int
random_evolve (double sys[], const double t)
/** Versió bona, suposo. */
/* Seguint arXiv:cond-mat/9707147, actualitza la part
* estocàstica segons \dot x = x_D + h^(1/2) * noise.
*/
{
gsl_rng * rng = random_generator_get_generator ("random_evolve");
double delta_t_ = t - t_ant;
double sqrt_h = sqrt(RATIO * delta_t_);
dimensions * dim = sys_dimensions_handle ();
double xl = dim -> x_phys_min;
double xr = dim -> x_phys_max;
int i = 0;
for (i = 0; i < phys_size; i++) {
double x = sys[i];
if ((xl < x) && (x < xr)) {
double ran_x = gsl_ran_gaussian (rng, 1.);
double ran_y = gsl_ran_gaussian (rng, 1.);
sys[i] = sys[i] + sqrt_h * ran_x;
sys[index_y(i)] = sys[index_y(i)] + sqrt_h * ran_y;
}
}
t_ant = t;
return 0;
}
double
r2_ab_couette (const int a, const int b, const double sys[])
{
dimensions *dim = sys_initial_dimensions_handle ();
double y_max = dim->y_max;
double y_min = dim->y_min;
double x = sys[a] - sys[b];
double ya = sys[index_y(a)];
double yb = sys[index_y(b)];
double yb_imatge = yb;
y_min = y_min - delta_y / 2.;
y_max = y_max + delta_y / 2.;
if (yb > y_max)
yb_imatge = y_min + (yb - y_max);
else if (yb < y_min)
yb_imatge = y_max - (y_min - yb);
double y = ya - yb_imatge;
return x*x + y*y;
}
int
data_stress_molecular_print (FILE * pfile, const sys_info_t * p_sys_info,
const int snap, const double t)
{
/*1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 */
/*snap t e_str xx xy yy Lxx Lxy Lyy Rxx Rxy Ryy fxL fyL fxR fyR */
fprintf (pfile, "mol "
"%d %.5e %.5e "
"%.5e %.5e %.5e " // mean
"%.5e %.5e %.5e " // L
"%.5e %.5e %.5e " // R
"%.5e %.5e %.5e %.5e\n", // forces
snap, t, e_strain,
mean_stress[index_xx(0)],
mean_stress[index_xy(0)],
mean_stress[index_yy(0)],
mean_stress_L[index_xx(0)],
mean_stress_L[index_xy(0)],
mean_stress_L[index_yy(0)],
mean_stress_R[index_xx(0)],
mean_stress_R[index_xy(0)],
mean_stress_R[index_yy(0)],
forca_L[index_x(0)], forca_L[index_y(0)],
forca_R[index_x(0)], forca_R[index_y(0)]);
return 0;
}
int
bottom_reflexive_force (double t, const double sys[],
double f[], void *params)
{
dimensions *dim = sys_initial_dimensions_handle ();
double y_min = dim -> y_phys_min;
y_min = y_min + dist_a * range_factor / 2.;
int i;
for (i = 0; i < phys_size; i++)
{
if (sys[index_y(i)] < y_min)
{
if (f[index_y(i)] < 0.)
