From 5d66dc6659718d2e16644a7b1c43ae50af134b6d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 May 2023 17:38:16 -0400 Subject: [PATCH] apply clang-format --- src/REPLICA/fix_pimd_langevin.cpp | 123 ++++++++++++++---------------- 1 file changed, 58 insertions(+), 65 deletions(-) diff --git a/src/REPLICA/fix_pimd_langevin.cpp b/src/REPLICA/fix_pimd_langevin.cpp index 733d38e038..67d7cabe02 100644 --- a/src/REPLICA/fix_pimd_langevin.cpp +++ b/src/REPLICA/fix_pimd_langevin.cpp @@ -47,7 +47,8 @@ using namespace LAMMPS_NS; using namespace FixConst; -using namespace MathConst; +using MathConst::MY_PI; +using MathConst::THIRD; enum { NMPIMD }; enum { PHYSICAL, NORMAL }; @@ -63,7 +64,7 @@ enum { SINGLE_PROC, MULTI_PROC }; /* ---------------------------------------------------------------------- */ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), random(nullptr), c_pe(nullptr), c_press(nullptr) + Fix(lmp, narg, arg), random(nullptr), c_pe(nullptr), c_press(nullptr) { restart_global = 1; time_integrate = 1; @@ -114,18 +115,18 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : int seed = -1; - for (int i = 0; i < 6; i++) - { + for (int i = 0; i < 6; i++) { p_flag[i] = 0; p_target[i] = 0.0; } for (int i = 3; i < narg - 1; i += 2) { if (strcmp(arg[i], "method") == 0) { - if (strcmp(arg[i + 1], "nmpimd") == 0)method = NMPIMD; - else error->universe_all(FLERR, "Unknown method parameter for fix pimd/langevin"); - } - else if (strcmp(arg[i], "integrator") == 0) { + if (strcmp(arg[i + 1], "nmpimd") == 0) + method = NMPIMD; + else + error->universe_all(FLERR, "Unknown method parameter for fix pimd/langevin"); + } else if (strcmp(arg[i], "integrator") == 0) { if (strcmp(arg[i + 1], "obabo") == 0) integrator = OBABO; else if (strcmp(arg[i + 1], "baoab") == 0) @@ -157,11 +158,11 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : "Unknown ensemble parameter for fix pimd/langevin. Only nve and nvt " "ensembles are supported!"); } else if (strcmp(arg[i], "fmass") == 0) { - fmass = utils::numeric(FLERR, arg[i+1], false, lmp); + fmass = utils::numeric(FLERR, arg[i + 1], false, lmp); if (fmass < 0.0 || fmass > np) error->universe_all(FLERR, "Invalid fmass value for fix pimd/langevin"); } else if (strcmp(arg[i], "sp") == 0) { - sp = utils::numeric(FLERR, arg[i+1], false, lmp); + sp = utils::numeric(FLERR, arg[i + 1], false, lmp); if (sp < 0.0) error->universe_all(FLERR, "Invalid sp value for fix pimd/nvt"); } else if (strcmp(arg[i], "fmmode") == 0) { if (strcmp(arg[i + 1], "physical") == 0) @@ -204,29 +205,29 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : error->universe_all(FLERR, "Unknown barostat parameter for fix pimd/langevin"); } else if (strcmp(arg[i], "iso") == 0) { pstyle = ISO; - Pext = utils::numeric(FLERR, arg[i+1], false, lmp); + Pext = utils::numeric(FLERR, arg[i + 1], false, lmp); p_target[0] = p_target[1] = p_target[2] = Pext; pdim = 3; } else if (strcmp(arg[i], "aniso") == 0) { pstyle = ANISO; p_flag[0] = p_flag[1] = p_flag[2] = 1; - Pext = utils::numeric(FLERR, arg[i+1], false, lmp); + Pext = utils::numeric(FLERR, arg[i + 1], false, lmp); p_target[0] = p_target[1] = p_target[2] = Pext; pdim = 3; } else if (strcmp(arg[i], "x") == 0) { pstyle = ANISO; p_flag[0] = 1; - p_target[0] = utils::numeric(FLERR, arg[i+1], false, lmp); + p_target[0] = utils::numeric(FLERR, arg[i + 1], false, lmp); pdim++; } else if (strcmp(arg[i], "y") == 0) { pstyle = ANISO; p_flag[1] = 1; - p_target[1] = utils::numeric(FLERR, arg[i+1], false, lmp); + p_target[1] = utils::numeric(FLERR, arg[i + 1], false, lmp); pdim++; } else if (strcmp(arg[i], "z") == 0) { pstyle = ANISO; p_flag[2] = 1; - p_target[2] = utils::numeric(FLERR, arg[i+1], false, lmp); + p_target[2] = utils::numeric(FLERR, arg[i + 1], false, lmp); pdim++; } else if (strcmp(arg[i], "taup") == 