public class AmpacReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
private int |
atomCount |
private javax.vecmath.Point3f[] |
atomPositions |
private int |
freqAtom0 |
private float[] |
partialCharges |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer
Constructor and Description |
---|
AmpacReader() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
checkLine() |
private void |
readCoordinates()
Reads a set of coordinates
|
private void |
readFrequencies()
Reads a set of vibrations.
|
private void |
readPartialCharges() |
private void |
setPositions() |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeReader, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
private int atomCount
private int freqAtom0
private float[] partialCharges
private javax.vecmath.Point3f[] atomPositions
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
private void readCoordinates() throws java.lang.Exception
java.lang.Exception
- if an I/O error occursprivate void setPositions()
private void readPartialCharges() throws java.lang.Exception
java.lang.Exception
private void readFrequencies() throws java.lang.Exception
java.lang.Exception
- if an I/O error occurs