enable and apply clang-format
This commit is contained in:
Axel Kohlmeyer
@ -1,4 +1,3 @@
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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@ -14,16 +13,16 @@
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#include "pair_lj_expand.h"
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#include <cmath>
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#include <cstring>
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#include "atom.h"
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#include "comm.h"
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#include "error.h"
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#include "force.h"
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#include "neigh_list.h"
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#include "math_const.h"
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#include "memory.h"
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#include "error.h"
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#include "neigh_list.h"
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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using namespace MathConst;
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@ -61,14 +60,14 @@ PairLJExpand::~PairLJExpand()
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void PairLJExpand::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
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double rsq,r2inv,r6inv,forcelj,factor_lj;
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double r,rshift,rshiftsq;
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int *ilist,*jlist,*numneigh,**firstneigh;
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int i, j, ii, jj, inum, jnum, itype, jtype;
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double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair;
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double rsq, r2inv, r6inv, forcelj, factor_lj;
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double r, rshift, rshiftsq;
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int *ilist, *jlist, *numneigh, **firstneigh;
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evdwl = 0.0;
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ev_init(eflag,vflag);
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ev_init(eflag, vflag);
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double **x = atom->x;
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double **f = atom->f;
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@ -101,35 +100,33 @@ void PairLJExpand::compute(int eflag, int vflag)
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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rsq = delx * delx + dely * dely + delz * delz;
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jtype = type[j];
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if (rsq < cutsq[itype][jtype]) {
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r = sqrt(rsq);
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rshift = r - shift[itype][jtype];
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rshiftsq = rshift*rshift;
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r2inv = 1.0/rshiftsq;
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r6inv = r2inv*r2inv*r2inv;
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forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
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fpair = factor_lj*forcelj/rshift/r;
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rshiftsq = rshift * rshift;
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r2inv = 1.0 / rshiftsq;
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r6inv = r2inv * r2inv * r2inv;
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forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
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fpair = factor_lj * forcelj / rshift / r;
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f[i][0] += delx*fpair;
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f[i][1] += dely*fpair;
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f[i][2] += delz*fpair;
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f[i][0] += delx * fpair;
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f[i][1] += dely * fpair;
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f[i][2] += delz * fpair;
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if (newton_pair || j < nlocal) {
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f[j][0] -= delx*fpair;
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f[j][1] -= dely*fpair;
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f[j][2] -= delz*fpair;
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f[j][0] -= delx * fpair;
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f[j][1] -= dely * fpair;
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f[j][2] -= delz * fpair;
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}
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if (eflag) {
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evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
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offset[itype][jtype];
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evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype];
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evdwl *= factor_lj;
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}
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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evdwl,0.0,fpair,delx,dely,delz);
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if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
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}
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}
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}
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@ -144,24 +141,23 @@ void PairLJExpand::compute(int eflag, int vflag)
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void PairLJExpand::allocate()
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{
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allocated = 1;
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int n = atom->ntypes;
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int np1 = atom->ntypes + 1;
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memory->create(setflag,n+1,n+1,"pair:setflag");
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for (int i = 1; i <= n; i++)
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for (int j = i; j <= n; j++)
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setflag[i][j] = 0;
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memory->create(setflag, np1, np1, "pair:setflag");
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for (int i = 1; i < np1; i++)
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for (int j = i; j < np1; j++) setflag[i][j] = 0;
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memory->create(cutsq,n+1,n+1,"pair:cutsq");
