Example: Adding ASE structures

This example demonstrates how to add ASE structures via the atomicrex Python interface.

Location

examples/python_interface

Input files

• adding_structures_aseatoms.py: main input file

  from __future__ import print_function, division
  import atomicrex
  from ase.io import read
  from numpy.random import rand
  
  print('Create job object.')
  job = atomicrex.Job()
  
  print('Parse XML input file with input parameters'
        ' and potential information.')
  job.parse_input_file('main.xml')
  
  print('Switch verbosity to "medium".')
  job.set_verbosity(2)
  
  print('Adding a user-defined structure')
  conf = read('aluminum_cell_with_forces.traj')
  structure = job.add_ase_structure("Al-ase", conf)
  structure.compute_energy(compute_forces=True)
  print('Potential energy: {}'.format(structure.get_potential_energy()))
  print('Forces:')
  for i, force in enumerate(structure.get_forces(), start=1):
      print('{:3}'.format(i), end='')
      print((3*' {:10.6f}').format(*force))
  print('')
  
  print('Forces:')
  for i, force in enumerate(structure.get_forces(), start=1):
      print('{:3}'.format(i), end='')
      print((3*' {:10.6f}').format(*force))
  print('')
  
  print('Testing some ASE like method calls and properties')
  structure = job.structures['Al-ase']
  print(' positions')
  print(structure.positions)
  print(' get_positions()')
  print(structure.get_positions())
  print(' get_forces()')
  print(structure.get_forces())
  print(' get_cell()')
  print(structure.get_cell())
  print(' get_number_of_atoms()')
  print(structure.get_number_of_atoms())
  
  print('Handling target forces')
  n = structure.get_number_of_atoms()
  target_forces = rand(n, 3)
  structure.set_target_forces(target_forces)
  print('target_forces (1): {}'.format(structure.target_forces[:3]))
  print('target_forces (2): {}'.format(structure.get_target_forces()[:3]))
  

• main.xml: file with definition of potential

  <?xml version='1.0' encoding='iso-8859-1'?>
  <job>
    <name>EAM potential</name>
  
    <atom-types>
      <species>Al</species>
    </atom-types>
  
    <potentials>
      <xi:include href='potential.xml' xmlns:xi='http://www.w3.org/2003/XInclude' />
    </potentials>
  
    <structures>
    </structures>
  
  </job>
  

• potential.xml: definition of potential form and parameters

  <eam id='Al potential' species-a='*' species-b='*'>
  
    <mapping>
      <pair-interaction species-a='*' species-b='*' function='V' />
      <electron-density species-a='*' species-b='*' function='rho' />
      <embedding-energy species='*' function='F' />
    </mapping>
    
    <functions>
  
      <user-function id='V'>
        <input-var>r</input-var>
        <expression>
  	A * exp(-lambda * r)
        </expression>
        <derivative>
  	-lambda * A * exp(-lambda * r)
        </derivative>
        <param name='A'>500</param>
        <param name='lambda'>2.73</param>
        <fit-dof>
  	<A/>
  	<lambda/>
        </fit-dof>
        <screening>
  	<user-function id='rho_screening'>
  	  <cutoff>6.5</cutoff>
  	  <input-var>r</input-var>
  	  <expression>
  	    1 - 1/(1 + ((r - cutoff) / h)^4)
  	  </expression>
  	  <derivative>
  	    4 * h^4 * (r - cutoff)^3 / ((h^4 + (r - cutoff)^4)^2)
  	  </derivative>
  	  <param name='h'>3</param>
  	</user-function>
        </screening>
      </user-function>
  
      <user-function id='rho'>
        <input-var>r</input-var>
        <expression>
  	exp(-twomu * r)
        </expression>
        <derivative>
  	-twomu * exp(-twomu * r)
        </derivative>
        <param name='twomu'>1.14</param>
        <fit-dof>
  	<twomu/>
        </fit-dof>
        <screening>
  	<user-function id='rho_screening'>
  	  <cutoff>6.5</cutoff>
  	  <input-var>r</input-var>
  	  <expression>
  	    1 - 1/(1 + ((r - cutoff) / h)^4)
  	  </expression>
  	  <derivative>
  	    4 * h^4 * (r - cutoff)^3 / ((h^4 + (r - cutoff)^4)^2)
  	  </derivative>
  	  <param name='h'>3</param>
  	</user-function>
        </screening>
      </user-function>
  
