private void dumpInfo(int shell) {
if (doShowShellType) {
Logger.debug(
"\n\t\t\tprocessShell: "
+ shell
+ " type="
+ QS.getQuantumShellTag(shell)
+ " nGaussians="
+ nGaussians
+ " atom="
+ atomIndex);
doShowShellType = false;
}
if (Logger.isActiveLevel(Logger.LEVEL_DEBUGHIGH))
for (int ig = 0; ig < nGaussians; ig++) {
double alpha = gaussians[gaussianPtr + ig][0];
double c1 = gaussians[gaussianPtr + ig][1];
Logger.debug("\t\t\tGaussian " + (ig + 1) + " alpha=" + alpha + " c=" + c1);
}
String[] so = getShellOrder(shell);
for (int i = 0; i < map.length; i++) {
double c = coeffs[i];
Logger.debug(
"MO coeff "
+ (so == null ? "?" : so[i])
+ " "
+ (map[i] + moCoeff - map.length + i + 1)
+ "\t"
+ c
+ "\t"
+ thisAtom.atom);
}
}
private double normalizeShell(int iShell) {
double c = 0;
int[] shell = shells.get(iShell);
basisType = QS.getItem(shell[1]);
gaussianPtr = shell[2];
nGaussians = shell[3];
doShowShellType = doDebug;
if (!setCoeffs(false)) return 0;
for (int i = map.length; --i >= 0; ) c += coeffs[i] * coeffs[i];
return c;
}
private String getMoState(int modelIndex) {
strID = getId(modelIndex);
if (!getSettings(strID)) return "";
SB s = new SB();
int modelCount = vwr.getModelCount();
if (modelCount > 1) appendCmd(s, "frame " + vwr.getModelNumberDotted(modelIndex));
if (moCutoff != null)
appendCmd(s, "mo cutoff " + (sg.getIsPositiveOnly() ? "+" : "") + moCutoff);
if (moScale != null) appendCmd(s, "mo scale " + moScale);
if (moMonteCarloCount != null)
appendCmd(s, "mo points " + moMonteCarloCount + " " + moRandomSeed);
if (moResolution != null) appendCmd(s, "mo resolution " + moResolution);
if (moPlane != null)
appendCmd(
s, "mo plane {" + moPlane.x + " " + moPlane.y + " " + moPlane.z + " " + moPlane.w + "}");
if (moTitleFormat != null) appendCmd(s, "mo titleFormat " + PT.esc(moTitleFormat));
// the following is a correct object==object test
if (moColorNeg != null)
appendCmd(
s,
"mo color "
+ Escape.escapeColor(moColorNeg.intValue())
+ (moColorNeg.equals(moColorPos)
? ""
: " " + Escape.escapeColor(moColorPos.intValue())));
if (moSlab != null) {
if (thisMesh.slabOptions != null) appendCmd(s, thisMesh.slabOptions.toString());
if (thisMesh.jvxlData.slabValue != Integer.MIN_VALUE)
appendCmd(s, "mo slab " + thisMesh.jvxlData.slabValue);
}
if (moLinearCombination == null) {
appendCmd(s, "mo " + (moSquareData == Boolean.TRUE ? "squared " : "") + moNumber);
} else {
appendCmd(
s,
"mo "
+ QS.getMOString(moLinearCombination)
+ (moSquareLinear == Boolean.TRUE ? " squared" : ""));
}
if (moTranslucency != null) appendCmd(s, "mo translucent " + moTranslucentLevel);
appendCmd(s, ((IsosurfaceMesh) thisModel.get("mesh")).getState("mo"));
return s.toString();
}
private void processShell(int iShell) {
int lastAtom = atomIndex;
int[] shell = shells.get(iShell);
atomIndex = shell[0] + firstAtomOffset;
basisType = QS.getItem(shell[1]);
gaussianPtr = shell[2];
nGaussians = shell[3];
doShowShellType = doDebug;
if (atomIndex != lastAtom && (thisAtom = qmAtoms[atomIndex]) != null)
thisAtom.setXYZ(this, true);
if (!setCoeffs(true)) return;
if (havePoints) setMinMax(-1);
switch (basisType) {
case S:
addDataS();
break;
case P:
addDataP();
break;
case SP:
addDataSP();
break;
case D_SPHERICAL:
addData5D();
break;
case D_CARTESIAN:
addData6D();
break;
case F_SPHERICAL:
addData7F();
break;
case F_CARTESIAN:
addData10F();
break;
default:
Logger.warn(" Unsupported basis type for atomno=" + (atomIndex + 1) + ": " + basisType.tag);
break;
}
}