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, 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 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, 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, 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 Exception
initializeReader in class AtomSetCollectionReaderExceptionprotected boolean checkLine()
throws Exception
checkLine in class AtomSetCollectionReaderExceptionvoid processTotalEnergy()
void processAtomicCharges()
throws 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.Exceptionvoid processCoordinates()
throws 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
Exceptionprivate void readFrequencies()
throws 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.
Exception - If an I/O error occurs