diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp index c271f27237..23ec79fa98 100644 --- a/src/ASPHERE/pair_resquared.cpp +++ b/src/ASPHERE/pair_resquared.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -18,32 +17,31 @@ #include "pair_resquared.h" -#include -#include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" #include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "math_extra.h" +#include "memory.h" +#include "neigh_list.h" +#include "neighbor.h" +#include using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairRESquared::PairRESquared(LAMMPS *lmp) : Pair(lmp), - cr60(pow(60.0,1.0/3.0)), - b_alpha(45.0/56.0) +PairRESquared::PairRESquared(LAMMPS *lmp) : + Pair(lmp), cr60(pow(60.0, 1.0 / 3.0)), b_alpha(45.0 / 56.0) { single_enable = 0; - cr60 = pow(60.0,1.0/3.0); - b_alpha = 45.0/56.0; - solv_f_a = 3.0/(16.0*atan(1.0)*-36.0); - solv_f_r = 3.0/(16.0*atan(1.0)*2025.0); + cr60 = pow(60.0, 1.0 / 3.0); + b_alpha = 45.0 / 56.0; + solv_f_a = 3.0 / (16.0 * atan(1.0) * -36.0); + solv_f_r = 3.0 / (16.0 * atan(1.0) * 2025.0); } /* ---------------------------------------------------------------------- @@ -68,8 +66,8 @@ PairRESquared::~PairRESquared() memory->destroy(lj3); memory->destroy(lj4); memory->destroy(offset); - delete [] lshape; - delete [] setwell; + delete[] lshape; + delete[] setwell; } } @@ -77,14 +75,14 @@ PairRESquared::~PairRESquared() void PairRESquared::compute(int eflag, int vflag) { - int i,j,ii,jj,inum,jnum,itype,jtype; - double evdwl,one_eng,rsq,r2inv,r6inv,forcelj,factor_lj; - double fforce[3],ttor[3],rtor[3],r12[3]; - int *ilist,*jlist,*numneigh,**firstneigh; - RE2Vars wi,wj; + int i, j, ii, jj, inum, jnum, itype, jtype; + double evdwl, one_eng, rsq, r2inv, r6inv, forcelj, factor_lj; + double fforce[3], ttor[3], rtor[3], r12[3]; + int *ilist, *jlist, *numneigh, **firstneigh; + RE2Vars wi, wj; evdwl = 0.0; - ev_init(eflag,vflag); + ev_init(eflag, vflag); double **x = atom->x; double **f = atom->f; @@ -107,7 +105,7 @@ void PairRESquared::compute(int eflag, int vflag) // not a LJ sphere - if (lshape[itype] != 0.0) precompute_i(i,wi); + if (lshape[itype] != 0.0) precompute_i(i, wi); jlist = firstneigh[i]; jnum = numneigh[i]; @@ -119,10 +117,10 @@ void PairRESquared::compute(int eflag, int vflag) // r12 = center to center vector - r12[0] = x[j][0]-x[i][0]; - r12[1] = x[j][1]-x[i][1]; - r12[2] = x[j][2]-x[i][2]; - rsq = MathExtra::dot3(r12,r12); + r12[0] = x[j][0] - x[i][0]; + r12[1] = x[j][1] - x[i][1]; + r12[2] = x[j][2] - x[i][2]; + rsq = MathExtra::dot3(r12, r12); jtype = type[j]; // compute if less than cutoff @@ -132,49 +130,50 @@ void PairRESquared::compute(int eflag, int vflag) switch (form[itype][jtype]) { - case SPHERE_SPHERE: - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); - forcelj *= -r2inv; - if (eflag) one_eng = - r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) - - offset[itype][jtype]; - fforce[0] = r12[0]*forcelj; - fforce[1] = r12[1]*forcelj; - fforce[2] = r12[2]*forcelj; - break; + case SPHERE_SPHERE: + r2inv = 1.0 / rsq; + r6inv = r2inv * r2inv * r2inv; + forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]); + forcelj *= -r2inv; + if (eflag) { + one_eng = r6inv * (r6inv * lj3[itype][jtype] - lj4[itype][jtype]); + one_eng -= offset[itype][jtype]; + } + fforce[0] = r12[0] * forcelj; + fforce[1] = r12[1] * forcelj; + fforce[2] = r12[2] * forcelj; + break; - case SPHERE_ELLIPSE: - precompute_i(j,wj); - if (newton_pair || j < nlocal) { - one_eng = resquared_lj(j,i,wj,r12,rsq,fforce,rtor,true); - tor[j][0] += rtor[0]*factor_lj; - tor[j][1] += rtor[1]*factor_lj; - tor[j][2] += rtor[2]*factor_lj; - } else - one_eng = resquared_lj(j,i,wj,r12,rsq,fforce,rtor,false); - break; + case SPHERE_ELLIPSE: + precompute_i(j, wj); + if (newton_pair || j < nlocal) { + one_eng = resquared_lj(j, i, wj, r12, rsq, fforce, rtor, true); + tor[j][0] += rtor[0] * factor_lj; + tor[j][1] += rtor[1] * factor_lj; + tor[j][2] += rtor[2] * factor_lj; + } else + one_eng = resquared_lj(j, i, wj, r12, rsq, fforce, rtor, false); + break; - case ELLIPSE_SPHERE: - one_eng = resquared_lj(i,j,wi,r12,rsq,fforce,ttor,true); - tor[i][0] += ttor[0]*factor_lj; - tor[i][1] += ttor[1]*factor_lj; - tor[i][2] += ttor[2]*factor_lj; - break; + case ELLIPSE_SPHERE: + one_eng = resquared_lj(i, j, wi, r12, rsq, fforce, ttor, true); + tor[i][0] += ttor[0] * factor_lj; + tor[i][1] += ttor[1] * factor_lj; + tor[i][2] += ttor[2] * factor_lj; + break; - default: - precompute_i(j,wj); - one_eng = resquared_analytic(i,j,wi,wj,r12,rsq,fforce,ttor,rtor); - tor[i][0] += ttor[0]*factor_lj; - tor[i][1] += ttor[1]*factor_lj; - tor[i][2] += ttor[2]*factor_lj; - if (newton_pair || j < nlocal) { - tor[j][0] += rtor[0]*factor_lj; - tor[j][1] += rtor[1]*factor_lj; - tor[j][2] += rtor[2]*factor_lj; - } - break; + default: + precompute_i(j, wj); + one_eng = resquared_analytic(i, j, wi, wj, r12, rsq, fforce, ttor, rtor); + tor[i][0] += ttor[0] * factor_lj; + tor[i][1] += ttor[1] * factor_lj; + tor[i][2] += ttor[2] * factor_lj; + if (newton_pair || j < nlocal) { + tor[j][0] += rtor[0] * factor_lj; + tor[j][1] += rtor[1] * factor_lj; + tor[j][2] += rtor[2] * factor_lj; + } + break; } fforce[0] *= factor_lj; @@ -190,11 +189,11 @@ void PairRESquared::compute(int eflag, int vflag) f[j][2] -= fforce[2]; } - if (eflag) evdwl = factor_lj*one_eng; + if (eflag) evdwl = factor_lj * one_eng; - if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, - evdwl,0.0,fforce[0],fforce[1],fforce[2], - -r12[0],-r12[1],-r12[2]); + if (evflag) + ev_tally_xyz(i, j, nlocal, newton_pair, evdwl, 0.0, fforce[0], fforce[1], fforce[2], + -r12[0], -r12[1], -r12[2]); } } } @@ -209,31 +208,30 @@ void PairRESquared::compute(int eflag, int vflag) void PairRESquared::allocate() { allocated = 1; - int n = atom->ntypes; + const int n = 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, n, n, "pair:setflag"); + for (int