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Coulomb pair style with smeared out charges (coul/slater)
This commit is contained in:
Axel Kohlmeyer
2020-03-18 20:52:47 -04:00
committed by GitHub
parent 2b39c9968f da2e6b2389
commit 164bf1b60e
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2
doc/src/Commands_pair.rst
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@ -77,6 +77,8 @@ OPT.
* :doc:`coul/long/cs (g) <pair_cs>`
* :doc:`coul/long/soft (o) <pair_fep_soft>`
* :doc:`coul/msm (o) <pair_coul>`
* :doc:`coul/slater/cut <pair_coul_slater>`
* :doc:`coul/slater/long <pair_coul_slater>`
* :doc:`coul/shield <pair_coul_shield>`
* :doc:`coul/streitz <pair_coul>`
* :doc:`coul/wolf (ko) <pair_coul>`

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.. index:: pair_style coul/slater
pair_style coul/slater/cut command
==================================
pair_style coul/slater/long command
===================================
Syntax
""""""
.. code-block:: LAMMPS
pair_style coul/slater/cut lamda cutoff
pair_style coul/slater/long lamda cutoff
lamda = decay length of the charge (distance units)
cutoff = cutoff (distance units)
Examples
""""""""
.. code-block:: LAMMPS
pair_style coul/slater/cut 1.0 3.5
pair_coeff * *
pair_coeff 2 2 2.5
pair_style coul/slater/long 1.0 12.0
pair_coeff * *
pair_coeff 1 1 5.0
Description
"""""""""""
Styles *coul/slater* compute electrostatic interactions in mesoscopic models
which employ potentials without explicit excluded-volume interactions.
The goal is to prevent artificial ionic pair formation by including a charge
distribution in the Coulomb potential, following the formulation of
:ref:`(Melchor) <Melchor>`:
.. math::
E = \frac{Cq_iq_j}{\epsilon r} \left( 1- \left( 1 + \frac{r_{ij}}{\lambda} exp\left( -2r_{ij}/\lambda \right) \right) \right) \qquad r < r_c
where :math:`r_c` is the cutoff distance and :math:`\lambda` is the decay length of the charge.
C is the same Coulomb conversion factor as in the pair\_styles coul/cut and coul/long. In this way the Coulomb
interaction between ions is corrected at small distances r.
For the *coul/slater/cut* style, the potential energy for distances larger than the cutoff is zero,
while for the *coul/slater/long*, the long-range interactions are computed either by the Ewald or the PPPM technique.
Phenomena that can be captured at a mesoscopic level using this type of electrostatic
interactions include the formation of polyelectrolyte-surfactant aggregates,
charge stabilization of colloidal suspensions, and the formation of
complexes driven by charged species in biological systems. :ref:`(Vaiwala) <Vaiwala>`.
The cutoff distance is optional. If it is not used,
the default global value specified in the pair_style command is used.
For each pair of atom types, a specific cutoff distance can be defined via the :doc:`pair_coeff <pair_coeff>` command as in the example
above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands:
* :math:`r_c` (distance units)
The global decay length of the charge (:math:`\lambda`) specified in the pair\_style command is used for all pairs.
----------
**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
For atom type pairs I,J and I != J, the cutoff distance for the
*coul/slater* styles can be mixed. The default mix value is *geometric*\ .
See the "pair\_modify" command for details.
The :doc:`pair_modify <pair_modify>` shift and table options are not relevant
for these pair styles.
These pair styles do not support the :doc:`pair_modify <pair_modify>`
tail option for adding long-range tail corrections to energy and
pressure.
These pair styles write their information to :doc:`binary restart files <restart>`, so pair\_style and pair\_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
*inner*\ , *middle*\ , *outer* keywords.
Restrictions
""""""""""""
The *coul/slater/long* style requires the long-range solvers included in the KSPACE package.
These styles are part of the "USER-MISC" package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style, hybrid/overlay <pair_hybrid>`, :doc:`kspace_style <kspace_style>`
**Default:** none
----------
.. _Melchor:
**(Melchor)** Gonzalez-Melchor, Mayoral, Velázquez, and Alejandre, J Chem Phys, 125, 224107 (2006).
.. _Vaiwala:
**(Vaiwala)** Vaiwala, Jadhav, and Thaokar, J Chem Phys, 146, 124904 (2017).

