org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xtal.CastepReader

All Implemented Interfaces:: javajs.api.GenericLineReader

public class CastepReader extends AtomSetCollectionReader

CASTEP (http://www.castep.org) .cell file format relevant section of .cell file are included as comments below preliminary .castep, .phonon frequency reader -- hansonr@stolaf.edu 9/2011 -- Many thanks to Keith Refson for his assistance with this implementation -- atom's mass is encoded as bfactor -- FILTER options include "q=n" where n is an integer "q={1/4 1/4 0}" "q=ALL" -- for non-simple fractions, you must use the exact form of the wavevector description: -- load "xxx.phonon" FILTER "q=(-0.083333 0.083333 0.500000) -- for simple fractions, you can also just specify SUPERCELL {a b c} where the number of cells matches a given wavevector -- SUPERCELL {4 4 1}, for example note: following was never implemented? -- following this with ".1" ".2" etc. gives first, second, third, etc. occurance: -- load "xxx.phonon" FILTER "q=1.3" .... -- load "xxx.phonon" FILTER "{0 0 0}.3" ....

Version:: 1.2
Author:: Joerg Meyer, FHI Berlin 2009 (meyer@fhi-berlin.mpg.de)

Field Summary

Fields

Modifier and Type

Field

Description

private float

a

private javajs.util.V3[]

abc

private int

ac

private float

alpha

private javajs.util.P3[]

atomPts

private float

b

private float

beta

private float

c

private String

chargeType

private String

desiredQ

private javajs.util.V3

desiredQpt

private float

gamma

private boolean

haveCharges

private boolean

havePhonons

private boolean

isAllQ

private boolean

isCell

private boolean

isOutput

private boolean

isPhonon

private boolean

isTS

private String

lastQPt

private static final float[]

lengthUnitFactors

private static final String[]

lengthUnitIds

private javajs.util.M4

matSupercell

private int

qpt2

private static final float

RAD_TO_DEG

private String[]

tokens

private String

tsType

private static final double

TWOPI

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

CastepReader()
Method Summary

Modifier and Type

Method

Description

protected boolean

checkLine()

protected void

finalizeSubclassReader()

optional reader-specific method run first.

private String

getFractionalCoord(javajs.util.V3 qvec)

private void

getTensor(Atom atom, String line0)

void

initializeReader()

private static boolean

isInt(float f)

private void

readAtomData(float factor)

private void

readEnergy(int pt, String prefix)

private boolean

readFileData()

private void

readLatticeAbc()

private void

readLatticeCart()

private float

readLengthUnit(String units)

private int

readOutputAtomIndex()

private void

readOutputAtoms()

private void

readOutputBornChargeTensors()

private void

readOutputCharges()

read Mulliken or Hirshfield charges

private void

readOutputUnitCell()

private void

readPhononFractionalCoord()

private void

readPhononFrequencies()

private void

readPhononTrajectories()

private void

readPhononUnitCell()

private void

readPositionsAbs()

private void

readPositionsFrac()

private void

setDesiredQpt(String s)

private void

setLatticeVectors()

private void

setPhononVector(float[] data, Atom atom, javajs.util.V3 rTrans, javajs.util.V3 qvec, javajs.util.V3 v)

transform complex vibration vector to a real vector by applying the appropriate translation, storing the results in v

private int

tokenizeCastepCell()

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, 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, 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 Details
- RAD_TO_DEG
  
  private static final float RAD_TO_DEG
  See Also:
  
  Constant Field Values
- tokens
  
  private String[] tokens
- isPhonon
  
  private boolean isPhonon
- isTS
  
  private boolean isTS
- isOutput
  
  private boolean isOutput
- isCell
  
  private boolean isCell
- a
  
  private float a
- b
  
  private float b
- c
  
  private float c
- alpha
  
  private float alpha
- beta
  
  private float beta
- gamma
  
  private float gamma
- abc
  
  private javajs.util.V3[] abc
- ac
  
  private int ac
- atomPts
  
  private javajs.util.P3[] atomPts
- havePhonons
  
  private boolean havePhonons
- lastQPt
  
  private String lastQPt
- qpt2
  
  private int qpt2
- desiredQpt
  
  private javajs.util.V3 desiredQpt
- desiredQ
  
  private String desiredQ
- chargeType
  
  private String chargeType
- isAllQ
  
  private boolean isAllQ
- haveCharges
  
  private boolean haveCharges
- tsType
  
  private String tsType
- lengthUnitIds
  
  private static final String[] lengthUnitIds
- lengthUnitFactors
  
  private static final float[] lengthUnitFactors
- matSupercell
  
  private javajs.util.M4 matSupercell
- TWOPI
  
  private static final double TWOPI
  See Also:
  
