diff --git a/src/EXTRA-PAIR/pair_born_coul_dsf.cpp b/src/EXTRA-PAIR/pair_born_coul_dsf.cpp index 3fac9a79c9..84bfed6908 100644 --- a/src/EXTRA-PAIR/pair_born_coul_dsf.cpp +++ b/src/EXTRA-PAIR/pair_born_coul_dsf.cpp @@ -280,7 +280,7 @@ void PairBornCoulDSF::init_style() if (!atom->q_flag) error->all(FLERR,"Pair style born/coul/dsf requires atom attribute q"); - neighbor->request(this,instance_me); + neighbor->add_request(this); cut_coulsq = cut_coul * cut_coul; double erfcc = erfc(alpha*cut_coul); diff --git a/src/EXTRA-PAIR/pair_born_coul_wolf.cpp b/src/EXTRA-PAIR/pair_born_coul_wolf.cpp index 2fe4316011..54eaed1dc2 100644 --- a/src/EXTRA-PAIR/pair_born_coul_wolf.cpp +++ b/src/EXTRA-PAIR/pair_born_coul_wolf.cpp @@ -283,7 +283,7 @@ void PairBornCoulWolf::init_style() if (!atom->q_flag) error->all(FLERR,"Pair style born/coul/wolf requires atom attribute q"); - neighbor->request(this,instance_me); + neighbor->add_request(this); cut_coulsq = cut_coul * cut_coul; } diff --git a/src/EXTRA-PAIR/pair_cosine_squared.cpp b/src/EXTRA-PAIR/pair_cosine_squared.cpp index 77bb7dc326..1e61142c0b 100644 --- a/src/EXTRA-PAIR/pair_cosine_squared.cpp +++ b/src/EXTRA-PAIR/pair_cosine_squared.cpp @@ -175,17 +175,6 @@ void PairCosineSquared::coeff(int narg, char **arg) error->all(FLERR, "Incorrect args for pair coefficients (none set)"); } -/* ---------------------------------------------------------------------- - init specific to this pair style (unnecessary) -------------------------------------------------------------------------- */ - -/* -void PairCosineSquared::init_style() -{ - neighbor->request(this,instance_me); -} -*/ - /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ diff --git a/src/EXTRA-PAIR/pair_coul_diel.cpp b/src/EXTRA-PAIR/pair_coul_diel.cpp index 4f45858725..fb110eed84 100644 --- a/src/EXTRA-PAIR/pair_coul_diel.cpp +++ b/src/EXTRA-PAIR/pair_coul_diel.cpp @@ -17,15 +17,15 @@ #include "pair_coul_diel.h" -#include #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include using namespace LAMMPS_NS; @@ -218,7 +218,7 @@ void PairCoulDiel::init_style() if (!atom->q_flag) error->all(FLERR,"Pair style coul/diel requires atom attribute q"); - neighbor->request(this,instance_me); + neighbor->add_request(this); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_coul_exclude.cpp b/src/EXTRA-PAIR/pair_coul_exclude.cpp index 74890bcf08..efd612d1d6 100644 --- a/src/EXTRA-PAIR/pair_coul_exclude.cpp +++ b/src/EXTRA-PAIR/pair_coul_exclude.cpp @@ -182,7 +182,7 @@ void PairCoulExclude::init_style() if (!atom->q_flag) error->all(FLERR,"Pair style coul/exclude requires atom attribute q"); - neighbor->request(this,instance_me); + neighbor->add_request(this); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_coul_slater_long.cpp b/src/EXTRA-PAIR/pair_coul_slater_long.cpp index 605305a7ef..d30d346fa0 100644 --- a/src/EXTRA-PAIR/pair_coul_slater_long.cpp +++ b/src/EXTRA-PAIR/pair_coul_slater_long.cpp @@ -241,7 +241,7 @@ void PairCoulSlaterLong::init_style() if (!atom->q_flag) error->all(FLERR,"Pair style coul/slater/long requires atom attribute q"); - neighbor->request(this,instance_me); + neighbor->add_request(this); cut_coulsq = cut_coul * cut_coul; diff --git a/src/EXTRA-PAIR/pair_e3b.cpp b/src/EXTRA-PAIR/pair_e3b.cpp index 3af8e754c0..f09a3bcae2 100644 --- a/src/EXTRA-PAIR/pair_e3b.cpp +++ b/src/EXTRA-PAIR/pair_e3b.cpp @@ -458,7 +458,7 @@ void PairE3B::init_style() if (typeO < 1 || typeO > atom->ntypes) error->all(FLERR, "Invalid Otype: out of bounds"); // need a half neighbor list - neighbor->request(this, instance_me); + neighbor->add_request(this); if (!force->pair_match("tip4p", false, 0)) if (comm->me == 0) diff --git a/src/EXTRA-PAIR/pair_lj96_cut.cpp b/src/EXTRA-PAIR/pair_lj96_cut.cpp index a762e7de6b..28038ea396 100644 --- a/src/EXTRA-PAIR/pair_lj96_cut.cpp +++ b/src/EXTRA-PAIR/pair_lj96_cut.cpp @@ -25,7 +25,6 @@ #include "math_const.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "respa.h" #include "update.h" @@ -485,21 +484,14 @@ void PairLJ96Cut::init_style() { // request regular or rRESPA neighbor list - int irequest; - int respa = 0; + int list_style = NeighConst::REQ_DEFAULT; - if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { - if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; - if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; + if (update->whichflag == 1 && utils::strmatch(update->integrate_style, "^respa")) { + auto respa = (Respa *) update->integrate; + if (respa->level_inner >= 0) list_style = NeighConst::REQ_RESPA_INOUT; + if (respa->level_middle >= 0) list_style = NeighConst::REQ_RESPA_ALL; } - - irequest = neighbor->request(this,instance_me); - - if (respa >= 1) { - neighbor->requests[irequest]->respaouter = 1; - neighbor->requests[irequest]->respainner = 1; - } - if (respa == 2) neighbor->requests[irequest]->respamiddle = 1; + neighbor->add_request(this, list_style); // set rRESPA cutoffs diff --git a/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp b/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp index 79afd1ebeb..9782844c26 100644 --- a/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp +++ b/src/EXTRA-PAIR/pair_lj_cut_coul_dsf.cpp @@ -19,17 +19,17 @@ #include "pair_lj_cut_coul_dsf.h" -#include -#include #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "math_const.h" #include "error.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -273,7 +273,7 @@ void PairLJCutCoulDSF::init_style() if (!atom->q_flag) error->all(FLERR,"Pair style lj/cut/coul/dsf requires atom attribute q"); - neighbor->request(this,instance_me); + neighbor->add_request(this); cut_coulsq = cut_coul * cut_coul; double erfcc = erfc(alpha*cut_coul); diff --git a/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp b/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp index a0b6e6587b..aa0875f11c 100644 --- a/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp +++ b/src/EXTRA-PAIR/pair_lj_cut_coul_wolf.cpp @@ -18,16 +18,16 @@ #include "pair_lj_cut_coul_wolf.h" -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neighbor.h" +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -270,9 +270,7 @@ void PairLJCutCoulWolf::init_style() cut_coulsq = cut_coul * cut_coul; - // request regular or rRESPA neighbor list - - neighbor->request(this,instance_me); + neighbor->add_request(this); } /* ---------------------------------------------------------------------- diff --git a/src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp b/src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp index 2791c28747..5d5ceff1e5 100644 --- a/src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp +++ b/src/EXTRA-PAIR/pair_lj_expand_coul_long.cpp @@ -18,21 +18,20 @@ #include "pair_lj_expand_coul_long.h" -#include -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "update.h" -#include "respa.