Examples with ReflectionSpline ffx.crystal.ReflectionSpline used on opensource projects

Example 1 with ReflectionSpline

use of ffx.crystal.ReflectionSpline in project ffx by mjschnie.

the class SigmaAMinimize method setWEstimate.

private void setWEstimate() {
    // generate initial w estimate
    ReflectionSpline spline = new ReflectionSpline(reflectionList, refinementData.nbins);
    int[] nmean = new int[refinementData.nbins];
    for (int i = 0; i < refinementData.nbins; i++) {
        nmean[i] = 0;
    }
    double mean = 0.0, tot = 0.0;
    double[][] fc = refinementData.fctot;
    double[][] fo = refinementData.fsigf;
    for (HKL ih : reflectionList.hkllist) {
        int i = ih.index();
        if (ih.allowed() == 0.0 || Double.isNaN(fc[i][0]) || Double.isNaN(fo[i][0])) {
            continue;
        }
        double s2 = Crystal.invressq(crystal, ih);
        double epsc = ih.epsilonc();
        ComplexNumber fct = new ComplexNumber(fc[i][0], fc[i][1]);
        double ecscale = spline.f(s2, refinementData.fcesq);
        double eoscale = spline.f(s2, refinementData.foesq);
        double ec = fct.times(sqrt(ecscale)).abs();
        double eo = fo[i][0] * sqrt(eoscale);
        double wi = pow(eo - ec, 2.0) / epsc;
        nmean[spline.i1()]++;
        tot++;
        x[spline.i1() + refinementData.nbins] += (wi - x[spline.i1() + refinementData.nbins]) / nmean[spline.i1()];
        mean += (wi - mean) / tot;
    }
    logger.info(String.format(" Starting mean w:    %8.3f", mean));
    logger.info(String.format(" Starting w scaling: %8.3f", 1.0 / mean));
    for (int i = 0; i < refinementData.nbins; i++) {
        x[i] -= x[i + refinementData.nbins];
        x[i] *= scaling[i];
        scaling[i + refinementData.nbins] = 1.0 / mean;
        x[i + refinementData.nbins] *= scaling[i + refinementData.nbins];
    }
    sigmaAEnergy.setScaling(scaling);
}

Example 2 with ReflectionSpline

use of ffx.crystal.ReflectionSpline in project ffx by mjschnie.

the class CrystalStats method getSigmaA.

/**
 * simply return the current sigmaA value
 *
 * @return sigmaA
 */
public double getSigmaA() {
    double sum = 0.0;
    int nhkl = 0;
    ReflectionSpline sigmaaspline = new ReflectionSpline(reflectionlist, refinementdata.sigmaa.length);
    for (HKL ih : reflectionlist.hkllist) {
        int i = ih.index();
        // ignored cases
        if (Double.isNaN(fc[i][0]) || Double.isNaN(fo[i][0]) || fo[i][1] <= 0.0) {
            continue;
        }
        // spline setup
        double ss = Crystal.invressq(crystal, ih);
        double fh = spline.f(ss, refinementdata.spline);
        double sa = sigmaaspline.f(ss, refinementdata.sigmaa);
        nhkl++;
        sum += (sa - sum) / nhkl;
    }
    return sum;
}

Example 3 with ReflectionSpline

use of ffx.crystal.ReflectionSpline in project ffx by mjschnie.

the class CrystalStats method getSigmaW.

/**
 * simply return the current sigmaW value
 *
 * @return sigmaW
 */
public double getSigmaW() {
    double sum = 0.0;
    int nhkl = 0;
    ReflectionSpline sigmaaspline = new ReflectionSpline(reflectionlist, refinementdata.sigmaa.length);
    for (HKL ih : reflectionlist.hkllist) {
        int i = ih.index();
        // ignored cases
        if (Double.isNaN(fc[i][0]) || Double.isNaN(fo[i][0]) || fo[i][1] <= 0.0) {
            continue;
        }
        // spline setup
        double ss = Crystal.invressq(crystal, ih);
        double fh = spline.f(ss, refinementdata.spline);
        double wa = sigmaaspline.f(ss, refinementdata.sigmaw);
        nhkl++;
        sum += (wa - sum) / nhkl;
    }
    return sum;
}

Example 4 with ReflectionSpline

use of ffx.crystal.ReflectionSpline in project ffx by mjschnie.

the class CrystalStats method printRStats.

