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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://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 "fix_pi.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixPI::FixPI(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg) {
if ((atom->esph_flag != 1) || (atom->rho_flag != 1))
error->all(FLERR,
"Fix sph command requires atom_style with both energy and density");
// Accept optional Oldroyd-B parameters:
// fix ID group pi (Newtonian, default)
// fix ID group pi tau (Oldroyd-B with G_p=1)
// fix ID group pi tau Gp (Oldroyd-B with explicit G_p)
if (narg < 3 || narg > 5)
error->all(FLERR,"Illegal number of arguments for fix pi (expected 3..5)");
tau_p = -1.0; // <0 -> polymer evolution OFF
Gp = 1.0;
if (narg >= 4) tau_p = utils::numeric(FLERR, arg[3], false, lmp);
if (narg == 5) Gp = utils::numeric(FLERR, arg[4], false, lmp);
if (tau_p > 0.0 && Gp < 0.0)
error->all(FLERR,"fix pi: polymer modulus Gp must be non-negative");
time_integrate = 1;
}
/* ---------------------------------------------------------------------- */
int FixPI::setmask() {
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= PRE_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixPI::init() {
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
}
void FixPI::setup_pre_force(int /*vflag*/)
{
// set vest equal to v
double **v = atom->v;
double **vest = atom->vest;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup)
nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
vest[i][0] = v[i][0];
vest[i][1] = v[i][1];
vest[i][2] = v[i][2];
}
}
}
void FixPI::pre_force(int /*vflag*/)
{
// set vest equal to v
// double **stfluid = atom->stfluid;
// double **gradv = atom->gradv;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup)
nlocal = atom->nfirst;
//for (int i = 0; i < nlocal; i++) {
// if (mask[i] & groupbit) {
// gradv[i][0] = 0.0;
// gradv[i][1] = 0.0;
// gradv[i][2] = 0.0;
// gradv[i][3] = 0.0;
// gradv[i][4] = 0.0;
// gradv[i][5] = 0.0;
// gradv[i][6] = 0.0;
//gradv[i][7] = 0.0;
// gradv[i][8] = 0.0;
//}
//}
}
/* ----------------------------------------------------------------------
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
void FixPI::initial_integrate(int /*vflag*/) {
// update v and x and rho and e of atoms in group
double **gradv = atom->gradv;
// double **stfluid = atom->stfluid;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **vest = atom->vest;
double *rho = atom->rho;
double *drho = atom->drho;
double *esph = atom->esph;
double *desph = atom->desph;
double *mass = atom->mass;
double *rmass = atom->rmass;
int rmass_flag = atom->rmass_flag;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int i;
double dtfm;
if (igroup == atom->firstgroup)
nlocal = atom->nfirst;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (rmass_flag) {
dtfm = dtf / rmass[i];
} else {
dtfm = dtf / mass[type[i]];
}
//Only 2d to test
// double trace;
//trace = gradv[i][0]+gradv[i][1];//+gradv[i][0]
// stfluid[i][0] = 0;//(2*gradv[i][0]+trace/2);
// stfluid[i][1] = 0;//(2*gradv[i][1]+trace/2);
// stfluid[i][2] = 0.0;//(gradv[i][2]-trace/2);
// stfluid[i][3] = (gradv[i][3]+gradv[i][6]);
// stfluid[i][4] = 0.0;//0.5*(gradv[i][4]+gradv[i][7]);
// stfluid[i][5] = 0.0;//0.5*(gradv[i][5]+gradv[i][8]);
gradv[i][0] = 0.0;
gradv[i][1] = 0.0;
gradv[i][2] = 0.0;
gradv[i][3] = 0.0;
gradv[i][4] = 0.0;
gradv[i][5] = 0.0;
gradv[i][6] = 0.0;
gradv[i][7] = 0.0;
gradv[i][8] = 0.0;
esph[i] += dtf * desph[i]; // half-step update of particle internal energy
rho[i] += dtf * drho[i]; // ... and density
// extrapolate velocity for use with velocity-dependent potentials, e.g. SPH
vest[i][0] = v[i][0] + 2.0 * dtfm * f[i][0];
vest[i][1] = v[i][1] + 2.0 * dtfm * f[i][1];
vest[i][2] = v[i][2] + 2.0 * dtfm * f[i][2];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
}
/* ---------------------------------------------------------------------- */
void FixPI::final_integrate() {
double **stfluid = atom->stfluid;
double **gradv = atom->gradv;
double **stmic = atom->stmic;
// update v, rho, and e of atoms in group
double **v = atom->v;
double **f = atom->f;
double *esph = atom->esph;
double *desph = atom->desph;
double *rho = atom->rho;
double *drho = atom->drho;
int *type = atom->type;
int *mask = atom->mask;
double *mass = atom->mass;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup)
nlocal = atom->nfirst;
double dtfm;
double *rmass = atom->rmass;
int rmass_flag = atom->rmass_flag;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (rmass_flag) {
dtfm = dtf / rmass[i];
} else {
dtfm = dtf / mass[type[i]];
}
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
esph[i] += dtf * desph[i];
rho[i] += dtf * drho[i];
// ---- Oldroyd-B polymer stress evolution (2D, Hookean dumbbell) ----
// Storage in stmic[i]: [0]=sxx [1]=syy [2]=szz [3]=sxy [4]=sxz [5]=syz.
// gradv[i] convention: [0]=du/dx [1]=dv/dy [2]=dw/dz
// [3]=du/dy [4]=du/dz [5]=dv/dz
// [6]=dv/dx [7]=dw/dx [8]=dw/dy
// Eq: d(sigma)/dt = Gp*(grad v + grad v^T) + grad v . sigma
// + sigma . grad v^T - sigma/tau
// For 2D we update sxx, syy, sxy only; the rest stay 0.
if (tau_p > 0.0) {
double sxx = stmic[i][0];
double syy = stmic[i][1];
double sxy = stmic[i][3];
double duxx = gradv[i][0];
double dvyy = gradv[i][1];
double duxy = gradv[i][3];
double dvyx = gradv[i][6];
double dsxx = 2.0*Gp*duxx + 2.0*(sxx*duxx + sxy*duxy) - sxx/tau_p;
double dsyy = 2.0*Gp*dvyy + 2.0*(sxy*dvyx + syy*dvyy) - syy/tau_p;
double dsxy = Gp*(duxy + dvyx)
+ sxx*dvyx + sxy*(duxx + dvyy) + syy*duxy
- sxy/tau_p;
// forward Euler over full dt (= 2*dtf in LJ units, force->ftm2v=1)
double dt_full = 2.0 * dtf / force->ftm2v;
stmic[i][0] = sxx + dt_full * dsxx;
stmic[i][1] = syy + dt_full * dsyy;
stmic[i][3] = sxy + dt_full * dsxy;
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixPI::reset_dt() {
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
}
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