diff --git a/examples/PACKAGES/pair_sw_3b_table/README b/examples/PACKAGES/pair_sw_3b_table/README index 690adbc30a..2d00030fea 100644 --- a/examples/PACKAGES/pair_sw_3b_table/README +++ b/examples/PACKAGES/pair_sw_3b_table/README @@ -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.