void kineticsmethods(int nlhs, mxArray* plhs[],
int nrhs, const mxArray* prhs[])
{
double vv = 0.0;
int job = getInt(prhs[2]);
int kin, irxn;
// construct a new instance
if (job == 0) {
checkNArgs(8, nrhs);
int root = getInt(prhs[1]);
int iph = getInt(prhs[3]);
int in1 = getInt(prhs[4]);
int in2 = getInt(prhs[5]);
int in3 = getInt(prhs[6]);
int in4 = getInt(prhs[7]);
vv = static_cast<int>(kin_newFromXML(root, iph, in1, in2, in3, in4));
plhs[0] = mxCreateNumericMatrix(1,1,mxDOUBLE_CLASS,mxREAL);
double* h = mxGetPr(plhs[0]);
*h = vv;
return;
} else if (job > 0) {
// methods
int isp = 1;
if (job < 5 || job > 6) {
checkNArgs(4,nrhs);
} else {
checkNArgs(5,nrhs);
isp = getInt(prhs[4]);
}
kin = getInt(prhs[1]);
irxn = getInt(prhs[3]);
// get scalar attributes
if (job < 10) {
switch (job) {
case 1:
vv = (double) kin_nReactions(kin);
break;
case 2:
vv = kin_multiplier(kin, irxn-1);
break;
case 3:
vv = (double) kin_nSpecies(kin);
break;
case 4:
vv = kin_isReversible(kin,irxn-1);
break;
case 5:
vv = kin_reactantStoichCoeff(kin, isp - 1, irxn-1);
break;
case 6:
vv = kin_productStoichCoeff(kin, isp - 1, irxn-1);
break;
default:
mexErrMsgTxt("unknown job");
}
plhs[0] = mxCreateNumericMatrix(1,1,mxDOUBLE_CLASS,mxREAL);
double* h = mxGetPr(plhs[0]);
*h = vv;
return;
} else if (job < 20) {
// get reaction array attributes
mwSize nr = (mwSize) kin_nReactions(kin);
plhs[0] = mxCreateNumericMatrix(nr,1,mxDOUBLE_CLASS,mxREAL);
double* h = mxGetPr(plhs[0]);
int ok = -10;
switch (job) {
case 11:
ok = kin_getFwdRatesOfProgress(kin,nr,h);
break;
case 12:
ok = kin_getRevRatesOfProgress(kin,nr,h);
break;
case 13:
ok = kin_getNetRatesOfProgress(kin,nr,h);
break;
case 14:
ok = kin_getEquilibriumConstants(kin,nr,h);
break;
case 15:
ok = kin_getFwdRateConstants(kin,nr,h);
break;
case 16:
ok = kin_getRevRateConstants(kin,1,nr,h);
break;
default:
;
}
if (ok < 0) {
mexErrMsgTxt("error computing rates of progress");
}
} else if (job < 30) {
mwSize nsp = (mwSize) kin_nSpecies(kin);
plhs[0] = mxCreateNumericMatrix(nsp,1,mxDOUBLE_CLASS,mxREAL);
double* h = mxGetPr(plhs[0]);
int ok = -10;
switch (job) {
case 21:
ok = kin_getCreationRates(kin,nsp,h);
break;
case 22:
ok = kin_getDestructionRates(kin,nsp,h);
break;
case 23:
ok = kin_getNetProductionRates(kin,nsp,h);
break;
case 24:
ok = kin_getSourceTerms(kin, nsp, h);
break;
default:
;
}
if (ok < 0) {
mexErrMsgTxt("error computing production rates");
}
} else if (job < 40) {
char* buf;
int iok = -1, buflen;
switch (job) {
case 31:
buflen = kin_getReactionString(kin, irxn-1, 0, 0);
if (buflen > 0) {
buf = (char*) mxCalloc(buflen, sizeof(char));
iok = kin_getReactionString(kin, irxn-1, buflen, buf);
}
break;
default:
;
}
if (iok == 0) {
plhs[0] = mxCreateString(buf);
return;
} else {
reportError();
}
}
} else {
// set attributes
int iok = -1;
job = -job;
kin = getInt(prhs[1]);
irxn = getInt(prhs[3]);
if (job < 10) {
checkNArgs(5,nrhs);
double v = getDouble(prhs[4]);
switch (job) {
case 1:
iok = kin_setMultiplier(kin,irxn-1,v);
break;
case 3:
iok = kin_del(kin);
break;
case 5:
iok = kin_advanceCoverages(kin,v);
break;
default:
mexErrMsgTxt("unknown job");
}
}
if (iok < 0) {
reportError();
}
}
}
static PyObject*
kin_getarray(PyObject *self, PyObject *args)
{
int kin;
int job;
if (!PyArg_ParseTuple(args, "ii:kin_getarray", &kin, &job))
return NULL;
// array attributes
int iok = -22;
size_t nrxns = kin_nReactions(kin);
size_t nsp = kin_nSpecies(kin);
size_t ix;
if (job < 45 || job >= 90) ix = nrxns; else ix = nsp;
#ifdef HAS_NUMPY
npy_intp nix = ix;
PyArrayObject* x = (PyArrayObject*)PyArray_SimpleNew(1, &nix, PyArray_DOUBLE);
#else
int nix = int(ix);
PyArrayObject* x =
(PyArrayObject*)PyArray_FromDims(1, &nix, PyArray_DOUBLE);
#endif
double* xd = (double*)x->data;
switch (job) {
case 10:
iok = kin_getFwdRatesOfProgress(kin, nrxns, xd);
break;
case 20:
iok = kin_getRevRatesOfProgress(kin, nrxns, xd);
break;
case 30:
iok = kin_getNetRatesOfProgress(kin, nrxns, xd);
break;
case 32:
iok = kin_getActivationEnergies(kin, nrxns, xd);
break;
case 34:
iok = kin_getFwdRateConstants(kin, nrxns, xd);
break;
case 35:
iok = kin_getRevRateConstants(kin, 1, nrxns, xd);
case 36:
iok = kin_getRevRateConstants(kin, 0, nrxns, xd);
break;
case 40:
iok = kin_getEquilibriumConstants(kin, nrxns, xd);
break;
case 50:
iok = kin_getCreationRates(kin, nsp, xd);
break;
case 60:
iok = kin_getDestructionRates(kin, nsp, xd);
break;
case 70:
iok = kin_getNetProductionRates(kin, nsp, xd);
break;
case 80:
iok = kin_getSourceTerms(kin, nsp, xd);
break;
case 90:
iok = kin_getDelta(kin, 0, nrxns, xd);
break;
case 91:
iok = kin_getDelta(kin, 1, nrxns, xd);
break;
case 92:
iok = kin_getDelta(kin, 2, nrxns, xd);
break;
case 93:
iok = kin_getDelta(kin, 3, nrxns, xd);
break;
case 94:
iok = kin_getDelta(kin, 4, nrxns, xd);
break;
case 95:
iok = kin_getDelta(kin, 5, nrxns, xd);
break;
default:
;
}
if (iok >= 0) {
return PyArray_Return(x);
}
else
return reportError(iok);
}