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Finally updated the github tutorial

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\documentclass[aps,pr,onecolumn,superscriptaddress,noshowpacs,a4paper,15pt]{revtex4}
\pdfoutput=1
\bibliographystyle{apsrev4}
\usepackage{color}
\usepackage{dcolumn} %Align table columns on decimal point
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{graphicx}
\usepackage[pdftex]{hyperref}
\hypersetup{colorlinks=true,citecolor=blue,linkcolor=red,urlcolor=blue}
\usepackage[all]{hypcap}
\newcommand{\red}{\color{red}}
\newcommand{\blue}{\color{blue}}
\definecolor{green}{rgb}{0,0.5,0}
\newcommand{\green}{\color{green}}
\newcommand{\white}{\color{white}}
%\newcommand{\cite}[1]{\hspace{-1 ex} % \nocite{#1}\citenum{#1}}
\thickmuskip=0.5\thickmuskip %shorter spaces in math
\begin{document}
\begingroup
\Large
\begin{eqnarray*}
E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\[15pt]
V_{ij} & = & {\rm Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\[15pt]
{\rm Tap}(r_{ij}) & = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
\end{eqnarray*}
\endgroup
\end{document}

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\documentclass[aps,pr,onecolumn,superscriptaddress,noshowpacs,a4paper,15pt]{revtex4}
\pdfoutput=1
\bibliographystyle{apsrev4}
\usepackage{color}
\usepackage{dcolumn} %Align table columns on decimal point
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{graphicx}
\usepackage[pdftex]{hyperref}
\hypersetup{colorlinks=true,citecolor=blue,linkcolor=red,urlcolor=blue}
\usepackage[all]{hypcap}
\newcommand{\red}{\color{red}}
\newcommand{\blue}{\color{blue}}
\definecolor{green}{rgb}{0,0.5,0}
\newcommand{\green}{\color{green}}
\newcommand{\white}{\color{white}}
%\newcommand{\cite}[1]{\hspace{-1 ex} % \nocite{#1}\citenum{#1}}
\thickmuskip=0.5\thickmuskip %shorter spaces in math
%
\begin{document}
%
\begingroup
\Large
\begin{eqnarray*}
E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\[15pt]
V_{ij} & = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
\left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
\frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
\cdot \frac{C_6}{r^6_{ij}} \right \}\\[15pt]
\rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\[15pt]
\rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\[15pt]
f(\rho) & = & C e^{ -( \rho / \delta )^2 }\\[15pt]
{\rm Tap}(r_{ij}) & = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
\end{eqnarray*}
\endgroup
%
\end{document}
%

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\documentclass[aps,pr,onecolumn,superscriptaddress,noshowpacs,a4paper,15pt]{revtex4}
\pdfoutput=1
\bibliographystyle{apsrev4}
\usepackage{color}
\usepackage{dcolumn} %Align table columns on decimal point
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{graphicx}
\usepackage[pdftex]{hyperref}
\hypersetup{colorlinks=true,citecolor=blue,linkcolor=red,urlcolor=blue}
\usepackage[all]{hypcap}
\newcommand{\red}{\color{red}}
\newcommand{\blue}{\color{blue}}
\definecolor{green}{rgb}{0,0.5,0}
\newcommand{\green}{\color{green}}
\newcommand{\white}{\color{white}}
%\newcommand{\cite}[1]{\hspace{-1 ex} % \nocite{#1}\citenum{#1}}
\thickmuskip=0.5\thickmuskip %shorter spaces in math
\begin{document}
\begingroup
\Large
\begin{eqnarray*}
E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\[15pt]
V_{ij} & = & e^{-\lambda (r_{ij} -z_0)} \left [ C + f(\rho_{ij}) + f(\rho_{ji}) - A \left ( \frac{r_{ij}}{z_0}\right )^{-6} \right ] \\
\rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{i})^2 \\[15pt]
\rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{j})^2 \\[15pt]
f(\rho) & = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { \rho/\delta }^{2n}
\end{eqnarray*}
\endgroup
\end{document}

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style coul/shield command :h3
[Syntax:]
pair_style coul/shield cutoff tap_flag :pre
cutoff = global cutoff (distance units)
tap_flag = 0/1 to turn off/on the Tapper function
[Examples:]
pair_style coul/shield 16.0 1
pair_coeff 1 2 0.70 :pre
[Description:]
Style {coul/shield} computes a Coulomb interaction for boron and nitrigon
atoms locate in different layers of hexagonal boron nitride. This potential must
be used in combination with the potential "pair_style pair_ilp_gr_hBN"_pair_ilp_gr_hBN.html
NOTE: This potential is intended for electrostatic interactions between two different
layers of hexagonal boron nitride. Therefore, to avoid interaction within the same layers,
each layer should have a separate molecule id and is recommended to use
"full" atom style in the data file.
