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region_prism.cpp
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Wed, Jul 16, 08:20

region_prism.cpp
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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: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "region_prism.h"
#include "domain.h"
#include "force.h"
#include "error.h"
using namespace LAMMPS_NS;
#define BIG 1.0e20
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
RegPrism::RegPrism(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
{
options(narg-11,&arg[11]);
if (strcmp(arg[2],"INF") == 0 || strcmp(arg[2],"EDGE") == 0) {
if (domain->box_exist == 0)
error->all("Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[2],"INF") == 0) xlo = -BIG;
else xlo = domain->boxlo[0];
} else xlo = xscale*atof(arg[2]);
if (strcmp(arg[3],"INF") == 0 || strcmp(arg[3],"EDGE") == 0) {
if (domain->box_exist == 0)
error->all("Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[3],"INF") == 0) xhi = BIG;
else xhi = domain->boxhi[0];
} else xhi = xscale*atof(arg[3]);
if (strcmp(arg[4],"INF") == 0 || strcmp(arg[4],"EDGE") == 0) {
if (domain->box_exist == 0)
error->all("Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[4],"INF") == 0) ylo = -BIG;
else ylo = domain->boxlo[1];
} else ylo = yscale*atof(arg[4]);
if (strcmp(arg[5],"INF") == 0 || strcmp(arg[5],"EDGE") == 0) {
if (domain->box_exist == 0)
error->all("Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[5],"INF") == 0) yhi = BIG;
else yhi = domain->boxhi[1];
} else yhi = yscale*atof(arg[5]);
if (strcmp(arg[6],"INF") == 0 || strcmp(arg[6],"EDGE") == 0) {
if (domain->box_exist == 0)
error->all("Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[6],"INF") == 0) zlo = -BIG;
else zlo = domain->boxlo[2];
} else zlo = zscale*atof(arg[6]);
if (strcmp(arg[7],"INF") == 0 || strcmp(arg[7],"EDGE") == 0) {
if (domain->box_exist == 0)
error->all("Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[7],"INF") == 0) zhi = BIG;
else zhi = domain->boxhi[2];
} else zhi = zscale*atof(arg[7]);
xy = xscale*atof(arg[8]);
xz = xscale*atof(arg[9]);
yz = yscale*atof(arg[10]);
// error check
// prism cannot be 0 thickness in any dim, else inverse blows up
// non-zero tilt values cannot be used if either dim is INF on both ends
if (xlo >= xhi || ylo >= yhi || zlo >= zhi)
error->all("Illegal region prism command");
if (xy != 0.0 && xlo == -BIG && xhi == BIG)
error->all("Illegal region prism command");
if (xy != 0.0 && ylo == -BIG && yhi == BIG)
error->all("Illegal region prism command");
if (xz != 0.0 && xlo == -BIG && xhi == BIG)
error->all("Illegal region prism command");
if (xz != 0.0 && zlo == -BIG && zhi == BIG)
error->all("Illegal region prism command");
if (yz != 0.0 && ylo == -BIG && yhi == BIG)
error->all("Illegal region prism command");
if (yz != 0.0 && zlo == -BIG && zhi == BIG)
error->all("Illegal region prism command");
// extent of prism
if (interior) {
bboxflag = 1;
extent_xlo = MIN(xlo,xlo+xy);
extent_xlo = MIN(extent_xlo,extent_xlo+xz);
extent_ylo = MIN(ylo,ylo+yz);
extent_zlo = zlo;
extent_xhi = MAX(xhi,xhi+xy);
extent_xhi = MAX(extent_xhi,extent_xhi+xz);
extent_yhi = MAX(yhi,yhi+yz);
extent_zhi = zhi;
} else bboxflag = 0;
// particle could contact all 6 planes
cmax = 6;
contact = new Contact[cmax];
// h = transformation matrix from tilt coords (0-1) to box coords (xyz)
// columns of h are edge vectors of tilted box
// hinv = transformation matrix from box coords to tilt coords
