diff --git a/src/USER-EFF/compute_temp_deform_eff.cpp b/src/USER-EFF/compute_temp_deform_eff.cpp index e05e4d131..ab6b51ea4 100644 --- a/src/USER-EFF/compute_temp_deform_eff.cpp +++ b/src/USER-EFF/compute_temp_deform_eff.cpp @@ -1,180 +1,178 @@ /* ---------------------------------------------------------------------- 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 "compute_temp_deform_eff.h" #include "update.h" #include "atom.h" #include "domain.h" #include "force.h" #include "modify.h" #include "group.h" #include "error.h" using namespace LAMMPS_NS; enum{NO_REMAP,X_REMAP,V_REMAP}; // same as fix_deform.cpp /* ---------------------------------------------------------------------- */ ComputeTempDeformEff::ComputeTempDeformEff(LAMMPS *lmp, int narg, char **arg) : ComputeTempDeform(lmp, narg, arg) { // error check if (!atom->spin_flag || !atom->ervel_flag) error->all("Compute temp/deform/eff requires atom attributes spin, ervel"); } /* ---------------------------------------------------------------------- */ void ComputeTempDeformEff::dof_compute() { double natoms = group->count(igroup); dof = domain->dimension * natoms; dof -= extra_dof + fix_dof; // just include nuclear dof int *spin = atom->spin; int *mask = atom->mask; int nlocal = atom->nlocal; int one = 0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { if (spin[i]) one++; } int nelectrons; MPI_Allreduce(&one,&nelectrons,1,MPI_INT,MPI_SUM,world); - // the -3 recovers an extra_dof taken out because it's used by eradius - - dof -= domain->dimension * nelectrons - 3; + dof -= domain->dimension * nelectrons; if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz); else tfactor = 0.0; } /* ---------------------------------------------------------------------- */ double ComputeTempDeformEff::compute_scalar() { double lamda[3],vstream[3],vthermal[3]; invoked_scalar = update->ntimestep; double **x = atom->x; double **v = atom->v; double *ervel = atom->ervel; double *mass = atom->mass; double *rmass = atom->rmass; int *spin = atom->spin; int *type = atom->type; int *mask = atom->mask; int nlocal = atom->nlocal; // lamda = 0-1 triclinic lamda coords // vstream = streaming velocity = Hrate*lamda + Hratelo // vthermal = thermal velocity = v - vstream double *h_rate = domain->h_rate; double *h_ratelo = domain->h_ratelo; double t = 0.0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { domain->x2lamda(x[i],lamda); vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] + h_rate[4]*lamda[2] + h_ratelo[0]; vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1]; vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2]; vthermal[0] = v[i][0] - vstream[0]; vthermal[1] = v[i][1] - vstream[1]; vthermal[2] = v[i][2] - vstream[2]; if (rmass) { t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] + vthermal[2]*vthermal[2]) * rmass[i]; if (spin[i]) t += 0.75*rmass[i]*ervel[i]*ervel[i]; } else { t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] + vthermal[2]*vthermal[2])* mass[type[i]]; if (spin[i]) t += 0.75*mass[type[i]]*ervel[i]*ervel[i]; } } MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world); if (dynamic) dof_compute(); scalar *= tfactor; return scalar; } /* ---------------------------------------------------------------------- */ void ComputeTempDeformEff::compute_vector() { double lamda[3],vstream[3],vthermal[3]; invoked_vector = update->ntimestep; double **x = atom->x; double **v = atom->v; double *ervel = atom->ervel; double *mass = atom->mass; double *rmass = atom->rmass; int *spin = atom->spin; int *type = atom->type; int *mask = atom->mask; int nlocal = atom->nlocal; double *h_rate = domain->h_rate; double *h_ratelo = domain->h_ratelo; double massone,t[6]; for (int i = 0; i < 6; i++) t[i] = 0.0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { domain->x2lamda(x[i],lamda); vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] + h_rate[4]*lamda[2] + h_ratelo[0]; vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1]; vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2]; vthermal[0] = v[i][0] - vstream[0]; vthermal[1] = v[i][1] - vstream[1]; vthermal[2] = v[i][2] - vstream[2]; if (rmass) massone = rmass[i]; else massone = mass[type[i]]; t[0] += massone * vthermal[0]*vthermal[0]; t[1] += massone * vthermal[1]*vthermal[1]; t[2] += massone * vthermal[2]*vthermal[2]; t[3] += massone * vthermal[0]*vthermal[1]; t[4] += massone * vthermal[0]*vthermal[2]; t[5] += massone * vthermal[1]*vthermal[2]; if (spin[i]) { t[0] += 0.75 * massone * ervel[i]*ervel[i]; t[1] += 0.75 * massone * ervel[i]*ervel[i]; t[2] += 0.75 * massone * ervel[i]*ervel[i]; } } MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world); for (int i = 0; i < 6; i++) vector[i] *= force->mvv2e; }