Revision: 20301
http://sourceforge.net/p/jmol/code/20301
Author: hansonr
Date: 2015-02-18 00:44:51 +0000 (Wed, 18 Feb 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.2.12_2015.02.17b"
bug fix: writing to PNGJ data to .ZIP file should create a standard ZIP file.
-- especially useful now that some zip readers will not open PNGJ files as
zip files
(with newer 7zip you can right-click file, then select 7zip...open
archive...zip)
var x = load("t.png", true)
write var x "t.zip"
bug fix: VASP POSCAR fix for atom symbols in header line
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/xtal/VaspPoscarReader.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/OutputManager.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xtal/VaspPoscarReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xtal/VaspPoscarReader.java
2015-02-17 12:02:59 UTC (rev 20300)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xtal/VaspPoscarReader.java
2015-02-18 00:44:51 UTC (rev 20301)
@@ -11,15 +11,16 @@
* http://cms.mpi.univie.ac.at/vasp/
*
* @author Pieremanuele Canepa, Wake Forest University, Department of Physics
- * Winston Salem, NC 27106, cane...@wfu.edu
+ * Winston Salem, NC 27106, cane...@wfu.edu (pcan...@mit.edu)
*
* @version 1.0
*/
public class VaspPoscarReader extends AtomSetCollectionReader {
- private Lst<String> atomLabels = new Lst<String>();
+ private Lst<String> atomLabels;
private int ac;
+ private String title;
@Override
protected void initializeReader() throws Exception {
@@ -31,7 +32,7 @@
}
private void readJobTitle() throws Exception {
- asc.setAtomSetName(rd().trim());
+ asc.setAtomSetName(title = rd().trim());
}
private void readUnitCellVectors() throws Exception {
@@ -51,10 +52,21 @@
private void readMolecularFormula() throws Exception {
// H C O Be C H
- String elementLabel[] = PT.getTokens(discardLinesUntilNonBlank());
+ String[] elementLabel = PT.getTokens(discardLinesUntilNonBlank());
+ String[] elementCounts;
+ if (PT.parseInt(elementLabel[0]) == Integer.MIN_VALUE) {
+ elementCounts = PT.getTokens(rd());
// 6 24 18 6 6 24
- String elementCounts[] = PT.getTokens(rd());
+ } else {
+ elementCounts = elementLabel;
+ elementLabel = PT.split(title, " ");
+ if (elementLabel.length != elementCounts.length) {
+ elementLabel = PT.split("Al B C Db Eu F Ga Hf I K Li Mn N O P Ru S Te
U V W Xe Yb Zn", " ");
+ appendLoadNote("using pseudo atoms Al B C Db...");
+ }
+ }
SB mf = new SB();
+ atomLabels = new Lst<String>();
for (int i = 0; i < elementCounts.length; i++) {
int n = Integer.parseInt(elementCounts[i]);
ac += n;
@@ -64,7 +76,7 @@
atomLabels.addLast(label);
}
String s = mf.toString();
- Logger.info("VaspPoscar reader: " + ac + " atoms identified for" + s);
+ appendLoadNote(ac + " atoms identified for" + s);
appendLoadNote(s);
asc.newAtomSet();
asc.setAtomSetName(s);
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-02-17 12:02:59 UTC
(rev 20300)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-02-18 00:44:51 UTC
(rev 20301)
@@ -4129,22 +4129,22 @@
isData = true;
loadScript.append(" /*data*/ data");
String key = stringParameter(++i).toLowerCase();
+ int ptVar = key.indexOf("@");
+ if (ptVar >= 0)
+ key = key.replace('@', '_');
loadScript.append(" ").append(PT.esc(key));
isAppend = key.startsWith("append");
doOrient = (key.indexOf("orientation") >= 0);
- String strModel = (key.indexOf("@") >= 0 ? ""
- + getParameter(key.substring(key.indexOf("@") + 1), T.string, true)
+ String strModel = (ptVar >= 0 ? ""
+ + getParameter(key.substring(ptVar + 1), T.string, true)
: paramAsStr(++i));
strModel = Viewer.fixInlineString(strModel, vwr.getInlineChar());
htParams.put("fileData", strModel);
htParams.put("isData", Boolean.TRUE);
//note: ScriptCompiler will remove an initial \n if present