      <user-function id='F'>
        <input-var>rho</input-var>
        <expression>
  	-D * sqrt(rho)
        </expression>
        <derivative>
          -D / (2 * sqrt(rho))
        </derivative>
        <param name='D'>8</param>
        <fit-dof>
  	<D/>
        </fit-dof>
      </user-function>
      
    </functions>
    
  </eam>
  

Output (files)

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

  -- Create job object.
  -- Parse XML input file with input parameters and potential information.
  -- Switch verbosity to "medium".
  -- Adding a user-defined structure
  -- Potential energy: -406.205
  -- Forces:
    1   0.228922  -0.414563   0.403548
    2   0.334428  -0.379682  -0.069397
    3  -0.378330   0.067553   0.136166
    4  -0.267490  -0.711869   0.103088
    5   0.041316  -0.103022   0.170451
    6  -0.072592   0.667039  -0.564620
    7  -0.084321  -0.048024   0.213219
    8  -0.115677   0.092934   0.172038
    9  -0.064267  -0.366829   0.832821
   10   0.058028   0.272147  -0.303900
   11   0.609686   0.504441  -0.109501
   12  -0.201763  -0.337560   0.344438
   13   0.181331  -0.382344  -0.239886
   14  -0.268898  -0.133752   0.163918
   15  -0.039570   0.339826  -0.169081
   16   0.214493  -0.078752  -0.294277
   17  -0.184247  -0.005420   0.204261
   18   0.071321   0.254455  -0.162130
   19  -0.174279   0.408565  -0.339281
   20   0.191058  -0.715959  -0.307583
   21   0.321434  -0.163229  -0.128408
   22  -0.675280   0.309515  -0.041442
   23   0.219854  -0.117558   0.116172
   24  -0.086597  -0.099163  -0.391950
   25  -0.231826  -0.338387   0.086434
   26   0.530835   0.048422  -0.403332
   27   0.341596   0.200922   0.070035
   28  -0.172922   0.033823   0.008343
   29   0.108258  -0.342995   0.143624
   30   0.662741   0.275639  -0.083324
   31  -0.301691   0.552812   0.867687
   32  -0.183424   0.091752   0.576055
   33  -0.246428  -0.031239  -0.036501
   34  -0.107925  -0.062948  -0.109163
   35   0.040014   0.274406   0.103698
   36   0.334733   0.272170  -0.399553
   37  -0.243321  -0.254463   0.118213
   38  -0.019562  -0.120828  -0.379838
   39   0.108252   0.192477   0.059798
   40   0.056310   0.159857   0.072343
   41  -0.041001  -0.599749  -0.012367
   42  -0.040833   0.065984  -0.005606
   43   0.132693  -0.324158  -0.042541
   44   0.541216   0.210147   0.139861
   45  -0.049268  -0.173836   0.033620
   46  -0.173325   0.218925  -0.106198
   47  -0.181661  -0.017519  -0.275766
   48  -0.406309  -0.095575  -0.105968
   49   0.627431   0.256956  -0.023413
   50   0.048451  -0.188717   0.169491
   51  -0.225842   0.067075   0.109482
   52   0.258366  -0.426346  -0.453674
   53  -0.089705  -0.020970  -0.344332
   54   0.134904  -0.347013  -0.382229
   55  -0.140402   0.033413   0.349354
   56   0.157963  -0.242563   0.266146
   57  -0.049528   0.089142  -0.546993
   58   0.095217   0.035059  -0.187862
   59   0.079393   0.077567   0.360967
   60  -0.195147  -0.014146   0.085351
   61  -0.354831   0.471337   0.027340
   62   0.432583  -0.341057   0.010506
   63  -0.179308   0.288969   0.057459
   64  -0.115056  -0.054860   0.064757
   65   0.027839  -0.178986  -0.588737
   66  -0.173004   0.597557  -0.049663
   67  -0.048882  -0.138456   0.091417
   68  -0.196630   0.094504  -0.285369
   69  -0.291099  -0.413900   0.537339
   70  -0.196607   0.215786  -0.086852
   71  -0.113973  -0.322237  -0.043920
   72   0.560492   0.424776   0.166814
   73  -0.061087   0.128668   0.322428
   74   0.120940  -0.281966  -0.002923
   75  -0.330124   0.804282   0.669875
   76  -0.189006   0.315214   0.115832
   77  -0.262314  -0.148664  -0.068018
   78   0.372951   0.211672  -0.610556
   79  -0.253618  -0.204521   0.254051
   80   0.054615   0.533164  -0.250822
   81   0.001499  -0.278007  -0.158165
   82   0.109897   0.448542   0.094093
   83  -0.048153   0.178814   0.135986
   84   0.070408  -0.333719  -0.176256
   85  -0.018817  -0.204087  -0.029193
   86   0.516421   0.034657   0.202886
   87  -0.184486   0.274774   0.381507
   88   0.036280   0.131803   0.006680
   89   0.050961  -0.086562  -0.592143
   90  -0.417281  -0.395419  -0.076470
   91   0.320950   0.000971   0.266972
   92   0.347855  -0.338514   0.025089
   93  -0.583493  -0.103524  -0.515571
   94  -0.280567   0.399732  -0.368744
   95   0.590736  -0.213561   0.546512
   96  -0.092683  -0.177060   0.066034
   97  -0.513592   0.417980   0.679979
   98   0.270410   0.292739   0.081619
   99   0.069373  -0.637980  -0.346315
  100   0.041867  -0.136503  -0.361105
  101  -0.627068   0.113209   0.185993
  102   0.071122   0.361615  -0.115911
  103  -0.113852  -0.420183   0.012828
  104  -0.221971   0.799182   0.437205
  105   0.170078  -0.184417   0.301193
  106   0.037502  -0.383577   0.015640
  107   0.393803  -0.207942   0.301298
  108   0.182111   0.231907  -0.793102
  
