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Fixing misc bugs with interfaces

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This commit is contained in:
jtclemm
2023-05-23 22:12:34 -06:00
parent b4e1effe5f
commit 6f59b7c5e0
7 changed files with 77 additions and 35 deletions
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2
doc/src/fix_rheo.rst
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@ -23,7 +23,7 @@ Syntax
*surface/detection* values = *sdstyle* *limit*
*sdstyle* = *coordination* or *divergence*
*limit* = threshold for surface particles (unitless)
*interface/reconstruction* values = none, reconstructs interfaces with solid particles
*interface/reconstruct* values = none, reconstructs interfaces with solid particles
*rho/sum* values = none, uses the kernel to compute the density of particles
*density* values = *rho0* (density)
*sound/squared* values = *csq* (velocity\^2)

7
src/RHEO/compute_rheo_grad.cpp
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@ -179,9 +179,6 @@ void ComputeRHEOGrad::compute_peratom()
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
vi[0] = v[i][0];
vi[1] = v[i][1];
vi[2] = v[i][2];
itype = type[i];
fluidi = !(status[i] & PHASECHECK);
jlist = firstneigh[i];
@ -203,6 +200,10 @@ void ComputeRHEOGrad::compute_peratom()
rhoi = rho[i];
rhoj = rho[j];
vi[0] = v[i][0];
vi[1] = v[i][1];
vi[2] = v[i][2];
vj[0] = v[j][0];
vj[1] = v[j][1];
vj[2] = v[j][2];

16
src/RHEO/compute_rheo_interface.cpp
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@ -170,9 +170,10 @@ void ComputeRHEOInterface::compute_peratom()
chi[i] += w;
} else {
if (!fluidi) {
dot = (-fp_store[0][j] + fp_store[0][i]) * delx;
dot += (-fp_store[1][j] + fp_store[1][i]) * dely;
dot += (-fp_store[2][j] + fp_store[2][i]) * delz;
dot = (-fp_store[j][0] + fp_store[i][0]) * delx;
dot += (-fp_store[j][1] + fp_store[i][1]) * dely;
dot += (-fp_store[j][2] + fp_store[i][2]) * delz;
rho[i] += w * (csq * (rho[j] - rho0) - rho[j] * dot);
normwf[i] += w;
}
@ -184,9 +185,10 @@ void ComputeRHEOInterface::compute_peratom()
chi[j] += w;
} else {
if (!fluidj) {
dot = (-fp_store[0][i] + fp_store[0][j]) * delx;
dot += (-fp_store[1][i] + fp_store[1][j]) * dely;
dot += (-fp_store[2][i] + fp_store[2][j]) * delz;
dot = (-fp_store[i][0] + fp_store[j][0]) * delx;
dot += (-fp_store[i][1] + fp_store[j][1]) * dely;
dot += (-fp_store[i][2] + fp_store[j][2]) * delz;
rho[j] += w * (csq * (rho[i] - rho0) + rho[i] * dot);
normwf[j] += w;
}
@ -342,7 +344,7 @@ void ComputeRHEOInterface::store_forces()
// If forces are overwritten by a fix, there are no pressure forces
// so just normalize
auto fixlist = modify->get_fix_by_style("setforce");
if (fixlist.size() == 0) {
if (fixlist.size() != 0) {
for (const auto &fix : fixlist) {
for (int i = 0; i < atom->nlocal; i++) {
minv = 1.0 / mass[type[i]];

8
src/RHEO/fix_rheo.cpp
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@ -105,7 +105,7 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
}
iarg += 2;
} else if (strcmp(arg[iarg],"interface/reconstruction") == 0) {
} else if (strcmp(arg[iarg],"interface/reconstruct") == 0) {
interface_flag = 1;
} else if (strcmp(arg[iarg],"rho/sum") == 0) {
rhosum_flag = 1;
@ -360,6 +360,7 @@ void FixRHEO::initial_integrate(int /*vflag*/)
}
if (!rhosum_flag) {
if (status[i] & PHASECHECK) continue;
for (a = 0; a < dim; a++) {
rho[i] += dtv * vshift[i][a] * gradr[i][a];
}
@ -380,7 +381,10 @@ void FixRHEO::pre_force(int /*vflag*/)
compute_grad->forward_fields(); // also forwards v and rho for chi
compute_kernel->compute_peratom();
if (interface_flag) compute_interface->compute_peratom();
if (interface_flag) {
// Note on first setup, have no forces for pressure to reference
compute_interface->compute_peratom();
}
compute_grad->compute_peratom();
compute_grad->forward_gradients();

