diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp index f3db5dea9..029b76cb2 100644 --- a/src/ASPHERE/compute_temp_asphere.cpp +++ b/src/ASPHERE/compute_temp_asphere.cpp @@ -1,401 +1,402 @@ /* ---------------------------------------------------------------------- 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: Mike Brown (SNL) ------------------------------------------------------------------------- */ #include #include #include "compute_temp_asphere.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_ellipsoid.h" #include "update.h" #include "force.h" #include "domain.h" #include "modify.h" #include "group.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; enum{ROTATE,ALL}; #define INERTIA 0.2 // moment of inertia prefactor for ellipsoid /* ---------------------------------------------------------------------- */ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), + id_bias(NULL), tbias(NULL), avec(NULL) { if (narg < 3) error->all(FLERR,"Illegal compute temp/asphere command"); scalar_flag = vector_flag = 1; size_vector = 6; extscalar = 0; extvector = 1; tempflag = 1; tempbias = 0; id_bias = NULL; mode = ALL; int iarg = 3; while (iarg < narg) { if (strcmp(arg[iarg],"bias") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/asphere command"); tempbias = 1; int n = strlen(arg[iarg+1]) + 1; id_bias = new char[n]; strcpy(id_bias,arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"dof") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal compute temp/asphere command"); if (strcmp(arg[iarg+1],"rotate") == 0) mode = ROTATE; else if (strcmp(arg[iarg+1],"all") == 0) mode = ALL; else error->all(FLERR,"Illegal compute temp/asphere command"); iarg += 2; } else error->all(FLERR,"Illegal compute temp/asphere command"); } vector = new double[6]; } /* ---------------------------------------------------------------------- */ ComputeTempAsphere::~ComputeTempAsphere() { delete [] id_bias; delete [] vector; } /* ---------------------------------------------------------------------- */ void ComputeTempAsphere::init() { // error check avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid"); if (!avec) error->all(FLERR,"Compute temp/asphere requires atom style ellipsoid"); // check that all particles are finite-size, no point particles allowed int *ellipsoid = atom->ellipsoid; int *mask = atom->mask; int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) if (ellipsoid[i] < 0) error->one(FLERR,"Compute temp/asphere requires extended particles"); if (tempbias) { int i = modify->find_compute(id_bias); if (i < 0) error->all(FLERR,"Could not find compute ID for temperature bias"); tbias = modify->compute[i]; if (tbias->tempflag == 0) error->all(FLERR,"Bias compute does not calculate temperature"); if (tbias->tempbias == 0) error->all(FLERR,"Bias compute does not calculate a velocity bias"); if (tbias->igroup != igroup) error->all(FLERR,"Bias compute group does not match compute group"); if (strcmp(tbias->style,"temp/region") == 0) tempbias = 2; else tempbias = 1; // init and setup bias compute because // this compute's setup()->dof_compute() may be called first tbias->init(); tbias->setup(); } } /* ---------------------------------------------------------------------- */ void ComputeTempAsphere::setup() { dynamic = 0; if (dynamic_user || group->dynamic[igroup]) dynamic = 1; dof_compute(); } /* ---------------------------------------------------------------------- */ void ComputeTempAsphere::dof_compute() { adjust_dof_fix(); // 6 dof for 3d, 3 dof for 2d // which dof are included also depends on mode // assume full rotation of extended particles // user should correct this via compute_modify if needed natoms_temp = group->count(igroup); int nper; if (domain->dimension == 3) { if (mode == ALL) nper = 6; else nper = 3; } else { if (mode == ALL) nper = 3; else nper = 1; } dof = nper*natoms_temp; // additional adjustments to dof if (tempbias == 1) { if (mode == ALL) dof -= tbias->dof_remove(-1) * natoms_temp; } else if (tempbias == 2) { int *mask = atom->mask; int nlocal = atom->nlocal; tbias->dof_remove_pre(); int count = 0; for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) if (tbias->dof_remove(i)) count++; int count_all; MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world); dof -= nper*count_all; } dof -= extra_dof + fix_dof; if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz); else tfactor = 0.0; } /* ---------------------------------------------------------------------- */ double ComputeTempAsphere::compute_scalar() { invoked_scalar = update->ntimestep; if (tempbias) { if (tbias->invoked_scalar != update->ntimestep) tbias->compute_scalar(); tbias->remove_bias_all(); } AtomVecEllipsoid::Bonus *bonus = avec->bonus; double **v = atom->v; double **angmom = atom->angmom; double *rmass = atom->rmass; int *ellipsoid = atom->ellipsoid; int *mask = atom->mask; int nlocal = atom->nlocal; double *shape,*quat; double