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -686,21 +685,14 @@ void PairLJExpandCoulLong::init_style() // request regular or rRESPA neighbor list - int irequest; - int respa = 0; + int list_style = NeighConst::REQ_DEFAULT; - if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { - if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; - if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; + if (update->whichflag == 1 && utils::strmatch(update->integrate_style, "^respa")) { + auto respa = (Respa *) update->integrate; + if (respa->level_inner >= 0) list_style = NeighConst::REQ_RESPA_INOUT; + if (respa->level_middle >= 0) list_style = NeighConst::REQ_RESPA_ALL; } - - irequest = neighbor->request(this,instance_me); - - if (respa >= 1) { - neighbor->requests[irequest]->respaouter = 1; - neighbor->requests[irequest]->respainner = 1; - } - if (respa == 2) neighbor->requests[irequest]->respamiddle = 1; + neighbor->add_request(this, list_style); cut_coulsq = cut_coul * cut_coul; diff --git a/src/EXTRA-PAIR/pair_lj_gromacs.cpp b/src/EXTRA-PAIR/pair_lj_gromacs.cpp index 83bf099649..c5b23d24d9 100644 --- a/src/EXTRA-PAIR/pair_lj_gromacs.cpp +++ b/src/EXTRA-PAIR/pair_lj_gromacs.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -18,14 +17,14 @@ #include "pair_lj_gromacs.h" -#include #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 using namespace LAMMPS_NS; @@ -67,14 +66,14 @@ PairLJGromacs::~PairLJGromacs() void PairLJGromacs::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,r6inv,forcelj,factor_lj; - double 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, r2inv, r6inv, forcelj, factor_lj; + double 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; @@ -107,43 +106,42 @@ void PairLJGromacs::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; - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + r2inv = 1.0 / rsq; + r6inv = r2inv * r2inv * r2inv; + forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]); if (rsq > cut_inner_sq[itype][jtype]) { r = sqrt(rsq); t = r - cut_inner[itype][jtype]; - fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t); + fswitch = r * t * t * (ljsw1[itype][jtype] + ljsw2[itype][jtype] * t); forcelj += fswitch; } - fpair = factor_lj*forcelj*r2inv; + fpair = factor_lj * forcelj * 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) { - evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); + evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]); evdwl += ljsw5[itype][jtype]; if (rsq > cut_inner_sq[itype][jtype]) { - eswitch = t*t*t*(ljsw3[itype][jtype] + ljsw4[itype][jtype]*t); + eswitch = t * t * t * (ljsw3[itype][jtype] + ljsw4[itype][jtype] * t); evdwl += eswitch; } 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); } } } @@ -158,29 +156,28 @@ void PairLJGromacs::compute(int eflag, int vflag) void PairLJGromacs::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(cutsq, np1, np1, "pair:cutsq"); - memory->create(cut,n+1,n+1,"pair:cut"); - memory->create(cut_inner,n+1,n+1,"pair:cut_inner"); - memory->create(cut_inner_sq,n+1,n+1,"pair:cut_inner_sq"); - memory->create(epsilon,n+1,n+1,"pair:epsilon"); - memory->create(sigma,n+1,n+1,"pair:sigma"); - memory->create(lj1,n+1,n+1,"pair:lj1"); - memory->create(lj2,n+1,n+1,"pair:lj2"); - memory->create(lj3,n+1,n+1,"pair:lj3"); - memory->create(lj4,n+1,n+1,"pair:lj4"); - memory->create(ljsw1,n+1,n+1,"pair:ljsw1"); - memory->create(ljsw2,n+1,n+1,"pair:ljsw2"); - memory->create(ljsw3,n+1,n+1,"pair:ljsw3"); - memory->create(ljsw4,n+1,n+1,"pair:ljsw4"); - memory->create(ljsw5,n+1,n+1,"pair:ljsw5"); + memory->create(cut, np1, np1, "pair:cut"); + memory->create(cut_inner, np1, np1, "pair:cut_inner"); + memory->create(cut_inner_sq, np1, np1, "pair:cut_inner_sq"); + memory->create(epsilon, np1, np1, "pair:epsilon"); + memory->create(sigma, np1, np1, "pair:sigma"); + memory->create(lj1, np1, np1, "pair:lj1"); + memory->create(lj2, np1, np1, "pair:lj2"); + memory->create(lj3, np1, np1, "pair:lj3"); + memory->create(lj4, np1, np1, "pair:lj4"); + memory->create(ljsw1, np1, np1, "pair:ljsw1"); + memory->create(ljsw2, np1, np1, "pair:ljsw2"); + memory->create(ljsw3, np1, np1, "pair:ljsw3"); + memory->create(ljsw4, np1, np1, "pair:ljsw4"); + memory->create(ljsw5, np1, np1, "pair:ljsw5"); } /* ---------------------------------------------------------------------- @@ -189,18 +186,18 @@ void PairLJGromacs::allocate() void PairLJGromacs::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_global = utils::numeric(FLERR,arg[0],false,lmp); - cut_global = utils::numeric(FLERR,arg[1],false,lmp); + cut_inner_global = utils::numeric(FLERR, arg[0], false, lmp); + cut_global = utils::numeric(FLERR, arg[1], false, lmp); if (cut_inner_global <= 0.0 || cut_inner_global > cut_global) - error->all(FLERR,"Illegal pair_style command"); + error->all(FLERR, "Illegal pair_style command"); // 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]) { @@ -216,30 +213,29 @@ void PairLJGromacs::settings(int narg, char **arg) void PairLJGromacs::coeff(int narg, char **arg) { - if (narg != 4 && narg != 6) - error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg != 4 && narg != 6) 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 epsilon_one = utils::numeric(FLERR,arg[2],false,lmp); - double sigma_one = utils::numeric(FLERR,arg[3],false,lmp); + double epsilon_one = utils::numeric(FLERR, arg[2], false, lmp); + double sigma_one = utils::numeric(FLERR, arg[3], false, lmp); double cut_inner_one = cut_inner_global; double cut_one = cut_global; if (narg == 6) { - cut_inner_one = utils::numeric(FLERR,arg[4],false,lmp); - cut_one = utils::numeric(FLERR,arg[5],false,lmp); + cut_inner_one = utils::numeric(FLERR, arg[4], false, lmp); + cut_one = utils::numeric(FLERR, arg[5], false, lmp); } if (cut_inner_one <= 0.0 || cut_inner_one > cut_one) - error->all(FLERR,"Incorrect args for pair coefficients"); + error->all(FLERR, "Incorrect args for pair coefficients"); 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++) { epsilon[i][j] = epsilon_one; sigma[i][j] = sigma_one; cut_inner[i][j] = cut_inner_one; @@ -249,7 +245,7 @@ void PairLJGromacs::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"); } /* ---------------------------------------------------------------------- @@ -259,37 +255,36 @@ void PairLJGromacs::coeff(int narg, char **arg) double PairLJGromacs::init_one(int i, int j) { if (setflag[i][j] == 0) { - epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j], - sigma[i][i],sigma[j][j]); - sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]); - cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]); - cut[i][j] = mix_distance(cut[i][i],cut[j][j]); + epsilon[i][j] = mix_energy(epsilon[i][i], epsilon[j][j], sigma[i][i], sigma[j][j]); + sigma[i][j] = mix_distance(sigma[i][i], sigma[j][j]); + cut_inner[i][j] = mix_distance(cut_inner[i][i], cut_inner[j][j]); + cut[i][j] = mix_distance(cut[i][i], cut[j][j]); } - cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[i][j]; - lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0); - lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0); - lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0); - lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0); + cut_inner_sq[i][j] = cut_inner[i][j] * cut_inner[i][j]; + lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j], 12.0); + lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j], 6.0); + lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j], 12.0); + lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j], 6.0); - double r6inv = 1.0/pow(cut[i][j],6.0); - double r8inv = 1.0/pow(cut[i][j],8.0); + double r6inv = 1.0 / pow(cut[i][j], 6.0); + double r8inv = 1.0 / pow(cut[i][j], 8.0); double t = cut[i][j] - cut_inner[i][j]; - double t2inv = 1.0/(t*t); - double t3inv = t2inv/t; - double t3 = 1.0/t3inv; - double a6 = (7.0*cut_inner[i][j] - 10.0*cut[i][j])*r8inv*t2inv; - double b6 = (9.0*cut[i][j] - 7.0*cut_inner[i][j])*r8inv*t3inv; - double a12 = (13.0*cut_inner[i][j] - 16.0*cut[i][j])*r6inv*r8inv*t2inv; - double b12 = (15.0*cut[i][j] - 13.0*cut_inner[i][j])*r6inv*r8inv*t3inv; - double c6 = r6inv - t3*(6.0*a6/3.0 + 6.0*b6*t/4.0); - double c12 = r6inv*r6inv - t3*(12.0*a12/3.0 + 12.0*b12*t/4.0); + double t2inv = 1.0 / (t * t); + double t3inv = t2inv / t; + double t3 = 1.0 / t3inv; + double a6 = (7.0 * cut_inner[i][j] - 10.0 * cut[i][j]) * r8inv * t2inv; + double b6 = (9.0 * cut[i][j] - 7.0 * cut_inner[i][j]) * r8inv * t3inv; + double a12 = (13.0 * cut_inner[i][j] - 16.0 * cut[i][j]) * r6inv * r8inv * t2inv; + double b12 = (15.0 * cut[i][j] - 13.0 * cut_inner[i][j]) * r6inv * r8inv * t3inv; + double c6 = r6inv - t3 * (6.0 * a6 / 3.0 + 6.0 * b6 * t / 4.0); + double c12 = r6inv * r6inv - t3 * (12.0 * a12 / 3.0 + 12.0 * b12 * t / 4.0); - ljsw1[i][j] = lj1[i][j]*a12 - lj2[i][j]*a6; - ljsw2[i][j] = lj1[i][j]*b12 - lj2[i][j]*b6; - ljsw3[i][j] = -lj3[i][j]*12.0*a12/3.0 + lj4[i][j]*6.0*a6/3.0; - ljsw4[i][j] = -lj3[i][j]*12.0*b12/4.0 + lj4[i][j]*6.0*b6/4.0; - ljsw5[i][j] = -lj3[i][j]*c12 + lj4[i][j]*c6; + ljsw1[i][j] = lj1[i][j] * a12 - lj2[i][j] * a6; + ljsw2[i][j] = lj1[i][j] * b12 - lj2[i][j] * b6; + ljsw3[i][j] = -lj3[i][j] * 12.0 * a12 / 3.0 + lj4[i][j] * 6.0 * a6 / 3.0; + ljsw4[i][j] = -lj3[i][j] * 12.0 * b12 / 4.0 + lj4[i][j] * 6.0 * b6 / 4.0; + ljsw5[i][j] = -lj3[i][j] * c12 + lj4[i][j] * c6; cut_inner[j][i] = cut_inner[i][j]; cut_inner_sq[j][i] = cut_inner_sq[i][j]; @@ -314,15 +309,15 @@ void PairLJGromacs::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(&epsilon[i][j],sizeof(double),1,fp); - fwrite(&sigma[i][j],sizeof(double),1,fp); - fwrite(&cut_inner[i][j],sizeof(double),1,fp); - fwrite(&cut[i][j],sizeof(double),1,fp); + fwrite(&epsilon[i][j], sizeof(double), 1, fp); + fwrite(&sigma[i][j], sizeof(double), 1, fp); + fwrite(&cut_inner[i][j], sizeof(double), 1, fp); + fwrite(&cut[i][j], sizeof(double), 1, fp); } } } @@ -336,23 +331,23 @@ void PairLJGromacs::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++) 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,&epsilon[i][j],sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR, &epsilon[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &sigma[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cut_inner[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cut[i][j], sizeof(double), 1, fp, nullptr, error); } - MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&epsilon[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&sigma[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_inner[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut[i][j], 1, MPI_DOUBLE, 0, world); } } } @@ -363,10 +358,10 @@ void PairLJGromacs::read_restart(FILE *fp) void PairLJGromacs::write_restart_settings(FILE *fp) { - fwrite(&cut_inner_global,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(&cut_inner_global, 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); } /* ---------------------------------------------------------------------- @@ -377,15 +372,15 @@ void PairLJGromacs::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - utils::sfread(FLERR,&cut_inner_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,&mix_flag,sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR, &cut_inner_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, &mix_flag, sizeof(int), 1, fp, nullptr, error); } - MPI_Bcast(&cut_inner_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(&mix_flag,1,MPI_INT,0,world); + MPI_Bcast(&cut_inner_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(&mix_flag, 1, MPI_INT, 0, world); } /* ---------------------------------------------------------------------- @@ -394,8 +389,7 @@ void PairLJGromacs::read_restart_settings(FILE *fp) void PairLJGromacs::write_data(FILE *fp) { - for (int i = 1; i <= atom->ntypes; i++) - fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]); + for (int i = 1; i <= atom->ntypes; i++) fprintf(fp, "%d %g %g\n", i, epsilon[i][i], sigma[i][i]); } /* ---------------------------------------------------------------------- @@ -406,37 +400,35 @@ void PairLJGromacs::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],cut_inner[i][j],cut[i][j]); + fprintf(fp, "%d %d %g %g %g %g\n", i, j, epsilon[i][j], sigma[i][j], cut_inner[i][j], + cut[i][j]); } /* ---------------------------------------------------------------------- */ -double PairLJGromacs::single(int /*i*/, int /*j*/, int itype, int jtype, - double rsq, - double /*factor_coul*/, double factor_lj, - double &fforce) +double PairLJGromacs::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &fforce) { - double