Package org.jmol.adapter.readers.xtal
Class SiestaReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.xtal.SiestaReader
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- 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
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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
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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, 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, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors Constructor Description SiestaReader()
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Method Summary
All Methods Instance Methods Concrete Methods 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()
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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
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Field Detail
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noAtoms
private int noAtoms
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acfUnits
private String acfUnits
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tokens
private String[] tokens
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STATE_UNKNOWN
private final int STATE_UNKNOWN
- See Also:
- Constant Field Values
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STATE_INPUT
private final int STATE_INPUT
- See Also:
- Constant Field Values
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STATE_OUTPUT
private final int STATE_OUTPUT
- See Also:
- Constant Field Values
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state
private int state
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acfFactor
private float acfFactor
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unitCellVectors
private float[] unitCellVectors
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unitCellParamsS
private float[] unitCellParamsS
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latticeConstant
private float latticeConstant
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latticeUnits
private String latticeUnits
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ACF_M
private static final double ACF_M
- See Also:
- Constant Field Values
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ACF_NM
private static final double ACF_NM
- See Also:
- Constant Field Values
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ACF_ANG
private static final double ACF_ANG
- See Also:
- Constant Field Values
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ACF_BOHR
private static final double ACF_BOHR
- See Also:
- Constant Field Values
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Method Detail
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initializeReader
protected void initializeReader()
- Overrides:
initializeReader
in classAtomSetCollectionReader
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checkLine
protected boolean checkLine() throws Exception
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
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fixToken
private String fixToken(int i)
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getACFValue
private float getACFValue(float v)
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readAtomicCoordinatesFormat
private void readAtomicCoordinatesFormat()
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setAtomCoordXYZ
public void setAtomCoordXYZ(Atom atom, float x, float y, float z)
- Overrides:
setAtomCoordXYZ
in classAtomSetCollectionReader
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