/* CardioWave - main include file */
/* Copyright John B. Pormann, 21 July 2000, all rights reserved */
/* RCSID: $Id: CardioWave.h,v 1.10 2005/02/17 18:38:25 john Exp $ */
#ifndef _SIMSYSTEM_H
#define _SIMSYSTEM_H
#include <stdlib.h>
#include <stdio.h>
#include <stddef.h>
#include <string.h>
#include <math.h>
#include <malloc.h>
#include <memory.h>
#include <time.h>
#include "mpi.h?"
#if defined(_SGL)
typedef float real;
#define MPI_SSREAL MPI_FLOAT
#else
typedef double real;
#define MPI_SSREAL MPI_DOUBLE
#endif
/* compute offset of a member in a structure */
#define OffsetOf?(type,member) (offsetof(type,member)/sizeof(real))
/* some other handy data types */
typedef enum { false = 0, true = -1, no = 0, yes = -1 } logical;
typedef unsigned char byte;
#define and &&
#define or ||
#define not !
#define mod %
/* simulation type */
typedef enum {
Error = -1,
Monodomain = 1,
ReducedBidomain? = 2,
FullBidomain? = 3,
ReducedBidomainBath? = 4,
FullBidomainBath? = 5
} sim_t;
/* domain type */
typedef enum {
Undefd = -1,
Tissue = 0,
Intracellular = 1,
Intra = 1,
Extracellular = 2,
Extra = 2,
Bath = 3,
Solver = 4,
State = 5,
StateVar? = 5,
Aux = 6,
AuxVar? = 6,
Memparam = 7,
Param = 7
} domain_t;
typedef enum {
TYPE_BYTE = 1,
TYPE_CHAR = 1,
TYPE_INT = 2,
TYPE_REAL = 3
} datatype_t;
/* this header is for the full-matrix, vector, and sparse-matrix operations */
#include "VectorOps.h"
/* the big matrix structure - for the solver */
/* : other arrays are size NumComm? */
typedef struct {
int Rows,Cols;
int NumBlocks?;
int* BlockSplit?;
sparse* MatrixInfo?;
} bigmatrix;
#define _INIT_BIGMATRIX {0,0,0,NULL,NULL}
/* some defined constants */
#define MAX_PROCS 256
#define MAX_RESOURCES 256
#define MAX_FILENAME 128
#define MAX_PATCHSIZE 64
#define MAX_STIM 32
#define MAX_MEMBRANE 8
#define G2L?_REMOTE -1
#define GETJ_ALL 0
#define GETJ_DIDV 1
/* for the byte type, -1 won't work */
#define ByteError? 255
/* for parsing the resource strings */
typedef struct {
char* txt;
int cmd;
} rword;
/* function prototypes */
int InitSimulation( char** resources );
void ExitSimulation( vector Vm, vector Vx, vector Q, vector Av );
int GetNodeInfo?( void );
int ComputeSizes( char** resources );
int DomainLocalSize( domain_t dt );
int DomainGlobalSize( domain_t dt );
int GetInitialValues( vector* Vm, vector* Vx, vector* Q, vector* Av );
int Checkpoint( real t, vector Vm, vector Vx, vector Q, vector Av );
int NextMsgTag( void );
real GetMemUsed( void );
/* : defined in SimSystem?.c - calls ??_GetF in Membrane models */
int GetF( vector Vm, vector Q, vector Fv, vector Fq, vector Av );
/* : for the membrane patches */
int InitMembrane?( char** resources );
void SetPatches?( vector Vm, vector Q );
void GetJ?( int flag, real dt, real theta, vector Vm, vector Q, vector Gv,
vector Gq, vector JJ, vector ZZ );
void GetDQ?( real dt, real theta, vector Vm, vector Q, vector Gv, vector Gq,
vector Dv, vector Dq );
void ExitMembrane?( void );
/* : for the time-steppers */
int InitTimeStepper( char** res, real* t );
int Update( real* t, vector Vm, vector Vx, vector Q, vector Av );
void ExitTimeStepper( void );
/* :: defined in time-stepper but called as an interrupt handler */
void CatchSignal( int i );
/* : for the domain model */
int InitDomain( char** resources );
void ExitDomain( void );
/* : for the stimulus model */
int InitStimulus( char** resources );
void ApplyStimulus( int IntraOrExtra?, real t, real alpha,vector Fv,vector Fq );
void ExitStimulus( void );
/* : for the linear solvers */
int InitLinearSolver( char** resources );
int Solve( bigmatrix A, vector x, vector b );
