Revision: 20160
http://sourceforge.net/p/jmol/code/20160
Author: hansonr
Date: 2014-12-09 23:42:28 +0000 (Tue, 09 Dec 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.11_2014.12.09"
new feature: Castep reading of .ts files
bug fix: array.add("\t",array) broken 2014.12.04
bug fix: array.split("",true) doesn't handle CSV with new lines in quotes
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
2014-12-09 13:05:53 UTC (rev 20159)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/CastepReader.java
2014-12-09 23:42:28 UTC (rev 20160)
@@ -92,6 +92,7 @@
private String[] tokens;
private boolean isPhonon;
+ private boolean isTS;
private boolean isOutput;
private boolean isCell;
@@ -235,7 +236,7 @@
continue;
}
}
- if (isPhonon || isOutput) {
+ if (isPhonon || isOutput || isTS) {
if (isPhonon) {
isTrajectory = (desiredVibrationNumber <= 0);
asc.allowMultiple = false;
@@ -262,11 +263,11 @@
} else if (doProcessLines && line.contains("Born Effective Charges")) {
readOutputBornChargeTensors();
} else if (line.contains("Final energy ")) { // not "Final energy, E"
- readEnergy(3);
+ readEnergy(3, null);
} else if (line.contains("Dispersion corrected final energy*")) {
- readEnergy(5);
+ readEnergy(5, null);
} else if (line.contains("Total energy corrected")) {
- readEnergy(8);
+ readEnergy(8, null);
}
return true;
}
@@ -327,13 +328,13 @@
}
- private void readEnergy(int pt) throws Exception {
+ private void readEnergy(int pt, String prefix) throws Exception {
if (isTrajectory)
applySymmetryAndSetTrajectory();
tokens = getTokens();
try {
Double energy = Double.valueOf(Double.parseDouble(tokens[pt]));
- asc.setAtomSetName("Energy = " + energy + " eV");
+ asc.setAtomSetName(prefix + "Energy = " + energy + " eV");
asc.setAtomSetEnergy("" + energy, energy.floatValue());
asc.setAtomSetAuxiliaryInfo("Energy", energy);
} catch (Exception e) {
@@ -357,12 +358,15 @@
}
private void readPhononTrajectories() throws Exception {
- isTrajectory = (desiredVibrationNumber <= 0);
+ if (!isTS) // force this only for .phonon, not .ts
+ isTrajectory = (desiredVibrationNumber <= 0);
if (isTrajectory)
asc.setTrajectory();
doApplySymmetry = true;
while (line != null && line.contains("<-- E")) {
asc.newAtomSetClear(false);
+ if (isTS)
+ readEnergy(0, getTokensStr(prevline + " -")[0] + " ");
discardLinesUntilContains("<-- h");
setSpaceGroupName("P1");
abc = read3Vectors(true);
@@ -381,7 +385,7 @@
@Override
protected void finalizeSubclassReader() throws Exception {
- if (isPhonon || isOutput) {
+ if (isPhonon || isOutput || isTS) {
isTrajectory = false;
} else {
doApplySymmetry = true;
@@ -530,6 +534,11 @@
isCell = true;
break;
}
+ if (line.startsWith("LST")) {
+ isTS = true;
+ Logger.info("reading CASTEP .ts file");
+ return -1;
+ }
if (line.startsWith("BEGIN header")) {
isPhonon = true;
Logger.info("reading CASTEP .phonon file");
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-09 13:05:53 UTC
(rev 20159)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-09 23:42:28 UTC
(rev 20160)
@@ -18,6 +18,8 @@
Jmol.___JmolVersion="14.3.11_2014.12.09"
+new feature: Castep reading of .ts files
+
bug fix: array.add("\t",array) broken 2014.12.04
bug fix: array.split("",true) doesn't handle CSV with new lines in quotes
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