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[Jmol-commits] SF.net SVN: jmol:[11085] trunk/Jmol/src/org
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From: <ha...@us...> - 2009-06-23 16:47:49
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Revision: 11085
http://jmol.svn.sourceforge.net/jmol/?rev=11085&view=rev
Author: hansonr
Date: 2009-06-23 16:47:45 +0000 (Tue, 23 Jun 2009)
Log Message:
-----------
version=11.7.44_dev
# new feature: MO LIST or SHOW MO LIST display listing of orbitals for all files
# new feature: GAMESS reader now sets calculationType, orbital type, and auxiliaryInfo.calculationOptions
# bug fix: select(x;{xxx};...) or for(x;{xxx};...) when {xxx} is empty returns incorrect result
# bug fix: dipoles cannot be colored by name
# bug fix: dipole settings not accessible via wildcards
# new feature: merging of label() and format() functions -- same in all respects.
# bug fix: spartan'08 reader not reading vibrations
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/more/GamessReader.java
trunk/Jmol/src/org/jmol/adapter/readers/more/MOReader.java
trunk/Jmol/src/org/jmol/shapesurface/MolecularOrbital.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/ScriptEvaluator.java
trunk/Jmol/src/org/openscience/jmol/app/webexport/WebPanel.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/GamessReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/GamessReader.java 2009-06-23 16:47:08 UTC (rev 11084)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/GamessReader.java 2009-06-23 16:47:45 UTC (rev 11085)
@@ -31,11 +31,11 @@
import org.jmol.api.JmolAdapter;
import org.jmol.util.Logger;
+import org.jmol.util.TextFormat;
abstract public class GamessReader extends MOReader {
protected Vector atomNames;
- protected boolean isUHF = false;
abstract protected void readAtomsInBohrCoordinates() throws Exception;
@@ -220,5 +220,99 @@
}
return line;
}
-
+
+ /*
+ BASIS OPTIONS
+ -------------
+ GBASIS=N311 IGAUSS= 6 POLAR=DUNNING
+ NDFUNC= 3 NFFUNC= 1 DIFFSP= T
+ NPFUNC= 3 DIFFS= T
+ SPLIT3= 4.00000000 1.00000000 0.25000000
+
+
+ $CONTRL OPTIONS
+ ---------------
+SCFTYP=UHF RUNTYP=OPTIMIZE EXETYP=RUN
+MPLEVL= 2 CITYP =NONE CCTYP =NONE VBTYP =NONE
+DFTTYP=NONE TDDFT =NONE
+MULT = 3 ICHARG= 0 NZVAR = 0 COORD =UNIQUE
+PP =NONE RELWFN=NONE LOCAL =NONE NUMGRD= F
+ISPHER= 1 NOSYM = 0 MAXIT = 30 UNITS =ANGS
+PLTORB= F MOLPLT= F AIMPAC= F FRIEND=
+NPRINT= 7 IREST = 0 GEOM =INPUT
+NORMF = 0 NORMP = 0 ITOL = 20 ICUT = 9
+INTTYP=BEST GRDTYP=BEST QMTTOL= 1.0E-06
+
+$SYSTEM OPTIONS
+*/
+
+
+
+ private Hashtable calcOptions;
+ private boolean isTypeSet;
+
+ protected void setCalculationType() {
+ if (calcOptions == null || isTypeSet)
+ return;
+ isTypeSet = true;
+ String SCFtype = (String) calcOptions.get("contrl_options_SCFTYP");
+ String Runtype = (String) calcOptions.get("contrl_options_RUNTYP");
+ String igauss = (String) calcOptions.get("basis_options_IGAUSS");
+ String gbasis = (String) calcOptions.get("basis_options_GBASIS");
+ if (igauss == null && SCFtype == null)
+ return;
+
+ if (calculationType.equals("?"))
