fix electrode/conp command — LAMMPS documentation

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# fix electrode/conp command

Accelerator Variant: electrode/conp/intel

# fix electrode/conq command

Accelerator Variant: electrode/conq/intel

# fix electrode/thermo command

Accelerator Variant: electrode/thermo/intel

## Syntax

    fix ID group-ID style args keyword value ...

- ID, group-ID are documented in fix command

- style = electrode/conp or electrode/conq or electrode/thermo

- args = arguments used by a particular style

      electrode/conp args = potential eta
      electrode/conq args = charge eta
      electrode/thermo args = potential eta temp values
           potential = electrode potential
           charge = electrode charge
           eta = reciprocal width of electrode charge smearing (can be NULL if eta keyword is used)
           temp values = T_v tau_v rng_v
               T_v = temperature of thermo-potentiostat
               tau_v = time constant of thermo-potentiostat
               rng_v = integer used to initialize random number generator

- zero or more keyword/value pairs may be appended

- keyword = algo or symm or couple or etypes or ffield or write_mat or write_inv or read_mat or read_inv or qtotal or eta

    algo values = mat_inv or mat_cg tol or cg tol
        specify the algorithm used to compute the electrode charges
    symm value = on or off
        turn on/off charge neutrality constraint for the electrodes
    couple values = group-ID val
        group-ID = group of atoms treated as additional electrode
        val = electric potential or charge on this electrode
    etypes value = on or off
        turn on/off type-based optimized neighbor lists (electrode and electrolyte types may not overlap)
    ffield value = on or off
        turn on/off finite-field implementation
    write_mat value = filename
        filename = file to which to write elastance matrix
    write_inv value = filename
        filename = file to which to write inverted matrix
    read_mat value = filename
        filename = file from which to read elastance matrix
    read_inv value = filename
        filename = file from which to read inverted matrix
    qtotal value = number or v_ equal-style variable
        add overall potential so that all electrode charges add up to qtotal
    eta value = d_propname
        d_propname = a custom double vector defined via fix property/atom

## Examples

    fix fxconp bot electrode/conp -1.0 1.805 couple top 1.0 couple ref 0.0 write_inv inv.csv symm on
    fix fxconp electrodes electrode/conq 0.0 1.805 algo cg 1e-5
    fix fxconp bot electrode/thermo -1.0 1.805 temp 298 100 couple top 1.0

## Description

The electrode fixes implement the constant potential method (CPM) (Siepmann, Reed), and modern variants, to accurately model electrified, conductive electrodes. This is primarily useful for studying electrode-electrolyte interfaces, especially at high potential differences or ionicities, with non-planar electrodes such as nanostructures or nanopores, and to study dynamic phenomena such as charging or discharging time scales or conductivity or ionic diffusivities.

Each electrode fix allows users to set additional electrostatic relationships between the specified groups which model useful electrostatic configurations:

- electrode/conp sets potentials or potential differences between electrodes

  - (resulting in changing electrode total charges)

- electrode/conq sets the total charge on each electrode

  - (resulting in changing electrode potentials)

- electrode/thermo sets a thermopotentiostat (Deissenbeck) between two electrodes

  - (resulting in changing charges and potentials with appropriate average potential difference and thermal variance)

The first group-ID provided to each fix specifies the first electrode group, and more group(s) are added using the couple keyword for each additional group. While electrode/thermo only accepts two groups, electrode/conp and electrode/conq accept any number of groups, up to LAMMPS’s internal restrictions (see Restrictions below). Electrode groups must not overlap, i.e. the fix will issue an error if any particle is detected to belong to at least two electrode groups.

CPM involves updating charges on groups of electrode particles, per time step, so that the system’s total energy is minimized with respect to those charges. From basic electrostatics, this is equivalent to making each group conductive, or imposing an equal electrostatic potential on every particle in the same group (hence the name CPM). The charges are usually modelled as a Gaussian distribution to make the charge-charge interaction matrix invertible (Gingrich). The keyword eta specifies the distribution’s width in units of inverse length.

Added in version 22Dec2022.

Three algorithms are available to minimize the energy, varying in how matrices are pre-calculated before a run to provide computational speedup. These algorithms can be selected using the keyword algo:

- algo mat_inv pre-calculates the capacitance matrix and obtains the charge configuration in one matrix-vector calculation per time step

- algo mat_cg pre-calculates the elastance matrix (inverse of capacitance matrix) and obtains the charge configuration using a conjugate gradient solver in multiple matrix-vector calculations per time step

- algo cg does not perform any pre-calculation and obtains the charge configuration using a conjugate gradient solver and multiple calculations of the electric potential per time step.

For both cg methods, the command must specify the conjugate gradient tolerance. fix electrode/thermo currently only supports the mat_inv algorithm.

The keyword symm can be set on (or off) to turn on (or turn off) the capacitance matrix constraint that sets total electrode charge to be zero. This has slightly different effects for each fix electrode variant. For fix electrode/conp, with symm off, the potentials specified are absolute potentials, but the charge configurations satisfying them may add up to an overall non-zero, varying charge for the electrodes (and thus the simulation box). With symm on, the total charge over all electrode groups is constrained to zero, and potential differences rather than absolute potentials are the physically relevant quantities.

