Examples of MinAtom

org.jmol.minimize.MinAtom

Examples of org.jmol.minimize.MinAtom

    calc = calculations[CALC_OOP] = new ArrayList();
    // set up the special atom arrays
    OOPCalc oopCalc = new OOPCalc();
    int elemNo;
    for (int i = 0; i < atomCount; i++) {
      MinAtom a = atoms[i];
      if (a.nBonds == 3 && isInvertible(elemNo = a.atom.getElementNumber()))
        oopCalc.setData(calc, i, elemNo);
    }


    pairSearch(calculations[CALC_VDW] = new ArrayList(), new VDWCalc());

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Examples of org.jmol.minimize.MinAtom

    }
  }


  private void pairSearch(List calc, PairCalc type) {
    /*A:*/ for (int i = 0; i < atomCount - 1; i++) { // one atom...
      MinAtom atomA = atoms[i];
      int[] atomList1 = atomA.getBondedAtomIndexes();
      B: for (int j = i + 1; j < atomCount; j++) { // another atom...
        MinAtom atomB = atoms[j];
        /*nbrA:*/ for (int k = atomList1.length; --k >= 0;) { // check bonded A-B
          MinAtom nbrA = atoms[atomList1[k]];
          if (nbrA == atomB)
            continue B; // pick another B
          if (nbrA.nBonds == 1)
            continue;
          int[] atomList2 = nbrA.getBondedAtomIndexes(); // check A-X-B
          /*nbrAA:*/ for (int l = atomList2.length; --l >= 0;) {
            MinAtom nbrAA = atoms[atomList2[l]];
            if (nbrAA == atomB)
              continue B; // pick another B
            
            //this next would exclude A-X-X-B, but Rappe does not do that, he says

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Examples of org.jmol.minimize.MinAtom

    sb.append("\n" + title + "\n\n"
        + " ATOM    X        Y        Z    TYPE     GRADX    GRADY    GRADZ  "
        + "---------BONDED ATOMS--------\n"
        + trailer);
    for (int i = 0; i < atomCount; i++) {
      MinAtom atom = atoms[i];
      int[] others = atom.getBondedAtomIndexes();
      int[] iVal = new int[others.length + 1];
      iVal[0] = atom.atom.getAtomNumber();
      String s = "   ";
      for (int j = 0; j < others.length; j++) {
        s += " %3d";

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Examples of org.jmol.minimize.MinAtom

        atoms[i].coord[j] = coordSaved[i][j];
  }
  
  public boolean detectExplosion() {
    for (int i = 0; i < atomCount; i++) {
      MinAtom atom = atoms[i];
      for (int j = 0; j < 3; j++)
        if (!Util.isFinite(atom.coord[j]))
          return true;
    }
    for (int i = 0; i < bondCount; i++) {

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