  -- Testing some ASE like method calls and properties
  --- positions
  [[ -3.98492678e-01  -4.08087682e-01  -9.96224456e-02]
   [ -6.65368939e-01   1.58496554e+00   2.03522790e+00]
   [  1.92614018e+00  -3.11957370e-01   1.76343425e+00]
   [  1.52233776e+00   1.91464834e+00  -3.81360448e-02]
   [ -3.76353681e-01  -6.17827119e-01   3.77766972e+00]
   [ -2.45451179e-01   1.25231869e+00   6.24846035e+00]
   [  1.80889924e+00  -7.91801346e-01   5.75907473e+00]
   [  1.68380145e+00   1.37330395e+00   4.08461856e+00]
   [ -1.26526489e-01  -7.08629922e-01   7.70665956e+00]
   [ -3.89087231e-01   1.40456726e+00   1.01351670e+01]
   [  1.32422427e+00  -8.78220250e-01   1.01126269e+01]
   [  1.80092503e+00   1.39130444e+00   8.07978827e+00]
   [ -5.64223959e-01   3.61639696e+00   1.13072941e-01]
   [ -3.41095178e-01   5.58650101e+00   1.98623098e+00]
   [  1.65039013e+00   3.32016212e+00   2.26021096e+00]
   [  1.62155452e+00   5.30820706e+00   2.11500325e-01]
   [ -3.31552511e-01   3.45137271e+00   4.02597028e+00]
   [ -3.66363775e-01   5.32917347e+00   6.11612712e+00]
   [  1.77097260e+00   3.35359965e+00   6.46908248e+00]
   [  1.51900009e+00   5.66211394e+00   4.05522922e+00]
   [ -5.80112967e-01   3.55931330e+00   8.17398089e+00]
   [ -3.06136884e-02   5.38635282e+00   1.02275746e+01]
   [  1.57245343e+00   3.41651378e+00   9.93689082e+00]
   [  1.89171841e+00   5.56704688e+00   8.30968863e+00]
   [ -2.21480182e-01   7.57939520e+00  -5.93704753e-02]
   [ -4.03733841e-01   9.47990245e+00   1.94076582e+00]
   [  1.61394213e+00   7.40802885e+00   1.91615268e+00]
   [  1.86595922e+00   9.50775061e+00   3.80589904e-02]
   [ -3.80576212e-01   7.66968473e+00   3.87668989e+00]
   [ -5.69026443e-01   9.42285279e+00   6.02016611e+00]
   [  1.71977733e+00   7.49245333e+00   5.65001120e+00]
   [  1.79716919e+00   9.57392097e+00   3.48303401e+00]
   [ -1.50316309e-01   7.34665345e+00   8.11038896e+00]
   [ -3.07559606e-01   9.32566549e+00   1.01998213e+01]
   [  1.85416465e+00   7.33754093e+00   1.02797059e+01]
   [  1.60098411e+00   9.23910187e+00   8.29066614e+00]
   [  3.90753284e+00  -4.20879775e-01  -3.45932872e-02]
   [  3.80580064e+00   1.70735633e+00   2.23680504e+00]
   [  5.83365713e+00  -6.50372672e-01   1.99270531e+00]
   [  5.85545370e+00   1.38172663e+00  -1.96040166e-02]
   [  3.79176689e+00  -3.26013047e-01   3.97304868e+00]
   [  3.78548089e+00   1.44729765e+00   6.20458419e+00]
   [  5.65168290e+00  -4.79335512e-01   6.12401041e+00]
   [  5.65091839e+00   1.46191490e+00   4.09724527e+00]
   [  3.62512157e+00  -6.43257778e-01   8.09228361e+00]
   [  3.72826410e+00   1.27662889e+00   1.01625413e+01]
   [  5.74349836e+00  -6.26872239e-01   1.01258525e+01]
   [  5.87676079e+00   1.47153879e+00   8.26379759e+00]
   [  3.55784533e+00   3.33242906e+00   7.45472063e-03]
