Package org.jmol.adapter.readers.xtal

Class VaspPoscarReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xtal.VaspPoscarReader

All Implemented Interfaces:

javajs.api.GenericLineReader

Direct Known Subclasses:

AFLOWReader, VaspChgcarReader

public class VaspPoscarReader
extends AtomSetCollectionReader

adjusted for AFLOW options - adding element names, environment radius on atom line http://cms.mpi.univie.ac.at/vasp/

Version:

1.0

Author:

Pieremanuele Canepa, Wake Forest University, Department of Physics Winston Salem, NC 27106, canepap@wfu.edu (pcanepa@mit.edu), Bob Hanson

Field Summary

Fields

Modifier and Type	Field	Description
protected int	ac
protected javajs.util.Lst<String>	atomLabels
private boolean	atomsLabeledInline
protected String[]	defaultLabels
protected String[]	elementLabel
(package private) int	elementPt
private boolean	haveAtomLabels
protected boolean	quiet
(package private) int	radiusPt
private float	scaleFac
protected String	title

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
VaspPoscarReader()

Method Summary

Modifier and Type	Method	Description
protected void	finalizeSubclassReader()	optional reader-specific method run first.
protected String	getElement(String token)	allow for any number of characters, for which the first one or two are an element symbol.
protected void	initializeReader()
protected String	rdline()
protected void	readCoordinates()
protected void	readMolecularFormula()	try various ways to read the optional atom labels.
protected void	readStructure(String titleMsg)
protected void	readUnitCellVectors()

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

addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, 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, setAtomCoordXYZ, 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

atomLabels

protected javajs.util.Lst<String> atomLabels

haveAtomLabels

private boolean haveAtomLabels

atomsLabeledInline

private boolean atomsLabeledInline

scaleFac

private float scaleFac

ac

protected int ac

title

protected String title

quiet

protected boolean quiet

defaultLabels

protected String[] defaultLabels

elementLabel

protected String[] elementLabel

radiusPt

int radiusPt

elementPt

int elementPt

Constructor Detail

VaspPoscarReader

public VaspPoscarReader()

Method Detail

initializeReader

protected void initializeReader()
                         throws Exception

Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

Exception

readStructure

protected void readStructure(String titleMsg)
                      throws Exception

Throws:

Exception

finalizeSubclassReader

protected void finalizeSubclassReader()
                               throws Exception

Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class AtomSetCollectionReader

Throws:

Exception

readUnitCellVectors

protected void readUnitCellVectors()
                            throws Exception

Throws:

Exception

readMolecularFormula

protected void readMolecularFormula()
                             throws Exception

try various ways to read the optional atom labels. There is no convention here.

Throws:

Exception

readCoordinates

protected void readCoordinates()
                        throws Exception

Throws:

Exception

getElement

protected String getElement(String token)

allow for any number of characters, for which the first one or two are an element symbol.

Parameters:

token -

Returns:

element symbol

rdline

protected String rdline()
                 throws Exception

Throws:

Exception