pair_style threebody/table command¶

Syntax¶

pair_style style

• style = threebody/table

Examples¶

pair_style threebody/table
pair_coeff * * spce2.3b type1 type2

pair_style hybrid/overlay table linear 1200 threebody/table
pair_coeff      1 1 table table_CG_CG.txt VOTCA
pair_coeff      * * threebody/table spce.3b type


Used in example input scripts:

examples/PACKAGES/manybody_table/in.spce
examples/PACKAGES/manybody_table/in.spce2


Description¶

New in version 2Jun2022.

The threebody/table style is a pair style for generic tabulated three-body interactions. It has been developed for (coarse-grained) simulations (of water) with Kernel-based machine learning (ML) potentials (Scherer2). As for many other MANYBODY package pair styles the energy of a system is computed as a sum over three-body terms:

$E = \sum_i \sum_{j \neq i} \sum_{k > j} \phi_3 (r_{ij}, r_{ik}, \theta_{ijk})$

The summations in the formula are over all neighbors J and K of atom I within a cutoff distance $$cut$$. In contrast to the Stillinger-Weber potential, all forces are not calculated analytically, but read in from a three-body force/energy table which can be generated with the csg_ml app of VOTCA as available at: https://gitlab.mpcdf.mpg.de/votca/votca.

Only a single pair_coeff command is used with the threebody/table style which specifies a threebody potential (“.3b”) file with parameters for all needed elements. These are then mapped to LAMMPS atom types by specifying N_el additional arguments after the “.3b” filename in the pair_coeff command, where N_el is the number of LAMMPS atom types:

• “.3b” filename

• N_el element names = mapping of threebody elements to atom types

See the pair_coeff page for alternate ways to specify the path for the potential file.

As an example, imagine a file SiC.3b has three-body values for Si and C. If your LAMMPS simulation has 4 atoms types and you want the first 3 to be Si, and the fourth to be C, you would use the following pair_coeff command:

pair_coeff * * SiC.3b Si Si Si C


The first 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the “.3b” file. The final C argument maps LAMMPS atom type 4 to the C element in the threebody file. If a mapping value is specified as NULL, the mapping is not performed. This can be used when a threebody/table potential is used as part of the hybrid pair style. The NULL values are placeholders for atom types that will be used with other potentials.

The three-body files have a “.3b” suffix. Lines that are not blank or comments (starting with #) define parameters for a triplet of elements. The parameters in a single entry specify to the (three-body) cutoff distance and the tabulated three-body interaction. A single entry then contains:

• element 1 (the center atom in a 3-body interaction)

• element 2

• element 3

• cut (distance units)

• filename

• keyword

• style

• N

The parameter $$cut$$ is the (three-body) cutoff distance. When set to 0, no interaction is calculated for this element triplet. The parameters filename, keyword, style, and N refer to the tabulated three-body potential.

The tabulation is done on a three-dimensional grid of the two distances $$r_{ij}$$ and $$r_{ik}$$ as well as the angle $$\theta_{ijk}$$ which is constructed in the following way. There are two different cases. If element 2 and element 3 are of the same type (e.g. SiCC), the distance $$r_{ij}$$ is varied in “N” steps from rmin to rmax and the distance $$r_{ik}$$ is varied from $$r_{ij}$$ to rmax. This can be done, due to the symmetry of the triplet. If element 2 and element 3 are not of the same type (e.g. SiCSi), there is no additional symmetry and the distance $$r_{ik}$$ is also varied from rmin to rmax in “N” steps. The angle $$\theta_{ijk}$$ is always varied in “2N” steps from (0.0 + 180.0/(4N)) to (180.0 - 180.0/(4N)). Therefore, the total number of table entries is “M = N * N * (N+1)” for the symmetric (element 2 and element 3 are of the same type) and “M = 2 * N * N * N” for the general case (element 2 and element 3 are not of the same type).

The forces on all three particles I, J, and K of a triplet of this type of three-body interaction potential ($$\phi_3 (r_{ij}, r_{ik}, \theta_{ijk})$$) lie within the plane defined by the three inter-particle distance vectors $${\mathbf r}_{ij}$$, $${\mathbf r}_{ik}$$, and $${\mathbf r}_{jk}$$. This property is used to project the forces onto the inter-particle distance vectors as follows

$\begin{split}\begin{pmatrix} {\mathbf f}_{i} \\ {\mathbf f}_{j} \\ {\mathbf f}_{k} \\ \end{pmatrix} = \begin{pmatrix} f_{i1} & f_{i2} & 0 \\ f_{j1} & 0 & f_{j2} \\ 0 & f_{k1} & f_{k2} \\ \end{pmatrix} \begin{pmatrix} {\mathbf r}_{ij} \\ {\mathbf r}_{ik} \\ {\mathbf r}_{jk} \\ \end{pmatrix}\end{split}$

and then tabulate the 6 force constants $$f_{i1}$$, $$f_{i2}$$, $$f_{j1}$$, $$f_{j2}$$, $$f_{k1}$$, and $$f_{k2}$$, as well as the energy of a triplet e. Due to symmetry reasons, the following relations hold: $$f_{i1}=-f_{j1}$$, $$f_{i2}=-f_{k1}$$, and $$f_{j2}=-f_{k2}$$. As in this pair style the forces are read in directly, a correct MD simulation is also performed in the case that the triplet energies are set to e=0.

