void Reset_Pressures( simulation_data *data )
{
data->flex_bar.P_scalar = 0;
rtensor_MakeZero( data->flex_bar.P );
data->iso_bar.P = 0;
rvec_MakeZero( data->int_press );
rvec_MakeZero( data->my_ext_press );
rvec_MakeZero( data->ext_press );
}
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] );
}
}
}
/************************ initialize system ************************/
int Reposition_Atoms( reax_system *system, control_params *control,
simulation_data *data, mpi_datatypes *mpi_data,
char *msg )
{
int i;
rvec dx;
/* reposition atoms */
if( control->reposition_atoms == 0 ) { //fit atoms to periodic box
rvec_MakeZero( dx );
}
else if( control->reposition_atoms == 1 ) { //put center of mass to center
rvec_Scale( dx, 0.5, system->big_box.box_norms );
rvec_ScaledAdd( dx, -1., data->xcm );
}
else if( control->reposition_atoms == 2 ) { //put center of mass to origin
rvec_Scale( dx, -1., data->xcm );
}
else {
strcpy( msg, "reposition_atoms: invalid option" );
return FAILURE;
}
for( i = 0; i < system->n; ++i )
// Inc_on_T3_Gen( system->my_atoms[i].x, dx, &(system->big_box) );
rvec_Add( system->my_atoms[i].x, dx );
return SUCCESS;
}
void Compute_Pressure(reax_system* system, control_params *control,
simulation_data* data, mpi_datatypes *mpi_data)
{
int i;
reax_atom *p_atom;
rvec tmp, tx, int_press;
simulation_box *big_box = &(system->big_box);
/* Calculate internal pressure */
rvec_MakeZero( int_press );
// 0: both int and ext, 1: ext only, 2: int only
if( control->press_mode == 0 || control->press_mode == 2 ) {
for( i = 0; i < system->n; ++i ) {
p_atom = &( system->my_atoms[i] );
/* transform x into unitbox coordinates */
Transform_to_UnitBox( p_atom->x, big_box, 1, tx );
/* this atom's contribution to internal pressure */
rvec_Multiply( tmp, p_atom->f, tx );
rvec_Add( int_press, tmp );
}
}
/* sum up internal and external pressure */
MPI_Allreduce( int_press, data->int_press,
3, MPI_DOUBLE, MPI_SUM, mpi_data->comm_mesh3D );
MPI_Allreduce( data->my_ext_press, data->ext_press,
3, MPI_DOUBLE, MPI_SUM, mpi_data->comm_mesh3D );
/* kinetic contribution */
data->kin_press = 2.*(E_CONV*data->sys_en.e_kin) / (3.*big_box->V*P_CONV);
/* Calculate total pressure in each direction */
data->tot_press[0] = data->kin_press -
(( data->int_press[0] + data->ext_press[0] ) /
( big_box->box_norms[1] * big_box->box_norms[2] * P_CONV ));
data->tot_press[1] = data->kin_press -
(( data->int_press[1] + data->ext_press[1] ) /
( big_box->box_norms[0] * big_box->box_norms[2] * P_CONV ));
data->tot_press[2] = data->kin_press -
(( data->int_press[2] + data->ext_press[2] ) /
( big_box->box_norms[0] * big_box->box_norms[1] * P_CONV ));
data->iso_bar.P =
( data->tot_press[0] + data->tot_press[1] + data->tot_press[2] ) / 3.;
}
void Calculate_Dipole_Moment( reax_system *system, control_params *control,
simulation_data *data, static_storage *workspace,
list *bonds, FILE *fout )
{
int i, atom, count;
molecule m;
real mu_sum;
rvec tmpvec, mu;
int *mark = workspace->mark;
//fprintf( fout, "starting dipole moment calculations...\n" );
mu_sum = 0;
count = 0;
for( atom = 0; atom < system->N; ++atom )
/* start discovering water molecules from the central O atom */
if( !mark[atom] && system->atoms[atom].type == 2 ) {
rvec_MakeZero( mu );
memset( &m, 0, sizeof(molecule) );
Get_Molecule( atom, &m, mark, system, control, bonds, 0, fout );
if( Get_Type_of_Molecule( &m ) == WATER ) {
++count;
for( i = 1; i < 2; ++i ) {
Distance_on_T3_Gen( system->atoms[ m.atom_list[0] ].x,
system->atoms[ m.atom_list[i] ].x,
&(system->box), tmpvec );
rvec_ScaledAdd( mu, -system->atoms[m.atom_list[0]].q / 2.0, tmpvec );
}
mu_sum += rvec_Norm( mu );
}
}
fprintf( fout, "%7d %10d %10.5f\n",
data->step, count, mu_sum / count * ECxA_to_DEBYE );
fflush( fout );
}
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 );
}
/* IMPORTANT: This function assumes that current kinetic energy
* the system is already computed
*
* IMPORTANT: In Klein's paper, it is stated that a dU/dV term needs
* to be added when there are long-range interactions or long-range
* corrections to short-range interactions present.
