void FKIN_SETVIN(char key_name[], realtype *vval, int *ier, int key_len)
{
N_Vector Vec;
if (!strncmp(key_name,"CONSTR_VEC", (size_t)key_len)) {
Vec = NULL;
Vec = N_VCloneEmpty(F2C_KINSOL_vec);
if (Vec == NULL) {
*ier = -1;
return;
}
N_VSetArrayPointer(vval, Vec);
KINSetConstraints(KIN_kinmem, Vec);
N_VDestroy(Vec);
} else {
*ier = -99;
printf("FKINSETVIN: Unrecognized key.\n\n");
}
}
int main(void)
{
int globalstrategy;
realtype fnormtol, scsteptol;
N_Vector cc, sc, constraints;
UserData data;
int flag, maxl, maxlrst;
void *kmem;
cc = sc = constraints = NULL;
kmem = NULL;
data = NULL;
/* Allocate memory, and set problem data, initial values, tolerances */
globalstrategy = KIN_NONE;
data = AllocUserData();
if (check_flag((void *)data, "AllocUserData", 2)) return(1);
InitUserData(data);
/* Create serial vectors of length NEQ */
cc = N_VNew_Serial(NEQ);
if (check_flag((void *)cc, "N_VNew_Serial", 0)) return(1);
sc = N_VNew_Serial(NEQ);
if (check_flag((void *)sc, "N_VNew_Serial", 0)) return(1);
data->rates = N_VNew_Serial(NEQ);
if (check_flag((void *)data->rates, "N_VNew_Serial", 0)) return(1);
constraints = N_VNew_Serial(NEQ);
if (check_flag((void *)constraints, "N_VNew_Serial", 0)) return(1);
N_VConst(TWO, constraints);
SetInitialProfiles(cc, sc);
fnormtol=FTOL; scsteptol=STOL;
/* Call KINCreate/KINInit to initialize KINSOL.
A pointer to KINSOL problem memory is returned and stored in kmem. */
kmem = KINCreate();
if (check_flag((void *)kmem, "KINCreate", 0)) return(1);
/* Vector cc passed as template vector. */
flag = KINInit(kmem, func, cc);
if (check_flag(&flag, "KINInit", 1)) return(1);
flag = KINSetUserData(kmem, data);
if (check_flag(&flag, "KINSetUserData", 1)) return(1);
flag = KINSetConstraints(kmem, constraints);
if (check_flag(&flag, "KINSetConstraints", 1)) return(1);
flag = KINSetFuncNormTol(kmem, fnormtol);
if (check_flag(&flag, "KINSetFuncNormTol", 1)) return(1);
flag = KINSetScaledStepTol(kmem, scsteptol);
if (check_flag(&flag, "KINSetScaledStepTol", 1)) return(1);
/* We no longer need the constraints vector since KINSetConstraints
creates a private copy for KINSOL to use. */
N_VDestroy_Serial(constraints);
/* Call KINSpgmr to specify the linear solver KINSPGMR with preconditioner
routines PrecSetupBD and PrecSolveBD. */
maxl = 15;
maxlrst = 2;
flag = KINSpgmr(kmem, maxl);
if (check_flag(&flag, "KINSpgmr", 1)) return(1);
flag = KINSpilsSetMaxRestarts(kmem, maxlrst);
if (check_flag(&flag, "KINSpilsSetMaxRestarts", 1)) return(1);
flag = KINSpilsSetPreconditioner(kmem,
PrecSetupBD,
PrecSolveBD);
if (check_flag(&flag, "KINSpilsSetPreconditioner", 1)) return(1);
/* Print out the problem size, solution parameters, initial guess. */
PrintHeader(globalstrategy, maxl, maxlrst, fnormtol, scsteptol);
/* Call KINSol and print output concentration profile */
flag = KINSol(kmem, /* KINSol memory block */
cc, /* initial guess on input; solution vector */
globalstrategy, /* global stragegy choice */
sc, /* scaling vector, for the variable cc */
sc); /* scaling vector for function values fval */
if (check_flag(&flag, "KINSol", 1)) return(1);
printf("\n\nComputed equilibrium species concentrations:\n");
PrintOutput(cc);
/* Print final statistics and free memory */
PrintFinalStats(kmem);
N_VDestroy_Serial(cc);
N_VDestroy_Serial(sc);
KINFree(&kmem);
FreeUserData(data);
return(0);
}
int main(int argc, char *argv[])
{
MPI_Comm comm;
void *kmem;
UserData data;
N_Vector cc, sc, constraints;
int globalstrategy;
long int Nlocal;
realtype fnormtol, scsteptol, dq_rel_uu;
int flag, maxl, maxlrst;
long int mudq, mldq, mukeep, mlkeep;
int my_pe, npes, npelast = NPEX*NPEY-1;
data = NULL;
kmem = NULL;
cc = sc = constraints = NULL;
/* Get processor number and total number of pe's */
MPI_Init(&argc, &argv);
comm = MPI_COMM_WORLD;
MPI_Comm_size(comm, &npes);
MPI_Comm_rank(comm, &my_pe);
if (npes != NPEX*NPEY) {
if (my_pe == 0)
printf("\nMPI_ERROR(0): npes=%d is not equal to NPEX*NPEY=%d\n", npes,
NPEX*NPEY);
return(1);
