java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.xtal.CrystalReader

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class CrystalReader
extends AtomSetCollectionReader
```
A reader of OUT and OUTP files for CRYSTAL http://www.crystal.unito.it/

Version:

1.4 for a specific model in the set, use load "xxx.out" n as for all readers, where n is an integer > 0 for final optimized geometry use load "xxx.out" 0 (that is, "read the last model") as for all readers for conventional unit cell -- input coordinates only, use load "xxx.out" filter "conventional" to NOT load vibrations, use load "xxx.out" FILTER "novibrations" to load just the input deck exactly as indicated, use load "xxx.out" FILTER "input" now allows reading of frequencies and atomic values with conventional as long as this is not an optimization.

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

Field Summary

Fields
Modifier and Type	Field	Description
`private int`	`ac`
`private int[]`	`atomFrag`
`private int`	`atomIndexLast`
`private javajs.util.V3[]`	`directLatticeVectors`
`private java.lang.Double`	`energy`
`private boolean`	`getLastConventional`
`private boolean`	`haveCharges`
`private boolean`	`havePrimitiveMapping`
`private boolean`	`inputOnly`
`private boolean`	`isLongMode`
`private boolean`	`isMolecular`
`private boolean`	`isPolymer`
`private boolean`	`isPrimitive`
`private boolean`	`isProperties`
`private boolean`	`isSlab`
`private boolean`	`isVersion3`
`private float[]`	`nuclearCharges`
`private float`	`primitiveDensity`
`private javajs.util.M3`	`primitiveToCryst`
`private int[]`	`primitiveToIndex`
`private float`	`primitiveVolume`
`private javajs.util.P3`	`ptOriginShift`
`private java.lang.String`	`spaceGroupName`
`private javajs.util.Lst<java.lang.String>`	`vCoords`
`private javajs.util.Lst<java.lang.String>`	`vPrimitiveMapping`

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, 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 Description

CrystalReader()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected boolean`	`checkLine()`
`private void`	`createAtomsFromCoordLines()`	Now create atoms from the coordinate lines.
`protected void`	`finalizeSubclassReader()`	optional reader-specific method run first.
`private static java.lang.String`	`fixAtomName(java.lang.String s)`	MN33 becomes Mn33
`private int`	`getAtomicNumber(java.lang.String token)`
`private int`	`getAtomIndexFromPrimitiveIndex(int iPrim)`
`private boolean`	`getQuadrupoleTensors()`
`protected void`	`initializeReader()`
`private void`	`newAtomSet()`
`private boolean`	`readAtoms()`
`private boolean`	`readBornChargeTensors()`
`private void`	`readCoordLines()`	Read coordinates, either input or crystallographic, just saving their lines in a vector for now.
`private boolean`	`readData(java.lang.String name, int nfields)`	For spin and magnetic moment data, read the data block and save it as property_spin or propert_magneticMoment.
`private boolean`	`readFreqFragments()`	Select only specific atoms for frequency generation.
`private boolean`	`readFrequencies()`
`private boolean`	`readGradient()`	Read minimization measures
`private boolean`	`readHeader()`
`private void`	`readLatticeParams(boolean isNewSet)`	Read the lattice parameters.
`private boolean`	`readPartialCharges()`
`private void`	`readPrimitiveMapping()`
`private boolean`	`readShift()`	Read the origin shift
`private boolean`	`readTotalAtomicCharges()`
`private void`	`readTransformationMatrix()`	Read transform matrix primitive to conventional.
`private boolean`	`setDirect()`
`private void`	`setEnergy()`
`private void`	`setFreqValue(float freq, java.lang.String[] data)`
`private boolean`	`setPrimitiveMapping()`	Create arrays that maps primitive atoms to conventional atoms in a 1:1 fashion.
`private void`	`setPrimitiveVolumeAndDensity()`	Read the primitive cell volume and density.

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

isVersion3
```
private boolean isVersion3
```

isPrimitive
```
private boolean isPrimitive
```

isPolymer
```
private boolean isPolymer
```

isSlab
```
private boolean isSlab
```

isMolecular
```
private boolean isMolecular
```

haveCharges
```
private boolean haveCharges
```

inputOnly
```
private boolean inputOnly
```

isLongMode
```
private boolean isLongMode
```

getLastConventional
```
private boolean getLastConventional
```

havePrimitiveMapping
```
private boolean havePrimitiveMapping
```

isProperties
```
private boolean isProperties
```

ac
```
private int ac
```

atomIndexLast
```
private int atomIndexLast
```

atomFrag
```
private int[] atomFrag
```

primitiveToIndex
```
private int[] primitiveToIndex
```

nuclearCharges
```
private float[] nuclearCharges
```

vCoords

private javajs.util.Lst<java.lang.String> vCoords

energy
```
private java.lang.Double energy
```

ptOriginShift
```
private javajs.util.P3 ptOriginShift
```

primitiveToCryst

private javajs.util.M3 primitiveToCryst

directLatticeVectors

private javajs.util.V3[] directLatticeVectors

spaceGroupName

private java.lang.String spaceGroupName

primitiveVolume
```
private float primitiveVolume
```

primitiveDensity
```
private float primitiveDensity
```

vPrimitiveMapping

private javajs.util.Lst<java.lang.String> vPrimitiveMapping

Constructor Detail
- CrystalReader
```
public CrystalReader()
```

Method Detail

initializeReader
```
protected void initializeReader()
                         throws java.lang.Exception
```
Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

checkLine
```
protected boolean checkLine()
                     throws java.lang.Exception
```
Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

java.lang.Exception

finalizeSubclassReader
```
protected void finalizeSubclassReader()
                               throws java.lang.Exception
```
Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

setDirect

private boolean setDirect()
                   throws java.lang.Exception

Throws:: java.lang.Exception

readTransformationMatrix

private void readTransformationMatrix()
                               throws java.lang.Exception

Read transform matrix primitive to conventional.

