Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F81268221
pair_sph_lj.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Thu, Sep 5, 01:50
Size
11 KB
Mime Type
text/x-c
Expires
Sat, Sep 7, 01:50 (2 d)
Engine
blob
Format
Raw Data
Handle
20539993
Attached To
rLAMMPS lammps
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(FLERR,arg[2]);
double cut_one = force->numeric(FLERR,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;
}
*/
Event Timeline
Log In to Comment