surface_energy_static calculation style

Lucas M. Hale, lucas.hale@nist.gov, Materials Science and Engineering Division, NIST.

Introduction

The surface_energy_static calculation style evaluates the formation energy for a free surface by slicing an atomic system along a specific plane.

Version notes

  • 2018-07-09: Notebook added.

  • 2019-07-30: Description updated and small changes due to iprPy version.

  • 2020-05-22: Version 0.10 update - potentials now loaded from database.

  • 2020-09-22: Calculation updated to use atomman.defect.FreeSurface class. Setup and parameter definition streamlined.

Additional dependencies

Disclaimers

  • NIST disclaimers

  • Other atomic configurations at the free surface for certain planar cuts may have lower energies. The atomic relaxation will find a local minimum, which may not be the global minimum. Additionally, the material cut is planar perfect and therefore does not explore the effects of atomic roughness.

Method and Theory

First, an initial system is generated. This is accomplished by

  1. Starting with a unit cell system.

  2. Generating a transformed system by rotating the unit cell such that the new system’s box vectors correspond to crystallographic directions, and filled in with atoms to remain a perfect bulk cell when the three boundaries are periodic.

  3. All atoms are shifted by a fractional amount of the box vectors if needed.

  4. A supercell system is constructed by combining multiple replicas of the transformed system.

Two LAMMPS simulations are then performed that apply an energy/force minimization on the system, and the total energy of the system after relaxing is measured, \(E_{total}\). In the first simulation, all of the box’s directions are kept periodic (ppp), while in the second simulation two are periodic and one is non-periodic (ppm). This effectively slices the system along the boundary plane creating two free surfaces, each with surface area

\[A = \left| \vec{a_1} \times \vec{a_2} \right|,\]

where \(\vec{a_1}\) and \(\vec{a_2}\) are the two lattice vectors corresponding to the periodic in-plane directions.

The formation energy of the free surface, \(E_{f}^{surf}\), is computed in units of energy over area as

\[E_{f}^{surf} = \frac{E_{total}^{surf} - E_{total}^{0}} {2 A}.\]

The calculation method allows for the specification of which of the three box dimensions the cut is made along. If not specified, the default behavior is to make the \(\vec{c}\) vector direction non-periodic. This choice is due to the limitations of how LAMMPS defines triclinic boxes. \(\vec{c}\) vector is the only box vector that is allowed to have a component in the Cartesian z direction. Because of this, the other two box vectors are normal to the z-axis and therefore will be in the cut plane.

Demonstration

1. Setup

1.1. Library imports

Import libraries needed by the calculation. The external libraries used are:

[1]:
# Standard library imports
from pathlib import Path
import os
import shutil
import datetime

# http://www.numpy.org/
import numpy as np

# https://github.com/usnistgov/atomman
import atomman as am
import atomman.lammps as lmp
import atomman.unitconvert as uc

# https://github.com/usnistgov/iprPy
import iprPy

print('Notebook last executed on', datetime.date.today(), 'using iprPy version', iprPy.__version__)
Notebook last executed on 2020-09-22 using iprPy version 0.10.2

1.2. Default calculation setup

[2]:
# Specify calculation style
calc_style = 'surface_energy_static'

# If workingdir is already set, then do nothing (already in correct folder)
try:
    workingdir = workingdir

# Change to workingdir if not already there
except:
    workingdir = Path('calculationfiles', calc_style)
    if not workingdir.is_dir():
        workingdir.mkdir(parents=True)
    os.chdir(workingdir)

# Initialize connection to library
with open('C:/Users/lmh1/Documents/potentials_nist_gov/password.txt') as f:
    user, pswd = f.read().strip().split()
library = iprPy.Library(load=['lammps_potentials'], username=user, password=pswd)

2. Assign values for the calculation’s run parameters

2.1. Specify system-specific paths

  • lammps_command is the LAMMPS command to use (required).

  • mpi_command MPI command for running LAMMPS in parallel. A value of None will run simulations serially.