19
src/RHEO/fix_rheo_pressure.cpp
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@ -122,20 +122,9 @@ void FixRHEOPressure::pre_force(int /*vflag*/)
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (pressure_style == LINEAR) {
pressure[i] = csq * (rho[i] - rho0);
} else if (pressure_style == CUBIC) {
dr = rho[i] - rho0;
pressure[i] = csq * (dr + c_cubic * dr * dr * dr);
} else if (pressure_style == TAITWATER) {
rho_ratio = rho[i] / rho0inv;
rr3 = rho_ratio * rho_ratio * rho_ratio;
pressure[i] = csq * rho0 * SEVENTH * (rr3 * rr3 * rho_ratio - 1.0);
}
}
}
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
pressure[i] = calc_pressure(rho[i]);
if (comm_forward) comm->forward_comm(this);
}
@ -186,5 +175,5 @@ double FixRHEOPressure::calc_pressure(double rho)
rr3 = rho_ratio * rho_ratio * rho_ratio;
p = csq * rho0 * SEVENTH * (rr3 * rr3 * rho_ratio - 1.0);
}
return rho;
return p;
}

58
src/RHEO/pair_rheo.cpp
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@ -56,6 +56,8 @@ PairRHEO::PairRHEO(LAMMPS *lmp) :
artificial_visc_flag = 0;
rho_damp_flag = 0;
thermal_flag = 0;
comm_reverse = 3;
}
/* ---------------------------------------------------------------------- */
@ -79,7 +81,7 @@ void PairRHEO::compute(int eflag, int vflag)
double rhoi, rhoj, voli, volj, Pi, Pj, etai, etaj, kappai, kappaj;
double mu, q, fp_prefactor, drho_damp, fmag, psi_ij, Fij;
double *dWij, *dWji, *dW1ij, *dW1ji;
double dx[3], du[3], fv[3], dfp[3], fsolid[3], ft[3], vi[3], vj[3];
double dx[3], du[3], dv[3], fv[3], dfp[3], fsolid[3], ft[3], vi[3], vj[3];
int *ilist, *jlist, *numneigh, **firstneigh;
double imass, jmass, rsq, r, rinv;
@ -113,6 +115,12 @@ void PairRHEO::compute(int eflag, int vflag)
if (compute_interface) {
fp_store = compute_interface->fp_store;
chi = compute_interface->chi;
for (i = 0; i < atom->nmax; i++) {
fp_store[i][0] = 0.0;
fp_store[i][1] = 0.0;
fp_store[i][2] = 0.0;
}
}
inum = list->inum;
@ -243,11 +251,12 @@ void PairRHEO::compute(int eflag, int vflag)
//Hydrostatic pressure forces
fp_prefactor = voli * volj * (Pj + Pi);
sub3(vi, vj, du);
sub3(vi, vj, dv);
//Add artificial viscous pressure if required
if (artificial_visc_flag && pair_avisc_flag) {
//Interpolate velocities to midpoint and use this difference for artificial viscosity
copy3(dv, du);
for (a = 0; a < dim; a++)
for (b = 0; b < dim; b++)
du[a] -= 0.5 * (gradv[i][a * dim + b] + gradv[j][a * dim + b]) * dx[b];
@ -257,10 +266,6 @@ void PairRHEO::compute(int eflag, int vflag)
mu = MIN(0.0, mu);
q = av * (-2.0 * cs * mu + mu * mu);
fp_prefactor += voli * volj * q * (rhoj + rhoi);
if (fabs(fp_prefactor*dWij[0]) > 1e-9)
if (atom->tag[i] == 643 or atom->tag[j] == 643 or atom->tag[i] == 963 or atom->tag[j] == 963)
printf("%d-%d (%d %d) fp_prefactor %g %g %g\n", atom->tag[i], atom->tag[j], i, j, fp_prefactor, dWij[0], -fp_prefactor*dWij[0]);
}
// -Grad[P + Q]
@ -270,7 +275,7 @@ void PairRHEO::compute(int eflag, int vflag)
for (a = 0; a < dim; a++) {
fv[a] = 0.0;
for (b = 0; b < dim; b++)
fv[a] += du[a] * dx[b] * dWij[b];
fv[a] += dv[a] * dx[b] * dWij[b];
fv[a] *= (etai + etaj) * voli * volj * rinv * rinv;
}
@ -346,6 +351,11 @@ void PairRHEO::compute(int eflag, int vflag)
}
if (vflag_fdotr) virial_fdotr_compute();
if (compute_interface) {
comm->reverse_comm(this);
comm->forward_comm(this);
}
}
/* ----------------------------------------------------------------------
@ -476,3 +486,37 @@ double PairRHEO::init_one(int i, int j)
return h;
}
/* ---------------------------------------------------------------------- */
int PairRHEO::pack_reverse_comm(int n, int first, double *buf)
{
int i, k, m, last;
double **fp_store = compute_interface->fp_store;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = fp_store[i][0];
buf[m++] = fp_store[i][1];
buf[m++] = fp_store[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void PairRHEO::unpack_reverse_comm(int n, int *list, double *buf)
{
int i, j, k, m;
double **fp_store = compute_interface->fp_store;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
fp_store[j][0] += buf[m++];
fp_store[j][1] += buf[m++];
fp_store[j][2] += buf[m++];
}
}

2
src/RHEO/pair_rheo.h
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@ -33,6 +33,8 @@ class PairRHEO : public Pair {
void coeff(int, char **) override;
void setup() override;
double init_one(int, int) override;
int pack_reverse_comm(int, int, double *) override;
void unpack_reverse_comm(int, int *, double *) override;
protected:
double h, csq, rho0; // From fix RHEO