diff --git a/src/USER-EFF/compute_temp_region_eff.cpp b/src/USER-EFF/compute_temp_region_eff.cpp index 0f9a85935..d0ee66e1b 100644 --- a/src/USER-EFF/compute_temp_region_eff.cpp +++ b/src/USER-EFF/compute_temp_region_eff.cpp @@ -1,285 +1,292 @@ /* ---------------------------------------------------------------------- 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: Andres Jaramillo-Botero (Caltech) ------------------------------------------------------------------------- */ #include "mpi.h" #include "math.h" #include "string.h" #include "compute_temp_region_eff.h" #include "atom.h" #include "update.h" #include "force.h" #include "modify.h" #include "domain.h" #include "region.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputeTempRegionEff::ComputeTempRegionEff(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg) { if (!atom->electron_flag) error->all(FLERR,"Compute temp/region/eff requires atom style electron"); if (narg != 4) error->all(FLERR,"Illegal compute temp/region/eff command"); iregion = domain->find_region(arg[3]); if (iregion == -1) error->all(FLERR,"Region ID for compute temp/region/eff does not exist"); int n = strlen(arg[3]) + 1; idregion = new char[n]; strcpy(idregion,arg[3]); scalar_flag = vector_flag = 1; size_vector = 6; extscalar = 0; extvector = 1; tempflag = 1; tempbias = 1; maxbias = 0; vbiasall = NULL; vector = new double[6]; } /* ---------------------------------------------------------------------- */ ComputeTempRegionEff::~ComputeTempRegionEff() { delete [] idregion; memory->destroy(vbiasall); delete [] vector; } /* ---------------------------------------------------------------------- */ void ComputeTempRegionEff::init() { // set index and check validity of region iregion = domain->find_region(idregion); if (iregion == -1) error->all(FLERR,"Region ID for compute temp/region/eff does not exist"); } /* ---------------------------------------------------------------------- */ void ComputeTempRegionEff::setup() { dof = 0.0; } /* ---------------------------------------------------------------------- */ +void ComputeTempRegionEff::dof_remove_pre() +{ + domain->regions[iregion]->prematch(); +} + +/* ---------------------------------------------------------------------- */ + int ComputeTempRegionEff::dof_remove(int i) { double *x = atom->x[i]; if (domain->regions[iregion]->match(x[0],x[1],x[2])) return 0; return 1; } /* ---------------------------------------------------------------------- */ double ComputeTempRegionEff::compute_scalar() { invoked_scalar = update->ntimestep; double **x = atom->x; double **v = atom->v; double *ervel = atom->ervel; double *mass = atom->mass; int *spin = atom->spin; int *type = atom->type; int *mask = atom->mask; int nlocal = atom->nlocal; double mefactor = domain->dimension/4.0; Region *region = domain->regions[iregion]; region->prematch(); int count = 0; int ecount = 0; double t = 0.0; if (mass) { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) { count++; t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * mass[type[i]]; if (fabs(spin[i])==1) { t += mefactor*mass[type[i]]*ervel[i]*ervel[i]; ecount++; } } } double tarray[2],tarray_all[2]; // Assume 3/2 k T per nucleus tarray[0] = count-ecount; tarray[1] = t; MPI_Allreduce(tarray,tarray_all,2,MPI_DOUBLE,MPI_SUM,world); dof = domain->dimension * tarray_all[0] - extra_dof; int one = 0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) { if (fabs(spin[i])==1) one++; } if (dof > 0) scalar = force->mvv2e * tarray_all[1] / (dof * force->boltz); else scalar = 0.0; return scalar; } /* ---------------------------------------------------------------------- */ void ComputeTempRegionEff::compute_vector() { int i; invoked_vector = update->ntimestep; double **x = atom->x; double **v = atom->v; double *ervel = atom->ervel; double *mass = atom->mass; int *spin = atom->spin; int *type = atom->type; int *mask = atom->mask; int nlocal = atom->nlocal; double mefactor = domain->dimension/4.0; Region *region = domain->regions[iregion]; region->prematch(); double massone,t[6]; for (i = 0; i < 6; i++) t[i] = 0.0; for (i = 0; i < nlocal; i++) if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) { massone = mass[type[i]]; t[0] += massone * v[i][0]*v[i][0]; t[1] += massone * v[i][1]*v[i][1]; t[2] += massone * v[i][2]*v[i][2]; t[3] += massone * v[i][0]*v[i][1]; t[4] += massone * v[i][0]*v[i][2]; t[5] += massone * v[i][1]*v[i][2]; if (fabs(spin[i])==1) { t[0] += mefactor * massone * ervel[i]*ervel[i]; t[1] += mefactor * massone * ervel[i]*ervel[i]; t[2] += mefactor * massone * ervel[i]*ervel[i]; } } MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world); for (i = 0; i < 6; i++) vector[i] *= force->mvv2e; } /* ---------------------------------------------------------------------- remove velocity bias from atom I to leave thermal velocity NOTE: the following commands do not bias the radial electron velocities ------------------------------------------------------------------------- */ void ComputeTempRegionEff::remove_bias(int i, double *v) { double *x = atom->x[i]; if (domain->regions[iregion]->match(x[0],x[1],x[2])) vbias[0] = vbias[1] = vbias[2] = 0.0; else { vbias[0] = v[0]; vbias[1] = v[1]; vbias[2] = v[2]; v[0] = v[1] = v[2] = 0.0; } } /* ---------------------------------------------------------------------- remove velocity bias from all atoms to leave thermal velocity ------------------------------------------------------------------------- */ void ComputeTempRegionEff::remove_bias_all() { double **x = atom->x; double **v = atom->v; int *mask = atom->mask; int nlocal = atom->nlocal; if (nlocal > maxbias) { memory->destroy(vbiasall); maxbias = atom->nmax; memory->create(vbiasall,maxbias,3,"temp/region:vbiasall"); } Region *region = domain->regions[iregion]; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { if (region->match(x[i][0],x[i][1],x[i][2])) vbiasall[i][0] = vbiasall[i][1] = vbiasall[i][2] = 0.0; else { vbiasall[i][0] = v[i][0]; vbiasall[i][1] = v[i][1]; vbiasall[i][2] = v[i][2]; v[i][0] = v[i][1] = v[i][2] = 0.0; } } } /* ---------------------------------------------------------------------- add back in velocity bias to atom I removed by remove_bias() assume remove_bias() was previously called ------------------------------------------------------------------------- */ void ComputeTempRegionEff::restore_bias(int i, double *v) { v[0] += vbias[0]; v[1] += vbias[1]; v[2] += vbias[2]; } /* ---------------------------------------------------------------------- add back in velocity bias to all atoms removed by remove_bias_all() assume remove_bias_all() was previously called ------------------------------------------------------------------------- */ void ComputeTempRegionEff::restore_bias_all() { double **v = atom->v; int *mask = atom->mask; int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { v[i][0] += vbiasall[i][0]; v[i][1] += vbiasall[i][1]; v[i][2] += vbiasall[i][2]; } } /* ---------------------------------------------------------------------- */ double ComputeTempRegionEff::memory_usage() { double bytes = maxbias * sizeof(double); return bytes; } diff --git a/src/USER-EFF/compute_temp_region_eff.h b/src/USER-EFF/compute_temp_region_eff.h index 60a5e3474..b5c5ee379 100644 --- a/src/USER-EFF/compute_temp_region_eff.h +++ b/src/USER-EFF/compute_temp_region_eff.h @@ -1,51 +1,52 @@ /* ---------------------------------------------------------------------- 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. ------------------------------------------------------------------------- */ #ifdef COMPUTE_CLASS ComputeStyle(temp/region/eff,ComputeTempRegionEff) #else #ifndef LMP_COMPUTE_TEMP_REGION_EFF_H #define LMP_COMPUTE_TEMP_REGION_EFF_H #include "compute.h" namespace LAMMPS_NS { class ComputeTempRegionEff : public Compute { public: ComputeTempRegionEff(class LAMMPS *, int, char **); virtual ~ComputeTempRegionEff(); void init(); void setup(); virtual double compute_scalar(); virtual void compute_vector(); + void dof_remove_pre(void); int dof_remove(int); void remove_bias(int, double *); void remove_bias_all(); void restore_bias(int, double *); void restore_bias_all(); double memory_usage(); protected: int iregion; char *idregion; }; } #endif #endif