  Constant Field Values
Constructor Details
- CastepReader
  
  public CastepReader()
Method Details
- initializeReader
  
  public void initializeReader() throws Exception
  
  Overrides:
  
  initializeReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- setDesiredQpt
  
  private void setDesiredQpt(String s)
- readFileData
  
  private boolean readFileData() throws Exception
  
  Throws:
  
  Exception
- checkLine
  
  protected boolean checkLine() throws Exception
  
  Overrides:
  
  checkLine in class AtomSetCollectionReader
  
  Returns:
  
  true if need to read new line
  
  Throws:
  
  Exception
- readOutputUnitCell
  
  private void readOutputUnitCell() throws Exception
  
  Throws:
  
  Exception
- readOutputAtoms
  
  private void readOutputAtoms() throws Exception
  
  Throws:
  
  Exception
- readEnergy
  
  private void readEnergy(int pt, String prefix) throws Exception
  
  Throws:
  
  Exception
- readPhononTrajectories
  
  private void readPhononTrajectories() 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
- setLatticeVectors
  
  private void setLatticeVectors()
- readLatticeAbc
  
  private void readLatticeAbc() throws Exception
  
  Throws:
  
  Exception
- readLatticeCart
  
  private void readLatticeCart() throws Exception
  
  Throws:
  
  Exception
- readPositionsFrac
  
  private void readPositionsFrac() throws Exception
  
  Throws:
  
  Exception
- readPositionsAbs
  
  private void readPositionsAbs() throws Exception
  
  Throws:
  
  Exception
- readLengthUnit
  
  private float readLengthUnit(String units) throws Exception
  
  Throws:
  
  Exception
- readAtomData
  
  private void readAtomData(float factor) throws Exception
  
  Throws:
  
  Exception
- tokenizeCastepCell
  
  private int tokenizeCastepCell() throws Exception
  
  Throws:
  
  Exception
- readOutputBornChargeTensors
  
  private void readOutputBornChargeTensors() throws Exception
  
  Throws:
  
  Exception
- readOutputAtomIndex
  
  private int readOutputAtomIndex()
- getTensor
  
  private void getTensor(Atom atom, String line0) throws Exception
  
  Throws:
  
  Exception
- readOutputCharges
  
  private void readOutputCharges() throws Exception
  
  read Mulliken or Hirshfield charges
  
  Throws:
  
  Exception
- readPhononUnitCell
  
  private void readPhononUnitCell() throws Exception
  
  Throws:
  
  Exception
- readPhononFractionalCoord
  
  private void readPhononFractionalCoord() throws Exception
  
  Throws:
  
  Exception
- readPhononFrequencies
  
  private void readPhononFrequencies() throws Exception
  
  Throws:
  
  Exception
- getFractionalCoord
  
  private String getFractionalCoord(javajs.util.V3 qvec)
- isInt
  
  private static boolean isInt(float f)
- setPhononVector
  
  private void setPhononVector(float[] data, Atom atom, javajs.util.V3 rTrans, javajs.util.V3 qvec, javajs.util.V3 v)
  
  transform complex vibration vector to a real vector by applying the appropriate translation, storing the results in v
  
  Parameters:
  
  data - from .phonon line parsed for floats
  
  atom -
  
  rTrans - translation vector in unit fractional coord
  
  qvec - q point vector
  
  v - return vector

Class CastepReader

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

RAD_TO_DEG

tokens

isPhonon

isTS

isOutput

isCell

a

b

c

alpha

beta

gamma

abc

ac

atomPts

havePhonons

lastQPt

qpt2

desiredQpt

desiredQ

chargeType

isAllQ

haveCharges

tsType

lengthUnitIds

lengthUnitFactors

matSupercell

TWOPI

Constructor Details

CastepReader

Method Details

initializeReader

setDesiredQpt

readFileData

checkLine

readOutputUnitCell

readOutputAtoms

readEnergy

readPhononTrajectories

finalizeSubclassReader

setLatticeVectors

readLatticeAbc

readLatticeCart

readPositionsFrac

readPositionsAbs

readLengthUnit

readAtomData

tokenizeCastepCell

readOutputBornChargeTensors

readOutputAtomIndex

getTensor

readOutputCharges

readPhononUnitCell

readPhononFractionalCoord

readPhononFrequencies

getFractionalCoord

isInt

setPhononVector