Class GulpReader

  • All Implemented Interfaces:
    javajs.api.GenericLineReader

    public class GulpReader
    extends AtomSetCollectionReader
    Problems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional. Default right now is to read conventional cell, not primitive celll -- Frequency data number of atoms does not correspond to initial atom count. It looks like there is a missing report of symmetry-generated atoms. see https://projects.ivec.org/gulp/
    Version:
    1.0
    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
    • Field Detail

      • isSlab

        private boolean isSlab
      • isPolymer

        private boolean isPolymer
      • isPrimitive

        private boolean isPrimitive
      • sep

        private java.lang.String sep
      • coordinatesArePrimitive

        private boolean coordinatesArePrimitive
      • atomCharges

        private java.util.Map<java.lang.String,​java.lang.Float> atomCharges
      • bTest

        private boolean bTest
      • a

        private float a
      • b

        private float b
      • c

        private float c
      • alpha

        private float alpha
      • beta

        private float beta
      • gamma

        private float gamma
      • primitiveData

        private float[] primitiveData
      • tags

        private static final java.lang.String[] tags
      • totEnergy

        private java.lang.Double totEnergy
      • energyUnits

        private java.lang.String energyUnits
    • Constructor Detail

      • GulpReader

        public GulpReader()
    • Method Detail

      • checkLine

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

        private boolean readDimensionality()
                                    throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readSpaceGroup

        private void readSpaceGroup()
                             throws java.lang.Exception
        Throws:
        java.lang.Exception
      • parameterIndex

        private static int parameterIndex​(java.lang.String key)
      • setParameter

        private void setParameter​(java.lang.String key,
                                  float value)
      • newAtomSet

        private void newAtomSet​(boolean doSetUnitCell)
      • setModelParameters

        private void setModelParameters​(boolean isPrimitive)
      • readCellParameters

        private void readCellParameters​(boolean isLatticeVectors)
                                 throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readFinalCell

        private void readFinalCell()
                            throws java.lang.Exception
        Throws:
        java.lang.Exception
      • scalePrimitiveData

        private void scalePrimitiveData​(int i,
                                        float value)
      • readAtomicPos

        private void readAtomicPos​(boolean finalizeSymmetry)
                            throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readPartialCharges

        private void readPartialCharges()
                                 throws java.lang.Exception
        Throws:
        java.lang.Exception
      • readEnergy

        private void readEnergy()
                         throws java.lang.Exception
        Throws:
        java.lang.Exception
      • setEnergy

        private void setEnergy()