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 final double

ACF_ANG

private static final double

ACF_BOHR

private static final double

ACF_M

private static final 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 final int

STATE_INPUT

private final int

STATE_OUTPUT

private final 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, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, 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, 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, getFilterWithCase, 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 Details
- 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 Details
- SiestaReader
  
  public SiestaReader()
Method Details
- 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

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 Details

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 Details

SiestaReader

Method Details

initializeReader

checkLine

readValue

readBlock

readSpecies

fixToken

rdSiesta

getACFValue

readAtomicCoordinatesFormat

skipModel

setCell

readAtoms

setAtomCoordXYZ

newAtomSet

readAtomsCartGeomThenCell