/**
 * print R factors and associated statistics in a binned fashion
 */
public void printRStats() {
    double[][] res = new double[n][2];
    double[] nhkl = new double[n + 1];
    double[][] rb = new double[n + 1][2];
    double[][] sumfo = new double[n + 1][2];
    double[][] s = new double[n + 1][4];
    double numer = 0.0;
    double denom = 0.0;
    double sumall = 0.0;
    double sumfoall = 0.0;
    ReflectionSpline sigmaaspline = new ReflectionSpline(reflectionlist, refinementdata.sigmaa.length);
    for (int i = 0; i < n; i++) {
        res[i][0] = Double.NEGATIVE_INFINITY;
        res[i][1] = Double.POSITIVE_INFINITY;
    }
    for (HKL ih : reflectionlist.hkllist) {
        int i = ih.index();
        int b = ih.bin();
        // ignored cases
        if (Double.isNaN(fc[i][0]) || Double.isNaN(fo[i][0]) || fo[i][1] <= 0.0) {
            continue;
        }
        // spline setup
        double ss = Crystal.invressq(crystal, ih);
        double fh = spline.f(ss, refinementdata.spline);
        double sa = sigmaaspline.f(ss, refinementdata.sigmaa);
        double wa = sigmaaspline.f(ss, refinementdata.sigmaw);
        double eoscale = sigmaaspline.f(ss, refinementdata.foesq);
        // determine res limits of each bin
        double rs = Crystal.res(crystal, ih);
        if (rs > res[b][0]) {
            res[b][0] = rs;
        }
        if (rs < res[b][1]) {
            res[b][1] = rs;
        }
        ComplexNumber c = new ComplexNumber(fc[i][0], fc[i][1]);
        numer = abs(abs(fo[i][0]) - fh * abs(c.abs()));
        denom = abs(fo[i][0]);
        if (refinementdata.isFreeR(i)) {
            rb[b][1] += numer;
            sumfo[b][1] += denom;
            rb[n][1] += numer;
            sumfo[n][1] += denom;
            sumall += numer;
            sumfoall += denom;
        } else {
            rb[b][0] += numer;
            sumfo[b][0] += denom;
            rb[n][0] += numer;
            sumfo[n][0] += denom;
            sumall += numer;
            sumfoall += denom;
        }
        nhkl[b]++;
        nhkl[n]++;
        s[b][0] += (sa - s[b][0]) / nhkl[b];
        s[b][1] += (wa - s[b][1]) / nhkl[b];
        s[b][2] += ((wa / Math.sqrt(eoscale)) - s[b][2]) / nhkl[b];
        s[b][3] += (fomphi[i][0] - s[b][3]) / nhkl[b];
        s[n][0] += (sa - s[n][0]) / nhkl[n];
        s[n][1] += (wa - s[n][1]) / nhkl[n];
        s[n][2] += ((wa / Math.sqrt(eoscale)) - s[n][2]) / nhkl[n];
        s[n][3] += (fomphi[i][0] - s[n][3]) / nhkl[n];
    }
    StringBuilder sb = new StringBuilder(String.format("\n %15s | %7s | %7s | %7s | %7s | %7s | %7s\n", "Res. Range", "  R", "Rfree", "s", "w(E)", "w(F)", "FOM"));
    for (int i = 0; i < n; i++) {
        sb.append(String.format(" %7.3f %7.3f | ", res[i][0], res[i][1]));
        sb.append(String.format("%7.2f | %7.2f | %7.4f | %7.4f | %7.2f | %7.4f\n", (rb[i][0] / sumfo[i][0]) * 100.0, (rb[i][1] / sumfo[i][1]) * 100.0, s[i][0], s[i][1], s[i][2], s[i][3]));
    }
    sb.append(String.format(" %7.3f %7.3f | ", res[0][0], res[n - 1][1]));
    sb.append(String.format("%7.2f | %7.2f | %7.4f | %7.4f | %7.2f | %7.4f\n", (rb[n][0] / sumfo[n][0]) * 100.0, (rb[n][1] / sumfo[n][1]) * 100.0, s[n][0], s[n][1], s[n][2], s[n][3]));
    sb.append(" s and w are analagous to D and sum_wc");
    reslow = res[0][0];
    reshigh = res[n - 1][1];
    highreslow = res[n - 1][0];
    highreshigh = res[n - 1][1];
    r = (rb[n][0] / sumfo[n][0]) * 100.0;
    rfree = (rb[n][1] / sumfo[n][1]) * 100.0;
    rall = (sumall / sumfoall) * 100.0;
    highr = (rb[n - 1][0] / sumfo[n - 1][0]) * 100.0;
    highrfree = (rb[n - 1][1] / sumfo[n - 1][1]) * 100.0;
    if (print) {
        logger.info(sb.toString());
    }
}

