pair_style mesocnt command — LAMMPS documentation

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# pair_style mesocnt command

# pair_style mesocnt/viscous command

## Syntax

    pair_style style neigh_cutoff mode neigh_mode

- style = mesocnt or mesocnt/viscous

- neigh_cutoff = neighbor list cutoff (distance units)

- mode = chain or segment (optional)

- neigh_mode = id or topology (optional)

## Examples

    pair_style mesocnt 30.0
    pair_coeff * * C_10_10.mesocnt 2

    pair_style mesocnt/viscous 60.0 chain topology
    pair_coeff * * C_10_10.mesocnt 0.001 20.0 0.2 2 4

## Description

Style mesocnt implements a mesoscopic potential for the interaction of carbon nanotubes (CNTs), or other quasi-1D objects such as other kinds of nanotubes or nanowires. In this potential, CNTs are modelled as chains of cylindrical segments in which each infinitesimal surface element interacts with all other CNT surface elements with the Lennard-Jones (LJ) term adopted from the airebo style. The interaction energy is then computed by integrating over the surfaces of all interacting CNTs.

In LAMMPS, cylindrical segments are represented by bonds. Each segment is defined by its two end points (“nodes”) which correspond to atoms in LAMMPS. For the exact functional form of the potential and implementation details, the reader is referred to the original papers (Volkov1) and (Volkov2).

Changed in version 15Sep2022.

The potential supports two modes, segment and chain. By default, chain mode is enabled. In segment mode, interactions are pair-wise between all neighboring segments based on a segment-segment approach (keyword segment in pair_style command). In chain mode, interactions are calculated between each segment and infinitely or semi-infinitely long CNTs as described in (Volkov1). Chains of segments are converted to these (semi-)infinite CNTs bases on an approximate chain approach outlined in (Volkov2). Hence, interactions are calculated on a segment-chain basis (keyword chain in the pair_style command). Using chain mode allows to simplify the computation of the interactions significantly and reduces the computational times to the same order of magnitude as for regular bead spring models where beads interact with the standard pair_lj/cut potential. However, this method is only valid when the curvature of the CNTs in the system is small. When CNTs are buckled (see angle_mesocnt), local curvature can be very high and the pair_style automatically switches to segment mode for interactions involving buckled CNTs.

The potential further implements two different neighbor list construction modes. Mode id uses atom and mol IDs to construct neighbor lists while topology modes uses only the bond topology of the system. While id mode requires bonded atoms to have consecutive LAMMPS atom IDs and atoms in different CNTs to have different LAMMPS molecule IDs, topology mode has no such requirement. Using id mode is faster and is enabled by default.

Note

Neighbor id mode requires all CNTs in the system to have distinct LAMMPS molecule IDs and bonded atoms to have consecutive LAMMPS atom IDs. If this is not possible (e.g. in simulations of CNT rings), topology mode needs to be enabled in the pair_style command.

Added in version 15Sep2022.

In addition to the LJ interactions described above, style mesocnt/viscous explicitly models friction between neighboring segments. Friction forces are a function of the relative velocity between a segment and its neighboring approximate chain (even in segment mode) and only act along the axes of the interacting segment and chain. In this potential, friction forces acting per unit length of a nanotube segment are modelled as a shifted logistic function:

\[F^{\text{FRICTION}}(v) / L = \frac{F^{\text{max}}}{1 + \exp(-k(v-v_0))} - \frac{F^{\text{max}}}{1 + \exp(k v_0)}\]

In the pair_style command, the modes described above can be toggled using the segment or chain keywords. The neighbor list cutoff defines the cutoff within which atoms are included in the neighbor list for constructing neighboring CNT chains. This is different from the potential cutoff, which is directly calculated from parameters specified in the potential file. We recommend using a neighbor list cutoff of at least 3 times the maximum segment length used in the simulation to ensure proper neighbor chain construction.

Note

CNT ends are treated differently by all mesocnt styles. Atoms on CNT ends need to be assigned different LAMMPS atom types than atoms not on CNT ends.

Style mesocnt requires tabulated data provided in a single ASCII text file, as well as a list of integers corresponding to all LAMMPS atom types representing CNT ends:

- filename

- \(N\) CNT end atom types

For example, if your LAMMPS simulation of (10, 10) nanotubes has 4 atom types where atom types 1 and 3 are assigned to ‘inner’ nodes and atom types 2 and 4 are assigned to CNT end nodes, the pair_coeff command would be:

    pair_coeff * * C_10_10.mesocnt 2 4

Likewise, style mesocnt/viscous also requires the same information as style mesocnt, with the addition of 3 parameters for the viscous friction forces as listed above:

- filename

- \(F^{\text{max}}\)

- \(k\)

- \(v_0\)

- \(N\) CNT end atom types

Using the same example system as with style mesocnt with the addition of friction, the pair_coeff command is:

    pair_coeff * * C_10_10.mesocnt 0.03 20.0 0.20 2 4

Potential files for CNTs can be readily generated using the freely available code provided on

    https://github.com/phankl/cntpot

Using the same approach, it should also be possible to generate potential files for other 1D systems mentioned above.

Note

Because of their size, mesocnt style potential files are not bundled with LAMMPS. When compiling LAMMPS from source code, the file `C_10_10.mesocnt` should be downloaded separately from https://download.lammps.org/potentials/C_10_10.mesocnt

The first line of the potential file provides a time stamp and general information. The second line lists four integers giving the number of data points provided in the subsequent four data tables. The third line lists four floating point numbers: the CNT radius R, the LJ parameter sigma and two numerical parameters delta1 and delta2. These four parameters are given in Angstroms. This is followed by four data tables each separated by a single empty line. The first two tables have two columns and list the parameters uInfParallel and Gamma respectively. The last two tables have three columns giving data on a quadratic array and list the parameters Phi and uSemiParallel respectively. uInfParallel and uSemiParallel are given in eV/Angstrom, Phi is given in eV and Gamma is unitless.

If a simulation produces many warnings about segment-chain interactions falling outside the interpolation range, we recommend generating a potential file with lower values of delta1 and delta2.

## Mixing, shift, table, tail correction, restart, rRESPA info

These pair styles does not support mixing.

These pair styles does not support the pair_modify shift, table, and tail options.

These pair styles do not write their information to binary restart files, since it is stored in tabulated potential files. Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file.

These pair styles can only be used via the pair keyword of the run_style respa command. They do not support the inner, middle, outer keywords.

## Restrictions

These styles are part of the MESONT package. They are only enabled if LAMMPS was built with that package. See the Build package page for more info.

These pair styles require the newton setting to be “on” for pair interactions.

These pair styles require all 3 special_bonds lj settings to be non-zero for proper neighbor list construction.

Pair style mesocnt/viscous requires you to use the comm_modify vel yes command so that velocities are stored by ghost atoms.

## Related commands

pair_coeff, bond_style mesocnt, angle_style mesocnt

## Default

mode = chain, neigh_mode = id

(Volkov1) Volkov and Zhigilei, J Phys Chem C, 114, 5513 (2010).

(Volkov2) Volkov, Simov and Zhigilei, APS Meeting Abstracts, Q31.013 (2008).