diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp index 5c0602a453..4210818c61 100644 --- a/src/ASPHERE/pair_resquared.cpp +++ b/src/ASPHERE/pair_resquared.cpp @@ -505,10 +505,10 @@ void PairRESquared::precompute_i(const int i,RE2Vars &ws) 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 i=0; i<3; i++) { - MathExtra::times3(aTs,ws.lA[i],ws.lAtwo[i]); - MathExtra::transpose_times3(ws.lA[i],ws.sa,ws.lAsa[i]); - MathExtra::plus3(ws.lAsa[i],ws.lAtwo[i],ws.lAsa[i]); + 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]); } } @@ -724,10 +724,10 @@ double PairRESquared::resquared_analytic(const int i, const int j, dspr = 7.0/h12-1.0/hsec+stemp; pbsr = b_alpha*sigma[type[i]][type[j]]/hsec; - for (int i=0; i<3; i++) { - u[0] = -rhat[i]*rhat[0]; - u[1] = -rhat[i]*rhat[1]; - u[2] = -rhat[i]*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[i] += 1.0; u[0] /= rnorm; u[1] /= rnorm; @@ -753,7 +753,7 @@ double PairRESquared::resquared_analytic(const int i, const int j, dh12 = rhat[i]+MathExtra::dot3(u,spr); dUa = pbsu*(eta*dchi+deta*chi)-dh12*dspu; dUr = pbsr*(eta*dchi+deta*chi)-dh12*dspr; - fforce[i]=dUr*Ur+dUa*Ua; + fforce[m]=dUr*Ur+dUa*Ua; } // torque on i @@ -950,19 +950,19 @@ double PairRESquared::resquared_lj(const int i, const int j, dspr = 7.0/h12-1.0/hsec+stemp; pbsr = b_alpha*sigma[type[i]][type[j]]/hsec; - for (int i=0; i<3; i++) { - u[0] = -rhat[i]*rhat[0]; - u[1] = -rhat[i]*rhat[1]; - u[2] = -rhat[i]*rhat[2]; - u[i] += 1.0; + 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[i]+MathExtra::dot3(u,spr); + dh12 = rhat[m]+MathExtra::dot3(u,spr); dUa = pbsu*dchi-dh12*dspu; dUr = pbsr*dchi-dh12*dspr; - fforce[i]=dUr*Ur+dUa*Ua; + fforce[m]=dUr*Ur+dUa*Ua; } // torque on i @@ -970,17 +970,17 @@ double PairRESquared::resquared_lj(const int i, const int j, if (calc_torque) { MathExtra::vecmat(fourw,wi.aTe,fwae); - for (int i=0; i<3; i++) { - MathExtra::matvec(wi.lA[i],rhat,p); + for (int m=0; m<3; m++) { + MathExtra::matvec(wi.lA[m],rhat,p); double tempv[3]; - MathExtra::matvec(wi.lA[i],w,tempv); + MathExtra::matvec(wi.lA[m],w,tempv); dchi = -MathExtra::dot3(fwae,tempv); - MathExtra::matvec(lAtwo[i],spr,tempv); + MathExtra::matvec(lAtwo[m],spr,tempv); dh12 = -MathExtra::dot3(s,tempv); dUa = pbsu*dchi-dh12*dspu; dUr = pbsr*dchi-dh12*dspr; - ttor[i] = -(dUa*Ua+dUr*Ur); + ttor[m] = -(dUa*Ua+dUr*Ur); } } diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index 7dc7956586..23a4da7f07 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -21,21 +21,21 @@ #include "pair_body_rounded_polygon.h" -#include -#include -#include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" #include "body_rounded_polygon.h" #include "comm.h" -#include "force.h" -#include "fix.h" -#include "modify.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" +#include "fix.h" +#include "force.h" +#include "math_extra.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index 65179ecb80..6deb06aafb 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -23,22 +23,22 @@ #include "pair_body_rounded_polyhedron.h" -#include -#include #include "atom.h" #include "atom_vec_body.h" #include "body_rounded_polyhedron.h" #include "comm.h" -#include "force.h" -#include "fix.h" -#include "modify.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" -#include "math_extra.h" +#include "fix.h" +#include "force.h" #include "math_const.h" +#include "math_extra.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -1212,10 +1212,7 @@ int PairBodyRoundedPolyhedron::interaction_edge_to_edge(int ibody, contact_list[num_contacts].unique = 1; num_contacts++; } - } else { - } - return interact; } diff --git a/src/DPD-REACT/pair_exp6_rx.cpp b/src/DPD-REACT/pair_exp6_rx.cpp index f5adfac7a1..8240cb88b7 100644 --- a/src/DPD-REACT/pair_exp6_rx.cpp +++ b/src/DPD-REACT/pair_exp6_rx.cpp @@ -617,8 +617,7 @@ void PairExp6rx::coeff(int narg, char **arg) if (strcmp(site1,"1fluid") == 0) isite1 = oneFluidApproxParameter; - else - { + else { int isp; for (isp = 0; isp < nspecies; isp++) if (strcmp(site1, &atom->dname[isp][0]) == 0) break; @@ -631,8 +630,7 @@ void PairExp6rx::coeff(int narg, char **arg) if (strcmp(site2,"1fluid") == 0) isite2 = oneFluidApproxParameter; - else - { + else { int isp; for (isp = 0; isp < nspecies; isp++) if (strcmp(site2, &atom->dname[isp][0]) == 0) break; @@ -644,8 +642,7 @@ void PairExp6rx::coeff(int narg, char **arg) } // Set the interaction potential type to the enumerated type. - for (int iparam = 0; iparam < nparams; ++iparam) - { + for (int iparam = 0; iparam < nparams; ++iparam) { if (strcmp( params[iparam].potential, "exp6") == 0) params[iparam].potentialType = exp6PotentialType; else @@ -663,7 +660,6 @@ void PairExp6rx::coeff(int narg, char **arg) scalingFlag = EXPONENT; exponentR = utils::numeric(FLERR,arg[6],false,lmp); exponentEpsilon = utils::numeric(FLERR,arg[7],false,lmp); - if (narg > 9) error->all(FLERR,"Incorrect args for pair coefficients"); if (narg == 9) cut_one = utils::numeric(FLERR,arg[8],false,lmp); } else if (strcmp(arg[5],"polynomial") == 0) { scalingFlag = POLYNOMIAL; diff --git a/src/EXTRA-FIX/fix_gld.cpp b/src/EXTRA-FIX/fix_gld.cpp index 34ed43301e..2e30882206 100644 --- a/src/EXTRA-FIX/fix_gld.cpp +++ b/src/EXTRA-FIX/fix_gld.cpp @@ -132,6 +132,7 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR, "Illegal fix gld command"); } if (strcmp(arg[iarg+1],"no") == 0) { + zeroflag = 0; } else if (strcmp(arg[iarg+1],"yes") == 0) { zeroflag = 1; } else { @@ -144,6 +145,7 @@ FixGLD::FixGLD(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR, "Illegal fix gld command"); } if (strcmp(arg[iarg+1],"no") == 0) { + freezeflag = 0; } else if (strcmp(arg[iarg+1],"yes") == 0) { freezeflag = 1; for (int i = 0; i < atom->nlocal; i++) { diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp index b98b105045..8e3ec2ace8 100644 --- a/src/GPU/pppm_gpu.cpp +++ b/src/GPU/pppm_gpu.cpp @@ -106,6 +106,8 @@ PPPMGPU::PPPMGPU(LAMMPS *lmp) : PPPM(lmp) PPPMGPU::~PPPMGPU() { PPPM_GPU_API(clear)(poisson_time); + destroy_3d_offset(density_brick_gpu,nzlo_out,nylo_out); + destroy_3d_offset(vd_brick,nzlo_out,nylo_out); } /* ---------------------------------------------------------------------- diff --git a/src/GRANULAR/fix_wall_gran.cpp b/src/GRANULAR/fix_wall_gran.cpp index a604782993..5f16176e49 100644 --- a/src/GRANULAR/fix_wall_gran.cpp +++ b/src/GRANULAR/fix_wall_gran.cpp @@ -437,7 +437,7 @@ FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) : // register with Atom class history_one = nullptr; - grow_arrays(atom->nmax); + FixWallGran::grow_arrays(atom->nmax); atom->add_callback(Atom::GROW); atom->add_callback(Atom::RESTART); @@ -1555,8 +1555,7 @@ double FixWallGran::memory_usage() void FixWallGran::grow_arrays(int nmax) { - if (use_history) memory->grow(history_one,nmax,size_history, - "fix_wall_gran:history_one"); + if (use_history) memory->grow(history_one,nmax,size_history,"fix_wall_gran:history_one"); if (peratom_flag) { memory->grow(array_atom,nmax,size_peratom_cols,"fix_wall_gran:array_atom"); } diff --git a/src/GRANULAR/fix_wall_gran_region.cpp b/src/GRANULAR/fix_wall_gran_region.cpp index 0a92bac543..37afe9632c 100644 --- a/src/GRANULAR/fix_wall_gran_region.cpp +++ b/src/GRANULAR/fix_wall_gran_region.cpp @@ -62,7 +62,7 @@ FixWallGranRegion::FixWallGranRegion(LAMMPS *lmp, int narg, char **arg) : ncontact = nullptr; walls = nullptr; history_many = nullptr; - grow_arrays(atom->nmax); + FixWallGranRegion::grow_arrays(atom->nmax); // initialize shear history as if particle is not touching region @@ -355,8 +355,7 @@ void FixWallGranRegion::grow_arrays(int nmax) if (use_history) { memory->grow(ncontact,nmax,"fix_wall_gran:ncontact"); memory->grow(walls,nmax,tmax,"fix_wall_gran:walls"); - memory->grow(history_many,nmax,tmax,size_history, - "fix_wall_gran:history_many"); + memory->grow(history_many,nmax,tmax,size_history,"fix_wall_gran:history_many"); } if (peratom_flag) memory->grow(array_atom,nmax,size_peratom_cols,"fix_wall_gran:array_atom"); diff --git a/src/GRANULAR/pair_granular.cpp b/src/GRANULAR/pair_granular.cpp index d0e75d4812..2846403e4c 100644 --- a/src/GRANULAR/pair_granular.cpp +++ b/src/GRANULAR/pair_granular.cpp @@ -109,7 +109,8 @@ PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp) PairGranular::~PairGranular() { - delete [] svector; + delete[] svector; + delete[] history_transfer_factors; if (!fix_history) modify->delete_fix("NEIGH_HISTORY_GRANULAR_DUMMY"); else modify->delete_fix("NEIGH_HISTORY_GRANULAR"); diff --git a/src/MANYBODY/pair_tersoff_table.cpp b/src/MANYBODY/pair_tersoff_table.cpp index e64e5bce02..94c4d88b09 100644 --- a/src/MANYBODY/pair_tersoff_table.cpp +++ b/src/MANYBODY/pair_tersoff_table.cpp @@ -91,7 +91,7 @@ PairTersoffTable::~PairTersoffTable() memory->destroy(cutsq); } deallocateGrids(); - deallocatePreLoops(); + PairTersoffTable::deallocatePreLoops(); } /* ---------------------------------------------------------------------- */ diff --git a/src/OPENMP/pair_tersoff_table_omp.cpp b/src/OPENMP/pair_tersoff_table_omp.cpp index 47ee2feca8..5367a3d043 100644 --- a/src/OPENMP/pair_tersoff_table_omp.cpp +++ b/src/OPENMP/pair_tersoff_table_omp.cpp @@ -53,7 +53,7 @@ PairTersoffTableOMP::PairTersoffTableOMP(LAMMPS *lmp) : PairTersoffTableOMP::~PairTersoffTableOMP() { if (allocated) { - deallocatePreLoops(); + PairTersoffTableOMP::deallocatePreLoops(); } } diff --git a/src/REAXFF/fix_qeq_reaxff.cpp b/src/REAXFF/fix_qeq_reaxff.cpp index fd197a156a..8c3b7df190 100644 --- a/src/REAXFF/fix_qeq_reaxff.cpp +++ b/src/REAXFF/fix_qeq_reaxff.cpp @@ -165,7 +165,7 @@ FixQEqReaxFF::~FixQEqReaxFF() memory->destroy(s_hist); memory->destroy(t_hist); - deallocate_storage(); + FixQEqReaxFF::deallocate_storage(); deallocate_matrix(); memory->destroy(shld); diff --git a/src/REPLICA/fix_pimd.cpp b/src/REPLICA/fix_pimd.cpp index ce1d41302f..bb4af16f1b 100644 --- a/src/REPLICA/fix_pimd.cpp +++ b/src/REPLICA/fix_pimd.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -24,69 +23,29 @@ #include "fix_pimd.h" -#include -#include - -#include "universe.h" -#include "comm.h" -#include "force.h" #include "atom.h" +#include "comm.h" #include "domain.h" -#include "update.h" +#include "error.h" +#include "force.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "universe.