i = 1; i < n; i++) + for (int j = i; j < n; j++) setflag[i][j] = 0; - memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cutsq, n, n, "pair:cutsq"); - memory->create(form,n+1,n+1,"pair:form"); - memory->create(epsilon,n+1,n+1,"pair:epsilon"); - memory->create(sigma,n+1,n+1,"pair:sigma"); - memory->create(shape1,n+1,3,"pair:shape1"); - memory->create(shape2,n+1,3,"pair:shape2"); - memory->create(well,n+1,3,"pair:well"); - memory->create(cut,n+1,n+1,"pair:cut"); - 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(offset,n+1,n+1,"pair:offset"); + memory->create(form, n, n, "pair:form"); + memory->create(epsilon, n, n, "pair:epsilon"); + memory->create(sigma, n, n, "pair:sigma"); + memory->create(shape1, n, 3, "pair:shape1"); + memory->create(shape2, n, 3, "pair:shape2"); + memory->create(well, n, 3, "pair:well"); + memory->create(cut, n, n, "pair:cut"); + memory->create(lj1, n, n, "pair:lj1"); + memory->create(lj2, n, n, "pair:lj2"); + memory->create(lj3, n, n, "pair:lj3"); + memory->create(lj4, n, n, "pair:lj4"); + memory->create(offset, n, n, "pair:offset"); - lshape = new double[n+1]; - setwell = new int[n+1]; - for (int i = 1; i <= n; i++) setwell[i] = 0; + lshape = new double[n]; + setwell = new int[n]; + for (int i = 1; i < n; i++) setwell[i] = 0; } /* ---------------------------------------------------------------------- @@ -242,14 +240,14 @@ void PairRESquared::allocate() void PairRESquared::settings(int narg, char **arg) { - if (narg != 1) error->all(FLERR,"Illegal pair_style command"); + if (narg != 1) error->all(FLERR, "Illegal pair_style command"); - cut_global = utils::numeric(FLERR,arg[0],false,lmp); + cut_global = utils::numeric(FLERR, arg[0], false, lmp); // reset cutoffs that have been explicitly set if (allocated) { - int i,j; + int i, j; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) if (setflag[i][j]) cut[i][j] = cut_global; @@ -262,29 +260,28 @@ void PairRESquared::settings(int narg, char **arg) void PairRESquared::coeff(int narg, char **arg) { - if (narg < 10 || narg > 11) - error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 10 || narg > 11) 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 eia_one = utils::numeric(FLERR,arg[4],false,lmp); - double eib_one = utils::numeric(FLERR,arg[5],false,lmp); - double eic_one = utils::numeric(FLERR,arg[6],false,lmp); - double eja_one = utils::numeric(FLERR,arg[7],false,lmp); - double ejb_one = utils::numeric(FLERR,arg[8],false,lmp); - double ejc_one = utils::numeric(FLERR,arg[9],false,lmp); + double epsilon_one = utils::numeric(FLERR, arg[2], false, lmp); + double sigma_one = utils::numeric(FLERR, arg[3], false, lmp); + double eia_one = utils::numeric(FLERR, arg[4], false, lmp); + double eib_one = utils::numeric(FLERR, arg[5], false, lmp); + double eic_one = utils::numeric(FLERR, arg[6], false, lmp); + double eja_one = utils::numeric(FLERR, arg[7], false, lmp); + double ejb_one = utils::numeric(FLERR, arg[8], false, lmp); + double ejc_one = utils::numeric(FLERR, arg[9], false, lmp); double cut_one = cut_global; - if (narg == 11) cut_one = utils::numeric(FLERR,arg[10],false,lmp); + if (narg == 11) cut_one = utils::numeric(FLERR, arg[10], 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; cut[i][j] = cut_one; @@ -292,22 +289,26 @@ void PairRESquared::coeff(int narg, char **arg) well[i][0] = eia_one; well[i][1] = eib_one; well[i][2] = eic_one; - if (eia_one == 1.0 && eib_one == 1.0 && eic_one == 1.0) setwell[i] = 2; - else setwell[i] = 1; + if (eia_one == 1.0 && eib_one == 1.0 && eic_one == 1.0) + setwell[i] = 2; + else + setwell[i] = 1; } if (eja_one != 0.0 || ejb_one != 0.0 || ejc_one != 0.0) { well[j][0] = eja_one; well[j][1] = ejb_one; well[j][2] = ejc_one; - if (eja_one == 1.0 && ejb_one == 1.0 && ejc_one == 1.0) setwell[j] = 2; - else setwell[j] = 1; + if (eja_one == 1.0 && ejb_one == 1.0 && ejc_one == 1.0) + setwell[j] = 2; + else + setwell[j] = 1; } setflag[i][j] = 1; count++; } } - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- @@ -317,21 +318,21 @@ void PairRESquared::coeff(int narg, char **arg) void PairRESquared::init_style() { avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); - if (!avec) error->all(FLERR,"Pair resquared requires atom style ellipsoid"); + if (!avec) error->all(FLERR, "Pair resquared requires atom style ellipsoid"); - neighbor->request(this,instance_me); + neighbor->request(this, instance_me); // per-type shape precalculations // require that atom shapes are identical within each type for (int i = 1; i <= atom->ntypes; i++) { - if (!atom->shape_consistency(i,shape1[i][0],shape1[i][1],shape1[i][2])) - error->all(FLERR,"Pair resquared requires atoms with same type have same shape"); + if (!atom->shape_consistency(i, shape1[i][0], shape1[i][1], shape1[i][2])) + error->all(FLERR, "Pair resquared requires atoms with same type have same shape"); if (setwell[i]) { - shape2[i][0] = shape1[i][0]*shape1[i][0]; - shape2[i][1] = shape1[i][1]*shape1[i][1]; - shape2[i][2] = shape1[i][2]*shape1[i][2]; - lshape[i] = shape1[i][0]*shape1[i][1]*shape1[i][2]; + shape2[i][0] = shape1[i][0] * shape1[i][0]; + shape2[i][1] = shape1[i][1] * shape1[i][1]; + shape2[i][2] = shape1[i][2] * shape1[i][2]; + lshape[i] = shape1[i][0] * shape1[i][1] * shape1[i][2]; } } } @@ -343,14 +344,12 @@ void PairRESquared::init_style() double PairRESquared::init_one(int i, int j) { if (setwell[i] == 0 || setwell[j] == 0) - error->all(FLERR,"Pair resquared epsilon a,b,c coeffs are not all set"); + error->all(FLERR, "Pair resquared epsilon a,b,c coeffs are not all set"); int ishape = 0; - if (shape1[i][0] != 0.0 && shape1[i][1] != 0.0 && shape1[i][2] != 0.0) - ishape = 1; + if (shape1[i][0] != 0.0 && shape1[i][1] != 0.0 && shape1[i][2] != 0.0) ishape = 1; int jshape = 0; - if (shape1[j][0] != 0.0 && shape1[j][1] != 0.0 && shape1[j][2] != 0.0) - jshape = 1; + if (shape1[j][0] != 0.0 && shape1[j][1] != 0.0 && shape1[j][2] != 0.0) jshape = 1; if (ishape == 0 && jshape == 0) { form[i][j] = SPHERE_SPHERE; @@ -371,28 +370,27 @@ double PairRESquared::init_one(int i, int j) if (setflag[i][j] == 0) { if (setflag[j][i] == 0) { if (ishape == 0 && jshape == 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[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[i][j] = mix_distance(cut[i][i], cut[j][j]); } else - error->all(FLERR, - "Pair resquared epsilon and sigma coeffs are not all set"); + error->all(FLERR, "Pair resquared epsilon and sigma coeffs are not all set"); } epsilon[i][j] = epsilon[j][i]; sigma[i][j] = sigma[j][i]; cut[i][j] = cut[j][i]; } - 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); if (offset_flag && (cut[i][j] > 0.0)) { double ratio = sigma[i][j] / cut[i][j]; - offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0)); - } else offset[i][j] = 0.0; + offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio, 12.0) - pow(ratio, 6.0)); + } else + offset[i][j] = 0.0; epsilon[j][i] = epsilon[i][j]; sigma[j][i] = sigma[i][j]; @@ -413,16 +411,16 @@ void PairRESquared::write_restart(FILE *fp) { write_restart_settings(fp); - int i,j; + int i, j; for (i = 1; i <= atom->ntypes; i++) { - fwrite(&setwell[i],sizeof(int),1,fp); - if (setwell[i]) fwrite(&well[i][0],sizeof(double),3,fp); + fwrite(&setwell[i], sizeof(int), 1, fp); + if (setwell[i]) fwrite(&well[i][0], sizeof(double), 3, fp); 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[i][j],sizeof(double),1,fp); + fwrite(&epsilon[i][j], sizeof(double), 1, fp); + fwrite(&sigma[i][j], sizeof(double), 1, fp); + fwrite(&cut[i][j], sizeof(double), 1, fp); } } } @@ -437,27 +435,27 @@ void PairRESquared::read_restart(FILE *fp) read_restart_settings(fp); allocate(); - int i,j; + int i, j; int me = comm->me; for (i = 1; i <= atom->ntypes; i++) { - if (me == 0) utils::sfread(FLERR,&setwell[i],sizeof(int),1,fp,nullptr,error); - MPI_Bcast(&setwell[i],1,MPI_INT,0,world); + if (me == 0) utils::sfread(FLERR, &setwell[i], sizeof(int), 1, fp, nullptr, error); + MPI_Bcast(&setwell[i], 1, MPI_INT, 0, world); if (setwell[i]) { - if (me == 0) utils::sfread(FLERR,&well[i][0],sizeof(double),3,fp,nullptr,error); - MPI_Bcast(&well[i][0],3,MPI_DOUBLE,0,world); + if (me == 0) utils::sfread(FLERR, &well[i][0], sizeof(double), 3, fp, nullptr, error); + MPI_Bcast(&well[i][0], 3, MPI_DOUBLE, 0, world); } 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[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[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[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[i][j], 1, MPI_DOUBLE, 0, world); } } } @@ -469,8 +467,8 @@ void PairRESquared::read_restart(FILE *fp) void PairRESquared::write_restart_settings(FILE *fp) { - fwrite(&cut_global,sizeof(double),1,fp); - fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&cut_global, sizeof(double), 1, fp); + fwrite(&mix_flag, sizeof(int), 1, fp); } /* ---------------------------------------------------------------------- @@ -481,34 +479,34 @@ void PairRESquared::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); - utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR, &cut_global, sizeof(double), 1, fp, nullptr, error); + utils::sfread(FLERR, &mix_flag, sizeof(int), 1, fp, nullptr, error); } - MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); - MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + MPI_Bcast(&cut_global, 1, MPI_DOUBLE, 0, world); + MPI_Bcast(&mix_flag, 1, MPI_INT, 0, world); } /* ---------------------------------------------------------------------- Precompute per-particle temporaries for RE-squared calculation ------------------------------------------------------------------------- */ -void PairRESquared::precompute_i(const int i,RE2Vars &ws) +void PairRESquared::precompute_i(const int i, RE2Vars &ws) { - double aTs[3][3]; // A1'*S1^2 + double aTs[3][3]; // A1'*S1^2 int *ellipsoid = atom->ellipsoid; AtomVecEllipsoid::Bonus *bonus = avec->bonus; - MathExtra::quat_to_mat_trans(bonus[ellipsoid[i]].quat,ws.A); - MathExtra::transpose_diag3(ws.A,well[atom->type[i]],ws.aTe); - MathExtra::transpose_diag3(ws.A,shape2[atom->type[i]],aTs); - MathExtra::diag_times3(shape2[atom->type[i]],ws.A,ws.sa); - MathExtra::times3(aTs,ws.A,ws.gamma); - MathExtra::rotation_generator_x(ws.A,ws.lA[0]); - MathExtra::rotation_generator_y(ws.A,ws.lA[1]); - MathExtra::rotation_generator_z(ws.A,ws.lA[2]); - for (int m=0; m<3; m++) { - MathExtra::times3(aTs,ws.lA[m],ws.lAtwo[m]); - MathExtra::transpose_times3(ws.lA[m],ws.sa,ws.lAsa[m]); - MathExtra::plus3(ws.lAsa[m],ws.lAtwo[m],ws.lAsa[m]); + MathExtra::quat_to_mat_trans(bonus[ellipsoid[i]].quat, ws.A); + MathExtra::transpose_diag3(ws.A, well[atom->type[i]], ws.aTe); + MathExtra::transpose_diag3(ws.A, shape2[atom->type[i]], aTs); + MathExtra::diag_times3(shape2[atom->type[i]], ws.A, ws.sa); + MathExtra::times3(aTs, ws.A, ws.gamma); + MathExtra::rotation_generator_x(ws.A, ws.lA[0]); + MathExtra::rotation_generator_y(ws.A, ws.lA[1]); + MathExtra::rotation_generator_z(ws.A, ws.lA[2]); + for (int m = 0; m < 3; m++) { + MathExtra::times3(aTs, ws.lA[m], ws.lAtwo[m]); + MathExtra::transpose_times3(ws.lA[m], ws.sa, ws.lAsa[m]); + MathExtra::plus3(ws.lAsa[m], ws.lAtwo[m], ws.lAsa[m]); } } @@ -517,6 +515,7 @@ void PairRESquared::precompute_i(const int i,RE2Vars &ws) derivative of m (m2) ------------------------------------------------------------------------- */ +// clang-format off double PairRESquared::det_prime(const double m[3][3], const double m2[3][3]) { double ans; @@ -531,458 +530,441 @@ double PairRESquared::det_prime(const double m[3][3], const double m2[3][3]) m2[2][0]*m[0][1]*m[1][2] - m2[2][0]*m[0][2]*m[1][1]; return ans; } +// clang-format on /* ---------------------------------------------------------------------- Compute the energy, force, torque for a pair (INTEGRATED-INTEGRATED) ------------------------------------------------------------------------- */ -double PairRESquared::resquared_analytic(const int i, const int j, - const RE2Vars &wi, const RE2Vars &wj, - const double *r, const double rsq, - double *fforce, double *ttor, - double *rtor) +double PairRESquared::resquared_analytic(const int i, const int j, const RE2Vars &wi, + const RE2Vars &wj, const double *r, const double rsq, + double *fforce, double *ttor, double *rtor) { int *type = atom->type; // pair computations for energy, force, torque - double z1[3],z2[3]; // A1*rhat # don't need to store - double v1[3],v2[3]; // inv(S1^2)*z1 # don't need to store - double sigma1,sigma2; // 1/sqrt(z1'*v1) - double sigma1p2,sigma2p2; // sigma1^2 - double rnorm; // L2 norm of r - double rhat[3]; // r/rnorm - double s[3]; // inv(gamma1+gamma2)*rhat - double sigma12; // 1/sqrt(0.5*s'*rhat) - double H12[3][3]; // gamma1/sigma1+gamma2/sigma2 - double dH; // det(H12) - double lambda; // dS1/sigma1p2+dS2/sigma2p2 - double nu; // sqrt(dH/(sigma1+sigma2)) - double w[3]; // inv(A1'*E1*A1+A2'*E2*A2)*rhat - double h12; // rnorm-sigma12; - double eta; // lambda/nu - double chi; // 2*rhat'*w - double sprod; // dS1*dS2 - double sigh; // sigma/h12 - double tprod; // eta*chi*sigh - double Ua,Ur; // attractive/repulsive parts of potential + double z1[3], z2[3]; // A1*rhat # don't need to store + double v1[3], v2[3]; // inv(S1^2)*z1 # don't need to store + double sigma1, sigma2; // 1/sqrt(z1'*v1) + double sigma1p2, sigma2p2; // sigma1^2 + double rnorm; // L2 norm of r + double rhat[3]; // r/rnorm + double s[3]; // inv(gamma1+gamma2)*rhat + double sigma12; // 1/sqrt(0.5*s'*rhat) + double H12[3][3]; // gamma1/sigma1+gamma2/sigma2 + double dH; // det(H12) + double lambda; // dS1/sigma1p2+dS2/sigma2p2 + double nu; // sqrt(dH/(sigma1+sigma2)) + double w[3]; // inv(A1'*E1*A1+A2'*E2*A2)*rhat + double h12; // rnorm-sigma12; + double eta; // lambda/nu + double chi; // 2*rhat'*w + double sprod; // dS1*dS2 + double sigh; // sigma/h12 + double tprod; // eta*chi*sigh + double Ua, Ur; // attractive/repulsive parts of potential // pair computations for force, torque - double sec; // sigma*eta*chi - double sigma1p3, sigma2p3; // sigma1^3 - double vsigma1[3], vsigma2[3]; // sigma1^3*v1; - double sigma12p3; // sigma12^3 - double gsigma1[3][3], gsigma2[3][3]; // -gamma1/sigma1^2 - double tsig1sig2; // eta/(2*(sigma1+sigma2)) - double tdH; // eta/(2*dH) - double teta1,teta2; // 2*eta/lambda*dS1/sigma1p3 - double fourw[3]; // 4*w; - double spr[3]; // 0.5*sigma12^3*s - double hsec; // h12+[3,b_alpha]*sec - double dspu; // 1/h12 - 1/hsec + temp - double pbsu; // 3*sigma/hsec - double dspr; // 7/h12-1/hsec+temp - double pbsr; // b_alpha*sigma/hsec; - double u[3]; // (-rhat(i)*rhat+eye(:,i))/rnorm - double u1[3],u2[3]; // A1*u - double dsigma1,dsigma2; // u1'*vsigma1 (force) p'*vsigma1 (tor) - double dH12[3][3]; // dsigma1*gsigma1 + dsigma2*gsigma2 - double ddH; // derivative of det(H12) - double deta,dchi,dh12; // derivatives of eta,chi,h12 - double dUr,dUa; // derivatives of Ua,Ur + double sec; // sigma*eta*chi + double sigma1p3, sigma2p3; // sigma1^3 + double vsigma1[3], vsigma2[3]; // sigma1^3*v1; + double sigma12p3; // sigma12^3 + double gsigma1[3][3], gsigma2[3][3]; // -gamma1/sigma1^2 + double tsig1sig2; // eta/(2*(sigma1+sigma2)) + double tdH; // eta/(2*dH) + double teta1, teta2; // 2*eta/lambda*dS1/sigma1p3 + double fourw[3]; // 4*w; + double spr[3]; // 0.5*sigma12^3*s + double hsec; // h12+[3,b_alpha]*sec + double dspu; // 1/h12 - 1/hsec + temp + double pbsu; // 3*sigma/hsec + double dspr; // 7/h12-1/hsec+temp + double pbsr; // b_alpha*sigma/hsec; + double u[3]; // (-rhat(i)*rhat+eye(:,i))/rnorm + double u1[3], u2[3]; // A1*u + double dsigma1, dsigma2; // u1'*vsigma1 (force) p'*vsigma1 (tor) + double dH12[3][3]; // dsigma1*gsigma1 + dsigma2*gsigma2 + double ddH; // derivative of det(H12) + double deta, dchi, dh12; // derivatives of eta,chi,h12 + double dUr, dUa; // derivatives of Ua,Ur // pair computations for torque - double fwae[3]; // -fourw'*aTe - double p[3]; // lA*rhat + double fwae[3]; // -fourw'*aTe + double p[3]; // lA*rhat rnorm = sqrt(rsq); - rhat[0] = r[0]/rnorm; - rhat[1] = r[1]/rnorm; - rhat[2] = r[2]/rnorm; + rhat[0] = r[0] / rnorm; + rhat[1] = r[1] / rnorm; + rhat[2] = r[2] / rnorm; // energy double temp[3][3]; - MathExtra::plus3(wi.gamma,wj.gamma,temp); - int ierror = MathExtra::mldivide3(temp,rhat,s); - if (ierror) error->all(FLERR,"Bad matrix inversion in mldivide3"); + MathExtra::plus3(wi.gamma, wj.gamma, temp); + int ierror = MathExtra::mldivide3(temp, rhat, s); + if (ierror) error->all(FLERR, "Bad matrix inversion in mldivide3"); - sigma12 = 1.0/sqrt(0.5*MathExtra::dot3(s,rhat)); - MathExtra::matvec(wi.A,rhat,z1); - MathExtra::matvec(wj.A,rhat,z2); - v1[0] = z1[0]/shape2[type[i]][0]; - v1[1] = z1[1]/shape2[type[i]][1]; - v1[2] = z1[2]/shape2[type[i]][2]; - v2[0] = z2[0]/shape2[type[j]][0]; - v2[1] = z2[1]/shape2[type[j]][1]; - v2[2] = z2[2]/shape2[type[j]][2]; - sigma1 = 1.0/sqrt(MathExtra::dot3(z1,v1)); - sigma2 = 1.0/sqrt(MathExtra::dot3(z2,v2)); - H12[0][0] = wi.gamma[0][0]/sigma1+wj.gamma[0][0]/sigma2; - H12[0][1] = wi.gamma[0][1]/sigma1+wj.gamma[0][1]/sigma2; - H12[0][2] = wi.gamma[0][2]/sigma1+wj.gamma[0][2]/sigma2; - H12[1][0] = wi.gamma[1][0]/sigma1+wj.gamma[1][0]/sigma2; - H12[1][1] = wi.gamma[1][1]/sigma1+wj.gamma[1][1]/sigma2; - H12[1][2] = wi.gamma[1][2]/sigma1+wj.gamma[1][2]/sigma2; - H12[2][0] = wi.gamma[2][0]/sigma1+wj.gamma[2][0]/sigma2; - H12[2][1] = wi.gamma[2][1]/sigma1+wj.gamma[2][1]/sigma2; - H12[2][2] = wi.gamma[2][2]/sigma1+wj.gamma[2][2]/sigma2; - dH=MathExtra::det3(H12); - sigma1p2 = sigma1*sigma1; - sigma2p2 = sigma2*sigma2; - lambda = lshape[type[i]]/sigma1p2 + lshape[type[j]]/sigma2p2; - nu = sqrt(dH/(sigma1+sigma2)); - MathExtra::times3(wi.aTe,wi.A,temp); + sigma12 = 1.0 / sqrt(0.5 * MathExtra::dot3(s, rhat)); + MathExtra::matvec(wi.A, rhat, z1); + MathExtra::matvec(wj.A, rhat, z2); + v1[0] = z1[0] / shape2[type[i]][0]; + v1[1] = z1[1] / shape2[type[i]][1]; + v1[2] = z1[2] / shape2[type[i]][2]; + v2[0] = z2[0] / shape2[type[j]][0]; + v2[1] = z2[1] / shape2[type[j]][1]; + v2[2] = z2[2] / shape2[type[j]][2]; + sigma1 = 1.0 / sqrt(MathExtra::dot3(z1, v1)); + sigma2 = 1.0 / sqrt(MathExtra::dot3(z2, v2)); + H12[0][0] = wi.gamma[0][0] / sigma1 + wj.gamma[0][0] / sigma2; + H12[0][1] = wi.gamma[0][1] / sigma1 + wj.gamma[0][1] / sigma2; + H12[0][2] = wi.gamma[0][2] / sigma1 + wj.gamma[0][2] / sigma2; + H12[1][0] = wi.gamma[1][0] / sigma1 + wj.gamma[1][0] / sigma2; + H12[1][1] = wi.gamma[1][1] / sigma1 + wj.gamma[1][1] / sigma2; + H12[1][2] = wi.gamma[1][2] / sigma1 + wj.gamma[1][2] / sigma2; + H12[2][0] = wi.gamma[2][0] / sigma1 + wj.gamma[2][0] / sigma2; + H12[2][1] = wi.gamma[2][1] / sigma1 + wj.gamma[2][1] / sigma2; + H12[2][2] = wi.gamma[2][2] / sigma1 + wj.gamma[2][2] / sigma2; + dH = MathExtra::det3(H12); + sigma1p2 = sigma1 * sigma1; + sigma2p2 = sigma2 * sigma2; + lambda = lshape[type[i]] / sigma1p2 + lshape[type[j]] / sigma2p2; + nu = sqrt(dH / (sigma1 + sigma2)); + MathExtra::times3(wi.aTe, wi.A, temp); double temp2[3][3]; - MathExtra::times3(wj.aTe,wj.A,temp2); - MathExtra::plus3(temp,temp2,temp); - ierror = MathExtra::mldivide3(temp,rhat,w); - if (ierror) error->all(FLERR,"Bad matrix inversion in mldivide3"); + MathExtra::times3(wj.aTe, wj.A, temp2); + MathExtra::plus3(temp, temp2, temp); + ierror = MathExtra::mldivide3(temp, rhat, w); + if (ierror) error->all(FLERR, "Bad matrix inversion in mldivide3"); - h12 = rnorm-sigma12; - eta = lambda/nu; - chi = 2.0*MathExtra::dot3(rhat,w); + h12 = rnorm - sigma12; + eta = lambda / nu; + chi = 2.0 * MathExtra::dot3(rhat, w); sprod = lshape[type[i]] * lshape[type[j]]; - sigh = sigma[type[i]][type[j]]/h12; - tprod = eta*chi*sigh; + sigh = sigma[type[i]][type[j]] / h12; + tprod = eta * chi * sigh; - double stemp = h12/2.0; - Ua = (shape1[type[i]][0]+stemp)*(shape1[type[i]][1]+stemp)* - (shape1[type[i]][2]+stemp)*(shape1[type[j]][0]+stemp)* - (shape1[type[j]][1]+stemp)*(shape1[type[j]][2]+stemp); - Ua = (1.0+3.0*tprod)*sprod/Ua; - Ua = epsilon[type[i]][type[j]]*Ua/-36.0; + double stemp = h12 / 2.0; + Ua = (shape1[type[i]][0] + stemp) * (shape1[type[i]][1] + stemp) * (shape1[type[i]][2] + stemp) * + (shape1[type[j]][0] + stemp) * (shape1[type[j]][1] + stemp) * (shape1[type[j]][2] + stemp); + Ua = (1.0 + 3.0 * tprod) * sprod / Ua; + Ua = epsilon[type[i]][type[j]] * Ua / -36.0; - stemp = h12/cr60; - Ur = (shape1[type[i]][0]+stemp)*(shape1[type[i]][1]+stemp)* - (shape1[type[i]][2]+stemp)*(shape1[type[j]][0]+stemp)* - (shape1[type[j]][1]+stemp)*(shape1[type[j]][2]+stemp); - Ur = (1.0+b_alpha*tprod)*sprod/Ur; - Ur = epsilon[type[i]][type[j]]*Ur*pow(sigh,6.0)/2025.0; + stemp = h12 / cr60; + Ur = (shape1[type[i]][0] + stemp) * (shape1[type[i]][1] + stemp) * (shape1[type[i]][2] + stemp) * + (shape1[type[j]][0] + stemp) * (shape1[type[j]][1] + stemp) * (shape1[type[j]][2] + stemp); + Ur = (1.0 + b_alpha * tprod) * sprod / Ur; + Ur = epsilon[type[i]][type[j]] * Ur * pow(sigh, 6.0) / 2025.0; // force - sec = sigma[type[i]][type[j]]*eta*chi; - sigma12p3 = pow(sigma12,3.0); - sigma1p3 = sigma1p2*sigma1; - sigma2p3 = sigma2p2*sigma2; - vsigma1[0] = -sigma1p3*v1[0]; - vsigma1[1] = -sigma1p3*v1[1]; - vsigma1[2] = -sigma1p3*v1[2]; - vsigma2[0] = -sigma2p3*v2[0]; - vsigma2[1] = -sigma2p3*v2[1]; - vsigma2[2] = -sigma2p3*v2[2]; - gsigma1[0][0] = -wi.gamma[0][0]/sigma1p2; - gsigma1[0][1] = -wi.gamma[0][1]/sigma1p2; - gsigma1[0][2] = -wi.gamma[0][2]/sigma1p2; - gsigma1[1][0] = -wi.gamma[1][0]/sigma1p2; - gsigma1[1][1] = -wi.gamma[1][1]/sigma1p2; - gsigma1[1][2] = -wi.gamma[1][2]/sigma1p2; - gsigma1[2][0] = -wi.gamma[2][0]/sigma1p2; - gsigma1[2][1] = -wi.gamma[2][1]/sigma1p2; - gsigma1[2][2] = -wi.gamma[2][2]/sigma1p2; - gsigma2[0][0] = -wj.gamma[0][0]/sigma2p2; - gsigma2[0][1] = -wj.gamma[0][1]/sigma2p2; - gsigma2[0][2] = -wj.gamma[0][2]/sigma2p2; - gsigma2[1][0] = -wj.gamma[1][0]/sigma2p2; - gsigma2[1][1] = -wj.gamma[1][1]/sigma2p2; - gsigma2[1][2] = -wj.gamma[1][2]/sigma2p2; - gsigma2[2][0] = -wj.gamma[2][0]/sigma2p2; - gsigma2[2][1] = -wj.gamma[2][1]/sigma2p2; - gsigma2[2][2] = -wj.gamma[2][2]/sigma2p2; - tsig1sig2 = eta/(2.0*(sigma1+sigma2)); - tdH = eta/(2.0*dH); - teta1 = 2.0*eta/lambda; - teta2 = teta1*lshape[type[j]]/sigma2p3; - teta1 = teta1*lshape[type[i]]/sigma1p3; - fourw[0] = 4.0*w[0]; - fourw[1] = 4.0*w[1]; - fourw[2] = 4.0*w[2]; - spr[0] = 0.5*sigma12p3*s[0]; - spr[1] = 0.5*sigma12p3*s[1]; - spr[2] = 0.5*sigma12p3*s[2]; + sec = sigma[type[i]][type[j]] * eta * chi; + sigma12p3 = pow(sigma12, 3.0); + sigma1p3 = sigma1p2 * sigma1; + sigma2p3 = sigma2p2 * sigma2; + vsigma1[0] = -sigma1p3 * v1[0]; + vsigma1[1] = -sigma1p3 * v1[1]; + vsigma1[2] = -sigma1p3 * v1[2]; + vsigma2[0] = -sigma2p3 * v2[0]; + vsigma2[1] = -sigma2p3 * v2[1]; + vsigma2[2] = -sigma2p3 * v2[2]; + gsigma1[0][0] = -wi.gamma[0][0] / sigma1p2; + gsigma1[0][1] = -wi.gamma[0][1] / sigma1p2; + gsigma1[0][2] = -wi.gamma[0][2] / sigma1p2; + gsigma1[1][0] = -wi.gamma[1][0] / sigma1p2; + gsigma1[1][1] = -wi.gamma[1][1] / sigma1p2; + gsigma1[1][2] = -wi.gamma[1][2] / sigma1p2; + gsigma1[2][0] = -wi.gamma[2][0] / sigma1p2; + gsigma1[2][1] = -wi.gamma[2][1] / sigma1p2; + gsigma1[2][2] = -wi.gamma[2][2] / sigma1p2; + gsigma2[0][0] = -wj.gamma[0][0] / sigma2p2; + gsigma2[0][1] = -wj.gamma[0][1] / sigma2p2; + gsigma2[0][2] = -wj.gamma[0][2] / sigma2p2; + gsigma2[1][0] = -wj.gamma[1][0] / sigma2p2; + gsigma2[1][1] = -wj.gamma[1][1] / sigma2p2; + gsigma2[1][2] = -wj.gamma[1][2] / sigma2p2; + gsigma2[2][0] = -wj.gamma[2][0] / sigma2p2; + gsigma2[2][1] = -wj.gamma[2][1] / sigma2p2; + gsigma2[2][2] = -wj.gamma[2][2] / sigma2p2; + tsig1sig2 = eta / (2.0 * (sigma1 + sigma2)); + tdH = eta / (2.0 * dH); + teta1 = 2.0 * eta / lambda; + teta2 = teta1 * lshape[type[j]] / sigma2p3; + teta1 = teta1 * lshape[type[i]] / sigma1p3; + fourw[0] = 4.0 * w[0]; + fourw[1] = 4.0 * w[1]; + fourw[2] = 4.0 * w[2]; + spr[0] = 0.5 * sigma12p3 * s[0]; + spr[1] = 0.5 * sigma12p3 * s[1]; + spr[2] = 0.5 * sigma12p3 * s[2]; - stemp = 1.0/(shape1[type[i]][0]*2.0+h12)+ - 1.0/(shape1[type[i]][1]*2.0+h12)+ - 1.0/(shape1[type[i]][2]*2.0+h12)+ - 1.0/(shape1[type[j]][0]*2.0+h12)+ - 1.0/(shape1[type[j]][1]*2.0+h12)+ - 1.0/(shape1[type[j]][2]*2.0+h12); - hsec = h12+3.0*sec; - dspu = 1.0/h12-1.0/hsec+stemp; - pbsu = 3.0*sigma[type[i]][type[j]]/hsec; + stemp = 1.0 / (shape1[type[i]][0] * 2.0 + h12) + 1.0 / (shape1[type[i]][1] * 2.0 + h12) + + 1.0 / (shape1[type[i]][2] * 2.0 + h12) + 1.0 / (shape1[type[j]][0] * 2.0 + h12) + + 1.0 / (shape1[type[j]][1] * 2.0 + h12) + 1.0 / (shape1[type[j]][2] * 2.0 + h12); + hsec = h12 + 3.0 * sec; + dspu = 1.0 / h12 - 1.0 / hsec + stemp; + pbsu = 3.0 * sigma[type[i]][type[j]] / hsec; - stemp = 1.0/(shape1[type[i]][0]*cr60+h12)+ - 1.0/(shape1[type[i]][1]*cr60+h12)+ - 1.0/(shape1[type[i]][2]*cr60+h12)+ - 1.0/(shape1[type[j]][0]*cr60+h12)+ - 1.0/(shape1[type[j]][1]*cr60+h12)+ - 1.0/(shape1[type[j]][2]*cr60+h12); - hsec = h12+b_alpha*sec; - dspr = 7.0/h12-1.0/hsec+stemp; - pbsr = b_alpha*sigma[type[i]][type[j]]/hsec; + stemp = 1.0 / (shape1[type[i]][0] * cr60 + h12) + 1.0 / (shape1[type[i]][1] * cr60 + h12) + + 1.0 / (shape1[type[i]][2] * cr60 + h12) + 1.0 / (shape1[type[j]][0] * cr60 + h12) + + 1.0 / (shape1[type[j]][1] * cr60 + h12) + 1.0 / (shape1[type[j]][2] * cr60 + h12); + hsec = h12 + b_alpha * sec; + dspr = 7.0 / h12 - 1.0 / hsec + stemp; + pbsr = b_alpha * sigma[type[i]][type[j]] / hsec; - for (int m=0; m<3; m++) { - u[0] = -rhat[m]*rhat[0]; - u[1] = -rhat[m]*rhat[1]; - u[2] = -rhat[m]*rhat[2]; + for (int m = 0; m < 3; m++) { + u[0] = -rhat[m] * rhat[0]; + u[1] = -rhat[m] * rhat[1]; + u[2] = -rhat[m] * rhat[2]; u[m] += 1.0; u[0] /= rnorm; u[1] /= rnorm; u[2] /= rnorm; - MathExtra::matvec(wi.A,u,u1); - MathExtra::matvec(wj.A,u,u2); - dsigma1=MathExtra::dot3(u1,vsigma1); - dsigma2=MathExtra::dot3(u2,vsigma2); - dH12[0][0] = dsigma1*gsigma1[0][0]+dsigma2*gsigma2[0][0]; - dH12[0][1] = dsigma1*gsigma1[0][1]+dsigma2*gsigma2[0][1]; - dH12[0][2] = dsigma1*gsigma1[0][2]+dsigma2*gsigma2[0][2]; - dH12[1][0] = dsigma1*gsigma1[1][0]+dsigma2*gsigma2[1][0]; - dH12[1][1] = dsigma1*gsigma1[1][1]+dsigma2*gsigma2[1][1]; - dH12[1][2] = dsigma1*gsigma1[1][2]+dsigma2*gsigma2[1][2]; - dH12[2][0] = dsigma1*gsigma1[2][0]+dsigma2*gsigma2[2][0]; - dH12[2][1] = dsigma1*gsigma1[2][1]+dsigma2*gsigma2[2][1]; - dH12[2][2] = dsigma1*gsigma1[2][2]+dsigma2*gsigma2[2][2]; - ddH = det_prime(H12,dH12); - deta = (dsigma1+dsigma2)*tsig1sig2; - deta -= ddH*tdH; - deta -= dsigma1*teta1+dsigma2*teta2; - dchi = MathExtra::dot3(u,fourw); - dh12 = rhat[m]+MathExtra::dot3(u,spr); - dUa = pbsu*(eta*dchi+deta*chi)-dh12*dspu; - dUr = pbsr*(eta*dchi+deta*chi)-dh12*dspr; - fforce[m]=dUr*Ur+dUa*Ua; + MathExtra::matvec(wi.A, u, u1); + MathExtra::matvec(wj.A, u, u2); + dsigma1 = MathExtra::dot3(u1, vsigma1); + dsigma2 = MathExtra::dot3(u2, vsigma2); + dH12[0][0] = dsigma1 * gsigma1[0][0] + dsigma2 * gsigma2[0][0]; + dH12[0][1] = dsigma1 * gsigma1[0][1] + dsigma2 * gsigma2[0][1]; + dH12[0][2] = dsigma1 * gsigma1[0][2] + dsigma2 * gsigma2[0][2]; + dH12[1][0] = dsigma1 * gsigma1[1][0] + dsigma2 * gsigma2[1][0]; + dH12[1][1] = dsigma1 * gsigma1[1][1] + dsigma2 * gsigma2[1][1]; + dH12[1][2] = dsigma1 * gsigma1[1][2] + dsigma2 * gsigma2[1][2]; + dH12[2][0] = dsigma1 * gsigma1[2][0] + dsigma2 * gsigma2[2][0]; + dH12[2][1] = dsigma1 * gsigma1[2][1] + dsigma2 * gsigma2[2][1]; + dH12[2][2] = dsigma1 * gsigma1[2][2] + dsigma2 * gsigma2[2][2]; + ddH = det_prime(H12, dH12); + deta = (dsigma1 + dsigma2) * tsig1sig2; + deta -= ddH * tdH; + deta -= dsigma1 * teta1 + dsigma2 * teta2; + dchi = MathExtra::dot3(u, fourw); + dh12 = rhat[m] + MathExtra::dot3(u, spr); + dUa = pbsu * (eta * dchi + deta * chi) - dh12 * dspu; + dUr = pbsr * (eta * dchi + deta * chi) - dh12 * dspr; + fforce[m] = dUr * Ur + dUa * Ua; } // torque on i - MathExtra::vecmat(fourw,wi.aTe,fwae); + MathExtra::vecmat(fourw, wi.aTe, fwae); - for (int i=0; i<3; i++) { - MathExtra::matvec(wi.lA[i],rhat,p); - dsigma1 = MathExtra::dot3(p,vsigma1); - dH12[0][0] = wi.lAsa[i][0][0]/sigma1+dsigma1*gsigma1[0][0]; - dH12[0][1] = wi.lAsa[i][0][1]/sigma1+dsigma1*gsigma1[0][1]; - dH12[0][2] = wi.lAsa[i][0][2]/sigma1+dsigma1*gsigma1[0][2]; - dH12[1][0] = wi.lAsa[i][1][0]/sigma1+dsigma1*gsigma1[1][0]; - dH12[1][1] = wi.lAsa[i][1][1]/sigma1+dsigma1*gsigma1[1][1]; - dH12[1][2] = wi.lAsa[i][1][2]/sigma1+dsigma1*gsigma1[1][2]; - dH12[2][0] = wi.lAsa[i][2][0]/sigma1+dsigma1*gsigma1[2][0]; - dH12[2][1] = wi.lAsa[i][2][1]/sigma1+dsigma1*gsigma1[2][1]; - dH12[2][2] = wi.lAsa[i][2][2]/sigma1+dsigma1*gsigma1[2][2]; - ddH = det_prime(H12,dH12); - deta = tsig1sig2*dsigma1-tdH*ddH; - deta -= teta1*dsigma1; + for (int i = 0; i < 3; i++) { + MathExtra::matvec(wi.lA[i], rhat, p); + dsigma1 = MathExtra::dot3(p, vsigma1); + dH12[0][0] = wi.lAsa[i][0][0] / sigma1 + dsigma1 * gsigma1[0][0]; + dH12[0][1] = wi.lAsa[i][0][1] / sigma1 + dsigma1 * gsigma1[0][1]; + dH12[0][2] = wi.lAsa[i][0][2] / sigma1 + dsigma1 * gsigma1[0][2]; + dH12[1][0] = wi.lAsa[i][1][0] / sigma1 + dsigma1 * gsigma1[1][0]; + dH12[1][1] = wi.lAsa[i][1][1] / sigma1 + dsigma1 * gsigma1[1][1]; + dH12[1][2] = wi.lAsa[i][1][2] / sigma1 + dsigma1 * gsigma1[1][2]; + dH12[2][0] = wi.lAsa[i][2][0] / sigma1 + dsigma1 * gsigma1[2][0]; + dH12[2][1] = wi.lAsa[i][2][1] / sigma1 + dsigma1 * gsigma1[2][1]; + dH12[2][2] = wi.lAsa[i][2][2] / sigma1 + dsigma1 * gsigma1[2][2]; + ddH = det_prime(H12, dH12); + deta = tsig1sig2 * dsigma1 - tdH * ddH; + deta -= teta1 * dsigma1; double tempv[3]; - MathExtra::matvec(wi.lA[i],w,tempv); - dchi = -MathExtra::dot3(fwae,tempv); - MathExtra::matvec(wi.lAtwo[i],spr,tempv); - dh12 = -MathExtra::dot3(s,tempv); + MathExtra::matvec(wi.lA[i], w, tempv); + dchi = -MathExtra::dot3(fwae, tempv); + MathExtra::matvec(wi.lAtwo[i], spr, tempv); + dh12 = -MathExtra::dot3(s, tempv); - dUa = pbsu*(eta*dchi + deta*chi)-dh12*dspu; - dUr = pbsr*(eta*dchi + deta*chi)-dh12*dspr; - ttor[i] = -(dUa*Ua+dUr*Ur); + dUa = pbsu * (eta * dchi + deta * chi) - dh12 * dspu; + dUr = pbsr * (eta * dchi + deta * chi) - dh12 * dspr; + ttor[i] = -(dUa * Ua + dUr * Ur); } // torque on j - if (!