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93a0d4c096d15ef7953565924b24958e24528a07
lammps/src/BODY/pair_body_rounded_polyhedron.cpp
Axel Kohlmeyer 93a0d4c096 fix up some comments
2020-09-12 14:26:34 -04:00

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
Ref: Wang, Yu, Langston, Fraige, Particle shape effects in discrete
element modelling of cohesive angular particles, Granular Matter 2011,
13:1-12.
Note: The current implementation has not taken into account
the contact history for friction forces.
------------------------------------------------------------------------- */
#include "pair_body_rounded_polyhedron.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "atom_vec_body.h"
#include "body_rounded_polyhedron.h"
#include "comm.h"
#include "force.h"
#include "fix.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "math_extra.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define DELTA 10000
#define EPSILON 1e-3
#define MAX_FACE_SIZE 4 // maximum number of vertices per face (same as BodyRoundedPolyhedron)
#define MAX_CONTACTS 32 // for 3D models (including duplicated counts)
//#define _POLYHEDRON_DEBUG
enum {EE_INVALID=0,EE_NONE,EE_INTERACT};
enum {EF_INVALID=0,EF_NONE,EF_PARALLEL,EF_SAME_SIDE_OF_FACE,
EF_INTERSECT_INSIDE,EF_INTERSECT_OUTSIDE};
/* ---------------------------------------------------------------------- */
PairBodyRoundedPolyhedron::PairBodyRoundedPolyhedron(LAMMPS *lmp) : Pair(lmp)
{
dmax = nmax = 0;
discrete = nullptr;
dnum = dfirst = nullptr;
edmax = ednummax = 0;
edge = nullptr;
ednum = edfirst = nullptr;
facmax = facnummax = 0;
face = nullptr;
facnum = facfirst = nullptr;
enclosing_radius = nullptr;
rounded_radius = nullptr;
maxerad = nullptr;
single_enable = 0;
restartinfo = 0;
c_n = 0.1;
c_t = 0.2;
mu = 0.0;
A_ua = 1.0;
k_n = nullptr;
k_na = nullptr;
}
/* ---------------------------------------------------------------------- */
PairBodyRoundedPolyhedron::~PairBodyRoundedPolyhedron()
{
memory->destroy(discrete);
memory->destroy(dnum);
memory->destroy(dfirst);
memory->destroy(edge);
memory->destroy(ednum);
memory->destroy(edfirst);
memory->destroy(face);
memory->destroy(facnum);
memory->destroy(facfirst);
memory->destroy(enclosing_radius);
memory->destroy(rounded_radius);
memory->destroy(maxerad);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(k_n);
memory->destroy(k_na);
}
}
/* ---------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
int ni,nj,npi,npj,ifirst,jfirst,nei,nej,iefirst,jefirst;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,facc[3];
double rsq,eradi,eradj;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
ev_init(eflag,vflag);
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **torque = atom->torque;
double **angmom = atom->angmom;
int *body = atom->body;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// grow the per-atom lists if necessary and initialize
if (atom->nmax > nmax) {
memory->destroy(dnum);
memory->destroy(dfirst);
memory->destroy(ednum);
memory->destroy(edfirst);
memory->destroy(facnum);
memory->destroy(facfirst);
memory->destroy(enclosing_radius);
memory->destroy(rounded_radius);
nmax = atom->nmax;
memory->create(dnum,nmax,"pair:dnum");
memory->create(dfirst,nmax,"pair:dfirst");
memory->create(ednum,nmax,"pair:ednum");
memory->create(edfirst,nmax,"pair:edfirst");
memory->create(facnum,nmax,"pair:facnum");
memory->create(facfirst,nmax,"pair:facfirst");
memory->create(enclosing_radius,nmax,"pair:enclosing_radius");
memory->create(rounded_radius,nmax,"pair:rounded_radius");
}
ndiscrete = nedge = nface = 0;
for (i = 0; i < nall; i++)
dnum[i] = ednum[i] = facnum[i] = 0;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
if (body[i] >= 0) {
if (dnum[i] == 0) body2space(i);
npi = dnum[i];
ifirst = dfirst[i];
nei = ednum[i];
iefirst = edfirst[i];
eradi = enclosing_radius[i];
}
for (jj = 0; jj < jnum; jj++) {
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;
jtype = type[j];
// body/body interactions
evdwl = 0.0;
facc[0] = facc[1] = facc[2] = 0;
if (body[i] < 0 || body[j] < 0) continue;
if (dnum[j] == 0) body2space(j);
npj = dnum[j];
jfirst = dfirst[j];
nej = ednum[j];
jefirst = edfirst[j];
eradj = enclosing_radius[j];
// no interaction
double r = sqrt(rsq);
if (r > eradi + eradj + cut_inner) continue;
// sphere-sphere interaction
if (npi == 1 && npj == 1) {
sphere_against_sphere(i, j, itype, jtype, delx, dely, delz,
rsq, v, f, evflag);
continue;
}
// reset vertex and edge forces
for (ni = 0; ni < npi; ni++) {
discrete[ifirst+ni][3] = 0;
discrete[ifirst+ni][4] = 0;
discrete[ifirst+ni][5] = 0;
discrete[ifirst+ni][6] = 0;
}
for (nj = 0; nj < npj; nj++) {
discrete[jfirst+nj][3] = 0;
discrete[jfirst+nj][4] = 0;
discrete[jfirst+nj][5] = 0;
discrete[jfirst+nj][6] = 0;
}
for (ni = 0; ni < nei; ni++) {
edge[iefirst+ni][2] = 0;
edge[iefirst+ni][3] = 0;
edge[iefirst+ni][4] = 0;
edge[iefirst+ni][5] = 0;
}
for (nj = 0; nj < nej; nj++) {
edge[jefirst+nj][2] = 0;
edge[jefirst+nj][3] = 0;
edge[jefirst+nj][4] = 0;
edge[jefirst+nj][5] = 0;
}
// one of the two bodies is a sphere
if (npj == 1) {
sphere_against_face(i, j, itype, jtype, x, v, f, torque,
angmom, evflag);
sphere_against_edge(i, j, itype, jtype, x, v, f, torque,
angmom, evflag);
continue;
} else if (npi == 1) {
sphere_against_face(j, i, jtype, itype, x, v, f, torque,
angmom, evflag);
sphere_against_edge(j, i, jtype, itype, x, v, f, torque,
angmom, evflag);
continue;
}
int num_contacts;
Contact contact_list[MAX_CONTACTS];
num_contacts = 0;
// check interaction between i's edges and j' faces
#ifdef _POLYHEDRON_DEBUG
printf("INTERACTION between edges of %d vs. faces of %d:\n", i, j);
#endif
edge_against_face(i, j, itype, jtype, x, contact_list,
num_contacts, evdwl, facc);
// check interaction between j's edges and i' faces
#ifdef _POLYHEDRON_DEBUG
printf("\nINTERACTION between edges of %d vs. faces of %d:\n", j, i);
#endif
edge_against_face(j, i, jtype, itype, x, contact_list,
num_contacts, evdwl, facc);
// check interaction between i's edges and j' edges
#ifdef _POLYHEDRON_DEBUG
printf("INTERACTION between edges of %d vs. edges of %d:\n", i, j);
#endif
edge_against_edge(i, j, itype, jtype, x, contact_list,
num_contacts, evdwl, facc);
// estimate the contact area
// also consider point contacts and line contacts
if (num_contacts > 0) {
rescale_cohesive_forces(x, f, torque, contact_list, num_contacts,
itype, jtype, facc);
}
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0,
facc[0],facc[1],facc[2],delx,dely,delz);
} // end for jj
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(k_n,n+1,n+1,"pair:k_n");
memory->create(k_na,n+1,n+1,"pair:k_na");
memory->create(maxerad,n+1,"pair:maxerad");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::settings(int narg, char **arg)
{
if (narg < 5) error->all(FLERR,"Illegal pair_style command");
c_n = utils::numeric(FLERR,arg[0],false,lmp);
c_t = utils::numeric(FLERR,arg[1],false,lmp);
mu = utils::numeric(FLERR,arg[2],false,lmp);
A_ua = utils::numeric(FLERR,arg[3],false,lmp);
cut_inner = utils::numeric(FLERR,arg[4],false,lmp);
if (A_ua < 0) A_ua = 1;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
double k_n_one = utils::numeric(FLERR,arg[2],false,lmp);
double k_na_one = utils::numeric(FLERR,arg[3],false,lmp);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
k_n[i][j] = k_n_one;
k_na[i][j] = k_na_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::init_style()
{
avec = (AtomVecBody *) atom->style_match("body");
if (!avec) error->all(FLERR,"Pair body/rounded/polyhedron requires "
"atom style body");
if (strcmp(avec->bptr->style,"rounded/polyhedron") != 0)