r2inv,r6inv,forcelj,philj; - double r,t,fswitch,phiswitch; + double r2inv, r6inv, forcelj, philj; + double r, t, fswitch, phiswitch; - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + r2inv = 1.0 / rsq; + r6inv = r2inv * r2inv * r2inv; + forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]); if (rsq > cut_inner_sq[itype][jtype]) { r = sqrt(rsq); t = r - cut_inner[itype][jtype]; - fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t); + fswitch = r * t * t * (ljsw1[itype][jtype] + ljsw2[itype][jtype] * t); forcelj += fswitch; } - fforce = factor_lj*forcelj*r2inv; + fforce = factor_lj * forcelj * r2inv; - philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); + philj = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]); philj += ljsw5[itype][jtype]; if (rsq > cut_inner_sq[itype][jtype]) { - phiswitch = t*t*t*(ljsw3[itype][jtype] + ljsw4[itype][jtype]*t); + phiswitch = t * t * t * (ljsw3[itype][jtype] + ljsw4[itype][jtype] * t); philj += phiswitch; } - return factor_lj*philj; + return factor_lj * philj; } diff --git a/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.cpp b/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.cpp index 96b8985b6b..71911169cf 100644 --- a/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.cpp +++ b/src/EXTRA-PAIR/pair_lj_gromacs_coul_gromacs.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -18,14 +17,15 @@ #include "pair_lj_gromacs_coul_gromacs.h" -#include #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" + +#include using namespace LAMMPS_NS; @@ -64,14 +64,14 @@ PairLJGromacsCoulGromacs::~PairLJGromacsCoulGromacs() void PairLJGromacsCoulGromacs::compute(int eflag, int vflag) { - int i,j,ii,jj,inum,jnum,itype,jtype; - double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; - double rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj; - double r,tlj,tc,fswitch,fswitchcoul,eswitch,ecoulswitch; - int *ilist,*jlist,*numneigh,**firstneigh; + int i, j, ii, jj, inum, jnum, itype, jtype; + double qtmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul, fpair; + double rsq, r2inv, r6inv, forcecoul, forcelj, factor_coul, factor_lj; + double r, tlj, tc, fswitch, fswitchcoul, eswitch, ecoulswitch; + int *ilist, *jlist, *numneigh, **firstneigh; evdwl = ecoul = 0.0; - ev_init(eflag,vflag); + ev_init(eflag, vflag); double **x = atom->x; double **f = atom->f; @@ -109,69 +109,72 @@ void PairLJGromacsCoulGromacs::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; if (rsq < cut_bothsq) { - r2inv = 1.0/rsq; + r2inv = 1.0 / rsq; // skip if qi or qj = 0.0 since this potential may be used as // coarse-grain model with many uncharged atoms if (rsq < cut_coulsq && qtmp != 0.0 && q[j] != 0.0) { - forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv); + forcecoul = qqrd2e * qtmp * q[j] * sqrt(r2inv); if (rsq > cut_coul_innersq) { r = sqrt(rsq); tc = r - cut_coul_inner; - fswitchcoul = qqrd2e * qtmp*q[j]*r*tc*tc*(coulsw1 + coulsw2*tc); + fswitchcoul = qqrd2e * qtmp * q[j] * r * tc * tc * (coulsw1 + coulsw2 * tc); forcecoul += fswitchcoul; } - } else forcecoul = 0.0; + } else + forcecoul = 0.0; if (rsq < cut_ljsq) { - r6inv = r2inv*r2inv*r2inv; + r6inv = r2inv * r2inv * r2inv; jtype = type[j]; - forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]); if (rsq > cut_lj_innersq) { r = sqrt(rsq); tlj = r - cut_lj_inner; - fswitch = r*tlj*tlj*(ljsw1[itype][jtype] + - ljsw2[itype][jtype]*tlj); + fswitch = r * tlj * tlj * (ljsw1[itype][jtype] + ljsw2[itype][jtype] * tlj); forcelj += fswitch; } - } else forcelj = 0.0; + } else + forcelj = 0.0; - fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv; + fpair = (factor_coul * forcecoul + factor_lj * forcelj) * 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) { if (rsq < cut_coulsq) { - ecoul = qqrd2e * qtmp*q[j] * (sqrt(r2inv) - coulsw5); + ecoul = qqrd2e * qtmp * q[j] * (sqrt(r2inv) - coulsw5); if (rsq > cut_coul_innersq) { - ecoulswitch = tc*tc*tc * (coulsw3 + coulsw4*tc); - ecoul += qqrd2e*qtmp*q[j]*ecoulswitch; + ecoulswitch = tc * tc * tc * (coulsw3 + coulsw4 * tc); + ecoul += qqrd2e * qtmp * q[j] * ecoulswitch; } ecoul *= factor_coul; - } else ecoul = 0.0; + } else + ecoul = 0.0; if (rsq < cut_ljsq) { - evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); + evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]); evdwl += ljsw5[itype][jtype]; if (rsq > cut_lj_innersq) { - eswitch = tlj*tlj*tlj * (ljsw3[itype][jtype] + ljsw4[itype][jtype]*tlj); + eswitch = tlj * tlj * tlj * (ljsw3[itype][jtype] + ljsw4[itype][jtype] * tlj); evdwl += eswitch; } evdwl *= factor_lj; - } else evdwl = 0.0; + } else + evdwl = 0.0; } - if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,ecoul,fpair,delx,dely,delz); + if (evflag) ev_tally(i, j, nlocal, newton_pair, evdwl, ecoul, fpair, delx, dely, delz); } } } @@ -186,26 +189,25 @@ void PairLJGromacsCoulGromacs::compute(int eflag, int vflag) void PairLJGromacsCoulGromacs::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(cutsq, np1, np1, "pair:cutsq"); - memory->create(epsilon,n+1,n+1,"pair:epsilon"); - memory->create(sigma,n+1,n+1,"pair:sigma"); - memory->create(lj1,n+1,n+1,"pair:lj1"); - memory->create(lj2,n+1,n+1,"pair:lj2"); - memory->create(lj3,n+1,n+1,"pair:lj3"); - memory->create(lj4,n+1,n+1,"pair:lj4"); - memory->create(ljsw1,n+1,n+1,"pair:ljsw1"); - memory->create(ljsw2,n+1,n+1,"pair:ljsw2"); - memory->create(ljsw3,n+1,n+1,"pair:ljsw3"); - memory->create(ljsw4,n+1,n+1,"pair:ljsw4"); - memory->create(ljsw5,n+1,n+1,"pair:ljsw5"); + memory->create(epsilon, np1, np1, "pair:epsilon"); + memory->create(sigma, np1, np1, "pair:sigma"); + memory->create(lj1, np1, np1, "pair:lj1"); + memory->create(lj2, np1, np1, "pair:lj2"); + memory->create(lj3, np1, np1, "pair:lj3"); + memory->create(lj4, np1, np1, "pair:lj4"); + memory->create(ljsw1, np1, np1, "pair:ljsw1"); + memory->create(ljsw2, np1, np1, "pair:ljsw2"); + memory->create(ljsw3, np1, np1, "pair:ljsw3"); + memory->create(ljsw4, np1, np1, "pair:ljsw4"); + memory->create(ljsw5, np1, np1, "pair:ljsw5"); } /* ---------------------------------------------------------------------- @@ -214,23 +216,21 @@ void PairLJGromacsCoulGromacs::allocate() void PairLJGromacsCoulGromacs::settings(int narg, char **arg) { - if (narg != 2 && narg != 4) - error->all(FLERR,"Illegal pair_style command"); + if (narg != 2 && narg != 4) error->all(FLERR, "Illegal pair_style command"); - cut_lj_inner = utils::numeric(FLERR,arg[0],false,lmp); - cut_lj = utils::numeric(FLERR,arg[1],false,lmp); + cut_lj_inner = utils::numeric(FLERR, arg[0], false, lmp); + cut_lj = utils::numeric(FLERR, arg[1], false, lmp); if (narg == 2) { cut_coul_inner = cut_lj_inner; cut_coul = cut_lj; } else { - cut_coul_inner = utils::numeric(FLERR,arg[2],false,lmp); - cut_coul = utils::numeric(FLERR,arg[3],false,lmp); + cut_coul_inner = utils::numeric(FLERR, arg[2], false, lmp); + cut_coul = utils::numeric(FLERR, arg[3], false, lmp); } - if (cut_lj_inner <= 0.0 || cut_coul_inner < 0.0) - error->all(FLERR,"Illegal pair_style command"); + if (cut_lj_inner <= 0.0 || cut_coul_inner < 0.0) error->all(FLERR, "Illegal pair_style command"); if (cut_lj_inner > cut_lj || cut_coul_inner > cut_coul) - error->all(FLERR,"Illegal pair_style command"); + error->all(FLERR, "Illegal pair_style command"); } /* ---------------------------------------------------------------------- @@ -239,19 +239,19 @@ void PairLJGromacsCoulGromacs::settings(int narg, char **arg) void PairLJGromacsCoulGromacs::coeff(int narg, char **arg) { - 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,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 epsilon_one = utils::numeric(FLERR,arg[2],false,lmp); - double sigma_one = utils::numeric(FLERR,arg[3],false,lmp); + double epsilon_one = utils::numeric(FLERR, arg[2], false, lmp); + double sigma_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++) { epsilon[i][j] = epsilon_one; sigma[i][j] = sigma_one; setflag[i][j] = 1; @@ -259,7 +259,7 @@ void PairLJGromacsCoulGromacs::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"); } /* ---------------------------------------------------------------------- @@ -269,16 +269,15 @@ void PairLJGromacsCoulGromacs::coeff(int narg, char **arg) void PairLJGromacsCoulGromacs::init_style() { if (!atom->q_flag) - error->all(FLERR, - "Pair style lj/gromacs/coul/gromacs requires atom attribute q"); + error->all(FLERR, "Pair style lj/gromacs/coul/gromacs requires atom attribute q"); - neighbor->request(this,instance_me); + neighbor->add_request(this); cut_lj_innersq = cut_lj_inner * cut_lj_inner; cut_ljsq = cut_lj * cut_lj; cut_coul_innersq = cut_coul_inner * cut_coul_inner; cut_coulsq = cut_coul * cut_coul; - cut_bothsq = MAX(cut_ljsq,cut_coulsq); + cut_bothsq = MAX(cut_ljsq, cut_coulsq); } /* ---------------------------------------------------------------------- @@ -288,48 +287,47 @@ void PairLJGromacsCoulGromacs::init_style() double PairLJGromacsCoulGromacs::init_one(int i, int j) { if (setflag[i][j] == 0) { - epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j], - sigma[i][i],sigma[j][j]); - sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]); + epsilon[i][j] = mix_energy(epsilon[i][i], epsilon[j][j], sigma[i][i], sigma[j][j]); + sigma[i][j] = mix_distance(sigma[i][i], sigma[j][j]); } - double cut = MAX(cut_lj,cut_coul); + double cut = MAX(cut_lj, cut_coul); - lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0); - lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0); - lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0); - lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0); + lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j], 12.0); + lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j], 6.0); + lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j], 12.0); + lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j], 6.0); - double r6inv = 1.0/pow(cut_lj,6.0); - double r8inv = 1.0/pow(cut_lj,8.0); + double r6inv = 1.0 / pow(cut_lj, 6.0); + double r8inv = 1.0 / pow(cut_lj, 8.0); double t = cut_lj - cut_lj_inner; - double t2inv = 1.0/(t*t); - double t3inv = t2inv/t; - double t3 = 1.0/t3inv; - double a6 = (7.0*cut_lj_inner - 10.0*cut_lj)*r8inv*t2inv; - double b6 = (9.0*cut_lj - 7.0*cut_lj_inner)*r8inv*t3inv; - double a12 = (13.0*cut_lj_inner - 16.0*cut_lj)*r6inv*r8inv*t2inv; - double b12 = (15.0*cut_lj - 13.0*cut_lj_inner)*r6inv*r8inv*t3inv; - double c6 = r6inv - t3*(6.0*a6/3.0 + 6.0*b6*t/4.0); - double c12 = r6inv*r6inv - t3*(12.0*a12/3.0 + 12.0*b12*t/4.0); + double t2inv = 1.0 / (t * t); + double t3inv = t2inv / t; + double t3 = 1.0 / t3inv; + double a6 = (7.0 * cut_lj_inner - 10.0 * cut_lj) * r8inv * t2inv; + double b6 = (9.0 * cut_lj - 7.0 * cut_lj_inner) * r8inv * t3inv; + double a12 = (13.0 * cut_lj_inner - 16.0 * cut_lj) * r6inv * r8inv * t2inv; + double b12 = (15.0 * cut_lj - 13.0 * cut_lj_inner) * r6inv * r8inv * t3inv; + double c6 = r6inv - t3 * (6.0 * a6 / 3.0 + 6.0 * b6 * t / 4.0); + double c12 = r6inv * r6inv - t3 * (12.0 * a12 / 3.0 + 12.0 * b12 * t / 4.0); - ljsw1[i][j] = lj1[i][j]*a12 - lj2[i][j]*a6; - ljsw2[i][j] = lj1[i][j]*b12 - lj2[i][j]*b6; - ljsw3[i][j] = -lj3[i][j]*12.0*a12/3.0 + lj4[i][j]*6.0*a6/3.0; - ljsw4[i][j] = -lj3[i][j]*12.0*b12/4.0 + lj4[i][j]*6.0*b6/4.0; - ljsw5[i][j] = -lj3[i][j]*c12 + lj4[i][j]*c6; + ljsw1[i][j] = lj1[i][j] * a12 - lj2[i][j] * a6; + ljsw2[i][j] = lj1[i][j] * b12 - lj2[i][j] * b6; + ljsw3[i][j] = -lj3[i][j] * 12.0 * a12 / 3.0 + lj4[i][j] * 6.0 * a6 / 3.0; + ljsw4[i][j] = -lj3[i][j] * 12.0 * b12 / 4.0 + lj4[i][j] * 6.0 * b6 / 4.0; + ljsw5[i][j] = -lj3[i][j] * c12 + lj4[i][j] * c6; - double r3inv = 1.0/pow(cut_coul,3.0); + double r3inv = 1.0 / pow(cut_coul, 3.0); t = cut_coul - cut_coul_inner; - t2inv = 1.0/(t*t); - t3inv = t2inv/t; - double a1 = (2.0*cut_coul_inner - 5.0*cut_coul) * r3inv*t2inv; - double b1 = (4.0*cut_coul - 2.0*cut_coul_inner) * r3inv*t3inv; + t2inv = 1.0 / (t * t); + t3inv = t2inv / t; + double a1 = (2.0 * cut_coul_inner - 5.0 * cut_coul) * r3inv * t2inv; + double b1 = (4.0 * cut_coul - 2.0 * cut_coul_inner) * r3inv * t3inv; coulsw1 = a1; coulsw2 = b1; - coulsw3 = -a1/3.0; - coulsw4 = -b1/4.0; - coulsw5 = 1.0/cut_coul - t*t*t*(a1/3.0 + b1*t/4.0); + coulsw3 = -a1 / 3.0; + coulsw4 = -b1 / 4.0; + coulsw5 = 1.0 / cut_coul - t * t * t * (a1 / 3.0 + b1 * t / 4.0); lj1[j][i] = lj1[i][j]; lj2[j][i] = lj2[i][j]; @@ -352,13 +350,13 @@ void PairLJGromacsCoulGromacs::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(&epsilon[i][j],sizeof(double),1,fp); - fwrite(&sigma[i][j],sizeof(double),1,fp); + fwrite(&epsilon[i][j], sizeof(double), 1, fp); + fwrite(&sigma[i][j], sizeof(double), 1, fp); } } } @@ -372,19 +370,19 @@ void PairLJGromacsCoulGromacs::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++) 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,&epsilon[i][j],sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR, &epsilon[i][j], sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &sigma[i][j], sizeof(double), 