Package org.jmol.adapter.readers.xtal

Class CrystalReader

java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.xtal.CrystalReader
All Implemented Interfaces:
javajs.api.GenericLineReader
public class CrystalReader extends AtomSetCollectionReader
A reader of OUT and OUTP files for CRYSTAL http://www.crystal.unito.it/
Version:
1.4 special model auxiliaryInfo include: primitiveToCrystal M3 transforming primitive lattice to conventional lattice mat4PrimitiveToCrystal M4 for use in transforming symmetry operations mat4CrystalToPrimitive M4 convenience inverse of mat4PrimitiveToCrystal fileSymmetryOperations List symmetry operators (primitive) Drawing primitive unitcell operations: ops = _M.fileSystemOperations DRAW SYMOP @{ops[2]} If using the conventional cell, you can use its operators, or you can limit yourself this primitive subset using: mp2c = _M.mat4PrimitiveToCrystal mc2p = _M.mat4CrystalToPrimitive DRAW SYMOP @{mc2p * ops[2] * mp2c} for a specific model in the set, use load "xxx.out" n as for all readers, where n is an integer > 0 for final optimized geometry use load "xxx.out" 0 (that is, "read the last model") as for all readers for conventional unit cell -- input coordinates only, use load "xxx.out" filter "conventional" to NOT load vibrations, use load "xxx.out" FILTER "novibrations" to load just the input deck exactly as indicated, use load "xxx.out" FILTER "input" now allows reading of frequencies and atomic values with conventional as long as this is not an optimization.
Author:
Pieremanuele Canepa, Room 104, FM Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom, pc229@kent.ac.uk, Bob Hanson hansonr@stolaf.edu

  • Field Details

    • isVersion3

      private boolean isVersion3

    • isPolymer

      private boolean isPolymer

    • isSlab

      private boolean isSlab

    • haveCharges

      private boolean haveCharges

    • inputOnly

      private boolean inputOnly

    • isLongMode

      private boolean isLongMode

    • getLastConventional

      private boolean getLastConventional

    • havePrimitiveMapping

      private boolean havePrimitiveMapping

    • isProperties

      private boolean isProperties

    • STATE_NONE

      private static final int STATE_NONE
      See Also:

    • STATE_INPUT

      private static final int STATE_INPUT
      See Also:

    • STATE_INPUT_FROM

      private static final int STATE_INPUT_FROM
      See Also:

    • STATE_WAVEFUNCTION

      private static final int STATE_WAVEFUNCTION
      See Also:

    • STATE_OPT_POINT

      private static final int STATE_OPT_POINT
      See Also:

    • STATE_OPT_FINAL

      private static final int STATE_OPT_FINAL
      See Also:

    • STATE_FREQ

      private static final int STATE_FREQ
      See Also:

    • state

      private int state

    • ac

      private int ac

    • atomIndexLast

      private int atomIndexLast

    • atomFrag

      private int[] atomFrag

    • primitiveToIndex

      private int[] primitiveToIndex

    • nuclearCharges

      private float[] nuclearCharges

    • lstCoords

      private javajs.util.Lst<String> lstCoords

    • energy

      private Double energy

    • ptOriginShift

      private javajs.util.P3 ptOriginShift

    • directLatticeVectors

      private javajs.util.V3[] directLatticeVectors

    • spaceGroupName

      private String spaceGroupName

    • checkModelTrigger

      private boolean checkModelTrigger

    • fullSymmetry

      private boolean fullSymmetry

    • htCriticalPoints

      private Map<String,javajs.util.Lst<Object>> htCriticalPoints

    • directLatticeVectorsFirst

      private boolean directLatticeVectorsFirst
      CRYSTAL 17 moves directLatticeVectors before LATTICE PARAMETERS

    • cpno

      private int cpno

    • crtypes

      private static final String[] crtypes

    • symops

      private javajs.util.Lst<String> symops

    • f14

      private final float[] f14

    • f16

      private final float[] f16

    • smap

      private static final int[] smap

    • primitiveVolume

      private float primitiveVolume

    • primitiveDensity

      private float primitiveDensity

    • firstLine

      private String firstLine

    • type

      private String type

  • Constructor Details

    • CrystalReader

      public CrystalReader()

  • Method Details

    • rd

      public String rd() throws Exception
      filter out unnecessary lines
      Overrides:
      rd in class AtomSetCollectionReader
      Throws:
      Exception