- loadScript.appendC('\n');
- loadScript.append(strModel);
- if (key.indexOf("@") < 0) {
- loadScript.append(" end ").append(PT.esc(key));
+ loadScript.appendC('\n').append(strModel).append(" end
").append(PT.esc(key));
+ if (ptVar < 0)
i += 2; // skip END "key"
- }
break;
case T.mutate:
isMutate = isAppend = true;
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-02-17 12:02:59 UTC
(rev 20300)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-02-18 00:44:51 UTC
(rev 20301)
@@ -3411,7 +3411,8 @@
break;
} else if (key.equals("_IMAGE_")) {
v.add(0, key);
- v.add(1, bytes);
+ v.add(1, null);
+ v.add(2, bytes);
} else {
v.addLast(key);
v.addLast(null);
Modified: trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-02-17 12:02:59 UTC
(rev 20300)
+++ trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-02-18 00:44:51 UTC
(rev 20301)
@@ -1936,12 +1936,12 @@
if (!isIsosurface)
invArg();
isCavity = true;
- if (chk)
- continue;
float cavityRadius = (isFloatParameter(i + 1) ? floatParameter(++i)
: 1.2f);
float envelopeRadius = (isFloatParameter(i + 1) ? floatParameter(++i)
: 10f);
+ if (chk)
+ continue;
if (envelopeRadius > 10f) {
eval.integerOutOfRange(0, 10);
return;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-17 12:02:59 UTC
(rev 20300)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-02-18 00:44:51 UTC
(rev 20301)
@@ -3,7 +3,7 @@
# THIS IS THE DEVELOPMENT TRUNK
-# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
+# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
# Developers: to add a description of changes you have made,
# add it on a line below the "Jmol.___JmolVersion=..." line.
@@ -15,11 +15,31 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
TODO: add 2D graphics panel for Ramachandran and NBO-style 2D graphics -- send
to browser as data uri?
-Jmol.___JmolVersion="14.2.12_2015.02.17"
+Jmol.___JmolVersion="14.2.12_2015.02.17b"
+bug fix: writing to PNGJ data to .ZIP file should create a standard ZIP file.
+ -- especially useful now that some zip readers will not open PNGJ files as
zip files
+ (with newer 7zip you can right-click file, then select 7zip...open
archive...zip)
+
+ var x = load("t.png", true)
+ write var x "t.zip"
+
+
+bug fix: VASP POSCAR fix for atom symbols in header line
+
+JmolVersion="14.2.12_2015.02.17"
+
new feature: set zshadePower 0
-- allows examination of depth buffer and writing to image for external
processing
+ set zShadePower 0
+ set zSlab 100
+ set zDepth 0
+ set zShade true
+ write z.jpg
+ set zShade false
+ write rgb.jpg
+
JmolVersion="14.2.12_2015.02.16"
new feature: x.dot(y) for planes and points -- was present but undocumented
and not working correctly
Modified: trunk/Jmol/src/org/jmol/viewer/OutputManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/OutputManager.java 2015-02-17 12:02:59 UTC
(rev 20300)
+++ trunk/Jmol/src/org/jmol/viewer/OutputManager.java 2015-02-18 00:44:51 UTC
(rev 20301)
@@ -259,12 +259,18 @@
private boolean createTheImage(Object objImage, String type, OC out,
Map<String, Object> params, String[] errRet) {
type = type.substring(0, 1) + type.substring(1).toLowerCase();
- if (type.equals("Zipdata") || type.equals("Binary")) {
+ boolean isZipData = type.equals("Zipdata");
+ if (isZipData || type.equals("Binary")) {
@SuppressWarnings("unchecked")
Lst<Object> v = (Lst<Object>) params.get("imageData");
if (v.size() >= 2 && v.get(0).equals("_IMAGE_")) {
+ if (isZipData) {
+ errRet[0] = writeZipFile(out, v, "OK JMOL", null);
+ return true;
+ }
objImage = null;
v.remove(0);
+ v.remove(0); // also "_IMAGE_"
params.put("pngImgData", v.remove(0));
OC oz = getOutputChannel(null, null);
errRet[0] = writeZipFile(oz, v, "OK JMOL", null);
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