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This commit is contained in:
Axel Kohlmeyer
2021-07-29 14:44:15 -04:00
parent 5b6b6b8767
commit ebe5e6c024
1 changed files with 115 additions and 108 deletions
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223
src/INTERLAYER/pair_coul_shield.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories https://www.lammps.org/, Sandia National Laboratories
@ -20,22 +19,24 @@
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "pair_coul_shield.h" #include "pair_coul_shield.h"
#include <cmath>
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "math_special.h"
#include "error.h" #include "error.h"
#include "force.h"
#include "math_special.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include <cmath>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
PairCoulShield::PairCoulShield(LAMMPS *lmp) : Pair(lmp) { PairCoulShield::PairCoulShield(LAMMPS *lmp) : Pair(lmp)
{
tap_flag = 1; tap_flag = 1;
} }
@ -57,13 +58,13 @@ PairCoulShield::~PairCoulShield()
void PairCoulShield::compute(int eflag, int vflag) void PairCoulShield::compute(int eflag, int vflag)
{ {
int i,j,ii,jj,inum,jnum,itype,jtype; int i, j, ii, jj, inum, jnum, itype, jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair,Tap,dTap; 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; double rsq, r, r3, rarg, th, depsdr, epsr, forcecoul, factor_coul, Vc, fvc;
int *ilist,*jlist,*numneigh,**firstneigh; int *ilist, *jlist, *numneigh, **firstneigh;
ecoul = 0.0; ecoul = 0.0;
ev_init(eflag,vflag); ev_init(eflag, vflag);
double **x = atom->x; double **x = atom->x;
double **f = atom->f; double **f = atom->f;
@ -100,47 +101,51 @@ void PairCoulShield::compute(int eflag, int vflag)
delx = xtmp - x[j][0]; delx = xtmp - x[j][0];
dely = ytmp - x[j][1]; dely = ytmp - x[j][1];
delz = ztmp - x[j][2]; delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz; rsq = delx * delx + dely * dely + delz * delz;
jtype = type[j]; jtype = type[j];
// only include the interaction between different layers // only include the interaction between different layers
if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) { if (rsq < cutsq[itype][jtype] && atom->molecule[i] != atom->molecule[j]) {
r = sqrt(rsq); r = sqrt(rsq);
r3 = rsq*r; r3 = rsq * r;
rarg = 1.0/sigmae[itype][jtype]; rarg = 1.0 / sigmae[itype][jtype];
th = r3 + MathSpecial::cube(rarg); th = r3 + MathSpecial::cube(rarg);
epsr = 1.0/pow(th,0.333333333333333333333333); epsr = 1.0 / pow(th, 1.0 / 3.0);
depsdr = MathSpecial::square(epsr); depsdr = MathSpecial::square(epsr);
depsdr *= depsdr; depsdr *= depsdr;
Vc = qqrd2e*qtmp*q[j]*epsr; Vc = qqrd2e * qtmp * q[j] * epsr;
// turn on/off taper function // turn on/off taper function
if (tap_flag) { if (tap_flag) {
Tap = calc_Tap(r,cut[itype][jtype]); Tap = calc_Tap(r, cut[itype][jtype]);
dTap = calc_dTap(r,cut[itype][jtype]); dTap = calc_dTap(r, cut[itype][jtype]);
} else {Tap = 1.0; dTap = 0.0;} } else {
Tap = 1.0;
dTap = 0.0;
}
forcecoul = qqrd2e*qtmp*q[j]*r*depsdr; forcecoul = qqrd2e * qtmp * q[j] * r * depsdr;
fvc = forcecoul*Tap - Vc*dTap/r; fvc = forcecoul * Tap - Vc * dTap / r;
fpair = factor_coul*fvc; fpair = factor_coul * fvc;
f[i][0] += delx*fpair; f[i][0] += delx * fpair;
f[i][1] += dely*fpair; f[i][1] += dely * fpair;
f[i][2] += delz*fpair; f[i][2] += delz * fpair;
if (newton_pair || j < nlocal) { if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair; f[j][0] -= delx * fpair;
f[j][1] -= dely*fpair; f[j][1] -= dely * fpair;
f[j][2] -= delz*fpair; f[j][2] -= delz * fpair;
} }
if (eflag) { if (eflag) {
if (tap_flag) ecoul = Vc*Tap; if (tap_flag)
else ecoul = Vc - offset[itype][jtype]; ecoul = Vc * Tap;
else
ecoul = Vc - offset[itype][jtype];
ecoul *= factor_coul; ecoul *= factor_coul;
} }
if (evflag) ev_tally(i,j,nlocal,newton_pair,0.0, if (evflag) ev_tally(i, j, nlocal, newton_pair, 0.0, ecoul, fpair, delx, dely, delz);
ecoul,fpair,delx,dely,delz);
} }
} }
} }
@ -157,15 +162,14 @@ void PairCoulShield::allocate()
allocated = 1; allocated = 1;
int n = atom->ntypes; int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag"); memory->create(setflag, n + 1, n + 1, "pair:setflag");
for (int i = 1; i <= n; i++) for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++) for (int j = i; j <= n; j++) setflag[i][j] = 0;