    • initializeReader

      protected void initializeReader() throws Exception
      Overrides:
      initializeReader in class AtomSetCollectionReader
      Throws:
      Exception

    • checkLine

      protected boolean checkLine() throws Exception
      Overrides:
      checkLine in class AtomSetCollectionReader
      Returns:
      true if need to read new line
      Throws:
      Exception

    • processNextCriticalPoint

      private void processNextCriticalPoint() throws Exception
      Throws:
      Exception

    • newLattice

      private void newLattice(boolean isConv) throws Exception
      Throws:
      Exception

    • addModel

      private boolean addModel() throws Exception
      Throws:
      Exception

    • readSymmetryOperators

      private void readSymmetryOperators() throws Exception
      Throws:
      Exception

    • finalizeSubclassReader

      protected void finalizeSubclassReader() throws Exception
      Description copied from class: AtomSetCollectionReader
      optional reader-specific method run first.
      Overrides:
      finalizeSubclassReader in class AtomSetCollectionReader
      Throws:
      Exception

    • getDirect

      private void getDirect() throws Exception
      Throws:
      Exception

    • setUnitCellOrientation

      private void setUnitCellOrientation()

    • readPrimitiveLatticeVectors

      private void readPrimitiveLatticeVectors() throws Exception
      Read transform matrix primitive to conventional.
      Throws:
      Exception

    • readHeader

      private boolean readHeader() throws Exception
      Throws:
      Exception

    • readLatticeParams

      private void readLatticeParams(boolean isPrimitive) throws Exception
      Read the lattice parameters.
      Parameters:
      isPrimitive -
      Throws:
      Exception

    • getAtomIndexFromPrimitiveIndex

      private int getAtomIndexFromPrimitiveIndex(int iPrim)
      Get the atom index from a primitive index. Used for atomic properties and frequency fragments. Note that primitive to conventional is not a 1:1 mapping. We don't consider that.
      Parameters:
      iPrim -
      Returns:
      the original number or the number from the primitive.

    • readAtoms

      private boolean readAtoms() throws Exception
      Throws:
      Exception

    • fixAtomName

      private static String fixAtomName(String s)
      MN33 becomes Mn33
      Parameters:
      s -
      Returns:
      fixed atom name

    • getAtomicNumber

      private int getAtomicNumber(String token)

    • readCoordLines

      private void readCoordLines() throws Exception
      Read coordinates, either input or crystallographic, just saving their lines in a vector for now.
      Throws:
      Exception

    • processCoordLines

      private void processCoordLines() throws Exception
      Now create atoms from the coordinate lines.
      Throws:
      Exception

    • applySymmetryAndSetTrajectory

      public void applySymmetryAndSetTrajectory() throws Exception
      Overrides:
      applySymmetryAndSetTrajectory in class AtomSetCollectionReader
      Throws:
      Exception

    • newAtomSet

      private void newAtomSet() throws Exception
      Throws:
      Exception

    • setEnergy

      private void setEnergy()

    • readPartialCharges

      private boolean readPartialCharges() throws Exception
      Throws:
      Exception

    • readTotalAtomicCharges

      private boolean readTotalAtomicCharges() throws Exception
      Throws:
      Exception

    • readFreqFragments

      private void readFreqFragments() throws Exception
      Select only specific atoms for frequency generation. (See freq_6for_001.out)
      Throws:
      Exception

    • readFrequencies

      private void readFrequencies() throws Exception
      Throws:
      Exception

    • setFreqValue

      private void setFreqValue(float freq, String[] data)

    • readRaman

      private javajs.util.Lst<String> readRaman(javajs.util.Lst<String> ramanData) throws Exception
      Throws:
      Exception

    • getModelForMode

      private int getModelForMode(int i0, int mode)

    • readGradient

      private boolean readGradient() throws Exception
      Read minimization measures
      Returns:
      true
      Throws:
      Exception

    • readData

      private boolean readData(String name, int nfields) throws Exception
      For spin and magnetic moment data, read the data block and save it as property_spin or propert_magneticMoment.
      Parameters:
      name -
      nfields -
      Returns:
      true
      Throws:
      Exception

    • getQuadrupoleTensors

      private boolean getQuadrupoleTensors() throws Exception
      Throws:
      Exception

    • readBornChargeTensors

      private boolean readBornChargeTensors() throws Exception
      Throws:
      Exception