{
f[index_y(i)] = - f[index_y(i)];
/* de fet, l'exponencial aquella ja
* era impenetrable, no sé perquè ho
* he tocat! Ara no recordo com coi
* era! :( */
}
}
}
return 0;
}
double
r2_ab_default (const int a, const int b, const double sys[])
{
double x = sys[a] - sys[b];
double y = sys[index_y(a)] - sys[index_y(b)];
return x*x + y*y;
}
int
right_y (double t, const double sys[],
double f[], void *params)
{
int i;
for (i = sys_paret_R_init (); i < sys_paret_R_fin (); i++)
f[index_y(i)] = f[index_y(i)] + V;
return 0;
}
int
inicia_cristall_paret_commensurada_amb_y (void)
{
double * sys = sys_handle ();
double delta_x = dist_a * sqrt(3.) / 2.;
double delta_y = dist_a;
double y_min = -ny_extra * delta_y;
double y_minR = y_min;
double x_min = -nx_paret * delta_x;
double x_max = NX * delta_x;
int paretLi = sys_paret_L_init ();
int paretRi = sys_paret_R_init ();
if (nx_paret % 2 == 1)
y_min = y_min - delta_y / 2.;
int i;
int j;
for (i = 0; i < nx_paret; i++)
{
for (j = 0; j < ny_paret; j++)
{
if (i % 2 == 0)
{
double x = x_min + i * delta_x;
double y = y_min + j * delta_y;
double yr = y_minR + j * delta_y;
int indexL = i + nx_paret * j + paretLi;
int indexR = i + nx_paret * j + paretRi;
sys[indexL] = x;
sys[index_y(indexL)] = y;
sys[indexR] = x + x_max - x_min;
sys[index_y(indexR)] = yr;
}
else
{
double x = x_min + i * delta_x;
double y = y_min + j * delta_y + delta_y / 2.;
double yr = y_minR + j * delta_y + delta_y / 2.;
int indexL = i + paretLi + nx_paret * j;
int indexR = i + paretRi + nx_paret * j;
sys[indexL] = x;
sys[index_y(indexL)] = y;
sys[indexR] = x + x_max - x_min;
sys[index_y(indexR)] = yr;
}
}
}
return 0;
}
int
inicia_cristall_paret_commensurada_amb_x (void)
{
double * sys = sys_handle ();
double delta_x = dist_a;
double delta_y = dist_a * sqrt(3.) / 2.;
double y_min = -ny_extra * delta_y;
double x_min = -nx_paret * delta_x;
double x = x_min;
double y = y_min;
int index;
for (index = sys_paret_L_init (); index < sys_paret_L_fin (); index++)
{
if (index % nx_paret == 0)
{
x = x_min;
y = y + delta_y;
}
sys[index] = x;
sys[index_y(index)] = y;
if (index / nx_paret % 2 == 0)
sys[index] = sys[index] + delta_x / 2.;
x = x + delta_x;
}
double x_max = NX * delta_x;
x = x_max;
y = y_min;
for (index = sys_paret_R_init (); index < sys_paret_R_fin (); index++)
{
if (index % nx_paret == 0)
{
x = x_max;
y = y + delta_y;
}
sys[index] = x;
sys[index_y(index)] = y;
if (index / nx_paret % 2 == 0)
sys[index] = sys[index] + delta_x / 2.;
x = x + delta_x;
}
return 0;
}
void Grid::putItem( GridItemPtr item)
{
const vec2 & location = item->getPos();
Cell& cell = cellRef( index_x( location.x ), index_y( location.y ) );
cell.add( item );
numItems += 1;
}
void Grid::removeItem( GridItemPtr item)
{
const vec2 & location = item->getPos();
Cell& cell = cellRef( index_x( location.x ), index_y( location.y ) );
cell.remove( item );
numItems -= 1;
}
int
historia_stress_writer (FILE * pfile, const double * sys,
const sys_info_t * p_sys_info)
/* implementacio de writer_funcp_t **/