:c,image(Eqs/pair_coul_shield.jpg)
Where Tap(r_ij) is the tapper function which provides a continuous cutoff (up to third derivative)
for interatomic separations larger than r_c "(Maaravi)"_#Maaravi. Here \lambda is the shielding
parameter that eliminates the short-range sigularity of the classical monopolar electrostatic
interaction expression "(Maaravi)"_#Maaravi.
The shielding parameter \lambda (1/distance units) must be defined for each pair of atom
types via the "pair_coeff"_pair_coeff.html command as in the example
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:
The global cutoff (r_c) specified in the pair_style command is used.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This pair style does not support parameter mixing. Coefficients must be given explicitly for each type of particle pairs.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
[Restrictions:]
This style is part of the "user-misc" package. It is only enabled
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_2_3 section for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html
"pair_style pair_ilp_gr_hBN"_pair_ilp_gr_hBN.html
[Default:] tap_flag = 1
:line
:link(Maaravi)
[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style ILP/graphene/hBN command :h3
[Syntax:]
pair_style hybrid/overlay ILP/graphene/hBN cutoff tap_flag :pre
cutoff = global cutoff (distance units)
tap_flag = 0/1 to turn off/on the Tapper function
[Examples:]
pair_style hybrid/overlay ILP/graphene/hBN 16.0 1
pair_coeff * * ILP/graphene/hBN BNCH.ILP B N C :pre
pair_style hybrid/overlay rebo tersoff ILP/graphene/hBN 16.0 coul/shield 16.0
pair_coeff * * rebo CH.airebo NULL NULL C
pair_coeff * * tersoff BNC.tersoff B N NULL
pair_coeff * * ILP/graphene/hBN BNCH.ILP B N C :pre
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 2 2 coul/shield 0.69
[Description:]
The {ILP/graphene/hBN} style computes the registry-dependent interlayer potential (RDILP)
potential as described in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi. The normals are calculated in
the way as described in "(Kolmogorov)"_#Kolmogorov.
:c,image(Eqs/pair_ilp_gr_hBN.jpg)
Where Tap(r_ij) is the tapper function which provides a continuous cutoff (up to third derivative)
for interatomic separations larger than r_c "(Maaravi)"_#Maaravi. The definitons of each parameter
in the above equation can be found in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi.
It is important to include all the pairs to build the neighbor list for
calculating the normals.
NOTE: This potential is intended for interactions between two different layers
of graphene or hexagonal boron nitride. Therefore, to avoid interaction within
the same layers, each layer should have a separate molecule id and is recommended
to use "full" atom style in the data file.
The parameter file (e.g. BNCH.ILP), is intended for use with metal
"units"_units.html, with energies in meV. Two additional parameters, {S},
and {rcut} are included in the parameter file. {S} is designed to
facilitate scaling of energies. {rcut} is designed to build the neighbor
list for calculating the normals for each atom pair.
NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP), are
fitted with tapper function by setting the cutoff equal to 16.0 Angstrom.
Using different cutoff or tapper function should be careful.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style {none}.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This pair style does not support the pair_modify mix, shift, table, and tail options.
This pair style does not write their 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.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
This pair potential requires the newton setting to be “on” for pair interactions.
The BNCH.ILP potential file provided with LAMMPS (see the potentials directory) are parameterized for metal units.
You can use this potential with any LAMMPS units, but you would need to create your BNCH.ILP potential file with
coefficients listed in the appropriate units, if your simulation doesn’t use “metal” units.