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doc/utils/sphinx-config/false_positives.txt
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@ -1027,6 +1027,7 @@ Gmask
gneb
GNEB
Goldfarb
Gonzalez-Melchor
googlemail
Gordan
GPa
@ -1290,6 +1291,7 @@ Izvekov
izz
Izz
Jacobsen
Jadhav
jagreat
Jalalvand
james
@ -1663,6 +1665,7 @@ maxwell
Maxwellian
maxX
Mayergoyz
Mayoral
mbt
Mbytes
MBytes
@ -1691,6 +1694,7 @@ mediumvioletred
Mees
Mehl
Mei
Melchor
Meloni
Melrose
Mem
@ -2260,6 +2264,7 @@ polyA
polybond
polydisperse
polydispersity
polyelectrolyte
polyhedra
popen
Popov
@ -2769,6 +2774,7 @@ superset
supersphere
Supinski
Surblys
surfactant
surfactants
Suter
Sutmann
@ -2831,6 +2837,7 @@ tfmc
tfMC
th
Thakkar
Thaokar
thb
thei
Theodorou
@ -3025,6 +3032,7 @@ uwo
Uzdin
vacf
Vaid
Vaiwala
valent
Valeriu
valgrind
@ -3053,6 +3061,7 @@ Vectorization
vectorized
Vegt
vel
Velázquez
Verlag
verlet
Verlet

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# Bulk polyelectrolyte as described in section IV of J. Chem. Phys. 125, 224107 (2006)
boundary p p p
units lj
atom_style charge
region my_sim_box block 0.0 10.0 0.0 10.0 0.0 10.0
create_box 3 my_sim_box
create_atoms 1 random 2804 100 my_sim_box
create_atoms 2 random 98 200 my_sim_box
create_atoms 3 random 98 300 my_sim_box
set type 2 charge -1.0
set type 3 charge 1.0
comm_modify mode single vel yes
mass 1 1.0
mass 2 1.0
mass 3 1.0
pair_style hybrid/overlay dpd 1.0 1.0 245455 coul/slater/long 0.929 3.0
pair_coeff * * dpd 25.0 4.5
pair_coeff * * coul/slater/long
kspace_style ewald 0.00001
dielectric 1.0
neighbor 2.0 bin
neigh_modify every 1 delay 0 check no once no
timestep 0.02
fix 2 all nve
thermo 10
thermo_style custom step spcpu temp press etotal pe ke ecoul elong evdwl
thermo_modify line one
run 100000
write_data data.after_equilibration
compute RDF_1_1 all rdf 50 1 1 cutoff 3.0
compute RDF_1_2 all rdf 50 1 2 cutoff 3.0
compute RDF_1_3 all rdf 50 1 3 cutoff 3.0
compute RDF_2_2 all rdf 50 2 2 cutoff 3.0
compute RDF_2_3 all rdf 50 2 3 cutoff 3.0
compute RDF_3_3 all rdf 50 3 3 cutoff 3.0
fix 11 all ave/time 50 1 50 c_RDF_1_1[*] file tmp_1_1.rdf mode vector
fix 12 all ave/time 50 1 50 c_RDF_1_2[*] file tmp_1_2.rdf mode vector
fix 13 all ave/time 50 1 50 c_RDF_1_3[*] file tmp_1_3.rdf mode vector
fix 14 all ave/time 50 1 50 c_RDF_2_2[*] file tmp_2_2.rdf mode vector
fix 15 all ave/time 50 1 50 c_RDF_2_3[*] file tmp_2_3.rdf mode vector
fix 16 all ave/time 50 1 50 c_RDF_3_3[*] file tmp_3_3.rdf mode vector
run 10000
write_data data.after_production_run

