ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Cleaning up math, fixing tension bug, patching bond creation

Browse Source
This commit is contained in:
jtclemm
2024-02-23 13:26:28 -07:00
parent 70ea1dd352
commit b3de75da97
4 changed files with 90 additions and 52 deletions
Download Patch File Download Diff File Expand all files Collapse all files

54
src/RHEO/compute_rheo_interface.cpp
View File

@ -26,6 +26,7 @@
#include "force.h"
#include "fix_rheo.h"
#include "fix_rheo_pressure.h"
#include "math_extra.h"
#include "memory.h"
#include "modify.h"
#include "neighbor.h"
@ -36,6 +37,7 @@
using namespace LAMMPS_NS;
using namespace RHEO_NS;
using namespace MathExtra;
static constexpr double EPSILON = 1e-1;
@ -107,8 +109,8 @@ void ComputeRHEOInterface::init_list(int /*id*/, NeighList *ptr)
void ComputeRHEOInterface::compute_peratom()
{
int i, j, ii, jj, jnum, itype, jtype, fluidi, fluidj, status_match;
double xtmp, ytmp, ztmp, delx, dely, delz, rsq, w, dot;
int a, i, j, ii, jj, jnum, itype, jtype, fluidi, fluidj, status_match;
double xtmp, ytmp, ztmp, rsq, w, dot, dx[3];
int inum, *ilist, *jlist, *numneigh, **firstneigh;
int nlocal = atom->nlocal;
@ -153,15 +155,15 @@ void ComputeRHEOInterface::compute_peratom()
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;
dx[0] = xtmp - x[j][0];
dx[1] = ytmp - x[j][1];
dx[2] = ztmp - x[j][2];
rsq = lensq3(dx);
if (rsq < cutsq) {
jtype = type[j];
fluidj = !(status[j] & PHASECHECK);
w = compute_kernel->calc_w_quintic(i, j, delx, dely, delz, sqrt(rsq));
w = compute_kernel->calc_w_quintic(i, j, dx[0], dx[1], dx[2], sqrt(rsq));
status_match = 0;
norm[i] += w;
@ -172,9 +174,9 @@ void ComputeRHEOInterface::compute_peratom()
chi[i] += w;
} else {
if (!fluidi) {
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;
dot = 0;
for (a = 0; a < 3; a++)
dot += (-fp_store[j][a] + fp_store[i][a]) * dx[a];
rho[i] += w * (fix_pressure->calc_pressure(rho[j], jtype) - rho[j] * dot);
normwf[i] += w;
@ -187,9 +189,9 @@ void ComputeRHEOInterface::compute_peratom()
chi[j] += w;
} else {
if (!fluidj) {
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;
dot = 0;
for (a = 0; a < 3; a++)
dot += (-fp_store[i][a] + fp_store[j][a]) * dx[a];
rho[j] += w * (fix_pressure->calc_pressure(rho[i], itype) + rho[i] * dot);
normwf[j] += w;
@ -225,7 +227,7 @@ void ComputeRHEOInterface::compute_peratom()
int ComputeRHEOInterface::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/, int * /*pbc*/)
{
int i,j,k,m;
int i, j, k, m;
m = 0;
double *rho = atom->rho;
@ -267,7 +269,7 @@ void ComputeRHEOInterface::unpack_forward_comm(int n, int first, double *buf)
int ComputeRHEOInterface::pack_reverse_comm(int n, int first, double *buf)
{
int i,k,m,last;
int i, k, m, last;
double *rho = atom->rho;
m = 0;
@ -285,7 +287,7 @@ int ComputeRHEOInterface::pack_reverse_comm(int n, int first, double *buf)
void ComputeRHEOInterface::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,k,j,m;
int i, k, j, m;
double *rho = atom->rho;
int *status = atom->status;
m = 0;
@ -350,23 +352,19 @@ void ComputeRHEOInterface::store_forces()
for (const auto &fix : fixlist) {
for (int i = 0; i < atom->nlocal; i++) {
minv = 1.0 / mass[type[i]];
if (mask[i] & fix->groupbit) {
fp_store[i][0] = f[i][0] * minv;
fp_store[i][1] = f[i][1] * minv;
fp_store[i][2] = f[i][2] * minv;
} else {
fp_store[i][0] = (f[i][0] - fp_store[i][0]) * minv;
fp_store[i][1] = (f[i][1] - fp_store[i][1]) * minv;
fp_store[i][2] = (f[i][2] - fp_store[i][2]) * minv;
}
if (mask[i] & fix->groupbit)
for (int a = 0; a < 3; a++)
fp_store[i][a] = f[i][a] * minv;
else
for (int a = 0; a < 3; a++)
fp_store[i][a] = (f[i][a] - fp_store[i][a]) * minv;
}
}
} else {
for (int i = 0; i < atom->nlocal; i++) {
minv = 1.0 / mass[type[i]];
fp_store[i][0] = (f[i][0] - fp_store[i][0]) * minv;
fp_store[i][1] = (f[i][1] - fp_store[i][1]) * minv;
fp_store[i][2] = (f[i][2] - fp_store[i][2]) * minv;
for (int a = 0; a < 3; a++)
fp_store[i][a] = (f[i][a] - fp_store[i][a]) * minv;
}
}