wbody[3],inertia[3]; double rot[3][3]; // sum translational and rotational energy for each particle // no point particles since divide by inertia double t = 0.0; if (mode == ALL) { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i]; // principal moments of inertia shape = bonus[ellipsoid[i]].shape; quat = bonus[ellipsoid[i]].quat; inertia[0] = INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]); inertia[1] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]); inertia[2] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]); // wbody = angular velocity in body frame MathExtra::quat_to_mat(quat,rot); MathExtra::transpose_matvec(rot,angmom[i],wbody); wbody[0] /= inertia[0]; wbody[1] /= inertia[1]; wbody[2] /= inertia[2]; t += inertia[0]*wbody[0]*wbody[0] + inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2]; } } else { for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { // principal moments of inertia shape = bonus[ellipsoid[i]].shape; quat = bonus[ellipsoid[i]].quat; inertia[0] = INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]); inertia[1] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]); inertia[2] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]); // wbody = angular velocity in body frame MathExtra::quat_to_mat(quat,rot); MathExtra::transpose_matvec(rot,angmom[i],wbody); wbody[0] /= inertia[0]; wbody[1] /= inertia[1]; wbody[2] /= inertia[2]; t += inertia[0]*wbody[0]*wbody[0] + inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2]; } } if (tempbias) tbias->restore_bias_all(); MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world); if (dynamic || tempbias == 2) dof_compute(); if (dof < 0.0 && natoms_temp > 0.0) error->all(FLERR,"Temperature compute degrees of freedom < 0"); scalar *= tfactor; return scalar; } /* ---------------------------------------------------------------------- */ void ComputeTempAsphere::compute_vector() { int i; invoked_vector = update->ntimestep; if (tempbias) { if (tbias->invoked_vector != update->ntimestep) tbias->compute_vector(); tbias->remove_bias_all(); } AtomVecEllipsoid::Bonus *bonus = avec->bonus; double **v = atom->v; double **angmom = atom->angmom; double *rmass = atom->rmass; int *ellipsoid = atom->ellipsoid; int *mask = atom->mask; int nlocal = atom->nlocal; double *shape,*quat; double wbody[3],inertia[3],t[6]; double rot[3][3]; double massone; // sum translational and rotational energy for each particle // no point particles since divide by inertia for (i = 0; i < 6; i++) t[i] = 0.0; if (mode == ALL) { for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) { massone = rmass[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]; // principal moments of inertia shape = bonus[ellipsoid[i]].shape; quat = bonus[ellipsoid[i]].quat; inertia[0] = INERTIA*massone * (shape[1]*shape[1]+shape[2]*shape[2]); inertia[1] = INERTIA*massone * (shape[0]*shape[0]+shape[2]*shape[2]); inertia[2] = INERTIA*massone * (shape[0]*shape[0]+shape[1]*shape[1]); // wbody = angular velocity in body frame MathExtra::quat_to_mat(quat,rot); MathExtra::transpose_matvec(rot,angmom[i],wbody); wbody[0] /= inertia[0]; wbody[1] /= inertia[1]; wbody[2] /= inertia[2]; // rotational kinetic energy t[0] += inertia[0]*wbody[0]*wbody[0]; t[1] += inertia[1]*wbody[1]*wbody[1]; t[2] += inertia[2]*wbody[2]*wbody[2]; t[3] += inertia[0]*wbody[0]*wbody[1]; t[4] += inertia[1]*wbody[0]*wbody[2]; t[5] += inertia[2]*wbody[1]*wbody[2]; } } else { for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) { // principal moments of inertia shape = bonus[ellipsoid[i]].shape; quat = bonus[ellipsoid[i]].quat; massone = rmass[i]; inertia[0] = INERTIA*massone * (shape[1]*shape[1]+shape[2]*shape[2]); inertia[1] = INERTIA*massone * (shape[0]*shape[0]+shape[2]*shape[2]); inertia[2] = INERTIA*massone * (shape[0]*shape[0]+shape[1]*shape[1]); // wbody = angular velocity in body frame MathExtra::quat_to_mat(quat,rot); MathExtra::transpose_matvec(rot,angmom[i],wbody); wbody[0] /= inertia[0]; wbody[1] /= inertia[1]; wbody[2] /= inertia[2]; // rotational kinetic energy t[0] += inertia[0]*wbody[0]*wbody[0]; t[1] += inertia[1]*wbody[1]*wbody[1]; t[2] += inertia[2]*wbody[2]*wbody[2]; t[3] += inertia[0]*wbody[0]*wbody[1]; t[4] += inertia[1]*wbody[0]*wbody[2]; t[5] += inertia[2]*wbody[1]*wbody[2]; } } if (tempbias) tbias->restore_bias_all(); 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 ------------------------------------------------------------------------- */ void ComputeTempAsphere::remove_bias(int i, double *v) { if (tbias) tbias->remove_bias(i,v); } /* ---------------------------------------------------------------------- add back in velocity bias to atom I removed by remove_bias() assume remove_bias() was previously called ------------------------------------------------------------------------- */ void ComputeTempAsphere::restore_bias(int i, double *v) { if (tbias) tbias->restore_bias(i,v); }