}
}
Set_End_Index( i, btop_i, bonds );
}
}*/
workspace->realloc.Htop = Htop;
workspace->realloc.num_bonds = num_bonds;
workspace->realloc.num_hbonds = num_hbonds;
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: Htop = %d num_bonds = %d num_hbonds = %d\n",
system->my_rank, data->step, Htop, num_bonds, num_hbonds );
MPI_Barrier( comm );
#endif
#if defined( DEBUG )
Print_Bonds( system, bonds, "debugbonds.out" );
Print_Bond_List2( system, bonds, "pbonds.out" );
Print_Sparse_Matrix( system, H );
for( i = 0; i < H->n; ++i )
for( j = H->start[i]; j < H->end[i]; ++j )
fprintf( stderr, "%d %d %.15e\n",
MIN(system->my_atoms[i].orig_id,
system->my_atoms[H->entries[j].j].orig_id),
MAX(system->my_atoms[i].orig_id,
system->my_atoms[H->entries[j].j].orig_id),
H->entries[j].val );
#endif
Validate_Lists( system, workspace, lists, data->step,
system->n, system->N, system->numH, comm );
}
void Compute_Center_of_Mass( reax_system *system, simulation_data *data,
mpi_datatypes *mpi_data, MPI_Comm comm )
{
int i;
double m, det; //xx, xy, xz, yy, yz, zz;
double tmp_mat[6], tot_mat[6];
rvec my_xcm, my_vcm, my_amcm, my_avcm;
rvec tvec, diff;
rtensor mat, inv;
rvec_MakeZero( my_xcm ); // position of CoM
rvec_MakeZero( my_vcm ); // velocity of CoM
rvec_MakeZero( my_amcm ); // angular momentum of CoM
rvec_MakeZero( my_avcm ); // angular velocity of CoM
/* Compute the position, vel. and ang. momentum about the centre of mass */
for( i = 0; i < system->n; ++i ) {
m = system->reax_param.sbp[ system->my_atoms[i].type ].mass;
rvec_ScaledAdd( my_xcm, m, system->my_atoms[i].x );
rvec_ScaledAdd( my_vcm, m, system->my_atoms[i].v );
rvec_Cross( tvec, system->my_atoms[i].x, system->my_atoms[i].v );
rvec_ScaledAdd( my_amcm, m, tvec );
}
MPI_Allreduce( my_xcm, data->xcm, 3, MPI_DOUBLE, MPI_SUM, comm );
MPI_Allreduce( my_vcm, data->vcm, 3, MPI_DOUBLE, MPI_SUM, comm );
MPI_Allreduce( my_amcm, data->amcm, 3, MPI_DOUBLE, MPI_SUM, comm );
rvec_Scale( data->xcm, data->inv_M, data->xcm );
rvec_Scale( data->vcm, data->inv_M, data->vcm );
rvec_Cross( tvec, data->xcm, data->vcm );
rvec_ScaledAdd( data->amcm, -data->M, tvec );
data->etran_cm = 0.5 * data->M * rvec_Norm_Sqr( data->vcm );
/* Calculate and then invert the inertial tensor */
for( i = 0; i < 6; ++i )
tmp_mat[i] = 0;
//my_xx = my_xy = my_xz = my_yy = my_yz = my_zz = 0;
for( i = 0; i < system->n; ++i ){
m = system->reax_param.sbp[ system->my_atoms[i].type ].mass;
rvec_ScaledSum( diff, 1., system->my_atoms[i].x, -1., data->xcm );
tmp_mat[0]/*my_xx*/ += diff[0] * diff[0] * m;
tmp_mat[1]/*my_xy*/ += diff[0] * diff[1] * m;
tmp_mat[2]/*my_xz*/ += diff[0] * diff[2] * m;
tmp_mat[3]/*my_yy*/ += diff[1] * diff[1] * m;
tmp_mat[4]/*my_yz*/ += diff[1] * diff[2] * m;
tmp_mat[5]/*my_zz*/ += diff[2] * diff[2] * m;
}
MPI_Reduce( tmp_mat, tot_mat, 6, MPI_DOUBLE, MPI_SUM, MASTER_NODE, comm );
if( system->my_rank == MASTER_NODE ) {
mat[0][0] = tot_mat[3] + tot_mat[5]; // yy + zz;
mat[0][1] = mat[1][0] = -tot_mat[1]; // -xy;
mat[0][2] = mat[2][0] = -tot_mat[2]; // -xz;
mat[1][1] = tot_mat[0] + tot_mat[5]; // xx + zz;
mat[2][1] = mat[1][2] = -tot_mat[4]; // -yz;
mat[2][2] = tot_mat[0] + tot_mat[3]; // xx + yy;
/* invert the inertial tensor */
det = ( mat[0][0] * mat[1][1] * mat[2][2] +
mat[0][1] * mat[1][2] * mat[2][0] +
mat[0][2] * mat[1][0] * mat[2][1] ) -
( mat[0][0] * mat[1][2] * mat[2][1] +
mat[0][1] * mat[1][0] * mat[2][2] +
mat[0][2] * mat[1][1] * mat[2][0] );
inv[0][0] = mat[1][1] * mat[2][2] - mat[1][2] * mat[2][1];
inv[0][1] = mat[0][2] * mat[2][1] - mat[0][1] * mat[2][2];
inv[0][2] = mat[0][1] * mat[1][2] - mat[0][2] * mat[1][1];
inv[1][0] = mat[1][2] * mat[2][0] - mat[1][0] * mat[2][2];
inv[1][1] = mat[0][0] * mat[2][2] - mat[0][2] * mat[2][0];
inv[1][2] = mat[0][2] * mat[1][0] - mat[0][0] * mat[1][2];
inv[2][0] = mat[1][0] * mat[2][1] - mat[2][0] * mat[1][1];
inv[2][1] = mat[2][0] * mat[0][1] - mat[0][0] * mat[2][1];
inv[2][2] = mat[0][0] * mat[1][1] - mat[1][0] * mat[0][1];
if( det > ALMOST_ZERO )
rtensor_Scale( inv, 1./det, inv );
else rtensor_MakeZero( inv );
/* Compute the angular velocity about the centre of mass */
rtensor_MatVec( data->avcm, inv, data->amcm );
}
MPI_Bcast( data->avcm, 3, MPI_DOUBLE, MASTER_NODE, comm );
/* Compute the rotational energy */
data->erot_cm = 0.5 * E_CONV * rvec_Dot( data->avcm, data->amcm );
}