Relaxation of a user defined structure

This example demonstrates the definition and relaxation of a user defined structure provided in the input file via the <user-structure> element. None of the parameters are fitted.

Location

examples/relaxing_user_structure

Input files

  • main.xml: main input file

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    <?xml version='1.0' encoding='iso-8859-1'?>
<job>
  <name>Relaxation of a user defined structure</name>

  <verbosity>maximum</verbosity>
  
  <validate-potentials />
  
  <atom-types>
    <species>Ga</species>
    <species>N</species>
  </atom-types>
  
  <potentials>
    <tersoff id='GaN potential' species-a='*' species-b='*'>
      <param-file>GaN.tersoff</param-file>
    </tersoff>
  </potentials>
  
  <structures>
    
    <user-structure id='B1'>
      <pbc x='true' y='true' z='true' />
      <cell>
	<a1 x='4.304' y='0' z='0' />
	<a2 x='0' y='4.304' z='0' />
	<a3 x='0' y='0' z='4.304' />
	<atoms>
	  <atom type='Ga' x='0.1' y='0.0' z='0.0' reduced='true' />
	  <atom type='Ga' x='0.56' y='0.5' z='0.2' reduced='true' />
	  <atom type='Ga' x='0.5' y='0.0' z='0.5' reduced='true' />
	  <atom type='Ga' x='0.0' y='0.5' z='0.5' reduced='true' />
	  <atom type='N' x='0.5' y='0.2' z='0.0' reduced='true' />
	  <atom type='N' x='0.0' y='0.5' z='0.0' reduced='true' />
	  <atom type='N' x='0.0' y='0.0' z='0.5' reduced='true' />
	  <atom type='N' x='0.5' y='0.6' z='0.8' reduced='true' />
	</atoms>
      </cell>
      <relax-dof>
	<atom-coordinates/>
      </relax-dof>
    </user-structure>
    
  </structures>
</job>

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

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    # Tersoff parameters for various elements and mixtures
# multiple entries can be added to this file, LAMMPS reads the ones it needs
# these entries are in LAMMPS "metal" units:
#   A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms
#   other quantities are unitless

# format of a single entry (one or more lines):
#   element 1, element 2, element 3, 
#   m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A

# The following GaN potential is from J. Nord, K. Albe, P. Erhart
# and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003).
# This file is from Xiaowang Zhou, xzhou @ sandia.gov

 Ga Ga Ga 1.0 0.007874 1.846 1.918000 0.75000 -0.301300 1.0 1.0 1.44970 410.132 2.87 0.15 1.60916 535.199
 N  N  N  1.0 0.766120 0.000 0.178493 0.20172 -0.045238 1.0 1.0 2.38426 423.769 2.20 0.20 3.55779 1044.77
 Ga Ga N  1.0 0.001632 0.000 65.20700 2.82100 -0.518000 1.0 0.0 0.00000 0.00000 2.90 0.20 0.00000 0.00000
 Ga N  N  1.0 0.001632 0.000 65.20700 2.82100 -0.518000 1.0 1.0 2.63906 3864.27 2.90 0.20 2.93516 6136.44
 N  Ga Ga 1.0 0.001632 0.000 65.20700 2.82100 -0.518000 1.0 1.0 2.63906 3864.27 2.90 0.20 2.93516 6136.44
 N  Ga N  1.0 0.766120 0.000 0.178493 0.20172 -0.045238 1.0 0.0 0.00000 0.00000 2.20 0.20 0.00000 0.00000
 N  N  Ga 1.0 0.001632 0.000 65.20700 2.82100 -0.518000 1.0 0.0 0.00000 0.00000 2.90 0.20 0.00000 0.00000
 Ga N  Ga 1.0 0.007874 1.846 1.918000 0.75000 -0.301300 1.0 0.0 0.00000 0.00000 2.87 0.15 0.00000 0.00000

