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Fixing various errors, reorganizing status variable

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This commit is contained in:
jtclemm
2023-05-12 23:33:02 -06:00
parent 35418afd6b
commit dfc47a5501
16 changed files with 113 additions and 120 deletions
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2
examples/PACKAGES/rheo/poiseuille/in.rheo.poiseuille
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@ -59,7 +59,7 @@ pair_coeff * *
# ------ Fixes & computes ------ #
fix 1 all rheo ${cut} Quintic 0 shift
fix 1 all rheo ${cut} quintic 0 shift
fix 2 all rheo/viscosity constant ${eta}
fix 3 all rheo/pressure linear
fix 4 rig setforce 0.0 0.0 0.0

2
src/.gitignore vendored
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@ -205,6 +205,8 @@
/compute_rheo_interface.h
/compute_rheo_kernel.cpp
/compute_rheo_kernel.h
/compute_rheo_property_atom.cpp
/compute_rheo_property_atom.h
/compute_rheo_rho_sum.cpp
/compute_rheo_rho_sum.h
/compute_rheo_surface.cpp

11
src/RHEO/compute_rheo_grad.cpp
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@ -125,7 +125,7 @@ void ComputeRHEOGrad::init_list(int /*id*/, NeighList *ptr)
void ComputeRHEOGrad::compute_peratom()
{
int i, j, k, ii, jj, jnum, itype, jtype, a, b;
int i, j, k, ii, jj, jnum, itype, jtype, a, b, fluidi, fluidj;
double xtmp, ytmp, ztmp, delx, dely, delz;
double rsq, imass, jmass;
double rhoi, rhoj, Voli, Volj, drho, dT, deta;
@ -183,6 +183,7 @@ void ComputeRHEOGrad::compute_peratom()
vi[1] = v[i][1];
vi[2] = v[i][2];
itype = type[i];
fluidi = !(status[i] & PHASECHECK);
jlist = firstneigh[i];
jnum = numneigh[i];
@ -197,6 +198,8 @@ void ComputeRHEOGrad::compute_peratom()
rsq = delx * delx + dely * dely + delz * delz;
if (rsq < cutsq) {
fluidj = !(status[j] & PHASECHECK);
rhoi = rho[i];
rhoj = rho[j];
@ -206,13 +209,13 @@ void ComputeRHEOGrad::compute_peratom()
// Add corrections for walls
if (interface_flag) {
if ((status[i] & STATUS_FLUID) && !(status[j] & STATUS_FLUID)) {
if (fluidi && (!fluidj)) {
compute_interface->correct_v(vi, vj, i, j);
rhoj = compute_interface->correct_rho(j, i);
} else if (!(status[i] & STATUS_FLUID) && (status[j] & STATUS_FLUID)) {
} else if ((!fluidi) && fluidj) {
compute_interface->correct_v(vj, vi, j, i);
rhoi = compute_interface->correct_rho(i, j);
} else if (!(status[i] & STATUS_FLUID) && !(status[j] & STATUS_FLUID)) {
} else if ((!fluidi) && (!fluidj)) {
rhoi = rho0;
rhoj = rho0;
}

10
src/RHEO/compute_rheo_interface.cpp
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@ -131,7 +131,7 @@ void ComputeRHEOInterface::compute_peratom()
}
for (i = 0; i < nall; i++) {
if (!(status[i] & STATUS_FLUID)) rho[i] = 0.0;
if (status[i] & PHASECHECK) rho[i] = 0.0;
normwf[i] = 0.0;
norm[i] = 0.0;
chi[i] = 0.0;
@ -143,7 +143,7 @@ void ComputeRHEOInterface::compute_peratom()
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
fluidi = status[i] & STATUS_FLUID;
fluidi = !(status[i] & PHASECHECK);
jlist = firstneigh[i];
jnum = numneigh[i];
@ -158,7 +158,7 @@ void ComputeRHEOInterface::compute_peratom()
if (rsq < cutsq) {
jtype = type[j];
fluidj = status[j] & STATUS_FLUID;
fluidj = !(status[j] & PHASECHECK);
w = compute_kernel->calc_w_quintic(i, j, delx, dely, delz, sqrt(rsq));
status_match = 0;
@ -202,7 +202,7 @@ void ComputeRHEOInterface::compute_peratom()
if (norm[i] != 0.0) chi[i] /= norm[i];
// Recalculate rho for non-fluid particles
if (!(status[i] & STATUS_FLUID)) {
if (status[i] & PHASECHECK) {
if (normwf[i] != 0.0) {
// Stores rho for solid particles 1+Pw in Adami Adams 2012
rho[i] = MAX(EPSILON, rho0 + (rho[i] / normwf[i]) * csq_inv);
@ -289,7 +289,7 @@ void ComputeRHEOInterface::unpack_reverse_comm(int n, int *list, double *buf)
j = list[i];
norm[j] += buf[m++];
chi[j] += buf[m++];
if (!(status[j] & STATUS_FLUID)){
if (status[j] & PHASECHECK){
normwf[j] += buf[m++];
rho[j] += buf[m++];
} else {