{
static const char * new_line = "\n";
static const char * particle_delim = ":";
/* historia stressos: i x y xx xy yy **/
const char * format_file = "%d %.5e %.5e %.5e %.5e %.5e";
int phys_size = p_sys_info->phys_size;
int i;
fprintf (pfile, particle_delim);
for (i = 0; i < phys_size; i++)
{
fprintf (pfile, format_file,
i, // 1. i
sys[index_x(i)], // 2. x
sys[index_y(i)], // 3. y
stress_tensor[index_xx(i)] - mean_stress[index_xx(0)], // 4. xx
stress_tensor[index_xy(i)] - mean_stress[index_xy(0)], // 5. xy
stress_tensor[index_yy(i)] - mean_stress[index_yy(0)]); // 6. yy
fprintf (pfile, particle_delim);
}
fprintf (pfile, new_line);
return 0;
}
void
readIndexSetFromFile(IndexSet<Index2D> &Lambda, string filename)
{
std::ifstream infile (filename.c_str());
if (infile.is_open()) {
cerr << " Indexset file is open." << endl;
}
else {
cerr << " Indexset file " << filename.c_str() << " is not open." << endl;
}
int t1,t2;
int j1,j2;
long k1,k2;
T coeff;
while(!infile.eof()) {
infile >> t1 >> j1 >> k1 >> t2 >> j2 >> k2 >> coeff;
if (t1 == 1 && t2 == 1) {
Index1D index_x(j1,k1,XWavelet);
Index1D index_y(j2,k2,XWavelet);
Lambda.insert(Index2D(index_x,index_y));
}
else if (t1 == 1 && t2 == 0) {
Index1D index_x(j1,k1,XWavelet);
Index1D index_y(j2,k2,XBSpline);
Lambda.insert(Index2D(index_x,index_y));
}
else if (t1 == 0 && t2 == 1) {
Index1D index_x(j1,k1,XBSpline);
Index1D index_y(j2,k2,XWavelet);
Lambda.insert(Index2D(index_x,index_y));
}
else if (t1 == 0 && t2 == 0) {
Index1D index_x(j1,k1,XBSpline);
Index1D index_y(j2,k2,XBSpline);
Lambda.insert(Index2D(index_x,index_y));
}
else {
std::cerr << "Could not read file." << std::endl;
exit(1); return;
}
}
}
int
boundary_resolve_couette (void)
/* Resol els conflictes deguts a que partícules surtin per
* la part superior o inferior i hagin de passar-se a la seva
* imatge periòdica. */
{
dimensions *dim = sys_initial_dimensions_handle ();
double y_max = dim -> y_max; // initial_dimensions -> y_max;
double y_min = dim -> y_min; // initial_dimensions -> y_min;
y_min = y_min - delta_y / 2.; // ups, ja estava bé, crec.
y_max = y_max + delta_y / 2.;
double *sys = sys_handle ();
int i;
for (i = 0; i < sys_size; i++)
{
double y = sys[index_y(i)];
double y_new = y;
if (y > y_max)
{
y_new = y_min + (y - y_max);
/* fprintf(stderr,"pbc_up_down: %d %f %f\t%f %f\n", */
/* i,y,y_new,y_max,y_min); */
}
if (y < y_min)
{
y_new = y_max - (y_min - y);
/* fprintf(stderr,"pbc_down_up: %d %f %f\t%f %f\n", */
/* i,y,y_new,y_max,y_min); */
}
sys[index_y(i)] = y_new;
}
return 0;
}
int
inicia_cristall_sistema_orientat_y (void)
{
double * sys = sys_handle ();
double delta_x = dist_a * sqrt(3.) / 2.;
double delta_y = dist_a;
int i;
int j;
for (i = 0; i < NX; i++)
{
for (j = 0; j < NY; j++)
{
if (i % 2 == 0)
{
double x = i * delta_x;
double y = j * delta_y;
int index = i + NX * j;
sys[index] = x;
sys[index_y(index)] = y;
}
else
{
double x = i * delta_x;
double y = j * delta_y + delta_y / 2.;
int index = i + NX * j;
sys[index] = x;