[Related commands:]
"pair_coeff"_pair_coeff.html
"pair_none"_pair_none.html
"pair_style hybrid/overlay"_pair_hybrid.html
"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html
"pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html
"pair_style pair_coul_shield"_pair_coul_shield.html
[Default:] tap_flag = 1
:line
:link(Leven)
[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016)
:link(Maaravi)
[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
:link(Kolmogorov)
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style kolmogorov/crespi/full command :h3
[Syntax:]
pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag:pre
cutoff = global cutoff (distance units)
tap_flag = 0/1 to turn off/on the Tapper function
[Examples:]
pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0
pair_coeff * * none
pair_coeff * * kolmogorov/crespi/full CC.KC C C :pre
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
pair_coeff * * rebo CH.airebo C C
pair_coeff * * kolmogorov/crespi/full CC.KC C C :pre
[Description:]
The {kolmogorov/crespi/full} style computes the Kolmogorov-Crespi interaction
potential as described in "(Kolmogorov)"_#Kolmogorov. No simplification is made,
:c,image(Eqs/pair_kolmogorov_crespi_full.jpg)
It is important to have a suffiently large cutoff to ensure smooth forces and
to include all the pairs to build the neighbor list for calculating the normals.
Energies are shifted so that they go continously to zero at the cutoff assuming
that the exponential part of {Vij} (first term) decays sufficiently fast.
This shift is achieved by the last term in the equation for {Vij} above.
NOTE: This potential is intended for interactions between two different graphene
layers. Therefore, to avoid interaction within the same layers, each layer
should have a separate molecule id and is recommended to use
"full" atom style in the data file.
The parameter file (e.g. CC.KC), is intended for use with metal
"units"_units.html, with energies in meV. Two additional parameters, {S},
and {rcut} are included in the parameter file. {S} is designed to
facilitate scaling of energies. {rcut} is designed to build the neighbor
list for calculating the normals for each atom pair.
This potential must be used in combination with hybrid/overlay.
Other interactions can be set to zero using pair_style {none}.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This pair style does not support the pair_modify mix, shift, table, and tail options.
This pair style does not write their 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.
[Restrictions:]
This fix is part of the USER-MISC package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
This pair potential requires the newton setting to be “on” for pair interactions.
The CC.KC potential file provided with LAMMPS (see the potentials directory) are parameterized for metal units.
You can use this potential with any LAMMPS units, but you would need to create your CC.KC potential file with
coefficients listed in the appropriate units, if your simulation doesn’t use “metal” units.
[Related commands:]
"pair_coeff"_pair_coeff.html
"pair_none"_pair_none.html
"pair_style hybrid/overlay"_pair_hybrid.html
"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html
"pair_style pair_ilp_gr_hBN"_pair_ilp_gr_hBN.html
[Default:] tap_flag = 0
:line
:link(Kolmogorov)
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Wengen Ouyang (Tel Aviv University)
e-mail: w.g.ouyang at gmail dot com
This is a Coulomb potential described in
[Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017)]
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_coul_shield.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairCoulshield::PairCoulshield(LAMMPS *lmp) : Pair(lmp) {
Tapflag = 1;
}
