Revision: 20813
http://sourceforge.net/p/jmol/code/20813
Author: hansonr
Date: 2015-10-09 21:24:05 +0000 (Fri, 09 Oct 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.16_2015.10.09"
new feature: Gaussian log file reader reads spin density scalars as
property_spin
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
2015-10-08 03:49:03 UTC (rev 20812)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/GaussianReader.java
2015-10-09 21:24:05 UTC (rev 20813)
@@ -203,9 +203,32 @@
// avoid next calculation to set the last title string
return true;
}
+ if (line.startsWith(" Mulliken atomic spin densities:")) {
+ getSpinDensities(11);
+ return true;
+ }
+ if (line.startsWith(" Mulliken charges and spin densities:")) {
+ getSpinDensities(21);
+ return true;
+ }
return checkNboLine();
}
+// Mulliken atomic spin densities:
+// 1
+// 1 O 1.086438
+// 2 H -.043219
+// 3 H -.043219
+
+ private void getSpinDensities(int pt) throws Exception {
+ rd();
+ float[] data = new float[asc.getLastAtomSetAtomCount()];
+ for (int i = 0; i < data.length; i++)
+ data[i] = parseFloatStr(rd().substring(pt, pt + 10));
+ asc.setAtomProperties("spin", data, -1, false);
+ appendLoadNote(data.length + " spin densities loaded into model " +
(asc.iSet + 1));
+ }
+
/**
* Interprets the SCF Done: section.
*
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-10-08 03:49:03 UTC
(rev 20812)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-10-09 21:24:05 UTC
(rev 20813)
@@ -447,7 +447,7 @@
"groupPropertyList");
if (ms.am[i].isBioModel && ms.getInfo(i, "dssr") != null)
vwr.getAnnotationParser(true).setGroup1(ms, i);
- if (atomProperties == null)
+ if (atomProperties == null)
continue;
for (Map.Entry<String, Object> entry : atomProperties.entrySet()) {
String key = entry.getKey();
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-08 03:49:03 UTC
(rev 20812)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-10-09 21:24:05 UTC
(rev 20813)
@@ -62,8 +62,13 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.3.16_2015.10.06"
+Jmol.___JmolVersion="14.3.16_2015.10.09"
+new feature: Gaussian log file reader reads spin density scalars as
property_spin
+
+
+JmolVersion="14.3.16_2015.10.06"
+
new feature: print within(distance, point, array_of_points)
-- point array distance iterator
-- returns subarray of points (in differing order, probably) of
array_of_points
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