@SuppressWarnings("unchecked")
public static String escape(Object x) {
if (x instanceof String) return escape((String) x);
if (x instanceof List<?>) return escape((ArrayList<ScriptVariable>) x);
if (x instanceof BitSet) return escape((BitSet) x, true);
if (x instanceof Matrix3f)
return TextFormat.simpleReplace(((Matrix3f) x).toString(), "\t", ",\t");
if (x instanceof Matrix4f)
return TextFormat.simpleReplace(((Matrix4f) x).toString(), "\t", ",\t");
if (x instanceof Tuple3f) return escape((Tuple3f) x);
if (x instanceof Point4f) {
Point4f xyzw = (Point4f) x;
return "{" + xyzw.x + " " + xyzw.y + " " + xyzw.z + " " + xyzw.w + "}";
}
if (x instanceof AxisAngle4f) {
AxisAngle4f a = (AxisAngle4f) x;
return "{" + a.x + " " + a.y + " " + a.z + " " + (float) (a.angle * 180d / Math.PI) + "}";
}
if (x instanceof String[]) return escape((String[]) x, true);
if (x instanceof int[]
|| x instanceof int[][]
|| x instanceof float[]
|| x instanceof double[]
|| x instanceof float[][]
|| x instanceof float[][][]) return toJSON(null, x);
if (x instanceof Point3f[]) return escapeArray(x);
if (x instanceof Map) return escape((Map<String, Object>) x);
return (x == null ? "null" : x.toString());
}
private static String fixString(String s) {
if (s == null || s.indexOf("{\"") == 0) // don't doubly fix JSON strings when retrieving status
return s;
s = TextFormat.simpleReplace(s, "\"", "''");
s = TextFormat.simpleReplace(s, "\n", " | ");
return "\"" + s + "\"";
}
public static String escapeUrl(String url) {
url = TextFormat.simpleReplace(url, "\n", "");
url = TextFormat.simpleReplace(url, "%", "%25");
url = TextFormat.simpleReplace(url, "[", "%5B");
url = TextFormat.simpleReplace(url, "]", "%5D");
url = TextFormat.simpleReplace(url, " ", "%20");
return url;
}
private void readAtoms() throws Exception {
// format (4X,I4,4X,F10.8,3X,F10.8,3X,F10.8)
readLine();
while (line != null && (line.indexOf("ATOM") == 0 || !doSymmetry && line.indexOf(":") == 8)) {
int thisAtom = atomSetCollection.getAtomCount();
addAtom();
if (readLine().indexOf("MULT=") == 10)
for (int i = parseInt(line.substring(15, 18)); --i >= 0; ) {
readLine();
if (!doSymmetry) addAtom();
}
// format (A10,5X,I5,5X,F10.8,5X,F10.5,5X,F5.2)
String atomName = line.substring(0, 10);
String sym = atomName.substring(0, 2).trim();
if (sym.length() == 2 && Character.isDigit(sym.charAt(1))) sym = sym.substring(0, 1);
atomName = TextFormat.simpleReplace(atomName, " ", "");
int n = 0;
for (int i = atomSetCollection.getAtomCount(); --i >= thisAtom; ) {
Atom atom = atomSetCollection.getAtom(i);
atom.elementSymbol = sym;
atom.atomName = atomName + "_" + (n++);
}
while (readLine() != null && line.indexOf("ATOM") < 0 && line.indexOf("SYMMETRY") < 0) {}
}
// return with "SYMMETRY" line in buffer
}
String getDebugFooter(int iType, double energy) {
String s = "";
switch (iType) {
case CALC_DISTANCE:
s = "BOND STRETCHING";
break;
case CALC_ANGLE:
s = "ANGLE BENDING";
break;
case CALC_TORSION:
s = "TORSIONAL";
break;
case CALC_OOP:
s = "OUT-OF-PLANE BENDING";
break;
case CALC_VDW:
s = "VAN DER WAALS";
break;
case CALC_ES:
s = "ELECTROSTATIC ENERGY";
