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, 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 |
---|
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, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, 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 chargesFound
private boolean haveHeader
private int mopacVersion
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
void 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 3.9079They are expected to be found in the file before the cartesian coordinate section.
java.lang.Exception
void 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 0.0000In 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.Exception
private 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