/* Initialize libstokes
* Basic parameters for the libstorks
* and pos[] are set from init_aggregate.
*/
void System::initLibStokes(){
if (init_aggregate.empty() && np == 0){
cerr << "configuration of particles are not imported yet.";
exit(1);
}
if (np == 0)
np = init_aggregate.size(); /* np : number of all particles */
nm = np; /* nm : number of mobile particles */
cerr << "number of the particles : " << np << endl;
sd = stokes_init();
sd->twobody_lub = lubrication;
sd->version = 2; /* 0 = F, 1 = FT, 2 = FTS */
sd->periodic = 0; /* 0 = non periodic, 1 = periodic */
stokes_set_np(sd, np, nm);
if (lx == 0 || ly == 0 || lz == 0 ){
cerr << "lx, ly, lz are not given." << endl;exit(1);
}
cerr << "=======" << endl;
stokes_set_l(sd, lx, ly, lz);
int n3=np*3;
int n5=np*5;
try{
velocity = new double [ n3 ];
omega = new double [ n3 ];
strain_velocity = new double [ n5 ];
force = new double [ n3 ];
torque = new double [ n3 ];
stresslet = new double [ n5 ];
dr = new vec3d [np];
} catch (bad_alloc &){
cerr << "bad_alloc at System::init()" << endl;
exit(1);
}
/*
* set pos[] for SD
*/
if (!init_aggregate.empty()){
double scale = 1.0;
for (int i = 0; i < np; i++){
setPosition(i,
scale*init_aggregate[i].x,
scale*init_aggregate[i].y,
scale*init_aggregate[i].z);
}
set_dr_from_sdpos();
}
}
/* check make_matrix_mob_ewald_3all() for mono and poly(a=1)
* with SC config with N=2
* INPUT
* version : 0 (F), 1 (FT), 2 (FTS)
* dir : direction of the config, 0 (x), 1 (y), 2(z).
* phi : volume fraction, that is, phi = (4/3)pi a^3/l^3
* ewald_tr :
* ewald_eps :
* verbose : if non-zero, print results
* tiny : small number for check
* OUTPUT
* (returned value) : 0 => passed
* otherwise => failed
*/
int
check_make_matrix_mob_ewald_3all_poly_SC_2
(int version,
int dir,
double phi,
double ewald_tr, double ewald_eps,
int verbose, double tiny)
{
if (verbose != 0)
{
fprintf (stdout,
"==================================================\n"
"check_make_matrix_mob_ewald_3all_poly_SC_2\n"
"(%d,dir=%d,phi=%f,tr=%f,eps=%f): start\n",
version, dir, phi, ewald_tr, ewald_eps);
}
// initialize struct stokes *sys
struct stokes *sys = stokes_init ();
CHECK_MALLOC (sys, "check_make_matrix_mob_ewald_3all_poly_SC_2");
sys->version = version;
int np = 2;
stokes_set_np (sys, np, np);
//sys->lubmin = 2.0000000001;
sys->lubmin2 = 4.0000000001;
stokes_set_iter (sys, "gmres", 2000, 20, 1.0e-6, 1, stderr);
// periodic
sys->periodic = 1;
double l;
l = pow (M_PI / 0.75 / phi, 1.0 / 3.0);
if (dir == 1)
{
// x direction
stokes_set_l (sys, 2.0*l, l, l);
sys->pos [0] = 0.0;
sys->pos [1] = 0.0;
sys->pos [2] = 0.0;
sys->pos [3] = l;
sys->pos [4] = 0.0;
sys->pos [5] = 0.0;
}
else if (dir == 2)
{
// y direction
stokes_set_l (sys, l, 2.0*l, l);
sys->pos [0] = 0.0;
sys->pos [1] = 0.0;
sys->pos [2] = 0.0;
sys->pos [3] = 0.0;
sys->pos [4] = l;
sys->pos [5] = 0.0;
}
else
{
// z direction
stokes_set_l (sys, l, l, 2.0*l);
