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java.lang.Objectorg.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.simple.CubeReader
public class CubeReader
Gaussian cube file format http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html this is good because it is source code http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm distances are in Bohrs because we are reading Gaussian cube OUTPUT files not Gaussian cube INPUT files. Miguel 2005 07 17 a negative atom count means that it is molecular orbital (MO) data with MO data, the extra line contains the number of orbitals and the orbital number these orbitals are interspersed -- all orbital values are given together for each coordinate point. also used for older JVXL and JVXL+ file format
Field Summary | |
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private int |
atomCount
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private boolean |
isAngstroms
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Constructor Summary | |
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CubeReader()
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Method Summary | |
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void |
initializeReader()
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private void |
readAtomCountAndOrigin()
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private void |
readAtoms()
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private void |
readTitleLines()
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private int atomCount
private boolean isAngstroms
Constructor Detail |
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public CubeReader()
Method Detail |
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public void initializeReader() throws java.lang.Exception
initializeReader
in class AtomSetCollectionReader
java.lang.Exception
private void readTitleLines() throws java.lang.Exception
java.lang.Exception
private void readAtomCountAndOrigin() throws java.lang.Exception
java.lang.Exception
private void readAtoms() throws java.lang.Exception
java.lang.Exception
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