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; -enum{PIMD,NMPIMD,CMD}; +enum { PIMD, NMPIMD, CMD }; /* ---------------------------------------------------------------------- */ FixPIMD::FixPIMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { - method = PIMD; - fmass = 1.0; - nhc_temp = 298.15; - nhc_nchain = 2; - sp = 1.0; - - for (int i=3; iuniverse_all(FLERR,"Unknown method parameter for fix pimd"); - } - else if (strcmp(arg[i],"fmass")==0) - { - fmass = atof(arg[i+1]); - if (fmass<0.0 || fmass>1.0) error->universe_all(FLERR,"Invalid fmass value for fix pimd"); - } - else if (strcmp(arg[i],"sp")==0) - { - sp = atof(arg[i+1]); - if (fmass<0.0) error->universe_all(FLERR,"Invalid sp value for fix pimd"); - } - else if (strcmp(arg[i],"temp")==0) - { - nhc_temp = atof(arg[i+1]); - if (nhc_temp<0.0) error->universe_all(FLERR,"Invalid temp value for fix pimd"); - } - else if (strcmp(arg[i],"nhc")==0) - { - nhc_nchain = atoi(arg[i+1]); - if (nhc_nchain<2) error->universe_all(FLERR,"Invalid nhc value for fix pimd"); - } - else error->universe_all(arg[i],i+1,"Unknown keyword for fix pimd"); - } - - /* Initiation */ - max_nsend = 0; tag_send = nullptr; buf_send = nullptr; @@ -110,25 +69,60 @@ FixPIMD::FixPIMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) nhc_eta_dotdot = nullptr; nhc_eta_mass = nullptr; + method = PIMD; + fmass = 1.0; + nhc_temp = 298.15; + nhc_nchain = 2; + sp = 1.0; + + for (int i = 3; i < narg - 1; i += 2) { + if (strcmp(arg[i], "method") == 0) { + if (strcmp(arg[i + 1], "pimd") == 0) + method = PIMD; + else if (strcmp(arg[i + 1], "nmpimd") == 0) + method = NMPIMD; + else if (strcmp(arg[i + 1], "cmd") == 0) + method = CMD; + else + error->universe_all(FLERR, "Unknown method parameter for fix pimd"); + } else if (strcmp(arg[i], "fmass") == 0) { + fmass = utils::numeric(FLERR, arg[i + 1], false, lmp); + if (fmass < 0.0 || fmass > 1.0) + error->universe_all(FLERR, "Invalid fmass value for fix pimd"); + } else if (strcmp(arg[i], "sp") == 0) { + sp = utils::numeric(FLERR, arg[i + 1], false, lmp); + if (fmass < 0.0) error->universe_all(FLERR, "Invalid sp value for fix pimd"); + } else if (strcmp(arg[i], "temp") == 0) { + nhc_temp = utils::numeric(FLERR, arg[i + 1], false, lmp); + if (nhc_temp < 0.0) error->universe_all(FLERR, "Invalid temp value for fix pimd"); + } else if (strcmp(arg[i], "nhc") == 0) { + nhc_nchain = utils::inumeric(FLERR, arg[i + 1], false, lmp); + if (nhc_nchain < 2) error->universe_all(FLERR, "Invalid nhc value for fix pimd"); + } else + error->universe_all(FLERR, fmt::format("Unknown keyword {} for fix pimd", arg[i])); + } + + /* Initiation */ + size_peratom_cols = 12 * nhc_nchain + 3; nhc_offset_one_1 = 3 * nhc_nchain; - nhc_offset_one_2 = 3 * nhc_nchain +3; + nhc_offset_one_2 = 3 * nhc_nchain + 3; nhc_size_one_1 = sizeof(double) * nhc_offset_one_1; nhc_size_one_2 = sizeof(double) * nhc_offset_one_2; restart_peratom = 1; - peratom_flag = 1; - peratom_freq = 1; + peratom_flag = 1; + peratom_freq = 1; global_freq = 1; vector_flag = 1; size_vector = 2; - extvector = 1; + extvector = 1; comm_forward = 3; - atom->add_callback(Atom::GROW); // Call LAMMPS to allocate memory for per-atom array - atom->add_callback(Atom::RESTART); // Call LAMMPS to re-assign restart-data for per-atom array + atom->add_callback(Atom::GROW); // Call LAMMPS to allocate memory for per-atom array + atom->add_callback(Atom::RESTART); // Call LAMMPS to re-assign restart-data for per-atom array grow_arrays(atom->nmax); @@ -138,7 +132,37 @@ FixPIMD::FixPIMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) } /* ---------------------------------------------------------------------- */ +FixPIMD::~FixPIMD() +{ + delete[] mass; + atom->delete_callback(id, Atom::GROW); + atom->delete_callback(id, Atom::RESTART); + memory->destroy(M_x2xp); + memory->destroy(M_xp2x); + memory->destroy(M_f2fp); + memory->destroy(M_fp2f); + memory->sfree(lam); + + if (buf_beads) + for (int i = 0; i < np; i++) memory->sfree(buf_beads[i]); + delete[] buf_beads; + delete[] plan_send; + delete[] plan_recv; + delete[] mode_index; + + memory->sfree(tag_send); + memory->sfree(buf_send); + memory->sfree(buf_recv); + + memory->destroy(array_atom); + memory->destroy(nhc_eta); + memory->destroy(nhc_eta_dot); + memory->destroy(nhc_eta_dotdot); + memory->destroy(nhc_eta_mass); +} + +/* ---------------------------------------------------------------------- */ int FixPIMD::setmask() { int mask = 0; @@ -153,9 +177,10 @@ int FixPIMD::setmask() void FixPIMD::init() { if (atom->map_style == Atom::MAP_NONE) - error->all(FLERR,"Fix pimd requires an atom map, see atom_modify"); + error->all(FLERR, "Fix pimd requires an atom map, see atom_modify"); - if (universe->me==0 && screen) fprintf(screen,"Fix pimd initializing Path-Integral ...\n"); + if (universe->me == 0 && universe->uscreen) + fprintf(universe->uscreen, "Fix pimd initializing Path-Integral ...