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examples/PACKAGES/pair_sw_3b_table/README: corrections in the text

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Christoph Scherer
2022-05-26 14:32:12 +02:00
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examples/PACKAGES/pair_sw_3b_table/README
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@ -1,8 +1,8 @@
Example for pair style sw/table
================================
Example for pair style sw/3b/table
This example contains all required input files for the simulation of CG SPC/E water with
the user pair style sw/table, as well as a run.sh script.
the user pair style sw/3b/table, as well as a run.sh script.
To run the example, you have to compile LAMMPS with the MANYBODY package, including pair_sw_3b_table.h and pair_sw_3b_table.cpp.
@ -10,10 +10,10 @@ Running the simulation, you will reproduce results of the following publication:
C. Scherer, and D. Andrienko, Understanding three-body contributions to coarse-grained force fields, Phys. Chem. Chem. Phys, 20(34):22387–22394, 2018, http://xlink.rsc.org/?DOI=C8CP00746B
Here, a water molecule is represented by one coarse-grained (CG) bead. The
two-body (table_CG_CG.txt) and three-body angular (table_CG_CG_CG.txt) interaction potentials
have been parametrized with force-matching (FM) with the VOTCA package (https://gitlab.mpcdf.mpg.de/votca/votca).
For more details, have a look at the publication. For a example on the parametrization, have a look at
Here, a water molecule is represented by one coarse-grained (CG) bead.
The two-body (table_CG_CG.txt) and three-body angular (table_CG_CG_CG.txt) interaction potentials have been parametrized with force-matching (FM) with the VOTCA package (https://gitlab.mpcdf.mpg.de/votca/votca).
For more details, have a look at the publication.
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/spce/3body_sw.
@ -22,20 +22,19 @@ of 1000 CG water molecules, an input file (spce.in) and a (modified) Stillinger-
The lammps input file contains the lines specifying the pair style and coefficients:
- pair_style hybrid/overlay table linear 1200 sw/3b/table - use a combination of pair_style table with 1200 linear table entries and the pair_style sw/3b/table
- pair_style hybrid/overlay table linear 1200 sw/3b/table - use a combination of pair style table with 1200 linear table entries and the pair style sw/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 * * sw/3b/table spce.sw type - set the name of the Stillinger-Weber file for the pair_style sw/3b/table
- pair_coeff * * sw/3b/table spce.sw type - set the name of the Stillinger-Weber file for the pair style sw/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 sw/table is only used to calculate the three-body forces. Therefore, in the Stillinger-Weber file all
parameters refering to two-body interactions are set to zero. As explained in the documentation of this pair
style, the .sw file contains the
additional lines refering to the tabulated angular potential:
A hybrid pair style is used, where pair forces are calculated as a tabulated interaction (table_CG_CG.txt) and the pair style sw/3b/table is only used to calculate the three-body forces.
Therefore, in the Stillinger-Weber file all parameters refering to two-body interactions are set to zero.
As explained in the documentation of this pair style, the .sw file contains the additional lines refering to the tabulated angular potential:
- table_CG_CG_CG.txt - file name of tabulated angular potential
- VOTCA - keyword for tabulated angular potential
- linear - angular table is of linear style
- 1001 - 1001 table entries
The LAMMPS simulation is a standard nvt simulation. A dump file is output with the positions and forces every 10 time steps.
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 one(s) in the publicattion.