(force->newton_pair || j < atom->nlocal)) - return Ua+Ur; + if (!(force->newton_pair || j < atom->nlocal)) return Ua + Ur; - MathExtra::vecmat(fourw,wj.aTe,fwae); + MathExtra::vecmat(fourw, wj.aTe, fwae); - for (int i=0; i<3; i++) { - MathExtra::matvec(wj.lA[i],rhat,p); - dsigma2 = MathExtra::dot3(p,vsigma2); - dH12[0][0] = wj.lAsa[i][0][0]/sigma2+dsigma2*gsigma2[0][0]; - dH12[0][1] = wj.lAsa[i][0][1]/sigma2+dsigma2*gsigma2[0][1]; - dH12[0][2] = wj.lAsa[i][0][2]/sigma2+dsigma2*gsigma2[0][2]; - dH12[1][0] = wj.lAsa[i][1][0]/sigma2+dsigma2*gsigma2[1][0]; - dH12[1][1] = wj.lAsa[i][1][1]/sigma2+dsigma2*gsigma2[1][1]; - dH12[1][2] = wj.lAsa[i][1][2]/sigma2+dsigma2*gsigma2[1][2]; - dH12[2][0] = wj.lAsa[i][2][0]/sigma2+dsigma2*gsigma2[2][0]; - dH12[2][1] = wj.lAsa[i][2][1]/sigma2+dsigma2*gsigma2[2][1]; - dH12[2][2] = wj.lAsa[i][2][2]/sigma2+dsigma2*gsigma2[2][2]; - ddH = det_prime(H12,dH12); - deta = tsig1sig2*dsigma2-tdH*ddH; - deta -= teta2*dsigma2; + for (int i = 0; i < 3; i++) { + MathExtra::matvec(wj.lA[i], rhat, p); + dsigma2 = MathExtra::dot3(p, vsigma2); + dH12[0][0] = wj.lAsa[i][0][0] / sigma2 + dsigma2 * gsigma2[0][0]; + dH12[0][1] = wj.lAsa[i][0][1] / sigma2 + dsigma2 * gsigma2[0][1]; + dH12[0][2] = wj.lAsa[i][0][2] / sigma2 + dsigma2 * gsigma2[0][2]; + dH12[1][0] = wj.lAsa[i][1][0] / sigma2 + dsigma2 * gsigma2[1][0]; + dH12[1][1] = wj.lAsa[i][1][1] / sigma2 + dsigma2 * gsigma2[1][1]; + dH12[1][2] = wj.lAsa[i][1][2] / sigma2 + dsigma2 * gsigma2[1][2]; + dH12[2][0] = wj.lAsa[i][2][0] / sigma2 + dsigma2 * gsigma2[2][0]; + dH12[2][1] = wj.lAsa[i][2][1] / sigma2 + dsigma2 * gsigma2[2][1]; + dH12[2][2] = wj.lAsa[i][2][2] / sigma2 + dsigma2 * gsigma2[2][2]; + ddH = det_prime(H12, dH12); + deta = tsig1sig2 * dsigma2 - tdH * ddH; + deta -= teta2 * dsigma2; double tempv[3]; - MathExtra::matvec(wj.lA[i],w,tempv); - dchi = -MathExtra::dot3(fwae,tempv); - MathExtra::matvec(wj.lAtwo[i],spr,tempv); - dh12 = -MathExtra::dot3(s,tempv); + MathExtra::matvec(wj.lA[i], w, tempv); + dchi = -MathExtra::dot3(fwae, tempv); + MathExtra::matvec(wj.lAtwo[i], spr, tempv); + dh12 = -MathExtra::dot3(s, tempv); - dUa = pbsu*(eta*dchi + deta*chi)-dh12*dspu; - dUr = pbsr*(eta*dchi + deta*chi)-dh12*dspr; - rtor[i] = -(dUa*Ua+dUr*Ur); + dUa = pbsu * (eta * dchi + deta * chi) - dh12 * dspu; + dUr = pbsr * (eta * dchi + deta * chi) - dh12 * dspr; + rtor[i] = -(dUa * Ua + dUr * Ur); } - return Ua+Ur; + return Ua + Ur; } /* ---------------------------------------------------------------------- Compute the energy, force, torque for a pair (INTEGRATED-LJ) ------------------------------------------------------------------------- */ -double PairRESquared::resquared_lj(const int i, const int j, - const RE2Vars &wi, const double *r, - const double rsq, double *fforce, - double *ttor, bool calc_torque) +double PairRESquared::resquared_lj(const int i, const int j, const RE2Vars &wi, const double *r, + const double rsq, double *fforce, double *ttor, bool calc_torque) { int *type = atom->type; // pair computations for energy, force, torque - double rnorm; // L2 norm of r - double rhat[3]; // r/rnorm - double s[3]; // inv(gamma1)*rhat - double sigma12; // 1/sqrt(0.5*s'*rhat) - double w[3]; // inv(A1'*E1*A1+I)*rhat - double h12; // rnorm-sigma12; - double chi; // 2*rhat'*w - double sigh; // sigma/h12 - double tprod; // chi*sigh - double Ua,Ur; // attractive/repulsive parts of potential + double rnorm; // L2 norm of r + double rhat[3]; // r/rnorm + double s[3]; // inv(gamma1)*rhat + double sigma12; // 1/sqrt(0.5*s'*rhat) + double w[3]; // inv(A1'*E1*A1+I)*rhat + double h12; // rnorm-sigma12; + double chi; // 2*rhat'*w + double sigh; // sigma/h12 + double tprod; // chi*sigh + double Ua, Ur; // attractive/repulsive parts of potential // pair computations for force, torque - double sec; // sigma*chi - double sigma12p3; // sigma12^3 - double fourw[3]; // 4*w; - double spr[3]; // 0.5*sigma12^3*s - double hsec; // h12+[3,b_alpha]*sec - double dspu; // 1/h12 - 1/hsec + temp - double pbsu; // 3*sigma/hsec - double dspr; // 7/h12-1/hsec+temp - double pbsr; // b_alpha*sigma/hsec; - double u[3]; // (-rhat(i)*rhat+eye(:,i))/rnorm - double dchi,dh12; // derivatives of chi,h12 - double dUr,dUa; // derivatives of Ua,Ur - double h12p3; // h12^3 + double sec; // sigma*chi + double sigma12p3; // sigma12^3 + double fourw[3]; // 4*w; + double spr[3]; // 0.5*sigma12^3*s + double hsec; // h12+[3,b_alpha]*sec + double dspu; // 1/h12 - 1/hsec + temp + double pbsu; // 3*sigma/hsec + double dspr; // 7/h12-1/hsec+temp + double pbsr; // b_alpha*sigma/hsec; + double u[3]; // (-rhat(i)*rhat+eye(:,i))/rnorm + double dchi, dh12; // derivatives of chi,h12 + double dUr, dUa; // derivatives of Ua,Ur + double h12p3; // h12^3 // pair computations for torque - double fwae[3]; // -fourw'*aTe - double p[3]; // lA*rhat + double fwae[3]; // -fourw'*aTe + double p[3]; // lA*rhat // distance of closest approach correction - double aTs[3][3]; // A1'*S1^2 - double gamma[3][3]; // A1'*S1^2*A - double lAtwo[3][3][3]; // A1'*S1^2*wi.lA + double aTs[3][3]; // A1'*S1^2 + double gamma[3][3]; // A1'*S1^2*A + double lAtwo[3][3][3]; // A1'*S1^2*wi.lA double scorrect[3]; - double half_sigma=sigma[type[i]][type[j]] / 2.0; - scorrect[0] = shape1[type[i]][0]+half_sigma; - scorrect[1] = shape1[type[i]][1]+half_sigma; - scorrect[2] = shape1[type[i]][2]+half_sigma; + double half_sigma = sigma[type[i]][type[j]] / 