error->all(FLERR,"Pair body/rounded/polyhedron requires "
"body style rounded/polyhedron");
bptr = (BodyRoundedPolyhedron *) avec->bptr;
if (force->newton_pair == 0)
error->all(FLERR,"Pair style body/rounded/polyhedron requires "
"newton pair on");
if (comm->ghost_velocity == 0)
error->all(FLERR,"Pair body/rounded/polyhedron requires "
"ghost atoms store velocity");
neighbor->request(this);
// find the maximum enclosing radius for each atom type
int i, itype;
double eradi;
int* body = atom->body;
int* type = atom->type;
int ntypes = atom->ntypes;
int nlocal = atom->nlocal;
if (atom->nmax > nmax) {
memory->destroy(dnum);
memory->destroy(dfirst);
memory->destroy(ednum);
memory->destroy(edfirst);
memory->destroy(facnum);
memory->destroy(facfirst);
memory->destroy(enclosing_radius);
memory->destroy(rounded_radius);
nmax = atom->nmax;
memory->create(dnum,nmax,"pair:dnum");
memory->create(dfirst,nmax,"pair:dfirst");
memory->create(ednum,nmax,"pair:ednum");
memory->create(edfirst,nmax,"pair:edfirst");
memory->create(facnum,nmax,"pair:facnum");
memory->create(facfirst,nmax,"pair:facfirst");
memory->create(enclosing_radius,nmax,"pair:enclosing_radius");
memory->create(rounded_radius,nmax,"pair:rounded_radius");
}
ndiscrete = nedge = nface = 0;
for (i = 0; i < nlocal; i++)
dnum[i] = ednum[i] = facnum[i] = 0;
double *merad = nullptr;
memory->create(merad,ntypes+1,"pair:merad");
for (i = 1; i <= ntypes; i++)
maxerad[i] = merad[i] = 0;
int ipour;
for (ipour = 0; ipour < modify->nfix; ipour++)
if (strcmp(modify->fix[ipour]->style,"pour") == 0) break;
if (ipour == modify->nfix) ipour = -1;
int idep;
for (idep = 0; idep < modify->nfix; idep++)
if (strcmp(modify->fix[idep]->style,"deposit") == 0) break;
if (idep == modify->nfix) idep = -1;
for (i = 1; i <= ntypes; i++) {
merad[i] = 0.0;
if (ipour >= 0) {
itype = i;
merad[i] =
*((double *) modify->fix[ipour]->extract("radius",itype));
}
if (idep >= 0) {
itype = i;
merad[i] =
*((double *) modify->fix[idep]->extract("radius",itype));
}
}
for (i = 0; i < nlocal; i++) {
itype = type[i];
if (body[i] >= 0) {
if (dnum[i] == 0) body2space(i);
eradi = enclosing_radius[i];
if (eradi > merad[itype]) merad[itype] = eradi;
} else
merad[itype] = 0;
}
MPI_Allreduce(&merad[1],&maxerad[1],ntypes,MPI_DOUBLE,MPI_MAX,world);
memory->destroy(merad);
sanity_check();
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairBodyRoundedPolyhedron::init_one(int i, int j)
{
k_n[j][i] = k_n[i][j];
k_na[j][i] = k_na[i][j];
return (maxerad[i]+maxerad[j]);
}
/* ----------------------------------------------------------------------
convert N sub-particles in body I to space frame using current quaternion
store sub-particle space-frame displacements from COM in discrete list
------------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::body2space(int i)
{
int ibonus = atom->body[i];
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
int nsub = bptr->nsub(bonus);
double *coords = bptr->coords(bonus);
int body_num_edges = bptr->nedges(bonus);
double* edge_ends = bptr->edges(bonus);
int body_num_faces = bptr->nfaces(bonus);
double* face_pts = bptr->faces(bonus);
double eradius = bptr->enclosing_radius(bonus);
double rradius = bptr->rounded_radius(bonus);
// get the number of sub-particles (vertices)
// and the index of the first vertex of my body in the list
dnum[i] = nsub;
dfirst[i] = ndiscrete;
// grow the vertex list if necessary
// the first 3 columns are for coords, the last 3 for forces
if (ndiscrete + nsub > dmax) {
dmax += DELTA;
memory->grow(discrete,dmax,7,"pair:discrete");
}
double p[3][3];
MathExtra::quat_to_mat(bonus->quat,p);
for (int m = 0; m < nsub; m++) {
MathExtra::matvec(p,&coords[3*m],discrete[ndiscrete]);
discrete[ndiscrete][3] = 0;
discrete[ndiscrete][4] = 0;
discrete[ndiscrete][5] = 0;
discrete[ndiscrete][6] = 0;
ndiscrete++;
}
// get the number of edges (vertices)
// and the index of the first edge of my body in the list
ednum[i] = body_num_edges;
edfirst[i] = nedge;
// grow the edge list if necessary
// the first 2 columns are for vertex indices within body, the last 3 for forces
if (nedge + body_num_edges > edmax) {
edmax += DELTA;
memory->grow(edge,edmax,6,"pair:edge");
}
for (int m = 0; m < body_num_edges; m++) {
edge[nedge][0] = static_cast<int>(edge_ends[2*m+0]);
edge[nedge][1] = static_cast<int>(edge_ends[2*m+1]);
edge[nedge][2] = 0;
edge[nedge][3] = 0;
edge[nedge][4] = 0;
edge[nedge][5] = 0;
nedge++;
}
// get the number of faces and the index of the first face
facnum[i] = body_num_faces;
facfirst[i] = nface;
// grow the face list if necessary
// the first 3 columns are for vertex indices within body, the last 3 for forces
if (nface + body_num_faces > facmax) {
facmax += DELTA;
memory->grow(face,facmax,MAX_FACE_SIZE,"pair:face");
}
for (int m = 0; m < body_num_faces; m++) {
for (int k = 0; k < MAX_FACE_SIZE; k++)
face[nface][k] = static_cast<int>(face_pts[MAX_FACE_SIZE*m+k]);
nface++;
}
enclosing_radius[i] = eradius;
rounded_radius[i] = rradius;
}
/* ----------------------------------------------------------------------
Interaction between two spheres with different radii
according to the 2D model from Fraige et al.
---------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::sphere_against_sphere(int ibody, int jbody,
int itype, int jtype, double delx, double dely, double delz, double rsq,
double** v, double** f, int evflag)
{
double rradi,rradj,contact_dist;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double rij,rsqinv,R,fx,fy,fz,fn[3],ft[3],fpair,energy;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
rradi = rounded_radius[ibody];
rradj = rounded_radius[jbody];
contact_dist = rradi + rradj;
rij = sqrt(rsq);
R = rij - contact_dist;
energy = 0;
kernel_force(R, itype, jtype, energy, fpair);
fx = delx*fpair/rij;
fy = dely*fpair/rij;
fz = delz*fpair/rij;
if (R <= 0) { // in contact
// relative translational velocity
vr1 = v[ibody][0] - v[jbody][0];
vr2 = v[ibody][1] - v[jbody][1];
vr3 = v[ibody][2] - v[jbody][2];
// normal component
rsqinv = 1.0/rsq;
vnnr = vr1*delx + vr2*dely + vr3*delz;
vn1 = delx*vnnr * rsqinv;
vn2 = dely*vnnr * rsqinv;
vn3 = delz*vnnr * rsqinv;
// tangential component
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// normal friction term at contact
fn[0] = -c_n * vn1;
fn[1] = -c_n * vn2;
fn[2] = -c_n * vn3;
// tangential friction term at contact,
// excluding the tangential deformation term for now
ft[0] = -c_t * vt1;
ft[1] = -c_t * vt2;
ft[2] = -c_t * vt3;
fx += fn[0] + ft[0];
fy += fn[1] + ft[1];
fz += fn[2] + ft[2];
}
f[ibody][0] += fx;
f[ibody][1] += fy;
f[ibody][2] += fz;
if (newton_pair || jbody < nlocal) {
f[jbody][0] -= fx;
f[jbody][1] -= fy;
f[jbody][2] -= fz;
}
if (evflag) ev_tally_xyz(ibody,jbody,nlocal,newton_pair,
energy,0.0,fx,fy,fz,delx,dely,delz);
}
/* ----------------------------------------------------------------------
Interaction bt the edges of a polyhedron (ibody) and a sphere (jbody)
---------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::sphere_against_edge(int ibody, int jbody,
int itype, int jtype, double** x, double** v, double** f, double** torque,
double** angmom, int evflag)
{
int ni,nei,ifirst,iefirst,npi1,npi2,ibonus;
double xi1[3],xi2[3],vti[3],h[3],fn[3],ft[3],d,t;
double delx,dely,delz,rsq,rij,rsqinv,R,fx,fy,fz,fpair,energy;
double rradi,rradj,contact_dist;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double *quat, *inertia;
AtomVecBody::Bonus *bonus;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
ifirst = dfirst[ibody];
iefirst = edfirst[ibody];
nei = ednum[ibody];
rradi = rounded_radius[ibody];
rradj = rounded_radius[jbody];