break;
}
return TextFormat.sprintf(
"\n TOTAL %s ENERGY = %8.3f %s\n",
new String[] {s, getUnit()}, new float[] {(float) energy});
}
private static String localizeFileReferences(String script, String[] origFileList, String [] copiedFileNames) {
for (int i = 0; i < origFileList.length; i++) {
String fullPathName = origFileList[i];
String fullCopiedName = copiedFileNames[i];
String name = fullCopiedName.substring(fullCopiedName.lastIndexOf('/') + 1);
if (!name.equals(fullPathName))
script = TextFormat.simpleReplace(script, fullPathName,name);
}
return script;
}
public static JmolData getJmol(int width, int height, String commandOptions) {
JmolApp jmolApp = new JmolApp();
jmolApp.startupHeight = height;
jmolApp.startupWidth = width;
jmolApp.haveConsole = false;
jmolApp.isDataOnly = true;
// jmolApp.info.put("exit", Boolean.TRUE);
String[] args = TextFormat.split(commandOptions, ' '); // doesn't allow for double-quoted
jmolApp.parseCommandLine(args);
return new JmolData(jmolApp);
}
/*
//
// f(x + 2delta) - 2f(x + delta) + f(x)
// f''(x) = ------------------------------------
// (delta)^2
//
void getNumericalSecondDerivative(MinAtom atom, int terms, Vector3d dir) {
double delta = 1.0e-5;
double e0 = getEnergy(terms, false);
double dx = getDx2(atom, terms, 0, e0, delta);
double dy = getDx2(atom, terms, 1, e0, delta);
double dz = getDx2(atom, terms, 2, e0, delta);
dir.set(dx, dy, dz);
}
private double getDx2(MinAtom atom, int terms, int i,
double e0, double delta) {
// calculate f(1)
atom.coord[i] += delta;
double e1 = getEnergy(terms, false);
// calculate f(2)
atom.coord[i] += delta;
double e2 = getEnergy(terms, false);
atom.coord[i] -= 2 * delta;
return (e2 - 2 * e1 + e0) / (delta * delta);
}
*/
public double energyFull(boolean gradients, boolean isSilent) {
double energy;
if (gradients) clearForces();
energy =
energyBond(gradients)
+ energyAngle(gradients)
+ energyTorsion(gradients)
+ energyStretchBend(gradients)
+ energyOOP(gradients)
+ energyVDW(gradients)
+ energyES(gradients);
if (!isSilent && calc.loggingEnabled)
calc.appendLogData(
TextFormat.sprintf(
"\nTOTAL %s ENERGY = %8.3f %s/mol\n",
new Object[] {name, Float.valueOf(toUserUnits(energy)), minimizer.units}));
return energy;
}
String getAtomList(String title) {
String trailer =
"----------------------------------------"
+ "-------------------------------------------------------\n";
StringBuffer sb = new StringBuffer();
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";
iVal[j + 1] = atoms[others[j]].atom.getAtomNumber();
}
sb.append(
TextFormat.sprintf(
"%3d %8.3f %8.3f %8.3f %-5s %8.3f %8.3f %8.3f" + s + "\n",
new String[] {atom.type},
new float[] {
(float) atom.coord[0],
(float) atom.coord[1],
(float) atom.coord[2],
(float) atom.force[0],
(float) atom.force[1],
(float) atom.force[2],
},
iVal));
}
sb.append(trailer + "\n\n");
return sb.toString();
}
public void steepestDescentInitialize(int stepMax, double criterion) {
this.stepMax = stepMax; // 1000
// The criterion must be in the units of the calculation.
// However, the user is setting this, so they will be in Minimizer units.