sys[index_y(index)] = y;
}
}
}
return 0;
}
int
print_particles (FILE * pfile, const double * sys)
/* Nota: en cas que es vulgui escriure en un altre format,
* es pot sobreescriure aquest metode. **/
{
const char * particle_format = "%.5e %.5e";
int i;
fprintf (pfile, particle_delim);
for (i = 0; i < sys_size; i++)
{
fprintf (pfile, particle_format, sys[i], sys[index_y(i)]);
fprintf (pfile, particle_delim);
}
fprintf (pfile, new_line);
return 0;
}
int
inicia_cristall_add_random_perturbation_if_necessary (void)
{
char *SIGMA_ = getenv ("SIGMA");
if (SIGMA_ == 0)
{
log_to_logfile ("Cristall inicial perfecte. Sinó posar SIGMA != 0.",
__FILE__, __LINE__);
return 0;
}
double SIGMA = strtod (SIGMA_, NULL);
char log_SIGMA[100];
sprintf (log_SIGMA, "SIGMA = %.5e, és la fracció [0,1) del delta_x(y)" \
" que es pertorben les posicions inicials.", SIGMA);
log_to_logfile (log_SIGMA, __FILE__, __LINE__);
double * sys = sys_handle ();
gsl_rng * rng = random_generator_get_generator
("inicia_cristall_add_random_perturbation");
if (rng == 0) abort_no_random ();
dimensions * dim = sys_initial_dimensions_handle ();
int valid_new_x (double new_x)
{
return ((new_x > dim->x_min)&&(new_x < dim->x_max));
}
int valid_new_y (double new_y)
{
return 1;
}
int can_be_changed (int i, double new_x, double new_y)
{
int j;
for (j = 0; j < i; j++)
{
double x_j = sys[j];
double y_j = sys[index_y(j)];
double r2 = (new_x - x_j) * (new_x - x_j)
+ (new_y - y_j) * (new_y - y_j);
if (r2 < MINIMUM_APART * MINIMUM_APART) return 0;
}
return 1;
}
int
boundary_resolve_bottom_reflexive_up_free (void)
{
dimensions *dim = sys_dimensions_handle ();
/* double y_max = dim -> y_max; // initial_dimensions -> y_max; */
double y_min = dim -> y_min; // initial_dimensions -> y_min;
double *sys = sys_handle ();
int i;
for (i = 0; i < phys_size; i++)
{
double y = sys[index_y(i)];
if (y < y_min)
abort ();
}
return 0;
}
int
data_stress_molecular_extract (const sys_info_t * p_sys_info,
const double * sys, const double * f,
const int snap, const double t)
{
mean_stress[index_xx(0)] = 0.;
mean_stress[index_xy(0)] = 0.;
mean_stress[index_yy(0)] = 0.;
mean_stress2[index_xx(0)] = 0.;
mean_stress2[index_xy(0)] = 0.;
mean_stress2[index_yy(0)] = 0.;
mean_stress_L[index_xx(0)] = 0.;
mean_stress_L[index_xy(0)] = 0.;
mean_stress_L[index_yy(0)] = 0.;
mean_stress2_L[index_xx(0)] = 0.;
mean_stress2_L[index_xy(0)] = 0.;
mean_stress2_L[index_yy(0)] = 0.;
mean_stress_R[index_xx(0)] = 0.;
mean_stress_R[index_xy(0)] = 0.;
mean_stress_R[index_yy(0)] = 0.;
mean_stress2_R[index_xx(0)] = 0.;
mean_stress2_R[index_xy(0)] = 0.;
mean_stress2_R[index_yy(0)] = 0.;
forca_L[index_x(0)] = 0.;
forca_L[index_y(0)] = 0.;
forca_R[index_x(0)] = 0.;
forca_R[index_y(0)] = 0.;
int sys_size = p_sys_info->sys_size;
int i;
for (i = 0; i < sys_size; i++)
{
stress_tensor[index_xx(i)] = 0.;
stress_tensor[index_xy(i)] = 0.;
stress_tensor[index_yy(i)] = 0.;
}
for (i = 0; i < sys_size; i++)
{
double x_i = sys[index_x(i)];
double y_i = sys[index_y(i)];
double s_xx_i = 0.;