\n"); // prepare the constants @@ -181,16 +206,16 @@ void FixPIMD::init() /* The current solution, using LAMMPS internal real units */ const double Boltzmann = force->boltz; - const double Plank = force->hplanck; + const double Plank = force->hplanck; - double hbar = Plank / ( 2.0 * MY_PI ); - double beta = 1.0 / (Boltzmann * nhc_temp); - double _fbond = 1.0 * np / (beta*beta*hbar*hbar) ; + double hbar = Plank / (2.0 * MY_PI); + double beta = 1.0 / (Boltzmann * nhc_temp); + double _fbond = 1.0 * np / (beta * beta * hbar * hbar); omega_np = sqrt(np) / (hbar * beta) * sqrt(force->mvv2e); - fbond = - _fbond * force->mvv2e; + fbond = -_fbond * force->mvv2e; - if (universe->me==0) + if (universe->me == 0) printf("Fix pimd -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond); dtv = update->dt; @@ -198,10 +223,12 @@ void FixPIMD::init() comm_init(); - mass = new double [atom->ntypes+1]; + mass = new double[atom->ntypes + 1]; - if (method==CMD || method==NMPIMD) nmpimd_init(); - else for (int i=1; i<=atom->ntypes; i++) mass[i] = atom->mass[i] / np * fmass; + if (method == CMD || method == NMPIMD) + nmpimd_init(); + else + for (int i = 1; i <= atom->ntypes; i++) mass[i] = atom->mass[i] / np * fmass; if (!nhc_ready) nhc_init(); } @@ -210,7 +237,8 @@ void FixPIMD::init() void FixPIMD::setup(int vflag) { - if (universe->me==0 && screen) fprintf(screen,"Setting up Path-Integral ...\n"); + if (universe->me == 0 && universe->uscreen) + fprintf(universe->uscreen, "Setting up Path-Integral ...\n"); post_force(vflag); } @@ -234,13 +262,13 @@ void FixPIMD::final_integrate() void FixPIMD::post_force(int /*flag*/) { - for (int i=0; inlocal; i++) for(int j=0; j<3; j++) atom->f[i][j] /= np; + for (int i = 0; i < atom->nlocal; i++) + for (int j = 0; j < 3; j++) atom->f[i][j] /= np; comm_exec(atom->x); spring_force(); - if (method==CMD || method==NMPIMD) - { + if (method == CMD || method == NMPIMD) { /* forward comm for the force on ghost atoms */ nmpimd_fill(atom->f); @@ -262,34 +290,38 @@ void FixPIMD::post_force(int /*flag*/) void FixPIMD::nhc_init() { double tau = 1.0 / omega_np; - double KT = force->boltz * nhc_temp; + double KT = force->boltz * nhc_temp; double mass0 = KT * tau * tau; int max = 3 * atom->nlocal; - for (int i=0; iiworld==0) ; else nhc_eta_mass[i][ichain] *= fmass; + nhc_eta_mass[i][ichain] = mass0; + if ((method == CMD || method == NMPIMD) && universe->iworld == 0) + ; + else + nhc_eta_mass[i][ichain] *= fmass; } - nhc_eta_dot[i][nhc_nchain] = 0.0; + nhc_eta_dot[i][nhc_nchain] = 0.0; - for (int ichain=1; ichainmvv2e - KT) / nhc_eta_mass[i][ichain]; + for (int ichain = 1; ichain < nhc_nchain; ichain++) + nhc_eta_dotdot[i][ichain] = (nhc_eta_mass[i][ichain - 1] * nhc_eta_dot[i][ichain - 1] * + nhc_eta_dot[i][ichain - 1] * force->mvv2e - + KT) / + nhc_eta_mass[i][ichain]; } // Zero NH acceleration for CMD - if (method==CMD && universe->iworld==0) for (int i=0; iiworld == 0) + for (int i = 0; i < max; i++) + for (int ichain = 0; ichain < nhc_nchain; ichain++) nhc_eta_dotdot[i][ichain] = 0.0; nhc_ready = true; } @@ -302,8 +334,7 @@ void FixPIMD::nhc_update_x() double **x = atom->x; double **v = atom->v; - if (method==CMD || method==NMPIMD) - { + if (method == CMD || method == NMPIMD) { nmpimd_fill(atom->v); comm_exec(atom->v); @@ -313,8 +344,7 @@ void FixPIMD::nhc_update_x() nmpimd_transform(buf_beads, v, M_xp2x[universe->iworld]); } - for (int i=0; iv; double **f = atom->f; - for (int i=0; iiworld==0) return; + if (method == CMD && universe->iworld == 0) return; double expfac; int nmax = 3 * atom->nlocal; double KT = force->boltz * nhc_temp; double kecurrent, t_current; - double dthalf = 0.5 * update->dt; - double dt4 = 0.25 * update->dt; - double dt8 = 0.125 * update->dt; + double dthalf = 0.5 * update->dt; + double dt4 = 0.25 * update->dt; + double dt8 = 0.125 * update->dt; - for (int i=0; imvv2e; + kecurrent = mass[type[iatm]] * vv[idim] * vv[idim] * force->mvv2e; t_current = kecurrent / force->boltz; double *eta = nhc_eta[i]; @@ -366,9 +394,8 @@ void FixPIMD::nhc_update_v() eta_dotdot[0] = (kecurrent - KT) / nhc_eta_mass[i][0]; - for (int ichain=nhc_nchain-1; ichain>0; ichain--) - { - expfac = exp(-dt8 * eta_dot[ichain+1]); + for (int ichain = nhc_nchain - 1; ichain > 0; ichain--) { + expfac = exp(-dt8 * eta_dot[ichain + 1]); eta_dot[ichain] *= expfac; eta_dot[ichain] += eta_dotdot[ichain] * dt4; eta_dot[ichain] *= expfac; @@ -388,19 +415,18 @@ void FixPIMD::nhc_update_v() kecurrent = force->boltz * t_current; eta_dotdot[0] = (kecurrent - KT) / nhc_eta_mass[i][0]; - for (int ichain=0; ichaincreate(M_f2fp, np, np, "fix_feynman:M_f2fp"); memory->create(M_fp2f, np, np, "fix_feynman:M_fp2f"); - lam = (double*) memory->smalloc(sizeof(double)*np, "FixPIMD::lam"); + lam = (double *) memory->smalloc(sizeof(double) * np, "FixPIMD::lam"); // Set up eigenvalues lam[0] = 0.0; - if (np%2==0) lam[np-1] = 4.0 * np; + if (np % 2 == 0) lam[np - 1] = 4.0 * np; - for (int i=2; i<=np/2; i++) - { - lam[2*i-3] = lam[2*i-2] = 2.0 * np * (1.0 - 1.0 *cos(2.0*MY_PI*(i-1)/np)); + for (int i = 2; i <= np / 2; i++) { + lam[2 * i - 3] = lam[2 * i - 2] = 2.0 * np * (1.0 - 1.0 * cos(2.0 * MY_PI * (i - 1) / np)); } // Set up eigenvectors for non-degenerated modes - for (int i=0; iiworld; - for (int i=1; i<=atom->ntypes; i++) - { + for (int i = 1; i <= atom->ntypes; i++) { mass[i] = atom->mass[i]; - if (iworld) - { + if (iworld) { mass[i] *= lam[iworld]; mass[i] *= fmass; } @@ -486,17 +507,17 @@ void FixPIMD::nmpimd_fill(double **ptr) /* ---------------------------------------------------------------------- */ -void FixPIMD::nmpimd_transform(double** src, double** des, double *vector) +void FixPIMD::nmpimd_transform(double **src, double **des, double *vector) { int n = atom->nlocal; int m = 0; - for (int i=0; ix; double **f = atom->f; - double* _mass = atom->mass; - int* type = atom->type; + double *_mass = atom->mass; + int *type = atom->type; int nlocal = atom->nlocal; - double* xlast = buf_beads[x_last]; - double* xnext = buf_beads[x_next]; + double *xlast = buf_beads[x_last]; + double *xnext = buf_beads[x_next]; - for (int i=0; ime - comm->nprocs; int rank_next = universe->me + comm->nprocs; - if (rank_last<0) rank_last += universe->nprocs; - if (rank_next>=universe->nprocs) rank_next -= universe->nprocs; + if (rank_last < 0) rank_last += universe->nprocs; + if (rank_next >= universe->nprocs) rank_next -= universe->nprocs; - plan_send[0] = rank_next; plan_send[1] = rank_last; - plan_recv[0] = rank_last; plan_recv[1] = rank_next; + plan_send[0] = rank_next; + plan_send[1] = rank_last; + plan_recv[0] = rank_last; + plan_recv[1] = rank_next; - mode_index[0] = 0; mode_index[1] = 1; - x_last = 1; x_next = 0; - } - else - { + mode_index[0] = 0; + mode_index[1] = 1; + x_last = 1; + x_next = 0; + } else { size_plan = np - 1; - plan_send = new int [size_plan]; - plan_recv = new int [size_plan]; - mode_index = new int [size_plan]; + plan_send = new int[size_plan]; + plan_recv = new int[size_plan]; + mode_index = new int[size_plan]; - for (int i=0; ime + comm->nprocs * (i+1); - if (plan_send[i]>=universe->nprocs) plan_send[i] -= universe->nprocs; + for (int i = 0; i < size_plan; i++) { + plan_send[i] = universe->me + comm->nprocs * (i + 1); + if (plan_send[i] >= universe->nprocs) plan_send[i] -= universe->nprocs; - plan_recv[i] = universe->me - comm->nprocs * (i+1); - if (plan_recv[i]<0) plan_recv[i] += universe->nprocs; + plan_recv[i] = universe->me - comm->nprocs * (i + 1); + if (plan_recv[i] < 0) plan_recv[i] += universe->nprocs; - mode_index[i]=(universe->iworld+i+1)%(universe->nworlds); + mode_index[i] = (universe->iworld + i + 1) % (universe->nworlds); } - x_next = (universe->iworld+1+universe->nworlds)%(universe->nworlds); - x_last = (universe->iworld-1+universe->nworlds)%(universe->nworlds); + x_next = (universe->iworld + 1 + universe->nworlds) % (universe->nworlds); + x_last = (universe->iworld - 1 + universe->nworlds) % (universe->nworlds); } - if (buf_beads) - { - for (int i=0; inlocal; - if (nlocal > max_nlocal) - { - max_nlocal = nlocal+200; + if (nlocal > max_nlocal) { + max_nlocal = nlocal + 200; int size = sizeof(double) * max_nlocal * 3; - buf_recv = (double*) memory->srealloc(buf_recv, size, "FixPIMD:x_recv"); + buf_recv = (double *) memory->srealloc(buf_recv, size, "FixPIMD:x_recv"); - for (int i=0; isrealloc(buf_beads[i], size, "FixPIMD:x_beads[i]"); + for (int i = 0; i < np; i++) + buf_beads[i] = (double *) memory->srealloc(buf_beads[i], size, "FixPIMD:x_beads[i]"); } // copy local positions - memcpy(buf_beads[universe->iworld], &(ptr[0][0]), sizeof(double)*nlocal*3); + memcpy(buf_beads[universe->iworld], &(ptr[0][0]), sizeof(double) * nlocal * 3); // go over comm plans - for (int iplan = 0; iplanuworld, MPI_STATUS_IGNORE); + MPI_Sendrecv(&(nlocal), 1, MPI_INT, plan_send[iplan], 0, &(nsend), 1, MPI_INT, plan_recv[iplan], + 0, universe->uworld, MPI_STATUS_IGNORE); // allocate arrays - if (nsend > max_nsend) - { - max_nsend = nsend+200; - tag_send = (tagint*) memory->srealloc(tag_send, sizeof(tagint)*max_nsend, "FixPIMD:tag_send"); - buf_send = (double*) memory->srealloc(buf_send, sizeof(double)*max_nsend*3, "FixPIMD:x_send"); + if (nsend > max_nsend) { + max_nsend = nsend + 200; + tag_send = + (tagint *) memory->srealloc(tag_send, sizeof(tagint) * max_nsend, "FixPIMD:tag_send"); + buf_send = + (double *) memory->srealloc(buf_send, sizeof(double) * max_nsend * 3, "FixPIMD:x_send"); } // send tags - MPI_Sendrecv( atom->tag, nlocal, MPI_LMP_TAGINT, plan_send[iplan], 0, - tag_send, nsend, MPI_LMP_TAGINT, plan_recv[iplan], 0, universe->uworld, MPI_STATUS_IGNORE); + MPI_Sendrecv(atom->tag, nlocal, MPI_LMP_TAGINT, plan_send[iplan], 0, tag_send, nsend, + MPI_LMP_TAGINT, plan_recv[iplan], 0, universe->uworld, MPI_STATUS_IGNORE); // wrap positions double *wrap_ptr = buf_send; - int ncpy = sizeof(double)*3; + int ncpy = sizeof(double) * 3; - for (int i=0; imap(tag_send[i]); - if (index<0) - { + if (index < 0) { char error_line[256]; - sprintf(error_line, "Atom " TAGINT_FORMAT " is missing at world [%d] " - "rank [%d] required by rank [%d] (" TAGINT_FORMAT ", " - TAGINT_FORMAT ", " TAGINT_FORMAT ").\n", tag_send[i], - universe->iworld, comm->me, plan_recv[iplan], - atom->tag[0], atom->tag[1], atom->tag[2]); + sprintf(error_line, + "Atom " TAGINT_FORMAT " is missing at world [%d] " + "rank [%d] required by rank [%d] (" TAGINT_FORMAT ", " TAGINT_FORMAT + ", " TAGINT_FORMAT ").