forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1685 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
parent
ed397f77ed
commit
8fc53cce58
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@ -11,6 +11,7 @@
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "mpi.h"
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#include "string.h"
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#include "stdlib.h"
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@ -21,14 +22,19 @@
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using namespace LAMMPS_NS;
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#define BIG 1.0e20
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// needs to be big, but not so big that lose precision when subtract velocity
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#define BIG 1.0e10
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#define MIN(A,B) ((A) < (B)) ? (A) : (B)
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#define MAX(A,B) ((A) > (B)) ? (A) : (B)
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/* ---------------------------------------------------------------------- */
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FixViscosity::FixViscosity(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg != 7) error->all("Illegal fix viscosity command");
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if (narg < 7) error->all("Illegal fix viscosity command");
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MPI_Comm_rank(world,&me);
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@ -52,11 +58,50 @@ FixViscosity::FixViscosity(LAMMPS *lmp, int narg, char **arg) :
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nbin = atoi(arg[6]);
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if (nbin < 3) error->all("Illegal fix viscosity command");
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// optional keywords
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nswap = 1;
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vtarget = BIG;
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int iarg = 7;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"swap") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix viscosity command");
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nswap = atoi(arg[iarg+1]);
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if (nswap <= 0) error->all("Fix viscosity swap value must be positive");
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iarg += 2;
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} else if (strcmp(arg[iarg],"vtarget") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix viscosity command");
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if (strcmp(arg[iarg+1],"INF") == 0) vtarget = BIG;
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else vtarget = atof(arg[iarg+1]);
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if (vtarget <= 0.0)
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error->all("Fix viscosity vtarget value must be positive");
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iarg += 2;
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} else error->all("Illegal fix viscosity command");
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}
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// initialize array sizes to nswap+1 so have space to shift values down
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pos_index = new int[nswap+1];
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neg_index = new int[nswap+1];
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pos_delta = new double[nswap+1];
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neg_delta = new double[nswap+1];
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flux = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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FixViscosity::~FixViscosity()
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{
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delete [] pos_index;
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delete [] neg_index;
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delete [] pos_delta;
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delete [] neg_delta;
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}
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/* ---------------------------------------------------------------------- */
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int FixViscosity::setmask()
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{
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int mask = 0;
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@ -92,8 +137,8 @@ void FixViscosity::init()
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void FixViscosity::end_of_step()
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{
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int i;
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double p,coord;
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int i,m,insert;
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double p,coord,delta;
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MPI_Status status;
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struct {
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double value;
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@ -113,8 +158,10 @@ void FixViscosity::end_of_step()
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slabhi_hi = boxlo + ((nbin-1)/2 + 1)*binsize;
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}
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// ipos,ineg = my 2 atoms with most pos/neg momenta in bottom/top slabs
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// map atom back into periodic box if necessary
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// make list of nswap atoms with velocity closest to +/- vtarget
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// only consider atoms in the bottom/middle slabs
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// map atoms back into periodic box if necessary
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// insert = location in list to insert new atom
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double **x = atom->x;
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double **v = atom->v;
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@ -124,78 +171,113 @@ void FixViscosity::end_of_step()
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int ipos = -1;
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int ineg = -1;
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double pmin = BIG;
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double pmax = -BIG;
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npositive = nnegative = 0;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (mass) p = mass[type[i]] * v[i][vdim];
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else p = rmass[i] * v[i][vdim];
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coord = x[i][pdim];
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if (coord < boxlo && periodicity) coord += prd;
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else if (coord >= boxhi && periodicity) coord -= prd;
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if (coord >= slablo_lo && coord < slablo_hi) {
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if (p > pmax) {
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pmax = p;
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ipos = i;
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if (v[i][vdim] < 0.0) continue;
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delta = fabs(v[i][vdim] - vtarget);
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if (npositive < nswap || delta < pos_delta[nswap-1]) {
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for (insert = npositive-1; insert >= 0; insert--)
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if (delta > pos_delta[insert]) break;
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insert++;
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for (m = npositive-1; m >= insert; m--) {
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pos_delta[m+1] = pos_delta[m];
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pos_index[m+1] = pos_index[m];
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}
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pos_delta[insert] = delta;
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pos_index[insert] = i;
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if (npositive < nswap) npositive++;
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}
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}
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if (coord >= slabhi_lo && coord < slabhi_hi) {
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if (p < pmin) {
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pmin = p;
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ineg = i;
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if (v[i][vdim] > 0.0) continue;
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delta = fabs(v[i][vdim] + vtarget);
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if (nnegative < nswap || delta < neg_delta[nswap-1]) {
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for (insert = nnegative-1; insert >= 0; insert--)
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if (delta > neg_delta[insert]) break;
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insert++;
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for (m = nnegative-1; m >= insert; m--) {
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neg_delta[m+1] = neg_delta[m];
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neg_index[m+1] = neg_index[m];
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}
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neg_delta[insert] = delta;
