diff --git a/src/fix_thermal_conductivity.cpp b/src/fix_thermal_conductivity.cpp
index 26d423f7c..8b46ff807 100644
--- a/src/fix_thermal_conductivity.cpp
+++ b/src/fix_thermal_conductivity.cpp
@@ -1,277 +1,277 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include "math.h"
#include "mpi.h"
#include "string.h"
#include "stdlib.h"
#include "fix_thermal_conductivity.h"
#include "atom.h"
#include "force.h"
#include "domain.h"
#include "error.h"
using namespace LAMMPS_NS;
#define BIG 1.0e10
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
FixThermalConductivity::FixThermalConductivity(LAMMPS *lmp,
int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 6) error->all("Illegal fix thermal/conductivity command");
MPI_Comm_rank(world,&me);
nevery = atoi(arg[3]);
if (nevery <= 0) error->all("Illegal fix thermal/conductivity command");
scalar_flag = 1;
scalar_vector_freq = nevery;
extscalar = 0;
if (strcmp(arg[4],"x") == 0) edim = 0;
else if (strcmp(arg[4],"y") == 0) edim = 1;
else if (strcmp(arg[4],"z") == 0) edim = 2;
else error->all("Illegal fix thermal/conductivity command");
nbin = atoi(arg[5]);
if (nbin < 3) error->all("Illegal fix thermal/conductivity command");
// optional keywords
nswap = 1;
int iarg = 6;
while (iarg < narg) {
if (strcmp(arg[iarg],"swap") == 0) {
if (iarg+2 > narg)
error->all("Illegal fix thermal/conductivity command");
nswap = atoi(arg[iarg+1]);
if (nswap <= 0)
error->all("Fix thermal/conductivity swap value must be positive");
iarg += 2;
} else error->all("Illegal fix thermal/conductivity command");
}
// initialize array sizes to nswap+1 so have space to shift values down
index_lo = new int[nswap+1];
index_hi = new int[nswap+1];
ke_lo = new double[nswap+1];
ke_hi = new double[nswap+1];
e_exchange = 0.0;
}
/* ---------------------------------------------------------------------- */
FixThermalConductivity::~FixThermalConductivity()
{
delete [] index_lo;
delete [] index_hi;
delete [] ke_lo;
delete [] ke_hi;
}
/* ---------------------------------------------------------------------- */
int FixThermalConductivity::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixThermalConductivity::init()
{
// set bounds of 2 slabs in edim
// only necessary for static box, else re-computed in end_of_step()
// lo bin is always bottom bin
- // if nbin even, hi bin is just below half height
+ // if nbin even, hi bin is just above half height
// if nbin odd, hi bin straddles half height
if (domain->box_change == 0) {
prd = domain->prd[edim];
boxlo = domain->boxlo[edim];
boxhi = domain->boxhi[edim];
double binsize = (boxhi-boxlo) / nbin;
slablo_lo = boxlo;
slablo_hi = boxlo + binsize;
- slabhi_lo = boxlo + ((nbin-1)/2)*binsize;
- slabhi_hi = boxlo + ((nbin-1)/2 + 1)*binsize;
+ slabhi_lo = boxlo + (nbin/2)*binsize;
+ slabhi_hi = boxlo + (nbin/2+1)*binsize;
}
periodicity = domain->periodicity[edim];
}
/* ---------------------------------------------------------------------- */
void FixThermalConductivity::end_of_step()
{
int i,j,m,insert;
double p,coord,ke;
MPI_Status status;
struct {
double value;
int proc;
} mine[2],all[2];
// if box changes, recompute bounds of 2 slabs in edim
if (domain->box_change) {
prd = domain->prd[edim];
boxlo = domain->boxlo[edim];
boxhi = domain->boxhi[edim];
double binsize = (boxhi-boxlo) / nbin;
slablo_lo = boxlo;
slablo_hi = boxlo + binsize;
- slabhi_lo = boxlo + ((nbin-1)/2)*binsize;
- slabhi_hi = boxlo + ((nbin-1)/2 + 1)*binsize;
+ slabhi_lo = boxlo + (nbin/2)*binsize;
+ slabhi_hi = boxlo + (nbin/2+1)*binsize;
}
