Revision: 21355
http://sourceforge.net/p/jmol/code/21355
Author: hansonr
Date: 2017-01-26 22:29:18 +0000 (Thu, 26 Jan 2017)
Log Message:
-----------
NBO message ***errmess***
isosurface enables NBO option; still not for alpha/beta
Modified Paths:
--------------
trunk/Jmol/src/org/gennbo/NBODialog.java
trunk/Jmol/src/org/gennbo/NBODialogView.java
trunk/Jmol/src/org/gennbo/NBOService.java
trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
Modified: trunk/Jmol/src/org/gennbo/NBODialog.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBODialog.java 2017-01-26 14:20:52 UTC (rev
21354)
+++ trunk/Jmol/src/org/gennbo/NBODialog.java 2017-01-26 22:29:18 UTC (rev
21355)
@@ -788,13 +788,13 @@
NBOFileHandler.getExt(inputFileHandler.inputFile).equals("47"));
}
- public void setStatus(String statusInfo) {
+ void setStatus(String statusInfo) {
if (statusInfo.length() > 0)
log(statusInfo, 'p');
statusLab.setText(statusInfo);
}
- public void processEnd(int dialogMode, AbstractListModel<String> list) {
+ void processEnd(int dialogMode, AbstractListModel<String> list) {
statusLab.setText("");
switch (dialogMode) {
case NBOService.MODE_IMAGE:
@@ -822,11 +822,15 @@
setStatus("OK mode=" + dialogMode);
}
- public void loadFromHandler(File file) {
+ void loadFromHandler(File file) {
isNewModel = true;
if (dialogMode == DIALOG_VIEW)
setViewerBasis();
else
loadModelFileQueued(file, false, false);
}
+
+ void setLicense(String line) {
+ licenseInfo.setText("<html><div style='text-align: center'>" + line +
"</html>");
+ }
}
Modified: trunk/Jmol/src/org/gennbo/NBODialogView.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBODialogView.java 2017-01-26 14:20:52 UTC
(rev 21354)
+++ trunk/Jmol/src/org/gennbo/NBODialogView.java 2017-01-26 22:29:18 UTC
(rev 21355)
@@ -1725,7 +1725,8 @@
DefaultListModel<String> model = (DefaultListModel<String>) getModel();
String script = "select all";
String beta = (betaSpin.isSelected() ? " beta" : "");
-
+ String type = basis.getSelectedItem().toString();
+
// get only the ones needing changing
BS bsSel = new BS();
int[] selected = getSelectedIndices();
@@ -1749,7 +1750,7 @@
String id = "mo" + i;
script += ";select *;if (" + bsKnown.get(i) + "){isosurface " + id + "
on} else {isosurface " + id
+ " color " + (bsNeg.get(i) ? color1 + " " + color2 : color2 + " "
+ color1)
- + " cutoff 0.0316 MO " + (i + 1) + beta + " frontonly "
+ + " cutoff 0.0316 NBO " + type + " " + (i + 1) + beta + "
frontonly "
+ (useWireMesh ? " mesh nofill" : " nomesh fill translucent " +
opacityOp) + "}";
}
Modified: trunk/Jmol/src/org/gennbo/NBOService.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBOService.java 2017-01-26 14:20:52 UTC (rev
21354)
+++ trunk/Jmol/src/org/gennbo/NBOService.java 2017-01-26 22:29:18 UTC (rev
21355)
@@ -310,13 +310,18 @@
//boolean haveStart = false;
boolean inOpener = false;
boolean inRequest = false;
+ boolean inError = false;
System.out.println("nboListener " + this + " running");
while (!Thread.currentThread().isInterrupted()) {
String line = null;
try {
while ((line = nboReader.readLine()) != null) {
-
- logServerLine(line);
+ if (line.indexOf("***errmess***") == 0) {
+ logServerLine(line, false);
+ inError = !inError;
+ continue;
+ }
+ logServerLine(line, inError);
// ignore the opener business
if (line.indexOf("DATA \" \"") >= 0) {
//nboDialog.logInfo(" DATA...", Logger.LEVEL_INFO);
@@ -349,10 +354,8 @@
nboDialog.alertError("NBOServe has stopped working");
restart();
}
- if (line.indexOf("NBOServe") >= 0) {
- nboDialog.licenseInfo
- .setText("<html><div style='text-align: center'>" + line
- + "</html>");
+ if (line.indexOf("NBOServe v") >= 0) {
+ nboDialog.setLicense(line);
isWorking = false;
continue;
}
@@ -467,14 +470,16 @@
private int lineNo = 0;
- protected void logServerLine(String line) {
+ protected void logServerLine(String line, boolean inError) {
+