1, fp, nullptr, error); } - MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&epsilon[i][j], 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&sigma[i][j], 1, MPI_DOUBLE, 0, world); } } } @@ -395,12 +393,12 @@ void PairLJGromacsCoulGromacs::read_restart(FILE *fp) void PairLJGromacsCoulGromacs::write_restart_settings(FILE *fp) { - fwrite(&cut_lj_inner,sizeof(double),1,fp); - fwrite(&cut_lj,sizeof(double),1,fp); - fwrite(&cut_coul_inner,sizeof(double),1,fp); - fwrite(&cut_coul,sizeof(double),1,fp); - fwrite(&offset_flag,sizeof(int),1,fp); - fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&cut_lj_inner, sizeof(double), 1, fp); + fwrite(&cut_lj, sizeof(double), 1, fp); + fwrite(&cut_coul_inner, sizeof(double), 1, fp); + fwrite(&cut_coul, sizeof(double), 1, fp); + fwrite(&offset_flag, sizeof(int), 1, fp); + fwrite(&mix_flag, sizeof(int), 1, fp); } /* ---------------------------------------------------------------------- @@ -410,19 +408,19 @@ void PairLJGromacsCoulGromacs::write_restart_settings(FILE *fp) void PairLJGromacsCoulGromacs::read_restart_settings(FILE *fp) { if (comm->me == 0) { - utils::sfread(FLERR,&cut_lj_inner,sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&cut_lj,sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&cut_coul_inner,sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&cut_coul,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_lj_inner, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cut_lj, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cut_coul_inner, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &cut_coul, 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_lj_inner,1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut_coul_inner,1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut_coul,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_lj_inner, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_lj, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_coul_inner, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&cut_coul, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&offset_flag, 1, MPI_INT, 0, world); + MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world); } /* ---------------------------------------------------------------------- @@ -431,8 +429,7 @@ void PairLJGromacsCoulGromacs::read_restart_settings(FILE *fp) void PairLJGromacsCoulGromacs::write_data(FILE *fp) { - for (int i = 1; i <= atom->ntypes; i++) - fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]); + for (int i = 1; i <= atom->ntypes; i++) fprintf(fp, "%d %g %g\n", i, epsilon[i][i], sigma[i][i]); } /* ---------------------------------------------------------------------- @@ -443,62 +440,63 @@ void PairLJGromacsCoulGromacs::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,epsilon[i][j],sigma[i][j]); + fprintf(fp, "%d %d %g %g\n", i, j, epsilon[i][j], sigma[i][j]); } /* ---------------------------------------------------------------------- */ -double PairLJGromacsCoulGromacs::single(int i, int j, int itype, int jtype, - double rsq, - double factor_coul, double factor_lj, - double &fforce) +double PairLJGromacsCoulGromacs::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_lj, double &fforce) { - double r2inv,r6inv,forcecoul,forcelj,phicoul,philj; - double r,tlj,tc,fswitch,phiswitch,fswitchcoul,phiswitchcoul; + double r2inv, r6inv, forcecoul, forcelj, phicoul, philj; + double r, tlj, tc, fswitch, phiswitch, fswitchcoul, phiswitchcoul; - r2inv = 1.0/rsq; + r2inv = 1.0 / rsq; if (rsq < cut_coulsq) { - forcecoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv); + forcecoul = force->qqrd2e * atom->q[i] * atom->q[j] * sqrt(r2inv); if (rsq > cut_coul_innersq) { r = sqrt(rsq); tc = r - cut_coul_inner; - fswitchcoul = force->qqrd2e * - atom->q[i]*atom->q[j] * r*tc*tc * (coulsw1 + coulsw2*tc); + fswitchcoul = + force->qqrd2e * atom->q[i] * atom->q[j] * r * tc * tc * (coulsw1 + coulsw2 * tc); forcecoul += fswitchcoul; } - } else forcecoul = 0.0; + } else + forcecoul = 0.0; if (rsq < cut_ljsq) { - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + r6inv = r2inv * r2inv * r2inv; + forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]); if (rsq > cut_lj_innersq) { r = sqrt(rsq); tlj = r - cut_lj_inner; - fswitch = r*tlj*tlj*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*tlj); + fswitch = r * tlj * tlj * (ljsw1[itype][jtype] + ljsw2[itype][jtype] * tlj); forcelj += fswitch; } - } else forcelj = 0.0; + } else + forcelj = 0.0; - fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv; + fforce = (factor_coul * forcecoul + factor_lj * forcelj) * r2inv; double eng = 0.0; if (rsq < cut_coulsq) { - phicoul = force->qqrd2e * atom->q[i]*atom->q[j] * (sqrt(r2inv)-coulsw5); + phicoul = force->qqrd2e * atom->q[i] * atom->q[j] * (sqrt(r2inv) - coulsw5); if (rsq > cut_coul_innersq) { - phiswitchcoul = force->qqrd2e * atom->q[i]*atom->q[j] * tc*tc*tc * (coulsw3 + coulsw4*tc); + phiswitchcoul = + force->qqrd2e * atom->q[i] * atom->q[j] * tc * tc * tc * (coulsw3 + coulsw4 * tc); phicoul += phiswitchcoul; } - eng += factor_coul*phicoul; + eng += factor_coul * phicoul; } if (rsq < cut_ljsq) { - philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); + philj = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]); philj += ljsw5[itype][jtype]; if (rsq > cut_lj_innersq) { - phiswitch = tlj*tlj*tlj * (ljsw3[itype][jtype] + ljsw4[itype][jtype]*tlj); + phiswitch = tlj * tlj * tlj * (ljsw3[itype][jtype] + ljsw4[itype][jtype] * tlj); philj += phiswitch; } - eng += factor_lj*philj; + eng += factor_lj * philj; } return eng; diff --git a/src/EXTRA-PAIR/pair_mie_cut.cpp b/src/EXTRA-PAIR/pair_mie_cut.cpp index 4fd5dedb69..729cac8ff8 100644 --- a/src/EXTRA-PAIR/pair_mie_cut.cpp +++ b/src/EXTRA-PAIR/pair_mie_cut.cpp @@ -18,20 +18,19 @@ #include "pair_mie_cut.h" -#include -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "respa.