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lammps/src/region_cylinder.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.
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "region_cylinder.h"
#include "update.h"
#include "domain.h"
#include "input.h"
#include "variable.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
#define BIG 1.0e20
enum{CONSTANT,VARIABLE};
/* ---------------------------------------------------------------------- */
RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) :
Region(lmp, narg, arg)
{
options(narg-8,&arg[8]);
// check open face settings
if (openflag && (open_faces[2] || open_faces[3] ||
open_faces[4] || open_faces[5]))
error->all(FLERR,"Invalid region cylinder open setting");
if (strcmp(arg[2],"x") && strcmp(arg[2],"y") && strcmp(arg[2],"z"))
error->all(FLERR,"Illegal region cylinder command");
axis = arg[2][0];
if (axis == 'x') {
c1 = yscale*force->numeric(FLERR,arg[3]);
c2 = zscale*force->numeric(FLERR,arg[4]);
} else if (axis == 'y') {
c1 = xscale*force->numeric(FLERR,arg[3]);
c2 = zscale*force->numeric(FLERR,arg[4]);
} else if (axis == 'z') {
c1 = xscale*force->numeric(FLERR,arg[3]);
c2 = yscale*force->numeric(FLERR,arg[4]);
}
rstr = NULL;
if (strstr(arg[5],"v_") == arg[5]) {
int n = strlen(&arg[5][2]) + 1;
rstr = new char[n];
strcpy(rstr,&arg[5][2]);
radius = 0.0;
rstyle = VARIABLE;
varshape = 1;
variable_check();
shape_update();
} else {
radius = force->numeric(FLERR,arg[5]);
if (axis == 'x') radius *= yscale;
else radius *= xscale;
rstyle = CONSTANT;
}
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 (axis == 'x') {
if (strcmp(arg[6],"INF") == 0) lo = -BIG;
else if (domain->triclinic == 0) lo = domain->boxlo[0];
else lo = domain->boxlo_bound[0];
}
if (axis == 'y') {
if (strcmp(arg[6],"INF") == 0) lo = -BIG;
else if (domain->triclinic == 0) lo = domain->boxlo[1];
else lo = domain->boxlo_bound[1];
}
if (axis == 'z') {
if (strcmp(arg[6],"INF") == 0) lo = -BIG;
else if (domain->triclinic == 0) lo = domain->boxlo[2];
else lo = domain->boxlo_bound[2];
}
} else {
if (axis == 'x') lo = xscale*force->numeric(FLERR,arg[6]);
if (axis == 'y') lo = yscale*force->numeric(FLERR,arg[6]);
if (axis == 'z') lo = 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 (axis == 'x') {
if (strcmp(arg[7],"INF") == 0) hi = BIG;
else if (domain->triclinic == 0) hi = domain->boxhi[0];
else hi = domain->boxhi_bound[0];
}
if (axis == 'y') {
if (strcmp(arg[7],"INF") == 0) hi = BIG;
else if (domain->triclinic == 0) hi = domain->boxhi[1];
else hi = domain->boxhi_bound[1];
}
if (axis == 'z') {
if (strcmp(arg[7],"INF") == 0) hi = BIG;
else if (domain->triclinic == 0) hi = domain->boxhi[2];
else hi = domain->boxhi_bound[2];
}
} else {
if (axis == 'x') hi = xscale*force->numeric(FLERR,arg[7]);
if (axis == 'y') hi = yscale*force->numeric(FLERR,arg[7]);
if (axis == 'z') hi = zscale*force->numeric(FLERR,arg[7]);
}
// error check
if (radius <= 0.0) error->all(FLERR,"Illegal region cylinder command");
// extent of cylinder
// for variable radius, uses initial radius
if (interior) {
bboxflag = 1;
if (axis == 'x') {
extent_xlo = lo;
extent_xhi = hi;