   [  3.59903406e+00   5.42579427e+00   2.07917571e+00]
   [  5.86528134e+00   3.45321042e+00   2.03005466e+00]
   [  5.60779524e+00   5.51510354e+00   1.93188830e-01]
   [  3.66883631e+00   3.58554913e+00   4.42815635e+00]
   [  3.68500564e+00   5.62939806e+00   6.31691606e+00]
   [  5.81660626e+00   3.52381944e+00   6.10946149e+00]
   [  5.67012883e+00   5.55891079e+00   3.92850433e+00]
   [  3.82785340e+00   3.39895668e+00   8.45388606e+00]
   [  3.73967088e+00   5.37107184e+00   1.03417215e+01]
   [  5.83340520e+00   3.35167658e+00   1.01154841e+01]
   [  5.94306063e+00   5.47994106e+00   8.07987790e+00]
   [  3.82945580e+00   7.33704750e+00   7.68453725e-02]
   [  3.77812395e+00   9.74919852e+00   1.90927719e+00]
   [  5.71909560e+00   7.42647476e+00   2.04311554e+00]
   [  5.75733686e+00   9.49060787e+00  -1.06663117e-01]
   [  3.79297915e+00   7.53811943e+00   4.10918987e+00]
   [  3.78487991e+00   9.36692883e+00   5.89320516e+00]
   [  5.87995550e+00   7.45914140e+00   5.91458515e+00]
   [  5.96833171e+00   9.52041582e+00   4.17340117e+00]
   [  3.82883059e+00   7.66963968e+00   7.85330021e+00]
   [  3.78284165e+00   9.41580210e+00   1.01766029e+01]
   [  5.75595296e+00   7.57935642e+00   1.00621137e+01]
   [  5.53989653e+00   9.49193346e+00   7.92059396e+00]
   [  7.78777085e+00  -7.46134240e-01  -2.22978105e-01]
   [  7.76047807e+00   1.52367336e+00   2.12012081e+00]
   [  9.74889883e+00  -1.19145227e+00   1.55594258e+00]
   [  9.72785672e+00   1.26089516e+00  -1.29083734e-01]
   [  7.93496588e+00  -6.56691273e-01   4.05123557e+00]
   [  7.62105466e+00   1.36621569e+00   6.38779115e+00]
   [  9.88033048e+00  -6.54111528e-01   6.05044120e+00]
   [  9.75839850e+00   1.21386431e+00   4.26842962e+00]
   [  7.81207721e+00  -6.21465481e-01   8.09265819e+00]
   [  7.82250901e+00   1.17092296e+00   1.00580471e+01]
   [  9.99256482e+00  -7.04426705e-01   9.92631673e+00]
   [  9.79882872e+00   1.51155846e+00   8.14549541e+00]
   [  7.79442867e+00   3.43229977e+00   2.04770800e-02]
   [  7.61820289e+00   5.52364271e+00   1.85063981e+00]
   [  9.67959354e+00   3.45845150e+00   1.95226490e+00]
   [  9.81047113e+00   5.53039805e+00  -1.17800119e-02]
   [  7.68699548e+00   3.60253150e+00   4.32547836e+00]
   [  8.08201019e+00   5.77230237e+00   6.09066837e+00]
   [  9.68227975e+00   3.41731266e+00   5.94582400e+00]
   [  9.76989510e+00   5.65279689e+00   3.89865250e+00]
   [  8.03978010e+00   3.56674316e+00   8.18669322e+00]
   [  7.74500599e+00   5.24057521e+00   1.02896606e+01]
   [  9.65717955e+00   3.52020877e+00   1.00797121e+01]
   [  9.86048396e+00   5.62076188e+00   8.04752698e+00]
   [  7.87247538e+00   7.33585600e+00  -4.15129030e-01]
   [  7.54773416e+00   9.25302243e+00   1.80327830e+00]
   [  9.73729606e+00   7.73019755e+00   1.83128029e+00]
