forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1793 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
653c8b5c62
commit
d2b7cad48c
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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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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#include "fix_thermal_conductivity.h"
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#include "atom.h"
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#include "force.h"
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#include "domain.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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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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FixThermalConductivity::FixThermalConductivity(LAMMPS *lmp,
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int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg < 6) error->all("Illegal fix thermal/conductivity command");
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MPI_Comm_rank(world,&me);
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nevery = atoi(arg[3]);
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if (nevery <= 0) error->all("Illegal fix thermal/conductivity command");
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scalar_flag = 1;
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scalar_vector_freq = nevery;
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extscalar = 0;
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if (strcmp(arg[4],"x") == 0) edim = 0;
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else if (strcmp(arg[4],"y") == 0) edim = 1;
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else if (strcmp(arg[4],"z") == 0) edim = 2;
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else error->all("Illegal fix thermal/conductivity command");
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nbin = atoi(arg[5]);
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if (nbin < 3) error->all("Illegal fix thermal/conductivity command");
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// optional keywords
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nswap = 1;
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int iarg = 6;
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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)
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error->all("Illegal fix thermal/conductivity command");
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nswap = atoi(arg[iarg+1]);
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if (nswap <= 0)
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error->all("Fix thermal/conductivity swap value must be positive");
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iarg += 2;
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} else error->all("Illegal fix thermal/conductivity 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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index_lo = new int[nswap+1];
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index_hi = new int[nswap+1];
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ke_lo = new double[nswap+1];
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ke_hi = new double[nswap+1];
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e_exchange = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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FixThermalConductivity::~FixThermalConductivity()
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{
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delete [] index_lo;
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delete [] index_hi;
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delete [] ke_lo;
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delete [] ke_hi;
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}
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/* ---------------------------------------------------------------------- */
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int FixThermalConductivity::setmask()
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{
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int mask = 0;
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mask |= END_OF_STEP;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixThermalConductivity::init()
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{
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// set bounds of 2 slabs in edim
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// only necessary for static box, else re-computed in end_of_step()
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// lo bin is always bottom bin
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// if nbin even, hi bin is just below half height
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// if nbin odd, hi bin straddles half height
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if (domain->box_change == 0) {
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prd = domain->prd[edim];
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boxlo = domain->boxlo[edim];
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boxhi = domain->boxhi[edim];
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double binsize = (boxhi-boxlo) / nbin;
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slablo_lo = boxlo;
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slablo_hi = boxlo + binsize;
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slabhi_lo = boxlo + ((nbin-1)/2)*binsize;
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slabhi_hi = boxlo + ((nbin-1)/2 + 1)*binsize;
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}
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periodicity = domain->periodicity[edim];
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}
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/* ---------------------------------------------------------------------- */
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void FixThermalConductivity::end_of_step()
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{
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int i,j,m,insert;
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double p,coord,ke;
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MPI_Status status;
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struct {
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double value;
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int proc;
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} mine[2],all[2];
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// if box changes, recompute bounds of 2 slabs in edim
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if (domain->box_change) {
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prd = domain->prd[edim];
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boxlo = domain->boxlo[edim];
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boxhi = domain->boxhi[edim];
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double binsize = (boxhi-boxlo) / nbin;
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slablo_lo = boxlo;
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slablo_hi = boxlo + binsize;
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slabhi_lo = boxlo + ((nbin-1)/2)*binsize;
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slabhi_hi = boxlo + ((nbin-1)/2 + 1)*binsize;
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}
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// make 2 lists of up to nswap atoms
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// hottest atoms in lo slab, coldest atoms in hi slab (really mid slab)
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// lo slab list is sorted by hottest, hi slab is sorted by coldest
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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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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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nhi = nlo = 0;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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coord = x[i][edim];
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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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ke = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
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if (mass) ke *= 0.5*mass[type[i]];
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else ke *= 0.5*rmass[i];
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if (nlo < nswap || ke > ke_lo[nswap-1]) {
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for (insert = nlo-1; insert >= 0; insert--)
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if (ke < ke_lo[insert]) break;
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insert++;
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for (m = nlo-1; m >= insert; m--) {
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ke_lo[m+1] = ke_lo[m];
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index_lo[m+1] = index_lo[m];
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}
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ke_lo[insert] = ke;
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index_lo[insert] = i;
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if (nlo < nswap) nlo++;
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}
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}
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if (coord >= slabhi_lo && coord < slabhi_hi) {
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ke = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
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if (mass) ke *= 0.5*mass[type[i]];
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else ke *= 0.5*rmass[i];
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if (nhi < nswap || ke < ke_hi[nswap-1]) {
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for (insert = nhi-1; insert >= 0; insert--)
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if (ke > ke_hi[insert]) break;
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insert++;
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for (m = nhi-1; m >= insert; m--) {
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ke_hi[m+1] = ke_hi[m];
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index_hi[m+1] = index_hi[m];
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}
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ke_hi[insert] = ke;
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index_hi[insert] = i;
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if (nhi < nswap) nhi++;
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}
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}
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}