/* ---------------------------------------------------------------------- */
PairCoulshield::~PairCoulshield()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(sigmae);
memory->destroy(offset);
memory->destroy(cutsq);
memory->destroy(cut);
allocated = 0;
}
}
/* ---------------------------------------------------------------------- */
void PairCoulshield::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair,Tap,dTap;
double rsq,r,r3,rarg,th,depsdr,epsr,forcecoul,factor_coul,Vc,fvc;
int *ilist,*jlist,*numneigh,**firstneigh;
ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
// only include the interation between different layers
if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) {
r = sqrt(rsq);
r3 = rsq*r;
rarg = 1.0/sigmae[itype][jtype];
th = r3 + pow(rarg,3.0);
epsr = 1.0/pow(th,0.333333333333333333333333);
depsdr = pow(epsr,4.0);
Vc = qqrd2e*qtmp*q[j]*epsr;
// turn on/off Tapper function
if (Tapflag) {
Tap = calc_Tap(r,sqrt(cutsq[itype][jtype]));
dTap = calc_dTap(r,sqrt(cutsq[itype][jtype]));
} else {Tap = 1.0; dTap = 0.0;}
forcecoul = qqrd2e*qtmp*q[j]*r*depsdr;
fvc = forcecoul*Tap - Vc*dTap/r;
fpair = factor_coul*fvc;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
if (Tapflag) ecoul = Vc*Tap;
else ecoul = Vc - offset[itype][jtype];
ecoul *= factor_coul;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,0.0,
ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairCoulshield::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(sigmae,n+1,n+1,"pair:sigmae");
//memory->create(rme,n+1,n+1,"pair:rme");
memory->create(offset,n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairCoulshield::settings(int narg, char **arg)
{
if (narg < 1 || narg > 2) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
if (narg == 2) Tapflag = force->numeric(FLERR,arg[1]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairCoulshield::coeff(int narg, char **arg)
{
if (narg < 3 || narg > 4) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
double sigmae_one = force->numeric(FLERR,arg[2]);
double cut_one = cut_global;
if (narg == 4) cut_one = force->numeric(FLERR,arg[3]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
sigmae[i][j] = sigmae_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairCoulshield::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style coul/shield requires atom attribute q");
neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairCoulshield::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
error->all(FLERR,"for pair style coul/shield, parameters need to be set explicitly for all pairs.");
}
double *q = atom->q;
double qqrd2e = force->qqrd2e;
double r,r3,rarg,th,epsr;
if (offset_flag) {
r = cut[i][j];
r3 = r*r*r;
rarg = 1.0/sigmae[i][j];
th = r3 + pow(rarg,3.0);
epsr = 1.0/pow(th,0.333333333333333333);
offset[i][j] = qqrd2e*q[i]*q[j]*epsr;
} else offset[i][j] = 0.0;
sigmae[j][i] = sigmae[i][j];
offset[j][i] = offset[i][j];
cut[j][i] = cut[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCoulshield::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&sigmae[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairCoulshield::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (setflag[i][j]) {
if (me == 0) {
fread(&sigmae[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&sigmae[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCoulshield::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairCoulshield::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
double PairCoulshield::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
double &fforce)
{
double r, rarg,Vc,fvc,forcecoul,phishieldec;
double r3,th,epsr,depsdr,Tap,dTap;
double *q = atom->q;
double qqrd2e = force->qqrd2e;
r = sqrt(rsq);
r3 = rsq*r;
rarg = 1.0/sigmae[itype][jtype];
th = r3 + pow(rarg,3.0);
epsr = 1.0/pow(th,0.333333333333333333);
