public class CrystalReader extends AtomSetCollectionReader
Modifier and Type | Field and 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 |
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
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CrystalReader() |
Modifier and Type | Method and 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 void |
readEnergy() |
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.
|
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, 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, processDSSR, 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
private boolean isVersion3
private boolean isPrimitive
private boolean isPolymer
private boolean isSlab
private boolean isMolecular
private boolean haveCharges
private boolean inputOnly
private boolean isLongMode
private boolean getLastConventional
private boolean havePrimitiveMapping
private boolean isProperties
private int ac
private int atomIndexLast
private int[] atomFrag
private int[] primitiveToIndex
private float[] nuclearCharges
private javajs.util.Lst<java.lang.String> vCoords
private java.lang.Double energy
private javajs.util.P3 ptOriginShift
private javajs.util.M3 primitiveToCryst
private javajs.util.V3[] directLatticeVectors
private java.lang.String spaceGroupName
private float primitiveVolume
private float primitiveDensity
private javajs.util.Lst<java.lang.String> vPrimitiveMapping
protected void initializeReader() throws java.lang.Exception
initializeReader
in class AtomSetCollectionReader
java.lang.Exception
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
protected void finalizeSubclassReader() throws java.lang.Exception
AtomSetCollectionReader
finalizeSubclassReader
in class AtomSetCollectionReader
java.lang.Exception
private boolean setDirect() throws java.lang.Exception
java.lang.Exception
private void readTransformationMatrix() throws java.lang.Exception
java.lang.Exception
private boolean readShift()
private void setPrimitiveVolumeAndDensity()
private boolean readHeader() throws java.lang.Exception
java.lang.Exception
private void readLatticeParams(boolean isNewSet) throws java.lang.Exception
isNewSet
- java.lang.Exception
private void readPrimitiveMapping() throws java.lang.Exception
java.lang.Exception
private boolean setPrimitiveMapping() throws java.lang.Exception
java.lang.Exception
private boolean readAtoms() throws java.lang.Exception
java.lang.Exception
private static java.lang.String fixAtomName(java.lang.String s)
s
- private int getAtomicNumber(java.lang.String token)
private void readCoordLines() throws java.lang.Exception
java.lang.Exception
private void createAtomsFromCoordLines() throws java.lang.Exception
java.lang.Exception
private void newAtomSet() throws java.lang.Exception
java.lang.Exception
private void readEnergy()
private void setEnergy()
private boolean readPartialCharges() throws java.lang.Exception
java.lang.Exception
private boolean readTotalAtomicCharges() throws java.lang.Exception
java.lang.Exception
private int getAtomIndexFromPrimitiveIndex(int iPrim)
private boolean readFreqFragments() throws java.lang.Exception
java.lang.Exception
private boolean readFrequencies() throws java.lang.Exception
java.lang.Exception
private void setFreqValue(float freq, java.lang.String[] data)
private boolean readGradient() throws java.lang.Exception
java.lang.Exception
private boolean readData(java.lang.String name, int nfields) throws java.lang.Exception
name
- nfields
- java.lang.Exception
private boolean getQuadrupoleTensors() throws java.lang.Exception
java.lang.Exception
private boolean readBornChargeTensors() throws java.lang.Exception
java.lang.Exception