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cp_evol.c
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cp_evol.c
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/* Copyright (c) 2014, Giuseppe Argentieri <[email protected]>
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
*
*/
/*
*
*
* Filename: cp_evol.c
*
* Description:
*
* Version: 1.0
* Created: 15/05/2014 19:36:38
* Revision: none
* License: BSD
*
* Author: Giuseppe Argentieri (ga), [email protected]
* Organization: Università degli Studi di Trieste
*
*
*/
#include <gsl/gsl_odeiv2.h>
#include <stdlib.h>
#include <string.h>
#include <gsl/gsl_ieee_utils.h>
#include "funcs.h"
#include "initial.h"
/*
* FUNCTION
* Name: cp_evol
* Description:
*
*/
int cp_evol ( void* params, const double r[], double time_end, double step,
const gsl_vector* req_cp, gsl_matrix* cp_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_cp = gsl_vector_calloc(4) ;
for ( i = 0 ; i < 4 ; i++ )
gsl_vector_set ( init_cp, i, r[i] ) ;
/*
*
* Initializing the system for Redfield dynamics
*
*/
gsl_odeiv2_system cp_sys = { generator, jac, 4, (void*) cp_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* c_s = gsl_odeiv2_step_alloc ( gsl_odeiv2_step_rkck , 4 ) ;
/* Setting the step control: abserr=1e-9, relerr=1e-3 */
gsl_odeiv2_control* c_c = gsl_odeiv2_control_standard_new ( 1e-9, 1e-3, 1, 1 ) ;
/* Allocating the space for evolution function */
gsl_odeiv2_evolve* c_e = gsl_odeiv2_evolve_alloc ( 4 ) ;
/* opening the files */
FILE* f_cp = fopen ( "CP-EVOLUTION.dat", "w" ) ;
FILE* g_cp = fopen ( "CP-ENTROPY-PROD.dat", "w" ) ;
FILE* h_cp = fopen ( "CP-CURRENT.dat", "w" ) ;
FILE* i_cp = fopen ( "CP-ENTROPY.dat", "w" ) ;
/* writing data */
while ( t < t_end )
{
evol ( t, init_cp, step, c_e, c_c, c_s, &cp_sys ) ;
fprintf ( f_cp, "%.2f %.9f %.9f %.9f %.9f\n", t,
VECTOR(init_cp,1), VECTOR(init_cp,2),
VECTOR(init_cp,3),
gsl_hypot3(VECTOR(init_cp,1),VECTOR(init_cp,2),
VECTOR(init_cp,3)) ) ;
fprintf ( g_cp, "%.2f %.9f\n",
t, entropy_production( init_cp, req_cp, cp_m )) ;
fprintf ( h_cp, "%.2f %.9f\n",
t, tot_current(init_cp, pars) ) ;
fprintf ( i_cp, "%.2f %.9f\n",
t, entropy_of_state(init_cp) ) ;
t += step ;
}
/* final entropy */
printf("Final entropy: %g\n", entropy_of_state(init_cp)) ;
/* close the files */
fclose (f_cp) ;
fclose (g_cp) ;
fclose (h_cp) ;
fclose (i_cp) ;
/* free memory for evolution */
gsl_odeiv2_evolve_free (c_e) ;
gsl_odeiv2_control_free (c_c) ;
gsl_odeiv2_step_free (c_s) ;
return 0;
} /* ----- end of function cp_evol ----- */
/*
* 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 CP matrix from a file */
gsl_matrix* cp_m = gsl_matrix_calloc ( 4, 4 ) ;
mat_read ( cp_m, "CP_MATRIX" ) ;
/*
* Find the stationary state by solving the linear systems
* and the associated stationary currents
*/
gsl_vector* req_cp = gsl_vector_calloc (4) ;
FILE* f_cp = fopen ( "CP_STATIONARY.dat", "r" ) ;
gsl_vector_fscanf ( f_cp, req_cp ) ;
if ( f_cp == NULL )
printf("Error: %s.\nFailed to open CP_STATIONARY.dat",
strerror(errno)) ;
fclose ( f_cp ) ;
printf("CP DYNAMICS\n") ;
printf("Stationary state: ( %.1f , %.9f , %.9f , %.9f )\n",
VECTOR(req_cp,0), VECTOR(req_cp,1),
VECTOR(req_cp,2), VECTOR(req_cp,3) ) ;
printf("Stationary normalized (I/I0) DC current: %.9f\n\n",
-VECTOR(req_cp,3)*OMEGA/omega_1) ;
int status = cp_evol ( ¶ms, R, t_end, STEP, req_cp, cp_m ) ;
if ( status != 0 )
exit (EXIT_FAILURE) ;
/* free memory for matrices */
gsl_matrix_free(cp_m) ;
return EXIT_SUCCESS;
} /* ---------- end of function main ---------- */