* We may want to add that for more accuracy.
*/
void Compute_Pressure(reax_system* system, control_params *control,
simulation_data* data, mpi_datatypes *mpi_data)
{
int i;
reax_atom *p_atom;
rvec tmp, tx, int_press;
simulation_box *big_box = &(system->big_box);
/* Calculate internal pressure */
rvec_MakeZero( int_press );
// 0: both int and ext, 1: ext only, 2: int only
if( control->press_mode == 0 || control->press_mode == 2 ) {
for( i = 0; i < system->n; ++i ) {
p_atom = &( system->my_atoms[i] );
/* transform x into unitbox coordinates */
Transform_to_UnitBox( p_atom->x, big_box, 1, tx );
/* this atom's contribution to internal pressure */
rvec_Multiply( tmp, p_atom->f, tx );
rvec_Add( int_press, tmp );
#if defined(DEBUG)
fprintf( stderr, "%8d%8.2f%8.2f%8.2f",
i+1, p_atom->x[0], p_atom->x[1], p_atom->x[2] );
fprintf( stderr, "%8.2f%8.2f%8.2f",
p_atom->f[0], p_atom->f[1], p_atom->f[2] );
fprintf( stderr, "%8.2f%8.2f%8.2f\n",
int_press[0], int_press[1], int_press[2] );
#endif
}
}
/* sum up internal and external pressure */
#if defined(DEBUG)
fprintf(stderr,"p%d:p_int(%10.5f %10.5f %10.5f)p_ext(%10.5f %10.5f %10.5f)\n",
system->my_rank, int_press[0], int_press[1], int_press[2],
data->my_ext_press[0], data->my_ext_press[1], data->my_ext_press[2] );
#endif
MPI_Allreduce( int_press, data->int_press,
3, MPI_DOUBLE, MPI_SUM, mpi_data->comm_mesh3D );
MPI_Allreduce( data->my_ext_press, data->ext_press,
3, MPI_DOUBLE, MPI_SUM, mpi_data->comm_mesh3D );
#if defined(DEBUG)
fprintf( stderr, "p%d: %10.5f %10.5f %10.5f\n",
system->my_rank,
data->int_press[0], data->int_press[1], data->int_press[2] );
fprintf( stderr, "p%d: %10.5f %10.5f %10.5f\n",
system->my_rank,
data->ext_press[0], data->ext_press[1], data->ext_press[2] );
#endif
/* kinetic contribution */
data->kin_press = 2.*(E_CONV*data->sys_en.e_kin) / (3.*big_box->V*P_CONV);
/* Calculate total pressure in each direction */
data->tot_press[0] = data->kin_press -
(( data->int_press[0] + data->ext_press[0] ) /
( big_box->box_norms[1] * big_box->box_norms[2] * P_CONV ));
data->tot_press[1] = data->kin_press -
(( data->int_press[1] + data->ext_press[1] ) /
( big_box->box_norms[0] * big_box->box_norms[2] * P_CONV ));
data->tot_press[2] = data->kin_press -
(( data->int_press[2] + data->ext_press[2] ) /
( big_box->box_norms[0] * big_box->box_norms[1] * P_CONV ));
/* Average pressure for the whole box */
data->iso_bar.P =
( data->tot_press[0] + data->tot_press[1] + data->tot_press[2] ) / 3.;
}