VaspOutcarReader

java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.xtal.VaspOutcarReader

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class VaspOutcarReader
extends AtomSetCollectionReader
```
http://cms.mpi.univie.ac.at/vasp/

Version:

1.0

Author:

Pieremanuele Canepa, Room 104, FM Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom, pc229@kent.ac.uk

Field Summary

Fields
Modifier and Type	Field and Description
`private int`	`ac`
`private String[]`	`atomNames`
`private Double`	`electronEne`
`private javajs.util.Lst<String>`	`elementNames`
`private Double`	`gibbsEnergy`
`private Double`	`gibbsEntropy`
`private boolean`	`inputOnly`
`private boolean`	`isVersion5`
`private Double`	`kinEne`
`private boolean`	`mDsimulation`
`private float`	`temp`
`private Double`	`totEne`

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors
Constructor and Description

VaspOutcarReader()

Constructors
Constructor and Description
`VaspOutcarReader()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected boolean`	`checkLine()`
`protected void`	`finalizeSubclassReader()` optional reader-specific method run first.
`private String`	`fixMinus(String line)`
`protected void`	`initializeReader()`
`private void`	`readAtomCountAndSetNames()`
`private void`	`readElementNames()`
`private void`	`readEnergy()`
`private void`	`readFrequency()`
`private void`	`readInitialCoordinates()`
`private void`	`readMdyn()`
`private void`	`readPOSITION()`
`private void`	`readUnitCellVectors()`
`private void`	`setAtomSetInfo()`
`private void`	`setAtomSetInfoMd()`
`private void`	`setSymmetry()`

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

atomNames
```
private String[] atomNames
```

ac
```
private int ac
```

inputOnly
```
private boolean inputOnly
```

mDsimulation
```
private boolean mDsimulation
```

isVersion5
```
private boolean isVersion5
```

elementNames

private javajs.util.Lst<String> elementNames

gibbsEnergy
```
private Double gibbsEnergy
```

gibbsEntropy
```
private Double gibbsEntropy
```

electronEne
```
private Double electronEne
```

kinEne
```
private Double kinEne
```

totEne
```
private Double totEne
```

temp
```
private float temp
```

Constructor Detail
- VaspOutcarReader
```
public VaspOutcarReader()
```

Method Detail

initializeReader
```
protected void initializeReader()
```
Overrides:

initializeReader in class AtomSetCollectionReader

checkLine
```
protected boolean checkLine()
                     throws Exception
```
Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

Exception

finalizeSubclassReader
```
protected void finalizeSubclassReader()
                               throws Exception
```
Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class AtomSetCollectionReader

Throws:

Exception

readElementNames

private void readElementNames()
                       throws Exception

Throws:: Exception

readAtomCountAndSetNames

private void readAtomCountAndSetNames()
                               throws Exception

Throws:: Exception

readUnitCellVectors

private void readUnitCellVectors()
                          throws Exception

Throws:: Exception

fixMinus
```
private String fixMinus(String line)
```

setSymmetry

private void setSymmetry()
                  throws Exception

Throws:: Exception

readInitialCoordinates

private void readInitialCoordinates()
                             throws Exception

Throws:: Exception

readPOSITION

private void readPOSITION()
                   throws Exception

Throws:: Exception

readEnergy

private void readEnergy()
                 throws Exception

Throws:: Exception

setAtomSetInfo
```
private void setAtomSetInfo()
```

readMdyn

private void readMdyn()
               throws Exception

Throws:: Exception

setAtomSetInfoMd
```
private void setAtomSetInfoMd()
```

readFrequency

private void readFrequency()
                    throws Exception

Throws:: Exception

Class VaspOutcarReader

Field Summary

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Methods inherited from class java.lang.Object

Field Detail

atomNames

ac

inputOnly

mDsimulation

isVersion5

elementNames

gibbsEnergy

gibbsEntropy

electronEne

kinEne

totEne

temp

Constructor Detail

VaspOutcarReader

Method Detail

initializeReader

checkLine

finalizeSubclassReader

readElementNames

readAtomCountAndSetNames

readUnitCellVectors

fixMinus

setSymmetry

readInitialCoordinates

readPOSITION

readEnergy

setAtomSetInfo

readMdyn

setAtomSetInfoMd

readFrequency