CastepReader

java.lang.Object
- 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 and 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 float[]`	`lengthUnitFactors`
`private static String[]`	`lengthUnitIds`
`private int`	`qpt2`
`private static float`	`RAD_TO_DEG`
`private String[]`	`tokens`
`private String`	`tsType`
`private static double`	`TWOPI`

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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors
Constructor and Description

CastepReader()

Constructors
Constructor and Description
`CastepReader()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, 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

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

TWOPI
```
private static final double TWOPI
```
See Also:

Constant Field Values

Constructor Detail
- CastepReader
```
public CastepReader()
```

Method Detail

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 Detail

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

TWOPI

Constructor Detail

CastepReader

Method Detail

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