6
src/RHEO/fix_rheo.cpp
View File

@ -422,12 +422,6 @@ void FixRHEO::pre_force(int /*vflag*/)
if (mask[i] & groupbit)
status[i] &= OPTIONSMASK;
// Reinstate temporary options
for (int i = 0; i < nall; i++)
if (mask[i] & groupbit)
if (status[i] & STATUS_SOLID)
status[i] |= STATUS_NO_SHIFT;
// Calculate surfaces, update status
if (surface_flag) {
compute_surface->compute_peratom();

2
src/RHEO/fix_rheo_tension.cpp
View File

@ -467,7 +467,7 @@ void FixRHEOTension::pre_force(int vflag)
if (wsame[i] < wmin) continue;
weight = MAX(1.0, wsame[i] * wmin_inv);
weight = MIN(1.0, wsame[i] * wmin_inv); //MAX -> MIN 2/14/24
itype = type[i];
if (norm[i] != 0)

80
src/RHEO/fix_rheo_thermal.cpp
View File

@ -423,6 +423,7 @@ void FixRHEOThermal::pre_force(int /*vflag*/)
double *energy = atom->esph;
double *temperature = atom->temperature;
int *type = atom->type;
int *status = atom->status;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
@ -444,6 +445,11 @@ void FixRHEOThermal::pre_force(int /*vflag*/)
}
}
}
// Add temporary options, wiped by preceding fix rheo preforce
for (int i = 0; i < nall; i++)
if (status[i] & STATUS_SOLID)
status[i] |= STATUS_NO_SHIFT;
}
/* ---------------------------------------------------------------------- */
@ -481,39 +487,79 @@ void FixRHEOThermal::break_bonds()
tagint **bond_atom = atom->bond_atom;
int *num_bond = atom->num_bond;
int nlocal = atom->nlocal;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
// Rapidly delete all bonds for local atoms that melt (no shifting)
for (int i = 0; i < nlocal; i++) {
if (!(status[i] & STATUS_MELTING)) continue;
for (m = 0; m < num_bond[i]; m++) {
j = atom->map(bond_atom[i][m]);
if (!(status[i] & STATUS_MELTING) && !(status[j] & STATUS_MELTING)) continue;
bond_type[i][m] = 0;
if (n_histories > 0)
for (auto &ihistory: histories)
dynamic_cast<FixBondHistory *>(ihistory)->delete_history(i, num_bond[i] - 1);
dynamic_cast<FixBondHistory *>(ihistory)->delete_history(i, m);
if (fix_update_special_bonds) fix_update_special_bonds->add_broken_bond(i, j);
if (fix_update_special_bonds)
fix_update_special_bonds->add_broken_bond(i, j);
}
num_bond[i] = 0;
}
// For non-melting neighbors, selectively delete bond if necessary
if (j >= nlocal || (status[j] & STATUS_MELTING)) continue;
for (n = 0; n < num_bond[j]; n++) {
if (bond_atom[j][n] == tag[i]) {
bond_type[j][n] = 0;
nmax = num_bond[j] - 1;
bond_type[j][n] = bond_type[j][nmax];
bond_atom[j][n] = bond_atom[j][nmax];
if (n_histories > 0) {
// Update bond list and break solid-melted bonds
for (n = 0; n < nbondlist; n++) {
// skip bond if already broken
if (bondlist[n][2] <= 0) continue;
i = bondlist[n][0];
j = bondlist[n][1];
if (!(status[i] & STATUS_MELTING) && !(status[j] & STATUS_MELTING)) continue;
bondlist[n][2] = 0;
// Delete bonds for non-melted local atoms (shifting)
if (i < nlocal) {
for (m = 0; m < num_bond[i]; m++) {
if (bond_atom[i][m] == tag[j]) {
nmax = num_bond[i] - 1;
bond_type[i][m] = bond_type[i][nmax];
bond_atom[i][m] = bond_atom[i][nmax];
if (n_histories > 0)
for (auto &ihistory: histories) {
dynamic_cast<FixBondHistory *>(ihistory)->shift_history(j, n, nmax);
dynamic_cast<FixBondHistory *>(ihistory)->delete_history(j, nmax);
auto fix_bond_history = dynamic_cast<FixBondHistory *> (ihistory);
fix_bond_history->shift_history(i, m, nmax);
fix_bond_history->delete_history(i, nmax);
}
}
bond_type[i][nmax] = 0;
num_bond[i]--;
break;
}
}
}
if (j < nlocal) {
for (m = 0; m < num_bond[j]; m++) {
if (bond_atom[j][m] == tag[i]) {
nmax = num_bond[j] - 1;
bond_type[j][m] = bond_type[j][nmax];
bond_atom[j][m] = bond_atom[j][nmax];
if (n_histories > 0)
for (auto &ihistory: histories) {
auto fix_bond_history = dynamic_cast<FixBondHistory *> (ihistory);
fix_bond_history->shift_history(j, m, nmax);
fix_bond_history->delete_history(j, nmax);
}
bond_type[j][nmax] = 0;
num_bond[j]--;
break;
}
}
}
num_bond[i] = 0;
}
}