+ calculationType = "";
+
+ if (igauss != null) {
+ if (calculationType.length() > 0)
+ calculationType += " ";
+ calculationType += igauss + "-"
+ + TextFormat.simpleReplace(gbasis, "N", "");
+ // Q: "N" here means what?
+ }
+ if (SCFtype != null) {
+ if (calculationType.length() > 0)
+ calculationType += " ";
+ calculationType += SCFtype + " " + Runtype;
+ }
+ }
+
+ protected void readControlInfo() throws Exception {
+ readCalculationInfo("contrl_options_");
+ }
+
+ protected void readBasisInfo() throws Exception {
+ readCalculationInfo("basis_options_");
+ }
+
+ private void readCalculationInfo(String type) throws Exception {
+ if (calcOptions == null) {
+ calcOptions = new Hashtable();
+ atomSetCollection.setAtomSetCollectionAuxiliaryInfo("calculationOptions",
+ calcOptions);
+ }
+ while (readLine() != null && (line = line.trim()).length() > 0) {
+ if (line.indexOf("=") < 0)
+ continue;
+ String[] tokens = getTokens(TextFormat.simpleReplace(line, "="," = "));
+ for (int i = 0; i < tokens.length; i++) {
+ if (!tokens[i].equals("="))
+ continue;
+ try {
+ String key = type + tokens[i - 1];
+ String value = (key.equals("basis_options_SPLIT3") ? tokens[++i] + " " + tokens[++i]
+ + " " + tokens[++i] : tokens[++i]);
+ if (Logger.debugging)
+ Logger.debug(key + " = " + value);
+ calcOptions.put(key, value);
+ } catch (Exception e) {
+ // not interested
+ }
+ }
+ }
+ }
+
+
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/MOReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/MOReader.java 2009-06-23 16:47:08 UTC (rev 11084)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/MOReader.java 2009-06-23 16:47:45 UTC (rev 11085)
@@ -103,6 +103,7 @@
protected boolean iHaveAtoms = false;
protected boolean continuing = true;
protected boolean ignoreMOs = false;
+ protected String alphaBeta = "";
final protected int HEADER_GAMESS_UK_MO = 3;
final protected int HEADER_GAMESS_OCCUPANCIES = 2;
@@ -127,12 +128,17 @@
while (line != null && continuing)
if (checkLine())
readLine();
+ finalizeMoReader();
} catch (Exception e) {
return setError(e);
}
return atomSetCollection;
}
+ protected void finalizeMoReader() {
+ // see subclasses
+ }
+
private void initializeMoReader(BufferedReader reader, String type) {
this.reader = reader;
atomSetCollection = new AtomSetCollection("type");
@@ -152,7 +158,7 @@
return true;
boolean isOK = true;
int nOK = 0;
- line = line.toLowerCase();
+ line = line.toLowerCase() + " " + alphaBeta;
if (filterTokens == null) {
filterIsNot = (filter.indexOf("!") >= 0);
filterTokens = getTokens(filter.replace('!', ' ').replace(',', ' ')
@@ -339,6 +345,11 @@
}
if (line.indexOf("end") >= 0)
break;
+ if (line.indexOf(" ALPHA SET ") >= 0)
+ alphaBeta = "alpha";
+ else if (line.indexOf(" BETA SET ") >= 0)
+ alphaBeta = "beta";
+
//not everyone has followed the conventions for ending a section of output
if (line.length() == 0 || line.indexOf("--") >= 0 || line.indexOf(".....") >=0
|| line.indexOf("NBO BASIS") >= 0 // reading NBOs
@@ -364,7 +375,9 @@
}
}
mos[iMo].put("coefficients", coefs);
- if (moTypes != null && moCount < moTypes.size())
+ if (alphaBeta.length() > 0)
+ mos[iMo].put("type", alphaBeta);
+ else if (moTypes != null && moCount < moTypes.size())
mos[iMo].put("type", moTypes.get(moCount++));
orbitals.addElement(mos[iMo]);
}
@@ -398,7 +411,7 @@
line = "";
}
energyUnits = "a.u.";
- setMOData(true);
