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); }