//
this.criterion = criterion / toUserUnits(1); // 1e-3
currentStep = 0;
clearForces();
calc.setLoggingEnabled(true);
calc.setLoggingEnabled(stepMax == 0 || Logger.isActiveLevel(Logger.LEVEL_DEBUGHIGH));
String s =
name
+ " "
+ calc.getDebugHeader(-1)
+ "Jmol Minimization Version "
+ Viewer.getJmolVersion()
+ "\n";
calc.appendLogData(s);
Logger.info(s);
calc.getConstraintList();
if (calc.loggingEnabled)
calc.appendLogData(calc.getAtomList("S T E E P E S T D E S C E N T"));
dE = 0;
calc.setPreliminary(stepMax > 0);
e0 = energyFull(false, false);
s =
TextFormat.sprintf(
" Initial "
+ name
+ " E = %10.3f "
+ minimizer.units
+ " criterion = %8.6f max steps = "
+ stepMax,
new Object[] {Float.valueOf(toUserUnits(e0)), Float.valueOf(toUserUnits(criterion))});
minimizer.report(s, false);
calc.appendLogData(s);
}
boolean fileWriter(File file, JList InstanceList) throws IOException { //returns true if successful.
useAppletJS = JmolViewer.checkOption(viewer, "webMakerCreateJS");
// JOptionPane.showMessageDialog(null, "Creating directory for data...");
String datadirPath = file.getPath();
String datadirName = file.getName();
String fileName = null;
if (datadirName.indexOf(".htm") > 0) {
fileName = datadirName;
datadirPath = file.getParent();
file = new File(datadirPath);
datadirName = file.getName();
} else {
fileName = datadirName + ".html";
}
datadirPath = datadirPath.replace('\\', '/');
boolean made_datadir = (file.exists() && file.isDirectory() || file.mkdir());
DefaultListModel listModel = (DefaultListModel) InstanceList.getModel();
LogPanel.log("");
if (made_datadir) {
LogPanel.log(GT._("Using directory {0}", datadirPath));
LogPanel.log(" " + GT._("adding JmolPopIn.js"));
viewer.writeTextFile(datadirPath + "/JmolPopIn.js",
WebExport.getResourceString(this, "JmolPopIn.js"));
for (int i = 0; i < listModel.getSize(); i++) {
JmolInstance thisInstance = (JmolInstance) (listModel.getElementAt(i));
String javaname = thisInstance.javaname;
String script = thisInstance.script;
LogPanel.log(" ...jmolApplet" + i);
LogPanel.log(" ..." + GT._("adding {0}.png", javaname));
try {
thisInstance.movepict(datadirPath);
} catch (IOException IOe) {
throw IOe;
}
String fileList = "";
fileList += addFileList(script, "/*file*/");
fileList += addFileList(script, "FILE0=");
fileList += addFileList(script, "FILE1=");
if (localAppletPath.getText().equals(".")
|| remoteAppletPath.getText().equals("."))
