Computing a derived property using a point defect structure

This example demonstrates the use of a derived property and a point defect structure to compute the vacancy formation energy of body centered cubic (BCC) Fe.

Location

examples/derived_properties

Input files

• main.xml: main input file

  <?xml version='1.0' encoding='iso-8859-1'?>
  <job>
    <name>Computing derived properties</name>
  
    <verbosity>medium</verbosity>
  
    <atom-types>
      <species>Fe</species>
    </atom-types>
  
    <potentials>
      <abop id='FeFe' classic-mode='true' species-a='*' species-b='*'>
        <param-file>Fe.tersoff</param-file>
        <fit-dof>
  	<D0 tag='FeFeFe'/>
  	<r0 tag='FeFeFe'/>
  	<beta tag='FeFeFe'/>
  	<S tag='FeFeFe'/>
  	<c tag='FeFeFe'/>
  	<d tag='FeFeFe'/>
  	<h tag='FeFeFe'/>
  	<gamma tag='FeFeFe'/>
  	<twomu tag='FeFeFe'/>
        </fit-dof>
      </abop>
    </potentials>
    
    <structures>
  
      <bcc-lattice id='bcc-Fe'>
        <atom-type>Fe</atom-type>
        <lattice-parameter> 2.86 </lattice-parameter>
        <properties>
  	<lattice-parameter/>
  	<atomic-energy/>
        </properties>
      </bcc-lattice>
  
      <point-defect id='Vac'>
        <atom-type-A>Fe</atom-type-A>
        <lattice-type>bcc</lattice-type>
        <cell-size>4</cell-size>
        <lattice-parameter> 2.86 </lattice-parameter>
        <output file="POSCAR.defect-structure" format="poscar"/>
        <defects>
  	<vacancy index='85' />
  	<!-- <substitutional index='1' atom-type='Y' /> -->
  	<!-- <interstitial x='0.5625' y='0.5625' z='0.5625' atom-type='Y' /> -->
        </defects>
        <relax-dof>
  	<atom-coordinates reset='true'/>
        </relax-dof>
        <properties>
  	<atomic-energy/>
  	<lattice-parameter equalto='bcc-Fe.lattice-parameter'/>
        </properties>
      </point-defect>
  
      <derived-property id='bccFe-Ev' unit='eV'
                        equation='[Vac.total-energy] - 127*[bcc-Fe.atomic-energy] '/>
                        
    </structures>
  
  </job>
  

• Fe.tersoff: initial parameter set in Lammps/Tersoff format

  # Values taken from:
  # Michael Mueller et al
  # J. Phys.: Condens. Matter 19 (2007) 326220
  
  # Potential file was prepared by A. Stukowski (TU Darmstadt)
  
  # Parameters converted from K. Albe's analytical bond-order formalism to LAMMPS Tersoff format:
  # gamma = gamma
  # lambda3 = 2*mu
  # c = c
  # d = d
  # R = Rc
  # D = Dc
  # costheta0 = -h
  # lambda1 = beta*sqrt(2*S)
  # lambda2 = beta*sqrt(2/S)
  # A = D0/(S-1)*exp(lambda1*r0)
  # B = S*D0/(S-1)*exp(lambda2*r0)
  
  Fe Fe Fe 1.0 0.0115751 0 1.2898716 0.3413219 0.26 1.0 1.0 1.37635404 67.8647723 3.15 0.2 2.84810441 953.948593
  

Output (files)

• The final properties (as well as parameters) are written to standard output.

  This is program version 0.1.6
  Reading job file main.xml
  -------------------------------------------------------
  Parsing input file(s)
  -------------------------------------------------------
  -------------------------------------------------------
  Computing structure properties
  Structure 'bcc-Fe':
     total-energy: -4.28 eV
     atomic-energy: -4.28 eV/atom
     total-volume: 11.6968 A^3
     atomic-volume: 11.6968 A^3/atom
     lattice-parameter: 2.86 A [0:]
  Structure 'Vac':
     total-energy: -541.996 eV
     atomic-energy: -4.26768 eV/atom
     total-volume: 1497.19 A^3
     atomic-volume: 11.7889 A^3/atom
     lattice-parameter: 2.86 A [0:]
  Writing structure 'Vac' to /home/erhart/progs/atomicrex/examples/derived_properties/POSCAR.defect-structure
  -------------------------------------------------------
  Computing derived properties
     bccFe-Ev: 1.5644 eV
  -------------------------------------------------------
  -------------------------------------------------------
  

• For reference the code also writes the defect structure in POSCAR file format.