contact_dist = rradi + rradj;
for (ni = 0; ni < nei; ni++) {
npi1 = static_cast<int>(edge[iefirst+ni][0]);
npi2 = static_cast<int>(edge[iefirst+ni][1]);
// compute the space-fixed coordinates for the vertices of the face
xi1[0] = x[ibody][0] + discrete[ifirst+npi1][0];
xi1[1] = x[ibody][1] + discrete[ifirst+npi1][1];
xi1[2] = x[ibody][2] + discrete[ifirst+npi1][2];
xi2[0] = x[ibody][0] + discrete[ifirst+npi2][0];
xi2[1] = x[ibody][1] + discrete[ifirst+npi2][1];
xi2[2] = x[ibody][2] + discrete[ifirst+npi2][2];
// find the projection of the jbody's COM on the edge
project_pt_line(x[jbody], xi1, xi2, h, d, t);
if (d > contact_dist + cut_inner) continue;
if (t < 0 || t > 1) continue;
if (fabs(t) < EPSILON) {
if (static_cast<int>(discrete[ifirst+npi1][6]) == 1)
continue;
else {
h[0] = xi1[0];
h[1] = xi1[1];
h[2] = xi1[2];
discrete[ifirst+npi1][6] = 1;
}
}
if (fabs(t-1) < EPSILON) {
if (static_cast<int>(discrete[ifirst+npi2][6]) == 1)
continue;
else {
h[0] = xi2[0];
h[1] = xi2[1];
h[2] = xi2[2];
discrete[ifirst+npi2][6] = 1;
}
}
delx = h[0] - x[jbody][0];
dely = h[1] - x[jbody][1];
delz = h[2] - x[jbody][2];
rsq = delx*delx + dely*dely + delz*delz;
rsqinv = (rsq == 0.0) ? 0.0 : 1.0/rsq;
rij = sqrt(rsq);
R = rij - contact_dist;
energy = 0;
kernel_force(R, itype, jtype, energy, fpair);
fx = delx*fpair/rij;
fy = dely*fpair/rij;
fz = delz*fpair/rij;
if (R <= 0) { // in contact
// compute the velocity of the vertex in the space-fixed frame
ibonus = atom->body[ibody];
bonus = &avec->bonus[ibonus];
quat = bonus->quat;
inertia = bonus->inertia;
total_velocity(h, x[ibody], v[ibody], angmom[ibody],
inertia, quat, vti);
// relative translational velocity
vr1 = vti[0] - v[jbody][0];
vr2 = vti[1] - v[jbody][1];
vr3 = vti[2] - v[jbody][2];
// normal component
vnnr = vr1*delx + vr2*dely + vr3*delz;
vn1 = delx*vnnr * rsqinv;
vn2 = dely*vnnr * rsqinv;
vn3 = delz*vnnr * rsqinv;
// tangential component
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// normal friction term at contact
fn[0] = -c_n * vn1;
fn[1] = -c_n * vn2;
fn[2] = -c_n * vn3;
// tangential friction term at contact,
// excluding the tangential deformation term
ft[0] = -c_t * vt1;
ft[1] = -c_t * vt2;
ft[2] = -c_t * vt3;
fx += fn[0] + ft[0];
fy += fn[1] + ft[1];
fz += fn[2] + ft[2];
}
f[ibody][0] += fx;
f[ibody][1] += fy;
f[ibody][2] += fz;
sum_torque(x[ibody], h, fx, fy, fz, torque[ibody]);
if (newton_pair || jbody < nlocal) {
f[jbody][0] -= fx;
f[jbody][1] -= fy;
f[jbody][2] -= fz;
}
if (evflag) ev_tally_xyz(ibody,jbody,nlocal,newton_pair,
energy,0.0,fx,fy,fz,delx,dely,delz);
}
}
/* ----------------------------------------------------------------------
Interaction bt the faces of a polyhedron (ibody) and a sphere (jbody)
---------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::sphere_against_face(int ibody, int jbody,
int itype, int jtype, double** x, double** v, double** f, double** torque,
double** angmom, int evflag)
{
int ni,nfi,inside,ifirst,iffirst,npi1,npi2,npi3,ibonus,tmp;
double xi1[3],xi2[3],xi3[3],ui[3],vi[3],vti[3],n[3],h[3],fn[3],ft[3],d;
double delx,dely,delz,rsq,rij,rsqinv,R,fx,fy,fz,fpair,energy;
double rradi,rradj,contact_dist;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double *quat, *inertia;
AtomVecBody::Bonus *bonus;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
ifirst = dfirst[ibody];
iffirst = facfirst[ibody];
nfi = facnum[ibody];
rradi = rounded_radius[ibody];
rradj = rounded_radius[jbody];
contact_dist = rradi + rradj;
for (ni = 0; ni < nfi; ni++) {
npi1 = static_cast<int>(face[iffirst+ni][0]);
npi2 = static_cast<int>(face[iffirst+ni][1]);
npi3 = static_cast<int>(face[iffirst+ni][2]);
// compute the space-fixed coordinates for the vertices of the face
xi1[0] = x[ibody][0] + discrete[ifirst+npi1][0];
xi1[1] = x[ibody][1] + discrete[ifirst+npi1][1];
xi1[2] = x[ibody][2] + discrete[ifirst+npi1][2];
xi2[0] = x[ibody][0] + discrete[ifirst+npi2][0];
xi2[1] = x[ibody][1] + discrete[ifirst+npi2][1];
xi2[2] = x[ibody][2] + discrete[ifirst+npi2][2];
xi3[0] = x[ibody][0] + discrete[ifirst+npi3][0];
xi3[1] = x[ibody][1] + discrete[ifirst+npi3][1];
xi3[2] = x[ibody][2] + discrete[ifirst+npi3][2];
// find the normal unit vector of the face
MathExtra::sub3(xi2, xi1, ui);
MathExtra::sub3(xi3, xi1, vi);
MathExtra::cross3(ui, vi, n);
MathExtra::norm3(n);
// skip if the COM of the two bodies are in the same side of the face
if (opposite_sides(n, xi1, x[ibody], x[jbody]) == 0) continue;
// find the projection of the sphere on the face
project_pt_plane(x[jbody], xi1, xi2, xi3, h, d, inside);
inside_polygon(ibody, ni, x[ibody], h, nullptr, inside, tmp);
if (inside == 0) continue;
delx = h[0] - x[jbody][0];
dely = h[1] - x[jbody][1];
delz = h[2] - x[jbody][2];
rsq = delx*delx + dely*dely + delz*delz;
rij = sqrt(rsq);
R = rij - contact_dist;
energy = 0;
kernel_force(R, itype, jtype, energy, fpair);
fx = delx*fpair/rij;
fy = dely*fpair/rij;
fz = delz*fpair/rij;
if (R <= 0) { // in contact
// compute the velocity of the vertex in the space-fixed frame
ibonus = atom->body[ibody];
bonus = &avec->bonus[ibonus];
quat = bonus->quat;
inertia = bonus->inertia;
total_velocity(h, x[ibody], v[ibody], angmom[ibody],
inertia, quat, vti);
// relative translational velocity
vr1 = vti[0] - v[jbody][0];
vr2 = vti[1] - v[jbody][1];
vr3 = vti[2] - v[jbody][2];
// normal component
rsqinv = 1.0/rsq;
vnnr = vr1*delx + vr2*dely + vr3*delz;
vn1 = delx*vnnr * rsqinv;
vn2 = dely*vnnr * rsqinv;
vn3 = delz*vnnr * rsqinv;
// tangential component
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// normal friction term at contact
fn[0] = -c_n * vn1;
fn[1] = -c_n * vn2;
fn[2] = -c_n * vn3;
// tangential friction term at contact,
// excluding the tangential deformation term for now
ft[0] = -c_t * vt1;
ft[1] = -c_t * vt2;
ft[2] = -c_t * vt3;
fx += fn[0] + ft[0];
fy += fn[1] + ft[1];
fz += fn[2] + ft[2];
}
f[ibody][0] += fx;
f[ibody][1] += fy;
f[ibody][2] += fz;
sum_torque(x[ibody], h, fx, fy, fz, torque[ibody]);
if (newton_pair || jbody < nlocal) {
f[jbody][0] -= fx;
f[jbody][1] -= fy;
f[jbody][2] -= fz;
}
if (evflag) ev_tally_xyz(ibody,jbody,nlocal,newton_pair,
energy,0.0,fx,fy,fz,delx,dely,delz);
}
}
/* ----------------------------------------------------------------------
Determine the interaction mode between i's edges against j's edges
i = atom i (body i)
j = atom j (body j)
x = atoms' coordinates
f = atoms' forces
torque = atoms' torques
tag = atoms' tags
contact_list = list of contacts
num_contacts = number of contacts between i's edges and j's edges
Return:
---------------------------------------------------------------------- */
int PairBodyRoundedPolyhedron::edge_against_edge(int ibody, int jbody,
int itype, int jtype, double** x, Contact* contact_list, int &num_contacts,
double &evdwl, double* facc)
{
int ni,nei,nj,nej,interact;
double rradi,rradj,energy;
nei = ednum[ibody];
rradi = rounded_radius[ibody];
nej = ednum[jbody];
rradj = rounded_radius[jbody];
energy = 0;
interact = EE_NONE;
// loop through body i's edges
for (ni = 0; ni < nei; ni++) {
for (nj = 0; nj < nej; nj++) {
// compute the distance between the edge nj to the edge ni
#ifdef _POLYHEDRON_DEBUG
printf("Compute interaction between edge %d of body %d "
"with edge %d of body %d:\n",
nj, jbody, ni, ibody);
#endif
interact = interaction_edge_to_edge(ibody, ni, x[ibody], rradi,
jbody, nj, x[jbody], rradj,
itype, jtype, cut_inner,
contact_list, num_contacts,
energy, facc);
}
} // end for looping through the edges of body i
evdwl += energy;
return interact;
}
/* ----------------------------------------------------------------------