4
src/RHEO/compute_rheo_kernel.cpp
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@ -533,7 +533,7 @@ void ComputeRHEOKernel::compute_peratom()
w = calc_w_quintic(i,j,dx[0],dx[1],dx[2],r);
rhoj = rho[j];
if (interface_flag)
if (!(status[j] & STATUS_FLUID))
if (status[j] & PHASECHECK)
rhoj = compute_interface->correct_rho(j,i);
vj = mass[type[j]] / rhoj;
@ -582,7 +582,7 @@ void ComputeRHEOKernel::compute_peratom()
rhoj = rho[j];
if (interface_flag)
if (!(status[j] & STATUS_FLUID))
if (status[j] & PHASECHECK)
rhoj = compute_interface->correct_rho(j,i);
vj = mass[type[j]] / rhoj;

8
src/RHEO/compute_rheo_property_atom.cpp
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@ -212,10 +212,8 @@ void ComputeRHEOPropertyAtom::pack_phase(int n)
int *mask = atom->mask;
int nlocal = atom->nlocal;
int inverse_mask = ~PHASEMASK;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = (status[i] & inverse_mask);
if (mask[i] & groupbit) buf[n] = (status[i] & PHASECHECK);
else buf[n] = 0.0;
n += nvalues;
}
@ -244,10 +242,8 @@ void ComputeRHEOPropertyAtom::pack_surface(int n)
int *mask = atom->mask;
int nlocal = atom->nlocal;
int inverse_mask = ~SURFACEMASK;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = (status[i] & inverse_mask);
if (mask[i] & groupbit) buf[n] = (status[i] & SURFACECHECK);
else buf[n] = 0.0;
n += nvalues;
}

1
src/RHEO/compute_rheo_rho_sum.cpp
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@ -74,7 +74,6 @@ void ComputeRHEORhoSum::compute_peratom()
double **x = atom->x;
double *rho = atom->rho;
int *type = atom->type;
int *status = atom->status;
double *mass = atom->mass;
int newton = force->newton;

4
src/RHEO/compute_rheo_surface.cpp
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@ -183,7 +183,7 @@ void ComputeRHEOSurface::compute_peratom()
jlist = firstneigh[i];
jnum = numneigh[i];
itype = type[i];
fluidi = status[i] & STATUS_FLUID;
fluidi = !(status[i] & PHASECHECK);
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
@ -196,7 +196,7 @@ void ComputeRHEOSurface::compute_peratom()
rsq = lensq3(dx);
if (rsq < cutsq) {
jtype = type[j];
fluidj = status[j] & STATUS_FLUID;
fluidj = !(status[j] & PHASECHECK);
rhoi = rho[i];
rhoj = rho[j];

13
src/RHEO/compute_rheo_vshift.cpp
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@ -91,7 +91,7 @@ void ComputeRHEOVShift::compute_peratom()
double xtmp, ytmp, ztmp, rsq, r, rinv;
double w, wp, dr, w0, w4, vmag, prefactor;
double imass, jmass, voli, volj, rhoi, rhoj;
double dx[3], vi[3], vj[3] = {0};
double dx[3], vi[3], vj[3];
int dim = domain->dimension;
int *jlist;
@ -123,6 +123,11 @@ void ComputeRHEOVShift::compute_peratom()
for (a = 0; a < dim; a++)
vshift[i][a] = 0.0;
for (a = 0; a < 3; a++) {
vi[a] = 0.0;
vj[a] = 0.0;
}
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
@ -132,15 +137,15 @@ void ComputeRHEOVShift::compute_peratom()
jlist = firstneigh[i];
jnum = numneigh[i];
imass = mass[itype];
fluidi = status[i] & STATUS_FLUID;
fluidi = !(status[i] & PHASECHECK);
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
fluidj = status[j] & STATUS_FLUID;
fluidj = !(status[j] & PHASECHECK);
if ((!fluidi) && (!fluidj)) continue;
if (!(status[i] & STATUS_SHIFT) && !(status[j] & STATUS_SHIFT)) continue;
if ((status[i] & STATUS_NO_SHIFT) && (status[j] & STATUS_NO_SHIFT)) continue;
dx[0] = xtmp - x[j][0];
dx[1] = ytmp - x[j][1];