  'Vac' written by atomicPoet.
     1.00000000000000
      11.4399999999999995    0.0000000000000000    0.0000000000000000
       0.0000000000000000   11.4399999999999995    0.0000000000000000
       0.0000000000000000    0.0000000000000000   11.4399999999999995
     Fe 
     127 
  Cartesian
    0.0056182025237690  0.0056182025237798  0.0056182025237962
    1.4412486992558771  1.4412486992558295  1.4412486992558695
    0.0055901211774126  0.0055901211773910  2.8679804570307108
    1.4402516616902654  1.4402516616903043  4.2972132214723180
    0.0055774171002552  0.0055774171002643  5.7255632037165762
    1.4402271033985408  1.4402271033984919  7.1539361607186525
    0.0055833489153745  0.0055833489153580  8.5831550546788034
    1.4411993876663729  1.4411993876664055 10.0099785698326134
    0.0055901211773922  2.8679804570307432  0.0055901211773599
    1.4402516616902608  4.2972132214723668  1.4402516616902805
    0.0056024736822050  2.8646819033554696  2.8646819033554944
    1.4335448515972780  4.2925159429341164  4.2925159429341369
    0.0055821158528663  2.8657066525337211  5.7255785677147850
    1.4335191236776850  4.2924820606456180  7.1586788894200764
    0.0055705746644709  2.8646465444083722  8.5864872005290973
    1.4402206360930181  4.2971926193813363 10.0109424730879581
    0.0055774171002496  5.7255632037165443  0.0055774171002953
    1.4402271033985343  7.1539361607186231  1.4402271033985332
    0.0055821158528877  5.7255785677148197  2.8657066525336803
    1.4335191236776832  7.1586788894201101  4.2924820606455700
    0.0055758788362858  5.7255798429807720  5.7255798429808022
    1.4334748560643824  7.1586775928395845  7.1586775928396165
    0.0055565459413301  5.7255625241834238  8.5854328819018590
    1.4401964419518083  7.1539389672820723 10.0109322308854409
    0.0055833489153698  8.5831550546788282  0.0055833489153323
    1.4411993876663733 10.0099785698326489  1.4411993876663891
    0.0055705746644786  8.5864872005290689  2.8646465444083931
    1.4402206360930112 10.0109424730879404  4.2971926193813514
    0.0055565459413159  8.5854328819018928  5.7255625241833892
    1.4401964419518087 10.0109322308854871  7.1539389672820395
    0.0055313585270664  8.5864848646494654  8.5864848646494956
    1.4411832840190151 10.0099703178056973 10.0099703178057169
    2.8679804570307526  0.0055901211774133  0.0055901211774316
    4.2972132214723278  1.4402516616902263  1.4402516616902461
    2.8646819033554443  0.0056024736821919  2.8646819033554087
    4.2925159429341662  1.4335448515973259  4.2925159429341750
    2.8657066525337314  0.0055821158528855  5.7255785677148765
    4.2924820606455700  1.4335191236776457  7.1586788894200444
    2.8646465444083513  0.0055705746644623  8.5864872005290120
    4.2971926193813692  1.4402206360930592 10.0109424730879937
    2.8646819033554665  2.8646819033554465  0.0056024736821471
    4.2925159429341688  4.2925159429342097  1.4335448515972757
    2.8850348069472509  2.8850348069472673  2.8850348069473033
    4.3436334777866810  4.3436334777866410  4.3436334777866765
    2.8801159843696995  2.8801159843696782  5.7255896377877828
    4.3435366947740599  4.3435366947740954  7.1076574132112933
    2.8849599262854237  2.8849599262854366  8.5662092720534702
    4.2924776561564357  4.2924776561563949 10.0176409098800097
    2.8657066525337362  5.7255785677148401  0.0055821158529101
    4.2924820606455771  7.1586788894200204  1.4335191236776670
    2.8801159843696831  5.7255896377878157  2.8801159843696436
    4.3435366947740741  7.1076574132113235  4.3435366947740830
    2.8049677195108709  5.7256035467522421  5.7256035467522715
    4.3435194777971473  7.1076187198888734  7.1076187198888885
    2.8800605322997685  5.7255715018581332  8.5710856980599033
    4.2924529986609485  7.1586701063708116 10.0176264357056279
    2.8646465444083686  8.5864872005290493  0.0055705746644196
    4.2971926193813799 10.0109424730880150  1.4402206360930159
    2.8849599262854078  8.5662092720534453  2.8849599262854548
    4.2924776561564553 10.0176409098799706  4.2924776561564411
    2.8800605322997859  8.5710856980599370  5.7255715018581048
