ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

add clang-format support to plugin examples

Browse Source
This commit is contained in:
Axel Kohlmeyer
2021-05-05 23:51:12 -04:00
parent 5fcd0d8b79
commit 49a7bb57de
21 changed files with 376 additions and 326 deletions
Download Patch File Download Diff File Expand all files Collapse all files

184
examples/plugins/pair_morse2.cpp
View File

@ -13,14 +13,14 @@
#include "pair_morse2.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neigh_list.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
@ -52,13 +52,13 @@ PairMorse2::~PairMorse2()
void PairMorse2::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,dr,dexp,factor_lj;
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, dr, dexp, factor_lj;
int *ilist, *jlist, *numneigh, **firstneigh;
evdwl = 0.0;
ev_init(eflag,vflag);
ev_init(eflag, vflag);
double **x = atom->x;
double **f = atom->f;
@ -91,32 +91,33 @@ void PairMorse2::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]) {
r = sqrt(rsq);
dr = r - r0[itype][jtype];
dexp = exp(-alpha[itype][jtype] * dr);
fpair = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
fpair = factor_lj * morse1[itype][jtype] * (dexp * dexp - dexp) / r;
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) {
evdwl = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
offset[itype][jtype];
evdwl = d0[itype][jtype] * (dexp * dexp - 2.0 * dexp) -
offset[itype][jtype];
evdwl *= factor_lj;
}
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);
}
}
}
@ -133,19 +134,18 @@ void PairMorse2::allocate()
allocated = 1;
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 j = i; j <= n; j++)
setflag[i][j] = 0;
for (int j = i; j <= n; j++) 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(d0,n+1,n+1,"pair:d0");
memory->create(alpha,n+1,n+1,"pair:alpha");
memory->create(r0,n+1,n+1,"pair:r0");
memory->create(morse1,n+1,n+1,"pair:morse1");
memory->create(offset,n+1,n+1,"pair:offset");
memory->create(cut, n + 1, n + 1, "pair:cut");
memory->create(d0, n + 1, n + 1, "pair:d0");
memory->create(alpha, n + 1, n + 1, "pair:alpha");
memory->create(r0, n + 1, n + 1, "pair:r0");
memory->create(morse1, n + 1, n + 1, "pair:morse1");
memory->create(offset, n + 1, n + 1, "pair:offset");
}
/* ----------------------------------------------------------------------
@ -154,14 +154,14 @@ void PairMorse2::allocate()
void PairMorse2::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
if (narg != 1) 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);
// 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;
@ -175,23 +175,23 @@ void PairMorse2::settings(int narg, char **arg)
void PairMorse2::coeff(int narg, char **arg)
{
if (narg < 5 || narg > 6)
error->all(FLERR,"Incorrect args for pair coefficients");
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 d0_one = utils::numeric(FLERR,arg[2],false,lmp);
double alpha_one = utils::numeric(FLERR,arg[3],false,lmp);
double r0_one = utils::numeric(FLERR,arg[4],false,lmp);
double d0_one = utils::numeric(FLERR, arg[2], false, lmp);
double alpha_one = utils::numeric(FLERR, arg[3], false, lmp);
double r0_one = utils::numeric(FLERR, arg[4], false, lmp);
double cut_one = cut_global;
if (narg == 6) cut_one = utils::numeric(FLERR,arg[5],false,lmp);
if (narg == 6) cut_one = utils::numeric(FLERR, arg[5], 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++) {
d0[i][j] = d0_one;
alpha[i][j] = alpha_one;
r0[i][j] = r0_one;
@ -201,24 +201,24 @@ void PairMorse2::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 for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairMorse2::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set");
morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];
morse1[i][j] = 2.0 * d0[i][j] * alpha[i][j];
if (offset_flag) {
double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
} else offset[i][j] = 0.0;
offset[i][j] = d0[i][j] * (exp(2.0 * alpha_dr) - 2.0 * exp(alpha_dr));
} else