fileList += "Jmol.js\nJmolApplet.jar";
String[] filesToCopy = fileList.split("\n");
String[] copiedFileNames = new String[filesToCopy.length];
String f;
int pt;
for (int iFile = 0; iFile < filesToCopy.length; iFile++) {
if ((pt = (f = filesToCopy[iFile]).indexOf("|")) >= 0)
filesToCopy[iFile] = f.substring(0, pt);
copiedFileNames[iFile] = copyBinaryFile(filesToCopy[iFile],
datadirPath);
}
script = localizeFileReferences(script, filesToCopy, copiedFileNames);
LogPanel.log(" ..." + GT._("adding {0}.spt", javaname));
viewer.writeTextFile(datadirPath + "/" + javaname + ".spt", script);
}
String html = WebExport.getResourceString(this, panelName + "_template");
html = fixHtml(html);
appletInfoDivs = "";
StringBuffer appletDefs = new StringBuffer();
if (!useAppletJS)
htmlAppletTemplate = WebExport.getResourceString(this, panelName + "_template2");
for (int i = 0; i < listModel.getSize(); i++)
html = getAppletDefs(i, html, appletDefs, (JmolInstance) listModel
.getElementAt(i));
html = TextFormat.simpleReplace(html, "@AUTHOR@", GT.escapeHTML(pageAuthorName
.getText()));
html = TextFormat.simpleReplace(html, "@TITLE@", GT.escapeHTML(webPageTitle.getText()));
html = TextFormat.simpleReplace(html, "@REMOTEAPPLETPATH@",
remoteAppletPath.getText());
html = TextFormat.simpleReplace(html, "@LOCALAPPLETPATH@",
localAppletPath.getText());
html = TextFormat.simpleReplace(html, "@DATADIRNAME@", datadirName);
if (appletInfoDivs.length() > 0)
appletInfoDivs = "\n<div style='display:none'>\n" + appletInfoDivs
+ "\n</div>\n";
String str = appletDefs.toString();
if (useAppletJS)
str = "<script type='text/javascript'>\n" + str + "\n</script>";
html = TextFormat.simpleReplace(html, "@APPLETINFO@", appletInfoDivs);
html = TextFormat.simpleReplace(html, "@APPLETDEFS@", str);
html = TextFormat.simpleReplace(html, "@CREATIONDATA@", GT.escapeHTML(WebExport
.TimeStamp_WebLink()));
html = TextFormat.simpleReplace(html, "@AUTHORDATA@",
GT.escapeHTML(GT._("Based on template by A. Herráez as modified by J. Gutow")));
html = TextFormat.simpleReplace(html, "@LOGDATA@", "<pre>\n"
+ LogPanel.getText() + "\n</pre>\n");
LogPanel.log(" ..." + GT._("creating {0}", fileName));
viewer.writeTextFile(datadirPath + "/" + fileName, html);
} else {
IOException IOe = new IOException("Error creating directory: "
+ datadirPath);
throw IOe;
}
LogPanel.log("");
return true;
}
// Vector3d dir = new Vector3d();
public boolean steepestDescentTakeNSteps(int n) {
if (stepMax == 0) return false;
boolean isPreliminary = true;
for (int iStep = 1; iStep <= n; iStep++) {
currentStep++;
calc.setSilent(true);
for (int i = 0; i < minAtomCount; i++)
if (bsFixed == null || !bsFixed.get(i))
setForcesUsingNumericalDerivative(minAtoms[i], ENERGY);
linearSearch();
calc.setSilent(false);
if (calc.loggingEnabled) calc.appendLogData(calc.getAtomList("S T E P " + currentStep));
double e1 = energyFull(false, false);
dE = e1 - e0;
boolean done = Util.isNear(e1, e0, criterion);
if (done || currentStep % 10 == 0 || stepMax <= currentStep) {
String s =
TextFormat.sprintf(
name + " Step %-4d E = %10.6f dE = %8.6f ",
new Object[] {
new float[] {(float) e1, (float) (dE), (float) criterion},
Integer.valueOf(currentStep)
});
minimizer.report(s, false);
calc.appendLogData(s);
}
e0 = e1;
if (done || stepMax <= currentStep) {
if (calc.loggingEnabled) calc.appendLogData(calc.getAtomList("F I N A L G E O M E T R Y"));
if (done) {
String s =
TextFormat.formatString(
"\n "
+ name
+ " STEEPEST DESCENT HAS CONVERGED: E = %8.5f "
+ minimizer.units
+ " after "
+ currentStep
+ " steps",
"f",
toUserUnits(e1));
calc.appendLogData(s);
minimizer.report(s, true);
Logger.info(s);
}
return false;
}
// System.out.println(isPreliminary + " " + getNormalizedDE() + " " + currentStep);
if (isPreliminary && getNormalizedDE() >= 2) {
// looking back at this after some time, I don't exactly see why I wanted
// this to stay in preliminary mode unless |DE| >= 2 * crit.