Determine the interaction mode between i's edges against j's faces
i = atom i (body i)
j = atom j (body j)
x = atoms' coordinates
f = atoms' forces
torque = atoms' torques
tag = atoms' tags
contact_list = list of contacts
num_contacts = number of contacts between i's edges and j's faces
Return:
---------------------------------------------------------------------- */
int PairBodyRoundedPolyhedron::edge_against_face(int ibody, int jbody,
int itype, int jtype, double** x, Contact* contact_list, int &num_contacts,
double &evdwl, double* facc)
{
int ni,nei,nj,nfj,interact;
double rradi,rradj,energy;
nei = ednum[ibody];
rradi = rounded_radius[ibody];
nfj = facnum[jbody];
rradj = rounded_radius[jbody];
energy = 0;
interact = EF_NONE;
// loop through body i's edges
for (ni = 0; ni < nei; ni++) {
// loop through body j's faces
for (nj = 0; nj < nfj; nj++) {
// compute the distance between the face nj to the edge ni
#ifdef _POLYHEDRON_DEBUG
printf("Compute interaction between face %d of body %d with "
"edge %d of body %d:\n",
nj, jbody, ni, ibody);
#endif
interact = interaction_face_to_edge(jbody, nj, x[jbody], rradj,
ibody, ni, x[ibody], rradi,
itype, jtype, cut_inner,
contact_list, num_contacts,
energy, facc);
}
} // end for looping through the edges of body i
evdwl += energy;
return interact;
}
/* -------------------------------------------------------------------------
Compute the distance between an edge of body i and an edge from
another body
Input:
ibody = body i (i.e. atom i)
face_index = face index of body i
xmi = atom i's coordinates (body i's center of mass)
rounded_radius_i = rounded radius of the body i
jbody = body i (i.e. atom j)
edge_index = coordinate of the tested edge from another body
xmj = atom j's coordinates (body j's center of mass)
rounded_radius_j = rounded radius of the body j
cut_inner = cutoff for vertex-vertex and vertex-edge interaction
Output:
d = Distance from a point x0 to an edge
hi = coordinates of the projection of x0 on the edge
contact = 0 no contact between the queried edge and the face
1 contact detected
return
INVALID if the face index is invalid
NONE if there is no interaction
------------------------------------------------------------------------- */
int PairBodyRoundedPolyhedron::interaction_edge_to_edge(int ibody,
int edge_index_i, double *xmi, double rounded_radius_i,
int jbody, int edge_index_j, double *xmj, double rounded_radius_j,
int itype, int jtype, double cut_inner,
Contact* contact_list, int &num_contacts, double &energy, double* facc)
{
int ifirst,iefirst,jfirst,jefirst,npi1,npi2,npj1,npj2,interact;
double xi1[3],xi2[3],xpj1[3],xpj2[3];
double r,t1,t2,h1[3],h2[3];
double contact_dist;
double** x = atom->x;
double** v = atom->v;
double** f = atom->f;
double** torque = atom->torque;
double** angmom = atom->angmom;
ifirst = dfirst[ibody];
iefirst = edfirst[ibody];
npi1 = static_cast<int>(edge[iefirst+edge_index_i][0]);
npi2 = static_cast<int>(edge[iefirst+edge_index_i][1]);
// compute the space-fixed coordinates for the edge ends
xi1[0] = xmi[0] + discrete[ifirst+npi1][0];
xi1[1] = xmi[1] + discrete[ifirst+npi1][1];
xi1[2] = xmi[2] + discrete[ifirst+npi1][2];
xi2[0] = xmi[0] + discrete[ifirst+npi2][0];
xi2[1] = xmi[1] + discrete[ifirst+npi2][1];
xi2[2] = xmi[2] + discrete[ifirst+npi2][2];
// two ends of the edge from body j
jfirst = dfirst[jbody];
jefirst = edfirst[jbody];
npj1 = static_cast<int>(edge[jefirst+edge_index_j][0]);
npj2 = static_cast<int>(edge[jefirst+edge_index_j][1]);
xpj1[0] = xmj[0] + discrete[jfirst+npj1][0];
xpj1[1] = xmj[1] + discrete[jfirst+npj1][1];
xpj1[2] = xmj[2] + discrete[jfirst+npj1][2];
xpj2[0] = xmj[0] + discrete[jfirst+npj2][0];
xpj2[1] = xmj[1] + discrete[jfirst+npj2][1];
xpj2[2] = xmj[2] + discrete[jfirst+npj2][2];
contact_dist = rounded_radius_i + rounded_radius_j;
int jflag = 1;
distance_bt_edges(xpj1, xpj2, xi1, xi2, h1, h2, t1, t2, r);
#ifdef _POLYHEDRON_DEBUG
double ui[3],uj[3];
MathExtra::sub3(xi1,xi2,ui);
MathExtra::norm3(ui);
MathExtra::sub3(xpj1,xpj2,uj);
MathExtra::norm3(uj);
double dot = MathExtra::dot3(ui, uj);
printf(" edge npi1 = %d (%f %f %f); npi2 = %d (%f %f %f) vs."
" edge npj1 = %d (%f %f %f); npj2 = %d (%f %f %f): "
"t1 = %f; t2 = %f; r = %f; dot = %f\n",
npi1, xi1[0], xi1[1], xi1[2], npi2, xi2[0], xi2[1], xi2[2],
npj1, xpj1[0], xpj1[1], xpj1[2], npj2, xpj2[0], xpj2[1], xpj2[2],
t1, t2, r, dot);
#endif
interact = EE_NONE;
// singularity case, ignore interactions
if (r < EPSILON) return interact;
// include the vertices for interactions
if (t1 >= 0 && t1 <= 1 && t2 >= 0 && t2 <= 1 &&
r < contact_dist + cut_inner) {
pair_force_and_torque(jbody, ibody, h1, h2, r, contact_dist,
jtype, itype, x, v, f, torque, angmom,
jflag, energy, facc);
interact = EE_INTERACT;
if (r <= contact_dist) {
// store the contact info
contact_list[num_contacts].ibody = ibody;
contact_list[num_contacts].jbody = jbody;
contact_list[num_contacts].xi[0] = h2[0];
contact_list[num_contacts].xi[1] = h2[1];
contact_list[num_contacts].xi[2] = h2[2];
contact_list[num_contacts].xj[0] = h1[0];
contact_list[num_contacts].xj[1] = h1[1];
contact_list[num_contacts].xj[2] = h1[2];
contact_list[num_contacts].type = 1;
contact_list[num_contacts].separation = r - contact_dist;
contact_list[num_contacts].unique = 1;
num_contacts++;
}
} else {
}
return interact;
}
/* -------------------------------------------------------------------------
Compute the interaction between a face of body i and an edge from
another body
Input:
ibody = body i (i.e. atom i)
face_index = face index of body i
xmi = atom i's coordinates (body i's center of mass)
rounded_radius_i = rounded radius of the body i
jbody = body i (i.e. atom j)
edge_index = coordinate of the tested edge from another body
xmj = atom j's coordinates (body j's center of mass)
rounded_radius_j = rounded radius of the body j
cut_inner = cutoff for vertex-vertex and vertex-edge interaction
Output:
d = Distance from a point x0 to an edge
hi = coordinates of the projection of x0 on the edge
contact = 0 no contact between the queried edge and the face
1 contact detected
return
INVALID if the face index is invalid
NONE if there is no interaction
------------------------------------------------------------------------- */
int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody,
int face_index, double *xmi, double rounded_radius_i,
int jbody, int edge_index, double *xmj, double rounded_radius_j,
int itype, int jtype, double cut_inner,
Contact* contact_list, int &num_contacts, double &energy, double* facc)
{
if (face_index >= facnum[ibody]) return EF_INVALID;
int ifirst,iffirst,jfirst,npi1,npi2,npi3;
int jefirst,npj1,npj2;
double xi1[3],xi2[3],xi3[3],xpj1[3],xpj2[3],ui[3],vi[3],n[3];
double** x = atom->x;
double** v = atom->v;
double** f = atom->f;
double** torque = atom->torque;
double** angmom = atom->angmom;
ifirst = dfirst[ibody];
iffirst = facfirst[ibody];
npi1 = static_cast<int>(face[iffirst+face_index][0]);
npi2 = static_cast<int>(face[iffirst+face_index][1]);
npi3 = static_cast<int>(face[iffirst+face_index][2]);
// compute the space-fixed coordinates for the vertices of the face
xi1[0] = xmi[0] + discrete[ifirst+npi1][0];
xi1[1] = xmi[1] + discrete[ifirst+npi1][1];
xi1[2] = xmi[2] + discrete[ifirst+npi1][2];
xi2[0] = xmi[0] + discrete[ifirst+npi2][0];
xi2[1] = xmi[1] + discrete[ifirst+npi2][1];
xi2[2] = xmi[2] + discrete[ifirst+npi2][2];
xi3[0] = xmi[0] + discrete[ifirst+npi3][0];
xi3[1] = xmi[1] + discrete[ifirst+npi3][1];
xi3[2] = xmi[2] + discrete[ifirst+npi3][2];
// find the normal unit vector of the face, ensure it point outward of the body
MathExtra::sub3(xi2, xi1, ui);