0) { tau_p = utils::numeric(FLERR, arg[i + 1], false, lmp); @@ -245,12 +246,12 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : global_freq = 1; vector_flag = 1; - if (!pstat_flag) size_vector = 10; + if (!pstat_flag) + size_vector = 10; else if (pstat_flag) { - if (pstyle == ISO){ - size_vector = 15; - } - else if (pstyle == ANISO){ + if (pstyle == ISO) { + size_vector = 15; + } else if (pstyle == ANISO) { size_vector = 17; } } @@ -271,7 +272,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : fixedpoint[0] = 0.5 * (domain->boxlo[0] + domain->boxhi[0]); fixedpoint[1] = 0.5 * (domain->boxlo[1] + domain->boxhi[1]); fixedpoint[2] = 0.5 * (domain->boxlo[2] + domain->boxhi[2]); - if (pstat_flag) { p_hydro = (p_target[0]+p_target[1]+p_target[2])/pdim; } + if (pstat_flag) { p_hydro = (p_target[0] + p_target[1] + p_target[2]) / pdim; } // initialize Marsaglia RNG with processor-unique seed @@ -293,8 +294,10 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) : nreplica = universe->nworlds; ireplica = universe->iworld; - if (nreplica == 1) mapflag = 0; - else mapflag = 1; + if (nreplica == 1) + mapflag = 0; + else + mapflag = 1; int *iroots = new int[nreplica]; MPI_Group uworldgroup, rootgroup; @@ -426,7 +429,8 @@ void FixPIMDLangevin::init() fbond = _fbond * force->mvv2e; if ((universe->me == 0) && (universe->uscreen)) - fprintf(universe->uscreen, "fix pimd/langevin -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond); + fprintf(universe->uscreen, + "fix pimd/langevin -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond); if (integrator == OBABO) { dtf = 0.5 * update->dt * force->ftm2v; @@ -724,13 +728,10 @@ void FixPIMDLangevin::qc_step() if (barostat == BZP) { for (int i = 0; i < nlocal; i++) { for (int j = 0; j < 3; j++) { - if (p_flag[j]) - { + if (p_flag[j]) { x[i][j] = expq[j] * x[i][j] + (expq[j] - expp[j]) / 2. / vw[j] * v[i][j]; v[i][j] = expp[j] * v[i][j]; - } - else - { + } else { x[i][j] += dtv * v[i][j]; } } @@ -844,10 +845,9 @@ void FixPIMDLangevin::press_v_step() } else if (pstyle == ANISO) { compute_stress_tensor(); for (int ii = 0; ii < 3; ii++) { - if (p_flag[ii]) - { - vw[ii] += - dtv * (volume * np * (stress_tensor[ii] - p_hydro) / force->nktv2p + Vcoeff / beta_np) / W; + if (p_flag[ii]) { + vw[ii] += dtv * + (volume * np * (stress_tensor[ii] - p_hydro) / force->nktv2p + Vcoeff / beta_np) / W; if (universe->iworld == 0) { double dvw_proc = 0.0, dvw = 0.0; for (int i = 0; i < nlocal; i++) { @@ -875,10 +875,8 @@ void FixPIMDLangevin::press_o_step() MPI_Bcast(&vw[0], 1, MPI_DOUBLE, 0, universe->uworld); } else if (pstyle == ANISO) { if (universe->me == 0) { - for (int ii=0; ii<3; ii++) - { - if (p_flag[ii]) - { + for (int ii = 0; ii < 3; ii++) { + if (p_flag[ii]) { r1 = random->gaussian(); vw[ii] = c1 * vw[ii] + c2 * sqrt(1.0 / W / beta_np) * r1; } @@ -1155,9 +1153,9 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr) m++; } MPI_Allgather(&m, 1, MPI_INT, counts, 1, MPI_INT, universe->uworld); - for (i = 0; i < nreplica; i++) { counts[i] *= 3; } + for (i = 0; i < nreplica; i++) counts[i] *= 3; displacements[0] = 0; - for (i = 0; i < nreplica - 1; i++) { displacements[i + 1] = displacements[i] + counts[i]; } + for (i = 0; i < nreplica - 1; i++) displacements[i + 1] = displacements[i] + counts[i]; MPI_Allgatherv(bufsorted[0], 3 * m, MPI_DOUBLE, bufsortedall[0], counts, displacements, MPI_DOUBLE, universe->uworld); } else if (cmode == MULTI_PROC) { @@ -1171,11 +1169,11 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr) } MPI_Gather(&m, 1, MPI_INT, counts, 1, MPI_INT, 0, world); displacements[0] = 0; - for (i = 0; i < nprocs - 1; i++) { displacements[i + 1] = displacements[i] + counts[i]; } + for (i = 0; i < nprocs - 1; i++) displacements[i + 