Homec4science
Diffusion lammps (master) Browse

lammps/src/region_block.cpp
b921b69f4792master

Last Change
Raw File

region_block.cpp
View Options

/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <string.h>
#include "region_block.h"
#include "force.h"
#include "domain.h"
#include "math_extra.h"
#include "error.h"
using namespace LAMMPS_NS;
#define BIG 1.0e20
/* ---------------------------------------------------------------------- */
RegBlock::RegBlock(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
{
options(narg-8,&arg[8]);
if (strcmp(arg[2],"INF") == 0 || strcmp(arg[2],"EDGE") == 0) {
if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[2],"INF") == 0) xlo = -BIG;
else if (domain->triclinic == 0) xlo = domain->boxlo[0];
else xlo = domain->boxlo_bound[0];
} else xlo = xscale*force->numeric(FLERR,arg[2]);
if (strcmp(arg[3],"INF") == 0 || strcmp(arg[3],"EDGE") == 0) {
if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[3],"INF") == 0) xhi = BIG;
else if (domain->triclinic == 0) xhi = domain->boxhi[0];
else xhi = domain->boxhi_bound[0];
} else xhi = xscale*force->numeric(FLERR,arg[3]);
if (strcmp(arg[4],"INF") == 0 || strcmp(arg[4],"EDGE") == 0) {
if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[4],"INF") == 0) ylo = -BIG;
else if (domain->triclinic == 0) ylo = domain->boxlo[1];
else ylo = domain->boxlo_bound[1];
} else ylo = yscale*force->numeric(FLERR,arg[4]);
if (strcmp(arg[5],"INF") == 0 || strcmp(arg[5],"EDGE") == 0) {
if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[5],"INF") == 0) yhi = BIG;
else if (domain->triclinic == 0) yhi = domain->boxhi[1];
else yhi = domain->boxhi_bound[1];
} else yhi = yscale*force->numeric(FLERR,arg[5]);
if (strcmp(arg[6],"INF") == 0 || strcmp(arg[6],"EDGE") == 0) {
if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[6],"INF") == 0) zlo = -BIG;
else if (domain->triclinic == 0) zlo = domain->boxlo[2];
else zlo = domain->boxlo_bound[2];
} else zlo = zscale*force->numeric(FLERR,arg[6]);
if (strcmp(arg[7],"INF") == 0 || strcmp(arg[7],"EDGE") == 0) {
if (domain->box_exist == 0)
error->all(FLERR,"Cannot use region INF or EDGE when box does not exist");
if (strcmp(arg[7],"INF") == 0) zhi = BIG;
else if (domain->triclinic == 0) zhi = domain->boxhi[2];
else zhi = domain->boxhi_bound[2];
} else zhi = zscale*force->numeric(FLERR,arg[7]);
// error check
if (xlo > xhi || ylo > yhi || zlo > zhi)
error->all(FLERR,"Illegal region block command");
// extent of block
if (interior) {
bboxflag = 1;
extent_xlo = xlo;
extent_xhi = xhi;
extent_ylo = ylo;
extent_yhi = yhi;
extent_zlo = zlo;
extent_zhi = zhi;
} else bboxflag = 0;
// particle could be close to all 6 planes
// particle can only touch 3 planes
cmax = 6;
contact = new Contact[cmax];
if (interior) tmax = 3;
else tmax = 1;
// open face data structs
face[0][0] = -1.0;
face[0][1] = 0.0;
face[0][2] = 0.0;
face[1][0] = 1.0;
face[1][1] = 0.0;
face[1][2] = 0.0;
face[2][0] = 0.0;
face[2][1] = -1.0;
face[2][2] = 0.0;
face[3][0] = 0.0;
face[3][1] = 1.0;
face[3][2] = 0.0;
face[4][0] = 0.0;
face[4][1] = 0.0;
face[4][2] = -1.0;
face[5][0] = 0.0;
face[5][1] = 0.0;
face[5][2] = 1.0;
// face[0]
corners[0][0][0] = xlo;
corners[0][0][1] = ylo;
corners[0][0][2] = zlo;
corners[0][1][0] = xlo;
corners[0][1][1] = ylo;
corners[0][1][2] = zhi;
corners[0][2][0] = xlo;
corners[0][2][1] = yhi;
corners[0][2][2] = zhi;
corners[0][3][0] = xlo;
corners[0][3][1] = yhi;
corners[0][3][2] = zlo;
// face[1]
corners[1][0][0] = xhi;
corners[1][0][1] = ylo;