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2
src/USER-MISC/README
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@ -76,6 +76,8 @@ pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
pair_style cosine/squared, Eugen Rozic, eugen.rozic.17 at ucl.ac.uk, 9 Aug 19
pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
pair_style coul/shield, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18
pair_style coul/slater/cut, Evangelos Voyiatzis, evoyiatzis at gmail.com, 26 February 2020
pair_style coul/slater/long, Evangelos Voyiatzis, evoyiatzis at gmail.com, 26 February 2020
pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
pair_style e3b, Steven Strong (U Chicago), stevene.strong at gmail dot com, 16 Apr 19
pair_style drip, Mingjian Wen, University of Minnesota, wenxx151 at umn.edu, 17 Apr 19

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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: Evangelos Voyiatzis (Royal DSM)
* ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_coul_slater_cut.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;
/* ---------------------------------------------------------------------- */
PairCoulSlaterCut::PairCoulSlaterCut(LAMMPS *lmp) : PairCoulCut(lmp) {}
/* ---------------------------------------------------------------------- */
void PairCoulSlaterCut::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
double rsq,r2inv,r,rinv,forcecoul,factor_coul,bracket_term;
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];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r = sqrt(rsq);
rinv = 1.0/r;
bracket_term = 1 - exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
forcecoul = qqrd2e * scale[itype][jtype] *
qtmp*q[j] * bracket_term * rinv;
fpair = factor_coul*forcecoul * r2inv;
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) ecoul = factor_coul * qqrd2e *
scale[itype][jtype] * qtmp*q[j] * rinv *
(1 - (1 + r/lamda)*exp(-2*r/lamda));
if (evflag) ev_tally(i,j,nlocal,newton_pair,
0.0,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairCoulSlaterCut::settings(int narg, char **arg)
{
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
lamda = force->numeric(FLERR,arg[0]);
cut_global = 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; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCoulSlaterCut::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&lamda,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 PairCoulSlaterCut::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&lamda,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(&lamda,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
double PairCoulSlaterCut::single(int i, int j, int /*itype*/, int /*jtype*/,
double rsq, double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r2inv,r,rinv,forcecoul,phicoul,bracket_term;
r2inv = 1.0/rsq;
r = sqrt(rsq);
rinv = 1.0/r;
bracket_term = 1 - exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
forcecoul = force->qqrd2e * atom->q[i]*atom->q[j] *
bracket_term * rinv;
fforce = factor_coul*forcecoul * r2inv;
phicoul = force->qqrd2e * atom->q[i]*atom->q[j] * rinv * (1 - (1 + r/lamda)*exp(-2*r/lamda));
return factor_coul*phicoul;
}

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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/slater/cut,PairCoulSlaterCut)
#else
#ifndef LMP_PAIR_COUL_SLATER_CUT_H
#define LMP_PAIR_COUL_SLATER_CUT_H
#include "pair_coul_cut.h"
namespace LAMMPS_NS {
class PairCoulSlaterCut : public PairCoulCut {
public:
PairCoulSlaterCut(class LAMMPS *);
virtual void compute(int, int);
void settings(int, char **);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
double single(int, int, int, int, double, double, double, double &);
protected:
double lamda;
};
}
#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.
*/