34
src/RHEO/fix_rheo.cpp
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@ -210,6 +210,8 @@ void FixRHEO::setup_pre_force(int /*vflag*/)
// Calculate surfaces
if (surface_flag) compute_surface->compute_peratom();
pre_force(0);
}
/* ---------------------------------------------------------------------- */
@ -258,8 +260,6 @@ void FixRHEO::setup(int /*vflag*/)
error->one(FLERR, "Fix rheo/viscosity does not fully cover all atoms");
if (!t_coverage_flag)
error->one(FLERR, "Fix rheo/thermal does not fully cover all atoms");
pre_force(0);
}
/* ---------------------------------------------------------------------- */
@ -283,7 +283,8 @@ void FixRHEO::initial_integrate(int /*vflag*/)
double **gradr = compute_grad->gradr;
double **gradv = compute_grad->gradv;
double **vshift;
if (shift_flag) compute_vshift->vshift;
if (shift_flag)
vshift = compute_vshift->vshift;
int nlocal = atom->nlocal;
int rmass_flag = atom->rmass_flag;
@ -294,7 +295,7 @@ void FixRHEO::initial_integrate(int /*vflag*/)
//Density Half-step
for (i = 0; i < nlocal; i++) {
if (status[i] & STATUS_NO_FORCE) continue;
if (status[i] & STATUS_NO_INTEGRATION) continue;
if (mask[i] & groupbit) {
if (rmass_flag) {
@ -331,8 +332,8 @@ void FixRHEO::initial_integrate(int /*vflag*/)
if (!rhosum_flag) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (status[i] & STATUS_NO_FORCE) continue;
if (!(status[i] & STATUS_FLUID)) continue;
if (status[i] & STATUS_NO_INTEGRATION) continue;
if (status[i] & PHASECHECK) continue;
divu = 0;
for (a = 0; a < dim; a++) {
@ -348,7 +349,7 @@ void FixRHEO::initial_integrate(int /*vflag*/)
compute_vshift->correct_surfaces(); // Could this be moved to preforce after the surface fix runs?
for (i = 0; i < nlocal; i++) {
if (!(status[i] & STATUS_SHIFT)) continue;
if (status[i] & STATUS_NO_SHIFT) continue;
if (mask[i] & groupbit) {
for (a = 0; a < dim; a++) {
@ -387,18 +388,13 @@ void FixRHEO::pre_force(int /*vflag*/)
if (shift_flag)
compute_vshift->compute_peratom();
// Remove extra shifting/no force options
// Remove temporary options
int *mask = atom->mask;
int *status = atom->status;
int nall = atom->nlocal + atom->nghost;
for (int i = 0; i < nall; i++) {
if (mask[i] & groupbit) {
status[i] &= ~STATUS_NO_FORCE;
if (status[i] & STATUS_FLUID)
status[i] &= ~STATUS_SHIFT;
}
}
for (int i = 0; i < nall; i++)
if (mask[i] & groupbit)
status[i] &= OPTIONSMASK;
// Calculate surfaces, update status
if (surface_flag) compute_surface->compute_peratom();
@ -433,7 +429,7 @@ void FixRHEO::final_integrate()
// Update velocity
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (status[i] & STATUS_NO_FORCE) continue;
if (status[i] & STATUS_NO_INTEGRATION) continue;
if (rmass_flag) {
dtfm = dtf / rmass[i];
@ -451,8 +447,8 @@ void FixRHEO::final_integrate()
if (!rhosum_flag) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (status[i] & STATUS_NO_FORCE) continue;
if (!(status[i] & STATUS_FLUID)) continue;
if (status[i] & STATUS_NO_INTEGRATION) continue;
if (status[i] & PHASECHECK) continue;
divu = 0;
for (a = 0; a < dim; a++) {