   [  9.69599141e+00   9.35455143e+00  -3.19634819e-01]
   [  7.96748192e+00   7.43576635e+00   3.88920347e+00]
   [  7.85548181e+00   9.40353265e+00   6.13241480e+00]
   [  9.88921030e+00   7.64907149e+00   6.11591151e+00]
   [  9.77373658e+00   9.28473772e+00   3.83252309e+00]
   [  7.61291574e+00   7.62759330e+00   8.03049720e+00]
   [  7.62930768e+00   9.66461528e+00   9.96645765e+00]
   [  9.64724245e+00   7.34756063e+00   9.91235165e+00]
   [  9.79362368e+00   9.34807755e+00   8.42652778e+00]]
  --- get_positions()
  [[ -3.98492678e-01  -4.08087682e-01  -9.96224456e-02]
   [ -6.65368939e-01   1.58496554e+00   2.03522790e+00]
   [  1.92614018e+00  -3.11957370e-01   1.76343425e+00]
   [  1.52233776e+00   1.91464834e+00  -3.81360448e-02]
   [ -3.76353681e-01  -6.17827119e-01   3.77766972e+00]
   [ -2.45451179e-01   1.25231869e+00   6.24846035e+00]
   [  1.80889924e+00  -7.91801346e-01   5.75907473e+00]
   [  1.68380145e+00   1.37330395e+00   4.08461856e+00]
   [ -1.26526489e-01  -7.08629922e-01   7.70665956e+00]
   [ -3.89087231e-01   1.40456726e+00   1.01351670e+01]
   [  1.32422427e+00  -8.78220250e-01   1.01126269e+01]
   [  1.80092503e+00   1.39130444e+00   8.07978827e+00]
   [ -5.64223959e-01   3.61639696e+00   1.13072941e-01]
   [ -3.41095178e-01   5.58650101e+00   1.98623098e+00]
   [  1.65039013e+00   3.32016212e+00   2.26021096e+00]
   [  1.62155452e+00   5.30820706e+00   2.11500325e-01]
   [ -3.31552511e-01   3.45137271e+00   4.02597028e+00]
   [ -3.66363775e-01   5.32917347e+00   6.11612712e+00]
   [  1.77097260e+00   3.35359965e+00   6.46908248e+00]
   [  1.51900009e+00   5.66211394e+00   4.05522922e+00]
   [ -5.80112967e-01   3.55931330e+00   8.17398089e+00]
   [ -3.06136884e-02   5.38635282e+00   1.02275746e+01]
   [  1.57245343e+00   3.41651378e+00   9.93689082e+00]
   [  1.89171841e+00   5.56704688e+00   8.30968863e+00]
   [ -2.21480182e-01   7.57939520e+00  -5.93704753e-02]
   [ -4.03733841e-01   9.47990245e+00   1.94076582e+00]
   [  1.61394213e+00   7.40802885e+00   1.91615268e+00]
   [  1.86595922e+00   9.50775061e+00   3.80589904e-02]
   [ -3.80576212e-01   7.66968473e+00   3.87668989e+00]
   [ -5.69026443e-01   9.42285279e+00   6.02016611e+00]
   [  1.71977733e+00   7.49245333e+00   5.65001120e+00]
   [  1.79716919e+00   9.57392097e+00   3.48303401e+00]
   [ -1.50316309e-01   7.34665345e+00   8.11038896e+00]
   [ -3.07559606e-01   9.32566549e+00   1.01998213e+01]
   [  1.85416465e+00   7.33754093e+00   1.02797059e+01]
   [  1.60098411e+00   9.23910187e+00   8.29066614e+00]
   [  3.90753284e+00  -4.20879775e-01  -3.45932872e-02]
   [  3.80580064e+00   1.70735633e+00   2.23680504e+00]
   [  5.83365713e+00  -6.50372672e-01   1.99270531e+00]
   [  5.85545370e+00   1.38172663e+00  -1.96040166e-02]