corners[1][0][2] = zlo;
corners[1][1][0] = xhi;
corners[1][1][1] = ylo;
corners[1][1][2] = zhi;
corners[1][2][0] = xhi;
corners[1][2][1] = yhi;
corners[1][2][2] = zhi;
corners[1][3][0] = xhi;
corners[1][3][1] = yhi;
corners[1][3][2] = zlo;
// face[2]
MathExtra::copy3(corners[2][0],corners[0][0]);
MathExtra::copy3(corners[2][1],corners[1][0]);
MathExtra::copy3(corners[2][2],corners[1][1]);
MathExtra::copy3(corners[2][3],corners[0][1]);
// face[3]
MathExtra::copy3(corners[3][0],corners[0][3]);
MathExtra::copy3(corners[3][1],corners[0][2]);
MathExtra::copy3(corners[3][2],corners[1][2]);
MathExtra::copy3(corners[3][3],corners[1][3]);
// face[4]
MathExtra::copy3(corners[4][0],corners[0][0]);
MathExtra::copy3(corners[4][1],corners[0][3]);
MathExtra::copy3(corners[4][2],corners[1][3]);
MathExtra::copy3(corners[4][3],corners[1][0]);
// face[5]
MathExtra::copy3(corners[5][0],corners[0][1]);
MathExtra::copy3(corners[5][1],corners[1][1]);
MathExtra::copy3(corners[5][2],corners[1][2]);
MathExtra::copy3(corners[5][3],corners[0][2]);
}
/* ---------------------------------------------------------------------- */
RegBlock::~RegBlock()
{
if (copymode) return;
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
------------------------------------------------------------------------- */
int RegBlock::inside(double x, double y, double z)
{
if (x >= xlo && x <= xhi && y >= ylo && y <= yhi && z >= zlo && z <= zhi)
return 1;
return 0;
}
/* ----------------------------------------------------------------------
contact if 0 <= x < cutoff from one or more inner surfaces of block
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 block to x
------------------------------------------------------------------------- */
int RegBlock::surface_interior(double *x, double cutoff)
{
double delta;
// x is exterior to block
if (x[0] < xlo || x[0] > xhi || x[1] < ylo || x[1] > yhi ||
x[2] < zlo || x[2] > zhi) return 0;
// x is interior to block or on its surface
int n = 0;
delta = x[0] - xlo;
if (delta < cutoff && !open_faces[0]) {
contact[n].r = delta;
contact[n].delx = delta;
contact[n].dely = contact[n].delz = 0.0;
contact[n].radius = 0;
contact[n].iwall = 0;
n++;
}
delta = xhi - x[0];
if (delta < cutoff && !open_faces[1]) {
contact[n].r = delta;
contact[n].delx = -delta;
contact[n].dely = contact[n].delz = 0.0;
contact[n].radius = 0;
contact[n].iwall = 1;
n++;
}
delta = x[1] - ylo;
if (delta < cutoff && !open_faces[2]) {
contact[n].r = delta;
contact[n].dely = delta;
contact[n].delx = contact[n].delz = 0.0;
contact[n].radius = 0;
contact[n].iwall = 2;
n++;
}
delta = yhi - x[1];
if (delta < cutoff && !open_faces[3]) {
contact[n].r = delta;
contact[n].dely = -delta;
contact[n].delx = contact[n].delz = 0.0;
contact[n].radius = 0;
contact[n].iwall = 3;
n++;
}
delta = x[2] - zlo;
if (delta < cutoff && !open_faces[4]) {
contact[n].r = delta;
contact[n].delz = delta;
contact[n].delx = contact[n].dely = 0.0;
contact[n].radius = 0;
contact[n].iwall = 4;
n++;
}
delta = zhi - x[2];
if (delta < cutoff && !open_faces[5]) {
contact[n].r = delta;
contact[n].delz = -delta;
contact[n].delx = contact[n].dely = 0.0;
contact[n].radius = 0;
contact[n].iwall = 5;
n++;
}
return n;
}
/* ----------------------------------------------------------------------
one contact if 0 <= x < cutoff from outer surface of block
no contact if inside (possible if called from union/intersect)
delxyz = vector from nearest point on block to x
------------------------------------------------------------------------- */