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -497,21 +496,14 @@ void PairMIECut::init_style() { // request regular or rRESPA neighbor list - int irequest; - int respa = 0; + int list_style = NeighConst::REQ_DEFAULT; - if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) { - if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; - if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; + if (update->whichflag == 1 && utils::strmatch(update->integrate_style, "^respa")) { + auto respa = (Respa *) update->integrate; + if (respa->level_inner >= 0) list_style = NeighConst::REQ_RESPA_INOUT; + if (respa->level_middle >= 0) list_style = NeighConst::REQ_RESPA_ALL; } - - irequest = neighbor->request(this,instance_me); - - if (respa >= 1) { - neighbor->requests[irequest]->respaouter = 1; - neighbor->requests[irequest]->respainner = 1; - } - if (respa == 2) neighbor->requests[irequest]->respamiddle = 1; + neighbor->add_request(this, list_style); // set rRESPA cutoffs diff --git a/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp b/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp index a0e31d3070..5758cd3956 100644 --- a/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp +++ b/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp @@ -18,17 +18,17 @@ #include "pair_nm_cut_coul_cut.h" -#include -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp b/src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp index ff8dd3d220..66f4e53ab2 100644 --- a/src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp +++ b/src/EXTRA-PAIR/pair_nm_cut_coul_long.cpp @@ -18,18 +18,18 @@ #include "pair_nm_cut_coul_long.h" -#include -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" -#include "neigh_list.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -304,7 +304,7 @@ void PairNMCutCoulLong::init_style() if (!atom->q_flag) error->all(FLERR,"Pair style nm/cut/coul/long requires atom attribute q"); - neighbor->request(this,instance_me); + neighbor->add_request(this); cut_coulsq = cut_coul * cut_coul; // insure use of KSpace long-range solver, set g_ewald diff --git a/src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp index b480a04b04..6f7d50ebdd 100644 --- a/src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp +++ b/src/MOFFF/pair_buck6d_coul_gauss_dsf.cpp @@ -20,19 +20,21 @@ ------------------------------------------------------------------------- */ #include "pair_buck6d_coul_gauss_dsf.h" -#include -#include + #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "math_const.h" #include "error.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" #include "math_special.h" +#include +#include + using namespace LAMMPS_NS; using namespace MathConst; @@ -314,7 +316,7 @@ void PairBuck6dCoulGaussDSF::init_style() if (!atom->q_flag) error->all(FLERR,"Pair style buck6d/coul/dsf requires atom attribute q"); - neighbor->request(this,instance_me); + neighbor->add_request(this); cut_coulsq = cut_coul * cut_coul; } diff --git a/src/MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/MOFFF/pair_buck6d_coul_gauss_long.cpp index 79849fad2a..946aeb4635 100644 --- a/src/MOFFF/pair_buck6d_coul_gauss_long.cpp +++ b/src/MOFFF/pair_buck6d_coul_gauss_long.cpp @@ -20,19 +20,20 @@ #include "pair_buck6d_coul_gauss_long.h" -#include -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "kspace.h" -#include "neighbor.h" -#include "neigh_list.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neighbor.h" #include "math_special.h" +#include +#include + using namespace LAMMPS_NS; #define EWALD_F 1.12837917 @@ -336,7 +337,7 @@ void PairBuck6dCoulGaussLong::init_style() error->all(FLERR,"Pair style requires a KSpace style"); g_ewald = force->kspace->g_ewald; - neighbor->request(this,instance_me); + neighbor->add_request(this); cut_coulsq = cut_coul * cut_coul; diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp index f2c24c6d26..bdca9446a0 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp @@ -17,21 +17,21 @@ ------------------------------------------------------------------------- */ #include "pair_hbond_dreiding_lj.h" -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "math_const.h" #include "math_special.h" #include "memory.h" -#include "error.h" +#include "molecule.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -441,9 +441,7 @@ void PairHbondDreidingLJ::init_style() // full neighbor list request - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp index cf83c6baa3..1530283f4d 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp @@ -17,21 +17,21 @@ ------------------------------------------------------------------------- */ #include "pair_hbond_dreiding_morse.h" -#include -#include + #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_request.h" -#include "neigh_list.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "math_const.h" #include "math_special.h" #include "memory.h" -#include "error.h" +#include "molecule.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -365,9 +365,7 @@ void PairHbondDreidingMorse::init_style() // full neighbor list request - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); } /* ---------------------------------------------------------------------- */ diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp index 5df54a0911..c1dd0ec48c 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp @@ -18,16 +18,16 @@ #include "pair_lj_charmm_coul_charmm.h" -#include -#include #include "atom.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; @@ -281,15 +281,14 @@ void PairLJCharmmCoulCharmm::coeff(int narg, char **arg) void PairLJCharmmCoulCharmm::init_style() { if (!atom->q_flag) - error->all(FLERR, - "Pair style lj/charmm/coul/charmm requires atom attribute q"); + error->all(FLERR, "Pair style lj/charmm/coul/charmm requires atom attribute q"); - neighbor->request(this,instance_me); + neighbor->add_request(this); // require cut_lj_inner < cut_lj, cut_coul_inner < cut_coul if (cut_lj_inner >= cut_lj || cut_coul_inner >= cut_coul) - error->all(FLERR,"Pair inner cutoff >= Pair outer cutoff"); + error->all(FLERR, "Pair inner cutoff >= Pair outer cutoff"); cut_lj_innersq = cut_lj_inner * cut_lj_inner; cut_ljsq = cut_lj * cut_lj; diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp index 1d9be47db2..1259dba07b 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp @@ -22,17 +22,17 @@ #include "pair_lj_charmmfsw_coul_charmmfsh.h" +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "update.h" + #include #include -#include "atom.h" -#include "update.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - using namespace LAMMPS_NS; @@ -305,10 +305,9 @@ void PairLJCharmmfswCoulCharmmfsh::coeff(int narg, char **arg) void PairLJCharmmfswCoulCharmmfsh::init_style() { if (!atom->q_flag) - error->all(FLERR,"Pair style lj/charmmfsw/coul/charmmfsh " - "requires atom attribute q"); + error->all(FLERR,"Pair style lj/charmmfsw/coul/charmmfsh requires atom attribute q"); - neighbor->request(this,instance_me); + neighbor->add_request(this); // require cut_lj_inner < cut_lj diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp index 60f55ea70d..1d46df3e13 100644 --- a/src/MOLECULE/pair_tip4p_cut.cpp +++ b/src/MOLECULE/pair_tip4p_cut.cpp @@ -18,18 +18,18 @@ #include "pair_tip4p_cut.h" -#include -#include "atom.