// make 2 lists of up to nswap atoms
// hottest atoms in lo slab, coldest atoms in hi slab (really mid slab)
// lo slab list is sorted by hottest, hi slab is sorted by coldest
// map atoms back into periodic box if necessary
// insert = location in list to insert new atom
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
nhi = nlo = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
coord = x[i][edim];
if (coord < boxlo && periodicity) coord += prd;
else if (coord >= boxhi && periodicity) coord -= prd;
if (coord >= slablo_lo && coord < slablo_hi) {
ke = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (mass) ke *= 0.5*mass[type[i]];
else ke *= 0.5*rmass[i];
if (nlo < nswap || ke > ke_lo[nswap-1]) {
for (insert = nlo-1; insert >= 0; insert--)
if (ke < ke_lo[insert]) break;
insert++;
for (m = nlo-1; m >= insert; m--) {
ke_lo[m+1] = ke_lo[m];
index_lo[m+1] = index_lo[m];
}
ke_lo[insert] = ke;
index_lo[insert] = i;
if (nlo < nswap) nlo++;
}
}
if (coord >= slabhi_lo && coord < slabhi_hi) {
ke = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (mass) ke *= 0.5*mass[type[i]];
else ke *= 0.5*rmass[i];
if (nhi < nswap || ke < ke_hi[nswap-1]) {
for (insert = nhi-1; insert >= 0; insert--)
if (ke > ke_hi[insert]) break;
insert++;
for (m = nhi-1; m >= insert; m--) {
ke_hi[m+1] = ke_hi[m];
index_hi[m+1] = index_hi[m];
}
ke_hi[insert] = ke;
index_hi[insert] = i;
if (nhi < nswap) nhi++;
}
}
}
// loop over nswap pairs
// pair 2 global atoms at beginning of sorted lo/hi slab lists via Allreduce
// BIG values are for procs with no atom to contribute
// use negative of hottest KE since is doing a MINLOC
// MINLOC also communicates which procs own them
// exchange kinetic energy between the 2 particles
// if I own both particles just swap, else point2point comm of velocities
double sbuf[3],rbuf[3];
mine[0].proc = mine[1].proc = me;
int ilo = 0;
int ihi = 0;
for (m = 0; m < nswap; m++) {
if (ilo < nlo) mine[0].value = -ke_lo[ilo];
else mine[0].value = BIG;
if (ihi < nhi) mine[1].value = ke_hi[ihi];
else mine[1].value = BIG;
MPI_Allreduce(mine,all,2,MPI_DOUBLE_INT,MPI_MINLOC,world);
if (all[0].value == BIG || all[1].value == BIG) continue;
all[0].value = -all[0].value;
e_exchange += force->mvv2e * (all[0].value - all[1].value);
if (me == all[0].proc && me == all[1].proc) {
i = index_lo[ilo++];
j = index_hi[ihi++];
rbuf[0] = v[i][0];
rbuf[1] = v[i][1];
rbuf[2] = v[i][2];
v[i][0] = v[j][0];
v[i][1] = v[j][1];
v[i][2] = v[j][2];
v[j][0] = rbuf[0];
v[j][1] = rbuf[1];
v[j][2] = rbuf[2];
} else if (me == all[0].proc) {
i = index_lo[ilo++];
sbuf[0] = v[i][0];
sbuf[1] = v[i][1];
sbuf[2] = v[i][2];
MPI_Sendrecv(sbuf,3,MPI_DOUBLE,all[1].proc,0,
rbuf,3,MPI_DOUBLE,all[1].proc,0,world,&status);
v[i][0] = rbuf[0];
v[i][1] = rbuf[1];
v[i][2] = rbuf[2];
} else if (me == all[1].proc) {
j = index_hi[ihi++];
sbuf[0] = v[j][0];
sbuf[1] = v[j][1];
sbuf[2] = v[j][2];
MPI_Sendrecv(sbuf,3,MPI_DOUBLE,all[0].proc,0,
rbuf,3,MPI_DOUBLE,all[0].proc,0,world,&status);
v[j][0] = rbuf[0];
v[j][1] = rbuf[1];
v[j][2] = rbuf[2];
}
}
}
/* ---------------------------------------------------------------------- */
double FixThermalConductivity::compute_scalar()
{
return e_exchange;
}
diff --git a/src/fix_viscosity.cpp b/src/fix_viscosity.cpp
index 3b6274630..cd29ac85f 100644
--- a/src/fix_viscosity.cpp
+++ b/src/fix_viscosity.cpp
@@ -1,290 +1,290 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include "math.h"
#include "mpi.h"
#include "string.h"
#include "stdlib.h"
#include "fix_viscosity.h"
#include "atom.h"
#include "domain.h"