void ExitLinearSolver( void );
/* : for the preconditioners */
int InitPreconditioner( char** resources );
void ComputeFactors( bigmatrix A );
int PreconditionSystem( bigmatrix A, vector x, vector b );
void ExitPreconditioner( void );
/* : for the boundary conditions */
int InitBCs?( char** resources );
void ApplyBCmatrix?( bigmatrix A );
void ApplyBCvector?( real t, bigmatrix A, vector x, vector y );
void ExitBCs?( void );
/* : Parallel kernel */
int InitParallel( char** resources );
int CreateRegularSplitting( domain_t dt, int xd, int yd, int zd );
int CreateIrregularSplitting( domain_t dt, int sz, int bw );
int WriteGlobalData( void* ptr, int num, datatype_t dtp,
domain_t d, FILE* fp );
int ReadGlobalData( void* ptr, int num, datatype_t dtp,
domain_t d, FILE* fp );
int Global2Local( domain_t dt, int gl );
int Local2Global( domain_t dt, int lc );
int OwnerOfLocal( domain_t dt, int lc );
int OwnerOfGlobal( domain_t dt, int gl );
/* defined in Parallel kernels */
int MatAlloc( bigmatrix* M, int nblks, int* blksz, domain_t* dtps,
int type, int mnz, int mnz2 );
int MatCommSetup?( bigmatrix M );
int MatVec( real alpha, bigmatrix A, vector x, real beta, vector y );
int MatAdd( real alpha, bigmatrix A, bigmatrix B );
int MatScale( real alpha, bigmatrix A );
int MatCopy( bigmatrix A, bigmatrix B );
real MatGet( bigmatrix A, int i, int j );
int MatPut( bigmatrix A, int i, int j, real v );
void MatGetNonzeros( bigmatrix A, int i, int* n, int* lst );
/* :: used in catching signals */
real ProcessSignal?( real x );
/* : alias into the Vx vector */
int AliasVxVi( vector Vx, vector* Vi );
int AliasVxVe( vector Vx, vector* Ve );
int AliasVxVb( vector Vx, vector* Vb );
/* helper functions */
int AppendResources( char** res, int ac, char** av );
int NumResources( char** res );
int NumWords( rword* list );
real GetRealValue( char* txt );
int GetIntValue( char* txt );
logical GetTFValue( char* txt );
byte GetByteValue( char* txt );
int GetNumValues( char* txt );
int* GetIntArray( char* txt );
real* GetRealArray( char* txt );
char* GetStringValue( char* txt );
int FindCommand( rword* list, char* res );
int FindNum( char* txt );
/* global variables */
/* : defined in SimSystem?.c */
extern int NumPEs,SelfPE,NextPE?,PrevPE?;
extern int NumMem;
/* : MaxComm? is defined in Parallel module */
extern int MaxComm?;
/* : filled in by Mem modules */
extern int PatchSize[MAX_MEMBRANE];
extern logical UseAuxvars;
extern int AuxiliarySize[MAX_MEMBRANE];
extern int MemParamSize[MAX_MEMBRANE];
extern int (*FunctionTable[MAX_MEMBRANE])();
extern void (*SetpatchTable[MAX_MEMBRANE])();
/* : in SimSystem? kernel */
extern int DebugLevel;
extern logical LoadState,SaveState;
extern FILE* FpResources;
extern char* LoadStateFilename;
extern char* SaveStateFilename;
extern real Beta,Cm;
extern vector Workspace;
/* : defined in the Time-stepper */
extern sim_t SimType;
extern logical NeedVolume, NeedInvVolume;
/* : defined in the kernel, but initialized by Grid routines */
extern vector Volume;
extern vector InvVolume;
extern vector MemParams;
extern bvector NodeType;
extern int TissueGlobalSize,TissueLocalSize;
extern int BathGlobalSize,BathLocalSize;
extern int StateGlobalSize,StateLocalSize;
extern int AuxiliaryGlobalSize,AuxiliaryLocalSize;
extern int SolverGlobalSize,SolverLocalSize;
extern int MemparamGlobalSize,MemparamLocalSize;
extern int* TissueSplit;
extern int* BathSplit;
extern int* SolverSplit;
extern int* StateSplit;
extern int* AuxiliarySplit;
extern int* MemparamSplit;
extern sparse MatrixINT,MatrixEXT,MatrixBATH;
extern sparse MatrixE2B,MatrixB2E;
#endif