For fix electrode/conq, with symm off, overall neutrality is explicitly obeyed or violated by the user input (which is not checked!). With symm on, overall neutrality is ensured by ignoring the user-input charge for the last listed electrode (instead, its charge will always be minus the total sum of all other electrode charges). For fix electrode/thermo, overall neutrality is always automatically imposed for any setting of symm, but symm on allows finite-field mode (ffield on, described below) for faster simulations.

For all three fixes, any potential (or charge for conq) can be specified as an equal-style variable prefixed with “v_”. For example, the following code will ramp the potential difference between electrodes from 0.0V to 2.0V over the course of the simulation:

    fix fxconp bot electrode/conp 0.0 1.805 couple top v_v symm on
    variable v equal ramp(0.0, 2.0)

Note that these fixes only parse their supplied variable name when starting a run, and so these fixes will accept equal-style variables defined after the fix definition, including variables dependent on the fix’s own output. This is useful, for example, in the fix’s internal finite-field commands (see below). For an advanced example of this see the in.conq2 input file in the directory `examples/PACKAGES/electrode/graph-il`.

This fix necessitates the use of a long range solver that calculates and provides the matrix of electrode-electrode interactions and a vector of electrode-electrolyte interactions. The Kspace styles ewald/electrode, pppm/electrode and pppm/electrode/intel are created specifically for this task (Ahrens-Iwers).

For systems with non-periodic boundaries in one or two directions dipole corrections are available with the kspace_modify. For ewald/electrode a two-dimensional Ewald summation (Hu) can be used by setting “slab ew2d”:

    kspace_modify slab <slab_factor>
    kspace_modify wire <wire_factor>
    kspace_modify slab ew2d

Two implementations for the calculation of the elastance matrix are available with pppm and can be selected using the amat onestep/twostep keyword. onestep is the default; twostep can be faster for large electrodes and a moderate mesh size but requires more memory.

    kspace_modify amat onestep/twostep

For all versions of the fix, the keyword-value ffield on enables the finite-field mode (Dufils, Tee), which uses an electric field across a periodic cell instead of non-periodic boundary conditions to impose a potential difference between the two electrodes bounding the cell. The fix (with name fix-ID) detects which of the two electrodes is “on top” (has the larger maximum z-coordinate among all particles). Assuming the first electrode group is on top, it then issues the following commands internally:

    variable fix-ID_ffield_zfield equal (f_fix-ID[2]-f_fix-ID[1])/lz
    efield fix-ID_efield all efield 0.0 0.0 v_fix-ID_ffield_zfield

which implements the required electric field as the potential difference divided by cell length. The internal commands use variable so that the electric field will correctly vary with changing potentials in the correct way (for example with equal-style potential difference or with fix electrode/conq). This keyword requires two electrodes and will issue an error with any other number of electrodes. This keyword requires electroneutrality to be imposed (symm on) and will issue an error otherwise.

Changed in version 22Dec2022.

For all versions of the fix, the keyword-value etypes on enables type-based optimized neighbor lists. With this feature enabled, LAMMPS provides the fix with an occasional neighbor list restricted to electrode-electrode interactions for calculating the electrode matrix, and a perpetual neighbor list restricted to electrode-electrolyte interactions for calculating the electrode potentials, using particle types to list only desired interactions, and typically resulting in 5–10% less computational time. Without this feature the fix will simply use the active pair style’s neighbor list. This feature cannot be enabled if any electrode particle has the same type as any electrolyte particle (which would be unusual in a typical simulation) and the fix will issue an error in that case.

Added in version 17Apr2024.

The keyword qtotal causes fix electrode/conp and fix electrode/thermo to add an overall potential to all electrodes so that the total charge on the electrodes is a specified amount (which may be an equal-style variable). For example, if a user wanted to simulate a solution of excess cations such that the total electrolyte charge is +2, setting qtotal -2 would cause the total electrode charge to be -2, so that the simulation box remains overall electroneutral. Since fix electrode/conq constrains the total charges of individual electrodes, and since symm on constrains the total charge of all electrodes to be zero, either option is incompatible with the qtotal keyword (even if qtotal is set to zero).

Added in version 17Apr2024.

The keyword eta takes the name of a custom double vector defined via fix property/atom. The values will be used instead of the standard eta value. The property/atom fix must be for vector of double values and use the ghost on option.

## Restart, fix_modify, output, run start/stop, minimize info

This fix currently does not write any information to restart files.

The fix_modify tf option enables the Thomas-Fermi metallicity model (Scalfi) and allows parameters to be set for each atom type.

    fix_modify ID tf type length voronoi

If this option is used, these two parameters must be set for all atom types of the electrode:

- tf is the Thomas-Fermi length \(l_{TF}\)

- voronoi is the Voronoi volume per atom in units of length cubed

Different types may have different tf and voronoi values. The following self-energy term is then added for all electrode atoms:

\[A_{ii} += \frac{1}{4 \pi \epsilon_0} \times \frac{4 \pi l_{TF}^2}{\mathrm{Voronoi volume}}\]

The fix_modify timer option turns on (off) additional timer outputs in the log file, for code developers to track optimization.

    fix_modify ID timer on/off

These fixes compute a global (extensive) scalar, a global (intensive) vector, and a global array, which can be accessed by various output commands.