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq"); memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut"); memory->create(cut, n + 1, n + 1, "pair:cut");
memory->create(sigmae,n+1,n+1,"pair:sigmae"); memory->create(sigmae, n + 1, n + 1, "pair:sigmae");
memory->create(offset,n+1,n+1,"pair:offset"); memory->create(offset, n + 1, n + 1, "pair:offset");
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -174,17 +178,17 @@ void PairCoulShield::allocate()
void PairCoulShield::settings(int narg, char **arg) void PairCoulShield::settings(int narg, char **arg)
{ {
if (narg < 1 || narg > 2) error->all(FLERR,"Illegal pair_style command"); if (narg < 1 || narg > 2) error->all(FLERR, "Illegal pair_style command");
cut_global = utils::numeric(FLERR,arg[0],false,lmp); cut_global = utils::numeric(FLERR, arg[0], false, lmp);
if (narg == 2) tap_flag = utils::numeric(FLERR,arg[1],false,lmp); if (narg == 2) tap_flag = utils::numeric(FLERR, arg[1], false, lmp);
// reset cutoffs that have been explicitly set // reset cutoffs that have been explicitly set
if (allocated) { if (allocated) {
int i,j; int i, j;
for (i = 1; i <= atom->ntypes; i++) for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++) for (j = i + 1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global; if (setflag[i][j]) cut[i][j] = cut_global;
} }
} }
@ -195,21 +199,21 @@ void PairCoulShield::settings(int narg, char **arg)
void PairCoulShield::coeff(int narg, char **arg) void PairCoulShield::coeff(int narg, char **arg)
{ {
if (narg < 3 || narg > 4) error->all(FLERR,"Incorrect args for pair coefficients"); if (narg < 3 || narg > 4) error->all(FLERR, "Incorrect args for pair coefficients");
if (!allocated) allocate(); if (!allocated) allocate();
int ilo,ihi,jlo,jhi; int ilo, ihi, jlo, jhi;
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error); utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
double sigmae_one = utils::numeric(FLERR,arg[2],false,lmp); double sigmae_one = utils::numeric(FLERR, arg[2], false, lmp);
double cut_one = cut_global; double cut_one = cut_global;
if (narg == 4) cut_one = utils::numeric(FLERR,arg[3],false,lmp); if (narg == 4) cut_one = utils::numeric(FLERR, arg[3], false, lmp);
int count = 0; int count = 0;
for (int i = ilo; i <= ihi; i++) { for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) { for (int j = MAX(jlo, i); j <= jhi; j++) {
sigmae[i][j] = sigmae_one; sigmae[i][j] = sigmae_one;
cut[i][j] = cut_one; cut[i][j] = cut_one;
setflag[i][j] = 1; setflag[i][j] = 1;
@ -217,22 +221,20 @@ void PairCoulShield::coeff(int narg, char **arg)
} }
} }
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
init specific to this pair style init specific to this pair style
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void PairCoulShield::init_style() void PairCoulShield::init_style()
{ {
if (!atom->q_flag) if (!atom->q_flag) error->all(FLERR, "Pair style coul/shield requires atom attribute q");
error->all(FLERR,"Pair style coul/shield requires atom attribute q");
if (!atom->molecule_flag) if (!atom->molecule_flag)
error->all(FLERR,"Pair style coul/shield requires atom attribute molecule"); error->all(FLERR, "Pair style coul/shield requires atom attribute molecule");
neighbor->request(this,instance_me); neighbor->request(this, instance_me);
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -242,22 +244,23 @@ void PairCoulShield::init_style()
double PairCoulShield::init_one(int i, int j) double PairCoulShield::init_one(int i, int j)
{ {
if (setflag[i][j] == 0) { if (setflag[i][j] == 0) {
error->all(FLERR,"for pair style coul/shield, parameters need to be set explicitly for all pairs."); error->all(FLERR,
"for pair style coul/shield, parameters need to be set explicitly for all pairs.");
} }
double *q = atom->q; double *q = atom->q;
double qqrd2e = force->qqrd2e; double qqrd2e = force->qqrd2e;
double r,r3,rarg,th,epsr; double r, r3, rarg, th, epsr;
if (offset_flag) { if (offset_flag) {
r = cut[i][j]; r = cut[i][j];
r3 = r*r*r; r3 = r * r * r;
rarg = 1.0/sigmae[i][j]; rarg = 1.0 / sigmae[i][j];
th = r3 + MathSpecial::cube(rarg); th = r3 + MathSpecial::cube(rarg);
epsr = 1.0/pow(th,0.333333333333333333); epsr = 1.0 / pow(th, 1.0/3.0);
offset[i][j] = qqrd2e*q[i]*q[j]*epsr; offset[i][j] = qqrd2e * q[i] * q[j] * epsr;
