示例#1
0
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();
        }
    }
}
示例#2
0
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);
}