Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/src/USER-SPH/pair_sph_lj.cpp
da77d5e62a9dlammm-devel

Last Change
Raw File

pair_sph_lj.cpp
View Options

/* ----------------------------------------------------------------------
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 "stdlib.h"
#include "pair_sph_lj.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "domain.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairSPHLJ::PairSPHLJ(LAMMPS *lmp) : Pair(lmp)
{
restartinfo = 0;
}
/* ---------------------------------------------------------------------- */
PairSPHLJ::~PairSPHLJ() {
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(viscosity);
}
}
/* ---------------------------------------------------------------------- */
void PairSPHLJ::compute(int eflag, int vflag) {
int i, j, ii, jj, inum, jnum, itype, jtype;
double xtmp, ytmp, ztmp, delx, dely, delz, fpair;
int *ilist, *jlist, *numneigh, **firstneigh;
double vxtmp, vytmp, vztmp, imass, jmass, fi, fj, fvisc, h, ih, ihsq, ihcub;
double rsq, wfd, delVdotDelR, mu, deltaE, ci, cj, lrc;
if (eflag || vflag)
ev_setup(eflag, vflag);
else
evflag = vflag_fdotr = 0;
double **v = atom->vest;
double **x = atom->x;
double **f = atom->f;
double *rho = atom->rho;
double *mass = atom->mass;
double *de = atom->de;
double *e = atom->e;
double *cv = atom->cv;
double *drho = atom->drho;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
vxtmp = v[i][0];
vytmp = v[i][1];
vztmp = v[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
imass = mass[itype];
// compute pressure of particle i with LJ EOS
LJEOS2(rho[i], e[i], cv[i], &fi, &ci);
fi /= (rho[i] * rho[i]);
//printf("fi = %f\n", fi);
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
jtype = type[j];
jmass = mass[jtype];
if (rsq < cutsq[itype][jtype]) {
h = cut[itype][jtype];
ih = 1.0 / h;
ihsq = ih * ih;
ihcub = ihsq * ih;
wfd = h - sqrt(rsq);
if (domain->dimension == 3) {
// Lucy Kernel, 3d
// Note that wfd, the derivative of the weight function with respect to r,
// is lacking a factor of r.
// The missing factor of r is recovered by
// (1) using delV . delX instead of delV . (delX/r) and
// (2) using f[i][0] += delx * fpair instead of f[i][0] += (delx/r) * fpair
wfd = -25.066903536973515383e0 * wfd * wfd * ihsq * ihsq * ihsq * ih;
} else {
// Lucy Kernel, 2d
wfd = -19.098593171027440292e0 * wfd * wfd * ihsq * ihsq * ihsq;
}
// function call to LJ EOS
LJEOS2(rho[j], e[j], cv[j], &fj, &cj);
fj /= (rho[j] * rho[j]);
// apply long-range correction to model a LJ fluid with cutoff
// this implies that the modelled LJ fluid has cutoff == SPH cutoff
lrc = - 11.1701 * (ihcub * ihcub * ihcub - 1.5 * ihcub);
fi += lrc;
fj += lrc;
// dot product of velocity delta and distance vector
delVdotDelR = delx * (vxtmp - v[j][0]) + dely * (vytmp - v[j][1])
+ delz * (vztmp - v[j][2]);
// artificial viscosity (Monaghan 1992)
if (delVdotDelR < 0.) {
mu = h * delVdotDelR / (rsq + 0.01 * h * h);
fvisc = -viscosity[itype][jtype] * (ci + cj) * mu / (rho[i] + rho[j]);
} else {
fvisc = 0.;
}
// total pair force & thermal energy increment
fpair = -imass * jmass * (fi + fj + fvisc) * wfd;
deltaE = -0.5 * fpair * delVdotDelR;
f[i][0] += delx * fpair;
f[i][1] += dely * fpair;
f[i][2] += delz * fpair;
// and change in density
drho[i] += jmass * delVdotDelR * wfd;
// change in thermal energy
de[i] += deltaE;
if (newton_pair || j < nlocal) {
f[j][0] -= delx * fpair;
f[j][1] -= dely * fpair;
f[j][2] -= delz * fpair;
de[j] += deltaE;
drho[j] += imass * delVdotDelR * wfd;
}
if (evflag)
ev_tally(i, j, nlocal, newton_pair, 0.0, 0.0, fpair, delx, dely, delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairSPHLJ::allocate() {
allocated = 1;
int n = atom->ntypes;
memory->create(setflag, n + 1, n + 1, "pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
memory->create(cut, n + 1, n + 1, "pair:cut");
memory->create(viscosity, n + 1, n + 1, "pair:viscosity");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairSPHLJ::settings(int narg, char **arg) {
if (narg != 0)
error->all(FLERR,
"Illegal number of setting arguments for pair_style sph/lj");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairSPHLJ::coeff(int narg, char **arg) {
if (narg != 4)
error->all(FLERR,
"Incorrect args for pair_style sph/lj coefficients");
if (!allocated)
allocate();
int ilo, ihi, jlo, jhi;