+ setMOData(!alphaBeta.equals("alpha"));
}
protected void getMOHeader(int headerType, String[] tokens, Hashtable[] mos, int nThisLine)
@@ -467,6 +480,7 @@
if (clearOrbitals) {
orbitals = new Vector();
moData = new Hashtable();
+ alphaBeta = "";
}
}
Modified: trunk/Jmol/src/org/jmol/shapesurface/MolecularOrbital.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/MolecularOrbital.java 2009-06-23 16:47:08 UTC (rev 11084)
+++ trunk/Jmol/src/org/jmol/shapesurface/MolecularOrbital.java 2009-06-23 16:47:45 UTC (rev 11085)
@@ -243,7 +243,7 @@
String s = (String) super.getProperty("list", param);
if (s.length() > 1)
s += "cutoff = " + super.getProperty("cutoff", 0) + "\n";
- return s;
+ return viewer.getMoInfo(-1) + "\n" + s;
}
if (propertyName == "moNumber")
return new Integer(moNumber);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-06-23 16:47:08 UTC (rev 11084)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-06-23 16:47:45 UTC (rev 11085)
@@ -3,16 +3,14 @@
version=11.7.44_dev
+# new feature: MO LIST or SHOW MO LIST display listing of orbitals for all files
+# new feature: GAMESS reader now sets calculationType, orbital type, and auxiliaryInfo.calculationOptions
# bug fix: select(x;{xxx};...) or for(x;{xxx};...) when {xxx} is empty returns incorrect result
# bug fix: dipoles cannot be colored by name
# bug fix: dipole settings not accessible via wildcards
# new feature: merging of label() and format() functions -- same in all respects.
# bug fix: spartan'08 reader not reading vibrations
-# bug fix: GAMESS reader now ignores orbitals in UHF calculations as it does not yet read them properly.
-# Added appropriate logger message. Will replace once fixed.
-# new feature: show mo energies -- lists molecular orbitals for all files.
-
# -----------------------------------------------------------------------------
#version=11.7.43
Modified: trunk/Jmol/src/org/jmol/viewer/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ScriptEvaluator.java 2009-06-23 16:47:08 UTC (rev 11084)
+++ trunk/Jmol/src/org/jmol/viewer/ScriptEvaluator.java 2009-06-23 16:47:45 UTC (rev 11085)
@@ -9892,7 +9892,7 @@
"jvxlFileData");
break;
case Token.mo:
- if (optParameterAsString(2).equalsIgnoreCase("energies")) {
+ if (optParameterAsString(2).equalsIgnoreCase("list")) {
msg = viewer.getMoInfo(-1);
len = 3;
} else {
Modified: trunk/Jmol/src/org/openscience/jmol/app/webexport/WebPanel.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/webexport/WebPanel.java 2009-06-23 16:47:08 UTC (rev 11084)
+++ trunk/Jmol/src/org/openscience/jmol/app/webexport/WebPanel.java 2009-06-23 16:47:45 UTC (rev 11085)
@@ -515,7 +515,7 @@
private static String copyBinaryFile(String fullPathName, String dataPath) {
String name = fullPathName.substring(fullPathName.lastIndexOf('/') + 1);
name = dataPath + "/" + name;
- String gzname = name.concat(".gz");
+ String gzname = name + ".gz";
File outFile = new File(name);
File gzoutFile = new File(gzname);
if (outFile.exists())
@@ -563,7 +563,7 @@
private static String writeFileBytes(String path, byte[] data) {
try {
if (data.length>=524288 && !path.endsWith("JmolApplet.jar") ){ //gzip it
- path = path.concat(".gz");
+ path += ".gz";
GZIPOutputStream gzFile = new GZIPOutputStream(new FileOutputStream(path));
gzFile.write(data);
LogPanel.log(" ..." + GT._("compressing large data file to") + "\n");
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