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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
         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 = symm or couple or etypes or ffield or write_mat or write_inv or read_mat or read_inv

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 values = type
    type = atom type (can be a range) exclusive to the electrode for optimized neighbor lists
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

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
fix fxconp bot electrode/thermo -1.0 1.805 temp 298 100 couple top 1.0

Description

fix electrode/conp mode implements a constant potential method (CPM) (Siepmann, Reed). Charges of groups specified via group-ID and optionally with the couple keyword are adapted to meet their respective potential at every time step. An arbitrary number of electrodes can be set but the respective groups may not overlap. Electrode charges have a Gaussian charge distribution with reciprocal width eta. The energy minimization is achieved via matrix inversion (Wang).

fix electrode/conq enforces a total charge specified in the input on each electrode. The energy is minimized w.r.t. the charge distribution within the electrode.

fix electrode/thermo implements a thermo-potentiostat (Deissenbeck). Temperature and time constant of the thermo-potentiostat need to be specified using the temp keyword. Currently, only two electrodes are possible with this style.

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

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 parameters must be set for all atom types of the electrode.

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

The fix_modify set options allow calculated quantities to be accessed via internal variables. Currently four types of quantities can be accessed:

fix-modify ID set v group-ID variablename
fix-modify ID set qsb group-ID variablename
fix-modify ID set mc group-ID1 group-ID2 variablename
fix-modify ID set me group-ID1 group-ID2 variablename

One use case is to output the potential that is internally calculated and applied to each electrode group by fix electrode/conq or fix electrode/thermo. For that case the v option makes fix electrode update the variable variablename with the potential applied to group group-ID, where group-ID must be a group whose charges are updated by fix electrode and variablename must be an internal-style variable:

fix conq bot electrode/conq -1.0 1.979 couple top 1.0
variable vbot internal 0.0
fix_modify conq set v bot vbot

The qsb option similarly outputs the total updated charge of the group if its potential were 0.0V. The mc option requires two group-IDs, and outputs the entry {group-ID1, group-ID2} of the (symmetric) macro-capacitance matrix (MC) which relates the electrodes’ applied potentials (V), total charges (Q), and total charges at 0.0 V (Qsb):

\[\mathbf{Q} = \mathbf{Q}_{SB} + \mathbf{MC} \cdot \mathbf{V}\]

Lastly, the me option also requires two group-IDs and outputs the entry {group-ID1, group-ID2} of the macro-elastance matrix, which is the inverse of the macro-capacitance matrix. (As the names denote, the macro-capacitance matrix gives electrode charges from potentials, and the macro-elastance matrix gives electrode potentials from charges).

Warning

Positions of electrode particles have to be immobilized at all times.

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).


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).

(Wang) Wang et al., J. Chem. Phys. 141, 184102 (2014).

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

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

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

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