force->bounds(arg[0], atom->ntypes, ilo, ihi);
force->bounds(arg[1], atom->ntypes, jlo, jhi);
double viscosity_one = force->numeric(arg[2]);
double cut_one = force->numeric(arg[3]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
viscosity[i][j] = viscosity_one;
printf("setting cut[%d][%d] = %f\n", i, j, cut_one);
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0)
error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairSPHLJ::init_one(int i, int j) {
if (setflag[i][j] == 0) {
error->all(FLERR,"All pair sph/lj coeffs are not set");
}
cut[j][i] = cut[i][j];
viscosity[j][i] = viscosity[i][j];
return cut[i][j];
}
/* ---------------------------------------------------------------------- */
double PairSPHLJ::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj, double &fforce) {
fforce = 0.0;
return 0.0;
}
/*double PairSPHLJ::LJEOS2(double rho, double e, double cv) {
double T = e / cv;
if (T < 1.e-2) T = 1.e-2;
//printf("%f %f\n", T, rho);
double iT = 0.1e1 / T;
//double itpow1_4 = exp(0.25 * log(iT)); //pow(iT, 0.1e1 / 0.4e1);
double itpow1_4 = pow(iT, 0.1e1 / 0.4e1);
double x = rho * itpow1_4;
double xsq = x * x;
double xpow3 = xsq * x;
double xpow4 = xsq * xsq;
double xpow9 = xpow3 * xpow3 * xpow3;
return (0.1e1 + rho * (0.3629e1 + 0.7264e1 * x + 0.104925e2 * xsq + 0.11460e2
* xpow3 + 0.21760e1 * xpow9 - itpow1_4 * itpow1_4 * (0.5369e1 + 0.13160e2
* x + 0.18525e2 * xsq - 0.17076e2 * xpow3 + 0.9320e1 * xpow4) + iT
* (-0.3492e1 + 0.18698e2 * x - 0.35505e2 * xsq + 0.31816e2 * xpow3
- 0.11195e2 * xpow4)) * itpow1_4) * rho * T;
}*/
/* --------------------------------------------------------------------------------------------- */
/* Lennard-Jones EOS,
Francis H. Ree
"Analytic representation of thermodynamic data for the Lennard‐Jones fluid",
Journal of Chemical Physics 73 pp. 5401-5403 (1980)
*/
void PairSPHLJ::LJEOS2(double rho, double e, double cv, double *p, double *c) {
double T = e/cv;
double beta = 1.0 / T;
double beta_sqrt = sqrt(beta);
double x = rho * sqrt(beta_sqrt);
double xsq = x * x;
double xpow3 = xsq * x;
double xpow4 = xsq * xsq;
/* differential of Helmholtz free energy w.r.t. x */
double diff_A_NkT = 3.629 + 7.264*x - beta*(3.492 - 18.698*x + 35.505*xsq - 31.816*xpow3 + 11.195*xpow4)
- beta_sqrt*(5.369 + 13.16*x + 18.525*xsq - 17.076*xpow3 + 9.32*xpow4)
+ 10.4925*xsq + 11.46*xpow3 + 2.176*xpow4*xpow4*x;
/* differential of Helmholtz free energy w.r.t. x^2 */
double d2A_dx2 = 7.264 + 20.985*x \
+ beta*(18.698 - 71.01*x + 95.448*xsq - 44.78*xpow3)\
- beta_sqrt*(13.16 + 37.05*x - 51.228*xsq + 37.28*xpow3)\
+ 34.38*xsq + 19.584*xpow4*xpow4;
// p = rho k T * (1 + rho * d(A/(NkT))/drho)
// dx/drho = rho/x
*p = rho * T * (1.0 + diff_A_NkT * x); // pressure
double csq = T * (1.0 + 2.0 * diff_A_NkT * x + d2A_dx2 * x * x); // soundspeed squared
if (csq > 0.0) {
*c = sqrt(csq); // soundspeed
} else {
*c = 0.0;
}
}
/* ------------------------------------------------------------------------------ */
/* Jirí Kolafa, Ivo Nezbeda
* "The Lennard-Jones fluid: an accurate analytic and theoretically-based equation of state",
* Fluid Phase Equilibria 100 pp. 1-34 (1994) */
/*double PairSPHLJ::LJEOS2(double rho, double e, double cv) {
double T = e / cv;
double sT = sqrt(T);
double isT = 1.0 / sT;
double dC = -0.063920968 * log(T) + 0.011117524 / T - 0.076383859 / sT
+ 1.080142248 + 0.000693129 * sT;
double eta = 3.141592654 / 6. * rho * (dC * dC * dC);
double zHS = (1 + eta * (1 + eta * (1 - eta / 1.5 * (1 + eta))))
/ ((1. - eta) * (1. - eta) * (1. - eta));
double BC = (((((-0.58544978 * isT + 0.43102052) * isT + .87361369) * isT
- 4.13749995) * isT + 2.90616279) * isT - 7.02181962) / T + 0.02459877;
double gammaBH = 1.92907278;
double sum = ((2.01546797 * 2 + rho * ((-28.17881636) * 3 + rho
* (28.28313847 * 4 + rho * (-10.42402873) * 5))) + (-19.58371655 * 2
+ rho * (+75.62340289 * 3 + rho * ((-120.70586598) * 4 + rho
* (+93.92740328 * 5 + rho * (-27.37737354) * 6)))) / sqrt(T)
+ ((29.34470520 * 2 + rho * ((-112.35356937) * 3 + rho * (+170.64908980
* 4 + rho * ((-123.06669187) * 5 + rho * 34.42288969 * 6))))
+ ((-13.37031968) * 2 + rho * (65.38059570 * 3 + rho
* ((-115.09233113) * 4 + rho * (88.91973082 * 5 + rho
* (-25.62099890) * 6)))) / T) / T) * rho * rho;
return ((zHS + BC / exp(gammaBH * rho * rho) * rho * (1 - 2 * gammaBH * rho
* rho)) * T + sum) * rho;
}
*/
c4science · Help