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// loop over nswap pairs
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// pair 2 global atoms at beginning of sorted lo/hi slab lists via Allreduce
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// BIG values are for procs with no atom to contribute
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// use negative of hottest KE since is doing a MINLOC
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// MINLOC also communicates which procs own them
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// exchange kinetic energy between the 2 particles
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// if I own both particles just swap, else point2point comm of velocities
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double sbuf[3],rbuf[3];
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mine[0].proc = mine[1].proc = me;
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int ilo = 0;
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int ihi = 0;
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for (m = 0; m < nswap; m++) {
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if (ilo < nlo) mine[0].value = -ke_lo[ilo];
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else mine[0].value = BIG;
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if (ihi < nhi) mine[1].value = ke_hi[ihi];
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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 (all[0].value == BIG || all[1].value == BIG) continue;
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all[0].value = -all[0].value;
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e_exchange += force->mvv2e * (all[0].value - all[1].value);
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if (me == all[0].proc && me == all[1].proc) {
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i = index_lo[ilo++];
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j = index_hi[ihi++];
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rbuf[0] = v[i][0];
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rbuf[1] = v[i][1];
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rbuf[2] = v[i][2];
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v[i][0] = v[j][0];
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v[i][1] = v[j][1];
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v[i][2] = v[j][2];
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v[j][0] = rbuf[0];
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v[j][1] = rbuf[1];
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v[j][2] = rbuf[2];
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} else if (me == all[0].proc) {
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i = index_lo[ilo++];
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sbuf[0] = v[i][0];
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sbuf[1] = v[i][1];
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sbuf[2] = v[i][2];
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MPI_Sendrecv(sbuf,3,MPI_DOUBLE,all[1].proc,0,
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rbuf,3,MPI_DOUBLE,all[1].proc,0,world,&status);
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v[i][0] = rbuf[0];
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v[i][1] = rbuf[1];
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v[i][2] = rbuf[2];
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} else if (me == all[1].proc) {
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j = index_hi[ihi++];
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sbuf[0] = v[j][0];
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sbuf[1] = v[j][1];
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sbuf[2] = v[j][2];
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MPI_Sendrecv(sbuf,3,MPI_DOUBLE,all[0].proc,0,
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rbuf,3,MPI_DOUBLE,all[0].proc,0,world,&status);
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v[j][0] = rbuf[0];
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v[j][1] = rbuf[1];
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v[j][2] = rbuf[2];
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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double FixThermalConductivity::compute_scalar()
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{
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return e_exchange;
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}
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@ -0,0 +1,45 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifndef FIX_THERMAL_CONDUCTIVITY_H
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#define FIX_THERMAL_CONDUCTIVITY_H
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#include "fix.h"
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namespace LAMMPS_NS {
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class FixThermalConductivity : public Fix {
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public:
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FixThermalConductivity(class LAMMPS *, int, char **);
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~FixThermalConductivity();
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int setmask();
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void init();
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void end_of_step();
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double compute_scalar();
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private:
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int me;
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int edim,nbin,periodicity;
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int nswap;
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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 e_exchange;
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int nlo,nhi;
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int *index_lo,*index_hi;
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double *ke_lo,*ke_hi;
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};
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}
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#endif
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@ -87,7 +87,7 @@ FixViscosity::FixViscosity(LAMMPS *lmp, int narg, char **arg) :
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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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p_exchange = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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@ -225,7 +225,7 @@ void FixViscosity::end_of_step()
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int ipos,ineg;
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double sbuf[2],rbuf[2];
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double dflux = 0.0;
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double pswap = 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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@ -251,7 +251,7 @@ void FixViscosity::end_of_step()
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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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pswap += 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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@ -261,7 +261,7 @@ void FixViscosity::end_of_step()
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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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pswap += 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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@ -271,20 +271,20 @@ void FixViscosity::end_of_step()
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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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pswap -= sbuf[0]*sbuf[1];
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}
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}
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// tally momentum flux from all swaps
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// tally momentum exchange from all swaps
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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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double pswap_all;
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MPI_Allreduce(&pswap,&pswap_all,1,MPI_DOUBLE,MPI_SUM,world);
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p_exchange += pswap_all;
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}
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/* ---------------------------------------------------------------------- */
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double FixViscosity::compute_scalar()
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{
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return flux;
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return p_exchange;
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}
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@ -34,7 +34,7 @@ class FixViscosity : public Fix {
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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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double p_exchange;
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int npositive,nnegative;
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int *pos_index,*neg_index;
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@ -188,6 +188,7 @@ DumpStyle(xyz,DumpXYZ)
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#include "fix_spring_self.h"
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#include "fix_temp_berendsen.h"
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#include "fix_temp_rescale.h"
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#include "fix_thermal_conductivity.h"
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#include "fix_tmd.h"
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#include "fix_viscosity.h"
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#include "fix_viscous.h"
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@ -246,6 +247,7 @@ FixStyle(spring/rg,FixSpringRG)
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FixStyle(spring/self,FixSpringSelf)
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FixStyle(temp/berendsen,FixTempBerendsen)
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FixStyle(temp/rescale,FixTempRescale)
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FixStyle(thermal/conductivity,FixThermalConductivity)
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FixStyle(tmd,FixTMD)
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FixStyle(viscosity,FixViscosity)
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FixStyle(viscous,FixViscous)
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