From 584b16682360d088f50ede69cbe38843d082ebe2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 2 Apr 2022 17:20:34 -0400 Subject: [PATCH] enable and apply clang-format --- src/EXTRA-COMPUTE/compute_msd_nongauss.cpp | 42 +++++----- src/compute_msd.cpp | 95 +++++++++++----------- 2 files changed, 69 insertions(+), 68 deletions(-) diff --git a/src/EXTRA-COMPUTE/compute_msd_nongauss.cpp b/src/EXTRA-COMPUTE/compute_msd_nongauss.cpp index 99c5cee715..0f68e03ca7 100644 --- a/src/EXTRA-COMPUTE/compute_msd_nongauss.cpp +++ b/src/EXTRA-COMPUTE/compute_msd_nongauss.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -19,17 +18,17 @@ #include "compute_msd_nongauss.h" #include "atom.h" -#include "update.h" -#include "group.h" #include "domain.h" #include "fix_store.h" +#include "group.h" +#include "update.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeMSDNonGauss::ComputeMSDNonGauss(LAMMPS *lmp, int narg, char **arg) : - ComputeMSD(lmp, narg, arg) + ComputeMSD(lmp, narg, arg) { size_vector = 3; } @@ -43,8 +42,10 @@ void ComputeMSDNonGauss::compute_vector() // cm = current center of mass double cm[3]; - if (comflag) group->xcm(igroup,masstotal,cm); - else cm[0] = cm[1] = cm[2] = 0.0; + if (comflag) + group->xcm(igroup, masstotal, cm); + else + cm[0] = cm[1] = cm[2] = 0.0; // dx,dy,dz = displacement of atom from original position // original unwrapped position is stored by fix @@ -63,8 +64,8 @@ void ComputeMSDNonGauss::compute_vector() double yprd = domain->yprd; double zprd = domain->zprd; - double dx,dy,dz; - int xbox,ybox,zbox; + double dx, dy, dz; + int xbox, ybox, zbox; double msd[2]; msd[0] = msd[1] = 0.0; @@ -75,11 +76,11 @@ void ComputeMSDNonGauss::compute_vector() xbox = (image[i] & IMGMASK) - IMGMAX; ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[i] >> IMG2BITS) - IMGMAX; - dx = x[i][0] + xbox*xprd - cm[0] - xoriginal[i][0]; - dy = x[i][1] + ybox*yprd - cm[1] - xoriginal[i][1]; - dz = x[i][2] + zbox*zprd - cm[2] - xoriginal[i][2]; - msd[0] += dx*dx + dy*dy + dz*dz; - msd[1] += (dx*dx + dy*dy + dz*dz)*(dx*dx + dy*dy + dz*dz); + dx = x[i][0] + xbox * xprd - cm[0] - xoriginal[i][0]; + dy = x[i][1] + ybox * yprd - cm[1] - xoriginal[i][1]; + dz = x[i][2] + zbox * zprd - cm[2] - xoriginal[i][2]; + msd[0] += dx * dx + dy * dy + dz * dz; + msd[1] += (dx * dx + dy * dy + dz * dz) * (dx * dx + dy * dy + dz * dz); } } else { @@ -88,19 +89,18 @@ void ComputeMSDNonGauss::compute_vector() xbox = (image[i] & IMGMASK) - IMGMAX; ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[i] >> IMG2BITS) - IMGMAX; - dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - - cm[0] - xoriginal[i][0]; - dy = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1] - xoriginal[i][1]; - dz = x[i][2] + h[2]*zbox - cm[2] - xoriginal[i][2]; - msd[0] += dx*dx + dy*dy + dz*dz; - msd[1] += (dx*dx + dy*dy + dz*dz)*(dx*dx + dy*dy + dz*dz); + dx = x[i][0] + h[0] * xbox + h[5] * ybox + h[4] * zbox - cm[0] - xoriginal[i][0]; + dy = x[i][1] + h[1] * ybox + h[3] * zbox - cm[1] - xoriginal[i][1]; + dz = x[i][2] + h[2] * zbox - cm[2] - xoriginal[i][2]; + msd[0] += dx * dx + dy * dy + dz * dz; + msd[1] += (dx * dx + dy * dy + dz * dz) * (dx * dx + dy * dy + dz * dz); } } - MPI_Allreduce(msd,vector,2,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(msd, vector, 2, MPI_DOUBLE, MPI_SUM, world); if (nmsd) { vector[0] /= nmsd; vector[1] /= nmsd; - vector[2] = (3*vector[1])/(5*vector[0]*vector[0]) - 1; + vector[2] = (3 * vector[1]) / (5 * vector[0] * vector[0]) - 1; } } diff --git a/src/compute_msd.cpp b/src/compute_msd.cpp index 8370e9f833..bff9dffd87 100644 --- a/src/compute_msd.cpp +++ b/src/compute_msd.