gsl_odeiv2_driver *
gsl_odeiv2_driver_alloc_standard_new (const gsl_odeiv2_system * sys,
const gsl_odeiv2_step_type * T,
const double hstart,
const double epsabs,
const double epsrel, const double a_y,
const double a_dydt)
{
/* Initializes an ODE driver system with control object of type
standard_new.
*/
gsl_odeiv2_driver *state = driver_alloc (sys, hstart, T);
if (state == NULL)
{
GSL_ERROR_NULL ("failed to allocate driver object", GSL_ENOMEM);
}
if (epsabs >= 0.0 && epsrel >= 0.0)
{
state->c =
gsl_odeiv2_control_standard_new (epsabs, epsrel, a_y, a_dydt);
if (state->c == NULL)
{
gsl_odeiv2_driver_free (state);
GSL_ERROR_NULL ("failed to allocate control object", GSL_ENOMEM);
}
}
else
{
gsl_odeiv2_driver_free (state);
GSL_ERROR_NULL ("epsabs and epsrel must be positive", GSL_EINVAL);
}
/* Distribute pointer to driver object */
gsl_odeiv2_step_set_driver (state->s, state);
gsl_odeiv2_evolve_set_driver (state->e, state);
gsl_odeiv2_control_set_driver (state->c, state);
return state;
}
void IzhikevichBranch::subthreshold_regimeRegime_::init_solver() {
IntegrationStep_ = cell->B_.step_;
static const gsl_odeiv2_step_type* T1 = gsl_odeiv2_step_rk2;
//FIXME: Could be reduced to include only the states which have a time
// derivative
N = 2;
if ( s_ == 0 )
s_ = gsl_odeiv2_step_alloc (T1, N);
else
gsl_odeiv2_step_reset(s_);
if ( c_ == 0 )
c_ = gsl_odeiv2_control_standard_new (0.001, 0.0, 1.0, 0.0);
else
gsl_odeiv2_control_init(c_, 0.001, 0.0, 1.0, 0.0);
if ( e_ == 0 )
e_ = gsl_odeiv2_evolve_alloc(N);
else
gsl_odeiv2_evolve_reset(e_);
sys_.function = IzhikevichBranch_subthreshold_regime_dynamics;
sys_.jacobian = IzhikevichBranch_subthreshold_regime_jacobian;
sys_.dimension = N;
sys_.params = reinterpret_cast<void*>(this->cell);
if (u == 0)
u = (double *)malloc(sizeof(double) * N);
assert (u);
if (jac == 0)
jac = (double *)malloc(sizeof(double) * N);
assert (jac);
}
/*
* FUNCTION
* Name: red_evol
* Description:
*
*/
int red_evol ( void* params, const double r[], double time_end, double step,
const gsl_vector* req_red, gsl_matrix* red_m )
{
struct f_params* pars = (struct f_params*) params ;
unsigned int i ; /* counter for the for loops */
/*
*
* evolving the systems
*
*/
double t = 0 ;
/* setting the initial vector */
gsl_vector* init_red = gsl_vector_calloc(4) ;
for ( i = 0 ; i < 4 ; i++ )
gsl_vector_set ( init_red, i, r[i] ) ;
/*
*
* Initializing the system for Redfield dynamics
*
*/
gsl_odeiv2_system red_sys = { generator, jac, 4, (void*) red_m } ;
/* Choosing the step function type: Runge-Kutta-Fehlberg (4,5) */
/* gsl_odeiv2_step* s = gsl_odeiv2_step_alloc ( gsl_odeiv2_step_rkf45 , 4 ) ; */
/* Choosing the step function type: Runge-Kutta Cash-Karp (4,5) */
gsl_odeiv2_step* r_s = gsl_odeiv2_step_alloc ( gsl_odeiv2_step_rkck , 4 ) ;
/* Setting the step control: abserr=1e-9, relerr=1e-3 */
gsl_odeiv2_control* r_c = gsl_odeiv2_control_standard_new ( 1e-9, 1e-3, 1, 1 ) ;
/* Allocating the space for evolution function */
gsl_odeiv2_evolve* r_e = gsl_odeiv2_evolve_alloc ( 4 ) ;
/* opening the files */
FILE* f_red = fopen ( "RED-EVOLUTION.dat", "w" ) ;
FILE* g_red = fopen ( "RED-ENTROPY-PROD.dat", "w" ) ;
FILE* h_red = fopen ( "RED-CURRENT.dat", "w" ) ;
FILE* i_red = fopen ( "RED-ENTROPY.dat", "w" ) ;
/* writing data */
while ( t < t_end )
{
evol ( t, init_red, step, r_e, r_c, r_s, &red_sys ) ;
fprintf ( f_red, "%.2f %.9f %.9f %.9f %.9f\n", t,
VECTOR(init_red,1), VECTOR(init_red,2),
VECTOR(init_red,3),
gsl_hypot3(VECTOR(init_red,1),VECTOR(init_red,2),
VECTOR(init_red,3)) ) ;
fprintf ( g_red, "%.2f %.9f\n",
t, entropy_production( init_red, req_red, red_m )) ;
fprintf ( h_red, "%.2f %.9f\n", t, tot_current(init_red, pars) ) ;
fprintf ( i_red, "%.2f %.9f\n",
t, entropy_of_state(init_red) ) ;
t += step ;
}
/* final entropy */
printf("Final entropy: %g\n", entropy_of_state(init_red) ) ;
/* close the files */
fclose (f_red) ;
fclose (g_red) ;
fclose (h_red) ;
fclose (i_red) ;
/* free memory for evolution */
gsl_odeiv2_evolve_free (r_e) ;
gsl_odeiv2_control_free (r_c) ;
gsl_odeiv2_step_free (r_s) ;
return 0;
} /* ----- end of function red_evol ----- */
gsl_odeiv2_control *
gsl_odeiv2_control_yp_new (double eps_abs, double eps_rel)
{
return gsl_odeiv2_control_standard_new (eps_abs, eps_rel, 0.0, 1.0);
}