double s_xy_i = 0.;
double s_yy_i = 0.;
int jotes = 0;
int j;
for (j = 0; j < sys_size; j++)
{
/* avoid self */
if (i == j) continue;
double x_j = sys[index_x(j)];
double y_j = sys[index_y(j)];
/* La i es l'origen, la f actua sobre la j. */
double x_ij = x_j - x_i;
double y_ij = y_j - y_i;
double r2_ij = x_ij * x_ij + y_ij * y_ij;
/* cut off */
if (r2_ij > range2) continue;
double f_x_ij = 0.;
double f_y_ij = 0.;
/* caluculo la forca entre _i_ i _j_*/
double over_r2 = 1./r2_ij;
double over_r6 = over_r2 * over_r2 * over_r2;
double factor;
factor = 24. * over_r2 * over_r6 * (2 * over_r6 - 1);
f_x_ij = factor * x_ij;
f_y_ij = factor * y_ij;
s_xx_i = s_xx_i + f_x_ij * x_ij;
s_xy_i = s_xy_i + f_x_ij * y_ij;
s_yy_i = s_yy_i + f_y_ij * y_ij;
/* valors propis */
/* double suma = 0.5 * (s_xx_i + s_yy_i); */
/* double resta = 0.5 * (s_xx_i - s_yy_i); */
/* double arrel = sqrt (resta * resta + s_xy_i * s_xy_i); */
/* double lambda_menys = suma - arrel; */
/* double lambda_mes = suma + arrel; */
jotes++;
}
double norm = 1./ ((double) jotes);
s_xx_i = norm * s_xx_i;
s_xy_i = norm * s_xy_i;
s_yy_i = norm * s_yy_i;
stress_tensor[index_xx(i)] = s_xx_i;
stress_tensor[index_xy(i)] = s_xy_i;
stress_tensor[index_yy(i)] = s_yy_i;
// fprintf (stderr, "%d %f %f %f\n", i, s_xx_i, s_xy_i, s_yy_i);
}
/* calculo les mitjanes, que haurien de coincidir */
int phys_size = p_sys_info->phys_size;
double norm = 1./ ((double) phys_size);
for (i = 0; i < phys_size; i++)
{
double s_xx_i = stress_tensor[index_xx(i)];
double s_xy_i = stress_tensor[index_xy(i)];
double s_yy_i = stress_tensor[index_yy(i)];
mean_stress[index_xx(0)] = mean_stress[index_xx(0)] + norm * s_xx_i;
mean_stress[index_xy(0)] = mean_stress[index_xy(0)] + norm * s_xy_i;
mean_stress[index_yy(0)] = mean_stress[index_yy(0)] + norm * s_yy_i;
mean_stress2[index_xx(0)] = mean_stress2[index_xx(0)]
+ norm * s_xx_i * s_xx_i;
mean_stress[index_xy(0)] = mean_stress[index_xy(0)]
+ norm * s_xy_i * s_xy_i;
mean_stress[index_yy(0)] = mean_stress[index_yy(0)]
+ norm * s_yy_i * s_yy_i;
}
/* e_strain **/
double V = p_sys_info->V;
double delta_x = p_sys_info->delta_x;
int NX = p_sys_info->NX;
double x_length_0 = (NX + 1) * delta_x;//(NX - 0.5) * delta_x;
double vt = 2 * V * t;
e_strain = vt / x_length_0;
int paret_size = p_sys_info->paret_size;
norm = 1. / ((double) paret_size);
int NY = p_sys_info->NY;
double delta_y = p_sys_info->delta_y;
double norm_f = 1. / (delta_y * ((double) NY));
// fprintf (stdout, "norm: %f\n", norm_f);
//forca total, no normalitzem / ((double) NY);
/* paretL */
for (i = phys_size; i < phys_size + paret_size; i++)
{
double xx = stress_tensor[index_xx(i)];
double xy = stress_tensor[index_xy(i)];
double yy = stress_tensor[index_yy(i)];
mean_stress_L[index_xx(0)] = mean_stress_L[index_xx(0)] + norm * xx;
mean_stress_L[index_xy(0)] = mean_stress_L[index_xy(0)] + norm * xy;
mean_stress_L[index_yy(0)] = mean_stress_L[index_yy(0)] + norm * yy;
mean_stress2_L[index_xx(0)] = mean_stress2_L[index_xx(0)]
+ norm * xx * xx;