[3]:
lammps_command = 'lmp_serial'
mpi_command = None

2.2. Load interatomic potential

  • potential_name gives the name of the potential_LAMMPS reference record in the iprPy library to use for the calculation.

  • potential is an atomman.lammps.Potential object (required).

[4]:
potential_name = '1999--Mishin-Y--Ni--LAMMPS--ipr1'

# Retrieve potential and parameter file(s)
potential = library.get_lammps_potential(id=potential_name, getfiles=True)

2.3. Load initial unit cell system

  • ucell is an atomman.System representing a fundamental unit cell of the system (required). Here, this is loaded from the database for the prototype.

[5]:
# Create ucell by loading prototype record
ucell = am.load('crystal', potential=potential, family='A1--Cu--fcc', database=library)

print(ucell)
avect =  [ 3.520,  0.000,  0.000]
bvect =  [ 0.000,  3.520,  0.000]
cvect =  [ 0.000,  0.000,  3.520]
origin = [ 0.000,  0.000,  0.000]
natoms = 4
natypes = 1
symbols = ('Ni',)
pbc = [ True  True  True]
per-atom properties = ['atype', 'pos']
     id   atype  pos[0]  pos[1]  pos[2]
      0       1   0.000   0.000   0.000
      1       1   0.000   1.760   1.760
      2       1   1.760   0.000   1.760
      3       1   1.760   1.760   0.000

2.4. Specify the defect parameters

  • hkl gives the Miller (hkl) or Miller-Bravais (hkil) plane to create the free surface on.

  • cutboxvector specifies which of the three box vectors (‘a’, ‘b’, or ‘c’) is to be made non-periodic to create the free surface.

  • shiftindex can be used for complex crystals to specify different termination planes.

[6]:
hkl = [1,0,0]
cutboxvector = 'c'
shiftindex = 0

2.5. Modify system

  • sizemults list of three integers specifying how many times the ucell vectors of \(a\), \(b\) and \(c\) are replicated in creating system.

  • minwidth specifies a minimum width that the system should be along the cutboxvector direction. The given sizemult in that direction will be increased if needed to ensure that the system is at least this wide.

[7]:
sizemults = [5, 5, 10]
minwidth = uc.set_in_units(0.0, 'angstrom')

2.6. Specify calculation-specific run parameters

  • energytolerance is the energy tolerance to use during the minimizations. This is unitless.

  • forcetolerance is the force tolerance to use during the minimizations. This is in energy/length units.

  • maxiterations is the maximum number of minimization iterations to use.

  • maxevaluations is the maximum number of minimization evaluations to use.

  • maxatommotion is the largest distance that an atom is allowed to move during a minimization iteration. This is in length units.

[8]:
energytolerance = 1e-8
forcetolerance = uc.set_in_units(0.0, 'eV/angstrom')
maxiterations = 10000
maxevaluations = 100000
maxatommotion = uc.set_in_units(0.01, 'angstrom')

3. Define calculation function(s) and generate template LAMMPS script(s)

3.1. min.template

[9]:
with open('min.template', 'w') as f:
    f.write("""#LAMMPS input script that performs an energy minimization

box tilt large

<atomman_system_pair_info>

thermo_style custom step lx ly lz pxx pyy pzz pe
thermo_modify format float %.13e

compute peatom all pe/atom

min_modify dmax <dmax>

dump dumpit all custom <maxeval> atom.* id type x y z c_peatom
dump_modify dumpit format <dump_modify_format>

minimize <etol> <ftol> <maxiter> <maxeval>""")

3.2. surface_energy()

[10]:
def surface_energy(lammps_command, ucell, potential, hkl,
                   mpi_command=None, sizemults=None, minwidth=None, even=False,
                   conventional_setting='p', cutboxvector='c',
                   atomshift=None, shiftindex=None,
                   etol=0.0, ftol=0.0, maxiter=10000,
                   maxeval=100000, dmax=uc.set_in_units(0.01, 'angstrom')):
    """
    Evaluates surface formation energies by slicing along one periodic
    boundary of a bulk system.

