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enable clang-format

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This commit is contained in:
Axel Kohlmeyer
2022-03-05 20:16:10 -05:00
parent 875560b827
commit c5c3c335c9
1 changed files with 139 additions and 154 deletions
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293
src/pair_zbl.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
@ -18,18 +17,18 @@
#include "pair_zbl.h"
#include <cmath>
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "pair_zbl_const.h"
#include <cmath>
// From J.F. Zeigler, J. P. Biersack and U. Littmark,
// "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985.
@ -38,7 +37,8 @@ using namespace PairZBLConstants;
/* ---------------------------------------------------------------------- */
PairZBL::PairZBL(LAMMPS *lmp) : Pair(lmp) {
PairZBL::PairZBL(LAMMPS *lmp) : Pair(lmp)
{
writedata = 1;
}
@ -70,13 +70,13 @@ PairZBL::~PairZBL()
void PairZBL::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,r,t,fswitch,eswitch;
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, r, t, fswitch, eswitch;
int *ilist, *jlist, *numneigh, **firstneigh;
evdwl = 0.0;
ev_init(eflag,vflag);
ev_init(eflag, vflag);
double **x = atom->x;
double **f = atom->f;
@ -107,7 +107,7 @@ void PairZBL::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 < cut_globalsq) {
@ -116,33 +116,30 @@ void PairZBL::compute(int eflag, int vflag)
if (rsq > cut_innersq) {
t = r - cut_inner;
fswitch = t*t *
(sw1[itype][jtype] + sw2[itype][jtype]*t);
fswitch = t * t * (sw1[itype][jtype] + sw2[itype][jtype] * t);
fpair += fswitch;
}
fpair *= -1.0/r;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
fpair *= -1.0 / r;
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) {
evdwl = e_zbl(r, itype, jtype);
evdwl += sw5[itype][jtype];
if (rsq > cut_innersq) {
eswitch = t*t*t *
(sw3[itype][jtype] + sw4[itype][jtype]*t);
eswitch = t * t * t * (sw3[itype][jtype] + sw4[itype][jtype] * t);
evdwl += eswitch;
}
}
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);
}
}
}
@ -157,26 +154,25 @@ void PairZBL::compute(int eflag, int vflag)
void PairZBL::allocate()
{
allocated = 1;
int n = atom->ntypes;
const 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(cutsq, np1, np1, "pair:cutsq");
memory->create(z,n+1,"pair:z");
memory->create(d1a,n+1,n+1,"pair:d1a");
memory->create(d2a,n+1,n+1,"pair:d2a");
memory->create(d3a,n+1,n+1,"pair:d3a");
memory->create(d4a,n+1,n+1,"pair:d4a");
memory->create(zze,n+1,n+1,"pair:zze");
memory->create(sw1,n+1,n+1,"pair:sw1");
memory->create(sw2,n+1,n+1,"pair:sw2");
memory->create(sw3,n+1,n+1,"pair:sw3");
memory->create(sw4,n+1,n+1,"pair:sw4");
memory->create(sw5,n+1,n+1,"pair:sw5");
memory->create(z, np1, "pair:z");
memory->create(d1a, np1, np1, "pair:d1a");
memory->create(d2a, np1, np1, "pair:d2a");
memory->create(d3a, np1, np1, "pair:d3a");
memory->create(d4a, np1, np1, "pair:d4a");
memory->create(zze, np1, np1, "pair:zze");
memory->create(sw1, np1, np1, "pair:sw1");
memory->create(sw2, np1, np1, "pair:sw2");
memory->create(sw3, np1, np1, "pair:sw3");
memory->create(sw4, np1, np1, "pair:sw4");
memory->create(sw5, np1, np1, "pair:sw5");
}
/* ----------------------------------------------------------------------
@ -185,15 +181,13 @@ void PairZBL::allocate()
void PairZBL::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");
cut_inner = utils::numeric(FLERR,arg[0],false,lmp);
cut_global = utils::numeric(FLERR,arg[1],false,lmp);
cut_inner = utils::numeric(FLERR, arg[0], false, lmp);