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memory->create(cutsq, np1, np1, "pair:cutsq");
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memory->create(cut,n+1,n+1,"pair:cut");
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memory->create(epsilon,n+1,n+1,"pair:epsilon");
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memory->create(sigma,n+1,n+1,"pair:sigma");
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memory->create(shift,n+1,n+1,"pair:shift");
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memory->create(lj1,n+1,n+1,"pair:lj1");
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memory->create(lj2,n+1,n+1,"pair:lj2");
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memory->create(lj3,n+1,n+1,"pair:lj3");
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memory->create(lj4,n+1,n+1,"pair:lj4");
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memory->create(offset,n+1,n+1,"pair:offset");
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memory->create(cut, np1, np1, "pair:cut");
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memory->create(epsilon, np1, np1, "pair:epsilon");
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memory->create(sigma, np1, np1, "pair:sigma");
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memory->create(shift, np1, np1, "pair:shift");
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memory->create(lj1, np1, np1, "pair:lj1");
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memory->create(lj2, np1, np1, "pair:lj2");
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memory->create(lj3, np1, np1, "pair:lj3");
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memory->create(lj4, np1, np1, "pair:lj4");
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memory->create(offset, np1, np1, "pair:offset");
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}
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/* ----------------------------------------------------------------------
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@ -170,14 +166,14 @@ void PairLJExpand::allocate()
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void PairLJExpand::settings(int narg, char **arg)
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{
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if (narg != 1) error->all(FLERR,"Illegal pair_style command");
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if (narg != 1) error->all(FLERR, "Illegal pair_style command");
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cut_global = utils::numeric(FLERR,arg[0],false,lmp);
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cut_global = utils::numeric(FLERR, arg[0], false, lmp);
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// reset cutoffs that have been explicitly set
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if (allocated) {
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int i,j;
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int i, j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++)
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if (setflag[i][j]) cut[i][j] = cut_global;
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@ -190,23 +186,23 @@ void PairLJExpand::settings(int narg, char **arg)
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void PairLJExpand::coeff(int narg, char **arg)
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{
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if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients");
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if (narg < 5 || narg > 6) error->all(FLERR, "Incorrect args for pair coefficients");
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if (!allocated) allocate();
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int ilo,ihi,jlo,jhi;
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utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
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utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
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int ilo, ihi, jlo, jhi;
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utils::bounds(FLERR, arg[0], 1, atom->ntypes, ilo, ihi, error);
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utils::bounds(FLERR, arg[1], 1, atom->ntypes, jlo, jhi, error);
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double epsilon_one = utils::numeric(FLERR,arg[2],false,lmp);
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double sigma_one = utils::numeric(FLERR,arg[3],false,lmp);
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double shift_one = utils::numeric(FLERR,arg[4],false,lmp);
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double epsilon_one = utils::numeric(FLERR, arg[2], false, lmp);
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double sigma_one = utils::numeric(FLERR, arg[3], false, lmp);
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double shift_one = utils::numeric(FLERR, arg[4], false, lmp);
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double cut_one = cut_global;
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if (narg == 6) cut_one = utils::numeric(FLERR,arg[5],false,lmp);
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if (narg == 6) cut_one = utils::numeric(FLERR, arg[5], false, lmp);
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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for (int j = MAX(jlo,i); j <= jhi; j++) {
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for (int j = MAX(jlo, i); j <= jhi; j++) {
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epsilon[i][j] = epsilon_one;
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sigma[i][j] = sigma_one;
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shift[i][j] = shift_one;
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@ -216,7 +212,7 @@ void PairLJExpand::coeff(int narg, char **arg)
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}
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}
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if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
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if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
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}
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/* ----------------------------------------------------------------------
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@ -228,22 +224,22 @@ double PairLJExpand::init_one(int i, int j)
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// always mix shift arithmetically
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if (setflag[i][j] == 0) {
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epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
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sigma[i][i],sigma[j][j]);
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sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
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cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
