public class MopacReader extends AtomSetCollectionReader
| Modifier and Type | Field and Description |
|---|---|
private boolean |
chargesFound |
private boolean |
haveHeader |
private int |
mopacVersion |
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, 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, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr| Constructor and Description |
|---|
MopacReader() |
| Modifier and Type | Method and Description |
|---|---|
protected boolean |
checkLine() |
protected void |
initializeReader() |
(package private) void |
processAtomicCharges()
Reads the section in MOPAC files with atomic charges.
|
(package private) void |
processCoordinates()
Reads the section in MOPAC files with cartesian coordinates.
|
(package private) void |
processTotalEnergy() |
private void |
readFrequencies()
Interprets the Harmonic frequencies section.
|
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, 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, finalizeSubclassReader, 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, setupASCRprivate boolean chargesFound
private boolean haveHeader
private int mopacVersion
protected void initializeReader()
throws java.lang.Exception
initializeReader in class AtomSetCollectionReaderjava.lang.Exceptionprotected boolean checkLine()
throws java.lang.Exception
checkLine in class AtomSetCollectionReaderjava.lang.Exceptionvoid processTotalEnergy()
void processAtomicCharges()
throws java.lang.Exception
NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS
ATOM NO. TYPE CHARGE ATOM ELECTRON DENSITY
1 C -0.077432 4.0774
2 C -0.111917 4.1119
3 C 0.092081 3.9079
They are expected to be found in the file before the
cartesian coordinate section.java.lang.Exceptionvoid processCoordinates()
throws java.lang.Exception
CARTESIAN COORDINATES
NO. ATOM X Y Z
1 C 0.0000 0.0000 0.0000
2 C 1.3952 0.0000 0.0000
3 C 2.0927 1.2078 0.0000
In a MOPAC2002 file the columns are different:
CARTESIAN COORDINATES
NO. ATOM X Y Z
1 H 0.00000000 0.00000000 0.00000000
2 O 0.95094500 0.00000000 0.00000000
3 H 1.23995160 0.90598439 0.00000000
java.lang.Exceptionprivate void readFrequencies()
throws java.lang.Exception
THE LAST 6 VIBRATIONS ARE THE TRANSLATION AND ROTATION MODES
THE FIRST THREE OF THESE BEING TRANSLATIONS IN X, Y, AND Z, RESPECTIVELY
NORMAL COORDINATE ANALYSIS
ROOT NO. 1 2 3 4 5 6
370.51248 370.82204 618.03031 647.68700 647.74806 744.32662
1 0.00002 0.00001 -0.00002 -0.05890 0.07204 -0.00002
2 0.00001 -0.00006 -0.00001 0.01860 0.13517 0.00000
3 0.00421 -0.11112 0.06838 -0.00002 -0.00003 -0.02449
4 0.00002 0.00001 -0.00002 -0.04779 0.07977 -0.00001
5 -0.00002 0.00002 0.00001 0.13405 -0.02908 0.00004
6 -0.10448 0.05212 -0.06842 -0.00005 -0.00002 -0.02447
The vectors are added to a clone of the last read AtomSet. Only the Frequencies are set as properties for each of the frequency type AtomSet generated.
java.lang.Exception - If an I/O error occurs