#include "error.h"
using namespace LAMMPS_NS;
// needs to be big, but not so big that lose precision when subtract velocity
#define BIG 1.0e10
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
FixViscosity::FixViscosity(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 7) error->all("Illegal fix viscosity command");
MPI_Comm_rank(world,&me);
nevery = atoi(arg[3]);
if (nevery <= 0) error->all("Illegal fix viscosity command");
scalar_flag = 1;
scalar_vector_freq = nevery;
extscalar = 0;
if (strcmp(arg[4],"x") == 0) vdim = 0;
else if (strcmp(arg[4],"y") == 0) vdim = 1;
else if (strcmp(arg[4],"z") == 0) vdim = 2;
else error->all("Illegal fix viscosity command");
if (strcmp(arg[5],"x") == 0) pdim = 0;
else if (strcmp(arg[5],"y") == 0) pdim = 1;
else if (strcmp(arg[5],"z") == 0) pdim = 2;
else error->all("Illegal fix viscosity command");
nbin = atoi(arg[6]);
if (nbin < 3) error->all("Illegal fix viscosity command");
// optional keywords
nswap = 1;
vtarget = BIG;
int iarg = 7;
while (iarg < narg) {
if (strcmp(arg[iarg],"swap") == 0) {
if (iarg+2 > narg) error->all("Illegal fix viscosity command");
nswap = atoi(arg[iarg+1]);
if (nswap <= 0) error->all("Fix viscosity swap value must be positive");
iarg += 2;
} else if (strcmp(arg[iarg],"vtarget") == 0) {
if (iarg+2 > narg) error->all("Illegal fix viscosity command");
if (strcmp(arg[iarg+1],"INF") == 0) vtarget = BIG;
else vtarget = atof(arg[iarg+1]);
if (vtarget <= 0.0)
error->all("Fix viscosity vtarget value must be positive");
iarg += 2;
} else error->all("Illegal fix viscosity command");
}
// initialize array sizes to nswap+1 so have space to shift values down
pos_index = new int[nswap+1];
neg_index = new int[nswap+1];
pos_delta = new double[nswap+1];
neg_delta = new double[nswap+1];
p_exchange = 0.0;
}
/* ---------------------------------------------------------------------- */
FixViscosity::~FixViscosity()
{
delete [] pos_index;
delete [] neg_index;
delete [] pos_delta;
delete [] neg_delta;
}
/* ---------------------------------------------------------------------- */
int FixViscosity::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixViscosity::init()
{
// set bounds of 2 slabs in pdim
// only necessary for static box, else re-computed in end_of_step()
// lo bin is always bottom bin
- // if nbin even, hi bin is just below half height
+ // if nbin even, hi bin is just above half height
// if nbin odd, hi bin straddles half height
if (domain->box_change == 0) {
prd = domain->prd[pdim];
boxlo = domain->boxlo[pdim];
boxhi = domain->boxhi[pdim];
double binsize = (boxhi-boxlo) / nbin;
slablo_lo = boxlo;
slablo_hi = boxlo + binsize;
- slabhi_lo = boxlo + ((nbin-1)/2)*binsize;
- slabhi_hi = boxlo + ((nbin-1)/2 + 1)*binsize;
+ slabhi_lo = boxlo + (nbin/2)*binsize;
+ slabhi_hi = boxlo + (nbin/2+1)*binsize;
}
periodicity = domain->periodicity[pdim];
}
/* ---------------------------------------------------------------------- */
void FixViscosity::end_of_step()
{
int i,m,insert;
double coord,delta;
MPI_Status status;
struct {
double value;
int proc;
} mine[2],all[2];
// if box changes, recompute bounds of 2 slabs in pdim
if (domain->box_change) {
prd = domain->prd[pdim];
boxlo = domain->boxlo[pdim];
boxhi = domain->boxhi[pdim];
double binsize = (boxhi-boxlo) / nbin;
slablo_lo = boxlo;
slablo_hi = boxlo + binsize;
- slabhi_lo = boxlo + ((nbin-1)/2)*binsize;
- slabhi_hi = boxlo + ((nbin-1)/2 + 1)*binsize;
+ slabhi_lo = boxlo + (nbin/2)*binsize;
+ slabhi_hi = boxlo + (nbin/2+1)*binsize;
}
