8.5.6. Adiabatic core/shell model — LAMMPS documentation

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# 8.5.6. Adiabatic core/shell model

The adiabatic core-shell model by Mitchell and Fincham is a simple method for adding polarizability to a system. In order to mimic the electron shell of an ion, a satellite particle is attached to it. This way the ions are split into a core and a shell where the latter is meant to react to the electrostatic environment inducing polarizability. See the Howto polarizable page for a discussion of all the polarizable models available in LAMMPS.

Technically, shells are attached to the cores by a spring force f = k*r where k is a parameterized spring constant and r is the distance between the core and the shell. The charges of the core and the shell add up to the ion charge, thus q(ion) = q(core) + q(shell). This setup introduces the ion polarizability (alpha) given by alpha = q(shell)^2 / k. In a similar fashion the mass of the ion is distributed on the core and the shell with the core having the larger mass.

To run this model in LAMMPS, atom_style full can be used since atom charge and bonds are needed. Each kind of core/shell pair requires two atom types and a bond type. The core and shell of a core/shell pair should be bonded to each other with a harmonic bond that provides the spring force. For example, a data file for NaCl, as found in examples/coreshell, has this format:

    432   atoms  # core and shell atoms
    216   bonds  # number of core/shell springs

    4     atom types  # 2 cores and 2 shells for Na and Cl
    2     bond types

    0.0 24.09597 xlo xhi
    0.0 24.09597 ylo yhi
    0.0 24.09597 zlo zhi

    Masses       # core/shell mass ratio = 0.1

    1 20.690784  # Na core
    2 31.90500   # Cl core
    3 2.298976   # Na shell
    4 3.54500    # Cl shell

    Atoms

    1    1    2   1.5005    0.00000000   0.00000000   0.00000000 # core of core/shell pair 1
    2    1    4  -2.5005    0.00000000   0.00000000   0.00000000 # shell of core/shell pair 1
    3    2    1   1.5056    4.01599500   4.01599500   4.01599500 # core of core/shell pair 2
    4    2    3  -0.5056    4.01599500   4.01599500   4.01599500 # shell of core/shell pair 2
    (...)

    Bonds   # Bond topology for spring forces

    1     2     1     2   # spring for core/shell pair 1
    2     2     3     4   # spring for core/shell pair 2
    (...)

Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only defined between the shells. Coulombic interactions are defined between all cores and shells. If desired, additional bonds can be specified between cores.

The special_bonds command should be used to turn-off the Coulombic interaction within core/shell pairs, since that interaction is set by the bond spring. This is done using the special_bonds command with a 1-2 weight = 0.0, which is the default value. It needs to be considered whether one has to adjust the special_bonds weighting according to the molecular topology since the interactions of the shells are bypassed over an extra bond.

Note that this core/shell implementation does not require all ions to be polarized. One can mix core/shell pairs and ions without a satellite particle if desired.

Since the core/shell model permits distances of r = 0.0 between the core and shell, a pair style with a “cs” suffix needs to be used to implement a valid long-range Coulombic correction. Several such pair styles are provided in the CORESHELL package. See this page for details. All of the core/shell enabled pair styles require the use of a long-range Coulombic solver, as specified by the kspace_style command. Either the PPPM or Ewald solvers can be used.

For the NaCL example problem, these pair style and bond style settings are used:

    pair_style      born/coul/long/cs 20.0 20.0
    pair_coeff      * *      0.0 1.000   0.00  0.00   0.00
    pair_coeff      3 3    487.0 0.23768 0.00  1.05   0.50 #Na-Na
    pair_coeff      3 4 145134.0 0.23768 0.00  6.99   8.70 #Na-Cl
    pair_coeff      4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl

    bond_style      harmonic
    bond_coeff      1 63.014 0.0
    bond_coeff      2 25.724 0.0

When running dynamics with the adiabatic core/shell model, the following issues should be considered. The relative motion of the core and shell particles corresponds to the polarization, hereby an instantaneous relaxation of the shells is approximated and a fast core/shell spring frequency ensures a nearly constant internal kinetic energy during the simulation. Thermostats can alter this polarization behavior, by scaling the internal kinetic energy, meaning the shell will not react freely to its electrostatic environment. Therefore it is typically desirable to decouple the relative motion of the core/shell pair, which is an imaginary degree of freedom, from the real physical system. To do that, the compute temp/cs command can be used, in conjunction with any of the thermostat fixes, such as fix nvt or fix langevin. This compute uses the center-of-mass velocity of the core/shell pairs to calculate a temperature, and ensures that velocity is what is rescaled for thermostatting purposes. This compute also works for a system with both core/shell pairs and non-polarized ions (ions without an attached satellite particle). The compute temp/cs command requires input of two groups, one for the core atoms, another for the shell atoms. Non-polarized ions which might also be included in the treated system should not be included into either of these groups, they are taken into account by the group-ID (second argument) of the compute. The groups can be defined using the group *type* command. Note that to perform thermostatting using this definition of temperature, the fix modify temp command should be used to assign the compute to the thermostat fix. Likewise the thermo_modify temp command can be used to make this temperature be output for the overall system.