mean_stress2_L[index_xy(0)] = mean_stress2_L[index_xy(0)]
+ norm * xy * xy;
mean_stress2_L[index_yy(0)] = mean_stress2_L[index_yy(0)]
+ norm * yy * yy;
forca_L[index_x(0)] = forca_L[index_x(0)] + norm_f * f[index_x(i)];
forca_L[index_y(0)] = forca_L[index_y(0)] + norm_f * f[index_y(i)];
}
norm = 1. / ((double) paret_size);
// norm_f = 1.; // forca total, no normalitzem / ((double) NY);
/* paretR */
for (i = phys_size + paret_size; i < phys_size + 2 * paret_size; i++)
{
double xx = stress_tensor[index_xx(i)];
double xy = stress_tensor[index_xy(i)];
double yy = stress_tensor[index_yy(i)];
mean_stress_R[index_xx(0)] = mean_stress_R[index_xx(0)] + norm * xx;
mean_stress_R[index_xy(0)] = mean_stress_R[index_xy(0)] + norm * xy;
mean_stress_R[index_yy(0)] = mean_stress_R[index_yy(0)] + norm * yy;
mean_stress2_R[index_xx(0)] = mean_stress2_R[index_xx(0)]
+ norm * xx * xx;
mean_stress2_R[index_xy(0)] = mean_stress2_R[index_xy(0)]
+ norm * xy * xy;
mean_stress2_R[index_yy(0)] = mean_stress2_R[index_yy(0)]
+ norm * yy * yy;
forca_R[index_x(0)] = forca_R[index_x(0)] + norm_f * f[index_x(i)];
forca_R[index_y(0)] = forca_R[index_y(0)] + norm_f * f[index_y(i)];
}
if (historia_stress_b)
dr_writer_write_frame (stress_history_pfile, sys,
p_sys_info, snap, t);
return 0;
}
int
data_energy_extract (const sys_info_t * p_sys_info,
const double * sys, const double * f,
const int snap, const double t)
{
energy_energy = 0.;
energy_energy2 = 0.;
dW_per_particle = 0.;
dW = 0.;
sum_modul_per_particle = 0.;
sum_modul = 0.;
int phys_size = p_sys_info->phys_size;
double norm = 1. / ((double) phys_size);
int i;
int sys_size = p_sys_info->sys_size;
for (i = 0; i < phys_size; i++)
//for (i = 0; i < sys_size; i++)
{
double x_i = sys[index_x(i)];
double y_i = sys[index_y(i)];
double e_i = 0.;
double fx_i = f[index_x(i)];
double fy_i = f[index_y(i)];
double vx_i = f[index_x(i)];
double vy_i = f[index_y(i)];
double dW_i = fx_i * vx_i + fy_i * vy_i; // v and f are the same, but...
double mod_v_i = sqrt(vx_i * vx_i + vy_i * vy_i);
int j;
//for (j = 0; j < phys_size; j++)
for (j = 0; j < sys_size; j++)
{
/* avoid self */
if (j == i) continue;
double x_j = sys[index_x(j)];
double y_j = sys[index_y(j)];
double r2 = (x_j - x_i) * (x_j - x_i) + (y_j - y_i) * (y_j - y_i);
double over_r2 = 1. / r2;
double over_r6 = over_r2 * over_r2 * over_r2;
double over_r12 = over_r6 * over_r6;
double e_ij = 4 * (over_r12 - over_r6);
e_i = e_i + e_ij;
}
// el 0.5 \sum_{i<j} = 0.5 \sum_{ij} !!!!!!!!!!!!!!
energy_energy = energy_energy + 0.5 * e_i;
energy_energy2 = energy_energy2 + 0.5 * e_i * e_i; //??? el 0.5 no ho sé
dW_per_particle = dW_per_particle + norm * dW_i;
dW = dW + dW_i;
sum_modul_per_particle = sum_modul_per_particle + norm * mod_v_i;
sum_modul = sum_modul + mod_v_i;
}
/* e_strain **/
double V = p_sys_info->V;
double delta_x = p_sys_info->delta_x;
int NX = p_sys_info->NX;
double x_length_0 = (NX + 1) * delta_x;//(NX - 0.5) * delta_x;
double vt = 2 * V * t;
e_strain = vt / x_length_0;
return 0;
}