1] = displacements[i] + counts[i]; MPI_Gatherv(tagsend, m, MPI_LMP_TAGINT, tagsendall, counts, displacements, MPI_LMP_TAGINT, 0, world); - for (i = 0; i < nprocs; i++) { counts[i] *= 3; } - for (i = 0; i < nprocs - 1; i++) { displacements[i + 1] = displacements[i] + counts[i]; } + for (i = 0; i < nprocs; i++) counts[i] *= 3; + for (i = 0; i < nprocs - 1; i++) displacements[i + 1] = displacements[i] + counts[i]; MPI_Gatherv(bufsend[0], 3 * m, MPI_DOUBLE, bufsendall[0], counts, displacements, MPI_DOUBLE, 0, world); for (int iplan = 0; iplan < sizeplan; iplan++) { @@ -1203,15 +1201,15 @@ void FixPIMDLangevin::inter_replica_comm(double **ptr) /* ---------------------------------------------------------------------- */ -void FixPIMDLangevin::remove_com_motion(){ - if(universe->iworld == 0) - { - double **v = atom->v; - int *mask = atom->mask; +void FixPIMDLangevin::remove_com_motion() +{ + if (universe->iworld == 0) { + double **v = atom->v; + int *mask = atom->mask; int nlocal = atom->nlocal; - if (dynamic) masstotal = group->mass(igroup); + if (dynamic) masstotal = group->mass(igroup); double vcm[3]; - group->vcm(igroup,masstotal,vcm); + group->vcm(igroup, masstotal, vcm); for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { v[i][0] -= vcm[0]; @@ -1372,7 +1370,8 @@ void FixPIMDLangevin::compute_t_vir() void FixPIMDLangevin::compute_p_prim() { double inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd); - p_prim = atom->natoms * np * force->boltz * temp * inv_volume - 1.0 / 1.5 * inv_volume * total_spring_energy; + p_prim = atom->natoms * np * force->boltz * temp * inv_volume - + 1.0 / 1.5 * inv_volume * total_spring_energy; p_prim *= force->nktv2p; } @@ -1415,14 +1414,14 @@ void FixPIMDLangevin::write_restart(FILE *fp) int nsize = size_restart_global(); double *list; - memory->create(list,nsize,"FixPIMDLangevin:list"); + memory->create(list, nsize, "FixPIMDLangevin:list"); pack_restart_data(list); if (comm->me == 0) { int size = nsize * sizeof(double); - fwrite(&size,sizeof(int),1,fp); - fwrite(list,sizeof(double),nsize,fp); + fwrite(&size, sizeof(int), 1, fp); + fwrite(list, sizeof(double), nsize, fp); } memory->destroy(list); @@ -1441,7 +1440,7 @@ int FixPIMDLangevin::size_restart_global() int FixPIMDLangevin::pack_restart_data(double *list) { int n = 0; - for (int i=0; i<6; i++) { list[n++] = vw[i]; } + for (int i = 0; i < 6; i++) list[n++] = vw[i]; return n; } @@ -1451,7 +1450,7 @@ void FixPIMDLangevin::restart(char *buf) { int n = 0; auto list = (double *) buf; - for (int i=0; i<6; i++) { vw[i] = list[n++]; } + for (int i = 0; i < 6; i++) vw[i] = list[n++]; } /* ---------------------------------------------------------------------- */ @@ -1470,7 +1469,7 @@ double FixPIMDLangevin::compute_vector(int n) if (n == 9) return p_cv; if (pstat_flag) { - volume = domain->xprd * domain->yprd * domain->zprd; + volume = domain->xprd * domain->yprd * domain->zprd; if (pstyle == ISO) { if (n == 10) return vw[0]; if (barostat == BZP) { @@ -1478,21 +1477,15 @@ double FixPIMDLangevin::compute_vector(int n) } else if (barostat == MTTK) { if (n == 11) return 1.5 * W * vw[0] * vw[0]; } - if (n == 12) { - return np * Pext * volume / force->nktv2p; - } - if (n == 13) { - return -Vcoeff * np * kBT * log(volume); - } + if (n == 12) { return np * Pext * volume / force->nktv2p; } + if (n == 13) { return -Vcoeff * np * kBT * log(volume); } if (n == 14) return totenthalpy; } else if (pstyle == ANISO) { if (n == 10) return vw[0]; if (n == 11) return vw[1]; if (n == 12) return vw[2]; if (n == 13) return 0.5 * W * (vw[0] * vw[0] + vw[1] * vw[1] + vw[2] * vw[2]); - if (n == 14) { - return np * Pext * volume / force->nktv2p; - } + if (n == 14) { return np * Pext * volume / force->nktv2p; } if (n == 15) { volume = domain->xprd * domain->yprd * domain->zprd; return -Vcoeff * np * kBT * log(volume);