MathExtra::sub3(xi3, xi1, vi);
MathExtra::cross3(ui, vi, n);
MathExtra::norm3(n);
double xc[3], dot, ans[3];
xc[0] = (xi1[0] + xi2[0] + xi3[0])/3.0;
xc[1] = (xi1[1] + xi2[1] + xi3[1])/3.0;
xc[2] = (xi1[2] + xi2[2] + xi3[2])/3.0;
MathExtra::sub3(xc, xmi, ans);
dot = MathExtra::dot3(ans, n);
if (dot < 0) MathExtra::negate3(n);
// two ends of the edge from body j
jfirst = dfirst[jbody];
jefirst = edfirst[jbody];
npj1 = static_cast<int>(edge[jefirst+edge_index][0]);
npj2 = static_cast<int>(edge[jefirst+edge_index][1]);
xpj1[0] = xmj[0] + discrete[jfirst+npj1][0];
xpj1[1] = xmj[1] + discrete[jfirst+npj1][1];
xpj1[2] = xmj[2] + discrete[jfirst+npj1][2];
xpj2[0] = xmj[0] + discrete[jfirst+npj2][0];
xpj2[1] = xmj[1] + discrete[jfirst+npj2][1];
xpj2[2] = xmj[2] + discrete[jfirst+npj2][2];
// no interaction if two ends of the edge
// are on the same side with the COM wrt the face
if (opposite_sides(n, xi1, xmi, xpj1) == 0 &&
opposite_sides(n, xi1, xmi, xpj2) == 0)
return EF_NONE;
// determine the intersection of the edge to the face
double hi1[3], hi2[3], d1, d2, contact_dist;
int inside1 = 0;
int inside2 = 0;
// enum {EF_PARALLEL=0,EF_SAME_SIDE_OF_FACE,
// EF_INTERSECT_INSIDE,EF_INTERSECT_OUTSIDE};
int interact = edge_face_intersect(xi1, xi2, xi3, xpj1, xpj2,
hi1, hi2, d1, d2, inside1, inside2);
inside_polygon(ibody, face_index, xmi, hi1, hi2, inside1, inside2);
contact_dist = rounded_radius_i + rounded_radius_j;
// both endpoints are on the same side of, or parallel to, the face
// and both are out of the interaction zone
if (interact == EF_SAME_SIDE_OF_FACE || interact == EF_PARALLEL) {
if (d1 > contact_dist + cut_inner && d2 > contact_dist + cut_inner)
return EF_NONE;
int num_outside = 0;
int jflag = 1;
#ifdef _POLYHEDRON_DEBUG
if (interact == EF_SAME_SIDE_OF_FACE)
printf(" - same side of face\n");
else if (interact == EF_PARALLEL)
printf(" - parallel\n");
printf(" face: xi1 (%f %f %f) xi2 (%f %f %f) xi3 (%f %f %f)\n",
xi1[0], xi1[1], xi1[2], xi2[0], xi2[1], xi2[2], xi3[0], xi3[1], xi3[2]);
printf(" edge: xpj1 (%f %f %f) xpj2 (%f %f %f)\n",
xpj1[0], xpj1[1], xpj1[2], xpj2[0], xpj2[1], xpj2[2]);
#endif
// xpj1 is in the interaction zone
// and its projection on the face is inside the triangle
// compute vertex-face interaction and accumulate force/torque to both bodies
if (d1 <= contact_dist + cut_inner) {
if (inside1) {
if (static_cast<int>(discrete[jfirst+npj1][6]) == 0) {
pair_force_and_torque(jbody, ibody, xpj1, hi1, d1, contact_dist,
jtype, itype, x, v, f, torque, angmom,
jflag, energy, facc);
#ifdef _POLYHEDRON_DEBUG
printf(" - compute pair force between vertex %d from edge %d of body %d "
"with face %d of body %d: d1 = %f\n",
npj1, edge_index, jbody, face_index, ibody, d1);
#endif
if (d1 <= contact_dist) {
// store the contact info
contact_list[num_contacts].ibody = ibody;
contact_list[num_contacts].jbody = jbody;
contact_list[num_contacts].xi[0] = hi1[0];
contact_list[num_contacts].xi[1] = hi1[1];
contact_list[num_contacts].xi[2] = hi1[2];
contact_list[num_contacts].xj[0] = xpj1[0];
contact_list[num_contacts].xj[1] = xpj1[1];
contact_list[num_contacts].xj[2] = xpj1[2];
contact_list[num_contacts].type = 0;
contact_list[num_contacts].separation = d1 - contact_dist;
contact_list[num_contacts].unique = 1;
num_contacts++;
}
discrete[jfirst+npj1][6] = 1;
}
} else {
num_outside++;
}
}
// xpj2 is in the interaction zone
// and its projection on the face is inside the triangle
// compute vertex-face interaction and accumulate force/torque to both bodies
if (d2 <= contact_dist + cut_inner) {
if (inside2) {
if (static_cast<int>(discrete[jfirst+npj2][6]) == 0) {
pair_force_and_torque(jbody, ibody, xpj2, hi2, d2, contact_dist,
jtype, itype, x, v, f, torque, angmom,
jflag, energy, facc);
#ifdef _POLYHEDRON_DEBUG
printf(" - compute pair force between vertex %d from edge %d of body %d "
"with face %d of body %d: d2 = %f\n",
npj2, edge_index, jbody, face_index, ibody, d2);
#endif
if (d2 <= contact_dist) {
// store the contact info
contact_list[num_contacts].ibody = ibody;
contact_list[num_contacts].jbody = jbody;
contact_list[num_contacts].xi[0] = hi2[0];
contact_list[num_contacts].xi[1] = hi2[1];
contact_list[num_contacts].xi[2] = hi2[2];
contact_list[num_contacts].xj[0] = xpj2[0];
contact_list[num_contacts].xj[1] = xpj2[1];
contact_list[num_contacts].xj[2] = xpj2[2];
contact_list[num_contacts].type = 0;
contact_list[num_contacts].separation = d2 - contact_dist;
contact_list[num_contacts].unique = 1;
num_contacts++;
}
discrete[jfirst+npj2][6] = 1;
}
} else {
num_outside++;
}
}
// both ends have projection outside of the face
// compute interaction between the edge with the three edges of the face
if (num_outside == 2) {
#ifdef _POLYHEDRON_DEBUG
printf(" - outside = 2\n");
printf(" - compute pair force between edge %d of body %d "
"with 3 edges of face %d of body %d\n",
edge_index, jbody, face_index, ibody);
#endif
interact = EF_INTERSECT_OUTSIDE;
}
} else if (interact == EF_INTERSECT_OUTSIDE) {
// compute interaction between the edge with the three edges of the face
#ifdef _POLYHEDRON_DEBUG
printf(" - intersect outside triangle\n");
printf(" - compute pair force between edge %d of body %d "
"with face %d of body %d\n", edge_index, jbody, face_index, ibody);
printf(" face: xi1 (%f %f %f) xi2 (%f %f %f) xi3 (%f %f %f)\n",
xi1[0], xi1[1], xi1[2], xi2[0], xi2[1], xi2[2], xi3[0], xi3[1], xi3[2]);
printf(" edge: xpj1 (%f %f %f) xpj2 (%f %f %f)\n",
xpj1[0], xpj1[1], xpj1[2], xpj2[0], xpj2[1], xpj2[2]);
#endif
} else if (interact == EF_INTERSECT_INSIDE) {
// need to do something here to resolve overlap!!
// p is the intersection between the edge and the face
int jflag = 1;
if (d1 < d2)
pair_force_and_torque(jbody, ibody, xpj1, hi1, d1, contact_dist,
jtype, itype, x, v, f, torque, angmom,
jflag, energy, facc);
else
pair_force_and_torque(jbody, ibody, xpj2, hi2, d2, contact_dist,
jtype, itype, x, v, f, torque, angmom,
jflag, energy, facc);
}
return interact;
}
/* ----------------------------------------------------------------------
Compute forces and torques between two bodies caused by the interaction
between a pair of points on either bodies (similar to sphere-sphere)
------------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::pair_force_and_torque(int ibody, int jbody,
double* pi, double* pj, double r, double contact_dist,
int itype, int jtype, double** x,
double** v, double** f, double** torque, double** angmom,
int jflag, double& energy, double* facc)
{
double delx,dely,delz,R,fx,fy,fz,fpair;
delx = pi[0] - pj[0];
dely = pi[1] - pj[1];
delz = pi[2] - pj[2];
R = r - contact_dist;
kernel_force(R, itype, jtype, energy, fpair);
fx = delx*fpair/r;
fy = dely*fpair/r;
fz = delz*fpair/r;
#ifdef _POLYHEDRON_DEBUG
printf(" - R = %f; r = %f; k_na = %f; shift = %f; fpair = %f;"
" energy = %f; jflag = %d\n", R, r, k_na, shift, fpair,
energy, jflag);
#endif
if (R <= 0) {
// contact: accumulate normal and tangential contact force components
contact_forces(ibody, jbody, pi, pj, delx, dely, delz, fx, fy, fz,
x, v, angmom, f, torque, facc);
} else {
// accumulate force and torque to both bodies directly
f[ibody][0] += fx;
f[ibody][1] += fy;
f[ibody][2] += fz;
sum_torque(x[ibody], pi, fx, fy, fz, torque[ibody]);
facc[0] += fx; facc[1] += fy; facc[2] += fz;
if (jflag) {
f[jbody][0] -= fx;
f[jbody][1] -= fy;
f[jbody][2] -= fz;
sum_torque(x[jbody], pj, -fx, -fy, -fz, torque[jbody]);
}
}
}
/* ----------------------------------------------------------------------
Kernel force is model-dependent and can be derived for other styles
here is the harmonic potential (linear piece-wise forces) in Wang et al.
