void scanf_vector(char* filename, gsl_vector* v)
{
FILE* fileptr;
fileptr = fopen(filename, "r");
gsl_vector_fscanf(fileptr, v);
fclose(fileptr);
}
void population_fscanf (Population *pop, FILE *stream)
{
int i;
for (i = 0; i < pop->n_e; i++){
gsl_vector_fscanf(stream, pop->y[i]);
gsl_matrix_fscanf(stream, pop->b[i]);
}
fscanf(stream, "%d", &pop->current_gen);
}
int read_vec( gsl_vector *a, const char * filename ) {
FILE *file = fopen(filename, "r");
if (file == NULL) {
Log::lprintf(Log::LOG_LEVEL_NOTIFY, "Error opening file %s\n", filename);
return 0;
}
gsl_vector_fscanf(file, a);
fclose(file);
return 1;
}
/*
* read/write a vector/matrix from a file
*
*/
void vct_fscanf(const char* filename, gsl_vector* v) {
outlog("reading %ld vector from %s", v->size, filename);
FILE* fileptr;
fileptr = fopen(filename, "r");
if (!fileptr) {
outlog("Error opening file %s. Failing.", filename);
exit(1);
}
gsl_vector_fscanf(fileptr, v);
fclose(fileptr);
}
/*
* FUNCTION
* Name: main
* Description:
*
*/
int main ( int argc, char *argv[] )
{
gsl_ieee_env_setup () ; /* read GSL_IEEE_MODE */
double beta = 1.0/T ; /* Boltzmann factor: beta */
double omega_1 = gsl_hypot(OMEGA,D) ; /* omega' */
struct f_params params;
params.omega_c = omega_c ;
params.beta = beta ;
params.Omega = OMEGA ;
params.omega_1 = omega_1 ;
params.alpha = alpha ;
/* read the Redfield matrix from a file */
gsl_matrix* red_m = gsl_matrix_calloc ( 4, 4 ) ;
mat_read ( red_m, "REDFIELD_MATRIX" ) ;
/*
* Find the stationary state by solving the linear systems
* and the associated stationary currents
*/
gsl_vector* req_red = gsl_vector_calloc (4) ;
FILE* f_red = fopen ( "RED_STATIONARY.dat", "r" ) ;
if ( f_red == NULL )
printf("Error: %s.\nFailed to open RED_STATIONARY.dat",
strerror(errno)) ;
gsl_vector_fscanf ( f_red, req_red ) ;
fclose ( f_red ) ;
printf("REDFIELD DYNAMICS\n") ;
printf("Stationary state: ( %.1f , %.9f , %.9f , %.9f )\n",
VECTOR(req_red,0), VECTOR(req_red,1),
VECTOR(req_red,2), VECTOR(req_red,3) ) ;
printf("Stationary normalized (I/I0) DC current: %.9f\n\n",
-VECTOR(req_red,3)*OMEGA/omega_1) ;
int status = red_evol ( ¶ms, R, t_end, STEP, req_red, red_m ) ;
if ( status != 0 )
exit (EXIT_FAILURE) ;
/* free memory for matrix */
gsl_matrix_free(red_m) ;
return EXIT_SUCCESS;
} /* ---------- end of function main ---------- */
int main(int argc, char *argv[]) {
// Declaring variables.
gsl_vector *z, *new_z;
int opt;
unsigned n;
double c;
char out_file[20];
// Default values.
sprintf(out_file, "%s", "out.dat");
// GNU getopt in action.