// both h and hinv are upper triangular
// since 1st edge of prism is along x-axis
// and bottom face of prism is in xy plane
h[0][0] = xhi - xlo;
h[0][1] = xy;
h[0][2] = xz;
h[1][1] = yhi - ylo;
h[1][2] = yz;
h[2][2] = zhi - zlo;
hinv[0][0] = 1.0/h[0][0];
hinv[0][1] = -h[0][1] / (h[0][0]*h[1][1]);
hinv[0][2] = (h[0][1]*h[1][2] - h[0][2]*h[1][1]) / (h[0][0]*h[1][1]*h[2][2]);
hinv[1][1] = 1.0/h[1][1];
hinv[1][2] = -h[1][2] / (h[1][1]*h[2][2]);
hinv[2][2] = 1.0/h[2][2];
// corners = 8 corner points of prism
// order = x varies fastest, then y, finally z
// clo/chi = lo and hi corner pts of prism
a[0] = xhi-xlo;
a[1] = 0.0;
a[2] = 0.0;
b[0] = xy;
b[1] = yhi-ylo;
b[2] = 0.0;
c[0] = xz;
c[1] = yz;
c[2] = zhi-zlo;
clo[0] = corners[0][0] = xlo;
clo[1] = corners[0][1] = ylo;
clo[2] = corners[0][2] = zlo;
corners[1][0] = xlo + a[0];
corners[1][1] = ylo + a[1];
corners[1][2] = zlo + a[2];
corners[2][0] = xlo + b[0];
corners[2][1] = ylo + b[1];
corners[2][2] = zlo + b[2];
corners[3][0] = xlo + a[0] + b[0];
corners[3][1] = ylo + a[1] + b[1];
corners[3][2] = zlo + a[2] + b[2];
corners[4][0] = xlo + c[0];
corners[4][1] = ylo + c[1];
corners[4][2] = zlo + c[2];
corners[5][0] = xlo + a[0] + c[0];
corners[5][1] = ylo + a[1] + c[1];
corners[5][2] = zlo + a[2] + c[2];
corners[6][0] = xlo + b[0] + c[0];
corners[6][1] = ylo + b[1] + c[1];
corners[6][2] = zlo + b[2] + c[2];
chi[0] = corners[7][0] = xlo + a[0] + b[0] + c[0];
chi[1] = corners[7][1] = ylo + a[1] + b[1] + c[1];
chi[2] = corners[7][2] = zlo + a[2] + b[2] + c[2];
// face = 6 inward-facing unit normals to prism faces
// order = xy plane, xz plane, yz plane
cross(a,b,face[0]);
cross(b,a,face[1]);
cross(c,a,face[2]);
cross(a,c,face[3]);
cross(b,c,face[4]);
cross(c,b,face[5]);
for (int i = 0; i < 6; i++) normalize(face[i]);
// tri = 3 vertices (0-7) in each of 12 triangles on 6 faces
// verts in each tri are ordered so that right-hand rule gives inward norm
// order = xy plane, xz plane, yz plane
tri[0][0] = 0; tri[0][1] = 1; tri[0][2] = 3;
tri[1][0] = 0; tri[1][1] = 3; tri[1][2] = 2;
tri[2][0] = 4; tri[2][1] = 7; tri[2][2] = 5;
tri[3][0] = 4; tri[3][1] = 6; tri[3][2] = 7;
tri[4][0] = 0; tri[4][1] = 4; tri[4][2] = 5;
tri[5][0] = 0; tri[5][1] = 5; tri[5][2] = 1;
tri[6][0] = 2; tri[6][1] = 7; tri[6][2] = 6;
tri[7][0] = 2; tri[7][1] = 3; tri[7][2] = 7;
tri[8][0] = 2; tri[8][1] = 6; tri[8][2] = 4;
tri[9][0] = 2; tri[9][1] = 4; tri[9][2] = 0;
tri[10][0] = 1; tri[10][1] = 5; tri[10][2] = 7;
tri[11][0] = 1; tri[11][1] = 7; tri[11][2] = 3;
}
/* ---------------------------------------------------------------------- */
RegPrism::~RegPrism()
{
delete [] contact;
}
/* ----------------------------------------------------------------------
inside = 1 if x,y,z is inside or on surface
inside = 0 if x,y,z is outside and not on surface
abc = Hinv * (xyz - xyz/lo)
abc = tilt coords (0-1)
Hinv = transformation matrix from box coords to tilt coords
xyz = box coords
xyz/lo = lower-left corner of prism
------------------------------------------------------------------------- */
int RegPrism::inside(double x, double y, double z)
{
double a = hinv[0][0]*(x-xlo) + hinv[0][1]*(y-ylo) + hinv[0][2]*(z-zlo);
double b = hinv[1][1]*(y-ylo) + hinv[1][2]*(z-zlo);
double c = hinv[2][2]*(z-zlo);
if (a >= 0.0 && a <= 1.0 && b >= 0.0 && b <= 1.0 && c >= 0.0 && c <= 1.0)
return 1;
return 0;
}
/* ----------------------------------------------------------------------
contact if 0 <= x < cutoff from one or more inner surfaces of prism
can be one contact for each of 6 faces