extent_ylo = c1 - radius;
extent_yhi = c1 + radius;
extent_zlo = c2 - radius;
extent_zhi = c2 + radius;
}
if (axis == 'y') {
extent_xlo = c1 - radius;
extent_xhi = c1 + radius;
extent_ylo = lo;
extent_yhi = hi;
extent_zlo = c2 - radius;
extent_zhi = c2 + radius;
}
if (axis == 'z') {
extent_xlo = c1 - radius;
extent_xhi = c1 + radius;
extent_ylo = c2 - radius;
extent_yhi = c2 + radius;
extent_zlo = lo;
extent_zhi = hi;
}
} else bboxflag = 0;
// particle could be close to cylinder surface and 2 ends
// particle can only touch surface and 1 end
cmax = 3;
contact = new Contact[cmax];
if (interior) tmax = 2;
else tmax = 1;
}
/* ---------------------------------------------------------------------- */
RegCylinder::~RegCylinder()
{
delete [] rstr;
delete [] contact;
}
/* ---------------------------------------------------------------------- */
void RegCylinder::init()
{
Region::init();
if (rstr) variable_check();
}
/* ----------------------------------------------------------------------
inside = 1 if x,y,z is inside or on surface
inside = 0 if x,y,z is outside and not on surface
------------------------------------------------------------------------- */
int RegCylinder::inside(double x, double y, double z)
{
double del1,del2,dist;
int inside;
if (axis == 'x') {
del1 = y - c1;
del2 = z - c2;
dist = sqrt(del1*del1 + del2*del2);
if (dist <= radius && x >= lo && x <= hi) inside = 1;
else inside = 0;
} else if (axis == 'y') {
del1 = x - c1;
del2 = z - c2;
dist = sqrt(del1*del1 + del2*del2);
if (dist <= radius && y >= lo && y <= hi) inside = 1;
else inside = 0;
} else {
del1 = x - c1;
del2 = y - c2;
dist = sqrt(del1*del1 + del2*del2);
if (dist <= radius && z >= lo && z <= hi) inside = 1;
else inside = 0;
}
return inside;
}
/* ----------------------------------------------------------------------
contact if 0 <= x < cutoff from one or more inner surfaces of cylinder
can be one contact for each of 3 cylinder surfaces
no contact if outside (possible if called from union/intersect)
delxyz = vector from nearest point on cylinder to x
special case: no contact with curved surf if x is on center axis
------------------------------------------------------------------------- */
int RegCylinder::surface_interior(double *x, double cutoff)
{
double del1,del2,r,delta;
int n = 0;
if (axis == 'x') {
del1 = x[1] - c1;
del2 = x[2] - c2;
r = sqrt(del1*del1 + del2*del2);
// x is exterior to cylinder
if (r > radius || x[0] < lo || x[0] > hi) return 0;
// x is interior to cylinder or on its surface
delta = radius - r;
if (delta < cutoff && r > 0.0 && !open_faces[2]) {
contact[n].r = delta;
contact[n].delx = 0.0;
contact[n].dely = del1*(1.0-radius/r);
contact[n].delz = del2*(1.0-radius/r);
contact[n].radius = -2.0*radius;
contact[n].iwall = 2;
contact[n].varflag = 1;
n++;
}
delta = x[0] - lo;
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;
contact[n].varflag = 0;
n++;
}
delta = hi - 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;
contact[n].varflag = 0;
n++;
}
} else if (axis == 'y') {
del1 = x[0] - c1;
del2 = x[2] - c2;
r = sqrt(del1*del1 + del2*del2);
// y is exterior to cylinder