------------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::kernel_force(double R, int itype, int jtype,
double& energy, double& fpair)
{
double kn = k_n[itype][jtype];
double kna = k_na[itype][jtype];
double shift = kna * cut_inner;
double e = 0;
if (R <= 0) { // deformation occurs
fpair = -kn * R - shift;
e = (0.5 * kn * R + shift) * R;
} else if (R <= cut_inner) { // not deforming but cohesive ranges overlap
fpair = kna * R - shift;
e = (-0.5 * kna * R + shift) * R;
} else fpair = 0.0;
energy += e;
}
/* ----------------------------------------------------------------------
Compute contact forces between two bodies
modify the force stored at the vertex and edge in contact by j_a
sum forces and torque to the corresponding bodies
fx,fy,fz = unscaled cohesive forces
fn = normal friction component
ft = tangential friction component (-c_t * v_t)
------------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::contact_forces(int ibody, int jbody,
double *xi, double *xj, double delx, double dely, double delz,
double fx, double fy, double fz, double** x, double** v, double** angmom,
double** f, double** torque, double* facc)
{
int ibonus,jbonus;
double rsq,rsqinv,vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
double fn[3],ft[3],vi[3],vj[3];
double *quat, *inertia;
AtomVecBody::Bonus *bonus;
// compute the velocity of the vertex in the space-fixed frame
ibonus = atom->body[ibody];
bonus = &avec->bonus[ibonus];
quat = bonus->quat;
inertia = bonus->inertia;
total_velocity(xi, x[ibody], v[ibody], angmom[ibody],
inertia, quat, vi);
// compute the velocity of the point on the edge in the space-fixed frame
jbonus = atom->body[jbody];
bonus = &avec->bonus[jbonus];
quat = bonus->quat;
inertia = bonus->inertia;
total_velocity(xj, x[jbody], v[jbody], angmom[jbody],
inertia, quat, vj);
// vector pointing from the contact point on ibody to that on jbody
rsq = delx*delx + dely*dely + delz*delz;
rsqinv = 1.0/rsq;
// relative translational velocity
vr1 = vi[0] - vj[0];
vr2 = vi[1] - vj[1];
vr3 = vi[2] - vj[2];
// normal component
vnnr = vr1*delx + vr2*dely + vr3*delz;
vn1 = delx*vnnr * rsqinv;
vn2 = dely*vnnr * rsqinv;
vn3 = delz*vnnr * rsqinv;
// tangential component
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// normal friction term at contact
fn[0] = -c_n * vn1;
fn[1] = -c_n * vn2;
fn[2] = -c_n * vn3;
// tangential friction term at contact
// excluding the tangential deformation term for now
ft[0] = -c_t * vt1;
ft[1] = -c_t * vt2;
ft[2] = -c_t * vt3;
// these are contact forces (F_n, F_t and F_ne) only
// cohesive forces will be scaled by j_a after contact area is computed
// mu * fne = tangential friction deformation during gross sliding
// see Eq. 4, Fraige et al.
fx = fn[0] + ft[0] + mu * fx;
fy = fn[1] + ft[1] + mu * fy;
fz = fn[2] + ft[2] + mu * fz;
f[ibody][0] += fx;
f[ibody][1] += fy;
f[ibody][2] += fz;
sum_torque(x[ibody], xi, fx, fy, fz, torque[ibody]);
f[jbody][0] -= fx;
f[jbody][1] -= fy;
f[jbody][2] -= fz;
sum_torque(x[jbody], xj, -fx, -fy, -fz, torque[jbody]);
facc[0] += fx; facc[1] += fy; facc[2] += fz;
#ifdef _POLYHEDRON_DEBUG
printf("contact ibody = %d: f = %f %f %f; torque = %f %f %f\n", ibody,
f[ibody][0], f[ibody][1], f[ibody][2],
torque[ibody][0], torque[ibody][1], torque[ibody][2]);
printf("contact jbody = %d: f = %f %f %f; torque = %f %f %f\n", jbody,
f[jbody][0], f[jbody][1], f[jbody][2],
torque[jbody][0], torque[jbody][1], torque[jbody][2]);
#endif
}
/* ----------------------------------------------------------------------
Rescale the forces and torques for all the contacts
------------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::rescale_cohesive_forces(double** x,
double** f, double** torque, Contact* contact_list, int &num_contacts,
int itype, int jtype, double* facc)
{
int m,ibody,jbody;
double delx,dely,delz,fx,fy,fz,R,fpair,r,contact_area;
int num_unique_contacts = 0;
if (num_contacts == 1) {
num_unique_contacts = 1;
contact_area = 0;
} else if (num_contacts == 2) {
num_unique_contacts = 2;
contact_area = num_contacts * A_ua;
} else {
find_unique_contacts(contact_list, num_contacts);
double xc[3],dx,dy,dz;
xc[0] = xc[1] = xc[2] = 0;
num_unique_contacts = 0;
for (int m = 0; m < num_contacts; m++) {
if (contact_list[m].unique == 0) continue;
xc[0] += contact_list[m].xi[0];
xc[1] += contact_list[m].xi[1];
xc[2] += contact_list[m].xi[2];
num_unique_contacts++;
}
xc[0] /= (double)num_unique_contacts;
xc[1] /= (double)num_unique_contacts;
xc[2] /= (double)num_unique_contacts;
contact_area = 0.0;
for (int m = 0; m < num_contacts; m++) {
if (contact_list[m].unique == 0) continue;
dx = contact_list[m].xi[0] - xc[0];
dy = contact_list[m].xi[1] - xc[1];
dz = contact_list[m].xi[2] - xc[2];
contact_area += (dx*dx + dy*dy + dz*dz);
}
contact_area *= (MY_PI/(double)num_unique_contacts);
}
double j_a = contact_area / (num_unique_contacts * A_ua);
if (j_a < 1.0) j_a = 1.0;
for (m = 0; m < num_contacts; m++) {
if (contact_list[m].unique == 0) continue;
ibody = contact_list[m].ibody;
jbody = contact_list[m].jbody;
delx = contact_list[m].xi[0] - contact_list[m].xj[0];
dely = contact_list[m].xi[1] - contact_list[m].xj[1];
delz = contact_list[m].xi[2] - contact_list[m].xj[2];
r = sqrt(delx*delx + dely*dely + delz*delz);
R = contact_list[m].separation;
double energy = 0;
kernel_force(R, itype, jtype, energy, fpair);
fpair *= j_a;
fx = delx*fpair/r;
fy = dely*fpair/r;
fz = delz*fpair/r;
f[ibody][0] += fx;
f[ibody][1] += fy;
f[ibody][2] += fz;
sum_torque(x[ibody], contact_list[m].xi, fx, fy, fz, torque[ibody]);
f[jbody][0] -= fx;
f[jbody][1] -= fy;
f[jbody][2] -= fz;
sum_torque(x[jbody], contact_list[m].xj, -fx, -fy, -fz, torque[jbody]);
facc[0] += fx; facc[1] += fy; facc[2] += fz;
}
}
/* ----------------------------------------------------------------------
Accumulate torque to body from the force f=(fx,fy,fz) acting at point x
------------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::sum_torque(double* xm, double *x, double fx,
double fy, double fz, double* torque)
{
double rx = x[0] - xm[0];
double ry = x[1] - xm[1];
double rz = x[2] - xm[2];
double tx = ry * fz - rz * fy;
double ty = rz * fx - rx * fz;
double tz = rx * fy - ry * fx;
torque[0] += tx;
torque[1] += ty;
torque[2] += tz;
}
/* ----------------------------------------------------------------------
Test if two points a and b are in opposite sides of a plane defined by
a normal vector n and a point x0
------------------------------------------------------------------------- */
int PairBodyRoundedPolyhedron::opposite_sides(double* n, double* x0,
double* a, double* b)
{
double m_a = n[0]*(a[0] - x0[0])+n[1]*(a[1] - x0[1])+n[2]*(a[2] - x0[2]);
double m_b = n[0]*(b[0] - x0[0])+n[1]*(b[1] - x0[1])+n[2]*(b[2] - x0[2]);
// equal to zero when either a or b is on the plane
if (m_a * m_b <= 0)
return 1;
else
return 0;
}
/* ----------------------------------------------------------------------
Test if a line segment defined by two points a and b intersects with
a triangle defined by three points x1, x2 and x3
------------------------------------------------------------------------- */
int PairBodyRoundedPolyhedron::edge_face_intersect(double* x1, double* x2,
double* x3, double* a, double* b, double* h_a, double* h_b,
double& d_a, double& d_b, int& inside_a, int& inside_b)
{
double s[3], u[3], v[3], n[3];
// line director
MathExtra::sub3(b, a, s);
