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[Jmol-commits] SF.net SVN: jmol:[15170] trunk/Jmol/src/org/jmol/adapter/readers/quantum
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From: <ha...@us...> - 2011-02-16 14:28:42
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Revision: 15170
http://jmol.svn.sourceforge.net/jmol/?rev=15170&view=rev
Author: hansonr
Date: 2011-02-16 14:28:35 +0000 (Wed, 16 Feb 2011)
Log Message:
-----------
Molden/Spartan reader upgrades
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java
trunk/Jmol/src/org/jmol/adapter/readers/quantum/SpartanArchive.java
trunk/Jmol/src/org/jmol/adapter/readers/quantum/SpartanSmolReader.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java 2011-02-16 14:23:52 UTC (rev 15169)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/MoldenReader.java 2011-02-16 14:28:35 UTC (rev 15170)
@@ -79,6 +79,7 @@
throw new Exception("out of order atom in [Atoms]");
}
nPrevAtom = nCurAtom;
+ atom.elementNumber = (short) parseInt(tokens[2]);
setAtomCoord(atom, parseFloat(tokens[3]) * f,
parseFloat(tokens[4]) * f,
parseFloat(tokens[5]) * f);
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/SpartanArchive.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/SpartanArchive.java 2011-02-16 14:23:52 UTC (rev 15169)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/SpartanArchive.java 2011-02-16 14:28:35 UTC (rev 15170)
@@ -232,14 +232,27 @@
readLine();
String[] tokens = getTokens();
int[] slater = new int[4];
- slater[0]= parseInt(tokens[3]) - 1; //atom pointer; 1-based
+ slater[0] = parseInt(tokens[3]) - 1; //atom pointer; 1-based
int iBasis = parseInt(tokens[0]); //0 = S, 1 = SP, 2 = D, 3 = F
- slater[1] = (iBasis == 0 ? 0 : iBasis + 1);//0 = S, 1 = P, 2 = SP, 3 = D, 4 = F
+ switch (iBasis) {
+ case 0:
+ iBasis = JmolAdapter.SHELL_S;
+ break;
+ case 1:
+ iBasis = JmolAdapter.SHELL_SP;
+ break;
+ case 2:
+ iBasis = JmolAdapter.SHELL_D_CARTESIAN;
+ break;
+ case 3:
+ iBasis = JmolAdapter.SHELL_F_CARTESIAN;
+ break;
+ }
+ slater[1] = iBasis;
int gaussianPtr = slater[2] = parseInt(tokens[2]) - 1;
int nGaussians = slater[3] = parseInt(tokens[1]);
- for (int j = 0; j < nGaussians; j++) {
+ for (int j = 0; j < nGaussians; j++)
typeArray[gaussianPtr + j] = iBasis;
- }
sdata.add(slater);
}
for (int i = 0; i < gaussianCount; i++) {
@@ -248,24 +261,64 @@
int nData = tokens.length;
float[] data = new float[nData + 1];
data[0] = alpha;
- int iBasis = typeArray[i];
//we put D and F into coef 1. This may change if I find that Gaussian output
//lists D and F in columns 3 and 4 as well.
- switch(iBasis) {
- case 1: //SP
- data[2] = parseFloat(tokens[1]);
- //fall through
- case 0: //S
+ switch (typeArray[i]) {
+ case JmolAdapter.SHELL_S:
data[1] = parseFloat(tokens[0]);
break;
- case 2: //D
+ case JmolAdapter.SHELL_SP:
+ data[1] = parseFloat(tokens[0]);
+ data[2] = parseFloat(tokens[1]);
+ if (data[1] == 0) {
+ data[1] = data[2];
+ typeArray[i] = JmolAdapter.SHELL_P;
+ }
+ break;
+ case JmolAdapter.SHELL_D_CARTESIAN:
data[1] = parseFloat(tokens[2]);
break;
- case 3: //F
+ case JmolAdapter.SHELL_F_CARTESIAN:
data[1] = parseFloat(tokens[3]);
+ break;
}
garray[i] = data;
}
+ int nCoeff = 0;
+ for (int i = 0; i < shellCount; i++) {
+ int[] slater = sdata.get(i);
+ switch(typeArray[slater[2]]) {
+ case JmolAdapter.SHELL_S:
+ nCoeff++;
+ break;
+ case JmolAdapter.SHELL_P:
+ slater[1] = JmolAdapter.SHELL_P;
+ nCoeff += 3;
+ break;
+ case JmolAdapter.SHELL_SP:
+ nCoeff += 4;
+ break;
+ case JmolAdapter.SHELL_D_CARTESIAN:
+ nCoeff += 6;
+ break;
+ case JmolAdapter.SHELL_F_CARTESIAN:
+ nCoeff += 10;
+ break;
+ }
+ }
+ boolean isD5F7 = (nCoeff < coefCount);
+ if (isD5F7)
+ for (int i = 0; i < shellCount; i++) {
+ int[] slater = sdata.get(i);
+ switch (typeArray[i]) {
+ case JmolAdapter.SHELL_D_CARTESIAN:
+ slater[1] = JmolAdapter.SHELL_D_SPHERICAL;
+ break;
+ case JmolAdapter.SHELL_F_CARTESIAN:
+ slater[1] = JmolAdapter.SHELL_F_SPHERICAL;
+ break;
+ }
+ }
moData.put("shells", sdata);
moData.put("gaussians", garray);
if (Logger.debugging) {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/SpartanSmolReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/SpartanSmolReader.java 2011-02-16 14:23:52 UTC (rev 15169)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/SpartanSmolReader.java 2011-02-16 14:28:35 UTC (rev 15170)
@@ -93,6 +93,7 @@
}
if (title != null)
atomSetCollection.setAtomSetName(title);
+ setProperties();
if (checkFilter("INPUT")) {
continuing = false;
return false;
@@ -192,23 +193,33 @@
}
}
- private void readProperties() throws Exception {
- if (spartanArchive == null) {
- readLine();
+ private boolean haveCharges;
+
+ private void setProperties() {
+ if (haveCharges || atomSetCollection.getAtomCount() == 0)
return;
- }
- spartanArchive.readProperties();
- boolean haveCharges = false;
if (checkFilter("ESPCHARGES"))
haveCharges = atomSetCollection.setAtomSetCollectionPartialCharges("ESPCHARGES");
if (!haveCharges && !atomSetCollection
.setAtomSetCollectionPartialCharges("MULCHARGES"))
- atomSetCollection.setAtomSetCollectionPartialCharges("Q1_CHARGES");
+ haveCharges = atomSetCollection.setAtomSetCollectionPartialCharges("Q1_CHARGES");
+ if (!haveCharges)
+ atomSetCollection.setAtomSetCollectionPartialCharges("ESPCHARGES");
+ haveCharges = true;
Float n = (Float) atomSetCollection
.getAtomSetCollectionAuxiliaryInfo("HOMO_N");
if (moData != null && n != null)
moData.put("HOMO", Integer.valueOf(n.intValue()));
+ }
+
+ private void readProperties() throws Exception {
+ if (spartanArchive == null) {
+ readLine();
+ return;
+ }
+ spartanArchive.readProperties();
readLine();
+ setProperties();
}
private int getModelNumber() {
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