diff --git a/src/fix_heat.cpp b/src/fix_heat.cpp index 97e0ed6a7..846531dbb 100644 --- a/src/fix_heat.cpp +++ b/src/fix_heat.cpp @@ -1,344 +1,344 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- Contributing author: Paul Crozier (SNL) ------------------------------------------------------------------------- */ #include #include #include #include "fix_heat.h" #include "atom.h" #include "domain.h" #include "region.h" #include "group.h" #include "force.h" #include "update.h" #include "modify.h" #include "input.h" #include "variable.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; using namespace FixConst; enum{CONSTANT,EQUAL,ATOM}; /* ---------------------------------------------------------------------- */ FixHeat::FixHeat(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), idregion(NULL), hstr(NULL), vheat(NULL), vscale(NULL) { if (narg < 4) error->all(FLERR,"Illegal fix heat command"); scalar_flag = 1; global_freq = 1; extscalar = 0; nevery = force->inumeric(FLERR,arg[3]); if (nevery <= 0) error->all(FLERR,"Illegal fix heat command"); hstr = NULL; if (strstr(arg[4],"v_") == arg[4]) { int n = strlen(&arg[4][2]) + 1; hstr = new char[n]; strcpy(hstr,&arg[4][2]); } else { heat_input = force->numeric(FLERR,arg[4]); hstyle = CONSTANT; } // optional args iregion = -1; int iarg = 5; while (iarg < narg) { if (strcmp(arg[iarg],"region") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix heat command"); iregion = domain->find_region(arg[iarg+1]); if (iregion == -1) error->all(FLERR,"Region ID for fix heat does not exist"); int n = strlen(arg[iarg+1]) + 1; idregion = new char[n]; strcpy(idregion,arg[iarg+1]); iarg += 2; } else error->all(FLERR,"Illegal fix heat command"); } scale = 1.0; maxatom = 0; } /* ---------------------------------------------------------------------- */ FixHeat::~FixHeat() { delete [] hstr; delete [] idregion; memory->destroy(vheat); memory->destroy(vscale); } /* ---------------------------------------------------------------------- */ int FixHeat::setmask() { int mask = 0; mask |= END_OF_STEP; return mask; } /* ---------------------------------------------------------------------- */ void FixHeat::init() { // set index and check validity of region if (iregion >= 0) { iregion = domain->find_region(idregion); if (iregion == -1) error->all(FLERR,"Region ID for fix heat does not exist"); } // check variable if (hstr) { hvar = input->variable->find(hstr); if (hvar < 0) error->all(FLERR,"Variable name for fix heat does not exist"); if (input->variable->equalstyle(hvar)) hstyle = EQUAL; else if (input->variable->atomstyle(hvar)) hstyle = ATOM; else error->all(FLERR,"Variable for fix heat is invalid style"); } // check for rigid bodies in region (done here for performance reasons) - if (modify->check_rigid_region_overlap(groupbit,domain->regions[iregion])) + if (iregion >= 0 && modify->check_rigid_region_overlap(groupbit,domain->regions[iregion])) error->warning(FLERR,"Cannot apply fix heat to atoms in rigid bodies"); // cannot have 0 atoms in group if (group->count(igroup) == 0) error->all(FLERR,"Fix heat group has no atoms"); masstotal = group->mass(igroup); if (masstotal <= 0.0) error->all(FLERR,"Fix heat group has invalid mass"); } /* ---------------------------------------------------------------------- */ void FixHeat::end_of_step() { int i; double heat,ke,massone; double vsub[3],vcm[3]; double **x = atom->x; double **v = atom->v; int *mask = atom->mask; int nlocal = atom->nlocal; int *type = atom->type; double *mass = atom->mass; double *rmass = atom->rmass; // reallocate per-atom arrays if necessary if (hstyle == ATOM && atom->nmax > maxatom) { maxatom = atom->nmax; memory->destroy(vheat); memory->destroy(vscale); memory->create(vheat,maxatom,"heat:vheat"); memory->create(vscale,maxatom,"heat:vscale"); } // evaluate variable if (hstyle != CONSTANT) { modify->clearstep_compute(); if (hstyle == EQUAL) heat_input = input->variable->compute_equal(hvar); else input->variable->compute_atom(hvar,igroup,vheat,1,0); modify->addstep_compute(update->ntimestep + nevery); } // vcm = center-of-mass velocity of scaled atoms if (iregion < 0) { ke = group->ke(igroup)*force->ftm2v; group->vcm(igroup,masstotal,vcm); } else { masstotal = group->mass(igroup,iregion); if (masstotal == 0.0) error->all(FLERR,"Fix