// plane normal vector
MathExtra::sub3(x2, x1, u);
MathExtra::sub3(x3, x1, v);
MathExtra::cross3(u, v, n);
MathExtra::norm3(n);
// find the projection of a and b to the plane and the corresponding distances
project_pt_plane(a, x1, x2, x3, h_a, d_a, inside_a);
project_pt_plane(b, x1, x2, x3, h_b, d_b, inside_b);
// check if the line segment is parallel to the plane
double dot = MathExtra::dot3(s, n);
if (fabs(dot) < EPSILON) return EF_PARALLEL;
// solve for the intersection between the line and the plane
double m[3][3], invm[3][3], p[3], ans[3];
m[0][0] = -s[0];
m[0][1] = u[0];
m[0][2] = v[0];
m[1][0] = -s[1];
m[1][1] = u[1];
m[1][2] = v[1];
m[2][0] = -s[2];
m[2][1] = u[2];
m[2][2] = v[2];
MathExtra::sub3(a, x1, p);
MathExtra::invert3(m, invm);
MathExtra::matvec(invm, p, ans);
// p is reused for the intersection point
// s = b - a
double t = ans[0];
p[0] = a[0] + s[0] * t;
p[1] = a[1] + s[1] * t;
p[2] = a[2] + s[2] * t;
// check if p is inside the triangle, excluding the edges and vertices
// the edge-edge and edge-vertices are handled separately
int inside = 0;
if (ans[1] > 0 && ans[2] > 0 && ans[1] + ans[2] < 1)
inside = 1;
int interact;
if (t < 0 || t > 1) {
interact = EF_SAME_SIDE_OF_FACE;
} else {
if (inside == 1)
interact = EF_INTERSECT_INSIDE;
else
interact = EF_INTERSECT_OUTSIDE;
}
return interact;
}
/* ----------------------------------------------------------------------
Find the projection of q on the plane defined by point p and the normal
unit vector n: q_proj = q - dot(q - p, n) * n
and the distance d from q to the plane
------------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::project_pt_plane(const double* q,
const double* p, const double* n,
double* q_proj, double &d)
{
double dot, ans[3], n_p[3];
n_p[0] = n[0]; n_p[1] = n[1]; n_p[2] = n[2];
MathExtra::sub3(q, p, ans);
dot = MathExtra::dot3(ans, n_p);
MathExtra::scale3(dot, n_p);
MathExtra::sub3(q, n_p, q_proj);
MathExtra::sub3(q, q_proj, ans);
d = MathExtra::len3(ans);
}
/* ----------------------------------------------------------------------
Check if points q1 and q2 are inside a convex polygon, i.e. a face of
a polyhedron
ibody = atom i's index
face_index = face index of the body
xmi = atom i's coordinates
q1 = tested point on the face (e.g. the projection of a point)
q2 = another point (can be a null pointer) for face-edge intersection
Output:
inside1 = 1 if q1 is inside the polygon, 0 otherwise
inside2 = 1 if q2 is inside the polygon, 0 otherwise
------------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::inside_polygon(int ibody, int face_index,
double* xmi, const double* q1, const double* q2,
int& inside1, int& inside2)
{
int i,n,ifirst,iffirst,npi1,npi2;
double xi1[3],xi2[3],u[3],v[3],costheta,anglesum1,anglesum2,magu,magv;
ifirst = dfirst[ibody];
iffirst = facfirst[ibody];
anglesum1 = anglesum2 = 0;;
for (i = 0; i < MAX_FACE_SIZE; i++) {
npi1 = static_cast<int>(face[iffirst+face_index][i]);
if (npi1 < 0) break;
n = i + 1;
if (n <= MAX_FACE_SIZE - 1) {
npi2 = static_cast<int>(face[iffirst+face_index][n]);
if (npi2 < 0) npi2 = static_cast<int>(face[iffirst+face_index][0]);
} else {
npi2 = static_cast<int>(face[iffirst+face_index][0]);
}
xi1[0] = xmi[0] + discrete[ifirst+npi1][0];
xi1[1] = xmi[1] + discrete[ifirst+npi1][1];
xi1[2] = xmi[2] + discrete[ifirst+npi1][2];
xi2[0] = xmi[0] + discrete[ifirst+npi2][0];
xi2[1] = xmi[1] + discrete[ifirst+npi2][1];
xi2[2] = xmi[2] + discrete[ifirst+npi2][2];
MathExtra::sub3(xi1,q1,u);
MathExtra::sub3(xi2,q1,v);
magu = MathExtra::len3(u);
magv = MathExtra::len3(v);
// the point is at either vertices
if (magu * magv < EPSILON) inside1 = 1;
else {
costheta = MathExtra::dot3(u,v)/(magu*magv);
anglesum1 += acos(costheta);
}
if (q2 != nullptr) {
MathExtra::sub3(xi1,q2,u);
MathExtra::sub3(xi2,q2,v);
magu = MathExtra::len3(u);
magv = MathExtra::len3(v);
if (magu * magv < EPSILON) inside2 = 1;
else {
costheta = MathExtra::dot3(u,v)/(magu*magv);
anglesum2 += acos(costheta);
}
}
}
if (fabs(anglesum1 - MY_2PI) < EPSILON) inside1 = 1;
else inside1 = 0;
if (q2 != nullptr) {
if (fabs(anglesum2 - MY_2PI) < EPSILON) inside2 = 1;
else inside2 = 0;
}
}
/* ----------------------------------------------------------------------
Find the projection of q on the plane defined by 3 points x1, x2 and x3
returns the distance d from q to the plane and whether the projected
point is inside the triangle defined by (x1, x2, x3)
------------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::project_pt_plane(const double* q,
const double* x1, const double* x2, const double* x3, double* q_proj,
double &d, int& inside)
{
double u[3],v[3],n[3];
// plane normal vector
MathExtra::sub3(x2, x1, u);
MathExtra::sub3(x3, x1, v);
MathExtra::cross3(u, v, n);
MathExtra::norm3(n);
// solve for the intersection between the line and the plane
double m[3][3], invm[3][3], p[3], ans[3];
m[0][0] = -n[0];
m[0][1] = u[0];
m[0][2] = v[0];
m[1][0] = -n[1];
m[1][1] = u[1];
m[1][2] = v[1];
m[2][0] = -n[2];
m[2][1] = u[2];
m[2][2] = v[2];
MathExtra::sub3(q, x1, p);
MathExtra::invert3(m, invm);
MathExtra::matvec(invm, p, ans);
double t = ans[0];
q_proj[0] = q[0] + n[0] * t;
q_proj[1] = q[1] + n[1] * t;
q_proj[2] = q[2] + n[2] * t;
// check if the projection point is inside the triangle
// exclude the edges and vertices
// edge-sphere and sphere-sphere interactions are handled separately
inside = 0;
if (ans[1] > 0 && ans[2] > 0 && ans[1] + ans[2] < 1) {
inside = 1;
}
// distance from q to q_proj
MathExtra::sub3(q, q_proj, ans);
d = MathExtra::len3(ans);
}
/* ---------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::project_pt_line(const double* q,
const double* xi1, const double* xi2, double* h, double& d, double& t)
{
double u[3],v[3],r[3],s;
MathExtra::sub3(xi2, xi1, u);
MathExtra::norm3(u);
MathExtra::sub3(q, xi1, v);
s = MathExtra::dot3(u, v);
h[0] = xi1[0] + s * u[0];
h[1] = xi1[1] + s * u[1];
h[2] = xi1[2] + s * u[2];
MathExtra::sub3(q, h, r);
d = MathExtra::len3(r);
if (fabs(xi2[0] - xi1[0]) > 0)
t = (h[0] - xi1[0])/(xi2[0] - xi1[0]);
else if (fabs(xi2[1] - xi1[1]) > 0)
t = (h[1] - xi1[1])/(xi2[1] - xi1[1]);
else if (fabs(xi2[2] - xi1[2]) > 0)
t = (h[2] - xi1[2])/(xi2[2] - xi1[2]);
}
/* ----------------------------------------------------------------------
compute the shortest distance between two edges (line segments)
x1, x2: two endpoints of the first edge
x3, x4: two endpoints of the second edge
h1: the end point of the shortest segment perpendicular to both edges
on the line (x1;x2)
h2: the end point of the shortest segment perpendicular to both edges
on the line (x3;x4)
t1: fraction of h1 in the segment (x1,x2)
t2: fraction of h2 in the segment (x3,x4)
------------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1,
const double* x2, const double* x3, const double* x4,
double* h1, double* h2, double& t1, double& t2, double& r)
{
double u[3],v[3],n[3],dot;
// set the default returned values
t1 = -2;
t2 = 2;
r = 0;
// find the edge unit directors and their dot product
MathExtra::sub3(x2, x1, u);
MathExtra::norm3(u);
MathExtra::sub3(x4, x3, v);
MathExtra::norm3(v);
dot = MathExtra::dot3(u,v);
dot = fabs(dot);
// check if two edges are parallel
// find the two ends of the overlapping segment, if any
if (fabs(dot - 1.0) < EPSILON) {
double s1,s2,x13[3],x23[3],x13h[3];
double t13,t23,t31,t41,x31[3],x41[3];
t13=t23=t31=t41=0.0;
MathExtra::sub3(x1,x3,x13); // x13 = x1 - x3
