org.jmol.adapter.readers.more

Class CubeReader

public class CubeReader extends AtomSetCollectionReader

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 JVXL and JVXL+ file format
Field Summary
intatomCount
booleanisAngstroms
booleannegativeAtomCount
float[]origin
int[]voxelCounts
float[][]voxelVectors
Method Summary
voidreadAtomCountAndOrigin()
voidreadAtoms()
AtomSetCollectionreadAtomSetCollection(BufferedReader br)
voidreadExtraLine()
voidreadTitleLines()
voidreadVoxelVector(int voxelVectorIndex)
voidreadVoxelVectors()

Field Detail

atomCount

int atomCount

isAngstroms

boolean isAngstroms

negativeAtomCount

boolean negativeAtomCount

origin

final float[] origin

voxelCounts

final int[] voxelCounts

voxelVectors

final float[][] voxelVectors

Method Detail

readAtomCountAndOrigin

void readAtomCountAndOrigin()

readAtoms

void readAtoms()

readAtomSetCollection

public AtomSetCollection readAtomSetCollection(BufferedReader br)

readExtraLine

void readExtraLine()

readTitleLines

void readTitleLines()

readVoxelVector

void readVoxelVector(int voxelVectorIndex)

readVoxelVectors

void readVoxelVectors()