sys->pos [0] = 0.0;
sys->pos [1] = 0.0;
sys->pos [2] = 0.0;
sys->pos [3] = 0.0;
sys->pos [4] = 0.0;
sys->pos [5] = l;
}
double xi = xi_by_tratio (sys, ewald_tr);
stokes_set_xi (sys, xi, ewald_eps);
int n;
if (version == 0) n = 3 * np;
else if (version == 1) n = 6 * np;
else n = 11 * np;
// case 1) -- mono
double *mat1 = (double *)malloc (sizeof (double) * n * n);
CHECK_MALLOC (mat1, "check_make_matrix_mob_ewald_3all_poly_SC_2");
double t0, t;
t0 = ptime_ms_d ();
make_matrix_mob_ewald_3all (sys, mat1);
t = ptime_ms_d ();
double ptime_mono = t - t0;
// set sys->a to test poly version
double a [2] = {1.0, 1.0};
stokes_set_radius (sys, a);
// case 2) -- poly
double *mat2 = (double *)malloc (sizeof (double) * n * n);
CHECK_MALLOC (mat2, "check_make_matrix_mob_ewald_3all_poly_SC_2");
t0 = ptime_ms_d ();
make_matrix_mob_ewald_3all (sys, mat2);
t = ptime_ms_d ();
double ptime_poly = t - t0;
// compare
int check = 0;
double max = 0.0;
char label [80];
int i, j;
for (i = 0; i < n; i ++)
{
for (j = 0; j < n; j ++)
{
sprintf (label, " (%d, %d) ", i, j);
check += compare_max (mat1[i*n+j], mat2[i*n+j],
label, verbose, tiny, &max);
}
}
free (mat1);
free (mat2);
stokes_free (sys);
if (verbose != 0)
{
fprintf (stdout, " ptime mono, poly = %.3f %.3f, poly/mono = %f\n",
ptime_mono, ptime_poly, ptime_poly / ptime_mono);
fprintf (stdout, " max error = %e vs tiny = %e\n", max, tiny);
if (check == 0) fprintf (stdout, " => PASSED\n\n");
else fprintf (stdout, " => FAILED\n\n");
}
return (check);
}
/* check atimes_ewald_3all() for mono and poly(a=1) with SC config with N=1
* INPUT
* version : 0 (F), 1 (FT), 2 (FTS)
* phi : volume fraction, that is, phi = (4/3)pi a^3/l^3
* ewald_tr :
* ewald_eps :
* verbose : if non-zero, print results
* tiny : small number for check
* OUTPUT
* (returned value) : 0 => passed
* otherwise => failed
*/
int
check_atimes_ewald_3all_poly_SC_1 (int version,
double phi,
double ewald_tr, double ewald_eps,
int verbose, double tiny)
{
if (verbose != 0)
{
fprintf (stdout,
"==================================================\n"
"check_atimes_ewald_3all_poly_SC_1\n"
"(%d,phi=%f,tr=%f,eps=%f)"
": start\n",
version, phi, ewald_tr, ewald_eps);
}
// initialize struct stokes *sys
struct stokes *sys = stokes_init ();
CHECK_MALLOC (sys, "check_atimes_ewald_3all_poly_SC_1");
sys->version = version;
int np = 1;
stokes_set_np (sys, np, np);
sys->pos [0] = 0.0;
sys->pos [1] = 0.0;
sys->pos [2] = 0.0;
sys->lubmin2 = 4.0000000001;
stokes_set_iter (sys, "gmres", 2000, 20, 1.0e-6, 1, stderr);
// periodic
sys->periodic = 1;
double l;
l = pow (M_PI / 0.75 / phi, 1.0 / 3.0);
stokes_set_l (sys, l, l, l);
double xi = xi_by_tratio (sys, ewald_tr);
stokes_set_xi (sys, xi, ewald_eps);
int n;
if (version == 0) n = 3 * np;
else if (version == 1) n = 6 * np;
else n = 11 * np;
double *x = (double *)malloc (sizeof (double) * n);
CHECK_MALLOC (x, "check_atimes_ewald_3all_poly_SC_1");