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neg_index[insert] = i;
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if (nnegative < nswap) nnegative++;
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}
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}
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}
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// find 2 global atoms with most pos/neg momenta in bottom/top slabs
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// MAXLOC also communicates which procs own them
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mine[0].value = pmax;
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mine[0].proc = me;
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mine[1].value = -pmin;
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mine[1].proc = me;
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MPI_Allreduce(mine,all,2,MPI_DOUBLE_INT,MPI_MAXLOC,world);
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// loop over nswap pairs
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// find 2 global atoms with smallest delta in bottom/top slabs
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// MINLOC also communicates which procs own them
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// exchange momenta between the 2 particles
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// if I own both particles just swap, else point2point comm of mass,vel
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// if I own both particles just swap, else point2point comm of vel,mass
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int ipos,ineg;
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double sbuf[2],rbuf[2];
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if (me == all[0].proc && me == all[1].proc) {
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sbuf[0] = v[ineg][vdim];
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if (mass) sbuf[1] = mass[type[ineg]];
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else sbuf[1] = rmass[ineg];
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rbuf[0] = v[ipos][vdim];
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if (mass) rbuf[1] = mass[type[ipos]];
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else rbuf[1] = rmass[ipos];
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v[ineg][vdim] = rbuf[0] * rbuf[1]/sbuf[1];
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v[ipos][vdim] = sbuf[0] * sbuf[1]/rbuf[1];
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double dflux = 0.0;
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mine[0].proc = mine[1].proc = me;
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int ipositive = 0;
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int inegative = 0;
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} else if (me == all[0].proc) {
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sbuf[0] = v[ipos][vdim];
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if (mass) sbuf[1] = mass[type[ipos]];
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else sbuf[1] = rmass[ipos];
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MPI_Sendrecv(sbuf,2,MPI_DOUBLE,all[1].proc,0,
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rbuf,2,MPI_DOUBLE,all[1].proc,0,world,&status);
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v[ipos][vdim] = rbuf[0] * rbuf[1]/sbuf[1];
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int nactual = MIN(nnegative,npositive);
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} else if (me == all[1].proc) {
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sbuf[0] = v[ineg][vdim];
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if (mass) sbuf[1] = mass[type[ineg]];
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else sbuf[1] = rmass[ineg];
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MPI_Sendrecv(sbuf,2,MPI_DOUBLE,all[0].proc,0,
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rbuf,2,MPI_DOUBLE,all[0].proc,0,world,&status);
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v[ineg][vdim] = rbuf[0] * rbuf[1]/sbuf[1];
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for (m = 0; m < nactual; m++) {
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if (ipositive < npositive) mine[0].value = pos_delta[ipositive];
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else mine[0].value = BIG;
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if (inegative < nnegative) mine[1].value = neg_delta[inegative];
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else mine[1].value = BIG;
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MPI_Allreduce(mine,all,2,MPI_DOUBLE_INT,MPI_MINLOC,world);
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if (me == all[0].proc && me == all[1].proc) {
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ipos = pos_index[ipositive++];
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ineg = neg_index[inegative++];
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rbuf[0] = v[ipos][vdim];
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if (mass) rbuf[1] = mass[type[ipos]];
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else rbuf[1] = rmass[ipos];
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sbuf[0] = v[ineg][vdim];
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if (mass) sbuf[1] = mass[type[ineg]];
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else sbuf[1] = rmass[ineg];
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v[ineg][vdim] = rbuf[0] * rbuf[1]/sbuf[1];
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v[ipos][vdim] = sbuf[0] * sbuf[1]/rbuf[1];
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dflux += rbuf[0]*rbuf[1] - sbuf[0]*sbuf[1];
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} else if (me == all[0].proc) {
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ipos = pos_index[ipositive++];
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sbuf[0] = v[ipos][vdim];
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if (mass) sbuf[1] = mass[type[ipos]];
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else sbuf[1] = rmass[ipos];
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MPI_Sendrecv(sbuf,2,MPI_DOUBLE,all[1].proc,0,
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rbuf,2,MPI_DOUBLE,all[1].proc,0,world,&status);
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v[ipos][vdim] = rbuf[0] * rbuf[1]/sbuf[1];
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dflux += sbuf[0]*sbuf[1];
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} else if (me == all[1].proc) {
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ineg = neg_index[inegative++];
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sbuf[0] = v[ineg][vdim];
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if (mass) sbuf[1] = mass[type[ineg]];
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else sbuf[1] = rmass[ineg];
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MPI_Sendrecv(sbuf,2,MPI_DOUBLE,all[0].proc,0,
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rbuf,2,MPI_DOUBLE,all[0].proc,0,world,&status);
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v[ineg][vdim] = rbuf[0] * rbuf[1]/sbuf[1];
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dflux -= sbuf[0]*sbuf[1];
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}
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}
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// tally momentum flux
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// sign of all[1].value was flipped for MPI_Allreduce
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// tally momentum flux from all swaps
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flux += all[0].value + all[1].value;
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double dflux_all;
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MPI_Allreduce(&dflux,&dflux_all,1,MPI_DOUBLE,MPI_SUM,world);
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flux += dflux_all;
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}
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/* ---------------------------------------------------------------------- */
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@ -21,7 +21,7 @@ namespace LAMMPS_NS {
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class FixViscosity : public Fix {
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public:
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FixViscosity(class LAMMPS *, int, char **);
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~FixViscosity() {}
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~FixViscosity();
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int setmask();
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void init();
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void end_of_step();
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@ -30,9 +30,15 @@ class FixViscosity : public Fix {
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private:
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int me;
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int vdim,pdim,nbin,periodicity;
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int nswap;
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double vtarget;
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double prd,boxlo,boxhi;
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double slablo_lo,slablo_hi,slabhi_lo,slabhi_hi;
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double flux;
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int npositive,nnegative;
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int *pos_index,*neg_index;
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double *pos_delta,*neg_delta;
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};
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}
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