}
/* Allocate memory, and set problem data, initial values, tolerances */
/* Set local length */
Nlocal = NUM_SPECIES*MXSUB*MYSUB;
/* Allocate and initialize user data block */
data = AllocUserData();
if (check_flag((void *)data, "AllocUserData", 2, my_pe)) MPI_Abort(comm, 1);
InitUserData(my_pe, Nlocal, comm, data);
/* Choose global strategy */
globalstrategy = KIN_NONE;
/* Allocate and initialize vectors */
cc = N_VNew_Parallel(comm, Nlocal, NEQ);
if (check_flag((void *)cc, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1);
sc = N_VNew_Parallel(comm, Nlocal, NEQ);
if (check_flag((void *)sc, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1);
data->rates = N_VNew_Parallel(comm, Nlocal, NEQ);
if (check_flag((void *)data->rates, "N_VNew_Parallel", 0, my_pe))
MPI_Abort(comm, 1);
constraints = N_VNew_Parallel(comm, Nlocal, NEQ);
if (check_flag((void *)constraints, "N_VNew_Parallel", 0, my_pe))
MPI_Abort(comm, 1);
N_VConst(ZERO, constraints);
SetInitialProfiles(cc, sc);
fnormtol = FTOL; scsteptol = STOL;
/* Call KINCreate/KINInit to initialize KINSOL:
nvSpec points to machine environment data
A pointer to KINSOL problem memory is returned and stored in kmem. */
kmem = KINCreate();
if (check_flag((void *)kmem, "KINCreate", 0, my_pe)) MPI_Abort(comm, 1);
/* Vector cc passed as template vector. */
flag = KINInit(kmem, func, cc);
if (check_flag(&flag, "KINInit", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSetUserData(kmem, data);
if (check_flag(&flag, "KINSetUserData", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSetConstraints(kmem, constraints);
if (check_flag(&flag, "KINSetConstraints", 1, my_pe)) MPI_Abort(comm, 1);
/* We no longer need the constraints vector since KINSetConstraints
creates a private copy for KINSOL to use. */
N_VDestroy_Parallel(constraints);
flag = KINSetFuncNormTol(kmem, fnormtol);
if (check_flag(&flag, "KINSetFuncNormTol", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSetScaledStepTol(kmem, scsteptol);
if (check_flag(&flag, "KINSetScaledStepTol", 1, my_pe)) MPI_Abort(comm, 1);
/* Call KINBBDPrecInit to initialize and allocate memory for the
band-block-diagonal preconditioner, and specify the local and
communication functions func_local and gcomm=NULL (all communication
needed for the func_local is already done in func). */
dq_rel_uu = ZERO;
mudq = mldq = 2*NUM_SPECIES - 1;
mukeep = mlkeep = NUM_SPECIES;
/* Call KINBBDSpgmr to specify the linear solver KINSPGMR */
maxl = 20; maxlrst = 2;
flag = KINSpgmr(kmem, maxl);
if (check_flag(&flag, "KINSpgmr", 1, my_pe)) MPI_Abort(comm, 1);
/* Initialize BBD preconditioner */
flag = KINBBDPrecInit(kmem, Nlocal, mudq, mldq, mukeep, mlkeep,
dq_rel_uu, func_local, NULL);
if (check_flag(&flag, "KINBBDPrecInit", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSpilsSetMaxRestarts(kmem, maxlrst);
if (check_flag(&flag, "KINSpilsSetMaxRestarts", 1, my_pe))
MPI_Abort(comm, 1);
/* Print out the problem size, solution parameters, initial guess. */
if (my_pe == 0)
PrintHeader(globalstrategy, maxl, maxlrst, mudq, mldq, mukeep,
mlkeep, fnormtol, scsteptol);
/* call KINSol and print output concentration profile */
flag = KINSol(kmem, /* KINSol memory block */
cc, /* initial guesss on input; solution vector */
globalstrategy, /* global stragegy choice */
sc, /* scaling vector, for the variable cc */
sc); /* scaling vector for function values fval */
if (check_flag(&flag, "KINSol", 1, my_pe)) MPI_Abort(comm, 1);
if (my_pe == 0) printf("\n\nComputed equilibrium species concentrations:\n");
if (my_pe == 0 || my_pe==npelast) PrintOutput(my_pe, comm, cc);
/* Print final statistics and free memory */
if (my_pe == 0)
PrintFinalStats(kmem);
N_VDestroy_Parallel(cc);
N_VDestroy_Parallel(sc);
KINFree(&kmem);
FreeUserData(data);
MPI_Finalize();
return(0);
}
int main()
{
UserData data;
realtype fnormtol, scsteptol;
N_Vector u1, u2, u, s, c;
int glstr, mset, flag;
void *kmem;
u1 = u2 = u = NULL;
s = c = NULL;
kmem = NULL;
data = NULL;