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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: Evangelos Voyiatzis (Royal DSM)
* ------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_coul_slater_long.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
/* ---------------------------------------------------------------------- */
PairCoulSlaterLong::PairCoulSlaterLong(LAMMPS *lmp) : Pair(lmp)
{
ewaldflag = pppmflag = 1;
//ftable = NULL;
qdist = 0.0;
}
/* ---------------------------------------------------------------------- */
PairCoulSlaterLong::~PairCoulSlaterLong()
{
if (!copymode) {
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(scale);
}
//if (ftable) free_tables();
}
}
/* ---------------------------------------------------------------------- */
void PairCoulSlaterLong::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
// double fraction,table;
double r,r2inv,forcecoul,factor_coul;
double grij,expm2,prefactor,t,erfc;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq;
double slater_term;
// int itable;
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];
if (rsq < cut_coulsq) {
r2inv = 1.0/rsq;
// if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
prefactor = qqrd2e * scale[itype][jtype] * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
/*
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = scale[itype][jtype] * qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = scale[itype][jtype] * qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
*/
fpair = forcecoul * r2inv;
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 (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
/*
else {
table = etable[itable] + fraction*detable[itable];
ecoul = scale[itype][jtype] * qtmp*q[j] * table;
}
*/
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
}
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 PairCoulSlaterLong::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(scale,n+1,n+1,"pair:scale");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairCoulSlaterLong::settings(int narg, char **arg)
{
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
lamda = force->numeric(FLERR,arg[0]);
cut_coul = force->numeric(FLERR,arg[1]);
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairCoulSlaterLong::coeff(int narg, char **arg)
{
if (narg != 2) 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);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
scale[i][j] = 1.0;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairCoulSlaterLong::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style coul/slater/long requires atom attribute q");
neighbor->request(this,instance_me);
cut_coulsq = cut_coul * cut_coul;
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == NULL)
error->all(FLERR,"Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;
// setup force tables
// if (ncoultablebits) init_tables(cut_coul,NULL);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairCoulSlaterLong::init_one(int i, int j)
{
scale[j][i] = scale[i][j];
return cut_coul+2.0*qdist;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCoulSlaterLong::write_restart(FILE *fp)
{
write_restart_settings(fp);
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j])
fwrite(&scale[i][j],sizeof(double),1,fp);
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairCoulSlaterLong::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 (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) fread(&scale[i][j],sizeof(double),1,fp);
MPI_Bcast(&scale[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCoulSlaterLong::write_restart_settings(FILE *fp)
{
fwrite(&cut_coul,sizeof(double),1,fp);
fwrite(&lamda,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
//fwrite(&ncoultablebits,sizeof(int),1,fp);
//fwrite(&tabinner,sizeof(double),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairCoulSlaterLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_coul,sizeof(double),1,fp);
fread(&lamda,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
//fread(&ncoultablebits,sizeof(int),1,fp);
//fread(&tabinner,sizeof(double),1,fp);
}
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
MPI_Bcast(&lamda,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
//MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world);
//MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world);
}
/* ---------------------------------------------------------------------- */
double PairCoulSlaterLong::single(int i, int j, int /*itype*/, int /*jtype*/,
double rsq,
double factor_coul, double /*factor_lj*/,
double &fforce)
{
double r2inv,r,grij,expm2,t,erfc,prefactor;
double slater_term;
// double fraction,table;
double forcecoul,phicoul;
// int itable;
r2inv = 1.0/rsq;
// if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
/*
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = atom->q[i]*atom->q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = atom->q[i]*atom->q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
*/
fforce = forcecoul * r2inv;
// if (!ncoultablebits || rsq <= tabinnersq)
phicoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
/*
else {
table = etable[itable] + fraction*detable[itable];
phicoul = atom->q[i]*atom->q[j] * table;
}
*/
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
return phicoul;
}
/* ---------------------------------------------------------------------- */
void *PairCoulSlaterLong::extract(const char *str, int &dim)
{
if (strcmp(str,"cut_coul") == 0) {
dim = 0;
return (void *) &cut_coul;
}
if (strcmp(str,"lamda") == 0) {
dim = 0;
return (void *) &lamda;
}
if (strcmp(str,"scale") == 0) {
dim = 2;
return (void *) scale;
}
return NULL;
}

78
src/USER-MISC/pair_coul_slater_long.h Normal file
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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/slater/long,PairCoulSlaterLong)
#else
#ifndef LMP_PAIR_COUL_SLATER_LONG_H
#define LMP_PAIR_COUL_SLATER_LONG_H
#include "pair.h"
namespace LAMMPS_NS {
class PairCoulSlaterLong : public Pair {
public:
PairCoulSlaterLong(class LAMMPS *);
~PairCoulSlaterLong();
virtual void compute(int, int);
virtual void settings(int, char **);
void coeff(int, char **);
virtual void init_style();
virtual double init_one(int, int);
void write_restart(FILE *);
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 &);
virtual void *extract(const char *, int &);
protected:
double cut_coul,cut_coulsq,qdist;
double lamda;
//double *cut_respa;
double g_ewald;
double **scale;
virtual void allocate();
};
}
#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: Pair style coul/slater/long requires atom attribute q
The atom style defined does not have this attribute.
E: Pair style requires a KSpace style
No kspace style is defined.
*/