Package org.jmol.adapter.readers.xtal

Class SiestaReader

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 String	acfUnits
(package private) Map<String,String[]>	htSpecies
private float	latticeConstant
private String	latticeUnits
private int	noAtoms
private int	state
private int	STATE_INPUT
private int	STATE_OUTPUT
private int	STATE_UNKNOWN
private 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, 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, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, 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

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

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

addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, 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 String acfUnits

tokens

private 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

Map<String,String[]> htSpecies

unitCellVectors

private float[] unitCellVectors

unitCellParamsS

private float[] unitCellParamsS

latticeConstant

private float latticeConstant

latticeUnits

private 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 Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

Exception

readValue

private void readValue(String key)
                throws Exception

Throws:

Exception

readBlock

private boolean readBlock(String key)
                   throws Exception

Throws:

Exception

readSpecies

private boolean readSpecies()
                     throws Exception

Throws:

Exception

fixToken

private String fixToken(int i)

rdSiesta

public String rdSiesta()
                throws Exception

Throws:

Exception

getACFValue

private float getACFValue(float v)

readAtomicCoordinatesFormat

private void readAtomicCoordinatesFormat()

skipModel

private void skipModel()
                throws Exception

Throws:

Exception

setCell

private boolean setCell(String key)
                 throws Exception

Throws:

Exception

readAtoms

private boolean readAtoms()
                   throws Exception

Throws:

Exception

setAtomCoordXYZ

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

Overrides:

setAtomCoordXYZ in class AtomSetCollectionReader

newAtomSet

private void newAtomSet()
                 throws Exception

Throws:

Exception

readAtomsCartGeomThenCell

private void readAtomsCartGeomThenCell()
                                throws Exception

Throws:

Exception