cut_global = utils::numeric(FLERR, arg[1], false, lmp);
if (cut_inner <= 0.0 )
error->all(FLERR,"Illegal pair_style command");
if (cut_inner > cut_global)
error->all(FLERR,"Illegal pair_style command");
if (cut_inner <= 0.0) error->all(FLERR, "Illegal pair_style command");
if (cut_inner > cut_global) error->all(FLERR, "Illegal pair_style command");
}
/* ----------------------------------------------------------------------
@ -205,28 +199,26 @@ void PairZBL::coeff(int narg, char **arg)
{
double z_one, z_two;
if (narg != 4)
error->all(FLERR,"Incorrect args for pair coefficients");
if (narg != 4) error->all(FLERR, "Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi;
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
int ilo, ihi;
utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
int jlo,jhi;
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
int jlo, jhi;
utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
z_one = utils::numeric(FLERR,arg[2],false,lmp);
z_two = utils::numeric(FLERR,arg[3],false,lmp);
z_one = utils::numeric(FLERR, arg[2], false, lmp);
z_two = utils::numeric(FLERR, arg[3], false, lmp);
// set flag for each i-j pair
// set z-parameter only for i-i pairs
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++) {
if (i == j) {
if (z_one != z_two)
error->all(FLERR,"Incorrect args for pair coefficients");
if (z_one != z_two) error->all(FLERR, "Incorrect args for pair coefficients");
z[i] = z_one;
}
setflag[i][j] = 1;
@ -235,7 +227,7 @@ void PairZBL::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");
}
/* ----------------------------------------------------------------------
@ -256,8 +248,7 @@ void PairZBL::init_style()
double PairZBL::init_one(int i, int j)
{
if (setflag[i][j] == 0)
set_coeff(i, j, z[i], z[j]);
if (setflag[i][j] == 0) set_coeff(i, j, z[i], z[j]);
return cut_global;
}
@ -272,8 +263,8 @@ void PairZBL::write_restart(FILE *fp)
int i;
for (i = 1; i <= atom->ntypes; i++) {
fwrite(&setflag[i][i],sizeof(int),1,fp);
if (setflag[i][i]) fwrite(&z[i],sizeof(double),1,fp);
fwrite(&setflag[i][i], sizeof(int), 1, fp);
if (setflag[i][i]) fwrite(&z[i], sizeof(double), 1, fp);
}
}
@ -286,20 +277,19 @@ void PairZBL::read_restart(FILE *fp)
read_restart_settings(fp);
allocate();
int i,j;
int i, j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++) {
if (me == 0) utils::sfread(FLERR,&setflag[i][i],sizeof(int),1,fp,nullptr,error);
MPI_Bcast(&setflag[i][i],1,MPI_INT,0,world);
if (me == 0) utils::sfread(FLERR, &setflag[i][i], sizeof(int), 1, fp, nullptr, error);
MPI_Bcast(&setflag[i][i], 1, MPI_INT, 0, world);
if (setflag[i][i]) {
if (me == 0) utils::sfread(FLERR,&z[i],sizeof(double),1,fp,nullptr,error);
MPI_Bcast(&z[i],1,MPI_DOUBLE,0,world);
if (me == 0) utils::sfread(FLERR, &z[i], sizeof(double), 1, fp, nullptr, error);
MPI_Bcast(&z[i], 1, MPI_DOUBLE, 0, world);
}
}
for (i = 1; i <= atom->ntypes; i++)
for (j = 1; j <= atom->ntypes; j++)
set_coeff(i,j,z[i],z[j]);
for (j = 1; j <= atom->ntypes; j++) set_coeff(i, j, z[i], z[j]);
}
/* ----------------------------------------------------------------------
@ -308,11 +298,11 @@ void PairZBL::read_restart(FILE *fp)
void PairZBL::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&cut_inner,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
fwrite(&tail_flag,sizeof(int),1,fp);
fwrite(&cut_global, sizeof(double), 1, fp);
fwrite(&cut_inner, sizeof(double), 1, fp);
fwrite(&offset_flag, sizeof(int), 1, fp);
fwrite(&mix_flag, sizeof(int), 1, fp);
fwrite(&tail_flag, sizeof(int), 1, fp);