depsdr = pow(epsr,4.0);
Vc = qqrd2e*q[i]*q[j]*epsr;
// turn on/off Tapper function
if (Tapflag) {
Tap = calc_Tap(r,sqrt(cutsq[itype][jtype]));
dTap = calc_dTap(r,sqrt(cutsq[itype][jtype]));
} else {Tap = 1.0; dTap = 0.0;}
forcecoul = qqrd2e*q[i]*q[j]*r*depsdr;
fvc = forcecoul*Tap - Vc*dTap/r;
fforce = factor_coul*fvc;
if (Tapflag) phishieldec = factor_coul*Vc*Tap;
else phishieldec = Vc - offset[itype][jtype];
return factor_coul*phishieldec;
}

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(coul/shield,PairCoulshield)
#else
#ifndef LMP_PAIR_COUL_SHIELD_H
#define LMP_PAIR_COUL_SHIELD_H
#include "pair.h"
namespace LAMMPS_NS {
class PairCoulshield : public Pair {
public:
PairCoulshield(class LAMMPS *);
virtual ~PairCoulshield();
virtual void compute(int, int);
virtual void settings(int, char **);
virtual void coeff(int, char **);
virtual void init_style();
virtual double init_one(int, int);
virtual void write_restart(FILE *);
virtual void read_restart(FILE *);
virtual void write_restart_settings(FILE *);
virtual void read_restart_settings(FILE *);
virtual double single(int, int, int, int, double, double, double, double &);
protected:
double cut_global;
double **cut;
double **sigmae, **offset;
//double a_eps, b_eps, eps_s;
int Tapflag;
void allocate();
/* ----Calculate the long-range cutoff term */
inline double calc_Tap(double r_ij, double Rcut) {
double Tap,r;
//int Tap_coeff[8] = {1,0,0,0,-35,84,-70,20};
double Tap_coeff[8] = {1.0,0.0,0.0,0.0,-35.0,84.0,-70.0,20.0};
r = r_ij/Rcut;
Tap = 0.0;
Tap = Tap_coeff[7] * r + Tap_coeff[6];
Tap = Tap * r + Tap_coeff[5];
Tap = Tap * r + Tap_coeff[4];
Tap = Tap * r + Tap_coeff[3];
Tap = Tap * r + Tap_coeff[2];
Tap = Tap * r + Tap_coeff[1];
Tap = Tap * r + Tap_coeff[0];
return(Tap);
}
/* ----Calculate the derivatives of long-range cutoff term */
inline double calc_dTap(double r_ij, double Rcut) {
double dTap,r;
double Tap_coeff[8] = {1.0,0.0,0.0,0.0,-35.0,84.0,-70.0,20.0};
r = r_ij/Rcut;
dTap = 0.0;
dTap = 7.0*Tap_coeff[7] * r + 6.0*Tap_coeff[6];
dTap = dTap * r + 5.0*Tap_coeff[5];
dTap = dTap * r + 4.0*Tap_coeff[4];
dTap = dTap * r + 3.0*Tap_coeff[3];
dTap = dTap * r + 2.0*Tap_coeff[2];
dTap = dTap * r + Tap_coeff[1];
dTap = dTap/Rcut;
return(dTap);
}
};
}
#endif
#endif

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(ILP/graphene/hBN,PairILP)
#else
#ifndef LMP_PAIR_ILP_H
#define LMP_PAIR_ILP_H
#include "pair.h"
#include "my_page.h"
#include <math.h>
namespace LAMMPS_NS {
class PairILP : public Pair {
public:
PairILP(class LAMMPS *);
virtual ~PairILP();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void init_style();
void calc_normal();
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
double single(int, int, int, int, double, double, double, double &);
protected:
int me;
int maxlocal; // size of numneigh, firstneigh arrays
int pgsize; // size of neighbor page
int oneatom; // max # of neighbors for one atom
MyPage<int> *ipage; // neighbor list pages
int *ILP_numneigh; // # of pair neighbors for each atom
int **ILP_firstneigh; // ptr to 1st neighbor of each atom
int tap_flag; // flag to turn on/off Tapper function
struct Param {
double z0,alpha,epsilon,C,delta,d,sR,reff,C6,S;
double delta2inv,seff,lambda,rcut;
int ielement,jelement;
};
Param *params; // parameter set for I-J interactions
char **elements; // names of unique elements
int **elem2param; // mapping from element pairs to parameters
int *map; // mapping from atom types to elements
int nelements; // # of unique elements
int nparams; // # of stored parameter sets
int maxparam; // max # of parameter sets
int nmax; // max # of atoms
double cut_global;
double cut_normal;
double **cut;
double **cutILPsq; // mapping the cutoff from element pairs to parameters
double **offset;
double **normal;
double ***dnormdri;
double ****dnormal;
