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
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
FieldsModifier and TypeFieldDescriptionprivate static final double
private static final double
private static final double
private static final double
private float
private String
private float
private String
private int
private int
private final int
private final int
private final int
private String[]
private float[]
private float[]
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, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noPack, 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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected boolean
private String
fixToken
(int i) private float
getACFValue
(float v) protected void
private void
rdSiesta()
private void
private boolean
private void
private boolean
private boolean
private void
void
setAtomCoordXYZ
(Atom atom, float x, float y, float z) private boolean
private void
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
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Field Details
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noAtoms
private int noAtoms -
acfUnits
-
tokens
-
STATE_UNKNOWN
private final int STATE_UNKNOWN- See Also:
-
STATE_INPUT
private final int STATE_INPUT- See Also:
-
STATE_OUTPUT
private final int STATE_OUTPUT- See Also:
-
state
private int state -
acfFactor
private float acfFactor -
htSpecies
-
unitCellVectors
private float[] unitCellVectors -
unitCellParamsS
private float[] unitCellParamsS -
latticeConstant
private float latticeConstant -
latticeUnits
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ACF_M
private static final double ACF_M- See Also:
-
ACF_NM
private static final double ACF_NM- See Also:
-
ACF_ANG
private static final double ACF_ANG- See Also:
-
ACF_BOHR
private static final double ACF_BOHR- See Also:
-
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Constructor Details
-
SiestaReader
public SiestaReader()
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Method Details
-
initializeReader
protected void initializeReader()- Overrides:
initializeReader
in classAtomSetCollectionReader
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checkLine
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
Exception
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readValue
- Throws:
Exception
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readBlock
- Throws:
Exception
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readSpecies
- Throws:
Exception
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fixToken
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rdSiesta
- Throws:
Exception
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getACFValue
private float getACFValue(float v) -
readAtomicCoordinatesFormat
private void readAtomicCoordinatesFormat() -
skipModel
- Throws:
Exception
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setCell
- Throws:
Exception
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readAtoms
- Throws:
Exception
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setAtomCoordXYZ
- Overrides:
setAtomCoordXYZ
in classAtomSetCollectionReader
-
newAtomSet
- Throws:
Exception
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readAtomsCartGeomThenCell
- Throws:
Exception
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