/* User data */
data = (UserData)malloc(sizeof *data);
data->lb[0] = PT25; data->ub[0] = ONE;
data->lb[1] = ONEPT5; data->ub[1] = TWO*PI;
/* Create serial vectors of length NEQ */
u1 = N_VNew_Serial(NEQ);
if (check_flag((void *)u1, "N_VNew_Serial", 0)) return(1);
u2 = N_VNew_Serial(NEQ);
if (check_flag((void *)u2, "N_VNew_Serial", 0)) return(1);
u = N_VNew_Serial(NEQ);
if (check_flag((void *)u, "N_VNew_Serial", 0)) return(1);
s = N_VNew_Serial(NEQ);
if (check_flag((void *)s, "N_VNew_Serial", 0)) return(1);
c = N_VNew_Serial(NEQ);
if (check_flag((void *)c, "N_VNew_Serial", 0)) return(1);
SetInitialGuess1(u1,data);
SetInitialGuess2(u2,data);
N_VConst_Serial(ONE,s); /* no scaling */
Ith(c,1) = ZERO; /* no constraint on x1 */
Ith(c,2) = ZERO; /* no constraint on x2 */
Ith(c,3) = ONE; /* l1 = x1 - x1_min >= 0 */
Ith(c,4) = -ONE; /* L1 = x1 - x1_max <= 0 */
Ith(c,5) = ONE; /* l2 = x2 - x2_min >= 0 */
Ith(c,6) = -ONE; /* L2 = x2 - x22_min <= 0 */
fnormtol=FTOL; scsteptol=STOL;
kmem = KINCreate();
if (check_flag((void *)kmem, "KINCreate", 0)) return(1);
flag = KINSetUserData(kmem, data);
if (check_flag(&flag, "KINSetUserData", 1)) return(1);
flag = KINSetConstraints(kmem, c);
if (check_flag(&flag, "KINSetConstraints", 1)) return(1);
flag = KINSetFuncNormTol(kmem, fnormtol);
if (check_flag(&flag, "KINSetFuncNormTol", 1)) return(1);
flag = KINSetScaledStepTol(kmem, scsteptol);
if (check_flag(&flag, "KINSetScaledStepTol", 1)) return(1);
flag = KINInit(kmem, func, u);
if (check_flag(&flag, "KINInit", 1)) return(1);
/* Call KINDense to specify the linear solver */
flag = KINDense(kmem, NEQ);
if (check_flag(&flag, "KINDense", 1)) return(1);
/* Print out the problem size, solution parameters, initial guess. */
PrintHeader(fnormtol, scsteptol);
/* --------------------------- */
printf("\n------------------------------------------\n");
printf("\nInitial guess on lower bounds\n");
printf(" [x1,x2] = ");
PrintOutput(u1);
N_VScale_Serial(ONE,u1,u);
glstr = KIN_NONE;
mset = 1;
SolveIt(kmem, u, s, glstr, mset);
/* --------------------------- */
N_VScale_Serial(ONE,u1,u);
glstr = KIN_LINESEARCH;
mset = 1;
SolveIt(kmem, u, s, glstr, mset);
/* --------------------------- */
N_VScale_Serial(ONE,u1,u);
glstr = KIN_NONE;
mset = 0;
SolveIt(kmem, u, s, glstr, mset);
/* --------------------------- */
N_VScale_Serial(ONE,u1,u);
glstr = KIN_LINESEARCH;
mset = 0;
SolveIt(kmem, u, s, glstr, mset);
/* --------------------------- */
printf("\n------------------------------------------\n");
printf("\nInitial guess in middle of feasible region\n");
printf(" [x1,x2] = ");
PrintOutput(u2);
N_VScale_Serial(ONE,u2,u);
glstr = KIN_NONE;
mset = 1;
SolveIt(kmem, u, s, glstr, mset);
/* --------------------------- */
N_VScale_Serial(ONE,u2,u);
glstr = KIN_LINESEARCH;
mset = 1;
SolveIt(kmem, u, s, glstr, mset);
/* --------------------------- */
N_VScale_Serial(ONE,u2,u);
glstr = KIN_NONE;
mset = 0;
SolveIt(kmem, u, s, glstr, mset);
/* --------------------------- */
N_VScale_Serial(ONE,u2,u);
glstr = KIN_LINESEARCH;
mset = 0;
SolveIt(kmem, u, s, glstr, mset);
/* Free memory */
N_VDestroy_Serial(u);
N_VDestroy_Serial(s);
N_VDestroy_Serial(c);
KINFree(&kmem);
free(data);
return(0);
}
int main()
{
realtype fnormtol, scsteptol;
N_Vector y, scale, constraints;
int mset, flag, i;
void *kmem;
SUNMatrix J;
SUNLinearSolver LS;
y = scale = constraints = NULL;
kmem = NULL;
J = NULL;
LS = NULL;
printf("\nRobot Kinematics Example\n");
printf("8 variables; -1 <= x_i <= 1\n");
printf("KINSOL problem size: 8 + 2*8 = 24 \n\n");
/* Create vectors for solution, scales, and constraints */
y = N_VNew_Serial(NEQ);
if (check_flag((void *)y, "N_VNew_Serial", 0)) return(1);
scale = N_VNew_Serial(NEQ);
if (check_flag((void *)scale, "N_VNew_Serial", 0)) return(1);
constraints = N_VNew_Serial(NEQ);
if (check_flag((void *)constraints, "N_VNew_Serial", 0)) return(1);
/* Initialize and allocate memory for KINSOL */
kmem = KINCreate();
if (check_flag((void *)kmem, "KINCreate", 0)) return(1);