Output

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

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    This is program version 0.1.6
Reading job file main.xml
-------------------------------------------------------
Parsing input file(s)
-------------------------------------------------------
Maximum cutoff for Tersoff potential 'GaN' is 3.1
Neighbor lists of structure 'B1' will be built for the first time.
-------------------------------------------------------
Validating potential routines.
Finite difference epsilon: 0.0001
Testing structure 'B1' with 24 atomic degrees of freedom.
Neighbor lists of structure 'B1' need to be rebuilt because of cell deformation (skin=0, cell_def=0 threshold=0).
Atom 0 pos(0.4304, 0, 0) dim=0   Numerical derivative: 13.8521 err: 1.1073e-08   Analytical derivative: 13.8521   Deviation: 3.07875e-10  0.0278041
Atom 0 pos(0.4304, 0, 0) dim=1   Numerical derivative: 5.11556 err: 4.16382e-08   Analytical derivative: 5.11556   Deviation: 2.49345e-10  0.00598839
Atom 0 pos(0.4304, 0, 0) dim=2   Numerical derivative: -0.30519 err: 7.27303e-08   Analytical derivative: -0.30519   Deviation: 2.02029e-10  0.00277779
Atom 1 pos(2.41024, 2.152, 0.8608) dim=0   Numerical derivative: -8.51022 err: 3.73012e-07   Analytical derivative: -8.51022   Deviation: 1.03178e-09  0.00276607
Atom 1 pos(2.41024, 2.152, 0.8608) dim=1   Numerical derivative: -36.1769 err: 4.80475e-07   Analytical derivative: -36.1769   Deviation: 8.6262e-10  0.00179535
Atom 1 pos(2.41024, 2.152, 0.8608) dim=2   Numerical derivative: -44.2624 err: 3.30148e-07   Analytical derivative: -44.2624   Deviation: 8.90907e-10  0.00269851
Atom 2 pos(2.152, 0, 2.152) dim=0   Numerical derivative: -2.65016 err: 1.67913e-07   Analytical derivative: -2.65016   Deviation: 6.53948e-11  0.000389455
Atom 2 pos(2.152, 0, 2.152) dim=1   Numerical derivative: 0.728396 err: 3.05131e-07   Analytical derivative: 0.728396   Deviation: 4.24452e-10  0.00139105
Atom 2 pos(2.152, 0, 2.152) dim=2   Numerical derivative: 2.82222 err: 9.58467e-08   Analytical derivative: 2.82222   Deviation: 5.40852e-11  0.000564289
Atom 3 pos(0, 2.152, 2.152) dim=0   Numerical derivative: -1.49171 err: 1.51867e-07   Analytical derivative: -1.49171   Deviation: 2.8947e-10  0.00190608
Atom 3 pos(0, 2.152, 2.152) dim=1   Numerical derivative: 0.743795 err: 1.28908e-08   Analytical derivative: 0.743795   Deviation: 7.38442e-11  0.00572844
Atom 3 pos(0, 2.152, 2.152) dim=2   Numerical derivative: -2.27849 err: 3.68302e-08   Analytical derivative: -2.27849   Deviation: 3.37614e-11  0.000916679
Atom 4 pos(2.152, 0.8608, 0) dim=0   Numerical derivative: -3.8569 err: 2.91654e-07   Analytical derivative: -3.8569   Deviation: 7.23626e-10  0.00248111
Atom 4 pos(2.152, 0.8608, 0) dim=1   Numerical derivative: 32.0262 err: 4.49265e-07   Analytical derivative: 32.0262   Deviation: 4.02665e-11  8.96275e-05
Atom 4 pos(2.152, 0.8608, 0) dim=2   Numerical derivative: 29.7458 err: 1.09448e-07   Analytical derivative: 29.7458   Deviation: 4.87226e-10  0.00445168
Atom 5 pos(0, 2.152, 0) dim=0   Numerical derivative: -1.5007 err: 1.36496e-06   Analytical derivative: -1.5007   Deviation: 3.04156e-10  0.000222832
Atom 5 pos(0, 2.152, 0) dim=1   Numerical derivative: 8.51754 err: 4.90494e-07   Analytical derivative: 8.51754   Deviation: 3.29276e-10  0.000671315
Atom 5 pos(0, 2.152, 0) dim=2   Numerical derivative: -21.3724 err: 1.88489e-06   Analytical derivative: -21.3724   Deviation: 4.89138e-11  2.59505e-05