Example 5 with ReflectionSpline

use of ffx.crystal.ReflectionSpline in project ffx by mjschnie.

the class MTZWriter method write.

/**
 * <p>
 * write</p>
 */
public void write() {
    ByteOrder byteOrder = ByteOrder.nativeOrder();
    FileOutputStream fileOutputStream;
    DataOutputStream dataOutputStream;
    try {
        if (logger.isLoggable(Level.INFO)) {
            StringBuilder sb = new StringBuilder();
            sb.append(format("\n Writing MTZ HKL file: \"%s\"\n", fileName));
            logger.info(sb.toString());
        }
        fileOutputStream = new FileOutputStream(fileName);
        dataOutputStream = new DataOutputStream(fileOutputStream);
        byte[] bytes = new byte[80];
        int offset = 0;
        int writeLen = 0;
        int iMapData;
        float fMapData;
        // Header.
        StringBuilder sb = new StringBuilder();
        sb.append("MTZ ");
        dataOutputStream.writeBytes(sb.toString());
        // Header offset.
        int headerOffset = n * nCol + 21;
        ByteBuffer byteBuffer = ByteBuffer.wrap(bytes);
        byteBuffer.order(byteOrder).putInt(headerOffset);
        // 0x4441 for LE, 0x1111 for BE
        if (ByteOrder.nativeOrder().equals(ByteOrder.LITTLE_ENDIAN)) {
            iMapData = 0x4441;
        } else {
            iMapData = 0x1111;
        }
        byteBuffer.order(byteOrder).putInt(iMapData);
        dataOutputStream.write(bytes, offset, 8);
        sb = new StringBuilder();
        sb.append(" ");
        sb.setLength(68);
        dataOutputStream.writeBytes(sb.toString());
        // Data.
        Vector<String> colname = new Vector<>(nCol);
        char[] colType = new char[nCol];
        double[] res = new double[2];
        res[0] = Double.POSITIVE_INFINITY;
        res[1] = Double.NEGATIVE_INFINITY;
        float[][] colMinMax = new float[nCol][2];
        for (int i = 0; i < nCol; i++) {
            colMinMax[i][0] = Float.POSITIVE_INFINITY;
            colMinMax[i][1] = Float.NEGATIVE_INFINITY;
        }
        ReflectionSpline sigmaASpline = new ReflectionSpline(reflectionList, refinementData.sigmaa.length);
        int col = 0;
        colname.add("H");
        colType[col++] = 'H';
        colname.add("K");
        colType[col++] = 'H';
        colname.add("L");
        colType[col++] = 'H';
        writeLen += 12;
        if (mtzType != MTZType.FCONLY) {
            colname.add("FO");
            colType[col++] = 'F';
            colname.add("SIGFO");
            colType[col++] = 'Q';
            colname.add("FreeR");
            colType[col++] = 'I';
            writeLen += 12;
        }
        if (mtzType != MTZType.DATAONLY) {
            colname.add("Fs");
            colType[col++] = 'F';
            colname.add("PHIFs");
            colType[col++] = 'P';
            colname.add("Fc");
            colType[col++] = 'F';
            colname.add("PHIFc");
            colType[col++] = 'P';
            writeLen += 16;
        }
        if (mtzType == MTZType.ALL) {
            colname.add("FOM");
            colType[col++] = 'W';
            colname.add("PHIW");
            colType[col++] = 'P';
            colname.add("SigmaAs");
            colType[col++] = 'F';
            colname.add("SigmaAw");
            colType[col++] = 'Q';
            colname.add("FWT");
            colType[col++] = 'F';
            colname.add("PHWT");
            colType[col++] = 'P';
            colname.add("DELFWT");
            colType[col++] = 'F';
            colname.add("PHDELWT");
            colType[col++] = 'P';
            writeLen += 32;
        }
        for (HKL ih : reflectionList.hkllist) {
            col = 0;
            int i = ih.index();
            // Skip the 0 0 0 reflection.
            if (ih.h() == 0 && ih.k() == 0 && ih.l() == 0) {
                continue;
            }
            double ss = Crystal.invressq(crystal, ih);
            res[0] = min(ss, res[0]);
            res[1] = max(ss, res[1]);
            // HKL first (3)
            fMapData = ih.h();
            colMinMax[col][0] = min(fMapData, colMinMax[0][0]);
            colMinMax[col][1] = max(fMapData, colMinMax[0][1]);
            byteBuffer.rewind();
            byteBuffer.order(byteOrder).putFloat(fMapData);
            col++;
            fMapData = ih.k();
            colMinMax[col][0] = min(fMapData, colMinMax[1][0]);
            colMinMax[col][1] = max(fMapData, colMinMax[1][1]);
            byteBuffer.order(byteOrder).putFloat(fMapData);
            col++;
            fMapData = ih.l();
            colMinMax[col][0] = min(fMapData, colMinMax[2][0]);
            colMinMax[col][1] = max(fMapData, colMinMax[2][1]);
            byteBuffer.order(byteOrder).putFloat(fMapData);
            col++;
            if (mtzType != MTZType.FCONLY) {
                // F/sigF (2)
                fMapData = (float) refinementData.getF(i);
