diff --git a/src/USER-DIELECTRIC/compute_efield_atom.cpp b/src/USER-DIELECTRIC/compute_efield_atom.cpp index f81cb06f18..c6ea0db94f 100644 --- a/src/USER-DIELECTRIC/compute_efield_atom.cpp +++ b/src/USER-DIELECTRIC/compute_efield_atom.cpp @@ -121,7 +121,6 @@ void ComputeEfieldAtom::setup() void ComputeEfieldAtom::compute_peratom() { int i,j; - double onemass; invoked_peratom = update->ntimestep; if (update->vflag_atom != invoked_peratom) @@ -143,7 +142,6 @@ void ComputeEfieldAtom::compute_peratom() // ntotal includes ghosts if either newton flag is set // KSpace includes ghosts if tip4pflag is set - double** f = atom->f; double* q = atom->q; int nlocal = atom->nlocal; int npair = nlocal; diff --git a/src/USER-DIELECTRIC/fix_polarize_bem_gmres.cpp b/src/USER-DIELECTRIC/fix_polarize_bem_gmres.cpp index 2fd3d14b3f..b25c7ce7b7 100644 --- a/src/USER-DIELECTRIC/fix_polarize_bem_gmres.cpp +++ b/src/USER-DIELECTRIC/fix_polarize_bem_gmres.cpp @@ -246,7 +246,7 @@ void FixPolarizeBEMGMRES::init() /* ---------------------------------------------------------------------- */ -void FixPolarizeBEMGMRES::setup(int vflag) +void FixPolarizeBEMGMRES::setup(int /*vflag*/) { // check if the pair styles in use are compatible @@ -308,7 +308,6 @@ void FixPolarizeBEMGMRES::compute_induced_charges() double *ed = atom->ed; double *em = atom->em; double *epsilon = atom->epsilon; - int *mask = atom->mask; int nlocal = atom->nlocal; double epsilon0 = force->dielectric; int eflag = 0; @@ -585,7 +584,7 @@ void FixPolarizeBEMGMRES::gmres_solve(double *x, double *r) matvec(A, v(k-1), v(k), n); ------------------------------------------------------------------------- */ -void FixPolarizeBEMGMRES::apply_operator(double *w, double *Aw, int n) +void FixPolarizeBEMGMRES::apply_operator(double *w, double *Aw, int /*n*/) { int i; double *q = atom->q; @@ -594,7 +593,6 @@ void FixPolarizeBEMGMRES::apply_operator(double *w, double *Aw, int n) double *ed = atom->ed; double *em = atom->em; double *epsilon = atom->epsilon; - int *mask = atom->mask; int nlocal = atom->nlocal; double epsilon0 = force->dielectric; int eflag = 0; @@ -655,7 +653,7 @@ void FixPolarizeBEMGMRES::apply_operator(double *w, double *Aw, int n) using Eq. (60) in Barros et al. ------------------------------------------------------------------------ */ -void FixPolarizeBEMGMRES::update_residual(double *w, double *r, int n) +void FixPolarizeBEMGMRES::update_residual(double *w, double *r, int /*n*/) { int i; double *q = atom->q; @@ -665,7 +663,6 @@ void FixPolarizeBEMGMRES::update_residual(double *w, double *r, int n) double *ed = atom->ed; double *em = atom->em; double *epsilon = atom->epsilon; - int *mask = atom->mask; int nlocal = atom->nlocal; double epsilon0 = force->dielectric; int eflag = 0; @@ -862,7 +859,7 @@ void FixPolarizeBEMGMRES::grow_arrays(int n) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixPolarizeBEMGMRES::copy_arrays(int i, int j, int delflag) +void FixPolarizeBEMGMRES::copy_arrays(int i, int j, int /*delflag*/) { induced_charge_idx[j] = induced_charge_idx[i]; } @@ -878,7 +875,7 @@ void FixPolarizeBEMGMRES::set_arrays(int i) /* ---------------------------------------------------------------------- */ -int FixPolarizeBEMGMRES::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) +int FixPolarizeBEMGMRES::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int m; for (m = 0; m < n; m++) buf[m] = atom->q[list[m]]; diff --git a/src/USER-DIELECTRIC/fix_polarize_bem_icc.cpp b/src/USER-DIELECTRIC/fix_polarize_bem_icc.cpp index 325e3044ff..10f4c62958 100644 --- a/src/USER-DIELECTRIC/fix_polarize_bem_icc.cpp +++ b/src/USER-DIELECTRIC/fix_polarize_bem_icc.cpp @@ -146,7 +146,7 @@ void FixPolarizeBEMICC::init() /* ---------------------------------------------------------------------- */ -void FixPolarizeBEMICC::setup(int vflag) +void FixPolarizeBEMICC::setup(int /*vflag*/) { // check if the pair styles in use are compatible @@ -236,7 +236,6 @@ void FixPolarizeBEMICC::compute_induced_charges() if (kspaceflag) force->kspace->compute(eflag, vflag); if (force->newton) comm->reverse_comm(); - int i10 = 0; for (int i = 0; i < nlocal; i++) { if (!(mask[i] & groupbit)) continue; @@ -397,7 +396,7 @@ int FixPolarizeBEMICC::modify_param(int narg, char **arg) /* ---------------------------------------------------------------------- */ -int FixPolarizeBEMICC::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) +int FixPolarizeBEMICC::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int m; for (m = 0; m < n; m++) buf[m] = atom->q[list[m]]; diff --git a/src/USER-DIELECTRIC/fix_polarize_functional.cpp b/src/USER-DIELECTRIC/fix_polarize_functional.cpp index 55fcd98bbe..4ca2de43d0 100644 --- a/src/USER-DIELECTRIC/fix_polarize_functional.cpp +++ b/src/USER-DIELECTRIC/fix_polarize_functional.cpp @@ -169,7 +169,6 @@ void FixPolarizeFunctional::init() // mapping induced charge matrix/vector to atom tags and vice versa int i, maxtag; - double *q = atom->q; int *mask = atom->mask; tagint *tag = atom->tag; int nlocal = atom->nlocal; @@ -287,14 +286,14 @@ void FixPolarizeFunctional::init() /* ---------------------------------------------------------------------- */ -void FixPolarizeFunctional::init_list(int id, NeighList *ptr) +void FixPolarizeFunctional::init_list(int /*id*/, NeighList *ptr) { list = ptr; } /* ---------------------------------------------------------------------- */ -void FixPolarizeFunctional::setup(int vflag) +void FixPolarizeFunctional::setup(int /*vflag*/) { // check if the pair styles in use are compatible @@ -338,7 +337,7 @@ void FixPolarizeFunctional::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixPolarizeFunctional::setup_pre_force(int vflag) +void FixPolarizeFunctional::setup_pre_force(int /*vflag*/) { // calculate Rww before the run (assuming that the interface is fixed for now) // otherwise this should be done every time step in pre_force() @@ -537,7 +536,7 @@ int FixPolarizeFunctional::unpack_exchange(int nlocal, double *buf) /* ---------------------------------------------------------------------- */ -int FixPolarizeFunctional::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) +int FixPolarizeFunctional::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { int m; for (m = 0; m < n; m++) buf[m] = atom->q[list[m]]; @@ -567,7 +566,7 @@ void FixPolarizeFunctional::grow_arrays(int n) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixPolarizeFunctional::copy_arrays(int i, int j, int delflag) +void FixPolarizeFunctional::copy_arrays(int i, int j, int /*delflag*/) { induced_charge_idx[j] = induced_charge_idx[i]; ion_idx[j] = ion_idx[i]; @@ -613,9 +612,7 @@ double FixPolarizeFunctional::memory_usage() void FixPolarizeFunctional::calculate_Rww_cutoff() { int *mask = atom->mask; - int *type = atom->type; tagint *tag = atom->tag; - int nlocal = atom->nlocal; double **x = atom->x; double *area = atom->area; double *curvature = atom->curvature; @@ -838,9 +835,7 @@ void FixPolarizeFunctional::calculate_qiRqw_cutoff() int ii, i, k, kk, jnum; double xtmp, ytmp, ztmp, delx, dely, delz, r; int *mask = atom->mask; - int *type = atom->type; tagint *tag = atom->tag; - int nlocal = atom->nlocal; double **x = atom->x; double *q = atom->q_unscaled; double *epsilon = atom->epsilon; diff --git a/src/USER-DIELECTRIC/pair_coul_cut_dielectric.cpp b/src/USER-DIELECTRIC/pair_coul_cut_dielectric.cpp index 1b540157e4..d5ead44512 100644 --- a/src/USER-DIELECTRIC/pair_coul_cut_dielectric.cpp +++ b/src/USER-DIELECTRIC/pair_coul_cut_dielectric.cpp @@ -56,7 +56,7 @@ PairCoulCutDielectric::~PairCoulCutDielectric() void PairCoulCutDielectric::compute(int eflag, int vflag) { int i,j,ii,jj,inum,jnum,itype,jtype; - double qtmp,etmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair; + double qtmp,etmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul; double fpair_i,fpair_j; double rsq,r2inv,rinv,forcecoul,factor_coul,efield_i; int *ilist,*jlist,*numneigh,**firstneigh; @@ -73,7 +73,6 @@ void PairCoulCutDielectric::compute(int eflag, int vflag) double **x = atom->x; double **f = atom->f; double *q = atom->q; - double *q_real = atom->q_unscaled; double* eps = atom->epsilon; double** norm = atom->mu; double* curvature = atom->curvature; @@ -177,16 +176,16 @@ void PairCoulCutDielectric::init_style() /* ---------------------------------------------------------------------- */ -double PairCoulCutDielectric::single(int i, int j, int itype, int jtype, +double PairCoulCutDielectric::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq, - double factor_coul, double factor_lj, + double factor_coul, double /*factor_lj*/, double &fforce) { - double r2inv,forcecoul,phicoul,ei,ej; + double r2inv,phicoul,ei,ej; double* eps = atom->epsilon; r2inv = 1.0/rsq; - forcecoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv)*eps[i]; + fforce = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv)*eps[i]; double eng = 0.0; if (eps[i] == 1) ei = 0; diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp b/src/USER-DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp index 82a5b0c99a..e4b330d485 100644 --- a/src/USER-DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp +++ b/src/USER-DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp @@ -57,7 +57,7 @@ PairLJCutCoulCutDielectric::~PairLJCutCoulCutDielectric() void PairLJCutCoulCutDielectric::compute(int eflag, int vflag) { int i, j, ii, jj, inum, jnum, itype, jtype; - double qtmp, etmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul, fpair; + double qtmp, etmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul; double fpair_i, fpair_j; double rsq, r2inv, r6inv, forcecoul, forcelj, factor_coul, factor_lj, efield_i, epot_i; int *ilist, *jlist, *numneigh, **firstneigh; @@ -76,7 +76,6 @@ void PairLJCutCoulCutDielectric::compute(int eflag, int vflag) double **x = atom->x; double **f = atom->f; double *q = atom->q; - double *q_real = atom->q_unscaled; double *eps = atom->epsilon; double **norm = atom->mu; double *curvature = atom->curvature; diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp b/src/USER-DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp index 4f8b2d63c8..4f3b46b14d 100644 --- a/src/USER-DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp +++ b/src/USER-DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp @@ -58,7 +58,7 @@ PairLJCutCoulDebyeDielectric::~PairLJCutCoulDebyeDielectric() void PairLJCutCoulDebyeDielectric::compute(int eflag, int vflag) { int i, j, ii, jj, inum, jnum, itype, jtype; - double qtmp, etmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul, fpair; + double qtmp, etmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul; double fpair_i, fpair_j; double rsq, r2inv, r6inv, forcecoul, forcelj, factor_coul, factor_lj, efield_i, epot_i; double