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "domain.h" #include "angle.h" +#include "atom.h" #include "bond.h" #include "comm.h" -#include "memory.h" +#include "domain.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include using namespace LAMMPS_NS; @@ -427,7 +427,7 @@ void PairTIP4PCut::init_style() if (force->angle == nullptr) error->all(FLERR,"Must use an angle style with TIP4P potential"); - neighbor->request(this); + neighbor->add_request(this); // set alpha parameter diff --git a/src/PERI/pair_peri.cpp b/src/PERI/pair_peri.cpp index a13b6adad1..4ed281489b 100644 --- a/src/PERI/pair_peri.cpp +++ b/src/PERI/pair_peri.cpp @@ -132,7 +132,7 @@ void PairPeri::init_style() if (!fix_peri_neigh) fix_peri_neigh = (FixPeriNeigh *) modify->add_fix("PERI_NEIGH all PERI_NEIGH"); - neighbor->request(this, instance_me); + neighbor->add_request(this); } /* ---------------------------------------------------------------------- */ diff --git a/src/PTM/compute_ptm_atom.cpp b/src/PTM/compute_ptm_atom.cpp index 3e7ea775ac..e024d45012 100644 --- a/src/PTM/compute_ptm_atom.cpp +++ b/src/PTM/compute_ptm_atom.cpp @@ -159,12 +159,7 @@ void ComputePTMAtom::init() { // need an occasional full neighbor list - int irequest = neighbor->request(this, instance_me); - neighbor->requests[irequest]->pair = 0; - neighbor->requests[irequest]->compute = 1; - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - neighbor->requests[irequest]->occasional = 1; + neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL); } /* ---------------------------------------------------------------------- */ diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index a74a0fa934..dd56e96e81 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -802,10 +802,7 @@ void FixBondReact::init() } // need a half neighbor list, built every Nevery steps - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->pair = 0; - neighbor->requests[irequest]->fix = 1; - neighbor->requests[irequest]->occasional = 1; + neighbor->add_request(this, NeighConst::REQ_OCCASIONAL); lastcheck = -1; } diff --git a/src/REPLICA/fix_hyper_global.cpp b/src/REPLICA/fix_hyper_global.cpp index bd96897a9e..232a72a9ad 100644 --- a/src/REPLICA/fix_hyper_global.cpp +++ b/src/REPLICA/fix_hyper_global.cpp @@ -14,8 +14,6 @@ #include "fix_hyper_global.h" -#include -#include #include "atom.h" #include "update.h" #include "group.h" @@ -23,12 +21,14 @@ #include "domain.h" #include "comm.h" #include "neighbor.h" -#include "neigh_request.h" #include "neigh_list.h" #include "math_extra.h" #include "memory.h" #include "error.h" +#include +#include + using namespace LAMMPS_NS; using namespace FixConst; @@ -138,10 +138,7 @@ void FixHyperGlobal::init() // need an occasional half neighbor list - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->pair = 0; - neighbor->requests[irequest]->fix = 1; - neighbor->requests[irequest]->occasional = 1; + neighbor->add_request(this, NeighConst::REQ_OCCASIONAL); } /* ---------------------------------------------------------------------- */ diff --git a/src/REPLICA/fix_hyper_local.cpp b/src/REPLICA/fix_hyper_local.cpp index 6b6a672fa0..9364a2f753 100644 --- a/src/REPLICA/fix_hyper_local.cpp +++ b/src/REPLICA/fix_hyper_local.cpp @@ -14,9 +14,6 @@ #include "fix_hyper_local.h" -#include -#include - #include "atom.h" #include "update.h" #include "group.h" @@ -32,6 +29,9 @@ #include "memory.h" #include "error.h" +#include +#include + using namespace LAMMPS_NS; using namespace FixConst; @@ -310,15 +310,9 @@ void FixHyperLocal::init() // NOTE: what if pair style list cutoff > Dcut // or what if neigh skin is huge? - int irequest_full = neighbor->request(this,instance_me); - neighbor->requests[irequest_full]->id = 1; - neighbor->requests[irequest_full]->pair = 0; - neighbor->requests[irequest_full]->fix = 1; - neighbor->requests[irequest_full]->half = 0; - neighbor->requests[irequest_full]->full = 1; - neighbor->requests[irequest_full]->cut = 1; - neighbor->requests[irequest_full]->cutoff = dcut; - neighbor->requests[irequest_full]->occasional = 1; + auto req = neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL); + req->set_id(1); + req->set_cutoff(dcut); // also need occasional half neighbor list derived from pair style // used for building local bond list @@ -326,11 +320,8 @@ void FixHyperLocal::init() // this list will also be built (or derived/copied) // every time build_bond() is called - int irequest_half = neighbor->request(this,instance_me); - neighbor->requests[irequest_half]->id = 2; - neighbor->requests[irequest_half]->pair = 0; - neighbor->requests[irequest_half]->fix = 1; - neighbor->requests[irequest_half]->occasional = 1; + req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL); + req->set_id(2); // extra timing output diff --git a/src/SMTBQ/pair_smtbq.cpp b/src/SMTBQ/pair_smtbq.cpp index b01c214ac6..be8af7f9bd 100644 --- a/src/SMTBQ/pair_smtbq.cpp +++ b/src/SMTBQ/pair_smtbq.cpp @@ -50,7 +50,6 @@ #include "math_special.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "update.h" @@ -286,9 +285,7 @@ void PairSMTBQ::init_style() // need a full neighbor list - int irequest = neighbor->request(this); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); pgsize = neighbor->pgsize; oneatom = neighbor->oneatom; diff --git a/src/SPH/pair_sph_rhosum.cpp b/src/SPH/pair_sph_rhosum.cpp index 09ec206b58..30fac93036 100644 --- a/src/SPH/pair_sph_rhosum.cpp +++ b/src/SPH/pair_sph_rhosum.cpp @@ -20,7 +20,6 @@ #include "error.h" #include "memory.h" #include "neigh_list.h" -#include "neigh_request.h" #include "neighbor.h" #include "update.h" @@ -55,9 +54,7 @@ PairSPHRhoSum::~PairSPHRhoSum() { void PairSPHRhoSum::init_style() { // need a full neighbor list - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); } /* ---------------------------------------------------------------------- */ diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp index 4247918499..c2fb771def 100644 --- a/src/SPIN/pair_spin.cpp +++ b/src/SPIN/pair_spin.cpp @@ -90,9 +90,7 @@ void PairSpin::init_style() // need a full neighbor list - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + neighbor->add_request(this, NeighConst::REQ_FULL); // get the lattice_flag from nve/spin