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Cleaning up math, fixing tension bug, patching bond creation

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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
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54
src/RHEO/compute_rheo_interface.cpp
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@ -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;
}
}