int i;
for (i = 0; i < n; i ++)
{
x[i] = 1.0;
}
// case 1) -- mono code
double *y1 = (double *)malloc (sizeof (double) * n);
CHECK_MALLOC (y1, "check_atimes_ewald_3all_poly_SC_1");
double t0, t;
t0 = ptime_ms_d ();
atimes_ewald_3all (n, x, y1, (void *)sys);
t = ptime_ms_d ();
double ptime_mono = t - t0;
// set sys->a to test poly version
double a [1] = {1.0};
stokes_set_radius (sys, a);
// case 2) -- poly code
double *y2 = (double *)malloc (sizeof (double) * n);
CHECK_MALLOC (y2, "check_atimes_ewald_3all_poly_SC_1");
t0 = ptime_ms_d ();
atimes_ewald_3all (n, x, y2, (void *)sys);
t = ptime_ms_d ();
double ptime_poly = t - t0;
// compare
int check = 0;
double max = 0.0;
char label [80];
for (i = 0; i < n; i ++)
{
sprintf (label, " (%d) ", i);
check += compare_max (y1[i], y2[i], label, verbose, tiny, &max);
}
free (x);
free (y1);
free (y2);
stokes_free (sys);
if (verbose != 0)
{
fprintf (stdout, " ptime mono, poly = %.3f %.3f, poly/mono = %f\n",
ptime_mono, ptime_poly, ptime_poly / ptime_mono);
fprintf (stdout, " max error = %e vs tiny = %e\n", max, tiny);
if (check == 0) fprintf (stdout, " => PASSED\n\n");
else fprintf (stdout, " => FAILED\n\n");
}
return (check);
}
/* main program */
int
main (int argc, char** argv)
{
struct stokes *sys = stokes_init ();
int np, nm;
np = 8;
nm = 8;
stokes_set_np (sys, np, nm);
sys->periodic = 1; // periodic boundary condition
double lx, ly, lz;
lx = 10.0;
ly = 10.0;
lz = 10.0;
stokes_set_l (sys, lx, ly, lz);
double ewald_tr = 60.25;
double xi = xi_by_tratio (sys, ewald_tr);
double ewald_eps = 1.0e-12;
stokes_set_xi (sys, xi, ewald_eps);
fprintf (stdout, "xi = %f\n", xi);
//sys->lubmin = 2.0000000001;
sys->lubmin2 = 4.0000000001;
sys->lubmax = 4.0;
stokes_set_iter (sys, "gmres", 2000, 20, 1.0e-6, 1, stdout);
int i;
double * pos;
double * u;
double * f;
pos = (double *)calloc (np * 3, sizeof (double));
u = (double *)calloc (np * 3, sizeof (double));
f = (double *)calloc (np * 3, sizeof (double));
pos[ 0] = 0.0; // x component
pos[ 1] = 0.0; // y component
pos[ 2] = 0.0; // z component
pos[ 3] = 5.0; pos[ 4] = 0.0; pos[ 5] = 0.0;
pos[ 6] = 0.0; pos[ 7] = 5.0; pos[ 8] = 0.0;
pos[ 9] = 0.0; pos[10] = 0.0; pos[11] = 5.0;
pos[12] = 5.0; pos[13] = 5.0; pos[14] = 0.0;
pos[15] = 0.0; pos[16] = 5.0; pos[17] = 5.0;
pos[18] = 5.0; pos[19] = 0.0; pos[20] = 5.0;
pos[21] = 5.0; pos[22] = 5.0; pos[23] = 5.0;
for (i = 0; i < np * 3; i ++)
{
u[i] = 1.0;
}
fprintf (stdout, "pos:\n");
for (i = 0; i < np; i ++)
{
fprintf (stdout, "%d %f %f %f\n",
i,
pos[i*3 + 0],
pos[i*3 + 1],
pos[i*3 + 2]);
}
fprintf (stdout, "u:\n");
for (i = 0; i < np; i ++)
{
fprintf (stdout, "%d %f %f %f\n",
i,
u[i*3 + 0],
u[i*3 + 1],
u[i*3 + 2]);
}
stokes_set_pos (sys, pos);
solve_res_3f (sys, u, f);
fprintf (stdout, "f:\n");
for (i = 0; i < np; i ++)
{
fprintf (stdout, "%d %f %f %f\n",
i,
f[i*3 + 0],
f[i*3 + 1],
f[i*3 + 2]);
}
return 0;
}