if (r > radius || x[1] < lo || x[1] > hi) return 0;
// y is interior to cylinder or on its surface
delta = radius - r;
if (delta < cutoff && r > 0.0 && !open_faces[2]) {
contact[n].r = delta;
contact[n].delx = del1*(1.0-radius/r);
contact[n].dely = 0.0;
contact[n].delz = del2*(1.0-radius/r);
contact[n].radius = -2.0*radius;
contact[n].iwall = 2;
contact[n].varflag = 1;
n++;
}
delta = x[1] - lo;
if (delta < cutoff && !open_faces[0]) {
contact[n].r = delta;
contact[n].dely = delta;
contact[n].delx = contact[n].delz = 0.0;
contact[n].radius = 0;
contact[n].iwall = 0;
contact[n].varflag = 0;
n++;
}
delta = hi - x[1];
if (delta < cutoff && !open_faces[1]) {
contact[n].r = delta;
contact[n].dely = -delta;
contact[n].delx = contact[n].delz = 0.0;
contact[n].radius = 0;
contact[n].iwall = 1;
contact[n].varflag = 0;
n++;
}
} else {
del1 = x[0] - c1;
del2 = x[1] - c2;
r = sqrt(del1*del1 + del2*del2);
// z is exterior to cylinder
if (r > radius || x[2] < lo || x[2] > hi) return 0;
// z is interior to cylinder or on its surface
delta = radius - r;
if (delta < cutoff && r > 0.0 && !open_faces[2]) {
contact[n].r = delta;
contact[n].delx = del1*(1.0-radius/r);
contact[n].dely = del2*(1.0-radius/r);
contact[n].delz = 0.0;
contact[n].radius = -2.0*radius;
contact[n].iwall = 2;
contact[n].varflag = 1;
n++;
}
delta = x[2] - lo;
if (delta < cutoff && !open_faces[0]) {
contact[n].r = delta;
contact[n].delz = delta;
contact[n].delx = contact[n].dely = 0.0;
contact[n].radius = 0;
contact[n].iwall = 0;
contact[n].varflag = 0;
n++;
}
delta = hi - x[2];
if (delta < cutoff && !open_faces[1]) {
contact[n].r = delta;
contact[n].delz = -delta;
contact[n].delx = contact[n].dely = 0.0;
contact[n].radius = 0;
contact[n].iwall = 1;
contact[n].varflag = 0;
n++;
}
}
return n;
}
/* ----------------------------------------------------------------------
one contact if 0 <= x < cutoff from outer surface of cylinder
no contact if inside (possible if called from union/intersect)
delxyz = vector from nearest point on cylinder to x
------------------------------------------------------------------------- */
int RegCylinder::surface_exterior(double *x, double cutoff)
{
double del1,del2,r;
double xp,yp,zp;
double dx, dr, dr2, d2, d2prev;
// radius of curvature for granular
// 0 for flat surfaces (infinite case), 2*radius for curved portion
double crad = 0.0;
int varflag = 0;
if (axis == 'x') {
del1 = x[1] - c1;
del2 = x[2] - c2;
r = sqrt(del1*del1 + del2*del2);
// x is far enough from cylinder that there is no contact
// x is interior to cylinder
if (r >= radius+cutoff || x[0] <= lo-cutoff || x[0] >= hi+cutoff) return 0;
if (r < radius && x[0] > lo && x[0] < hi) return 0;
// x is exterior to cylinder or on its surface
// xp,yp,zp = point on surface of cylinder that x is closest to
// could be edge of cylinder
// do not add contact point if r >= cutoff
d2prev = BIG;
if (!openflag) {
if (r > radius) {
yp = c1 + del1*radius/r;
zp = c2 + del2*radius/r;
crad = 2.0*radius;
varflag = 1;
} else {
yp = x[1];
zp = x[2];
}
if (x[0] < lo) xp = lo;
else if (x[0] > hi) xp = hi;
else xp = x[0];
}
// closest point on curved surface
else {
