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enable and apply clang-format

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This commit is contained in:
Axel Kohlmeyer
2022-05-20 06:51:36 -04:00
parent 21c2f8a74b
commit a16974ca48
1 changed files with 78 additions and 84 deletions
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162
src/pair_yukawa.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -14,14 +13,14 @@
#include "pair_yukawa.h"
#include <cmath>
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neigh_list.h"
#include <cmath>
using namespace LAMMPS_NS;
@ -53,13 +52,13 @@ PairYukawa::~PairYukawa()
void PairYukawa::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r,rinv,screening,forceyukawa,factor;
int *ilist,*jlist,*numneigh,**firstneigh;
int i, j, ii, jj, inum, jnum, itype, jtype;
double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair;
double rsq, r2inv, r, rinv, screening, forceyukawa, factor;
int *ilist, *jlist, *numneigh, **firstneigh;
evdwl = 0.0;
ev_init(eflag,vflag);
ev_init(eflag, vflag);
double **x = atom->x;
double **f = atom->f;
@ -92,25 +91,25 @@ void PairYukawa::compute(int eflag, int vflag)
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
rsq = delx * delx + dely * dely + delz * delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r2inv = 1.0 / rsq;
r = sqrt(rsq);
rinv = 1.0/r;
screening = exp(-kappa*r);
rinv = 1.0 / r;
screening = exp(-kappa * r);
forceyukawa = a[itype][jtype] * screening * (kappa + rinv);
fpair = factor*forceyukawa * r2inv;
fpair = factor * forceyukawa * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
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;
f[j][0] -= delx * fpair;
f[j][1] -= dely * fpair;
f[j][2] -= delz * fpair;
}
if (eflag) {
@ -118,8 +117,7 @@ void PairYukawa::compute(int eflag, int vflag)
evdwl *= factor;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
}
}
}
@ -134,18 +132,17 @@ void PairYukawa::compute(int eflag, int vflag)
void PairYukawa::allocate()
{
allocated = 1;
int n = atom->ntypes;
int np1 = atom->ntypes + 1;
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(setflag, np1, np1, "pair:setflag");
for (int i = 1; i < np1; i++)
for (int j = i; j < np1; j++) setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(rad,n+1,"pair:rad");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(a,n+1,n+1,"pair:a");
memory->create(offset,n+1,n+1,"pair:offset");
memory->create(cutsq, np1, np1, "pair:cutsq");
memory->create(rad, np1, "pair:rad");
memory->create(cut, np1, np1, "pair:cut");
memory->create(a, np1, np1, "pair:a");
memory->create(offset, np1, np1, "pair:offset");
}
/* ----------------------------------------------------------------------
@ -154,15 +151,15 @@ void PairYukawa::allocate()
void PairYukawa::settings(int narg, char **arg)
{
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
if (narg != 2) error->all(FLERR, "Illegal pair_style command");
kappa = utils::numeric(FLERR,arg[0],false,lmp);
cut_global = utils::numeric(FLERR,arg[1],false,lmp);
kappa = utils::numeric(FLERR, arg[0], false, lmp);
cut_global = utils::numeric(FLERR, arg[1], false, lmp);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
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;
@ -175,22 +172,21 @@ void PairYukawa::settings(int narg, char **arg)
void PairYukawa::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();
int ilo,ihi,jlo,jhi;
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
int ilo, ihi, jlo, jhi;
utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
double a_one = utils::numeric(FLERR,arg[2],false,lmp);
double a_one = utils::numeric(FLERR, arg[2], false, lmp);
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;
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++) {
a[i][j] = a_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
@ -198,7 +194,7 @@ void PairYukawa::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");
}
/* ----------------------------------------------------------------------
@ -208,14 +204,15 @@ void PairYukawa::coeff(int narg, char **arg)
double PairYukawa::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
a[i][j] = mix_energy(a[i][i],a[j][j],1.0,1.0);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
a[i][j] = mix_energy(a[i][i], a[j][j], 1.0, 1.0);
cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
}
if (offset_flag && (cut[i][j] > 0.0)) {
double screening = exp(-kappa * cut[i][j]);
offset[i][j] = a[i][j] * screening / cut[i][j];
} else offset[i][j] = 0.0;
} else
offset[i][j] = 0.0;
a[j][i] = a[i][j];
offset[j][i] = offset[i][j];
@ -231,13 +228,13 @@ void PairYukawa::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
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);
fwrite(&setflag[i][j], sizeof(int), 1, fp);
if (setflag[i][j]) {
fwrite(&a[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
fwrite(&a[i][j], sizeof(double), 1, fp);
fwrite(&cut[i][j], sizeof(double), 1, fp);
}
}
}
@ -252,19 +249,19 @@ void PairYukawa::read_restart(FILE *fp)
allocate();
int i,j;
int i, j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
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);
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);
if (setflag[i][j]) {
if (me == 0) {
utils::sfread(FLERR,&a[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR, &a[i][j], sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
}
MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&a[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
}
}
}
@ -275,10 +272,10 @@ void PairYukawa::read_restart(FILE *fp)
void PairYukawa::write_restart_settings(FILE *fp)
{
fwrite(&kappa,sizeof(double),1,fp);
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
fwrite(&kappa, sizeof(double), 1, fp);
fwrite(&cut_global, sizeof(double), 1, fp);
fwrite(&offset_flag, sizeof(int), 1, fp);
fwrite(&mix_flag, sizeof(int), 1, fp);
}
/* ----------------------------------------------------------------------
@ -288,15 +285,15 @@ void PairYukawa::write_restart_settings(FILE *fp)
void PairYukawa::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
utils::sfread(FLERR,&kappa,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,&mix_flag,sizeof(int),1,fp,nullptr,error);
utils::sfread(FLERR, &kappa, 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, &mix_flag, sizeof(int), 1, fp, nullptr, error);
}
MPI_Bcast(&kappa,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(&mix_flag,1,MPI_INT,0,world);
MPI_Bcast(&kappa, 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(&mix_flag, 1, MPI_INT, 0, world);
}
/* ----------------------------------------------------------------------
@ -305,8 +302,7 @@ void PairYukawa::read_restart_settings(FILE *fp)
void PairYukawa::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g\n",i,a[i][i]);
for (int i = 1; i <= atom->ntypes; i++) fprintf(fp, "%d %g\n", i, a[i][i]);
}
/* ----------------------------------------------------------------------
@ -316,25 +312,23 @@ void PairYukawa::write_data(FILE *fp)
void PairYukawa::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %d %g %g\n",i,j,a[i][j],cut[i][j]);
for (int j = i; j <= atom->ntypes; j++) fprintf(fp, "%d %d %g %g\n", i, j, a[i][j], cut[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairYukawa::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
double /*factor_coul*/, double factor_lj,
double &fforce)
double /*factor_coul*/, double factor_lj, double &fforce)
{
double r2inv,r,rinv,screening,forceyukawa,phi;
double r2inv, r, rinv, screening, forceyukawa, phi;
r2inv = 1.0/rsq;
r2inv = 1.0 / rsq;
r = sqrt(rsq);
rinv = 1.0/r;
screening = exp(-kappa*r);
rinv = 1.0 / r;
screening = exp(-kappa * r);
forceyukawa = a[itype][jtype] * screening * (kappa + rinv);
fforce = factor_lj*forceyukawa * r2inv;
fforce = factor_lj * forceyukawa * r2inv;
phi = a[itype][jtype] * screening * rinv - offset[itype][jtype];
return factor_lj*phi;
return factor_lj * phi;
}