29
src/RHEO/fix_rheo.h
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@ -74,22 +74,27 @@ namespace RHEO_NS {
// Status variables
enum Status{
// Phase status
STATUS_FLUID = 1 << 0,
STATUS_SOLID = 1 << 1,
STATUS_REACTIVE = 1 << 2,
STATUS_FREEZING = 1 << 3,
STATUS_SOLID = 1 << 0,
STATUS_REACTIVE = 1 << 1,
// Surface status
STATUS_BULK = 1 << 4,
STATUS_LAYER = 1 << 5,
STATUS_SURFACE = 1 << 6,
STATUS_SPLASH = 1 << 7,
STATUS_BULK = 1 << 2,
STATUS_LAYER = 1 << 3,
STATUS_SURFACE = 1 << 4,
STATUS_SPLASH = 1 << 5,
// Temporary status options - reset in preforce
STATUS_SHIFT = 1 << 8,
STATUS_NO_FORCE = 1 << 9
STATUS_NO_SHIFT = 1 << 6,
STATUS_NO_INTEGRATION = 1 << 7,
STATUS_FREEZING = 1 << 8
};
#define PHASEMASK 0xFFFFFFF0;
#define SURFACEMASK 0xFFFFFF0F;
// Masks and their inverses
#define PHASEMASK 0xFFFFFFFC
#define PHASECHECK 0x00000003
#define SURFACEMASK 0xFFFFFFC3
#define SURFACECHECK 0x0000003C
#define OPTIONSMASK 0xFFFFFE3F
} // namespace RHEO_NS
} // namespace LAMMPS_NS

37
src/RHEO/fix_rheo_pressure.cpp
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@ -43,9 +43,7 @@ FixRHEOPressure::FixRHEOPressure(LAMMPS *lmp, int narg, char **arg) :
if (narg < 4) error->all(FLERR,"Illegal fix command");
pressure_style = NONE;
comm_forward = 1;
nmax_store = 0;
// Currently can only have one instance of fix rheo/pressure
if (igroup != 0)
@ -73,10 +71,6 @@ FixRHEOPressure::FixRHEOPressure(LAMMPS *lmp, int narg, char **arg) :
FixRHEOPressure::~FixRHEOPressure()
{
// Remove custom property if it exists
int tmp1, tmp2, index;
index = atom->find_custom("rheo_pressure", tmp1, tmp2);
if (index != -1) atom->remove_custom(index, 1, 0);
}
/* ---------------------------------------------------------------------- */
@ -110,20 +104,6 @@ void FixRHEOPressure::init()
void FixRHEOPressure::setup_pre_force(int /*vflag*/)
{
fix_rheo->pressure_fix_defined = 1;
// Create pressure array if it doesn't already exist
// Create a custom atom property so it works with compute property/atom
// Do not create grow callback as there's no reason to copy/exchange data
// Manually grow if nmax_store exceeded
int tmp1, tmp2;
int index = atom->find_custom("rheo_pressure", tmp1, tmp2);
if (index == -1) {
index = atom->add_custom("rheo_pressure", 1, 0);
nmax_store = atom->nmax;
}
pressure = atom->dvector[index];
pre_force(0);
}
@ -138,14 +118,10 @@ void FixRHEOPressure::pre_force(int /*vflag*/)
int *mask = atom->mask;
double *rho = atom->rho;
double *pressure = atom->pressure;
int nlocal = atom->nlocal;
if (nmax_store < atom->nmax) {
memory->grow(pressure, atom->nmax, "atom:rheo_pressure");
nmax_store = atom->nmax;
}
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (pressure_style == LINEAR) {
@ -170,6 +146,7 @@ int FixRHEOPressure::pack_forward_comm(int n, int *list, double *buf,
int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,m;
double *pressure = atom->pressure;
m = 0;
for (i = 0; i < n; i++) {
@ -184,6 +161,7 @@ int FixRHEOPressure::pack_forward_comm(int n, int *list, double *buf,
void FixRHEOPressure::unpack_forward_comm(int n, int first, double *buf)
{
int i, k, m, last;
double *pressure = atom->pressure;
m = 0;
last = first + n;
@ -210,12 +188,3 @@ double FixRHEOPressure::calc_pressure(double rho)
}
return rho;
}
/* ---------------------------------------------------------------------- */
double FixRHEOPressure::memory_usage()
{
double bytes = 0.0;
bytes += (size_t) nmax_store * sizeof(double);
return bytes;
}

3
src/RHEO/fix_rheo_pressure.h
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@ -34,14 +34,11 @@ class FixRHEOPressure : public Fix {
void pre_force(int) override;
int pack_forward_comm(int, int *, double *, int, int *) override;
void unpack_forward_comm(int, int, double *) override;
double memory_usage() override;
double calc_pressure(double);
private:
double c_cubic, csq, rho0, rho0inv;
double *pressure;
int pressure_style;
int nmax_store;
class FixRHEO *fix_rheo;
};