heat group has no atoms"); ke = group->ke(igroup,iregion)*force->ftm2v; group->vcm(igroup,masstotal,vcm,iregion); } double vcmsq = vcm[0]*vcm[0] + vcm[1]*vcm[1] + vcm[2]*vcm[2]; // add heat via scale factor on velocities for CONSTANT and EQUAL cases // scale = velocity scale factor to accomplish eflux change in energy // vsub = velocity subtracted from each atom to preserve momentum // overall KE cannot go negative Region *region = NULL; if (iregion >= 0) { region = domain->regions[iregion]; region->prematch(); } if (hstyle != ATOM) { heat = heat_input*nevery*update->dt*force->ftm2v; double escale = (ke + heat - 0.5*vcmsq*masstotal)/(ke - 0.5*vcmsq*masstotal); if (escale < 0.0) error->all(FLERR,"Fix heat kinetic energy went negative"); scale = sqrt(escale); vsub[0] = (scale-1.0) * vcm[0]; vsub[1] = (scale-1.0) * vcm[1]; vsub[2] = (scale-1.0) * vcm[2]; if (iregion < 0) { for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) { v[i][0] = scale*v[i][0] - vsub[0]; v[i][1] = scale*v[i][1] - vsub[1]; v[i][2] = scale*v[i][2] - vsub[2]; } } else { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) { v[i][0] = scale*v[i][0] - vsub[0]; v[i][1] = scale*v[i][1] - vsub[1]; v[i][2] = scale*v[i][2] - vsub[2]; } } // add heat via per-atom scale factor on velocities for ATOM case // vscale = velocity scale factor to accomplish eflux change in energy // vsub = velocity subtracted from each atom to preserve momentum // KE of an atom cannot go negative } else { vsub[0] = vsub[1] = vsub[2] = 0.0; if (iregion < 0) { for (i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { heat = vheat[i]*nevery*update->dt*force->ftm2v; vscale[i] = (ke + heat - 0.5*vcmsq*masstotal)/(ke - 0.5*vcmsq*masstotal); if (vscale[i] < 0.0) error->all(FLERR, "Fix heat kinetic energy of an atom went negative"); scale = sqrt(vscale[i]); if (rmass) massone = rmass[i]; else massone = mass[type[i]]; vsub[0] += (scale-1.0) * v[i][0]*massone; vsub[1] += (scale-1.0) * v[i][1]*massone; vsub[2] += (scale-1.0) * v[i][2]*massone; } } vsub[0] /= masstotal; vsub[1] /= masstotal; vsub[2] /= masstotal; for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) { scale = sqrt(vscale[i]); v[i][0] = scale*v[i][0] - vsub[0]; v[i][1] = scale*v[i][1] - vsub[1]; v[i][2] = scale*v[i][2] - vsub[2]; } } else { for (i = 0; i < nlocal; i++) { if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) { heat = vheat[i]*nevery*update->dt*force->ftm2v; vscale[i] = (ke + heat - 0.5*vcmsq*masstotal)/(ke - 0.5*vcmsq*masstotal); if (vscale[i] < 0.0) error->all(FLERR, "Fix heat kinetic energy of an atom went negative"); scale = sqrt(vscale[i]); if (rmass) massone = rmass[i]; else massone = mass[type[i]]; vsub[0] += (scale-1.0) * v[i][0]*massone; vsub[1] += (scale-1.0) * v[i][1]*massone; vsub[2] += (scale-1.0) * v[i][2]*massone; } } vsub[0] /= masstotal; vsub[1] /= masstotal; vsub[2] /= masstotal; for (i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) { scale = sqrt(vscale[i]); v[i][0] = scale*v[i][0] - vsub[0]; v[i][1] = scale*v[i][1] - vsub[1]; v[i][2] = scale*v[i][2] - vsub[2]; } } } } /* ---------------------------------------------------------------------- */ double FixHeat::compute_scalar() { double average_scale = scale; if (hstyle == ATOM) { double scale_sum = 0.0; int ncount = 0; int *mask = atom->mask; double **x = atom->x; int nlocal = atom->nlocal; if (iregion < 0) { for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { scale_sum += sqrt(vscale[i]); ncount++; } } } else { Region *region = domain->regions[iregion]; region->prematch(); for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) { scale_sum += sqrt(vscale[i]); ncount++; } } } double scale_sum_all = 0.0; int ncount_all = 0; MPI_Allreduce(&scale_sum,&scale_sum_all,1,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(&ncount,&ncount_all,1,MPI_INT,MPI_SUM,world); if (ncount_all == 0) average_scale = 0.0; else average_scale = scale_sum_all/static_cast(ncount_all); } return average_scale; } /* ---------------------------------------------------------------------- memory usage of local atom-based arrays ------------------------------------------------------------------------- */ double FixHeat::memory_usage() { double bytes = 0.0; if (hstyle == ATOM) bytes = atom->nmax*2 * sizeof(double); return bytes; }