cvodedata.h

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/*
  Last changed Time-stamp: <2005-12-21 18:09:54 raim>
  $Id: cvodedata.h,v 1.27 2005/12/21 17:02:53 raimc Exp $
*/
/* 
 *
 * This library is free software; you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as published
 * by the Free Software Foundation; either version 2.1 of the License, or
 * any later version.
 *
 * This library is distributed in the hope that it will be useful, but
 * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
 * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
 * documentation provided hereunder is on an "as is" basis, and the
 * authors have no obligations to provide maintenance, support,
 * updates, enhancements or modifications.  In no event shall the
 * authors be liable to any party for direct, indirect, special,
 * incidental or consequential damages, including lost profits, arising
 * out of the use of this software and its documentation, even if the
 * authors have been advised of the possibility of such damage.  See
 * the GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this library; if not, write to the Free Software Foundation,
 * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
 *
 * The original code contained here was initially developed by:
 *
 *     Rainer Machne
 *
 * Contributor(s):
 *     Andrew Finney
 *     
 */

#ifndef _CVODEDATA_H_
#define _CVODEDATA_H_

/* Header Files for CVODE: required only for realtype *p  */
#include "nvector_serial.h"

#include <stdio.h>
#include <sbml/SBMLTypes.h>

#include "sbmlsolver/cvodedatatype.h"
#include "sbmlsolver/odemodeldatatype.h"
#include "sbmlsolver/integratorSettings.h"
#include "sbmlsolver/exportdefs.h"
#include "sbmlsolver/odeModel.h"


struct cvodeResults {
  int nout;        
  double *time;    
  int nvalues;     
  double **value;

  /* number of variables x(t) for which sensitivities are calculated */
  int neq;
  int nsens;
  double ***sensitivity;

} ;

struct cvodeData {

  odeModel_t *model;
  
  /* ODEs f(x,p,t) = dx/dt and values x. The ODEs are usually
     optimized versions of the same array in odeModel */
  int neq;         
  ASTNode_t **ode; 
  int nvalues; 
  double *value; 

  float currenttime;

  /* current sensitivities: dx(t)/dp */
  int nsens;            
  double **sensitivity; 
  realtype *p;
  
  cvodeSettings_t *opt;
  
  int *trigger;
  int steadystate; 

  cvodeResults_t *results;

  int run;

} ;

#ifdef __cplusplus
extern "C" {
#endif
  /* create data for formula evaluation */
  SBML_ODESOLVER_API cvodeData_t *CvodeData_create(odeModel_t *);
  SBML_ODESOLVER_API void CvodeData_initializeValues(cvodeData_t *);
  SBML_ODESOLVER_API void CvodeData_free(cvodeData_t *);
  /* get values from cvodeResults */
  SBML_ODESOLVER_API double CvodeResults_getTime(cvodeResults_t *, int);
  SBML_ODESOLVER_API double CvodeResults_getValue(cvodeResults_t *, variableIndex_t *, int);
  SBML_ODESOLVER_API int CvodeResults_getNout(cvodeResults_t *);
  SBML_ODESOLVER_API void CvodeData_free(cvodeData_t *);
  SBML_ODESOLVER_API cvodeData_t *CvodeData_create(odeModel_t *);
  SBML_ODESOLVER_API double CvodeResults_getSensitivityByNum(cvodeResults_t *,  int value, int parameter, int timestep);
  SBML_ODESOLVER_API double CvodeResults_getSensitivity(cvodeResults_t *,  variableIndex_t *y,  variableIndex_t *p, int timestep);
  SBML_ODESOLVER_API void CvodeResults_free(cvodeResults_t *);
#ifdef __cplusplus
}
#endif


/* internal functions used by integratorInstance.c */
int CvodeData_initialize(cvodeData_t *, cvodeSettings_t *, odeModel_t *);
cvodeResults_t *CvodeResults_create(cvodeData_t *, int);
int CvodeResults_allocateSens(cvodeResults_t *, int neq, int nsens, int nout);


#endif

/* End of file */

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