flag = KINInit(kmem, func, y); /* y passed as a template */
if (check_flag(&flag, "KINInit", 1)) return(1);
/* Set optional inputs */
N_VConst_Serial(ZERO,constraints);
for (i = NVAR+1; i <= NEQ; i++) Ith(constraints, i) = ONE;
flag = KINSetConstraints(kmem, constraints);
if (check_flag(&flag, "KINSetConstraints", 1)) return(1);
fnormtol = FTOL;
flag = KINSetFuncNormTol(kmem, fnormtol);
if (check_flag(&flag, "KINSetFuncNormTol", 1)) return(1);
scsteptol = STOL;
flag = KINSetScaledStepTol(kmem, scsteptol);
if (check_flag(&flag, "KINSetScaledStepTol", 1)) return(1);
/* Create dense SUNMatrix */
J = SUNDenseMatrix(NEQ, NEQ);
if(check_flag((void *)J, "SUNDenseMatrix", 0)) return(1);
/* Create dense SUNLinearSolver object */
LS = SUNLinSol_Dense(y, J);
if(check_flag((void *)LS, "SUNLinSol_Dense", 0)) return(1);
/* Attach the matrix and linear solver to KINSOL */
flag = KINSetLinearSolver(kmem, LS, J);
if(check_flag(&flag, "KINSetLinearSolver", 1)) return(1);
/* Set the Jacobian function */
flag = KINSetJacFn(kmem, jac);
if (check_flag(&flag, "KINSetJacFn", 1)) return(1);
/* Indicate exact Newton */
mset = 1;
flag = KINSetMaxSetupCalls(kmem, mset);
if (check_flag(&flag, "KINSetMaxSetupCalls", 1)) return(1);
/* Initial guess */
N_VConst_Serial(ONE, y);
for(i = 1; i <= NVAR; i++) Ith(y,i) = SUNRsqrt(TWO)/TWO;
printf("Initial guess:\n");
PrintOutput(y);
/* Call KINSol to solve problem */
N_VConst_Serial(ONE,scale);
flag = KINSol(kmem, /* KINSol memory block */
y, /* initial guess on input; solution vector */
KIN_LINESEARCH, /* global strategy choice */
scale, /* scaling vector, for the variable cc */
scale); /* scaling vector for function values fval */
if (check_flag(&flag, "KINSol", 1)) return(1);
printf("\nComputed solution:\n");
PrintOutput(y);
/* Print final statistics and free memory */
PrintFinalStats(kmem);
N_VDestroy_Serial(y);
N_VDestroy_Serial(scale);
N_VDestroy_Serial(constraints);
KINFree(&kmem);
SUNLinSolFree(LS);
SUNMatDestroy(J);
return(0);
}
/*! \fn kinsol_initialization
*
* \param [ref] [data]
* \param [in] [initData]
* \param [ref] [initialResiduals]
*
* \author lochel
*/
int kinsol_initialization(DATA* data, INIT_DATA* initData, int useScaling)
{
long i, indz;
KINSOL_DATA* kdata = NULL;
double fnormtol = 1.e-9; /* function tolerance */
double scsteptol = 1.e-9; /* step tolerance */
long int nni, nfe, nje, nfeD;
N_Vector z = NULL;
N_Vector sVars = NULL;
N_Vector sEqns = NULL;
N_Vector c = NULL;
int glstr = KIN_NONE; /* globalization strategy applied to the Newton method. It must be one of KIN_NONE or KIN_LINESEARCH */
long int mset = 1; /* maximum number of nonlinear iterations without a call to the preconditioner setup function. Pass 0 to indicate the default [10]. */
void *kmem = NULL;
int error_code = -1;
ASSERT(data->modelData.nInitResiduals == initData->nz, "The number of initial equations are not consistent with the number of unfixed variables. Select a different initialization.");
do /* Try it first with KIN_NONE. If that fails, try it with KIN_LINESEARCH. */
{
if(mset == 1 && glstr == KIN_NONE)
DEBUG_INFO(LOG_INIT, "using exact Newton");
else if(mset == 1)
DEBUG_INFO(LOG_INIT, "using exact Newton with line search");
else if(glstr == KIN_NONE)
DEBUG_INFO(LOG_INIT, "using modified Newton");
else
DEBUG_INFO(LOG_INIT, "using modified Newton with line search");
DEBUG_INFO_AL1(LOG_INIT, "| mset = %10ld", mset);
DEBUG_INFO_AL1(LOG_INIT, "| function tolerance = %10.6g", fnormtol);
DEBUG_INFO_AL1(LOG_INIT, "| step tolerance = %10.6g", scsteptol);
kdata = (KINSOL_DATA*)malloc(sizeof(KINSOL_DATA));
ASSERT(kdata, "out of memory");
kdata->initData = initData;
kdata->data = data;
z = N_VNew_Serial(3*initData->nz);
ASSERT(z, "out of memory");
sVars = N_VNew_Serial(3*initData->nz);
ASSERT(sVars, "out of memory");
sEqns = N_VNew_Serial(3*initData->nz);
ASSERT(sEqns, "out of memory");
c = N_VNew_Serial(3*initData->nz);
ASSERT(c, "out of memory");
/* initial guess */