   [  3.79176689e+00  -3.26013047e-01   3.97304868e+00]
   [  3.78548089e+00   1.44729765e+00   6.20458419e+00]
   [  5.65168290e+00  -4.79335512e-01   6.12401041e+00]
   [  5.65091839e+00   1.46191490e+00   4.09724527e+00]
   [  3.62512157e+00  -6.43257778e-01   8.09228361e+00]
   [  3.72826410e+00   1.27662889e+00   1.01625413e+01]
   [  5.74349836e+00  -6.26872239e-01   1.01258525e+01]
   [  5.87676079e+00   1.47153879e+00   8.26379759e+00]
   [  3.55784533e+00   3.33242906e+00   7.45472063e-03]
   [  3.59903406e+00   5.42579427e+00   2.07917571e+00]
   [  5.86528134e+00   3.45321042e+00   2.03005466e+00]
   [  5.60779524e+00   5.51510354e+00   1.93188830e-01]
   [  3.66883631e+00   3.58554913e+00   4.42815635e+00]
   [  3.68500564e+00   5.62939806e+00   6.31691606e+00]
   [  5.81660626e+00   3.52381944e+00   6.10946149e+00]
   [  5.67012883e+00   5.55891079e+00   3.92850433e+00]
   [  3.82785340e+00   3.39895668e+00   8.45388606e+00]
   [  3.73967088e+00   5.37107184e+00   1.03417215e+01]
   [  5.83340520e+00   3.35167658e+00   1.01154841e+01]
   [  5.94306063e+00   5.47994106e+00   8.07987790e+00]
   [  3.82945580e+00   7.33704750e+00   7.68453725e-02]
   [  3.77812395e+00   9.74919852e+00   1.90927719e+00]
   [  5.71909560e+00   7.42647476e+00   2.04311554e+00]
   [  5.75733686e+00   9.49060787e+00  -1.06663117e-01]
   [  3.79297915e+00   7.53811943e+00   4.10918987e+00]
   [  3.78487991e+00   9.36692883e+00   5.89320516e+00]
   [  5.87995550e+00   7.45914140e+00   5.91458515e+00]
   [  5.96833171e+00   9.52041582e+00   4.17340117e+00]
   [  3.82883059e+00   7.66963968e+00   7.85330021e+00]
   [  3.78284165e+00   9.41580210e+00   1.01766029e+01]
   [  5.75595296e+00   7.57935642e+00   1.00621137e+01]
   [  5.53989653e+00   9.49193346e+00   7.92059396e+00]
   [  7.78777085e+00  -7.46134240e-01  -2.22978105e-01]
   [  7.76047807e+00   1.52367336e+00   2.12012081e+00]
   [  9.74889883e+00  -1.19145227e+00   1.55594258e+00]
   [  9.72785672e+00   1.26089516e+00  -1.29083734e-01]
   [  7.93496588e+00  -6.56691273e-01   4.05123557e+00]
   [  7.62105466e+00   1.36621569e+00   6.38779115e+00]
   [  9.88033048e+00  -6.54111528e-01   6.05044120e+00]
   [  9.75839850e+00   1.21386431e+00   4.26842962e+00]
   [  7.81207721e+00  -6.21465481e-01   8.09265819e+00]
   [  7.82250901e+00   1.17092296e+00   1.00580471e+01]
   [  9.99256482e+00  -7.04426705e-01   9.92631673e+00]
   [  9.79882872e+00   1.51155846e+00   8.14549541e+00]
   [  7.79442867e+00   3.43229977e+00   2.04770800e-02]
   [  7.61820289e+00   5.52364271e+00   1.85063981e+00]
   [  9.67959354e+00   3.45845150e+00   1.95226490e+00]
   [  9.81047113e+00   5.53039805e+00  -1.17800119e-02]
   [  7.68699548e+00   3.60253150e+00   4.32547836e+00]
   [  8.08201019e+00   5.77230237e+00   6.09066837e+00]