while ((opt = getopt(argc, argv, "n:c:i:")) != -1) {
switch (opt) {
case 'n':
n = atoi(optarg);
break;
case 'c':
c = atof(optarg);
break;
case 'i':
sprintf(out_file, "%s", optarg);
break;
default:
exit(EXIT_FAILURE);
}
}
z = gsl_vector_alloc(3 * n + 3);
new_z = gsl_vector_alloc(6 * n + 3);
FILE *f = fopen(out_file, "r");
gsl_vector_fscanf(f, z);
fclose(f);
gsl_vector_set(new_z, 2 * n - 1, (gsl_vector_get(z, 0) + gsl_vector_get(z, n - 1)) / 2);
gsl_vector_set(new_z, 2 * n - 2, gsl_vector_get(z, n - 2));
for (unsigned i = 0; i < n - 1; i ++) {
gsl_vector_set(new_z, 2 * i, gsl_vector_get(z, i));
gsl_vector_set(new_z, 2 * i + 1,
(gsl_vector_get(z, i) + gsl_vector_get(z, i + 1)) / 2);
}
gsl_vector_set(new_z, 2 * n, gsl_vector_get(z, n) / 2);
gsl_vector_set(new_z, 2 * n + 1, gsl_vector_get(z, n));
gsl_vector_set(new_z, 4 * n - 2, gsl_vector_get(z, 2 * n - 2) / 2);
gsl_vector_set(new_z, 4 * n - 3, gsl_vector_get(z, 2 * n - 2));
for (unsigned i = 1; i < n - 1; i ++) {
gsl_vector_set(new_z, 2 * (n + i) + 1, gsl_vector_get(z, n + i));
gsl_vector_set(new_z, 2 * (n + i) ,
(gsl_vector_get(z, n + i - 1) + gsl_vector_get(z, n + i)) / 2);
}
gsl_vector_set(new_z, 4 * n - 1, gsl_vector_get(z, 2 * n -1));
gsl_vector_set(new_z, 4 * n, gsl_vector_get(z, 2 * n));
for (unsigned i = 0; i < n; i++) {
gsl_vector_set(new_z, 4 * n + 1 + 2 * i, gsl_vector_get(z, 2 * n + 1 + i));
gsl_vector_set(new_z, 4 * n + 2 + 2 * i, gsl_vector_get(z, 2 * n + 1 + i));
}
gsl_vector_set(new_z, 6 * n + 1, gsl_vector_get(z, 3 * n + 1));
gsl_vector_set(new_z, 6 * n + 2, gsl_vector_get(z, 3 * n + 2));
int result;
result = domain_minimize_fixed(new_z, 2 * n, c, 1e-8, 0.00001, 5000, 4, 2);
if (result) printf("Converging failed.");
else {
FILE *fout = fopen(out_file, "w");
gsl_vector_fprintf(fout, new_z, "%.10g");
fclose(fout);
}
gsl_vector_free(z);
gsl_vector_free(new_z);
}
// Initializes the program.
int main(int argc, char *argv[]) {
int opt, min_fails, eigen_follow, eigen_num, examining;
unsigned n, N, ord, size, params, j, M;
double d, c, dc0, dc, g0, g, eigen_thres, approach_thres, eps, eps2, state, old_state, h, bound, da, w, ss;
char *in_filename, *out_filename, *k_filename, *a_filename, *phi_filename, str[19], in;
bool subcrit, reset, rand, verbose, fixed, well;
// Setting default values.