The global scalar outputs the energy added to the system by this fix, which is the negative of the total charge on each electrode multiplied by that electrode’s potential.

The global vector outputs the potential on each electrode (and thus has N entries if the fix manages N electrode groups), in units of electric field multiplied by distance (thus volts for real and metal units). The electrode groups’ ordering follows the order in which they were input in the fix command using couple. The global vector output is useful for fix electrode/conq and fix electrode/thermo, where potential is dynamically updated based on electrolyte configuration instead of being directly set.

The global array has N rows and 2N+1 columns, where the fix manages N electrode groups managed by the fix. For the I-th row of the array, the elements are:

- array[I][1] = total charge that group I would have had if it were at 0 V applied potential

- array[I][2 to N + 1] = the N entries of the I-th row of the electrode capacitance matrix (definition follows)

- array[I][N + 2 to 2N + 1] = the N entries of the I-th row of the electrode elastance matrix (the inverse of the electrode capacitance matrix)

The \(N \times N\) electrode capacitance matrix, denoted \(\mathbf{C}\) in the following equation, summarizes how the total charge induced on each electrode (\(\mathbf{Q}\) as an N-vector) is related to the potential on each electrode, \(\mathbf{V}\), and the charge-at-0V \(\mathbf{Q}_{0V}\) (which is influenced by the local electrolyte structure):

\[\mathbf{Q} = \mathbf{Q}_{0V} + \mathbf{C} \cdot \mathbf{V}\]

The charge-at-0V, electrode capacitance and elastance matrices are internally used to calculate the potentials required to induce the specified total electrode charges in fix electrode/conq and fix electrode/thermo. With the symm on option, the electrode capacitance matrix would be singular, and thus its last row is replaced with N copies of its top-left entry (\(\mathbf{C}_{11}\)) for invertibility.

The global array output is mainly useful for quickly determining the ‘vacuum capacitance’ of the system (capacitance with only electrodes, no electrolyte), and can also be used for advanced simulations setting the potential as some function of the charge-at-0V (such as the `in.conq2` example mentioned above).

Please cite (Ahrens-Iwers2022) in any publication that uses this implementation. Please cite also the publication on the combination of the CPM with PPPM if you use pppm/electrode (Ahrens-Iwers).

## Restrictions

For algorithms that use a matrix for the electrode-electrode interactions, positions of electrode particles have to be immobilized at all times.

With ffield off (i.e. the default), the box geometry is expected to be z-non-periodic (i.e. boundary p p f), and this fix will issue an error if the box is z-periodic. With ffield on, the box geometry is expected to be z-periodic, and this fix will issue an error if the box is z-non-periodic.

The parallelization for the fix works best if electrode atoms are evenly distributed across processors. For a system with two electrodes at the bottom and top of the cell this can be achieved with processors * * 2, or with the line

    if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"

which avoids an error if the script is run on an odd number of processors (such as on just one processor for testing).

The fix creates an additional group named [fix-ID]_group which is the union of all electrode groups supplied to LAMMPS. This additional group counts towards LAMMPS’s limitation on the total number of groups (currently 32), which may not allow scripts that use that many groups to run with this fix.

The matrix-based algorithms (algo mat_inv and algo mat_cg) currently store an interaction matrix (either elastance or capacitance) of N by N doubles for each MPI process. This memory requirement may be prohibitive for large electrode groups. The fix will issue a warning if it expects to use more than 0.5 GiB of memory.

## Default

The default keyword-option settings are algo mat_inv, symm off, etypes off and ffield off.

Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the Accelerator packages page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.

These accelerated styles are part of the GPU, INTEL, KOKKOS, OPENMP, and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the Build package page for more info.

You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.

See the Accelerator packages page for more instructions on how to use the accelerated styles effectively.

(Siepmann) Siepmann and Sprik, J. Chem. Phys. 102, 511 (1995).

(Reed) Reed et al., J. Chem. Phys. 126, 084704 (2007).

(Deissenbeck) Deissenbeck et al., Phys. Rev. Letters 126, 136803 (2021).

(Gingrich) Gingrich, MSc thesis <https://gingrich.chem.northwestern.edu/papers/ThesiswCorrections.pdf>` (2010).

(Ahrens-Iwers) Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021).

(Hu) Hu, J. Chem. Theory Comput. 10, 5254 (2014).

(Dufils) Dufils et al., Phys. Rev. Letters 123, 195501 (2019).

(Tee) Tee and Searles, J. Chem. Phys. 156, 184101 (2022).

(Scalfi) Scalfi et al., J. Chem. Phys., 153, 174704 (2020).

(Ahrens-Iwers2022) Ahrens-Iwers et al., J. Chem. Phys. 157, 084801 (2022).