Atom 6 pos(0, 0, 2.152) dim=0   Numerical derivative: 0.40748 err: 4.87943e-09   Analytical derivative: 0.40748   Deviation: 1.2907e-10  0.0264519
Atom 6 pos(0, 0, 2.152) dim=1   Numerical derivative: -0.308894 err: 6.86895e-09   Analytical derivative: -0.308894   Deviation: 5.64106e-11  0.0082124
Atom 6 pos(0, 0, 2.152) dim=2   Numerical derivative: 0.434478 err: 1e-09   Analytical derivative: 0.434478   Deviation: 5.08127e-11  0.0508127
Atom 7 pos(2.152, 2.5824, 3.4432) dim=0   Numerical derivative: 3.75013 err: 2.14176e-07   Analytical derivative: 3.75013   Deviation: 1.30607e-10  0.000609811
Atom 7 pos(2.152, 2.5824, 3.4432) dim=1   Numerical derivative: -10.6457 err: 9.11384e-07   Analytical derivative: -10.6457   Deviation: 2.83357e-10  0.000310909
Atom 7 pos(2.152, 2.5824, 3.4432) dim=2   Numerical derivative: 35.216 err: 1.26092e-06   Analytical derivative: 35.216   Deviation: 3.19467e-10  0.000253361
Validation successful.
-------------------------------------------------------
-------------------------------------------------------
Computing structure properties
Relaxing atomic d.o.f. of structure B1 (#dof=21):
        force_rlx_iter=1 E=7.13911 fnorm=77.7135
        force_rlx_iter=2 E=-1.46156 fnorm=34.7045
        force_rlx_iter=3 E=-1.46156 fnorm=34.7045
        force_rlx_iter=4 E=-7.43048 fnorm=17.3768
        force_rlx_iter=5 E=-7.43048 fnorm=17.3768
        force_rlx_iter=6 E=-11.5514 fnorm=37.9108
        force_rlx_iter=7 E=-11.5514 fnorm=37.9108
Neighbor lists of structure 'B1' need to be rebuilt because of atomic displacement (skin=1.7216, threshold=0.8608).
        force_rlx_iter=8 E=140.376 fnorm=282.454
Neighbor lists of structure 'B1' need to be rebuilt because of atomic displacement (skin=1.7216, threshold=0.8608).
        force_rlx_iter=9 E=14.7855 fnorm=225.067
        force_rlx_iter=10 E=-17.5515 fnorm=32.2691
        force_rlx_iter=11 E=-17.5515 fnorm=32.2691
        force_rlx_iter=12 E=-17.1346 fnorm=32.6048
        force_rlx_iter=13 E=-18.309 fnorm=20.2751
        force_rlx_iter=14 E=-18.309 fnorm=20.2751
        force_rlx_iter=15 E=-20.1917 fnorm=31.4942
        force_rlx_iter=16 E=-20.1917 fnorm=31.4942
        force_rlx_iter=17 E=-20.9584 fnorm=39.4341
        force_rlx_iter=18 E=-20.9584 fnorm=39.4341
        force_rlx_iter=19 E=-21.6398 fnorm=20.1743
        force_rlx_iter=20 E=-21.6398 fnorm=20.1743
        force_rlx_iter=21 E=-22.2835 fnorm=9.9512
        force_rlx_iter=22 E=-22.2835 fnorm=9.9512
        force_rlx_iter=23 E=-22.8377 fnorm=13.3711
        force_rlx_iter=24 E=-22.8377 fnorm=13.3711
        force_rlx_iter=25 E=-23.179 fnorm=6.89407
        force_rlx_iter=26 E=-23.179 fnorm=6.89407
        force_rlx_iter=27 E=-23.4691 fnorm=6.68285
        force_rlx_iter=28 E=-23.4691 fnorm=6.68285
        force_rlx_iter=29 E=-24.2948 fnorm=4.80567
        force_rlx_iter=30 E=-24.2948 fnorm=4.80567
Neighbor lists of structure 'B1' need to be rebuilt because of atomic displacement (skin=1.7216, threshold=0.8608).
        force_rlx_iter=31 E=-25.3725 fnorm=9.23799
        force_rlx_iter=32 E=-25.3725 fnorm=9.23799
        force_rlx_iter=33 E=-24.1837 fnorm=17.5088
        force_rlx_iter=34 E=-26.2755 fnorm=10.1217
        force_rlx_iter=35 E=-26.2755 fnorm=10.1217
        force_rlx_iter=36 E=-27.2469 fnorm=9.00067
        force_rlx_iter=37 E=-27.2469 fnorm=9.00067
        force_rlx_iter=38 E=-28.0786 fnorm=5.84743
        force_rlx_iter=39 E=-28.0786 fnorm=5.84743
        force_rlx_iter=40 E=-28.5226 fnorm=4.47269
        force_rlx_iter=41 E=-28.5226 fnorm=4.47269
        force_rlx_iter=42 E=-29.1394 fnorm=3.18133