For the NaCl example, this can be done as follows:

    group cores type 1 2
    group shells type 3 4
    compute CSequ all temp/cs cores shells
    fix thermoberendsen all temp/berendsen 1427 1427 0.4    # thermostat for the true physical system
    fix thermostatequ all nve                               # integrator as needed for the berendsen thermostat
    fix_modify thermoberendsen temp CSequ
    thermo_modify temp CSequ                                # output of center-of-mass derived temperature

The pressure for the core/shell system is computed via the regular LAMMPS convention by treating the cores and shells as individual particles. For the thermo output of the pressure as well as for the application of a barostat, it is necessary to use an additional pressure compute based on the default temperature and specifying it as a second argument in fix modify and thermo_modify resulting in:

    (...)
    compute CSequ all temp/cs cores shells
    compute thermo_press_lmp all pressure thermo_temp       # pressure for individual particles
    thermo_modify temp CSequ press thermo_press_lmp         # modify thermo to regular pressure
    fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4
    fix_modify press_bar temp CSequ press thermo_press_lmp  # pressure modification for correct kinetic scalar

If compute temp/cs is used, the decoupled relative motion of the core and the shell should in theory be stable. However numerical fluctuation can introduce a small momentum to the system, which is noticeable over long trajectories. Therefore it is recommendable to use the fix momentum command in combination with compute temp/cs when equilibrating the system to prevent any drift.

When initializing the velocities of a system with core/shell pairs, it is also desirable to not introduce energy into the relative motion of the core/shell particles, but only assign a center-of-mass velocity to the pairs. This can be done by using the bias keyword of the velocity create command and assigning the compute temp/cs command to the temp keyword of the velocity command, e.g.

    velocity all create 1427 134 bias yes temp CSequ
    velocity all scale 1427 temp CSequ

To maintain the correct polarizability of the core/shell pairs, the kinetic energy of the internal motion shall remain nearly constant. Therefore the choice of spring force and mass ratio need to ensure much faster relative motion of the two atoms within the core/shell pair than their center-of-mass velocity. This allows the shells to effectively react instantaneously to the electrostatic environment and limits energy transfer to or from the core/shell oscillators. This fast movement also dictates the timestep that can be used.

The primary literature of the adiabatic core/shell model suggests that the fast relative motion of the core/shell pairs only allows negligible energy transfer to the environment. The mentioned energy transfer will typically lead to a small drift in total energy over time. This internal energy can be monitored using the compute chunk/atom and compute temp/chunk commands. The internal kinetic energies of each core/shell pair can then be summed using the sum() special function of the variable command. Or they can be time/averaged and output using the fix ave/time command. To use these commands, each core/shell pair must be defined as a “chunk”. If each core/shell pair is defined as its own molecule, the molecule ID can be used to define the chunks. If cores are bonded to each other to form larger molecules, the chunks can be identified by the fix property/atom via assigning a core/shell ID to each atom using a special field in the data file read by the read_data command. This field can then be accessed by the compute property/atom command, to use as input to the compute chunk/atom command to define the core/shell pairs as chunks.

For example if core/shell pairs are the only molecules:

    read_data NaCl_CS_x0.1_prop.data
    compute prop all property/atom molecule
    compute cs_chunk all chunk/atom c_prop
    compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0     # note the chosen degrees of freedom for the core/shell pairs
    fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector

For example if core/shell pairs and other molecules are present:

    fix csinfo all property/atom i_CSID                       # property/atom command
    read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info  # atom property added in the data-file
    compute prop all property/atom i_CSID
    (...)

The additional section in the date file would be formatted like this:

    CS-Info         # header of additional section

    1   1           # column 1 = atom ID, column 2 = core/shell ID
    2   1
    3   2
    4   2
    5   3
    6   3
    7   4
    8   4
    (...)

(Mitchell and Fincham) Mitchell, Fincham, J Phys Condensed Matter, 5, 1031-1038 (1993).

(Fincham) Fincham, Mackrodt and Mitchell, J Phys Condensed Matter, 6, 393-404 (1994).