2.0; + scorrect[0] = shape1[type[i]][0] + half_sigma; + scorrect[1] = shape1[type[i]][1] + half_sigma; + scorrect[2] = shape1[type[i]][2] + half_sigma; scorrect[0] = scorrect[0] * scorrect[0] / 2.0; scorrect[1] = scorrect[1] * scorrect[1] / 2.0; scorrect[2] = scorrect[2] * scorrect[2] / 2.0; - MathExtra::transpose_diag3(wi.A,scorrect,aTs); - MathExtra::times3(aTs,wi.A,gamma); - for (int ii=0; ii<3; ii++) - MathExtra::times3(aTs,wi.lA[ii],lAtwo[ii]); + MathExtra::transpose_diag3(wi.A, scorrect, aTs); + MathExtra::times3(aTs, wi.A, gamma); + for (int ii = 0; ii < 3; ii++) MathExtra::times3(aTs, wi.lA[ii], lAtwo[ii]); - rnorm=sqrt(rsq); - rhat[0] = r[0]/rnorm; - rhat[1] = r[1]/rnorm; - rhat[2] = r[2]/rnorm; + rnorm = sqrt(rsq); + rhat[0] = r[0] / rnorm; + rhat[1] = r[1] / rnorm; + rhat[2] = r[2] / rnorm; // energy - int ierror = MathExtra::mldivide3(gamma,rhat,s); - if (ierror) error->all(FLERR,"Bad matrix inversion in mldivide3"); + int ierror = MathExtra::mldivide3(gamma, rhat, s); + if (ierror) error->all(FLERR, "Bad matrix inversion in mldivide3"); - sigma12 = 1.0/sqrt(0.5*MathExtra::dot3(s,rhat)); + sigma12 = 1.0 / sqrt(0.5 * MathExtra::dot3(s, rhat)); double temp[3][3]; - MathExtra::times3(wi.aTe,wi.A,temp); + MathExtra::times3(wi.aTe, wi.A, temp); temp[0][0] += 1.0; temp[1][1] += 1.0; temp[2][2] += 1.0; - ierror = MathExtra::mldivide3(temp,rhat,w); - if (ierror) error->all(FLERR,"Bad matrix inversion in mldivide3"); + ierror = MathExtra::mldivide3(temp, rhat, w); + if (ierror) error->all(FLERR, "Bad matrix inversion in mldivide3"); - h12 = rnorm-sigma12; - chi = 2.0*MathExtra::dot3(rhat,w); - sigh = sigma[type[i]][type[j]]/h12; - tprod = chi*sigh; + h12 = rnorm - sigma12; + chi = 2.0 * MathExtra::dot3(rhat, w); + sigh = sigma[type[i]][type[j]] / h12; + tprod = chi * sigh; - h12p3 = pow(h12,3.0); - double sigmap3 = pow(sigma[type[i]][type[j]],3.0); - double stemp = h12/2.0; - Ua = (shape1[type[i]][0]+stemp)*(shape1[type[i]][1]+stemp)* - (shape1[type[i]][2]+stemp)*h12p3/8.0; - Ua = (1.0+3.0*tprod)*lshape[type[i]]/Ua; - Ua = epsilon[type[i]][type[j]]*Ua*sigmap3*solv_f_a; + h12p3 = pow(h12, 3.0); + double sigmap3 = pow(sigma[type[i]][type[j]], 3.0); + double stemp = h12 / 2.0; + Ua = (shape1[type[i]][0] + stemp) * (shape1[type[i]][1] + stemp) * (shape1[type[i]][2] + stemp) * + h12p3 / 8.0; + Ua = (1.0 + 3.0 * tprod) * lshape[type[i]] / Ua; + Ua = epsilon[type[i]][type[j]] * Ua * sigmap3 * solv_f_a; - stemp = h12/cr60; - Ur = (shape1[type[i]][0]+stemp)*(shape1[type[i]][1]+stemp)* - (shape1[type[i]][2]+stemp)*h12p3/60.0; - Ur = (1.0+b_alpha*tprod)*lshape[type[i]]/Ur; - Ur = epsilon[type[i]][type[j]]*Ur*sigmap3*pow(sigh,6.0)*solv_f_r; + stemp = h12 / cr60; + Ur = (shape1[type[i]][0] + stemp) * (shape1[type[i]][1] + stemp) * (shape1[type[i]][2] + stemp) * + h12p3 / 60.0; + Ur = (1.0 + b_alpha * tprod) * lshape[type[i]] / Ur; + Ur = epsilon[type[i]][type[j]] * Ur * sigmap3 * pow(sigh, 6.0) * solv_f_r; // force - sec = sigma[type[i]][type[j]]*chi; - sigma12p3 = pow(sigma12,3.0); - fourw[0] = 4.0*w[0]; - fourw[1] = 4.0*w[1]; - fourw[2] = 4.0*w[2]; - spr[0] = 0.5*sigma12p3*s[0]; - spr[1] = 0.5*sigma12p3*s[1]; - spr[2] = 0.5*sigma12p3*s[2]; + sec = sigma[type[i]][type[j]] * chi; + sigma12p3 = pow(sigma12, 3.0); + fourw[0] = 4.0 * w[0]; + fourw[1] = 4.0 * w[1]; + fourw[2] = 4.0 * w[2]; + spr[0] = 0.5 * sigma12p3 * s[0]; + spr[1] = 0.5 * sigma12p3 * s[1]; + spr[2] = 0.5 * sigma12p3 * s[2]; - stemp = 1.0/(shape1[type[i]][0]*2.0+h12)+ - 1.0/(shape1[type[i]][1]*2.0+h12)+ - 1.0/(shape1[type[i]][2]*2.0+h12)+ - 3.0/h12; - hsec = h12+3.0*sec; - dspu = 1.0/h12-1.0/hsec+stemp; - pbsu = 3.0*sigma[type[i]][type[j]]/hsec; + stemp = 1.0 / (shape1[type[i]][0] * 2.0 + h12) + 1.0 / (shape1[type[i]][1] * 2.0 + h12) + + 1.0 / (shape1[type[i]][2] * 2.0 + h12) + 3.0 / h12; + hsec = h12 + 3.0 * sec; + dspu = 1.0 / h12 - 1.0 / hsec + stemp; + pbsu = 3.0 * sigma[type[i]][type[j]] / hsec; - stemp = 1.0/(shape1[type[i]][0]*cr60+h12)+ - 1.0/(shape1[type[i]][1]*cr60+h12)+ - 1.0/(shape1[type[i]][2]*cr60+h12)+ - 3.0/h12; - hsec = h12+b_alpha*sec; - dspr = 7.0/h12-1.0/hsec+stemp; - pbsr = b_alpha*sigma[type[i]][type[j]]/hsec; + stemp = 1.0 / (shape1[type[i]][0] * cr60 + h12) + 1.0 / (shape1[type[i]][1] * cr60 + h12) + + 1.0 / (shape1[type[i]][2] * cr60 + h12) + 3.0 / h12; + hsec = h12 + b_alpha * sec; + dspr = 7.0 / h12 - 1.0 / hsec + stemp; + pbsr = b_alpha * sigma[type[i]][type[j]] / hsec; - for (int m=0; m<3; m++) { - u[0] = -rhat[m]*rhat[0]; - u[1] = -rhat[m]*rhat[1]; - u[2] = -rhat[m]*rhat[2]; + for (int m = 0; m < 3; m++) { + u[0] = -rhat[m] * rhat[0]; + u[1] = -rhat[m] * rhat[1]; + u[2] = -rhat[m] * rhat[2]; u[m] += 1.0; u[0] /= rnorm; u[1] /= rnorm; u[2] /= rnorm; - dchi = MathExtra::dot3(u,fourw); - dh12 = rhat[m]+MathExtra::dot3(u,spr); - dUa = pbsu*dchi-dh12*dspu; - dUr = pbsr*dchi-dh12*dspr; - fforce[m]=dUr*Ur+dUa*Ua; + dchi = MathExtra::dot3(u, fourw); + dh12 = rhat[m] + MathExtra::dot3(u, spr); + dUa = pbsu * dchi - dh12 * dspu; + dUr = pbsr * dchi - dh12 * dspr; + fforce[m] = dUr * Ur + dUa * Ua; } // torque on i if (calc_torque) { - MathExtra::vecmat(fourw,wi.aTe,fwae); + MathExtra::vecmat(fourw, wi.aTe, fwae); - for (int m=0; m<3; m++) { - MathExtra::matvec(wi.lA[m],rhat,p); + for (int m = 0; m < 3; m++) { + MathExtra::matvec(wi.lA[m], rhat, p); double tempv[3]; - MathExtra::matvec(wi.lA[m],w,tempv); - dchi = -MathExtra::dot3(fwae,tempv); - MathExtra::matvec(lAtwo[m],spr,tempv); - dh12 = -MathExtra::dot3(s,tempv); + MathExtra::matvec(wi.lA[m], w, tempv); + dchi = -MathExtra::dot3(fwae, tempv); + MathExtra::matvec(lAtwo[m], spr, tempv); + dh12 = -MathExtra::dot3(s, tempv); - dUa = pbsu*dchi-dh12*dspu; - dUr = pbsr*dchi-dh12*dspr; - ttor[m] = -(dUa*Ua+dUr*Ur); + dUa = pbsu * dchi - dh12 * dspu; + dUr = pbsr * dchi - dh12 * dspr; + ttor[m] = -(dUa * Ua + dUr * Ur); } } - return Ua+Ur; + return Ua + Ur; }