Example: Adding library structures

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

Location

examples/python_interface

Input files

  • adding_structures_library.py: main input file

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    from __future__ import print_function, division
import atomicrex

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 structure from the library')
structure = job.add_library_structure('Al-fcc',
                                      'fcc',
                                      {'alat': 4.032, 'type': 'Al'})
structure.modify_property('atomic-energy', -3.36, 200.0)
structure.modify_property('bulk-modulus', 80.9, 0.1)
structure.modify_property('C11', 114.0, 100.0)
structure.modify_property('C12', 61.9)
structure.modify_property('C44', 31.6)
print('')

print('Testing some ASE like method calls')
print('.positions: ', structure.positions)
print('.get_positions: ', structure.get_positions())
print('.get_cell:')
print(structure.get_cell())
print('.get_number_of_atoms: ', structure.get_number_of_atoms())
print('')

print('Computing properties.')
structure.compute_properties()
print('')

print('Printing properties.')
structure.print_properties()
print('')

print('Adding another structure from the library')
structure = job.add_library_structure('Al-bcc',
                                      'body-centered cubic',
                                      {'alat': 4.032, 'type': 'Al'})
print('')

print('Demonstrating the conversion to an ASE atoms object.')
conf = structure.get_atoms(job)
print(' cell')
print(conf.cell)
print(' atoms')
for k, atom in enumerate(conf, start=1):
    print(' {:3}'.format(k))
    print(atom)
print('')

print('Adding more structures from the library')
structure = job.add_library_structure('my-simple-cubic',
                                      'sc',
                                      {'alat': 3.0, 'type': 'Al'})
print(' id: {} (nat = {})'.format(structure.id,
                                  structure.get_number_of_atoms()))
print(structure.cell)
structure = job.add_library_structure('my-diamond',
                                      'dia',
                                      {'alat': 1.0, 'type': 'Al'})
print(' id: {} (nat = {})'.format(structure.id,
                                  structure.get_number_of_atoms()))
print(structure.cell)
structure = job.add_library_structure('my-hcp',
                                      'hcp',
                                      {'alat': 2.5,
                                       'clat': 4.0,
                                       'type': 'Al'})
print(' id: {} (nat = {})'.format(structure.id,
                                  structure.get_number_of_atoms()))
print(structure.cell)
structure = job.add_library_structure('my-omega',
                                      'omega',
                                      {'alat': 2.5,
                                       'ca_ratio': 0.69,
                                       'type': 'Al'})
print(' id: {} (nat = {})'.format(structure.id,
                                  structure.get_number_of_atoms()))
print(structure.cell)
structure = job.add_library_structure('my-L10',
                                      'L10',
                                      {'alat': 2.5,
                                       'ca_ratio': 0.69,
                                       'type_A': 'Al',
                                       'type_B': 'Al'})
print(' id: {} (nat = {})'.format(structure.id,
                                  structure.get_number_of_atoms()))
print(structure.cell)
print('')

  • main.xml: file with definition of potential

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    <?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

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    <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.

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    -- Create job object
-- Parse XML input file with input parameters and potential information.
-- Switch verbosity to "medium"
-- Adding a structure from the library

-- Testing some ASE like method calls
('.positions: ', array([[ 0.,  0.,  0.]]))
('.get_positions: ', array([[ 0.,  0.,  0.]]))
.get_cell:
[[ 0.     2.016  2.016]
 [ 2.016  0.     2.016]
 [ 2.016  2.016  0.   ]]
('.get_number_of_atoms: ', 1)

-- Computing properties.

-- Printing properties.
total-energy: -3.82797 eV
atomic-energy: -3.82797 eV/atom (target: -3.36 eV/atom) Rel. weight: 200; Abs. weight: 1; Weighted residual: 0.218993
total-volume: 16.3871 A^3
atomic-volume: 16.3871 A^3/atom
bulk-modulus: 35.5454 GPa (target: 80.9 GPa) Rel. weight: 0.1; Abs. weight: 1; Weighted residual: 2057.04
C11: 43.1185 GPa (target: 114 GPa) Rel. weight: 100; Abs. weight: 1; Weighted residual: 5024.19
C12: 31.7592 GPa (target: 61.9 GPa) Rel. weight: 1; Abs. weight: 1; Weighted residual: 908.47
C44: 25.7187 GPa (target: 31.6 GPa) Rel. weight: 1; Abs. weight: 1; Weighted residual: 34.5897

-- Adding another structure from the library

-- Demonstrating the conversion to an ASE atoms object.
--- cell
[[-2.016  2.016  2.016]
 [ 2.016 -2.016  2.016]
 [ 2.016  2.016 -2.016]]
--- atoms
  1 Atom('Al', [0.0, 0.0, 0.0], index=0)

-- Adding more structures from the library
--- id: my-simple-cubic (nat = 1)
[[ 3.  0.  0.]
 [ 0.  3.  0.]
 [ 0.  0.  3.]]
--- id: my-diamond (nat = 2)
[[ 0.   0.5  0.5]
 [ 0.5  0.   0.5]
 [ 0.5  0.5  0. ]]
--- id: my-hcp (nat = 2)
[[  2.50000000e+00  -2.22044605e-16   0.00000000e+00]
 [ -1.25000000e+00   2.16506351e+00   0.00000000e+00]
 [  0.00000000e+00   0.00000000e+00   4.00000000e+00]]
--- id: my-omega (nat = 3)
[[  2.50000000e+00  -2.22044605e-16   0.00000000e+00]
 [ -1.25000000e+00   2.16506351e+00   0.00000000e+00]
 [  0.00000000e+00   0.00000000e+00   1.72500000e+00]]
--- id: my-L10 (nat = 4)
[[ 2.5    0.     0.   ]
 [ 0.     2.5    0.   ]
 [ 0.     0.     1.725]]