16
src/RHEO/fix_rheo_thermal.cpp
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@ -205,7 +205,7 @@ void FixRHEOThermal::initial_integrate(int /*vflag*/)
nlocal = atom->nfirst;
for (i = 0; i < nlocal; i++) {
if (!(status[i] & STATUS_SHIFT)) continue;
if (status[i] & STATUS_NO_SHIFT) continue;
if (mask[i] & groupbit) {
for (a = 0; a < dim; a++) {
@ -231,7 +231,7 @@ void FixRHEOThermal::post_integrate()
//Integrate temperature and check status
for (int i = 0; i < atom->nlocal; i++) {
if (mask[i] & groupbit) {
if (status[i] & STATUS_NO_FORCE) continue;
if (status[i] & STATUS_NO_INTEGRATION) continue;
cvi = calc_cv(i);
temperature[i] += dtf * heatflow[i] / cvi;
@ -245,16 +245,22 @@ void FixRHEOThermal::post_integrate()
}
if (Ti > Tci) {
// If solid, melt
if (status[i] & STATUS_SOLID) {
status[i] &= PHASEMASK;
status[i] |= STATUS_FLUID;
} else if (!(status[i] & STATUS_SOLID)) {
}
} else {
// If fluid, freeze
if (!(status[i] & STATUS_SOLID)) {
status[i] &= PHASEMASK;
status[i] |= STATUS_SOLID;
status[i] |= STATUS_FREEZING;
}
}
}
}
}
}
/* ----------------------------------------------------------------------
Only need to update non-evolving conductivity styles after atoms exchange
@ -300,7 +306,7 @@ void FixRHEOThermal::final_integrate()
//Integrate temperature and check status
for (int i = 0; i < atom->nlocal; i++) {
if (mask[i] & groupbit) {
if (status[i] & STATUS_NO_FORCE) continue;
if (status[i] & STATUS_NO_INTEGRATION) continue;
cvi = calc_cv(i);
temperature[i] += dtf * heatflow[i] / cvi;

18
src/RHEO/pair_rheo.cpp
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@ -120,6 +120,16 @@ void PairRHEO::compute(int eflag, int vflag)
numneigh = list->numneigh;
firstneigh = list->firstneigh;
for (a = 0; a < 3; a++) {
vi[a] = 0.0;
vj[a] = 0.0;
du[a] = 0.0;
fv[a] = 0.0;
dfp[a] = 0.0;
fsolid[a] = 0.0;
ft[0] = 0.0;
}
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@ -132,7 +142,7 @@ void PairRHEO::compute(int eflag, int vflag)
jnum = numneigh[i];
imass = mass[itype];
etai = viscosity[i];
fluidi = status[i] & STATUS_FLUID;
fluidi = !(status[i] & PHASECHECK);
if (thermal_flag) {
kappai = conductivity[i];
Ti = temperature[i];
@ -154,7 +164,7 @@ void PairRHEO::compute(int eflag, int vflag)
jmass = mass[jtype];
etaj = viscosity[j];
fluidj = status[j] & STATUS_FLUID;
fluidj = !(status[j] & PHASECHECK);
if (thermal_flag) {
Tj = temperature[j];
kappaj = conductivity[j];
@ -186,6 +196,7 @@ void PairRHEO::compute(int eflag, int vflag)
Pi = pressure[i];
Pj = pressure[j];
fmag = 0;
if (interface_flag) {
if (fluidi && (!fluidj)) {
compute_interface->correct_v(vi, vj, i, j);
rhoj = compute_interface->correct_rho(j, i);
@ -206,6 +217,7 @@ void PairRHEO::compute(int eflag, int vflag)
rhoi = rho0;
rhoj = rho0;
}
}
// Repel if close to inner solid particle
scale3(fmag, dx, fsolid);
@ -328,6 +340,7 @@ void PairRHEO::compute(int eflag, int vflag)
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
@ -421,6 +434,7 @@ void PairRHEO::setup()
compute_grad = fix_rheo->compute_grad;
compute_interface = fix_rheo->compute_interface;
thermal_flag = fix_rheo->thermal_flag;
interface_flag = fix_rheo->interface_flag;
csq = fix_rheo->csq;
rho0 = fix_rheo->rho0;

1
src/RHEO/pair_rheo.h
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@ -42,6 +42,7 @@ class PairRHEO : public Pair {
int artificial_visc_flag;
int rho_damp_flag;
int thermal_flag;
int interface_flag;
void allocate();