   [  9.68227975e+00   3.41731266e+00   5.94582400e+00]
   [  9.76989510e+00   5.65279689e+00   3.89865250e+00]
   [  8.03978010e+00   3.56674316e+00   8.18669322e+00]
   [  7.74500599e+00   5.24057521e+00   1.02896606e+01]
   [  9.65717955e+00   3.52020877e+00   1.00797121e+01]
   [  9.86048396e+00   5.62076188e+00   8.04752698e+00]
   [  7.87247538e+00   7.33585600e+00  -4.15129030e-01]
   [  7.54773416e+00   9.25302243e+00   1.80327830e+00]
   [  9.73729606e+00   7.73019755e+00   1.83128029e+00]
   [  9.69599141e+00   9.35455143e+00  -3.19634819e-01]
   [  7.96748192e+00   7.43576635e+00   3.88920347e+00]
   [  7.85548181e+00   9.40353265e+00   6.13241480e+00]
   [  9.88921030e+00   7.64907149e+00   6.11591151e+00]
   [  9.77373658e+00   9.28473772e+00   3.83252309e+00]
   [  7.61291574e+00   7.62759330e+00   8.03049720e+00]
   [  7.62930768e+00   9.66461528e+00   9.96645765e+00]
   [  9.64724245e+00   7.34756063e+00   9.91235165e+00]
   [  9.79362368e+00   9.34807755e+00   8.42652778e+00]]
  --- get_forces()
  [[ 0.22892154 -0.41456274  0.40354777]
   [ 0.33442756 -0.37968235 -0.06939719]
   [-0.37832989  0.06755346  0.13616561]
   [-0.26748974 -0.71186862  0.10308841]
   [ 0.04131579 -0.10302224  0.17045124]
   [-0.07259232  0.66703872 -0.56461986]
   [-0.08432065 -0.0480242   0.21321879]
   [-0.11567734  0.09293361  0.17203778]
   [-0.06426676 -0.36682936  0.83282081]
   [ 0.05802804  0.27214725 -0.3039002 ]
   [ 0.60968639  0.50444127 -0.10950088]
   [-0.2017634  -0.33756022  0.34443838]
   [ 0.18133141 -0.38234394 -0.23988576]
   [-0.26889752 -0.13375198  0.16391797]
   [-0.03957044  0.33982645 -0.1690814 ]
   [ 0.21449267 -0.07875218 -0.2942773 ]
   [-0.18424724 -0.00541966  0.20426084]
   [ 0.07132073  0.25445519 -0.16213021]
   [-0.17427888  0.40856469 -0.33928067]
   [ 0.19105847 -0.71595869 -0.30758279]
   [ 0.32143431 -0.16322855 -0.12840826]
   [-0.67527976  0.30951546 -0.04144172]
   [ 0.21985361 -0.11755798  0.11617204]
   [-0.08659679 -0.09916311 -0.39195035]
   [-0.23182556 -0.33838654  0.08643442]
   [ 0.53083485  0.04842197 -0.4033323 ]
   [ 0.34159555  0.2009216   0.07003484]
   [-0.17292164  0.03382334  0.00834344]
   [ 0.10825778 -0.34299516  0.14362393]
   [ 0.66274085  0.27563949 -0.08332353]
   [-0.30169149  0.55281221  0.86768695]
   [-0.18342438  0.09175157  0.57605505]
   [-0.24642782 -0.03123893 -0.03650125]
   [-0.10792478 -0.0629481  -0.10916315]
   [ 0.04001394  0.27440637  0.10369848]
   [ 0.33473268  0.2721702  -0.39955316]
   [-0.2433211  -0.25446262  0.11821327]
   [-0.01956225 -0.12082819 -0.37983809]
   [ 0.10825182  0.19247699  0.05979798]
   [ 0.0563102   0.15985714  0.07234288]
   [-0.04100094 -0.59974928 -0.0123671 ]
   [-0.04083294  0.06598362 -0.00560583]
   [ 0.13269326 -0.32415768 -0.04254086]