}
/* ----------------------------------------------------------------------
@ -323,17 +313,17 @@ void PairZBL::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut_inner,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,&tail_flag,sizeof(int),1,fp,nullptr,error);
utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error);
utils::sfread(FLERR, &cut_inner, 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, &tail_flag, sizeof(int), 1, fp, nullptr, error);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_inner,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(&tail_flag,1,MPI_INT,0,world);
MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut_inner, 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(&tail_flag, 1, MPI_INT, 0, world);
}
/* ----------------------------------------------------------------------
@ -342,8 +332,7 @@ void PairZBL::read_restart_settings(FILE *fp)
void PairZBL::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g\n",i,z[i],z[i]);
for (int i = 1; i <= atom->ntypes; i++) fprintf(fp, "%d %g %g\n", i, z[i], z[i]);
}
/* ----------------------------------------------------------------------
@ -353,33 +342,29 @@ void PairZBL::write_data(FILE *fp)
void PairZBL::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,z[i],z[j]);
for (int j = i; j <= atom->ntypes; j++) fprintf(fp, "%d %d %g %g\n", i, j, z[i], z[j]);
}
/* ---------------------------------------------------------------------- */
double PairZBL::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
double /*dummy1*/, double /*dummy2*/,
double &fforce)
double PairZBL::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, double /*dummy1*/,
double /*dummy2*/, double &fforce)
{
double phi,r,t,eswitch,fswitch;
double phi, r, t, eswitch, fswitch;
r = sqrt(rsq);
fforce = dzbldr(r, itype, jtype);
if (rsq > cut_innersq) {
t = r - cut_inner;
fswitch = t*t *
(sw1[itype][jtype] + sw2[itype][jtype]*t);
fswitch = t * t * (sw1[itype][jtype] + sw2[itype][jtype] * t);
fforce += fswitch;
}
fforce *= -1.0/r;
fforce *= -1.0 / r;
phi = e_zbl(r, itype, jtype);
phi += sw5[itype][jtype];
if (rsq > cut_innersq) {
eswitch = t*t*t *
(sw3[itype][jtype] + sw4[itype][jtype]*t);
eswitch = t * t * t * (sw3[itype][jtype] + sw4[itype][jtype] * t);
phi += eswitch;
}
@ -390,55 +375,56 @@ double PairZBL::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
compute ZBL pair energy
------------------------------------------------------------------------- */
double PairZBL::e_zbl(double r, int i, int j) {
double PairZBL::e_zbl(double r, int i, int j)
{
double d1aij = d1a[i][j];
double d2aij = d2a[i][j];
double d3aij = d3a[i][j];
double d4aij = d4a[i][j];
double zzeij = zze[i][j];
double rinv = 1.0/r;
double rinv = 1.0 / r;
double sum = c1*exp(-d1aij*r);
sum += c2*exp(-d2aij*r);
sum += c3*exp(-d3aij*r);
sum += c4*exp(-d4aij*r);
double sum = c1 * exp(-d1aij * r);
sum += c2 * exp(-d2aij * r);
sum += c3 * exp(-d3aij * r);
sum += c4 * exp(-d4aij * r);
double result = zzeij*sum*rinv;
double result = zzeij * sum * rinv;
return result;
}
/* ----------------------------------------------------------------------
compute ZBL first derivative
------------------------------------------------------------------------- */
double PairZBL::dzbldr(double r, int i, int j) {
double PairZBL::dzbldr(double r, int i, int j)
{
double d1aij = d1a[i][j];
double d2aij = d2a[i][j];
double d3aij = d3a[i][j];
double d4aij = d4a[i][j];
double zzeij = zze[i][j];
double rinv = 1.0/r;
double rinv = 1.0 / r;
