Revision: 20142
http://sourceforge.net/p/jmol/code/20142
Author: hansonr
Date: 2014-11-27 05:01:33 +0000 (Thu, 27 Nov 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.11_2014.11.27"
new feature: ZMatrixReader also serves as simple input file reader
for Q-Chem, Jaguar, MolPro, and ADF, as produced by NBO6Pro
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java
2014-11-27 01:10:19 UTC (rev 20141)
+++ trunk/Jmol/src/org/jmol/adapter/readers/simple/ZMatrixReader.java
2014-11-27 05:01:33 UTC (rev 20142)
@@ -46,7 +46,8 @@
public class ZMatrixReader extends AtomSetCollectionReader {
/*
- * a simple Z-matrix reader
+ * a simple Z-matrix reader, also serves as simple
+ * input file reader for Q-Chem, Jaguar, MolPro, and ADF, as produced by
NBO6Pro
*
* Can be invoked using ZMATRIX:: or with file starting with #ZMATRIX
* # are comments; can include jmolscript: xxxx
@@ -217,6 +218,34 @@
line = line.substring(0, line.indexOf("#"));
if (line.indexOf(":") >= 0)
return true; // Variables: or Constants:
+ if (line.contains("$molecule")) {
+ // Q-Chem input
+ rd(); // spin
+ return readBlock("$end");
+ }
+ if (line.startsWith("$"))
+ return true; // $NBO
+ if (line.contains("%mem")) {
+ // Gaussian
+ discardLinesUntilBlank();
+ discardLinesUntilBlank();
+ rd(); // spin
+ return readBlock(null);
+ }
+ if (line.contains("ATOMS cartesian")) {
+ // ADF input
+ return readBlock("END");
+ }
+ if (line.contains("&zmat")) {
+ // Jaguar input
+ return readBlock("&");
+ }
+ if (line.contains("geometry={")) {
+ // MolPRO via NBO6
+ readLines(2);
+ return readBlock("}");
+ }
+
tokens = getTokensStr(line);
if (tokens.length == 2) {
getSymbolic();
@@ -226,13 +255,21 @@
return true;
}
- private void cleanLine() {
+ private boolean readBlock(String strEnd) throws Exception {
+ lineBuffer.clear();
+ while (rd() != null && cleanLine() != null
+ && (strEnd == null ? line.length() > 0 : line.indexOf(strEnd) < 0))
+ lineBuffer.addLast(getTokens());
+ return (continuing = false);
+ }
+
+ private String cleanLine() {
// remove commas for Gaussian and parenthetical expressions for MOPAC
line = line.replace(',', ' ');
int pt1, pt2;
while ((pt1 = line.indexOf('(')) >= 0 && (pt2 = line.indexOf('(', pt1)) >=
0)
line = line.substring(0, pt1) + " " + line.substring(pt2 + 1);
- line = line.trim();
+ return (line = line.trim());
}
@Override
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2014-11-27
01:10:19 UTC (rev 20141)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2014-11-27
05:01:33 UTC (rev 20142)
@@ -675,7 +675,7 @@
{"TlsDataOnly", "REFMAC\n\nTL", "REFMAC\r\n\r\n", "REFMAC\r\rTL"};
private final static String[] zMatrixFileStartRecords =
- {"ZMatrix", "#ZMATRIX"};
+ {"ZMatrix", "#ZMATRIX", "%mem="};
private final static String[] magresFileStartRecords =
{"Magres", "#$magres", "# magres"};
@@ -847,6 +847,8 @@
private final static String[] gaussianFchkContainsRecords =
{ "GaussianFchk", "Number of point charges in /Mol/" };
+ private final static String[] zmatrixContainsRecords =
+ { "ZMatrix", " ATOMS cartesian", "$molecule", "&zmat", "geometry={" };
private final static String[][] headerContainsRecords =
@@ -860,6 +862,7 @@
dmolContainsRecords, gulpContainsRecords,
espressoContainsRecords, siestaContainsRecords, xcrysDenContainsRecords,
mopacArchiveContainsRecords,abinitContainsRecords,gaussianFchkContainsRecords,
+ zmatrixContainsRecords
};
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-27 01:10:19 UTC
(rev 20141)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-27 05:01:33 UTC
(rev 20142)
@@ -17,6 +17,10 @@
Jmol.___JmolVersion="14.3.11_2014.11.27"
+new feature: ZMatrixReader also serves as simple input file reader
+ for Q-Chem, Jaguar, MolPro, and ADF, as produced by NBO6Pro
+
+
JmolVersion="14.3.10_2014.11.27"
released as 14.3.10
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
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