gsl_vector *z, *k, *a, *phi, *old_z;
rand = false;
fixed = false;
well = false;
verbose = false;
j=0;
ss=1;
while ((opt = getopt(argc, argv, "n:c:i:o:O:K:A:P:e:g:N:b:rvd:M:a:fws:W:j:")) != -1) {
switch (opt) {
case 'n':
n = atoi(optarg);
break;
case 'b':
bound = atof(optarg);
break;
case 'c':
c = atof(optarg);
break;
case 'i':
in_filename = optarg;
break;
case 'o':
out_filename = optarg;
break;
case 'O':
ord = atoi(optarg);
break;
case 'K':
k_filename = optarg;
break;
case 'A':
a_filename = optarg;
break;
case 'P':
phi_filename = optarg;
break;
case 'g':
g0 = atof(optarg);
break;
case 'N':
N = atoi(optarg);
break;
case 'j':
j = atoi(optarg);
break;
case 'M':
M = atoi(optarg);
break;
case 'e':
eps = atof(optarg);
break;
case 'd':
dc0 = atof(optarg);
break;
case 'a':
da = atof(optarg);
break;
case 'r':
rand = true;
break;
case 'f':
fixed = true;
break;
case 'w':
well = true;
break;
case 'W':
w = atof(optarg);
break;
case 's':
ss = atof(optarg);
break;
case 'v':
verbose = true;
break;
default:
exit(EXIT_FAILURE);
}
}
if (rand || !fixed) {
size = 3 * n + 2;
params = 2 * n + 1;
} else {
size = 3 * n + 3;
params = 2 * n;
}
z = gsl_vector_alloc(size);
old_z = gsl_vector_alloc(size);
if (rand) {
k = gsl_vector_alloc(2 * ord);
a = gsl_vector_alloc(ord);
phi = gsl_vector_alloc(ord);
}
FILE *in_file = fopen(in_filename, "r");
gsl_vector_fscanf(in_file, z);
fclose(in_file);
if (rand) {
FILE *k_file = fopen(k_filename, "r");
gsl_vector_fscanf(k_file, k);
fclose(k_file);
FILE *a_file = fopen(a_filename, "r");
gsl_vector_fscanf(a_file, a);
fclose(a_file);
FILE *phi_file = fopen(phi_filename, "r");
gsl_vector_fscanf(phi_file, phi);
fclose(phi_file);
}
g = g0;
dc = dc0;
double beta = 0.9;
double s = 1;
double sigma = 0.5;
if (rand && well) min_fails = domain_minimize_randWell(z, n, c, ord, k, a, phi, w, ss, eps, N, beta, s, sigma, g, bound, verbose);
else if (rand) min_fails = domain_minimize_rand(z, n, c, ord, k, a, phi, eps, N, beta, s, sigma, g, bound, verbose);
else {
if (fixed) min_fails = domain_minimize_fixedmin(z, n, c, eps, N, beta, ss, sigma, g, bound, verbose);
else {
if (well) min_fails = domain_minimize_nakedWell(z, n, c, w, ss, eps, N, beta, s, sigma, g, bound, verbose);
else min_fails = domain_minimize_naked(z, n, c, eps, N, beta, s, sigma, g, bound, verbose);
}
}
if (min_fails) {
printf("BIFUR: Initial relaxation failed, exiting.\n");
FILE *out_file = fopen(out_filename, "w");
gsl_vector_fprintf(out_file, z, "%.10e");
fclose(out_file);
return 1;
}
while (j < M) {
j += 1;
c += dc;
g = g0;
if (rand) gsl_vector_scale(a, da);
gsl_vector_memcpy(old_z, z);
printf("EVOLVE: Step %05d, starting with c = %f.\n", j, c);
while (true) {
if (rand && well) min_fails = domain_minimize_randWell(z, n, c, ord, k, a, phi, w, ss, eps, N, beta, s, sigma, g, bound, verbose);
else if (rand) min_fails = domain_minimize_rand(z, n, c, ord, k, a, phi, eps, N, beta, s, sigma, g, bound, verbose);
else if (fixed) min_fails = domain_minimize_fixedmin(z, n, c, eps, N, beta, s, sigma, g, bound, verbose);
else if (well) min_fails = domain_minimize_nakedWell(z, n, c, w, ss, eps, N, beta, s, sigma, g, bound, verbose);
else min_fails = domain_minimize_naked(z, n, c, eps, N, beta, s, sigma, g, bound, verbose);
if (!min_fails) break;
printf("EVOLVE: Newton's method failed to converge, reducing gamma.\n");
gsl_vector_memcpy(z, old_z);
g *= 0.1;
}
sprintf(str, "output/out-%05d.dat", j);
FILE *fout = fopen(str, "w");
fprintf(fout, "%.10e\n", c);
gsl_vector_fprintf(fout, z, "%.10e");
fclose(fout);
}
FILE *out_file = fopen(out_filename, "w");
gsl_vector_fprintf(out_file, z, "%.10e");
fclose(out_file);
gsl_vector_free(z);
return 0;
}