\n", + tag_send[i], universe->iworld, comm->me, plan_recv[iplan], atom->tag[0], + atom->tag[1], atom->tag[2]); - error->universe_one(FLERR,error_line); + error->universe_one(FLERR, error_line); } memcpy(wrap_ptr, ptr[index], ncpy); @@ -677,21 +694,20 @@ void FixPIMD::comm_exec(double **ptr) // sendrecv x - MPI_Sendrecv( buf_send, nsend*3, MPI_DOUBLE, plan_recv[iplan], 0, - buf_recv, nlocal*3, MPI_DOUBLE, plan_send[iplan], 0, universe->uworld, MPI_STATUS_IGNORE); + MPI_Sendrecv(buf_send, nsend * 3, MPI_DOUBLE, plan_recv[iplan], 0, buf_recv, nlocal * 3, + MPI_DOUBLE, plan_send[iplan], 0, universe->uworld, MPI_STATUS_IGNORE); // copy x - memcpy(buf_beads[mode_index[iplan]], buf_recv, sizeof(double)*nlocal*3); + memcpy(buf_beads[mode_index[iplan]], buf_recv, sizeof(double) * nlocal * 3); } } /* ---------------------------------------------------------------------- */ -int FixPIMD::pack_forward_comm(int n, int *list, double *buf, - int /*pbc_flag*/, int * /*pbc*/) +int FixPIMD::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/) { - int i,j,m; + int i, j, m; m = 0; @@ -709,7 +725,7 @@ int FixPIMD::pack_forward_comm(int n, int *list, double *buf, void FixPIMD::unpack_forward_comm(int n, int first, double *buf) { - int i,m,last; + int i, m, last; m = 0; last = first + n; @@ -726,47 +742,51 @@ void FixPIMD::unpack_forward_comm(int n, int first, double *buf) double FixPIMD::memory_usage() { - return (double)atom->nmax * size_peratom_cols * sizeof(double); + return (double) atom->nmax * size_peratom_cols * sizeof(double); } /* ---------------------------------------------------------------------- */ void FixPIMD::grow_arrays(int nmax) { - if (nmax==0) return; - int count = nmax*3; + if (nmax == 0) return; + int count = nmax * 3; memory->grow(array_atom, nmax, size_peratom_cols, "FixPIMD::array_atom"); - memory->grow(nhc_eta, count, nhc_nchain, "FixPIMD::nh_eta"); - memory->grow(nhc_eta_dot, count, nhc_nchain+1, "FixPIMD::nh_eta_dot"); - memory->grow(nhc_eta_dotdot, count, nhc_nchain, "FixPIMD::nh_eta_dotdot"); - memory->grow(nhc_eta_mass, count, nhc_nchain, "FixPIMD::nh_eta_mass"); + memory->grow(nhc_eta, count, nhc_nchain, "FixPIMD::nh_eta"); + memory->grow(nhc_eta_dot, count, nhc_nchain + 1, "FixPIMD::nh_eta_dot"); + memory->grow(nhc_eta_dotdot, count, nhc_nchain, "FixPIMD::nh_eta_dotdot"); + memory->grow(nhc_eta_mass, count, nhc_nchain, "FixPIMD::nh_eta_mass"); } /* ---------------------------------------------------------------------- */ void FixPIMD::copy_arrays(int i, int j, int /*delflag*/) { - int i_pos = i*3; - int j_pos = j*3; + int i_pos = i * 3; + int j_pos = j * 3; - memcpy(nhc_eta [j_pos], nhc_eta [i_pos], nhc_size_one_1); - memcpy(nhc_eta_dot [j_pos], nhc_eta_dot [i_pos], nhc_size_one_2); + memcpy(nhc_eta[j_pos], nhc_eta[i_pos], nhc_size_one_1); + memcpy(nhc_eta_dot[j_pos], nhc_eta_dot[i_pos], nhc_size_one_2); memcpy(nhc_eta_dotdot[j_pos], nhc_eta_dotdot[i_pos], nhc_size_one_1); - memcpy(nhc_eta_mass [j_pos], nhc_eta_mass [i_pos], nhc_size_one_1); + memcpy(nhc_eta_mass[j_pos], nhc_eta_mass[i_pos], nhc_size_one_1); } /* ---------------------------------------------------------------------- */ int FixPIMD::pack_exchange(int i, double *buf) { - int offset=0; + int offset = 0; int pos = i * 3; - memcpy(buf+offset, nhc_eta[pos], nhc_size_one_1); offset += nhc_offset_one_1; - memcpy(buf+offset, nhc_eta_dot[pos], nhc_size_one_2); offset += nhc_offset_one_2; - memcpy(buf+offset, nhc_eta_dotdot[pos], nhc_size_one_1); offset += nhc_offset_one_1; - memcpy(buf+offset, nhc_eta_mass[pos], nhc_size_one_1); offset += nhc_offset_one_1; + memcpy(buf + offset, nhc_eta[pos], nhc_size_one_1); + offset += nhc_offset_one_1; + memcpy(buf + offset, nhc_eta_dot[pos], nhc_size_one_2); + offset += nhc_offset_one_2; + memcpy(buf + offset, nhc_eta_dotdot[pos], nhc_size_one_1); + offset += nhc_offset_one_1; + memcpy(buf + offset, nhc_eta_mass[pos], nhc_size_one_1); + offset += nhc_offset_one_1; return size_peratom_cols; } @@ -775,13 +795,17 @@ int FixPIMD::pack_exchange(int i, double *buf) int FixPIMD::unpack_exchange(int nlocal, double *buf) { - int offset=0; - int pos = nlocal*3; + int offset = 0; + int pos = nlocal * 3; - memcpy(nhc_eta[pos], buf+offset, nhc_size_one_1); offset += nhc_offset_one_1; - memcpy(nhc_eta_dot[pos], buf+offset, nhc_size_one_2); offset += nhc_offset_one_2; - memcpy(nhc_eta_dotdot[pos], buf+offset, nhc_size_one_1); offset += nhc_offset_one_1; - memcpy(nhc_eta_mass[pos], buf+offset, nhc_size_one_1); offset += nhc_offset_one_1; + memcpy(nhc_eta[pos], buf + offset, nhc_size_one_1); + offset += nhc_offset_one_1; + memcpy(nhc_eta_dot[pos], buf + offset, nhc_size_one_2); + offset += nhc_offset_one_2; + memcpy(nhc_eta_dotdot[pos], buf + offset, nhc_size_one_1); + offset += nhc_offset_one_1; + memcpy(nhc_eta_mass[pos], buf + offset, nhc_size_one_1); + offset += nhc_offset_one_1; return size_peratom_cols; } @@ -790,17 +814,21 @@ int FixPIMD::unpack_exchange(int nlocal, double *buf) int FixPIMD::pack_restart(int i, double *buf) { - int offset=0; + int offset = 0; int pos = i * 3; // pack buf[0] this way because other fixes unpack it - buf[offset++] = size_peratom_cols+1; + buf[offset++] = size_peratom_cols + 1; - memcpy(buf+offset, nhc_eta[pos], nhc_size_one_1); offset += nhc_offset_one_1; - memcpy(buf+offset, nhc_eta_dot[pos], nhc_size_one_2); offset += nhc_offset_one_2; - memcpy(buf+offset, nhc_eta_dotdot[pos], nhc_size_one_1); offset += nhc_offset_one_1; - memcpy(buf+offset, nhc_eta_mass[pos], nhc_size_one_1); offset += nhc_offset_one_1; + memcpy(buf + offset, nhc_eta[pos], nhc_size_one_1); + offset += nhc_offset_one_1; + memcpy(buf + offset, nhc_eta_dot[pos], nhc_size_one_2); + offset += nhc_offset_one_2; + memcpy(buf + offset, nhc_eta_dotdot[pos], nhc_size_one_1); + offset += nhc_offset_one_1; + memcpy(buf + offset, nhc_eta_mass[pos], nhc_size_one_1); + offset += nhc_offset_one_1; - return size_peratom_cols+1; + return size_peratom_cols + 1; } /* ---------------------------------------------------------------------- */ @@ -813,15 +841,19 @@ void FixPIMD::unpack_restart(int nlocal, int nth) // unpack the Nth first values this way because other fixes pack them int m = 0; - for (int i=0; i (extra[nlocal][m]); + for (int i = 0; i < nth; i++) m += static_cast(extra[nlocal][m]); m++; int pos = nlocal * 3; - memcpy(nhc_eta[pos], extra[nlocal]+m, nhc_size_one_1); m += nhc_offset_one_1; - memcpy(nhc_eta_dot[pos], extra[nlocal]+m, nhc_size_one_2); m += nhc_offset_one_2; - memcpy(nhc_eta_dotdot[pos], extra[nlocal]+m, nhc_size_one_1); m += nhc_offset_one_1; - memcpy(nhc_eta_mass[pos], extra[nlocal]+m, nhc_size_one_1); m += nhc_offset_one_1; + memcpy(nhc_eta[pos], extra[nlocal] + m, nhc_size_one_1); + m += nhc_offset_one_1; + memcpy(nhc_eta_dot[pos], extra[nlocal] + m, nhc_size_one_2); + m += nhc_offset_one_2; + memcpy(nhc_eta_dotdot[pos], extra[nlocal] + m, nhc_size_one_1); + m += nhc_offset_one_1; + memcpy(nhc_eta_mass[pos], extra[nlocal] + m, nhc_size_one_1); + m += nhc_offset_one_1; nhc_ready = true; } @@ -830,21 +862,21 @@ void FixPIMD::unpack_restart(int nlocal, int nth) int FixPIMD::maxsize_restart() { - return size_peratom_cols+1; + return size_peratom_cols + 1; } /* ---------------------------------------------------------------------- */ int FixPIMD::size_restart(int /*nlocal*/) { - return size_peratom_cols+1; + return size_peratom_cols + 1; } /* ---------------------------------------------------------------------- */ double FixPIMD::compute_vector(int n) { - if (n==0) { return spring_energy; } - if (n==1) { return t_sys; } + if (n == 0) { return spring_energy; } + if (n == 1) { return t_sys; } return 0.0; } diff --git a/src/REPLICA/fix_pimd.h b/src/REPLICA/fix_pimd.h index 2c13663f23..05a24dedce 100644 --- a/src/REPLICA/fix_pimd.h +++ b/src/REPLICA/fix_pimd.h @@ -27,6 +27,7 @@ namespace LAMMPS_NS { class FixPIMD : public Fix { public: FixPIMD(class LAMMPS *, int, char **); + virtual ~FixPIMD(); int setmask(); diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index 66a1dd83d5..a445ace756 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -94,7 +94,8 @@ NEB::~NEB() { MPI_Comm_free(&roots); memory->destroy(all); - delete [] rdist; + delete[] rdist; + if (fp) fclose(fp); } /* ---------------------------------------------------------------------- @@ -379,8 +380,8 @@ void NEB::readfile(char *file, int flag) char line[MAXLINE]; double xx,yy,zz,delx,dely,delz; - if (me_universe == 0 && screen) - fprintf(screen,"Reading NEB coordinate file(s) ...\n"); + if (me_universe == 0 && universe->uscreen) + fprintf(universe->uscreen,"Reading NEB coordinate file(s) ...\n"); // flag = 0, universe root reads header of file, bcast to universe // flag = 1, each replica's root reads header of file, bcast to world @@ -534,6 +535,7 @@ void NEB::readfile(char *file, int flag) else fclose(fp); } } + fp = nullptr; } /* ---------------------------------------------------------------------- diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index a07a16350a..1b798166a1 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -78,7 +78,8 @@ NEBSpin::~NEBSpin() { MPI_Comm_free(&roots); memory->destroy(all); - delete [] rdist; + delete[] rdist; + if (fp) fclose(fp); } /* ---------------------------------------------------------------------- @@ -373,8 +374,8 @@ void NEBSpin::readfile(char *file, int flag) double xx,yy,zz; double musp,spx,spy,spz; - if (me_universe == 0 && screen) - fprintf(screen,"Reading NEBSpin coordinate file(s) ...\n"); + if (me_universe == 0 && universe->uscreen) + fprintf(universe->uscreen,"Reading NEBSpin coordinate file(s) ...\n"); // flag = 0, universe root reads header of file, bcast to universe // flag = 1, each replica's root reads header of file, bcast to world @@ -546,8 +547,8 @@ void NEBSpin::readfile(char *file, int flag) // clean up - delete [] buffer; - delete [] values; + delete[] buffer; + delete[] values; if (flag == 0) { if (me_universe == 0) { @@ -560,6 +561,7 @@ void NEBSpin::readfile(char *file, int flag) else fclose(fp); } } + fp = nullptr; } /* ---------------------------------------------------------------------- diff --git a/src/compute_dipole.cpp b/src/compute_dipole.cpp index 053f11e6f9..b67c3df3ce 100644 --- a/src/compute_dipole.cpp +++ b/src/compute_dipole.cpp @@ -29,7 +29,7 @@ enum { MASSCENTER, GEOMCENTER }; ComputeDipole::ComputeDipole(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg) { - if (narg != 3) error->all(FLERR, "Illegal compute com command"); + if ((narg < 3) || (narg > 4)) error->all(FLERR, "Illegal compute dipole command"); scalar_flag = 1; vector_flag = 1; @@ -39,11 +39,8 @@ ComputeDipole::ComputeDipole(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, n vector = new double[size_vector]; vector[0] = vector[1] = vector[2] = 0.0; - usecenter = MASSCENTER; - if ((narg != 3) && (narg != 4)) error->all(FLERR, "Illegal compute dipole command"); - if (narg == 4) { if (utils::strmatch(arg[3], "^geom")) usecenter = GEOMCENTER; diff --git a/src/read_restart.cpp b/src/read_restart.cpp index faf9fd1620..e42bb59272 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -44,7 +44,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -ReadRestart::ReadRestart(LAMMPS *lmp) : Command(lmp) {} +ReadRestart::ReadRestart(LAMMPS *lmp) : Command(lmp), mpiio(nullptr) {} /* ---------------------------------------------------------------------- */ @@ -110,8 +110,7 @@ void ReadRestart::command(int narg, char **arg) } fp = fopen(hfile.c_str(),"rb"); if (fp == nullptr) - error->one(FLERR,"Cannot open restart file {}: {}", - hfile, utils::getsyserror()); + error->one(FLERR,"Cannot open restart file {}: {}", hfile, utils::getsyserror()); } // read magic string, endian flag, format revision @@ -336,8 +335,7 @@ void ReadRestart::command(int narg, char **arg) procfile.replace(procfile.find("%"),1,fmt::format("{}",icluster)); fp = fopen(procfile.c_str(),"rb"); if (fp == nullptr) - error->one(FLERR,"Cannot open restart file {}: {}", - procfile, utils::getsyserror()); + error->one(FLERR,"Cannot open restart file {}: {}", procfile, utils::getsyserror()); } int procsperfile; @@ -401,7 +399,7 @@ void ReadRestart::command(int narg, char **arg) // clean-up memory - delete [] file; + delete[] file; memory->destroy(buf); // for multiproc or MPI-IO files: @@ -525,8 +523,9 @@ void ReadRestart::command(int narg, char **arg) MPI_Barrier(world); if (comm->me == 0) - utils::logmesg(lmp," read_restart CPU = {:.3f} seconds\n", - MPI_Wtime()-time1); + utils::logmesg(lmp," read_restart CPU = {:.3f} seconds\n",MPI_Wtime()-time1); + + delete mpiio; } /* ---------------------------------------------------------------------- @@ -599,7 +598,7 @@ void ReadRestart::header() if (me == 0) utils::logmesg(lmp," restart file = {}, LAMMPS = {}\n", version,lmp->version); - delete [] version; + delete[] version; // we have no forward compatibility, thus exit with error @@ -638,7 +637,7 @@ void ReadRestart::header() } else if (flag == UNITS) { char *style = read_string(); if (strcmp(style,update->unit_style) != 0) update->set_units(style); - delete [] style; + delete[] style; } else if (flag == NTIMESTEP) { update->ntimestep = read_bigint(); @@ -772,9 +771,9 @@ void ReadRestart::header() atom->create_avec(style,nargcopy,argcopy,1); if (comm->me ==0) utils::logmesg(lmp," restoring atom style {} from restart\n",style); - for (int i = 0; i < nargcopy; i++) delete [] argcopy[i]; - delete [] argcopy; - delete [] style; + for (int i = 0; i < nargcopy; i++) delete[] argcopy[i]; + delete[] argcopy; + delete[] style; } else if (flag == NATOMS) { atom->natoms = read_bigint(); @@ -889,7 +888,7 @@ void ReadRestart::type_arrays() double *mass = new double[atom->ntypes+1]; read_double_vec(atom->ntypes,&mass[1]); atom->set_mass(mass); - delete [] mass; + delete[] mass; } else error->all(FLERR, "Invalid flag in type arrays section of restart file"); @@ -910,7 +909,7 @@ void ReadRestart::force_fields() if (flag == PAIR) { style = read_string(); force->create_pair(style,1); - delete [] style; + delete[] style; if (comm->me ==0) utils::logmesg(lmp," restoring pair style {} from restart\n", force->pair_style); @@ -926,7 +925,7 @@ void ReadRestart::force_fields() } else if (flag == BOND) { style = read_string(); force->create_bond(style,1); - delete [] style; + delete[] style; if (comm->me ==0) utils::logmesg(lmp," restoring bond style {} from restart\n", force->bond_style); @@ -935,7 +934,7 @@ void ReadRestart::force_fields() } else if (flag == ANGLE) { style = read_string(); force->create_angle(style,1); - delete [] style; + delete[] style; if (comm->me ==0) utils::logmesg(lmp," restoring angle style {} from restart\n", force->angle_style); @@ -944,7 +943,7 @@ void ReadRestart::force_fields() } else if (flag == DIHEDRAL) { style = read_string(); force->create_dihedral(style,1); - delete [] style; + delete[] style; if (comm->me ==0) utils::logmesg(lmp," restoring dihedral style {} from restart\n", force->dihedral_style); @@ -953,7 +952,7 @@ void ReadRestart::force_fields() } else if (flag == IMPROPER) { style = read_string(); force->create_improper(style,1); - delete [] style; + delete[] style; if (comm->me ==0) utils::logmesg(lmp," restoring improper style {} from restart\n", force->improper_style); @@ -1117,7 +1116,7 @@ void ReadRestart::magic_string() MPI_Bcast(str,n,MPI_CHAR,0,world); if (strcmp(str,MAGIC_STRING) != 0) error->all(FLERR,"Invalid LAMMPS restart file"); - delete [] str; + delete[] str; } /* ---------------------------------------------------------------------- @@ -1164,7 +1163,7 @@ void ReadRestart::check_eof_magic() if (strcmp(str,MAGIC_STRING) != 0) error->all(FLERR,"Incomplete or corrupted LAMMPS restart file"); - delete [] str; + delete[] str; } /* ----------------------------------------------------------------------