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epsilon[i][j] = mix_energy(epsilon[i][i], epsilon[j][j], sigma[i][i], sigma[j][j]);
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sigma[i][j] = mix_distance(sigma[i][i], sigma[j][j]);
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cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
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shift[i][j] = 0.5 * (shift[i][i] + shift[j][j]);
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}
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lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
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lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
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lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
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lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
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lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j], 12.0);
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lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j], 6.0);
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lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j], 12.0);
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lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j], 6.0);
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if (offset_flag && (cut[i][j] > 0.0)) {
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double ratio = sigma[i][j] / cut[i][j];
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offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
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} else offset[i][j] = 0.0;
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double ratio = sigma[i][j] / (cut[i][j] + shift[i][j]);
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offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio, 12.0) - pow(ratio, 6.0));
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} else
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offset[i][j] = 0.0;
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lj1[j][i] = lj1[i][j];
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lj2[j][i] = lj2[i][j];
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@ -259,32 +255,34 @@ double PairLJExpand::init_one(int i, int j)
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int *type = atom->type;
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int nlocal = atom->nlocal;
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double count[2],all[2];
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double count[2], all[2];
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count[0] = count[1] = 0.0;
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for (int k = 0; k < nlocal; k++) {
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if (type[k] == i) count[0] += 1.0;
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if (type[k] == j) count[1] += 1.0;
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}
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MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
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MPI_Allreduce(count, all, 2, MPI_DOUBLE, MPI_SUM, world);
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double sig2 = sigma[i][j]*sigma[i][j];
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double sig6 = sig2*sig2*sig2;
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double sig2 = sigma[i][j] * sigma[i][j];
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double sig6 = sig2 * sig2 * sig2;
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double rc1 = cut[i][j];
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double rc2 = rc1*rc1;
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double rc3 = rc2*rc1;
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double rc9 = rc3*rc3*rc3;
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double rc2 = rc1 * rc1;
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double rc3 = rc2 * rc1;
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double rc9 = rc3 * rc3 * rc3;
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double shift1 = shift[i][j];
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double shift2 = shift1*shift1;
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double shift3 = shift2*shift1;
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double shift2 = shift1 * shift1;
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double shift3 = shift2 * shift1;
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etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] * sig6 *
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((1.0/9.0 + 2.0*shift1/(10.0*rc1) + shift2/(11.0*rc2))*sig6/rc9 -
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(1.0/3.0 + 2.0*shift1/(4.0*rc1) + shift2/(5.0*rc2))/rc3);
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ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] * sig6 *
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((1.0/9.0 + 3.0*shift1/(10.0*rc1) +
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3.0*shift2/(11.0*rc2) + shift3/(12.0*rc3))*2.0*sig6/rc9 -
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(1.0/3.0 + 3.0*shift1/(4.0*rc1) +
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3.0*shift2/(5.0*rc2) + shift3/(6.0*rc3))/rc3);
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etail_ij = 8.0 * MY_PI * all[0] * all[1] * epsilon[i][j] * sig6 *
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((1.0 / 9.0 + 2.0 * shift1 / (10.0 * rc1) + shift2 / (11.0 * rc2)) * sig6 / rc9 -
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(1.0 / 3.0 + 2.0 * shift1 / (4.0 * rc1) + shift2 / (5.0 * rc2)) / rc3);
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ptail_ij = 16.0 * MY_PI * all[0] * all[1] * epsilon[i][j] * sig6 *
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((1.0 / 9.0 + 3.0 * shift1 / (10.0 * rc1) + 3.0 * shift2 / (11.0 * rc2) +
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shift3 / (12.0 * rc3)) *
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2.0 * sig6 / rc9 -
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(1.0 / 3.0 + 3.0 * shift1 / (4.0 * rc1) + 3.0 * shift2 / (5.0 * rc2) +
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shift3 / (6.0 * rc3)) /
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rc3);
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}
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return cut[i][j] + shift[i][j];
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@ -298,15 +296,15 @@ void PairLJExpand::write_restart(FILE *fp)
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{
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write_restart_settings(fp);
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int i,j;
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int i, j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++) {
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fwrite(&setflag[i][j],sizeof(int),1,fp);