nboDialog.logInfo((++lineNo) + "< " + line,
- isFortranError(line) ? Logger.LEVEL_ERROR : Logger.LEVEL_DEBUG);
+ isFortranError(line) || inError ? Logger.LEVEL_ERROR :
Logger.LEVEL_DEBUG);
}
protected boolean isFortranError(String line) {
return line.indexOf("Permission denied") >= 0
- || line.indexOf("PGFIO-F") >= 0 || line.indexOf("Invalid command") >=
0;
+ || line.indexOf("PGFIO-F") >= 0
+ || line.indexOf("Invalid command") >= 0;
}
public void closeProcess() {
Modified: trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2017-01-26 14:20:52 UTC
(rev 21354)
+++ trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2017-01-26 22:29:18 UTC
(rev 21355)
@@ -1016,8 +1016,8 @@
@SuppressWarnings("unchecked")
- private void setNBOType(Map<String, Object> moData, String type)
- throws ScriptException {
+ private void setNBOType(Map<String, Object> moData, String type,
+ boolean isBeta) throws ScriptException {
// 31 32 33 34 35 36 37 38 39 40 41
int ext = ";AO; ;PNAO;;NAO; ;PNHO;;NHO; ;PNBO;;NBO; ;PNLMO;NLMO;;MO;
;NO;"
.indexOf(";" + type + ";");
@@ -1030,7 +1030,8 @@
if (chk)
return;
try {
- Lst<Map<String, Object>> orbitals = (Lst<Map<String, Object>>)
moData.get(type + "_coefs");
+ Lst<Map<String, Object>> orbitals = (Lst<Map<String, Object>>) moData
+ .get(type + "_coefs");
if (orbitals == null) {
String fileName = moData.get("nboRoot") + "." + ext;
String data = vwr.getFileAsString3(fileName, true, null);
@@ -1045,8 +1046,17 @@
orbitals.addLast(mo);
mo.put("dfCoefMaps", dfCoefMaps);
}
- ((QS) Interface.getInterface("org.jmol.quantum.QS", vwr,
"script")).setNboLabels(nboLabels, n, orbitals, 0, type);
+ ((QS) Interface.getInterface("org.jmol.quantum.QS", vwr, "script"))
+ .setNboLabels(nboLabels, n, orbitals, 0, type);
data = data.substring(data.lastIndexOf("--") + 2);
+ if (data.indexOf("alpha") >= 0) {
+ if (isBeta) {
+ if (data.indexOf("beta") >= 0)
+ data = data.substring(data.indexOf("beta") + 4);
+ else
+ data = "";
+ }
+ }
int len = data.length();
int[] next = new int[1];
for (int i = 0; i < n; i++) {
@@ -1112,7 +1122,7 @@
error(ScriptError.ERROR_moModelError);
vwr.checkMenuUpdate();
if (nboType != null) {
- setNBOType(moData, nboType);
+ setNBOType(moData, nboType, isBeta);
if (lc == null && moNumber == Integer.MAX_VALUE)
return;
}
@@ -1246,6 +1256,7 @@
boolean haveSlab = false;
boolean haveIntersection = false;
boolean isFrontOnly = false;
+ String nbotype = null;
float[] data = null;
String cmd = null;
int thisSetNumber = Integer.MIN_VALUE;
@@ -1870,7 +1881,12 @@
error(ScriptError.ERROR_expressionExpected);
}
break;
+ case T.nbo:
+ nbotype = paramAsStr(++i).toUpperCase();
+ sbCommand.append(" nbo ").append(nbotype).append(" ");
case T.mo:
+ if (nbotype == null)
+ sbCommand.append(" mo ");
// mo 1-based-index
int moNumber = Integer.MAX_VALUE;
int offset = Integer.MAX_VALUE;
@@ -1883,7 +1899,7 @@
eval.bad();
break;
case T.density:
- sbCommand.append("mo [1] squared ");
+ sbCommand.append("[1] squared ");
addShapeProperty(propertyList, "squareLinear", Boolean.TRUE);
linearCombination = new float[] { 1 };
offset = moNumber = 0;
@@ -1895,7 +1911,7 @@
moNumber = 0;
i = eval.iToken;
//if (surfaceObjectSeen) {
- sbCommand.append(" mo " + (isNegOffset ? "-" : "") + "HOMO ");
+ sbCommand.append((isNegOffset ? "-" : "") + "HOMO ");
if (offset > 0)
sbCommand.append("+");
if (offset != 0)
@@ -1905,7 +1921,7 @@
case T.integer:
moNumber = intParameter(i);
//if (surfaceObjectSeen)
- sbCommand.append(" mo ").appendI(moNumber);
+ sbCommand.appendI(moNumber);
if (tokAt(i + 1) == T.beta) {
isBeta = true;
i++;
@@ -1935,7 +1951,7 @@
.appendI(seed);
}
setMoData(propertyList, moNumber, linearCombination, offset,
- isNegOffset, modelIndex, null, null, isBeta);
+ isNegOffset, modelIndex, null, nbotype, isBeta);
surfaceObjectSeen = true;
continue;
case T.nci:
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