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

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class SiestaReader
extends AtomSetCollectionReader
```
SIESTA http://www.icmab.es/siesta/

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	Description
`private static double`	`ACF_ANG`
`private static double`	`ACF_BOHR`
`private static double`	`ACF_M`
`private static double`	`ACF_NM`
`private float`	`acfFactor`
`private java.lang.String`	`acfUnits`
`(package private) java.util.Map<java.lang.String,java.lang.String[]>`	`htSpecies`
`private float`	`latticeConstant`
`private java.lang.String`	`latticeUnits`
`private int`	`noAtoms`
`private int`	`state`
`private int`	`STATE_INPUT`
`private int`	`STATE_OUTPUT`
`private int`	`STATE_UNKNOWN`
`private java.lang.String[]`	`tokens`
`private float[]`	`unitCellParamsS`
`private float[]`	`unitCellVectors`

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, 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, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors
Constructor Description

SiestaReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected boolean`	`checkLine()`
`private java.lang.String`	`fixToken(int i)`
`private float`	`getACFValue(float v)`
`protected void`	`initializeReader()`
`private void`	`newAtomSet()`
`java.lang.String`	`rdSiesta()`
`private void`	`readAtomicCoordinatesFormat()`
`private boolean`	`readAtoms()`
`private void`	`readAtomsCartGeomThenCell()`
`private boolean`	`readBlock(java.lang.String key)`
`private boolean`	`readSpecies()`
`private void`	`readValue(java.lang.String key)`
`void`	`setAtomCoordXYZ(Atom atom, float x, float y, float z)`
`private boolean`	`setCell(java.lang.String key)`
`private void`	`skipModel()`

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, 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, 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

noAtoms
```
private int noAtoms
```

acfUnits
```
private java.lang.String acfUnits
```

tokens
```
private java.lang.String[] tokens
```

STATE_UNKNOWN
```
private final int STATE_UNKNOWN
```
See Also:

Constant Field Values

STATE_INPUT
```
private final int STATE_INPUT
```
See Also:

Constant Field Values

STATE_OUTPUT
```
private final int STATE_OUTPUT
```
See Also:

Constant Field Values

state
```
private int state
```

acfFactor
```
private float acfFactor
```

htSpecies

java.util.Map<java.lang.String,java.lang.String[]> htSpecies

unitCellVectors
```
private float[] unitCellVectors
```

unitCellParamsS
```
private float[] unitCellParamsS
```

latticeConstant
```
private float latticeConstant
```

latticeUnits
```
private java.lang.String latticeUnits
```

ACF_M
```
private static final double ACF_M
```
See Also:

Constant Field Values

ACF_NM
```
private static final double ACF_NM
```
See Also:

Constant Field Values

ACF_ANG
```
private static final double ACF_ANG
```
See Also:

Constant Field Values

ACF_BOHR
```
private static final double ACF_BOHR
```
See Also:

Constant Field Values

Constructor Detail
- SiestaReader
```
public SiestaReader()
```

Method Detail

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

initializeReader in class AtomSetCollectionReader

checkLine
```
protected boolean checkLine()
                     throws java.lang.Exception
```
Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

java.lang.Exception

readValue

private void readValue(java.lang.String key)
                throws java.lang.Exception

Throws:: java.lang.Exception

readBlock

private boolean readBlock(java.lang.String key)
                   throws java.lang.Exception

Throws:: java.lang.Exception

readSpecies

private boolean readSpecies()
                     throws java.lang.Exception

Throws:: java.lang.Exception

fixToken

private java.lang.String fixToken(int i)

rdSiesta

public java.lang.String rdSiesta()
                          throws java.lang.Exception

Throws:: java.lang.Exception

getACFValue

private float getACFValue(float v)

readAtomicCoordinatesFormat

private void readAtomicCoordinatesFormat()

skipModel

private void skipModel()
                throws java.lang.Exception

Throws:: java.lang.Exception

setCell

private boolean setCell(java.lang.String key)
                 throws java.lang.Exception

Throws:: java.lang.Exception

readAtoms

private boolean readAtoms()
                   throws java.lang.Exception

Throws:: java.lang.Exception

setAtomCoordXYZ

public void setAtomCoordXYZ(Atom atom,
                            float x,
                            float y,
                            float z)

Overrides:: setAtomCoordXYZ in class AtomSetCollectionReader

newAtomSet

private void newAtomSet()
                 throws java.lang.Exception

Throws:: java.lang.Exception

readAtomsCartGeomThenCell

private void readAtomsCartGeomThenCell()
                                throws java.lang.Exception

Throws:: java.lang.Exception

Class SiestaReader

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

noAtoms

acfUnits

tokens

STATE_UNKNOWN

STATE_INPUT

STATE_OUTPUT

state

acfFactor

htSpecies

unitCellVectors

unitCellParamsS

latticeConstant

latticeUnits

ACF_M

ACF_NM

ACF_ANG

ACF_BOHR

Constructor Detail

SiestaReader

Method Detail

initializeReader

checkLine

readValue

readBlock

readSpecies

fixToken

rdSiesta

getACFValue

readAtomicCoordinatesFormat

skipModel

setCell

readAtoms

setAtomCoordXYZ

newAtomSet

readAtomsCartGeomThenCell