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fwrite(&setflag[i][j], sizeof(int), 1, fp);
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if (setflag[i][j]) {
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fwrite(&epsilon[i][j],sizeof(double),1,fp);
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fwrite(&sigma[i][j],sizeof(double),1,fp);
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fwrite(&shift[i][j],sizeof(double),1,fp);
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fwrite(&cut[i][j],sizeof(double),1,fp);
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fwrite(&epsilon[i][j], sizeof(double), 1, fp);
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fwrite(&sigma[i][j], sizeof(double), 1, fp);
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fwrite(&shift[i][j], sizeof(double), 1, fp);
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fwrite(&cut[i][j], sizeof(double), 1, fp);
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}
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}
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}
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@ -321,23 +319,23 @@ void PairLJExpand::read_restart(FILE *fp)
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allocate();
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int i,j;
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int i, j;
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int me = comm->me;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++) {
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if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
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MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
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if (me == 0) utils::sfread(FLERR, &setflag[i][j], sizeof(int), 1, fp, nullptr, error);
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MPI_Bcast(&setflag[i][j], 1, MPI_INT, 0, world);
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if (setflag[i][j]) {
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if (me == 0) {
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utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&shift[i][j],sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
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utils::sfread(FLERR, &epsilon[i][j], sizeof(double), 1, fp, nullptr, error);
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utils::sfread(FLERR, &sigma[i][j], sizeof(double), 1, fp, nullptr, error);
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utils::sfread(FLERR, &shift[i][j], sizeof(double), 1, fp, nullptr, error);
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utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error);
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}
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MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&shift[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&epsilon[i][j], 1, MPI_DOUBLE, 0, world);
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MPI_Bcast(&sigma[i][j], 1, MPI_DOUBLE, 0, world);
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MPI_Bcast(&shift[i][j], 1, MPI_DOUBLE, 0, world);
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MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world);
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}
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}
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}
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@ -348,10 +346,10 @@ void PairLJExpand::read_restart(FILE *fp)
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void PairLJExpand::write_restart_settings(FILE *fp)
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{
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fwrite(&cut_global,sizeof(double),1,fp);
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fwrite(&offset_flag,sizeof(int),1,fp);
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fwrite(&mix_flag,sizeof(int),1,fp);
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fwrite(&tail_flag,sizeof(int),1,fp);
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fwrite(&cut_global, sizeof(double), 1, fp);
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fwrite(&offset_flag, sizeof(int), 1, fp);
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fwrite(&mix_flag, sizeof(int), 1, fp);
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||||
fwrite(&tail_flag, sizeof(int), 1, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -361,15 +359,15 @@ void PairLJExpand::write_restart_settings(FILE *fp)
|
||||
void PairLJExpand::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,&tail_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);
|
||||
utils::sfread(FLERR, &tail_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(&tail_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);
|
||||
MPI_Bcast(&tail_flag, 1, MPI_INT, 0, world);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -379,7 +377,7 @@ void PairLJExpand::read_restart_settings(FILE *fp)
|
||||
void PairLJExpand::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],shift[i][i]);
|
||||
fprintf(fp, "%d %g %g %g\n", i, epsilon[i][i], sigma[i][i], shift[i][i]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -390,29 +388,26 @@ void PairLJExpand::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,
|
||||
epsilon[i][j],sigma[i][j],shift[i][j],cut[i][j]);
|
||||
fprintf(fp, "%d %d %g %g %g %g\n", i, j, epsilon[i][j], sigma[i][j], shift[i][j], cut[i][j]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJExpand::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 r,rshift,rshiftsq,r2inv,r6inv,forcelj,philj;
|
||||
double r, rshift, rshiftsq, r2inv, r6inv, forcelj, philj;
|
||||
|
||||
r = sqrt(rsq);
|
||||
rshift = r - shift[itype][jtype];
|
||||
rshiftsq = rshift*rshift;
|
||||
r2inv = 1.0/rshiftsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||
fforce = factor_lj*forcelj/rshift/r;
|
||||
rshiftsq = rshift * rshift;
|
||||
r2inv = 1.0 / rshiftsq;
|
||||
r6inv = r2inv * r2inv * r2inv;
|
||||
forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]);
|
||||
fforce = factor_lj * forcelj / rshift / r;
|
||||
|
||||
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
|
||||
offset[itype][jtype];
|
||||
return factor_lj*philj;
|
||||
philj = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype];
|
||||
return factor_lj * philj;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -420,8 +415,8 @@ double PairLJExpand::single(int /*i*/, int /*j*/, int itype, int jtype, double r
|
||||
void *PairLJExpand::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 2;
|
||||
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
|
||||
if (strcmp(str,"sigma") == 0) return (void *) sigma;
|
||||
if (strcmp(str,"delta") == 0) return (void *) shift;
|
||||
if (strcmp(str, "epsilon") == 0) return (void *) epsilon;
|
||||
if (strcmp(str, "sigma") == 0) return (void *) sigma;
|
||||
if (strcmp(str, "delta") == 0) return (void *) shift;
|
||||
return nullptr;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user