        force_rlx_iter=43 E=-29.1394 fnorm=3.18133
Neighbor lists of structure 'B1' need to be rebuilt because of atomic displacement (skin=1.7216, threshold=0.8608).
        force_rlx_iter=44 E=-29.4139 fnorm=4.1065
        force_rlx_iter=45 E=-29.4139 fnorm=4.1065
        force_rlx_iter=46 E=-29.635 fnorm=2.09631
        force_rlx_iter=47 E=-29.635 fnorm=2.09631
        force_rlx_iter=48 E=-29.7691 fnorm=1.13437
        force_rlx_iter=49 E=-29.7691 fnorm=1.13437
        force_rlx_iter=50 E=-29.8357 fnorm=0.665141
        force_rlx_iter=51 E=-29.8357 fnorm=0.665141
        force_rlx_iter=52 E=-29.8467 fnorm=0.68019
        force_rlx_iter=53 E=-29.8467 fnorm=0.68019
        force_rlx_iter=54 E=-29.8567 fnorm=0.276079
        force_rlx_iter=55 E=-29.8567 fnorm=0.276079
        force_rlx_iter=56 E=-29.8597 fnorm=0.124064
        force_rlx_iter=57 E=-29.8597 fnorm=0.124064
        force_rlx_iter=58 E=-29.861 fnorm=0.145802
        force_rlx_iter=59 E=-29.861 fnorm=0.145802
        force_rlx_iter=60 E=-29.8621 fnorm=0.138224
        force_rlx_iter=61 E=-29.8621 fnorm=0.138224
        force_rlx_iter=62 E=-29.8627 fnorm=0.0927194
        force_rlx_iter=63 E=-29.8627 fnorm=0.0927194
        force_rlx_iter=64 E=-29.8633 fnorm=0.0587317
        force_rlx_iter=65 E=-29.8633 fnorm=0.0587317
        force_rlx_iter=66 E=-29.8635 fnorm=0.0718047
        force_rlx_iter=67 E=-29.8635 fnorm=0.0718047
        force_rlx_iter=68 E=-29.8638 fnorm=0.0842552
        force_rlx_iter=69 E=-29.8638 fnorm=0.0842552
        force_rlx_iter=70 E=-29.8641 fnorm=0.0587966
        force_rlx_iter=71 E=-29.8641 fnorm=0.0587966
        force_rlx_iter=72 E=-29.8643 fnorm=0.046053
        force_rlx_iter=73 E=-29.8643 fnorm=0.046053
        force_rlx_iter=74 E=-29.8644 fnorm=0.0454129
        force_rlx_iter=75 E=-29.8644 fnorm=0.0454129
        force_rlx_iter=76 E=-29.8645 fnorm=0.0607217
        force_rlx_iter=77 E=-29.8645 fnorm=0.0607217
        force_rlx_iter=78 E=-29.8646 fnorm=0.0262235
        force_rlx_iter=79 E=-29.8646 fnorm=0.0262235
        force_rlx_iter=80 E=-29.8646 fnorm=0.0211356
        force_rlx_iter=81 E=-29.8646 fnorm=0.0211356
        force_rlx_iter=82 E=-29.8647 fnorm=0.0224202
        force_rlx_iter=83 E=-29.8647 fnorm=0.0224202
        force_rlx_iter=84 E=-29.8647 fnorm=0.0241339
        force_rlx_iter=85 E=-29.8647 fnorm=0.0241339
        force_rlx_iter=86 E=-29.8647 fnorm=0.0448303
        force_rlx_iter=87 E=-29.8647 fnorm=0.0132578
        force_rlx_iter=88 E=-29.8647 fnorm=0.0132578
        force_rlx_iter=89 E=-29.8647 fnorm=0.00517589
        force_rlx_iter=90 E=-29.8647 fnorm=0.00517589
        force_rlx_iter=91 E=-29.8647 fnorm=0.00493333
        force_rlx_iter=92 E=-29.8647 fnorm=0.00493333
        force_rlx_iter=93 E=-29.8647 fnorm=0.00470475
        force_rlx_iter=94 E=-29.8647 fnorm=0.00470475
        force_rlx_iter=95 E=-29.8647 fnorm=0.00282684
        force_rlx_iter=96 E=-29.8647 fnorm=0.00282684
        force_rlx_iter=97 E=-29.8647 fnorm=0.00201777
        force_rlx_iter=98 E=-29.8647 fnorm=0.00201777
        force_rlx_iter=99 E=-29.8647 fnorm=0.000957771
        force_rlx_iter=100 E=-29.8647 fnorm=0.000957771
        force_rlx_iter=101 E=-29.8647 fnorm=0.000805027
        force_rlx_iter=102 E=-29.8647 fnorm=0.000805027
Structure 'B1':
   total-energy: -29.8647 eV
   atomic-energy: -3.73309 eV/atom
   total-volume: 79.7291 A^3
   atomic-volume: 9.96614 A^3/atom
-------------------------------------------------------
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