no contact if outside (possible if called from union/intersect)
delxyz = vector from nearest point on prism to x
------------------------------------------------------------------------- */
int RegPrism::surface_interior(double *x, double cutoff)
{
int i;
double dot;
double *corner;
// x is exterior to prism
for (i = 0; i < 6; i++) {
if (i % 2) corner = chi;
else corner = clo;
dot = (x[0]-corner[0])*face[i][0] + (x[1]-corner[1])*face[i][1] +
(x[2]-corner[2])*face[i][2];
if (dot < 0.0) return 0;
}
// x is interior to prism or on its surface
int n = 0;
for (int i = 0; i < 6; i++) {
if (i % 2) corner = chi;
else corner = clo;
dot = (x[0]-corner[0])*face[i][0] + (x[1]-corner[1])*face[i][1] +
(x[2]-corner[2])*face[i][2];
if (dot < cutoff) {
contact[n].r = dot;
contact[n].delx = dot*face[i][0];
contact[n].dely = dot*face[i][1];
contact[n].delz = dot*face[i][2];
n++;
}
}
return n;
}
/* ----------------------------------------------------------------------
one contact if 0 <= x < cutoff from outer surface of prism
no contact if inside (possible if called from union/intersect)
delxyz = vector from nearest point on prism to x
------------------------------------------------------------------------- */
int RegPrism::surface_exterior(double *x, double cutoff)
{
int i;
double dot;
double *corner;
double xp,yp,zp;
// x is far enough from prism that there is no contact
for (i = 0; i < 6; i++) {
if (i % 2) corner = chi;
else corner = clo;
dot = (x[0]-corner[0])*face[i][0] + (x[1]-corner[1])*face[i][1] +
(x[2]-corner[2])*face[i][2];
if (dot <= -cutoff) return 0;
}
// x is interior to prism
for (i = 0; i < 6; i++) {
if (i % 2) corner = chi;
else corner = clo;
dot = (x[0]-corner[0])*face[i][0] + (x[1]-corner[1])*face[i][1] +
(x[2]-corner[2])*face[i][2];
if (dot <= 0.0) break;
}
if (i == 6) return 0;
// x is exterior to prism or on its surface
// xp,yp,zp = point on surface of prism that x is closest to
// could be edge or corner pt of prism
// do not add contact point if r >= cutoff
find_nearest(x,xp,yp,zp);
add_contact(0,x,xp,yp,zp);
if (contact[0].r < cutoff) return 1;
return 0;
}
/* ----------------------------------------------------------------------
x is exterior to prism or on its surface
return (xp,yp,zp) = nearest pt to x that is on surface of prism
------------------------------------------------------------------------- */
void RegPrism::find_nearest(double *x, double &xp, double &yp, double &zp)
{
int i,j,k,iface;
double xproj[3],xline[3],nearest[3];
double dot;
// generate successive xnear points, one nearest to x is (xp,yp,zp)
// loop over 6 faces and 2 triangles in each face
// xproj = x projected to plane of triangle
// if xproj is inside or on triangle boundary, that is xnear
// else: loop over 3 edges of triangle
// compute distance to edge line
// xnear = nearest point on line to xproj, bounded by segment end pts
double distsq = BIG;
for (int itri = 0; itri < 12; itri++) {
iface = itri/2;
i = tri[itri][0];
j = tri[itri][1];
k = tri[itri][2];
dot = (x[0]-corners[i][0])*face[iface][0] +
(x[1]-corners[i][1])*face[iface][1] +
(x[2]-corners[i][2])*face[iface][2];
xproj[0] = x[0] - dot*face[iface][0];
xproj[1] = x[1] - dot*face[iface][1];
xproj[2] = x[2] - dot*face[iface][2];
if (inside_tri(xproj,corners[i],corners[j],corners[k],face[iface]))
distsq = closest(x,xproj,nearest,distsq);
else {
point_on_line_segment(corners[i],corners[j],xproj,xline);
distsq = closest(x,xline,nearest,distsq);
point_on_line_segment(corners[j],corners[k],xproj,xline);