// make 2 lists of up to nswap atoms with velocity closest to +/- vtarget
// lists are sorted by closeness to vtarget
// only consider atoms in the bottom/middle slabs
// map atoms back into periodic box if necessary
// insert = location in list to insert new atom
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
npositive = nnegative = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
coord = x[i][pdim];
if (coord < boxlo && periodicity) coord += prd;
else if (coord >= boxhi && periodicity) coord -= prd;
if (coord >= slablo_lo && coord < slablo_hi) {
if (v[i][vdim] < 0.0) continue;
delta = fabs(v[i][vdim] - vtarget);
if (npositive < nswap || delta < pos_delta[nswap-1]) {
for (insert = npositive-1; insert >= 0; insert--)
if (delta > pos_delta[insert]) break;
insert++;
for (m = npositive-1; m >= insert; m--) {
pos_delta[m+1] = pos_delta[m];
pos_index[m+1] = pos_index[m];
}
pos_delta[insert] = delta;
pos_index[insert] = i;
if (npositive < nswap) npositive++;
}
}
if (coord >= slabhi_lo && coord < slabhi_hi) {
if (v[i][vdim] > 0.0) continue;
delta = fabs(v[i][vdim] + vtarget);
if (nnegative < nswap || delta < neg_delta[nswap-1]) {
for (insert = nnegative-1; insert >= 0; insert--)
if (delta > neg_delta[insert]) break;
insert++;
for (m = nnegative-1; m >= insert; m--) {
neg_delta[m+1] = neg_delta[m];
neg_index[m+1] = neg_index[m];
}
neg_delta[insert] = delta;
neg_index[insert] = i;
if (nnegative < nswap) nnegative++;
}
}
}
// loop over nswap pairs
// find 2 global atoms with smallest delta in bottom/top slabs
// BIG values are for procs with no atom to contribute
// MINLOC also communicates which procs own them
// exchange momenta between the 2 particles
// if I own both particles just swap, else point2point comm of vel,mass
int ipos,ineg;
double sbuf[2],rbuf[2];
double pswap = 0.0;
mine[0].proc = mine[1].proc = me;
int ipositive = 0;
int inegative = 0;
for (m = 0; m < nswap; m++) {
if (ipositive < npositive) mine[0].value = pos_delta[ipositive];
else mine[0].value = BIG;
if (inegative < nnegative) mine[1].value = neg_delta[inegative];
else mine[1].value = BIG;
MPI_Allreduce(mine,all,2,MPI_DOUBLE_INT,MPI_MINLOC,world);
if (all[0].value == BIG || all[1].value == BIG) continue;
if (me == all[0].proc && me == all[1].proc) {
ipos = pos_index[ipositive++];
ineg = neg_index[inegative++];
rbuf[0] = v[ipos][vdim];
if (mass) rbuf[1] = mass[type[ipos]];
else rbuf[1] = rmass[ipos];
sbuf[0] = v[ineg][vdim];
if (mass) sbuf[1] = mass[type[ineg]];
else sbuf[1] = rmass[ineg];
v[ineg][vdim] = rbuf[0] * rbuf[1]/sbuf[1];
v[ipos][vdim] = sbuf[0] * sbuf[1]/rbuf[1];
pswap += rbuf[0]*rbuf[1] - sbuf[0]*sbuf[1];
} else if (me == all[0].proc) {
ipos = pos_index[ipositive++];
sbuf[0] = v[ipos][vdim];
if (mass) sbuf[1] = mass[type[ipos]];
else sbuf[1] = rmass[ipos];
MPI_Sendrecv(sbuf,2,MPI_DOUBLE,all[1].proc,0,
rbuf,2,MPI_DOUBLE,all[1].proc,0,world,&status);
v[ipos][vdim] = rbuf[0] * rbuf[1]/sbuf[1];
pswap += sbuf[0]*sbuf[1];
} else if (me == all[1].proc) {
ineg = neg_index[inegative++];
sbuf[0] = v[ineg][vdim];
if (mass) sbuf[1] = mass[type[ineg]];
else sbuf[1] = rmass[ineg];
MPI_Sendrecv(sbuf,2,MPI_DOUBLE,all[0].proc,0,
rbuf,2,MPI_DOUBLE,all[0].proc,0,world,&status);
v[ineg][vdim] = rbuf[0] * rbuf[1]/sbuf[1];
pswap -= sbuf[0]*sbuf[1];
}
}
// tally momentum exchange from all swaps
double pswap_all;
MPI_Allreduce(&pswap,&pswap_all,1,MPI_DOUBLE,MPI_SUM,world);
p_exchange += pswap_all;
}
/* ---------------------------------------------------------------------- */
double FixViscosity::compute_scalar()
{
return p_exchange;
}