for(i=0; i<initData->nz; ++i)
{
NV_Ith_S(z, i) = initData->start[i];
NV_Ith_S(z, initData->nInitResiduals+2*i+0) = NV_Ith_S(z, i) - initData->min[i];
NV_Ith_S(z, initData->nInitResiduals+2*i+1) = NV_Ith_S(z, i) - initData->max[i];
}
kdata->useScaling=useScaling;
if(useScaling)
{
computeInitialResidualScalingCoefficients(data, initData);
for(i=0; i<initData->nz; ++i)
{
NV_Ith_S(sVars, i) = 1.0 / (initData->nominal[i] == 0.0 ? 1.0 : initData->nominal[i]);
NV_Ith_S(sVars, initData->nInitResiduals+2*i+0) = NV_Ith_S(sVars, i);
NV_Ith_S(sVars, initData->nInitResiduals+2*i+1) = NV_Ith_S(sVars, i);
NV_Ith_S(sEqns, i) = 1.0 / (initData->residualScalingCoefficients[i] == 0.0 ? 1.0 : initData->residualScalingCoefficients[i]);
NV_Ith_S(sEqns, initData->nInitResiduals+2*i+0) = NV_Ith_S(sEqns, i);
NV_Ith_S(sEqns, initData->nInitResiduals+2*i+1) = NV_Ith_S(sEqns, i);
}
}
else
{
N_VConst_Serial(1.0, sVars); /* no scaling */
N_VConst_Serial(1.0, sEqns); /* no scaling */
}
for(i=0; i<initData->nz; ++i)
{
NV_Ith_S(c, i) = 0.0; /* no constraint on z[i] */
NV_Ith_S(c, initData->nInitResiduals+2*i+0) = 1.0;
NV_Ith_S(c, initData->nInitResiduals+2*i+1) = -1.0;
}
kmem = KINCreate();
ASSERT(kmem, "out of memory");
KINSetErrHandlerFn(kmem, kinsol_errorHandler, NULL);
KINSetUserData(kmem, kdata);
KINSetConstraints(kmem, c);
KINSetFuncNormTol(kmem, fnormtol);
KINSetScaledStepTol(kmem, scsteptol);
KINInit(kmem, kinsol_residuals, z);
/* Call KINDense to specify the linear solver */
KINDense(kmem, 3*initData->nz);
KINSetMaxSetupCalls(kmem, mset);
/*KINSetNumMaxIters(kmem, 2000);*/
globalInitialResiduals = initData->initialResiduals;
error_code = KINSol(kmem, /* KINSol memory block */
z, /* initial guess on input; solution vector */
glstr, /* global stragegy choice */
sVars, /* scaling vector, for the variable cc */
sEqns); /* scaling vector for function values fval */
globalInitialResiduals = NULL;
KINGetNumNonlinSolvIters(kmem, &nni);
KINGetNumFuncEvals(kmem, &nfe);
KINDlsGetNumJacEvals(kmem, &nje);
KINDlsGetNumFuncEvals(kmem, &nfeD);
DEBUG_INFO(LOG_INIT, "final kinsol statistics");
DEBUG_INFO_AL1(LOG_INIT, "| KINGetNumNonlinSolvIters = %5ld", nni);
DEBUG_INFO_AL1(LOG_INIT, "| KINGetNumFuncEvals = %5ld", nfe);
DEBUG_INFO_AL1(LOG_INIT, "| KINDlsGetNumJacEvals = %5ld", nje);
DEBUG_INFO_AL1(LOG_INIT, "| KINDlsGetNumFuncEvals = %5ld", nfeD);
/* Free memory */
N_VDestroy_Serial(z);
N_VDestroy_Serial(sVars);
N_VDestroy_Serial(sEqns);
N_VDestroy_Serial(c);
KINFree(&kmem);
free(kdata);
if(error_code < 0)
glstr++; /* try next globalization strategy */
}while(error_code < 0 && glstr <= KIN_LINESEARCH);
/* debug output */
indz = 0;
DEBUG_INFO(LOG_INIT, "solution");
for(i=0; i<data->modelData.nStates; ++i)
if(data->modelData.realVarsData[i].attribute.fixed==0)
DEBUG_INFO_AL2(LOG_INIT, "| %s = %g", initData->name[indz++], data->localData[0]->realVars[i]);
for(i=0; i<data->modelData.nParametersReal; ++i)
if(data->modelData.realParameterData[i].attribute.fixed == 0)
DEBUG_INFO_AL2(LOG_INIT, "| %s = %g", initData->name[indz++], data->simulationInfo.realParameter[i]);
if(error_code < 0)
THROW("kinsol failed. see last warning. use [-lv LOG_INIT] for more output.");
return 0;
}
int main(int argc, char *argv[])
{
int globalstrategy;
long int local_N;
realtype fnormtol, scsteptol;
N_Vector cc, sc, constraints;
UserData data;
int flag, maxl, maxlrst;
int my_pe, npes, npelast = NPEX*NPEY-1;
void *kmem;
MPI_Comm comm;
cc = sc = constraints = NULL;
data = NULL;
kmem = NULL;
/* Get processor number and total number of pe's */
MPI_Init(&argc, &argv);
comm = MPI_COMM_WORLD;
MPI_Comm_size(comm, &npes);
MPI_Comm_rank(comm, &my_pe);
if (npes != NPEX*NPEY) {
if (my_pe == 0)
fprintf(stderr, "\nMPI_ERROR(0); npes = %d is not equal to NPEX*NPEY = %d\n",
npes,NPEX*NPEY);
MPI_Finalize();
return(1);
}
/* Allocate memory, and set problem data, initial values, tolerances */
/* Set local vector length */
local_N = NUM_SPECIES*MXSUB*MYSUB;
/* Allocate and initialize user data block */