distsq = closest(x,xline,nearest,distsq);
point_on_line_segment(corners[i],corners[k],xproj,xline);
distsq = closest(x,xline,nearest,distsq);
}
}
xp = nearest[0];
yp = nearest[1];
zp = nearest[2];
}
/* ----------------------------------------------------------------------
test if x is inside triangle with vertices v1,v2,v3
norm = normal to triangle, defined by right-hand rule for v1,v2,v3 ordering
edge = edge vector of triangle
pvec = vector from vertex to x
xproduct = cross product of edge with pvec
if xproduct dot norm < 0.0 for any of 3 edges, then x is outside triangle
------------------------------------------------------------------------- */
int RegPrism::inside_tri(double *x, double *v1, double *v2, double *v3,
double *norm)
{
double edge[3],pvec[3],xproduct[3];
subtract(v1,v2,edge);
subtract(v1,x,pvec);
cross(edge,pvec,xproduct);
if (dotproduct(xproduct,norm) < 0.0) return 0;
subtract(v2,v3,edge);
subtract(v2,x,pvec);
cross(edge,pvec,xproduct);
if (dotproduct(xproduct,norm) < 0.0) return 0;
subtract(v3,v1,edge);
subtract(v3,x,pvec);
cross(edge,pvec,xproduct);
if (dotproduct(xproduct,norm) < 0.0) return 0;
return 1;
}
/* ----------------------------------------------------------------------
find nearest point to C on line segment A,B and return it as D
project (C-A) onto (B-A)
t = length of that projection, normalized by length of (B-A)
t <= 0, C is closest to A
t >= 1, C is closest to B
else closest point is between A and B
------------------------------------------------------------------------- */
void RegPrism::point_on_line_segment(double *a, double *b,
double *c, double *d)
{
double ba[3],ca[3];
subtract(a,b,ba);
subtract(a,c,ca);
double t = dotproduct(ca,ba) / dotproduct(ba,ba);
if (t <= 0.0) {
d[0] = a[0];
d[1] = a[1];
d[2] = a[2];
} else if (t >= 1.0) {
d[0] = b[0];
d[1] = b[1];
d[2] = b[2];
} else {
d[0] = a[0] + t*ba[0];
d[1] = a[1] + t*ba[1];
d[2] = a[2] + t*ba[2];
}
}
/* ---------------------------------------------------------------------- */
double RegPrism::closest(double *x, double *near, double *nearest, double dsq)
{
double delx = x[0] - near[0];
double dely = x[1] - near[1];
double delz = x[2] - near[2];
double rsq = delx*delx + dely*dely + delz*delz;
if (rsq >= dsq) return dsq;
nearest[0] = near[0];
nearest[1] = near[1];
nearest[2] = near[2];
return rsq;
}
/* ----------------------------------------------------------------------
v3 = v2 - v1
------------------------------------------------------------------------- */
void RegPrism::subtract(double *v1, double *v2, double *v3)
{
v3[0] = v2[0] - v1[0];
v3[1] = v2[1] - v1[1];
v3[2] = v2[2] - v1[2];
}
/* ----------------------------------------------------------------------
v3 = v1 x v2
------------------------------------------------------------------------- */
void RegPrism::cross(double *v1, double *v2, double *v3)
{
v3[0] = v1[1]*v2[2] - v1[2]*v2[1];
v3[1] = v1[2]*v2[0] - v1[0]*v2[2];
v3[2] = v1[0]*v2[1] - v1[1]*v2[0];
}
/* ----------------------------------------------------------------------
return dotproduct = v1 dot v2
------------------------------------------------------------------------- */
double RegPrism::dotproduct(double *v1, double *v2)
{
return (v1[0]*v2[0] + v1[1]*v2[1] + v1[2]*v2[2]);
}
/* ---------------------------------------------------------------------- */
void RegPrism::normalize(double *x)
{
double invlen = 1.0/sqrt(x[0]*x[0] + x[1]*x[1] + x[2]*x[2]);
x[0] *= invlen;
x[1] *= invlen;
x[2] *= invlen;
}

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