offset[i][j] = 0.0;
d0[j][i] = d0[i][j];
alpha[j][i] = alpha[i][j];
@ -237,15 +237,15 @@ void PairMorse2::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(&d0[i][j],sizeof(double),1,fp);
fwrite(&alpha[i][j],sizeof(double),1,fp);
fwrite(&r0[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
fwrite(&d0[i][j], sizeof(double), 1, fp);
fwrite(&alpha[i][j], sizeof(double), 1, fp);
fwrite(&r0[i][j], sizeof(double), 1, fp);
fwrite(&cut[i][j], sizeof(double), 1, fp);
}
}
}
@ -260,23 +260,29 @@ void PairMorse2::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,&d0[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&alpha[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&r0[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
utils::sfread(FLERR, &d0[i][j], sizeof(double), 1, fp, nullptr,
error);
utils::sfread(FLERR, &alpha[i][j], sizeof(double), 1, fp, nullptr,
error);
utils::sfread(FLERR, &r0[i][j], sizeof(double), 1, fp, nullptr,
error);
utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr,
error);
}
MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&d0[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&alpha[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&r0[i][j], 1, MPI_DOUBLE, 0, world);
MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
}
}
}
@ -287,9 +293,9 @@ void PairMorse2::read_restart(FILE *fp)
void PairMorse2::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);
fwrite(&cut_global, sizeof(double), 1, fp);
fwrite(&offset_flag, sizeof(int), 1, fp);
fwrite(&mix_flag, sizeof(int), 1, fp);
}
/* ----------------------------------------------------------------------
@ -299,13 +305,13 @@ void PairMorse2::write_restart_settings(FILE *fp)
void PairMorse2::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
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, &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(&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(&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);
}
/* ----------------------------------------------------------------------
@ -315,7 +321,7 @@ void PairMorse2::read_restart_settings(FILE *fp)
void PairMorse2::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g %g\n",i,d0[i][i],alpha[i][i],r0[i][i]);
fprintf(fp, "%d %g %g %g\n", i, d0[i][i], alpha[i][i], r0[i][i]);
}
/* ----------------------------------------------------------------------
@ -326,25 +332,25 @@ void PairMorse2::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 %g %g\n",
i,j,d0[i][j],alpha[i][j],r0[i][j],cut[i][j]);
fprintf(fp, "%d %d %g %g %g %g\n", i, j, d0[i][j], alpha[i][j], r0[i][j],
cut[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairMorse2::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
double /*factor_coul*/, double factor_lj,
double &fforce)
double PairMorse2::single(int /*i*/, int /*j*/, int itype, int jtype,
double rsq, double /*factor_coul*/, double factor_lj,
double &fforce)
{
double r,dr,dexp,phi;
double r, dr, dexp, phi;
r = sqrt(rsq);
dr = r - r0[itype][jtype];
dexp = exp(-alpha[itype][jtype] * dr);
fforce = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
fforce = factor_lj * morse1[itype][jtype] * (dexp * dexp - dexp) / r;
phi = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - offset[itype][jtype];
return factor_lj*phi;
phi = d0[itype][jtype] * (dexp * dexp - 2.0 * dexp) - offset[itype][jtype];
return factor_lj * phi;
}
/* ---------------------------------------------------------------------- */
@ -352,8 +358,8 @@ double PairMorse2::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq
void *PairMorse2::extract(const char *str, int &dim)
{
dim = 2;
if (strcmp(str,"d0") == 0) return (void *) d0;
if (strcmp(str,"r0") == 0) return (void *) r0;
if (strcmp(str,"alpha") == 0) return (void *) alpha;
if (strcmp(str, "d0") == 0) return (void *) d0;
if (strcmp(str, "r0") == 0) return (void *) r0;
if (strcmp(str, "alpha") == 0) return (void *) alpha;
return nullptr;
}