data = AllocUserData();
if (check_flag((void *)data, "AllocUserData", 0, my_pe)) MPI_Abort(comm, 1);
InitUserData(my_pe, comm, data);
/* Set global strategy flag */
globalstrategy = KIN_NONE;
/* Allocate and initialize vectors */
cc = N_VNew_Parallel(comm, local_N, NEQ);
if (check_flag((void *)cc, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1);
sc = N_VNew_Parallel(comm, local_N, NEQ);
if (check_flag((void *)sc, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1);
data->rates = N_VNew_Parallel(comm, local_N, NEQ);
if (check_flag((void *)data->rates, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1);
constraints = N_VNew_Parallel(comm, local_N, NEQ);
if (check_flag((void *)constraints, "N_VNew_Parallel", 0, my_pe)) MPI_Abort(comm, 1);
N_VConst(ZERO, constraints);
SetInitialProfiles(cc, sc);
fnormtol=FTOL; scsteptol=STOL;
/* Call KINCreate/KINMalloc to initialize KINSOL:
nvSpec is the nvSpec pointer used in the parallel version
A pointer to KINSOL problem memory is returned and stored in kmem. */
kmem = KINCreate();
if (check_flag((void *)kmem, "KINCreate", 0, my_pe)) MPI_Abort(comm, 1);
/* Vector cc passed as template vector. */
flag = KINMalloc(kmem, funcprpr, cc);
if (check_flag(&flag, "KINMalloc", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSetNumMaxIters(kmem, 250);
if (check_flag(&flag, "KINSetNumMaxIters", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSetFdata(kmem, data);
if (check_flag(&flag, "KINSetFdata", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSetConstraints(kmem, constraints);
if (check_flag(&flag, "KINSetConstraints", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSetFuncNormTol(kmem, fnormtol);
if (check_flag(&flag, "KINSetFuncNormTol", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSetScaledStepTol(kmem, scsteptol);
if (check_flag(&flag, "KINSetScaledStepTop", 1, my_pe)) MPI_Abort(comm, 1);
/* We no longer need the constraints vector since KINSetConstraints
creates a private copy for KINSOL to use. */
N_VDestroy_Parallel(constraints);
/* Call KINSpgmr to specify the linear solver KINSPGMR with preconditioner
routines Precondbd and PSolvebd, and the pointer to the user data block. */
maxl = 20; maxlrst = 2;
flag = KINSpgmr(kmem, maxl);
if (check_flag(&flag, "KINSpgmr", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSpilsSetMaxRestarts(kmem, maxlrst);
if (check_flag(&flag, "KINSpilsSetMaxRestarts", 1, my_pe)) MPI_Abort(comm, 1);
flag = KINSpilsSetPreconditioner(kmem,
Precondbd,
PSolvebd,
data);
if (check_flag(&flag, "KINSpilsSetPreconditioner", 1, my_pe)) MPI_Abort(comm, 1);
/* Print out the problem size, solution parameters, initial guess. */
if (my_pe == 0)
PrintHeader(globalstrategy, maxl, maxlrst, fnormtol, scsteptol);
/* Call KINSol and print output concentration profile */
flag = KINSol(kmem, /* KINSol memory block */
cc, /* initial guess on input; solution vector */
globalstrategy, /* global stragegy choice */
sc, /* scaling vector for the variable cc */
sc); /* scaling vector for function values fval */
if (check_flag(&flag, "KINSol", 1, my_pe)) MPI_Abort(comm, 1);
if (my_pe == 0)
printf("\n\nComputed equilibrium species concentrations:\n");
if (my_pe == 0 || my_pe == npelast)
PrintOutput(my_pe, comm, cc);
/* Print final statistics and free memory */
if (my_pe == 0)
PrintFinalStats(kmem);
N_VDestroy_Parallel(cc);
N_VDestroy_Parallel(sc);
KINFree(&kmem);
FreeUserData(data);
MPI_Finalize();
return(0);
}
static void KIM_Malloc(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
int status;
mxArray *mx_in[3], *mx_out[2];
int mxiter, msbset, msbsetsub, etachoice, mxnbcf;
double eta, egamma, ealpha, mxnewtstep, relfunc, fnormtol, scsteptol;
booleantype verbose, noInitSetup, noMinEps;
double *constraints;
N_Vector NVconstraints;
int ptype;
int mudq, mldq, mupper, mlower;
int maxl, maxrs;
double dqrely;
/*
* -----------------------------
* Find out the vector type and
* then pass it to the vector
* library.