The filename specifies the file containing the tabulated energy and derivative values of $$\phi_3 (r_{ij}, r_{ik}, \theta_{ijk})$$. The keyword then specifies a section of the file. The format of this file is as follows (without the parenthesized comments):

# Tabulated three-body potential for spce water (one or more comment or blank lines)

ENTRY1                                                                      (keyword is the first text on line)
N 12 rmin 2.55 rmax 3.65                                                    (N, rmin, rmax parameters)
(blank line)
1 2.55 2.55 3.75 -867.212 -611.273 867.212 21386.8 611.273 -21386.8  0.0    (index, r_ij, r_ik, theta, f_i1, f_i2, f_j1, f_j2, f_k1, f_k2, e)
2 2.55 2.55 11.25 -621.539 -411.189 621.539 5035.95 411.189 -5035.95  0.0
...
1872 3.65 3.65 176.25 -0.00215132 -0.00412886 0.00215137 0.00111754 0.00412895 -0.00111757  0.0


A section begins with a non-blank line whose first character is not a “#”; blank lines or lines starting with “#” can be used as comments between sections. The first line begins with a keyword which identifies the section. The next line lists (in any order) one or more parameters for the table. Each parameter is a keyword followed by one or more numeric values.

The parameter “N” is required. It should be the same than the parameter “N” of the “.3b” file, otherwise its value is overwritten. “N” determines the number of table entries “M” that follow: “M = N * N * (N+1)” (symmetric triplet, e.g. SiCC) or “M = 2 * N * N * N” (asymmetric triplet, e.g. SiCSi). Therefore “M = 12 * 12 * 13 = 1872” in the above symmetric example. The parameters “rmin” and “rmax” are also required and determine the minimum and maximum of the inter-particle distances $$r_{ij}$$ and $$r_{ik}$$.

Following a blank line, the next M lines of the angular table file list the tabulated values. On each line, the first value is the index from 1 to M, the second value is the distance $$r_{ij}$$, the third value is the distance $$r_{ik}$$, the fourth value is the angle $$\theta_{ijk})$$, the next six values are the force constants $$f_{i1}$$, $$f_{i2}$$, $$f_{j1}$$, $$f_{j2}$$, $$f_{k1}$$, and $$f_{k2}$$, and the last value is the energy e.

Note that one three-body potential file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds one that matches the specified keyword of appropriate section of the “.3b” file.

At the moment, only the style linear is allowed and implemented. After reading in the force table, it is internally stored in LAMMPS as a lookup table. For each triplet configuration occurring in the simulation within the cutoff distance, the next nearest tabulated triplet configuration is looked up. No interpolation is done. This allows for a very efficient force calculation with the stored force constants and energies. Due to the know table structure, the lookup can be done efficiently. It has been tested (Scherer2) that with a reasonably small bin size, the accuracy and speed is comparable to that of a Stillinger-Weber potential with tabulated three-body interactions (pair_style sw/angle/table) while the table format of this pair style allows for more flexible three-body interactions.

As for the Stillinger-Weber potential, the three-body potential file must contain entries for all the elements listed in the pair_coeff command. It can also contain entries for additional elements not being used in a particular simulation; LAMMPS ignores those entries.

For a single-element simulation, only a single entry is required (e.g. SiSiSi). For a two-element simulation, the file must contain 8 entries (for SiSiSi, SiSiC, SiCSi, SiCC, CSiSi, CSiC, CCSi, CCC), that specify threebody parameters for all permutations of the two elements interacting in three-body configurations. Thus for 3 elements, 27 entries would be required, etc.

As annotated above, the first element in the entry is the center atom in a three-body interaction. Thus an entry for SiCC means a Si atom with 2 C atoms as neighbors. The tabulated three-body forces can in principle be specific to the three elements of the configuration. However, the user must ensure that it makes physically sense. E.g., the tabulated three-body forces for the entries CSiC and CCSi should be the same exchanging $$r_{ij}$$ with r_{ik}, $$f_{j1}$$ with $$f_{k1}$$, and $$f_{j2}$$ with $$f_{k2}$$.

Additional input files and reference data can be found at: https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-tutorials/ml

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

As all interactions are tabulated, no mixing is performed.

This pair style does not support the pair_modify shift, table, and tail options.

This pair style does not write its information to binary restart files, since it is stored in potential files. Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file.

This pair style can only be used via the pair keyword of the run_style respa command. It does not support the inner, middle, outer keywords.

Restrictions¶

This pair style is part of the MANYBODY package. It is only enabled if LAMMPS was built with that package. See the Build package page for more info.

This pair style requires the newton setting to be “on” for pair interactions.