Throws:: java.lang.Exception

readShift
```
private boolean readShift()
```
Read the origin shift

Returns:

true

setPrimitiveVolumeAndDensity
```
private void setPrimitiveVolumeAndDensity()
```
Read the primitive cell volume and density. Not sure why we are rounding here.

readHeader

private boolean readHeader()
                    throws java.lang.Exception

Throws:: java.lang.Exception

readLatticeParams

private void readLatticeParams(boolean isNewSet)
                        throws java.lang.Exception

Read the lattice parameters.

Parameters:: isNewSet -
Throws:: java.lang.Exception

readPrimitiveMapping

private void readPrimitiveMapping()
                           throws java.lang.Exception

Throws:: java.lang.Exception

setPrimitiveMapping
```
private boolean setPrimitiveMapping()
                             throws java.lang.Exception
```
Create arrays that maps primitive atoms to conventional atoms in a 1:1 fashion. Creates int[] primitiveToIndex -- points to model-based atomIndex

Returns:

TRUE if coordinates have been created

Throws:

java.lang.Exception

readAtoms

private boolean readAtoms()
                   throws java.lang.Exception

Throws:: java.lang.Exception

fixAtomName

private static java.lang.String fixAtomName(java.lang.String s)

MN33 becomes Mn33

Parameters:: s -
Returns:: fixed atom name

getAtomicNumber

private int getAtomicNumber(java.lang.String token)

readCoordLines
```
private void readCoordLines()
                     throws java.lang.Exception
```
Read coordinates, either input or crystallographic, just saving their lines in a vector for now.

Throws:

java.lang.Exception

createAtomsFromCoordLines

private void createAtomsFromCoordLines()
                                throws java.lang.Exception

Now create atoms from the coordinate lines.

Throws:: java.lang.Exception

newAtomSet

private void newAtomSet()
                 throws java.lang.Exception

Throws:: java.lang.Exception

setEnergy
```
private void setEnergy()
```

readPartialCharges

private boolean readPartialCharges()
                            throws java.lang.Exception

Throws:: java.lang.Exception

readTotalAtomicCharges

private boolean readTotalAtomicCharges()
                                throws java.lang.Exception

Throws:: java.lang.Exception

getAtomIndexFromPrimitiveIndex

private int getAtomIndexFromPrimitiveIndex(int iPrim)

readFreqFragments
```
private boolean readFreqFragments()
                           throws java.lang.Exception
```
Select only specific atoms for frequency generation. (See freq_6for_001.out)

Returns:

true

Throws:

java.lang.Exception

readFrequencies

private boolean readFrequencies()
                         throws java.lang.Exception

Throws:: java.lang.Exception

setFreqValue

private void setFreqValue(float freq,
                          java.lang.String[] data)

readGradient

private boolean readGradient()
                      throws java.lang.Exception

Read minimization measures

Returns:: true
Throws:: java.lang.Exception

readData
```
private boolean readData(java.lang.String name,
                         int nfields)
                  throws java.lang.Exception
```
For spin and magnetic moment data, read the data block and save it as property_spin or propert_magneticMoment.

Parameters:

name -

nfields -

Returns:

true

Throws:

java.lang.Exception

getQuadrupoleTensors

private boolean getQuadrupoleTensors()
                              throws java.lang.Exception

Throws:: java.lang.Exception

readBornChargeTensors

private boolean readBornChargeTensors()
                               throws java.lang.Exception

Throws:: java.lang.Exception

Class CrystalReader

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

isVersion3

isPrimitive

isPolymer

isSlab

isMolecular

haveCharges

inputOnly

isLongMode

getLastConventional

havePrimitiveMapping

isProperties

ac

atomIndexLast

atomFrag

primitiveToIndex

nuclearCharges

vCoords

energy

ptOriginShift

primitiveToCryst

directLatticeVectors

spaceGroupName

primitiveVolume

primitiveDensity

vPrimitiveMapping

Constructor Detail

CrystalReader

Method Detail

initializeReader

checkLine

finalizeSubclassReader

setDirect

readTransformationMatrix

readShift

setPrimitiveVolumeAndDensity

readHeader

readLatticeParams

readPrimitiveMapping

setPrimitiveMapping

readAtoms

fixAtomName

getAtomicNumber

readCoordLines

createAtomsFromCoordLines

newAtomSet

setEnergy

readPartialCharges

readTotalAtomicCharges

getAtomIndexFromPrimitiveIndex

readFreqFragments

readFrequencies

setFreqValue

readGradient

readData

getQuadrupoleTensors

readBornChargeTensors