* -----------------------------
*/
/* Send vec_type and mx_comm */
InitVectors();
/*
* -----------------------------
* Extract stuff from arguments:
* - SYS function
* - problem dimension
* - solver options
* - user data
* -----------------------------
*/
/* Matlab user-provided function */
mxDestroyArray(mx_SYSfct);
mx_SYSfct = mxDuplicateArray(prhs[0]);
/* problem dimension */
N = (int) mxGetScalar(prhs[1]);
/* Solver Options -- optional argument */
status = get_SolverOptions(prhs[2],
&verbose,
&mxiter, &msbset, &msbsetsub, &etachoice, &mxnbcf,
&eta, &egamma, &ealpha, &mxnewtstep,
&relfunc, &fnormtol, &scsteptol,
&constraints,
&noInitSetup, &noMinEps);
/* User data -- optional argument */
mxDestroyArray(mx_data);
mx_data = mxDuplicateArray(prhs[3]);
/*
* -----------------------------------------------------
* Set solution vector (used as a template to KINMAlloc)
* -----------------------------------------------------
*/
y = NewVector(N);
/*
* ----------------------------------------
* Create kinsol object and allocate memory
* ----------------------------------------
*/
kin_mem = KINCreate();
/* attach error handler function */
status = KINSetErrHandlerFn(kin_mem, mtlb_KINErrHandler, NULL);
if (verbose) {
status = KINSetPrintLevel(kin_mem,3);
/* attach info handler function */
status = KINSetInfoHandlerFn(kin_mem, mtlb_KINInfoHandler, NULL);
/* initialize the output window */
mx_in[0] = mxCreateScalarDouble(0);
mx_in[1] = mxCreateScalarDouble(0); /* ignored */
mx_in[2] = mxCreateScalarDouble(0); /* ignored */
mexCallMATLAB(1,mx_out,3,mx_in,"kim_info");
fig_handle = (int)*mxGetPr(mx_out[0]);
}
/* Call KINMalloc */
status = KINMalloc(kin_mem, mtlb_KINSys, y);
/* Redirect output */
status = KINSetErrFile(kin_mem, stdout);
/* Optional inputs */
status = KINSetNumMaxIters(kin_mem,mxiter);
status = KINSetNoInitSetup(kin_mem,noInitSetup);
status = KINSetNoMinEps(kin_mem,noMinEps);
status = KINSetMaxSetupCalls(kin_mem,msbset);
status = KINSetMaxSubSetupCalls(kin_mem,msbsetsub);
status = KINSetMaxBetaFails(kin_mem,mxnbcf);
status = KINSetEtaForm(kin_mem,etachoice);
status = KINSetEtaConstValue(kin_mem,eta);
status = KINSetEtaParams(kin_mem,egamma,ealpha);
status = KINSetMaxNewtonStep(kin_mem,mxnewtstep);
status = KINSetRelErrFunc(kin_mem,relfunc);
status = KINSetFuncNormTol(kin_mem,fnormtol);
status = KINSetScaledStepTol(kin_mem,scsteptol);
if (constraints != NULL) {
NVconstraints = N_VCloneEmpty(y);
N_VSetArrayPointer(constraints, NVconstraints);
status = KINSetConstraints(kin_mem,NVconstraints);
N_VDestroy(NVconstraints);
}
status = get_LinSolvOptions(prhs[2],
&mupper, &mlower,
&mudq, &mldq, &dqrely,
&ptype, &maxrs, &maxl);
switch (ls) {
case LS_NONE:
mexErrMsgTxt("KINMalloc:: no linear solver specified.");
break;
case LS_DENSE:
status = KINDense(kin_mem, N);
if (!mxIsEmpty(mx_JACfct))
status = KINDenseSetJacFn(kin_mem, mtlb_KINDenseJac, NULL);
break;
case LS_BAND:
status = KINBand(kin_mem, N, mupper, mlower);
if (!mxIsEmpty(mx_JACfct))
status = KINBandSetJacFn(kin_mem, mtlb_KINBandJac, NULL);
break;
case LS_SPGMR:
switch(pm) {
case PM_NONE:
status = KINSpgmr(kin_mem, maxl);
if (!mxIsEmpty(mx_PSOLfct)) {
if (!mxIsEmpty(mx_PSETfct))
status = KINSpilsSetPreconditioner(kin_mem, mtlb_KINSpilsPset, mtlb_KINSpilsPsol, NULL);
else
status = KINSpilsSetPreconditioner(kin_mem, NULL, mtlb_KINSpilsPsol, NULL);
}
break;
case PM_BBDPRE:
if (!mxIsEmpty(mx_GCOMfct))
bbd_data = KINBBDPrecAlloc(kin_mem, N, mudq, mldq, mupper, mlower, dqrely, mtlb_KINGloc, mtlb_KINGcom);
else
bbd_data = KINBBDPrecAlloc(kin_mem, N, mudq, mldq, mupper, mlower, dqrely, mtlb_KINGloc, NULL);
status = KINBBDSpgmr(kin_mem, maxl, bbd_data);
break;
}
