Revision: 21680
http://sourceforge.net/p/jmol/code/21680
Author: hansonr
Date: 2017-07-27 13:42:02 +0000 (Thu, 27 Jul 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.20.4"
bug fix: SpartanSMOL reader for iSpartan files does not read charges or
vibrational mode data
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/spartan/SpartanArchive.java
trunk/Jmol/src/org/jmol/adapter/readers/spartan/SpartanReader.java
trunk/Jmol/src/org/jmol/adapter/readers/spartan/SpartanSmolReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/spartan/SpartanArchive.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/spartan/SpartanArchive.java
2017-07-27 13:15:02 UTC (rev 21679)
+++ trunk/Jmol/src/org/jmol/adapter/readers/spartan/SpartanArchive.java
2017-07-27 13:42:02 UTC (rev 21680)
@@ -51,6 +51,7 @@
private int modelCount = 0;
+ private int modelAtomCount = 0;
private int ac = 0;
private String bondData; // not in archive; may or may not have
private int moCount = 0;
@@ -62,8 +63,9 @@
private BasisFunctionReader r;
- SpartanArchive(BasisFunctionReader r, String bondData, String endCheck) {
+ SpartanArchive(BasisFunctionReader r, String bondData, String endCheck, int
smolAtomCount) {
initialize(r, bondData);
+ this.modelAtomCount = smolAtomCount;
this.endCheck = endCheck;
isSMOL = (endCheck != null);
}
@@ -130,8 +132,6 @@
r.asc.setAtomSetEnergy(tokens[0], value);
}
- int modelAtomCount;
-
private int setInfo(String info) throws Exception {
// 5 17 11 18 0 1 17 0 RHF 3-21G(d) NOOPT FREQ
// 0 1 2 3 4 5 6 7 8 9
Modified: trunk/Jmol/src/org/jmol/adapter/readers/spartan/SpartanReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/spartan/SpartanReader.java
2017-07-27 13:15:02 UTC (rev 21679)
+++ trunk/Jmol/src/org/jmol/adapter/readers/spartan/SpartanReader.java
2017-07-27 13:42:02 UTC (rev 21680)
@@ -47,7 +47,7 @@
String cartesianHeader = "Cartesian Coordinates (Ang";
if (isSpartanArchive(cartesianHeader)) {
moData = new Hashtable<String, Object>();
- SpartanArchive spartanArchive = new SpartanArchive(this, "", null);
+ SpartanArchive spartanArchive = new SpartanArchive(this, "", null, 0);
int ac = spartanArchive.readArchive(line, true, 0, true);
if (ac > 0)
asc.setAtomSetName("Spartan file");
Modified: trunk/Jmol/src/org/jmol/adapter/readers/spartan/SpartanSmolReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/spartan/SpartanSmolReader.java
2017-07-27 13:15:02 UTC (rev 21679)
+++ trunk/Jmol/src/org/jmol/adapter/readers/spartan/SpartanSmolReader.java
2017-07-27 13:42:02 UTC (rev 21680)
@@ -163,10 +163,6 @@
return false;
} else if (lcline.endsWith("proparc")
|| lcline.endsWith("propertyarchive")) {
- if (spartanArchive == null) {
- spartanArchive = new SpartanArchive(this, bondData, endCheck);
- spartanArchive.modelAtomCount = asc.getAtomSetAtomCount(asc.iSet);
- }
readProperties();
return false;
} else if (lcline.endsWith("archive")) {
@@ -246,7 +242,7 @@
}
private String readArchive() throws Exception {
- spartanArchive = new SpartanArchive(this, bondData, endCheck);
+ spartanArchive = new SpartanArchive(this, bondData, endCheck, 0);
String modelName = readArchiveHeader();
if (modelName != null)
modelAtomCount = spartanArchive.readArchive(line, false, asc.ac, false);
@@ -266,10 +262,13 @@
}
private void readProperties() throws Exception {
- if (spartanArchive == null) {
+ if (modelAtomCount == 0) {
rd();
return;
}
+ if (spartanArchive == null)
+ spartanArchive = new SpartanArchive(this, bondData, endCheck,
+ modelAtomCount);
spartanArchive.readProperties();
rd();
setCharges();
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2017-07-27 13:15:02 UTC (rev 21679)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2017-07-27 13:42:02 UTC (rev 21680)
@@ -738,8 +738,9 @@
if (!atomSetInfo.containsKey(auxKey))
return false;
Lst<Float> atomData = (Lst<Float>) atomSetInfo.get(auxKey);
- for (int i = atomData.size(); --i >= 0;)
- atoms[i].partialCharge = atomData.get(i).floatValue();
+ int n = atomData.size();
+ for (int i = ac; --i >= 0;)
+ atoms[i].partialCharge = atomData.get(i % n).floatValue();
Logger.info("Setting partial charges type " + auxKey);
return true;
}
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