org.jmol.adapter.readers.simple
public class MopacReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
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private int |
baseAtomIndex |
private boolean |
chargesFound |
private boolean |
haveHeader |
private int |
mopacVersion |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer
Constructor and Description |
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MopacReader() |
Modifier and Type | Method and Description |
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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.
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(package private) void |
processTotalEnergy() |
private void |
readFrequencies()
Interprets the Harmonic frequencies section.
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addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
private int baseAtomIndex
private boolean chargesFound
private boolean haveHeader
private int mopacVersion
protected void initializeReader() throws Exception
initializeReader
in class AtomSetCollectionReader
Exception
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
void 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 3.9079They are expected to be found in the file before the cartesian coordinate section.
Exception
void 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 0.0000In 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
Exception
private 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