status = KINSpilsSetMaxRestarts(kin_mem, maxrs);
if (!mxIsEmpty(mx_JACfct))
status = KINSpilsSetJacTimesVecFn(kin_mem, mtlb_KINSpilsJac, NULL);
break;
case LS_SPBCG:
switch(pm) {
case PM_NONE:
status = KINSpbcg(kin_mem, maxl);
if (!mxIsEmpty(mx_PSOLfct)) {
if (!mxIsEmpty(mx_PSETfct))
status = KINSpilsSetPreconditioner(kin_mem, mtlb_KINSpilsPset, mtlb_KINSpilsPsol, NULL);
else
status = KINSpilsSetPreconditioner(kin_mem, NULL, mtlb_KINSpilsPsol, NULL);
}
break;
case PM_BBDPRE:
if (!mxIsEmpty(mx_GCOMfct))
bbd_data = KINBBDPrecAlloc(kin_mem, N, mudq, mldq, mupper, mlower, dqrely, mtlb_KINGloc, mtlb_KINGcom);
else
bbd_data = KINBBDPrecAlloc(kin_mem, N, mudq, mldq, mupper, mlower, dqrely, mtlb_KINGloc, NULL);
status = KINBBDSpbcg(kin_mem, maxl, bbd_data);
break;
}
if (!mxIsEmpty(mx_JACfct))
status = KINSpilsSetJacTimesVecFn(kin_mem, mtlb_KINSpilsJac, NULL);
break;
case LS_SPTFQMR:
switch(pm) {
case PM_NONE:
status = KINSptfqmr(kin_mem, maxl);
if (!mxIsEmpty(mx_PSOLfct)) {
if (!mxIsEmpty(mx_PSETfct))
status = KINSpilsSetPreconditioner(kin_mem, mtlb_KINSpilsPset, mtlb_KINSpilsPsol, NULL);
else
status = KINSpilsSetPreconditioner(kin_mem, NULL, mtlb_KINSpilsPsol, NULL);
}
break;
case PM_BBDPRE:
if (!mxIsEmpty(mx_GCOMfct))
bbd_data = KINBBDPrecAlloc(kin_mem, N, mudq, mldq, mupper, mlower, dqrely, mtlb_KINGloc, mtlb_KINGcom);
else
bbd_data = KINBBDPrecAlloc(kin_mem, N, mudq, mldq, mupper, mlower, dqrely, mtlb_KINGloc, NULL);
status = KINBBDSptfqmr(kin_mem, maxl, bbd_data);
break;
}
if (!mxIsEmpty(mx_JACfct))
status = KINSpilsSetJacTimesVecFn(kin_mem, mtlb_KINSpilsJac, NULL);
break;
}
return;
}
bool kinsol_solve(void) {
double fnormtol;
N_Vector y, scale, constraints;
int mset, flag;
void *kmem;
y = scale = constraints = NULL;
kmem = NULL;
/* Create vectors for solution, scales, and constraints */
y = N_VMake_Serial(nvariables, variables);
if (y == NULL) goto cleanup;
scale = N_VNew_Serial(nvariables);
if (scale == NULL) goto cleanup;
constraints = N_VNew_Serial(nvariables);
if (constraints == NULL) goto cleanup;
/* Initialize and allocate memory for KINSOL */
kmem = KINCreate();
if (kmem == NULL) goto cleanup;
flag = KINInit(kmem, _f, y);
if (flag < 0) goto cleanup;
// This constrains metabolites >= 0
N_VConst_Serial(1.0, constraints);
flag = KINSetConstraints(kmem, constraints);
if (flag < 0) goto cleanup;
fnormtol = ARGS.ABSTOL;
flag = KINSetFuncNormTol(kmem, fnormtol);
if (flag < 0) goto cleanup;
//scsteptol = ARGS.RELTOL;
//flag = KINSetScaledStepTol(kmem, scsteptol);
//if (flag < 0) goto cleanup;
/* Attach dense linear solver */
flag = KINDense(kmem, nvariables);
if (flag < 0) goto cleanup;
flag = KINDlsSetDenseJacFn(kmem, _dfdy);
if (flag < 0) goto cleanup;
/* Indicate exact Newton */
//This makes sure that the user-supplied Jacobian gets evaluated onevery step.
mset = 1;
flag = KINSetMaxSetupCalls(kmem, mset);
if (flag < 0) goto cleanup;
/* Initial guess is the intial variable concentrations */
/* Call KINSol to solve problem */
N_VConst_Serial(1.0,scale);
flag = KINSol(kmem, /* KINSol memory block */
y, /* initial guess on input; solution vector */
KIN_NONE, /* basic Newton iteration */
scale, /* scaling vector, for the variable cc */
scale); /* scaling vector for function values fval */
if((ARGS.MODE != ABC) and (ARGS.MODE != ABCSIM) and (ARGS.MODE != Prior))
OUT_nums();
if (flag < 0) goto cleanup;
N_VDestroy_Serial(y);
N_VDestroy_Serial(scale);
N_VDestroy_Serial(constraints);
KINFree(&kmem);
return true;
cleanup:
error("Could not integrate!\n");
if (y!=NULL) N_VDestroy_Serial(y);
if (scale!=NULL) N_VDestroy_Serial(scale);
if (constraints!=NULL) N_VDestroy_Serial(constraints);
if (kmem!=NULL) KINFree(&kmem);
return false;
}