void read_file( char * );
void allocate();
void ILP_neigh();
/* ----Calculate the long-range cutoff term */
inline double calc_Tap(double r_ij, double Rcut) {
double Tap,r;
double Tap_coeff[8] = {1.0,0.0,0.0,0.0,-35.0,84.0,-70.0,20.0};
r = r_ij/Rcut;
if(r >= 1.0) {Tap = 0.0;}
else {
Tap = Tap_coeff[7] * r + Tap_coeff[6];
Tap = Tap * r + Tap_coeff[5];
Tap = Tap * r + Tap_coeff[4];
Tap = Tap * r + Tap_coeff[3];
Tap = Tap * r + Tap_coeff[2];
Tap = Tap * r + Tap_coeff[1];
Tap = Tap * r + Tap_coeff[0];
}
return(Tap);
}
/* ----Calculate the derivatives of long-range cutoff term */
inline double calc_dTap(double r_ij, double Rcut) {
double dTap,r;
double Tap_coeff[8] = {1.0,0.0,0.0,0.0,-35.0,84.0,-70.0,20.0};
r = r_ij/Rcut;
if(r >= 1.0) {dTap = 0.0;}
else {
dTap = 7.0*Tap_coeff[7] * r + 6.0*Tap_coeff[6];
dTap = dTap * r + 5.0*Tap_coeff[5];
dTap = dTap * r + 4.0*Tap_coeff[4];
dTap = dTap * r + 3.0*Tap_coeff[3];
dTap = dTap * r + 2.0*Tap_coeff[2];
dTap = dTap * r + Tap_coeff[1];
dTap = dTap/Rcut;
}
return(dTap);
}
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
*/

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(kolmogorov/crespi/full,PairKolmogorovCrespiFull)
#else
#ifndef LMP_PAIR_KolmogorovCrespi_FULL_H
#define LMP_PAIR_KolmogorovCrespi_FULL_H
#include "pair.h"
#include "my_page.h"
#include <math.h>
namespace LAMMPS_NS {
class PairKolmogorovCrespiFull : public Pair {
public:
PairKolmogorovCrespiFull(class LAMMPS *);
virtual ~PairKolmogorovCrespiFull();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void init_style();
void calc_normal();
int pack_forward_comm(int, int *, double *, int, int *);
void unpack_forward_comm(int, int, double *);
double single(int, int, int, int, double, double, double, double &);
protected:
int me;
int maxlocal; // size of numneigh, firstneigh arrays
int pgsize; // size of neighbor page
int oneatom; // max # of neighbors for one atom
MyPage<int> *ipage; // neighbor list pages
int *KC_numneigh; // # of pair neighbors for each atom
int **KC_firstneigh; // ptr to 1st neighbor of each atom
int tap_flag; // flag to turn on/off Tapper function
struct Param {
double z0,C0,C2,C4,C,delta,lambda,A,S;
double delta2inv,z06,rcut;
int ielement,jelement;
};
Param *params; // parameter set for I-J interactions
char **elements; // names of unique elements
int **elem2param; // mapping from element pairs to parameters
int *map; // mapping from atom types to elements
int nelements; // # of unique elements
int nparams; // # of stored parameter sets
int maxparam; // max # of parameter sets
int nmax; // max # of atoms
double cut_global;
double cut_normal;
double **cut;
double **cutKCsq;
double **offset;
double **normal;
double ***dnormdri;
double ****dnormal;
void read_file( char * );
void allocate();
void KC_neigh();
/* ----Calculate the long-range cutoff term */
inline double calc_Tap(double r_ij, double Rcut) {
double Tap,r;
double Tap_coeff[8] = {1.0,0.0,0.0,0.0,-35.0,84.0,-70.0,20.0};
r = r_ij/Rcut;
if(r >= 1.0) {Tap = 0.0;}
else{
Tap = Tap_coeff[7] * r + Tap_coeff[6];
Tap = Tap * r + Tap_coeff[5];
Tap = Tap * r + Tap_coeff[4];
Tap = Tap * r + Tap_coeff[3];
Tap = Tap * r + Tap_coeff[2];
Tap = Tap * r + Tap_coeff[1];
Tap = Tap * r + Tap_coeff[0];
}
return(Tap);
}
/* ----Calculate the derivatives of long-range cutoff term */
inline double calc_dTap(double r_ij, double Rcut) {
double dTap,r;
double Tap_coeff[8] = {1.0,0.0,0.0,0.0,-35.0,84.0,-70.0,20.0};
r = r_ij/Rcut;
if(r >= 1.0) {dTap = 0.0;}
else {
dTap = 7.0*Tap_coeff[7] * r + 6.0*Tap_coeff[6];
dTap = dTap * r + 5.0*Tap_coeff[5];
dTap = dTap * r + 4.0*Tap_coeff[4];
dTap = dTap * r + 3.0*Tap_coeff[3];
dTap = dTap * r + 2.0*Tap_coeff[2];
dTap = dTap * r + Tap_coeff[1];
dTap = dTap/Rcut;
}
return(dTap);
}
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
*/