    Parameters
    ----------
    lammps_command :str
        Command for running LAMMPS.
    ucell : atomman.System
        The crystal unit cell to use as the basis of the stacking fault
        configurations.
    potential : atomman.lammps.Potential
        The LAMMPS implemented potential to use.
    hkl : array-like object
        The Miller(-Bravais) crystal fault plane relative to ucell.
    mpi_command : str, optional
        The MPI command for running LAMMPS in parallel.  If not given, LAMMPS
        will run serially.
    sizemults : list or tuple, optional
        The three System.supersize multipliers [a_mult, b_mult, c_mult] to use on the
        rotated cell to build the final system. Note that the cutboxvector sizemult
        must be an integer and not a tuple.  Default value is [1, 1, 1].
    minwidth : float, optional
        If given, the sizemult along the cutboxvector will be selected such that the
        width of the resulting final system in that direction will be at least this
        value. If both sizemults and minwidth are given, then the larger of the two
        in the cutboxvector direction will be used.
    even : bool, optional
        A True value means that the sizemult for cutboxvector will be made an even
        number by adding 1 if it is odd.  Default value is False.
    conventional_setting : str, optional
        Allows for rotations of a primitive unit cell to be determined from
        (hkl) indices specified relative to a conventional unit cell.  Allowed
        settings: 'p' for primitive (no conversion), 'f' for face-centered,
        'i' for body-centered, and 'a', 'b', or 'c' for side-centered.  Default
        behavior is to perform no conversion, i.e. take (hkl) relative to the
        given ucell.
    cutboxvector : str, optional
        Indicates which of the three system box vectors, 'a', 'b', or 'c', to
        cut with a non-periodic boundary (default is 'c').
    atomshift : array-like object, optional
        A Cartesian vector shift to apply to all atoms.  Can be used to shift
        atoms perpendicular to the fault plane to allow different termination
        planes to be cut.  Cannot be given with shiftindex.
    shiftindex : int, optional
        Allows for selection of different termination planes based on the
        preferred shift values determined by the underlying fault generation.
        Cannot be given with atomshift. If neither atomshift nor shiftindex
        given, then shiftindex will be set to 0.
    etol : float, optional
        The energy tolerance for the structure minimization. This value is
        unitless. (Default is 0.0).
    ftol : float, optional
        The force tolerance for the structure minimization. This value is in
        units of force. (Default is 0.0).
    maxiter : int, optional
        The maximum number of minimization iterations to use (default is
        10000).
    maxeval : int, optional
        The maximum number of minimization evaluations to use (default is
        100000).
    dmax : float, optional
        The maximum distance in length units that any atom is allowed to relax
        in any direction during a single minimization iteration (default is
        0.01 Angstroms).

    Returns
    -------
    dict
        Dictionary of results consisting of keys:

        - **'dumpfile_base'** (*str*) - The filename of the LAMMPS dump file
          of the relaxed bulk system.
        - **'dumpfile_surf'** (*str*) - The filename of the LAMMPS dump file
          of the relaxed system containing the free surfaces.
        - **'E_total_base'** (*float*) - The total potential energy of the
          relaxed bulk system.
        - **'E_total_surf'** (*float*) - The total potential energy of the
          relaxed system containing the free surfaces.
        - **'A_surf'** (*float*) - The area of the free surface.
        - **'E_coh'** (*float*) - The cohesive energy of the relaxed bulk
          system.
        - **'E_surf_f'** (*float*) - The computed surface formation energy.