} else offset[i][j] = 0.0; } else
offset[i][j] = 0.0;
sigmae[j][i] = sigmae[i][j]; sigmae[j][i] = sigmae[i][j];
offset[j][i] = offset[i][j]; offset[j][i] = offset[i][j];
@ -274,13 +277,13 @@ void PairCoulShield::write_restart(FILE *fp)
{ {
write_restart_settings(fp); write_restart_settings(fp);
int i,j; int i, j;
for (i = 1; i <= atom->ntypes; i++) for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) { for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp); fwrite(&setflag[i][j], sizeof(int), 1, fp);
if (setflag[i][j]) { if (setflag[i][j]) {
fwrite(&sigmae[i][j],sizeof(double),1,fp); fwrite(&sigmae[i][j], sizeof(double), 1, fp);
fwrite(&cut[i][j],sizeof(double),1,fp); fwrite(&cut[i][j], sizeof(double), 1, fp);
} }
} }
} }
@ -294,19 +297,19 @@ void PairCoulShield::read_restart(FILE *fp)
read_restart_settings(fp); read_restart_settings(fp);
allocate(); allocate();
int i,j; int i, j;
int me = comm->me; int me = comm->me;
for (i = 1; i <= atom->ntypes; i++) for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) { for (j = i; j <= atom->ntypes; j++) {
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
if (setflag[i][j]) { if (setflag[i][j]) {
if (me == 0) { if (me == 0) {
utils::sfread(FLERR,&sigmae[i][j],sizeof(double),1,fp,nullptr,error); utils::sfread(FLERR, &sigmae[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
} }
MPI_Bcast(&sigmae[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigmae[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
} }
} }
} }
@ -317,9 +320,9 @@ void PairCoulShield::read_restart(FILE *fp)
void PairCoulShield::write_restart_settings(FILE *fp) void PairCoulShield::write_restart_settings(FILE *fp)
{ {
fwrite(&cut_global,sizeof(double),1,fp); fwrite(&cut_global, sizeof(double), 1, fp);
fwrite(&offset_flag,sizeof(int),1,fp); fwrite(&offset_flag, sizeof(int), 1, fp);
fwrite(&mix_flag,sizeof(int),1,fp); fwrite(&mix_flag, sizeof(int), 1, fp);
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -329,23 +332,22 @@ void PairCoulShield::write_restart_settings(FILE *fp)
void PairCoulShield::read_restart_settings(FILE *fp) void PairCoulShield::read_restart_settings(FILE *fp)
{ {
if (comm->me == 0) { if (comm->me == 0) {
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error); utils::sfread(FLERR, &offset_flag, sizeof(int), 1, fp, nullptr, error);
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error);
} }
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world); MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world);
MPI_Bcast(&mix_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 PairCoulShield::single(int i, int j, int itype, int jtype, double rsq, double factor_coul,
double rsq, double factor_coul, double /*factor_lj*/, double /*factor_lj*/, double &fforce)
double &fforce)
{ {
double r, rarg,Vc,fvc,forcecoul,phishieldec; double r, rarg, Vc, fvc, forcecoul, phishieldec;
double r3,th,epsr,depsdr,Tap,dTap; double r3, th, epsr, depsdr, Tap, dTap;
double *q = atom->q; double *q = atom->q;
double qqrd2e = force->qqrd2e; double qqrd2e = force->qqrd2e;
@ -357,25 +359,30 @@ double PairCoulShield::single(int i, int j, int itype, int jtype,
} }
r = sqrt(rsq); r = sqrt(rsq);
r3 = rsq*r; r3 = rsq * r;
rarg = 1.0/sigmae[itype][jtype]; rarg = 1.0 / sigmae[itype][jtype];
th = r3 + MathSpecial::cube(rarg); th = r3 + MathSpecial::cube(rarg);
epsr = 1.0/pow(th,0.333333333333333333); epsr = 1.0 / pow(th, 1.0/3.0);
depsdr = epsr*epsr; depsdr = epsr * epsr;
depsdr *= depsdr; depsdr *= depsdr;
Vc = qqrd2e*q[i]*q[j]*epsr; Vc = qqrd2e * q[i] * q[j] * epsr;
// turn on/off taper function // turn on/off taper function
if (tap_flag) { if (tap_flag) {
Tap = calc_Tap(r,cut[itype][jtype]); Tap = calc_Tap(r, cut[itype][jtype]);
dTap = calc_dTap(r,cut[itype][jtype]); dTap = calc_dTap(r, cut[itype][jtype]);
} else {Tap = 1.0; dTap = 0.0;} } else {
Tap = 1.0;
dTap = 0.0;
}
forcecoul = qqrd2e*q[i]*q[j]*r*depsdr; forcecoul = qqrd2e * q[i] * q[j] * r * depsdr;
fvc = forcecoul*Tap - Vc*dTap/r; fvc = forcecoul * Tap - Vc * dTap / r;
fforce = factor_coul*fvc; fforce = factor_coul * fvc;
if (tap_flag) phishieldec = Vc*Tap; if (tap_flag)
else phishieldec = Vc - offset[itype][jtype]; phishieldec = Vc * Tap;
return factor_coul*phishieldec; else
phishieldec = Vc - offset[itype][jtype];
return factor_coul * phishieldec;
} }