                if (!isNaN(fMapData)) {
                    colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                    colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                }
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
                fMapData = (float) refinementData.getSigF(i);
                if (!isNaN(fMapData)) {
                    colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                    colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                }
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
                // Free R (1)
                fMapData = (float) refinementData.getFreeR(i);
                if (!isNaN(fMapData)) {
                    colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                    colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                }
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
            }
            if (mtzType == MTZType.FCONLY) {
                // Fs (2)
                fMapData = (float) refinementData.fsF(i);
                colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
                fMapData = (float) toDegrees(refinementData.fsPhi(i));
                colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
                // Fc (unscaled!) (2)
                fMapData = (float) refinementData.fcF(i);
                if (!isNaN(fMapData)) {
                    colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                    colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                }
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
                fMapData = (float) Math.toDegrees(refinementData.fcPhi(i));
                if (!isNaN(fMapData)) {
                    colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                    colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                }
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
            }
            if (mtzType == MTZType.ALL) {
                // Fs (2)
                fMapData = (float) refinementData.fsF(i);
                colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
                fMapData = (float) toDegrees(refinementData.fsPhi(i));
                colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
                // Fctot (2)
                fMapData = (float) refinementData.fcTotF(i);
                if (!isNaN(fMapData)) {
                    colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                    colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                }
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
                fMapData = (float) toDegrees(refinementData.fcTotPhi(i));
                if (!isNaN(fMapData)) {
                    colMinMax[col][0] = Math.min(fMapData, colMinMax[col][0]);
                    colMinMax[col][1] = Math.max(fMapData, colMinMax[col][1]);
                }
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
                // FOM/phase (2)
                fMapData = (float) refinementData.fomphi[i][0];
                if (!isNaN(fMapData)) {
                    colMinMax[col][0] = Math.min(fMapData, colMinMax[col][0]);
                    colMinMax[col][1] = Math.max(fMapData, colMinMax[col][1]);
                }
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
                fMapData = (float) toDegrees(refinementData.fomphi[i][1]);
                colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
                // Spline setup.
                double fh = spline.f(ss, refinementData.spline);
                double sa = sigmaASpline.f(ss, refinementData.sigmaa);
                double wa = sigmaASpline.f(ss, refinementData.sigmaw);
                // sigmaA/w (2)
                fMapData = (float) sa;
                if (!isNaN(fMapData)) {
                    colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                    colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                }
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
                fMapData = (float) wa;
                if (!isNaN(fMapData)) {
                    colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                    colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                }
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
                // Map coeffs (4).
                fMapData = (float) refinementData.FoFc2F(i);
                colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
                fMapData = (float) toDegrees(refinementData.FoFc2Phi(i));
                colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
                fMapData = (float) refinementData.foFc1F(i);
                colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
                fMapData = (float) toDegrees(refinementData.foFc1Phi(i));
                colMinMax[col][0] = min(fMapData, colMinMax[col][0]);
                colMinMax[col][1] = max(fMapData, colMinMax[col][1]);
                byteBuffer.order(byteOrder).putFloat(fMapData);
                col++;
            }
            dataOutputStream.write(bytes, offset, writeLen);
        }
        // Header.
        sb = new StringBuilder();
        sb.append("VERS MTZ:V1.1 ");
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dataOutputStream.writeBytes(sb.toString());
        Date now = new Date();
        SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss ");
        sb = new StringBuilder();
        sb.append("TITLE FFX output: " + sdf.format(now));
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dataOutputStream.writeBytes(sb.toString());
        sb = new StringBuilder();
        sb.append(String.format("NCOL %8d %12d %8d", nCol, n, 0));
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dataOutputStream.writeBytes(sb.toString());
        sb = new StringBuilder();
        sb.append("SORT    0    0    0    0    0 ");
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dataOutputStream.writeBytes(sb.toString());
        sb = new StringBuilder();
        char cdata = spaceGroup.shortName.charAt(0);
        if (cdata == 'H') {
            cdata = 'R';
        }
        sb.append(String.format("SYMINF %3d %2d %c %5d %22s %5s", spaceGroup.getNumberOfSymOps(), spaceGroup.numPrimitiveSymEquiv, cdata, spaceGroup.number, "'" + spaceGroup.shortName + "'", spaceGroup.pointGroupName));
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dataOutputStream.writeBytes(sb.toString());
        for (int i = 0; i < spaceGroup.symOps.size(); i++) {
            sb = new StringBuilder();
            sb.append("SYMM ");
            SymOp symop = spaceGroup.symOps.get(i);
            sb.append(symop.toXYZString());
            while (sb.length() < 80) {
                sb.append(" ");
            }
            dataOutputStream.writeBytes(sb.toString());
        }
        sb = new StringBuilder();
        sb.append(String.format("RESO %8.6f%13s%8.6f", res[0], " ", res[1]));
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dataOutputStream.writeBytes(sb.toString());
        sb = new StringBuilder();
        sb.append("VALM NAN ");
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dataOutputStream.writeBytes(sb.toString());
        sb = new StringBuilder();
        sb.append("NDIF        1 ");
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dataOutputStream.writeBytes(sb.toString());
        sb = new StringBuilder();
        sb.append("PROJECT       1 project ");
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dataOutputStream.writeBytes(sb.toString());
        sb = new StringBuilder();
        sb.append("CRYSTAL       1 crystal ");
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dataOutputStream.writeBytes(sb.toString());
        sb = new StringBuilder();
        sb.append("DATASET       1 dataset ");
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dataOutputStream.writeBytes(sb.toString());
        for (int j = 0; j < nCol; j++) {
            sb = new StringBuilder();
            sb.append(String.format("COLUMN %-30s %c %17.4f %17.4f    1", colname.get(j), colType[j], colMinMax[j][0], colMinMax[j][1]));
            dataOutputStream.writeBytes(sb.toString());
        }
        sb = new StringBuilder();
        sb.append(String.format("CELL %10.4f %9.4f %9.4f %9.4f %9.4f %9.4f ", crystal.a, crystal.b, crystal.c, crystal.alpha, crystal.beta, crystal.gamma));
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dataOutputStream.writeBytes(sb.toString());
        sb = new StringBuilder();
        sb.append(String.format("DCELL %9d %10.4f %9.4f %9.4f %9.4f %9.4f %9.4f ", 1, crystal.a, crystal.b, crystal.c, crystal.alpha, crystal.beta, crystal.gamma));
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dataOutputStream.writeBytes(sb.toString());
        sb = new StringBuilder();
        sb.append("DWAVEL        1    1.00000 ");
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dataOutputStream.writeBytes(sb.toString());
        sb = new StringBuilder();
        sb.append("END ");
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dataOutputStream.writeBytes(sb.toString());
        sb = new StringBuilder();
        sb.append("MTZENDOFHEADERS ");
        while (sb.length() < 80) {
            sb.append(" ");
        }
        dataOutputStream.writeBytes(sb.toString());
        dataOutputStream.close();
    } catch (Exception e) {
        String message = "Fatal exception evaluating structure factors.\n";
        logger.log(Level.SEVERE, message, e);
    }
}