double e1 = exp(-d1aij*r);
double e2 = exp(-d2aij*r);
double e3 = exp(-d3aij*r);
double e4 = exp(-d4aij*r);
double e1 = exp(-d1aij * r);
double e2 = exp(-d2aij * r);
double e3 = exp(-d3aij * r);
double e4 = exp(-d4aij * r);
double sum = c1*e1;
sum += c2*e2;
sum += c3*e3;
sum += c4*e4;
double sum = c1 * e1;
sum += c2 * e2;
sum += c3 * e3;
sum += c4 * e4;
double sum_p = -c1*d1aij*e1;
sum_p -= c2*d2aij*e2;
sum_p -= c3*d3aij*e3;
sum_p -= c4*d4aij*e4;
double sum_p = -c1 * d1aij * e1;
sum_p -= c2 * d2aij * e2;
sum_p -= c3 * d3aij * e3;
sum_p -= c4 * d4aij * e4;
double result = zzeij*(sum_p - sum*rinv)*rinv;
double result = zzeij * (sum_p - sum * rinv) * rinv;
return result;
}
@ -447,37 +433,37 @@ double PairZBL::dzbldr(double r, int i, int j) {
compute ZBL second derivative
------------------------------------------------------------------------- */
double PairZBL::d2zbldr2(double r, int i, int j) {
double PairZBL::d2zbldr2(double r, int i, int j)
{
double d1aij = d1a[i][j];
double d2aij = d2a[i][j];
double d3aij = d3a[i][j];
double d4aij = d4a[i][j];
double zzeij = zze[i][j];
double rinv = 1.0/r;
double rinv = 1.0 / r;
double e1 = exp(-d1aij*r);
double e2 = exp(-d2aij*r);
double e3 = exp(-d3aij*r);
double e4 = exp(-d4aij*r);
double e1 = exp(-d1aij * r);
double e2 = exp(-d2aij * r);
double e3 = exp(-d3aij * r);
double e4 = exp(-d4aij * r);
double sum = c1*e1;
sum += c2*e2;
sum += c3*e3;
sum += c4*e4;
double sum = c1 * e1;
sum += c2 * e2;
sum += c3 * e3;
sum += c4 * e4;
double sum_p = c1*e1*d1aij;
sum_p += c2*e2*d2aij;
sum_p += c3*e3*d3aij;
sum_p += c4*e4*d4aij;
double sum_p = c1 * e1 * d1aij;
sum_p += c2 * e2 * d2aij;
sum_p += c3 * e3 * d3aij;
sum_p += c4 * e4 * d4aij;
double sum_pp = c1*e1*d1aij*d1aij;
sum_pp += c2*e2*d2aij*d2aij;
sum_pp += c3*e3*d3aij*d3aij;
sum_pp += c4*e4*d4aij*d4aij;
double sum_pp = c1 * e1 * d1aij * d1aij;
sum_pp += c2 * e2 * d2aij * d2aij;
sum_pp += c3 * e3 * d3aij * d3aij;
sum_pp += c4 * e4 * d4aij * d4aij;
double result = zzeij*(sum_pp + 2.0*sum_p*rinv +
2.0*sum*rinv*rinv)*rinv;
double result = zzeij * (sum_pp + 2.0 * sum_p * rinv + 2.0 * sum * rinv * rinv) * rinv;
return result;
}
@ -488,12 +474,12 @@ double PairZBL::d2zbldr2(double r, int i, int j) {
void PairZBL::set_coeff(int i, int j, double zi, double zj)
{
double ainv = (pow(zi,pzbl) + pow(zj,pzbl))/(a0*force->angstrom);
d1a[i][j] = d1*ainv;
d2a[i][j] = d2*ainv;
d3a[i][j] = d3*ainv;
d4a[i][j] = d4*ainv;
zze[i][j] = zi*zj*force->qqr2e*force->qelectron*force->qelectron;
double ainv = (pow(zi, pzbl) + pow(zj, pzbl)) / (a0 * force->angstrom);
d1a[i][j] = d1 * ainv;
d2a[i][j] = d2 * ainv;
d3a[i][j] = d3 * ainv;
d4a[i][j] = d4 * ainv;
zze[i][j] = zi * zj * force->qqr2e * force->qelectron * force->qelectron;
d1a[j][i] = d1a[i][j];
d2a[j][i] = d2a[i][j];
@ -529,14 +515,14 @@ void PairZBL::set_coeff(int i, int j, double zi, double zj)
double fcp = dzbldr(cut_global, i, j);
double fcpp = d2zbldr2(cut_global, i, j);
double swa = (-3.0*fcp + tc*fcpp)/(tc*tc);
double swb = ( 2.0*fcp - tc*fcpp)/(tc*tc*tc);
double swc = -fc + (tc/2.0)*fcp - (tc*tc/12.0)*fcpp;
double swa = (-3.0 * fcp + tc * fcpp) / (tc * tc);
double swb = (2.0 * fcp - tc * fcpp) / (tc * tc * tc);
double swc = -fc + (tc / 2.0) * fcp - (tc * tc / 12.0) * fcpp;
sw1[i][j] = swa;
sw2[i][j] = swb;
sw3[i][j] = swa/3.0;
sw4[i][j] = swb/4.0;
sw3[i][j] = swa / 3.0;
sw4[i][j] = swb / 4.0;
sw5[i][j] = swc;
sw1[j][i] = sw1[i][j];
@ -545,4 +531,3 @@ void PairZBL::set_coeff(int i, int j, double zi, double zj)
sw4[j][i] = sw4[i][j];
sw5[j][i] = sw5[i][j];
}