    Raises
    ------
    ValueError
        For invalid cutboxvectors
    """
    # Construct free surface configuration generator
    surf_gen = am.defect.FreeSurface(hkl, ucell, cutboxvector=cutboxvector,
                                     conventional_setting=conventional_setting)

    # Check shift parameters
    if shiftindex is not None:
        assert atomshift is None, 'shiftindex and atomshift cannot both be given'
        atomshift = surf_gen.shifts[shiftindex]
    elif atomshift is None:
        atomshift = surf_gen.shifts[0]

    # Generate the free surface configuration
    system = surf_gen.surface(shift=atomshift, minwidth=minwidth,
                                  sizemults=sizemults, even=even)
    A_surf= surf_gen.surfacearea

    # Identify lammps_date version
    lammps_date = lmp.checkversion(lammps_command)['date']

    # Evaluate system with free surface
    surf_results = relax_system(lammps_command, system, potential,
                                mpi_command=mpi_command, etol=etol, ftol=ftol,
                                maxiter=maxiter, maxeval=maxeval, dmax=dmax,
                                lammps_date=lammps_date)

    # Extract results from system with free surface
    dumpfile_surf = 'surface.dump'
    shutil.move(surf_results['finaldumpfile'], dumpfile_surf)
    shutil.move('log.lammps', 'surface-log.lammps')
    E_total_surf = surf_results['potentialenergy']

    # Evaluate perfect system (all pbc removes cut)
    system.pbc = [True, True, True]
    perf_results = relax_system(lammps_command, system, potential,
                                mpi_command=mpi_command, etol=etol, ftol=ftol,
                                maxiter=maxiter, maxeval=maxeval, dmax=dmax,
                                lammps_date=lammps_date)

    # Extract results from perfect system
    dumpfile_base = 'perfect.dump'
    shutil.move(perf_results['finaldumpfile'], dumpfile_base)
    shutil.move('log.lammps', 'perfect-log.lammps')
    E_total_base = perf_results['potentialenergy']

    # Compute the free surface formation energy
    E_surf_f = (E_total_surf - E_total_base) / (2 * A_surf)

    # Save values to results dictionary
    results_dict = {}

    results_dict['dumpfile_base'] = dumpfile_base
    results_dict['dumpfile_surf'] = dumpfile_surf
    results_dict['E_total_base'] = E_total_base
    results_dict['E_total_surf'] = E_total_surf
    results_dict['A_surf'] = A_surf
    results_dict['E_coh'] = E_total_base / system.natoms
    results_dict['E_surf_f'] = E_surf_f

    return results_dict

3.3. relax_system()

[11]:
def relax_system(lammps_command, system, potential,
                 mpi_command=None, etol=0.0, ftol=0.0, maxiter=10000,
                 maxeval=100000, dmax=uc.set_in_units(0.01, 'angstrom'),
                 lammps_date=None):
    """
    Sets up and runs the min.in LAMMPS script for performing an energy/force
    minimization to relax a system.

    Parameters
    ----------
    lammps_command :str
        Command for running LAMMPS.
    system : atomman.System
        The system to perform the calculation on.
    potential : atomman.lammps.Potential
        The LAMMPS implemented potential to use.
    mpi_command : str, optional
        The MPI command for running LAMMPS in parallel.  If not given, LAMMPS
        will run serially.
    etol : float, optional
        The energy tolerance for the structure minimization. This value is
        unitless. (Default is 0.0).
    ftol : float, optional
        The force tolerance for the structure minimization. This value is in
        units of force. (Default is 0.0).
    maxiter : int, optional
        The maximum number of minimization iterations to use (default is
        10000).
    maxeval : int, optional
        The maximum number of minimization evaluations to use (default is
        100000).
    dmax : float, optional
        The maximum distance in length units that any atom is allowed to relax
        in any direction during a single minimization iteration (default is
        0.01 Angstroms).
    lammps_date : datetime.date or None, optional
        The date version of the LAMMPS executable.  If None, will be identified
        from the lammps_command (default is None).