   [ 0.54121591  0.2101466   0.139861  ]
   [-0.04926772 -0.17383622  0.03361989]
   [-0.17332534  0.21892472 -0.1061978 ]
   [-0.18166131 -0.01751918 -0.27576625]
   [-0.40630948 -0.09557508 -0.10596759]
   [ 0.62743061  0.25695605 -0.02341336]
   [ 0.04845146 -0.1887169   0.16949145]
   [-0.225842    0.06707538  0.10948211]
   [ 0.25836649 -0.42634597 -0.4536744 ]
   [-0.08970468 -0.0209698  -0.34433183]
   [ 0.1349041  -0.34701284 -0.38222863]
   [-0.14040196  0.03341312  0.34935396]
   [ 0.15796267 -0.2425633   0.26614575]
   [-0.04952779  0.08914239 -0.54699332]
   [ 0.0952173   0.03505894 -0.18786207]
   [ 0.07939277  0.07756744  0.36096656]
   [-0.19514725 -0.01414554  0.08535054]
   [-0.35483078  0.47133731  0.02734019]
   [ 0.43258259 -0.34105733  0.01050649]
   [-0.17930849  0.28896942  0.05745858]
   [-0.11505644 -0.05486027  0.06475662]
   [ 0.02783919 -0.17898572 -0.58873713]
   [-0.17300439  0.59755673 -0.04966261]
   [-0.04888241 -0.13845628  0.09141721]
   [-0.19662985  0.09450413 -0.28536864]
   [-0.29109897 -0.41390004  0.53733942]
   [-0.19660719  0.21578595 -0.08685193]
   [-0.11397296 -0.3222374  -0.04391983]
   [ 0.56049229  0.42477553  0.16681359]
   [-0.06108686  0.1286679   0.3224278 ]
   [ 0.12094032 -0.28196649 -0.00292332]
   [-0.33012441  0.804282    0.66987457]
   [-0.18900617  0.31521362  0.11583179]
   [-0.26231413 -0.14866436 -0.06801825]
   [ 0.37295135  0.2116719  -0.61055625]
   [-0.25361846 -0.20452072  0.25405109]
   [ 0.05461469  0.53316423 -0.25082207]
   [ 0.00149923 -0.27800738 -0.1581645 ]
   [ 0.1098966   0.44854248  0.09409307]
   [-0.04815347  0.17881374  0.13598582]
   [ 0.07040803 -0.33371938 -0.17625625]
   [-0.01881686 -0.2040866  -0.02919286]
   [ 0.51642115  0.03465716  0.20288642]
   [-0.1844863   0.27477392  0.38150728]
   [ 0.03627966  0.13180339  0.00668023]
   [ 0.05096143 -0.08656156 -0.59214342]
   [-0.41728103 -0.39541931 -0.07647021]
   [ 0.32095011  0.00097142  0.26697166]
   [ 0.347855   -0.33851362  0.02508909]
   [-0.58349336 -0.10352412 -0.51557139]
   [-0.28056713  0.39973245 -0.3687442 ]
   [ 0.5907364  -0.21356093  0.54651238]
   [-0.09268285 -0.17705962  0.06603417]
   [-0.51359216  0.41797985  0.67997871]
   [ 0.27040993  0.29273941  0.08161858]
   [ 0.06937297 -0.63798033 -0.34631549]
   [ 0.04186678 -0.13650258 -0.36110524]
   [-0.62706844  0.11320925  0.1859929 ]
   [ 0.07112217  0.36161508 -0.11591099]
   [-0.11385197 -0.42018308  0.01282795]
   [-0.22197115  0.79918194  0.437205  ]
   [ 0.17007785 -0.18441728  0.30119314]
   [ 0.03750233 -0.38357746  0.01564046]
   [ 0.39380315 -0.20794233  0.30129756]
   [ 0.18211137  0.2319073  -0.79310226]]
  --- get_cell()
  [[ 12.15   0.     0.  ]
   [  0.    12.15   0.  ]
   [  0.     0.    12.15]]
  --- get_number_of_atoms()
  108