lammps/examples/PACKAGES/pair_3b_table

Example for pair style 3b/table


This example contains all required input files for the simulation of CG SPC/E water with
the user pair style 3b/table, as well as a run.sh script.

To run the example, you have to compile LAMMPS with the MANYBODY package, including pair_3b_table.h and pair_3b_table.cpp.

Running the simulations, you will reproduce results of the following publication:

C. Scherer, R. Scheid, D. Andrienko, and T. Bereau, Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids, J. Chem. Theor. Comp., 16(5):3194–3204, 2020, https://doi.org/10.1021/acs.jctc.9b01256

Here, a water molecule is represented by one coarse-grained (CG) bead. The example contains
two parts.
The three-body (force) tables for both parts (1-1-1.table and 1-1-2.table) have been parametrized with the kernel-based machine learning (ML) with the VOTCA package (https://gitlab.mpcdf.mpg.de/votca/votca).
For a general description of the table format have a look at the documentation of this pair style.
For a example on the parametrization, have a look at https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/guide and
https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml.
In both cases, the parametrization has been done according to the three-body forces of the FM tabulated Stillinger-Weber (sw/3b/table) potential with the covariant meshing technique with the settings files used in https://gitlab.mpcdf.mpg.de/votca/votca/-/tree/master/csg-examples/ml/3body/with_binning.

For the first part of example, the folder contains the contains the LAMMPS data file (spce.data) with the starting configuration of 1000 CG water molecules, an input file (spce.in) and a three-body file (spce.3b).

The lammps input file contains the lines specifying the pair style and coefficients:

- pair_style   hybrid/overlay table linear 1200 3b/table - use a combination of pair style table with 1200 linear table entries and the pair style 3b/table
- pair_coeff   1 1 table table_CG_CG.txt VOTCA - set the table name and keyword for the pair style table
- pair_coeff   * * 3b/table spce.3b type - set the name of 3body file and bead type for the pair style 3b/table

A hybrid pair style is used, where pair forces are calculated as a tabulated interaction (table_CG_CG.txt) and the pair style 3b/table is only used to calculate the three-body forces.
The tabulated pair interaction is the same as in the example of the sw/3b/table pair style: examples/PACKAGES/pair_sw_3b_table

To run the simulation, one needs an additional 3body file (spce.3b).
It has the following structure:

- type - relates to keyword type in LAMMPS input file
- type - relates to keyword type in LAMMPS input file
- type - relates to keyword type in LAMMPS input file
- 3.7 - cutoff in Ang
- 1-1-1.table - name of 3-body force table
- ENTRY1 - keyword in 3-body force table for this interaction
- linear - interpolation is linear
- 12 - number of grid points in radial direction (automatically sets grid size, in this case to 1872)

As there is only one atom type (1), the force table is symmetric and contains "M = N * N * (N+1)" (12 * 12 * 13 = 1872) entries.

The LAMMPS simulation is a standard nvt simulation. A dump file is output with the positions and forces every 10 time steps.
You can calculate the pair distribution and compare it to the ones in the publication.

For the second part of the example, have a look at the LAMMPS data file (spce_2.data), the input file (spce_2.in) and the three-body file (spce_2.3b).
Running the second part, you will in fact perform the same MD simulation as in the first part of the example. However, the atom type of the first 100 CG water molecules has been changed from 1 to 2.
This is done to demonstrate how to run a simulation with different atom types.

Again, lammps input file (spce_2.in) contains the lines specifying the pair style and coefficients:

- pair_style  hybrid/overlay table linear 1200 3b/table - use a combination of pair style table with 1200 linear table entries and the pair style 3b/table
- pair_coeff  1 1 table table_CG_CG.txt VOTCA - set the table name and keyword for the pair style table
- pair_coeff  * * 3b/table spce_2.3b type1 type2 - set the name of 3body file and bead type for the pair style 3b/table

Now, the atom type 1 is mapped to the element type1 and the atom type 2 is mapped to the element type2 in the 3body file (spce_2.3b).
For this (artificial) two-element simulation, the 3body file now contain 8 entries for: type1 type1 type1, type1 type1 type2, type1 type2 type1, type1 type2 type2, type2 type1 type1, type2 type1 type2, type2 type2 type1, type2 type2 type2.
Each entry has the same structure as above. However, entries where the second and the third element are different require a different force table (1-1-2.table) instead of (1-1-1.table).
1-1-2.table contains exactly the force constants as 1-1-1.table.
However it has to have the asymmetric structure where both interparticle distances (r_ij and r_ik) are varied from rmin to rmax and therefore contains "M = 2 * N * N * N" (2 * 12 * 12 * 12 = 3456) entries.

Now run the simulation. The theromodynamic output, as well as, the pair correlation function should be exactly the same as for the first part of the example.