    Returns
    -------
    dict
        Dictionary of results consisting of keys:

        - **'logfile'** (*str*) - The name of the LAMMPS log file.
        - **'initialdatafile'** (*str*) - The name of the LAMMPS data file
          used to import an inital configuration.
        - **'initialdumpfile'** (*str*) - The name of the LAMMPS dump file
          corresponding to the inital configuration.
        - **'finaldumpfile'** (*str*) - The name of the LAMMPS dump file
          corresponding to the relaxed configuration.
        - **'potentialenergy'** (*float*) - The total potential energy of
          the relaxed system.
    """
    # Build filedict if function was called from iprPy
    try:
        assert __name__ == pkg_name
        calc = iprPy.load_calculation(calculation_style)
        filedict = calc.filedict
    except:
        filedict = {}

    # Ensure all atoms are within the system's box
    system.wrap()

    # Get lammps units
    lammps_units = lmp.style.unit(potential.units)

    #Get lammps version date
    if lammps_date is None:
        lammps_date = lmp.checkversion(lammps_command)['date']

    # Define lammps variables
    lammps_variables = {}
    system_info = system.dump('atom_data', f='system.dat',
                              potential=potential,
                              return_pair_info=True)
    lammps_variables['atomman_system_pair_info'] = system_info
    lammps_variables['etol'] = etol
    lammps_variables['ftol'] = uc.get_in_units(ftol, lammps_units['force'])
    lammps_variables['maxiter'] = maxiter
    lammps_variables['maxeval'] = maxeval
    lammps_variables['dmax'] = uc.get_in_units(dmax, lammps_units['length'])

    # Set dump_modify format based on dump_modify_version
    if lammps_date < datetime.date(2016, 8, 3):
        lammps_variables['dump_modify_format'] = '"%i %i %.13e %.13e %.13e %.13e"'
    else:
        lammps_variables['dump_modify_format'] = 'float %.13e'

    # Write lammps input script
    template_file = 'min.template'
    lammps_script = 'min.in'
    template = iprPy.tools.read_calc_file(template_file, filedict)
    with open(lammps_script, 'w') as f:
        f.write(iprPy.tools.filltemplate(template, lammps_variables,
                                         '<', '>'))

    # Run LAMMPS
    output = lmp.run(lammps_command, lammps_script, mpi_command)

    # Extract output values
    thermo = output.simulations[-1]['thermo']
    results = {}
    results['logfile'] = 'log.lammps'
    results['initialdatafile'] = 'system.dat'
    results['initialdumpfile'] = 'atom.0'
    results['finaldumpfile'] = 'atom.%i' % thermo.Step.values[-1]
    results['potentialenergy'] = uc.set_in_units(thermo.PotEng.values[-1],
                                                 lammps_units['energy'])

    return results

4. Run calculation function(s)

[12]:
results_dict = surface_energy(lammps_command, ucell, potential, hkl,
                              mpi_command = mpi_command,
                              sizemults = sizemults,
                              minwidth = minwidth,
                              cutboxvector = cutboxvector,
                              shiftindex = shiftindex,
                              etol = energytolerance,
                              ftol = forcetolerance,
                              maxiter = maxiterations,
                              maxeval = maxevaluations,
                              dmax = maxatommotion)
[13]:
results_dict.keys()
[13]:
dict_keys(['dumpfile_base', 'dumpfile_surf', 'E_total_base', 'E_total_surf', 'A_surf', 'E_coh', 'E_surf_f'])

5. Report results

5.1. Define units for outputting values

  • area_unit is the unit of area to display surface area in.

  • energy_unit is the unit of energy to display cohesive energies in.

  • energy_area_unit is the energy per area to report the surface energy in.

[14]:
area_unit = 'nm^2'
energy_unit = 'eV'

energy_area_unit = 'mJ/m^2'

5.2. Print \(E_{coh}\), \(A_{surface}\), and \(E_{surface}^f\)

[15]:
print('E_coh =  ', uc.get_in_units(results_dict['E_coh'], energy_unit), energy_unit)
print('A_surface =', uc.get_in_units(results_dict['A_surf'], area_unit), area_unit)
print('E_surface_f =', uc.get_in_units(results_dict['E_surf_f'], energy_area_unit), energy_area_unit)
E_coh =   -4.4499999983449 eV
A_surface = 3.0975990100882553 nm^2
E_surface_f = 1877.9483735323636 mJ/m^2