examples/PACKAGES/pair_sw_3b_table: added example for new pair style sw/3b/table

examples/PACKAGES/pair_sw_3b_table/README

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+Example for pair style sw/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.
+
+To run the example, you have to compile LAMMPS with the MANYBODY package, including pair_sw_3b_table.h and pair_sw_3b_table.h.
+
+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
+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.
+
+The folder contains the LAMMPS data file (spce.data) with the starting configuration
+of 1000 CG water molecules, an input file (spce.in) and a (modified) Stillinger-Weber file (spce.sw).
+
+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_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
+
+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:
+
+- 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.
+You can calculate the pair distribution and compare it to the one(s) in the publicattion.

examples/PACKAGES/pair_sw_3b_table/run.sh

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+#! /bin/bash -e
+
+#run the LAMMPS simulation (needs a current LAMMPS version compiled with the user pair_style sw/table)
+lmp < spce.in > spce.out
+

examples/PACKAGES/pair_sw_3b_table/spce.in

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+log none
+
+#SPC/E water
+
+units		real	
+atom_style	atomic
+
+read_data	spce.data
+
+#hybrid pair style consisting of
+#pair_style table to read in CG pair potential
+#pair_style sw/table for tabulated sw interactions
+pair_style      hybrid/overlay table linear 1200 sw/3b/table
+
+#pair coefficients
+pair_coeff	1 1 table table_CG_CG.txt VOTCA
+pair_coeff      * * sw/3b/table spce.sw type
+
+#nvt run with nose-hoover thermostat
+#time coupling of 100 ts for thermostat
+#target T is 300 K
+fix		1 all nvt temp 300.0 300.0 200.0
+
+#create initial velocities
+velocity	all create 300 432567 dist uniform
+#remove center of mass linear momentum
+velocity	all zero linear
+
+#remove center of mass linear momentum every 1000 time steps in each cartesian direction
+fix             remove all momentum 1000 linear 1 1 1
+
+#timestep of 2 fs
+timestep	2.0
+
+#print out thermodynamic info every 100 ts
+thermo		100
+
+#run 10000 ts
+run		10000
+
+#write out dump file every 10 ts for 100000 ts
+dump            2 all custom 10 spce.dump id type x y z fx fy fz
+run		100000
+
+undump          2

examples/PACKAGES/pair_sw_3b_table/spce.sw

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+type
+type
+type
+1 #epsilon in kcal/mol
+1 #sigma in dimensionless
+3.7 # a in Ang
+1.0 #lambda dimensionless
+0.8 #gamma in Ang
+0.0 #costheta0 dimensionless
+0 #two body part A=0
+0 #two body part B=0
+0 #two body part p=0
+0 #two body part q=0
+0.0 # use the standard Stillinger-Weber cutoff
+table_CG_CG_CG.txt
+VOTCA
+linear
+1001