r, rinv, screening; diff --git a/src/USER-DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp b/src/USER-DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp index c273fc2132..5fd8b499f8 100644 --- a/src/USER-DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp +++ b/src/USER-DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp @@ -64,7 +64,7 @@ PairLJCutCoulMSMDielectric::~PairLJCutCoulMSMDielectric() void PairLJCutCoulMSMDielectric::compute(int eflag, int vflag) { int i, ii, j, jj, inum, jnum, itype, jtype, itable; - double qtmp, etmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul, fpair, fcoul; + double qtmp, etmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul, fpair; double fpair_i, fpair_j; double fraction, table; double r, r2inv, r6inv, forcecoul, forcelj, factor_coul, factor_lj; diff --git a/src/USER-DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp b/src/USER-DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp index 564a156a04..53e9998f31 100644 --- a/src/USER-DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp +++ b/src/USER-DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp @@ -75,7 +75,7 @@ PairLJLongCoulLongDielectric::~PairLJLongCoulLongDielectric() void PairLJLongCoulLongDielectric::init_style() { - PairLJLongCoulLongDielectric::init_style(); + PairLJLongCoulLong::init_style(); avec = (AtomVecDielectric *) atom->style_match("dielectric"); if (!avec) error->all(FLERR, "Pair lj/long/coul/long/dielectric requires atom style dielectric"); @@ -91,7 +91,7 @@ void PairLJLongCoulLongDielectric::init_style() void PairLJLongCoulLongDielectric::compute(int eflag, int vflag) { - double evdwl, ecoul, fpair; + double evdwl, ecoul; evdwl = ecoul = 0.0; ev_init(eflag, vflag); @@ -117,10 +117,10 @@ void PairLJLongCoulLongDielectric::compute(int eflag, int vflag) int newton_pair = force->newton_pair; double qqrd2e = force->qqrd2e; - int i, ii, j, jj, inum, jnum, itype, jtype, itable; + int i, j, itype, jtype, itable; double qtmp, etmp, xtmp, ytmp, ztmp, delx, dely, delz; int order1 = ewald_order & (1 << 1), order6 = ewald_order & (1 << 6); - int *ineigh, *ineighn, *jneigh, *jneighn, typei, typej, ni; + int *ineigh, *ineighn, *jneigh, *jneighn, ni; double qi = 0.0, qri = 0.0; double fpair_i, fpair_j; double fraction, table; @@ -128,7 +128,7 @@ void PairLJLongCoulLongDielectric::compute(int eflag, int vflag) double grij, expm2, prefactor, t, erfc, prefactorE, efield_i, epot_i; double r, rsq, r2inv, force_coul, force_lj, factor_coul, factor_lj; double g2 = g_ewald_6 * g_ewald_6, g6 = g2 * g2 * g2, g8 = g6 * g2; - double xi[3], d[3]; + double xi[3]; ineighn = (ineigh = list->ilist) + list->inum; @@ -136,15 +136,19 @@ void PairLJLongCoulLongDielectric::compute(int eflag, int vflag) i = *ineigh; fi = f0 + 3 * i; qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + etmp = eps[i]; if (order1) qri = (qi = q[i]) * qqrd2e; // initialize constants - offseti = offset[typei = type[i]]; - lj1i = lj1[typei]; - lj2i = lj2[typei]; - lj3i = lj3[typei]; - lj4i = lj4[typei]; - cutsqi = cutsq[typei]; - cut_ljsqi = cut_ljsq[typei]; + offseti = offset[itype = type[i]]; + lj1i = lj1[itype]; + lj2i = lj2[itype]; + lj3i = lj3[itype]; + lj4i = lj4[itype]; + cutsqi = cutsq[itype]; + cut_ljsqi = cut_ljsq[itype]; memcpy(xi, x0 + (i + (i << 1)), 3 * sizeof(double)); jneighn = (jneigh = list->firstneigh[i]) + list->numneigh[i]; @@ -174,7 +178,7 @@ void PairLJLongCoulLongDielectric::compute(int eflag, int vflag) rsq = delx * delx + dely * dely + delz * delz; jtype = type[j]; - if (rsq >= cutsq[typei][typej]) continue; + if (rsq >= cutsq[itype][jtype]) continue; r2inv = 1.0 / rsq; r = sqrt(rsq); @@ -216,22 +220,22 @@ void PairLJLongCoulLongDielectric::compute(int eflag, int vflag) } else epot_i = efield_i = force_coul = ecoul = 0.0; - if (rsq < cut_ljsqi[typej]) { // lj + if (rsq < cut_ljsqi[jtype]) { // lj if (order6) { // long-range lj if (!ndisptablebits || rsq <= tabinnerdispsq) { // series real space double rn = r2inv * r2inv * r2inv; double x2 = g2 * rsq, a2 = 1.0 / x2; - x2 = a2 * exp(-x2) * lj4i[typej]; + x2 = a2 * exp(-x2) * lj4i[jtype]; if (ni == 0) { - force_lj = (rn *= rn) * lj1i[typej] - + force_lj = (rn *= rn) * lj1i[jtype] - g8 * (((6.0 * a2 + 6.0) * a2 + 3.0) * a2 + 1.0) * x2 * rsq; - if (eflag) evdwl = rn * lj3i[typej] - g6 * ((a2 + 1.0) * a2 + 0.5) * x2; + if (eflag) evdwl = rn * lj3i[jtype] - g6 * ((a2 + 1.0) * a2 + 0.5) * x2; } else { // special case double f = special_lj[ni], t = rn * (1.0 - f); - force_lj = f * (rn *= rn) * lj1i[typej] - - g8 * (((6.0 * a2 + 6.0) * a2 + 3.0) * a2 + 1.0) * x2 * rsq + t * lj2i[typej]; + force_lj = f * (rn *= rn) * lj1i[jtype] - + g8 * (((6.0 * a2 + 6.0) * a2 + 3.0) * a2 + 1.0) * x2 * rsq + t * lj2i[jtype]; if (eflag) - evdwl = f * rn * lj3i[typej] - g6 * ((a2 + 1.0) * a2 + 0.5) * x2 + t * lj4i[typej]; + evdwl = f * rn * lj3i[jtype] - g6 * ((a2 + 1.0) * a2 + 0.5) * x2 + t * lj4i[jtype]; } } else { // table real space union_int_float_t disp_t; @@ -240,39 +244,36 @@ void PairLJLongCoulLongDielectric::compute(int eflag, int vflag) double f_disp = (rsq - rdisptable[disp_k]) * drdisptable[disp_k]; double rn = r2inv * r2inv * r2inv; if (ni == 0) { - force_lj = (rn *= rn) * lj1i[typej] - - (fdisptable[disp_k] + f_disp * dfdisptable[disp_k]) * lj4i[typej]; + force_lj = (rn *= rn) * lj1i[jtype] - + (fdisptable[disp_k] + f_disp * dfdisptable[disp_k]) * lj4i[jtype]; if (eflag) - evdwl = rn * lj3i[typej] - - (edisptable[disp_k] + f_disp * dedisptable[disp_k]) * lj4i[typej]; + evdwl = rn * lj3i[jtype] - + (edisptable[disp_k] + f_disp * dedisptable[disp_k]) * lj4i[jtype]; } else { // special case double f = special_lj[ni], t = rn * (1.0 - f); - force_lj = f * (rn *= rn) * lj1i[typej] - - (fdisptable[disp_k] + f_disp * dfdisptable[disp_k]) * lj4i[typej] + - t * lj2i[typej]; + force_lj = f * (rn *= rn) * lj1i[jtype] - + (fdisptable[disp_k] + f_disp * dfdisptable[disp_k]) * lj4i[jtype] + + t * lj2i[jtype]; if (eflag) - evdwl = f * rn * lj3i[typej] - - (edisptable[disp_k] + f_disp * dedisptable[disp_k]) * lj4i[typej] + - t * lj4i[typej]; + evdwl = f * rn * lj3i[jtype] - + (edisptable[disp_k] + f_disp * dedisptable[disp_k]) * lj4i[jtype] + + t * lj4i[jtype]; } } } else { // cut lj double rn = r2inv * r2inv * r2inv; if (ni == 0) { - force_lj = rn * (rn * lj1i[typej] - lj2i[typej]); - if (eflag) evdwl = rn * (rn * lj3i[typej] - lj4i[typej]) - offseti[typej]; + force_lj = rn * (rn * lj1i[jtype] - lj2i[jtype]); + if (eflag) evdwl = rn * (rn * lj3i[jtype] - lj4i[jtype]) - offseti[jtype]; } else { // special case double f = special_lj[ni]; - force_lj = f * rn * (rn * lj1i[typej] - lj2i[typej]); - if (eflag) evdwl = f * (rn * (rn * lj3i[typej] - lj4i[typej]) - offseti[typej]); + force_lj = f * rn * (rn * lj1i[jtype] - lj2i[jtype]); + if (eflag) evdwl = f * (rn * (rn * lj3i[jtype] - lj4i[jtype]) - offseti[jtype]); } } - } + } else force_lj = evdwl = 0.0; - else - force_lj = evdwl = 0.0; - - fpair = (force_coul * etmp + force_lj) * r2inv; + fpair_i = (force_coul * etmp + force_lj) * r2inv; f[i][0] += delx * fpair_i; f[i][1] += dely * fpair_i; f[i][2] += delz * fpair_i;