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -28,11 +27,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg), - id_fix(nullptr) +ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), id_fix(nullptr) { - if (narg < 3) error->all(FLERR,"Illegal compute msd command"); + if (narg < 3) error->all(FLERR, "Illegal compute msd command"); vector_flag = 1; size_vector = 4; @@ -47,15 +44,16 @@ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) : int iarg = 3; while (iarg < narg) { - if (strcmp(arg[iarg],"com") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal compute msd command"); - comflag = utils::logical(FLERR,arg[iarg+1],false,lmp); + if (strcmp(arg[iarg], "com") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute msd command"); + comflag = utils::logical(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else if (strcmp(arg[iarg],"average") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal compute msd command"); - avflag = utils::logical(FLERR,arg[iarg+1],false,lmp); + } else if (strcmp(arg[iarg], "average") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal compute msd command"); + avflag = utils::logical(FLERR, arg[iarg + 1], false, lmp); iarg += 2; - } else error->all(FLERR,"Illegal compute msd command"); + } else + error->all(FLERR, "Illegal compute msd command"); } if (group->dynamic[igroup]) @@ -65,13 +63,14 @@ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) : // id = compute-ID + COMPUTE_STORE, fix group = compute group id_fix = utils::strdup(id + std::string("_COMPUTE_STORE")); - fix = (FixStore *) modify->add_fix(fmt::format("{} {} STORE peratom 1 3", - id_fix, group->names[igroup])); + fix = (FixStore *) modify->add_fix( + fmt::format("{} {} STORE peratom 1 3", id_fix, group->names[igroup])); // calculate xu,yu,zu for fix store array // skip if reset from restart file - if (fix->restart_reset) fix->restart_reset = 0; + if (fix->restart_reset) + fix->restart_reset = 0; else { double **xoriginal = fix->astore; @@ -81,15 +80,17 @@ ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) : int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit) domain->unmap(x[i],image[i],xoriginal[i]); - else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0; + if (mask[i] & groupbit) + domain->unmap(x[i], image[i], xoriginal[i]); + else + xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0; // adjust for COM if requested if (comflag) { double cm[3]; masstotal = group->mass(igroup); - group->xcm(igroup,masstotal,cm); + group->xcm(igroup, masstotal, cm); for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { xoriginal[i][0] -= cm[0]; @@ -127,7 +128,7 @@ void ComputeMSD::init() // set fix which stores reference atom coords fix = (FixStore *) modify->get_fix_by_id(id_fix); - if (!fix) error->all(FLERR,"Could not find compute msd fix with ID {}", id_fix); + if (!fix) error->all(FLERR, "Could not find compute msd fix with ID {}", id_fix); // nmsd = # of atoms in group @@ -144,8 +145,10 @@ void ComputeMSD::compute_vector() // cm = current center of mass double cm[3]; - if (comflag) group->xcm(igroup,masstotal,cm); - else cm[0] = cm[1] = cm[2] = 0.0; + if (comflag) + group->xcm(igroup, masstotal, cm); + else + cm[0] = cm[1] = cm[2] = 0.0; // dx,dy,dz = displacement of atom from reference position // reference unwrapped position is stored by fix @@ -164,8 +167,8 @@ void ComputeMSD::compute_vector() double yprd = domain->yprd; double zprd = domain->zprd; - double dx,dy,dz; - int xbox,ybox,zbox; + double dx, dy, dz; + int xbox, ybox, zbox; double msd[4]; msd[0] = msd[1] = msd[2] = msd[3] = 0.0; @@ -177,36 +180,34 @@ void ComputeMSD::compute_vector() double navfac; if (avflag) { naverage++; - navfac = 1.0/(naverage+1); + navfac = 1.0 / (naverage + 1); } - if (domain->triclinic == 0) { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { xbox = (image[i] & IMGMASK) - IMGMAX; ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[i] >> IMG2BITS) - IMGMAX; - xtmp = x[i][0] + xbox*xprd - cm[0]; - ytmp = x[i][1] + ybox*yprd - cm[1]; - ztmp = x[i][2] + zbox*zprd - cm[2]; + xtmp = x[i][0] + xbox * xprd - cm[0]; + ytmp = x[i][1] + ybox * yprd - cm[1]; + ztmp = x[i][2] + zbox * zprd - cm[2]; // use running average position for reference if requested if (avflag) { - xoriginal[i][0] = (xoriginal[i][0]*naverage + xtmp)*navfac; - xoriginal[i][1] = (xoriginal[i][1]*naverage + ytmp)*navfac; - xoriginal[i][2] = (xoriginal[i][2]*naverage + ztmp)*navfac; + xoriginal[i][0] = (xoriginal[i][0] * naverage + xtmp) * navfac; + xoriginal[i][1] = (xoriginal[i][1] * naverage + ytmp) * navfac; + xoriginal[i][2] = (xoriginal[i][2] * naverage + ztmp) * navfac; } dx = xtmp - xoriginal[i][0]; dy = ytmp - xoriginal[i][1]; dz = ztmp - xoriginal[i][2]; - msd[0] += dx*dx; - msd[1] += dy*dy; - msd[2] += dz*dz; - msd[3] += dx*dx + dy*dy + dz*dz; - + msd[0] += dx * dx; + msd[1] += dy * dy; + msd[2] += dz * dz; + msd[3] += dx * dx + dy * dy + dz * dz; } } else { for (int i = 0; i < nlocal; i++) @@ -214,29 +215,29 @@ void ComputeMSD::compute_vector() xbox = (image[i] & IMGMASK) - IMGMAX; ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[i] >> IMG2BITS) - IMGMAX; - xtmp = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - cm[0]; - ytmp = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1]; - ztmp = x[i][2] + h[2]*zbox - cm[2]; + xtmp = x[i][0] + h[0] * xbox + h[5] * ybox + h[4] * zbox - cm[0]; + ytmp = x[i][1] + h[1] * ybox + h[3] * zbox - cm[1]; + ztmp = x[i][2] + h[2] * zbox - cm[2]; // use running average position for reference if requested if (avflag) { - xoriginal[i][0] = (xoriginal[i][0]*naverage + xtmp)*navfac; - xoriginal[i][1] = (xoriginal[i][0]*naverage + xtmp)*navfac; - xoriginal[i][2] = (xoriginal[i][0]*naverage + xtmp)*navfac; + xoriginal[i][0] = (xoriginal[i][0] * naverage + xtmp) * navfac; + xoriginal[i][1] = (xoriginal[i][0] * naverage + xtmp) * navfac; + xoriginal[i][2] = (xoriginal[i][0] * naverage + xtmp) * navfac; } dx = xtmp - xoriginal[i][0]; dy = ytmp - xoriginal[i][1]; dz = ztmp - xoriginal[i][2]; - msd[0] += dx*dx; - msd[1] += dy*dy; - msd[2] += dz*dz; - msd[3] += dx*dx + dy*dy + dz*dz; + msd[0] += dx * dx; + msd[1] += dy * dy; + msd[2] += dz * dz; + msd[3] += dx * dx + dy * dy + dz * dz; } } - MPI_Allreduce(msd,vector,4,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(msd, vector, 4, MPI_DOUBLE, MPI_SUM, world); if (nmsd) { vector[0] /= nmsd; vector[1] /= nmsd;