Package org.jmol.adapter.readers.aflow

Class AFLOWReader

  • All Implemented Interfaces:
    javajs.api.GenericLineReader
    public class AFLOWReader
extends VaspPoscarReader
    A reader for various AFLOW file types. For starters, we have output from the binaries page. see http://www.aflowlib.org/binary_alloys.php or, in Jmol, from: print load("http://aflowlib.mems.duke.edu/php/apool.php?POST?job=awrapper_apool&lattice=all&alloy=AgAu") Unit cells are centered. Selected compositions can be obtained using the filter "Ca=0.5" for example.
    Version:
    1.0
    Author:
    Bob Hanson

    • Field Detail

      • aabb

        private java.lang.String aabb

      • readPRE

        private boolean readPRE

      • fracB

        private float fracB

      • compositions

        private java.util.Map<java.lang.String,​float[]> compositions

      • getComposition

        private boolean getComposition

      • listKey

        private java.lang.String listKey

      • listKeyCase

        private java.lang.String listKeyCase

      • fileModelNumber

        private int fileModelNumber

      • havePRE

        private boolean havePRE

      • titleMsg

        private java.lang.String titleMsg

      • keyMap

        private java.util.Map<java.lang.String,​java.lang.String> keyMap

    • Constructor Detail

      • AFLOWReader

        public AFLOWReader()

    • Method Detail

      • initializeReader

        protected void initializeReader()
                         throws java.lang.Exception
        Overrides:
        initializeReader in class VaspPoscarReader
        Throws:
        java.lang.Exception

      • 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

      • readPrePost

        private boolean readPrePost()
                     throws java.lang.Exception
        Throws:
        java.lang.Exception

      • finalizeModel

        private void finalizeModel()
                    throws java.lang.Exception
        Throws:
        java.lang.Exception

      • readElementLabelsOnly

        private void readElementLabelsOnly()
                            throws java.lang.Exception
        scan the AFLOWReader PRE structure for elements in coord section
        Throws:
        java.lang.Exception

      • getData

        private boolean getData()
                 throws java.lang.Exception
        Throws:
        java.lang.Exception

      • cleanKey

        private java.lang.String cleanKey​(java.lang.String key)
        cleans key to just letters and digits
        Parameters:
        key -
        Returns:
        cleaned key

      • listCompositions

        private void listCompositions()

      • alignUnitCells

        private void alignUnitCells()