    4.2924529986609548 10.0176264357056581  7.1586701063707556
    2.8849386427668797  8.5661892455538826  8.5661892455539199
    4.2971681396222996 10.0109183271886000 10.0109183271886426
    5.7255632037165336  0.0055774171002641  0.0055774171002934
    7.1539361607186613  1.4402271033984999  1.4402271033985339
    5.7255785677148374  0.0055821158528655  2.8657066525336816
    7.1586788894200648  1.4335191236777232  4.2924820606455727
    5.7255798429807578  0.0055758788362977  5.7255798429807960
    7.1586775928396271  1.4334748560643389  7.1586775928396227
    5.7255625241834478  0.0055565459413156  8.5854328819018555
    7.1539389672820333  1.4401964419518443 10.0109322308854427
    5.7255785677148232  2.8657066525337171  0.0055821158528345
    7.1586788894200568  4.2924820606456242  1.4335191236776927
    5.7255896377878264  2.8801159843696897  2.8801159843697230
    7.1076574132112809  4.3435366947740430  4.3435366947740617
    5.7256035467522208  2.8049677195108558  5.7256035467521826
    7.1076187198889009  4.3435194777971935  7.1076187198889160
    5.7255715018581483  2.8800605322997908  8.5710856980599814
    7.1586701063707618  4.2924529986609157 10.0176264357055960
    5.7255798429807614  5.7255798429807694  0.0055758788363471
    7.1586775928396253  7.1586775928395756  1.4334748560643693
    5.7256035467522386  5.7256035467522208  2.8049677195108171
    7.1076187198888947  7.1076187198889231  4.3435194777971642
    7.1075693775587858  7.1075693775587450  7.1075693775587832
    5.7255552224559771  5.7255552224559505  8.6461760277923467
    7.1586653416983941  7.1586653416984296 10.0176134414063842
    5.7255625241834265  8.5854328819018964  0.0055565459412803
    7.1539389672820288 10.0109322308854818  1.4401964419518176
    5.7255715018581430  8.5710856980599655  2.8800605322998130
    7.1586701063707565 10.0176264357055818  4.2924529986609405
    5.7255552224559505  8.6461760277923894  5.7255552224559132
    7.1586653416983914 10.0176134414064339  7.1586653416984030
    5.7255537179058811  8.5710501948302511  8.5710501948302813
    7.1539367919864869 10.0109171105905546 10.0109171105905723
    8.5831550546788478  0.0055833489153765  0.0055833489153977
   10.0099785698326009  1.4411993876663398  1.4411993876663560
    8.5864872005290565  0.0055705746644623  2.8646465444083158
   10.0109424730879741  1.4402206360930578  4.2971926193813825
    8.5854328819019088  0.0055565459413325  5.7255625241834736
   10.0109322308854445  1.4401964419517703  7.1539389672820120
    8.5864848646494547  0.0055313585270450  8.5864848646494192
   10.0099703178057293  1.4411832840190522 10.0099703178057453
    8.5864872005290689  2.8646465444083473  0.0055705746644255
   10.0109424730879830  4.2971926193814118  1.4402206360930125
    8.5662092720534400  2.8849599262854162  2.8849599262854539
   10.0176409098800185  4.2924776561563993  4.2924776561564393
    8.5710856980599583  2.8800605322997685  5.7255715018581004
   10.0176264357056226  4.2924529986609947  7.1586701063707547
    8.5661892455538720  2.8849386427668877  8.5661892455539181
   10.0109183271886479  4.2971681396222596 10.0109183271886373
    8.5854328819019052  5.7255625241834469  0.0055565459413629
   10.0109322308854427  7.1539389672819933  1.4401964419517852
    8.5710856980599388  5.7255715018581368  2.8800605322997348
   10.0176264357056191  7.1586701063708036  4.2924529986609707
    8.6461760277923982  5.7255552224559727  5.7255552224559931
   10.0176134414063931  7.1586653416983488  7.1586653416983657
    8.5710501948302387  5.7255537179058686  8.5710501948302049
   10.0109171105905919  7.1539367919865198 10.0109171105906007
    8.5864848646494618  8.5864848646494494  0.0055313585270225
   10.0099703178057240 10.0099703178057649  1.4411832840190211
    8.5661892455538879  8.5661892455539004  2.8849386427669077
   10.0109183271886444 10.0109183271886035  4.2971681396222916
    8.5710501948302582  8.5710501948302369  5.7255537179058349
   10.0109171105905901 10.0109171105906309  7.1539367919864807
    8.5661851872871750  8.5661851872871893  8.5661851872872177
   10.0099999999999998 10.0099999999999998 10.0099999999999998