MathExtra::sub3(x2,x3,x23); // x23 = x2 - x3
s1 = MathExtra::dot3(x13,v);
x13h[0] = x13[0] - s1*v[0];
x13h[1] = x13[1] - s1*v[1];
x13h[2] = x13[2] - s1*v[2];
r = MathExtra::len3(x13h);
// x13 is the projection of x1 on x3-x4
x13[0] = x3[0] + s1*v[0];
x13[1] = x3[1] + s1*v[1];
x13[2] = x3[2] + s1*v[2];
// x23 is the projection of x2 on x3-x4
s2 = MathExtra::dot3(x23,v);
x23[0] = x3[0] + s2*v[0];
x23[1] = x3[1] + s2*v[1];
x23[2] = x3[2] + s2*v[2];
// find the fraction of the projection points on the edges
if (fabs(x4[0] - x3[0]) > 0)
t13 = (x13[0] - x3[0])/(x4[0] - x3[0]);
else if (fabs(x4[1] - x3[1]) > 0)
t13 = (x13[1] - x3[1])/(x4[1] - x3[1]);
else if (fabs(x4[2] - x3[2]) > 0)
t13 = (x13[2] - x3[2])/(x4[2] - x3[2]);
if (fabs(x4[0] - x3[0]) > 0)
t23 = (x23[0] - x3[0])/(x4[0] - x3[0]);
else if (fabs(x4[1] - x3[1]) > 0)
t23 = (x23[1] - x3[1])/(x4[1] - x3[1]);
else if (fabs(x4[2] - x3[2]) > 0)
t23 = (x23[2] - x3[2])/(x4[2] - x3[2]);
if (fabs(x23[0] - x13[0]) > 0)
t31 = (x3[0] - x13[0])/(x23[0] - x13[0]);
else if (fabs(x23[1] - x13[1]) > 0)
t31 = (x3[1] - x13[1])/(x23[1] - x13[1]);
else if (fabs(x23[2] - x13[2]) > 0)
t31 = (x3[2] - x13[2])/(x23[2] - x13[2]);
// x31 is the projection of x3 on x1-x2
x31[0] = x1[0] + t31*(x2[0] - x1[0]);
x31[1] = x1[1] + t31*(x2[1] - x1[1]);
x31[2] = x1[2] + t31*(x2[2] - x1[2]);
if (fabs(x23[0] - x13[0]) > 0)
t41 = (x4[0] - x13[0])/(x23[0] - x13[0]);
else if (fabs(x23[1] - x13[1]) > 0)
t41 = (x4[1] - x13[1])/(x23[1] - x13[1]);
else if (fabs(x23[2] - x13[2]) > 0)
t41 = (x4[2] - x13[2])/(x23[2] - x13[2]);
// x41 is the projection of x4 on x1-x2
x41[0] = x1[0] + t41*(x2[0] - x1[0]);
x41[1] = x1[1] + t41*(x2[1] - x1[1]);
x41[2] = x1[2] + t41*(x2[2] - x1[2]);
// determine two ends from the overlapping segments
int n1 = 0;
int n2 = 0;
if (t13 >= 0 && t13 <= 1) {
h1[0] = x1[0];
h1[1] = x1[1];
h1[2] = x1[2];
h2[0] = x13[0];
h2[1] = x13[1];
h2[2] = x13[2];
t1 = 0;
t2 = t13;
n1++;
n2++;
}
if (t23 >= 0 && t23 <= 1) {
if (n1 == 0) {
h1[0] = x2[0];
h1[1] = x2[1];
h1[2] = x2[2];
h2[0] = x23[0];
h2[1] = x23[1];
h2[2] = x23[2];
t1 = 1;
t2 = t23;
n1++;
n2++;
} else {
h1[0] = (x1[0]+x2[0])/2;
h1[1] = (x1[1]+x2[1])/2;
h1[2] = (x1[2]+x2[2])/2;
h2[0] = (x13[0]+x23[0])/2;
h2[1] = (x13[1]+x23[1])/2;
h2[2] = (x13[2]+x23[2])/2;
t1 = 0.5;
t2 = (t13+t23)/2;
n1++;
n2++;
}
}
if (n1 == 0 && n2 == 0) {
if (t31 >= 0 && t31 <= 1) {
h1[0] = x31[0];
h1[1] = x31[1];
h1[2] = x31[2];
h2[0] = x3[0];
h2[1] = x3[1];
h2[2] = x3[2];
t1 = t31;
t2 = 0;
n1++;
n2++;
}
if (t41 >= 0 && t41 <= 1) {
if (n1 == 0) {
h1[0] = x41[0];
h1[1] = x41[1];
h1[2] = x41[2];
h2[0] = x4[0];
h2[1] = x4[1];
h2[2] = x4[2];
t1 = t41;
t2 = 1;
n1++;
n2++;
} else {
h1[0] = (x31[0]+x41[0])/2;
h1[1] = (x31[1]+x41[1])/2;
h1[2] = (x31[2]+x41[2])/2;
h2[0] = (x3[0]+x4[0])/2;
h2[1] = (x3[1]+x4[1])/2;
h2[2] = (x3[2]+x4[2])/2;
t1 = (t31+t41)/2;
t2 = 0.5;
n1++;
n2++;
}
}
}
// if n1 == 0 and n2 == 0 at this point,
// which means no overlapping segments bt two parallel edges,
// return the default values of t1 and t2
return;
}
// find the vector n perpendicular to both edges
MathExtra::cross3(u, v, n);
MathExtra::norm3(n);
// find the intersection of the line (x3,x4) and the plane (x1,x2,n)
// s = director of the line (x3,x4)
// n_p = plane normal vector of the plane (x1,x2,n)
double s[3], n_p[3];
MathExtra::sub3(x4, x3, s);
MathExtra::sub3(x2, x1, u);
MathExtra::cross3(u, n, n_p);
MathExtra::norm3(n_p);
// solve for the intersection between the line and the plane
double m[3][3], invm[3][3], p[3], ans[3];
m[0][0] = -s[0];
m[0][1] = u[0];
m[0][2] = n[0];
m[1][0] = -s[1];
m[1][1] = u[1];
m[1][2] = n[1];
m[2][0] = -s[2];
m[2][1] = u[2];
m[2][2] = n[2];
MathExtra::sub3(x3, x1, p);
MathExtra::invert3(m, invm);
MathExtra::matvec(invm, p, ans);
t2 = ans[0];
h2[0] = x3[0] + s[0] * t2;
h2[1] = x3[1] + s[1] * t2;
h2[2] = x3[2] + s[2] * t2;
project_pt_plane(h2, x1, n, h1, r);
if (fabs(x2[0] - x1[0]) > 0)
t1 = (h1[0] - x1[0])/(x2[0] - x1[0]);
else if (fabs(x2[1] - x1[1]) > 0)
t1 = (h1[1] - x1[1])/(x2[1] - x1[1]);
else if (fabs(x2[2] - x1[2]) > 0)
t1 = (h1[2] - x1[2])/(x2[2] - x1[2]);
}
/* ----------------------------------------------------------------------
Calculate the total velocity of a point (vertex, a point on an edge):
vi = vcm + omega ^ (p - xcm)
------------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::total_velocity(double* p, double *xcm,
double* vcm, double *angmom, double *inertia, double *quat, double* vi)
{
double r[3],omega[3],ex_space[3],ey_space[3],ez_space[3];
r[0] = p[0] - xcm[0];
r[1] = p[1] - xcm[1];
r[2] = p[2] - xcm[2];
MathExtra::q_to_exyz(quat,ex_space,ey_space,ez_space);
MathExtra::angmom_to_omega(angmom,ex_space,ey_space,ez_space,
inertia,omega);
vi[0] = omega[1]*r[2] - omega[2]*r[1] + vcm[0];
vi[1] = omega[2]*r[0] - omega[0]*r[2] + vcm[1];
vi[2] = omega[0]*r[1] - omega[1]*r[0] + vcm[2];
}
/* ----------------------------------------------------------------------
Determine the length of the contact segment, i.e. the separation between
2 contacts, should be extended for 3D models.
------------------------------------------------------------------------- */
double PairBodyRoundedPolyhedron::contact_separation(const Contact& c1,
const Contact& c2)
{
double x1 = 0.5*(c1.xi[0] + c1.xj[0]);
double y1 = 0.5*(c1.xi[1] + c1.xj[1]);
double z1 = 0.5*(c1.xi[2] + c1.xj[2]);
double x2 = 0.5*(c2.xi[0] + c2.xj[0]);
double y2 = 0.5*(c2.xi[1] + c2.xj[1]);
double z2 = 0.5*(c2.xi[2] + c2.xj[2]);
double rsq = (x2 - x1)*(x2 - x1) + (y2 - y1)*(y2 - y1) + (z2 - z1)*(z2 - z1);
return rsq;
}
/* ----------------------------------------------------------------------
find the number of unique contacts
------------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::find_unique_contacts(Contact* contact_list,
int& num_contacts)
{
int n = num_contacts;
for (int i = 0; i < n - 1; i++) {
for (int j = i + 1; j < n; j++) {
if (contact_list[i].unique == 0) continue;
double d = contact_separation(contact_list[i], contact_list[j]);
if (d < EPSILON) contact_list[j].unique = 0;
}
}
}
/* ---------------------------------------------------------------------- */
void PairBodyRoundedPolyhedron::sanity_check()
{
double x1[3],x2[3],h_a[3],h_b[3],d_a,d_b;
double a[3],b[3],t_a,t_b;
x1[0] = 0; x1[1] = 3; x1[2] = 0;
x2[0] = 3; x2[1] = 0; x2[2] = 0;
a[0] = 0; a[1] = 0; a[2] = 0;
b[0] = 4; b[1] = 0; b[2] = 0;
project_pt_line(a, x1, x2, h_a, d_a, t_a);
project_pt_line(b, x1, x2, h_b, d_b, t_b);
/*
printf("h_a: %f %f %f; h_b: %f %f %f; t_a = %f; t_b = %f; d = %f; d_b = %f\n",
h_a[0], h_a[1], h_a[2], h_b[0], h_b[1], h_b[2], t_a, t_b, d_a, d_b);
*/
/*
int inside_a, inside_b;
int mode = edge_face_intersect(x1, x2, x3, a, b, h_a, h_b, d_a, d_b,
inside_a, inside_b);
double u[3],v[3],n[3];
MathExtra::sub3(x2, x1, u);
MathExtra::sub3(x3, x1, v);
MathExtra::cross3(u, v, n);
MathExtra::norm3(n);
*/
/*
project_pt_plane(a, x1, x2, x3, h_a, d_a, inside_a);
printf("h_a: %f %f %f; d = %f: inside %d\n",
h_a[0], h_a[1], h_a[2], d_a, inside_a);
project_pt_plane(b, x1, x2, x3, h_b, d_b, inside_b);
printf("h_b: %f %f %f; d = %f: inside %d\n",
h_b[0], h_b[1], h_b[2], d_b, inside_b);
*/
/*
distance_bt_edges(x1, x2, x3, x4, h_a, h_b, t_a, t_b, d_a);
printf("h_a: %f %f %f; h_b: %f %f %f; t_a = %f; t_b = %f; d = %f\n",
h_a[0], h_a[1], h_a[2], h_b[0], h_b[1], h_b[2], t_a, t_b, d_a);
*/
}
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