// It's hard to ever have |DE| NOT >= 2 * crit -- that would be very close to the criterion.
// And when that IS the case, why would you want to STAY in preliminary mode? Hmm.
calc.setPreliminary(isPreliminary = false);
e0 = energyFull(false, false);
}
}
return true; // continue
}
String getDebugLine(int iType, Calculation c) {
switch (iType) {
case CALC_DISTANCE:
return TextFormat.sprintf(
"%3d %3d %-5s %-5s %4.2f%8.3f %8.3f %8.3f %8.3f %8.3f",
new String[] {atoms[c.ia].type, atoms[c.ib].type},
new float[] {
(float) c.dData[2] /*rab*/,
(float) c.rab,
(float) c.dData[0],
(float) c.dData[1],
(float) c.delta,
(float) c.energy
},
new int[] {atoms[c.ia].atom.getAtomNumber(), atoms[c.ib].atom.getAtomNumber()});
case CALC_ANGLE:
return TextFormat.sprintf(
"%3d %3d %3d %-5s %-5s %-5s %8.3f %8.3f %8.3f %8.3f",
new String[] {atoms[c.ia].type, atoms[c.ib].type, atoms[c.ic].type},
new float[] {
(float) (c.theta * RAD_TO_DEG),
(float) c.dData[4] /*THETA0*/,
(float) c.dData[0] /*Kijk*/,
(float) c.energy
},
new int[] {
atoms[c.ia].atom.getAtomNumber(),
atoms[c.ib].atom.getAtomNumber(),
atoms[c.ic].atom.getAtomNumber()
});
case CALC_TORSION:
return TextFormat.sprintf(
"%3d %3d %3d %3d %-5s %-5s %-5s %-5s %8.3f %8.3f %8.3f",
new String[] {atoms[c.ia].type, atoms[c.ib].type, atoms[c.ic].type, atoms[c.id].type},
new float[] {
(float) c.dData[0] /*V*/, (float) (c.theta * RAD_TO_DEG), (float) c.energy
},
new int[] {
atoms[c.ia].atom.getAtomNumber(),
atoms[c.ib].atom.getAtomNumber(),
atoms[c.ic].atom.getAtomNumber(),
atoms[c.id].atom.getAtomNumber()
});
case CALC_OOP:
return TextFormat.sprintf(
"" + "%3d %3d %3d %3d %-5s %-5s %-5s %-5s %8.3f %8.3f %8.3f",
new String[] {atoms[c.ia].type, atoms[c.ib].type, atoms[c.ic].type, atoms[c.id].type},
new float[] {
(float) (c.theta * RAD_TO_DEG), (float) c.dData[0] /*koop*/, (float) c.energy
},
new int[] {
atoms[c.ia].atom.getAtomNumber(),
atoms[c.ib].atom.getAtomNumber(),
atoms[c.ic].atom.getAtomNumber(),
atoms[c.id].atom.getAtomNumber()
});
case CALC_VDW:
return TextFormat.sprintf(
"%3d %3d %-5s %-5s %6.3f %8.3f %8.3f",
new String[] {atoms[c.iData[0]].type, atoms[c.iData[1]].type},
new float[] {(float) c.rab, (float) c.dData[0] /*kab*/, (float) c.energy},
new int[] {atoms[c.ia].atom.getAtomNumber(), atoms[c.ib].atom.getAtomNumber()});
case CALC_ES:
return TextFormat.sprintf(
"%3d %3d %-5s %-5s %6.3f %8.3f %8.3f",
new String[] {atoms[c.iData[0]].type, atoms[c.iData[1]].type},
new float[] {(float) c.rab, (float) c.dData[0] /*qq*/, (float) c.energy},
new int[] {atoms[c.ia].atom.getAtomNumber(), atoms[c.ib].atom.getAtomNumber()});
}
return "";
}