int RegBlock::surface_exterior(double *x, double cutoff)
{
double xp,yp,zp;
double xc,yc,zc,dist,mindist;
// x is far enough from block that there is no contact
// x is interior to block
if (x[0] <= xlo-cutoff || x[0] >= xhi+cutoff ||
x[1] <= ylo-cutoff || x[1] >= yhi+cutoff ||
x[2] <= zlo-cutoff || x[2] >= zhi+cutoff) return 0;
if (x[0] > xlo && x[0] < xhi && x[1] > ylo && x[1] < yhi &&
x[2] > zlo && x[2] < zhi) return 0;
// x is exterior to block or on its surface
// xp,yp,zp = point on surface of block that x is closest to
// could be edge or corner pt of block
// do not add contact point if r >= cutoff
if (!openflag){
if (x[0] < xlo) xp = xlo;
else if (x[0] > xhi) xp = xhi;
else xp = x[0];
if (x[1] < ylo) yp = ylo;
else if (x[1] > yhi) yp = yhi;
else yp = x[1];
if (x[2] < zlo) zp = zlo;
else if (x[2] > zhi) zp = zhi;
else zp = x[2];
}
else{
mindist = BIG;
for (int i = 0; i < 6; i++){
if (open_faces[i]) continue;
dist = find_closest_point(i,x,xc,yc,zc);
if (dist < mindist){
xp = xc;
yp = yc;
zp = zc;
mindist = dist;
}
}
}
add_contact(0,x,xp,yp,zp);
contact[0].iwall = 0;
if (contact[0].r < cutoff) return 1;
return 0;
}
/*------------------------------------------------------------------------
return distance to closest point on surface I of block region
store closest point in xc,yc,zc
--------------------------------------------------------------------------*/
double RegBlock::find_closest_point(int i, double *x,
double &xc, double &yc, double &zc)
{
double dot,d2,d2min;
double xr[3],xproj[3],p[3];
xr[0] = x[0] - corners[i][0][0];
xr[1] = x[1] - corners[i][0][1];
xr[2] = x[2] - corners[i][0][2];
dot = face[i][0]*xr[0] + face[i][1]*xr[1] + face[i][2]*xr[2];
xproj[0] = xr[0] - dot*face[i][0];
xproj[1] = xr[1] - dot*face[i][1];
xproj[2] = xr[2] - dot*face[i][2];
d2min = BIG;
// check if point projects inside of face
if (inside_face(xproj, i)){
d2 = d2min = dot*dot;
xc = xproj[0] + corners[i][0][0];
yc = xproj[1] + corners[i][0][1];
zc = xproj[2] + corners[i][0][2];
// check each edge
} else {
point_on_line_segment(corners[i][0],corners[i][1],x,p);
d2 = (p[0]-x[0])*(p[0]-x[0]) + (p[1]-x[1])*(p[1]-x[1]) +
(p[2]-x[2])*(p[2]-x[2]);
if (d2 < d2min) {
d2min = d2;
xc = p[0];
yc = p[1];
zc = p[2];
}
point_on_line_segment(corners[i][1],corners[i][2],x,p);
d2 = (p[0]-x[0])*(p[0]-x[0]) + (p[1]-x[1])*(p[1]-x[1]) +
(p[2]-x[2])*(p[2]-x[2]);
if (d2 < d2min) {
d2min = d2;
xc = p[0];
yc = p[1];
zc = p[2];
}
point_on_line_segment(corners[i][2],corners[i][3],x,p);
d2 = (p[0]-x[0])*(p[0]-x[0]) + (p[1]-x[1])*(p[1]-x[1]) +
(p[2]-x[2])*(p[2]-x[2]);
if (d2 < d2min) {
d2min = d2;
xc = p[0];
yc = p[1];
zc = p[2];
}
point_on_line_segment(corners[i][3],corners[i][0],x,p);
d2 = (p[0]-x[0])*(p[0]-x[0]) + (p[1]-x[1])*(p[1]-x[1]) +
(p[2]-x[2])*(p[2]-x[2]);
if (d2 < d2min) {
d2min = d2;
xc = p[0];
yc = p[1];
zc = p[2];
}
}
return d2min;
}
/*------------------------------------------------------------------------
determine if projected point is inside given face of the block
--------------------------------------------------------------------------*/
int RegBlock::inside_face(double *xproj, int iface)
{
if (iface < 2) {
if (xproj[1] > 0 && (xproj[1] < yhi-ylo) &&
xproj[2] > 0 && (xproj[2] < zhi-zlo)) return 1;
} else if (iface < 4) {
if (xproj[0] > 0 && (xproj[0] < (xhi-xlo)) &&
xproj[2] > 0 && (xproj[2] < (zhi-zlo))) return 1;
} else {
if (xproj[0] > 0 && xproj[0] < (xhi-xlo) &&
xproj[1] > 0 && xproj[1] < (yhi-ylo)) return 1;
}
return 0;
}
c4science · Help