dr = r - radius;
dr2 = dr*dr;
if (!open_faces[2]){
yp = c1 + del1*radius/r;
zp = c2 + del2*radius/r;
if (x[0] < lo) {
dx = lo-x[0];
xp = lo;
}
else if (x[0] > hi) {
dx = x[0]-hi;
xp = hi;
}
else {
dx = 0;
xp = x[0];
}
d2 = d2prev = dr2 + dx*dx;
}
// closest point on bottom cap
if (!open_faces[0]) {
dx = lo - x[0];
if (r < radius) d2 = dx*dx;
else d2 = dr2 + dx*dx;
if (d2 < d2prev) {
xp = lo;
if (r < radius){
yp = x[1];
zp = x[2];
}
d2prev = d2;
}
}
// closest point on top cap
if (!open_faces[1]) {
dx = hi - x[0];
if (r < radius) d2 = dx*dx;
else d2 = dr2 + dx*dx;
if (d2 < d2prev) {
xp = hi;
if (r < radius){
yp = x[1];
zp = x[2];
}
}
}
}
add_contact(0,x,xp,yp,zp);
contact[0].radius = crad;
contact[0].varflag = varflag;
contact[0].iwall = 0;
if (contact[0].r < cutoff) return 1;
return 0;
} else if (axis == 'y') {
del1 = x[0] - c1;
del2 = x[2] - c2;
r = sqrt(del1*del1 + del2*del2);
// y is far enough from cylinder that there is no contact
// y is interior to cylinder
if (r >= radius+cutoff || x[1] <= lo-cutoff || x[1] >= hi+cutoff) return 0;
if (r < radius && x[1] > lo && x[1] < hi) return 0;
// y is exterior to cylinder or on its surface
// xp,yp,zp = point on surface of cylinder that x is closest to
// could be edge of cylinder
// do not add contact point if r >= cutoff
d2prev = BIG;
if (!openflag) {
if (r > radius) {
xp = c1 + del1*radius/r;
zp = c2 + del2*radius/r;
crad = 2.0*radius;
varflag = 1;
} else {
xp = x[0];
zp = x[2];
}
if (x[1] < lo) yp = lo;
else if (x[1] > hi) yp = hi;
else yp = x[1];
}
// closest point on curved surface
else {
dr = r - radius;
dr2 = dr*dr;
if (!open_faces[2]){
xp = c1 + del1*radius/r;
zp = c2 + del2*radius/r;
if (x[1] < lo) {
dx = lo-x[1];
yp = lo;
}
else if (x[1] > hi) {
dx = x[1]-hi;
yp = hi;
}
else {
dx = 0;
yp = x[1];
}
d2 = d2prev = dr2 + dx*dx;
}
// closest point on bottom cap
if (!open_faces[0]) {
dx = lo - x[1];
if (r < radius) d2 = dx*dx;
else d2 = dr2 + dx*dx;
if (d2 < d2prev) {
yp = lo;
if (r < radius) {
xp = x[0];
zp = x[2];
}
d2prev = d2;
}
}
// closest point on top cap
if (!open_faces[1]) {
dx = hi - x[1];
if (r < radius) d2 = dx*dx;
else d2 = dr2 + dx*dx;
if (d2 < d2prev) {
yp = hi;
if (r < radius) {
xp = x[0];
zp = x[2];
}
}
}
}
add_contact(0,x,xp,yp,zp);
contact[0].radius = crad;
contact[0].varflag = varflag;
contact[0].iwall = 0;
if (contact[0].r < cutoff) return 1;
return 0;
} else {
del1 = x[0] - c1;
del2 = x[1] - c2;
r = sqrt(del1*del1 + del2*del2);
// z is far enough from cylinder that there is no contact
// z is interior to cylinder
if (r >= radius+cutoff || x[2] <= lo-cutoff || x[2] >= hi+cutoff) return 0;
if (r < radius && x[2] > lo && x[2] < hi) return 0;
// z is exterior to cylinder or on its surface
// xp,yp,zp = point on surface of cylinder that x is closest to
// could be edge of cylinder
// do not add contact point if r >= cutoff
d2prev = BIG;
if (!openflag) {
if (r > radius) {
xp = c1 + del1*radius/r;
yp = c2 + del2*radius/r;
crad = 2.0*radius;
varflag = 1;
} else {
xp = x[0];
yp = x[1];
}
if (x[2] < lo) zp = lo;
else if (x[2] > hi) zp = hi;
else zp = x[2];
}
// closest point on curved surface
else {
dr = r - radius;
dr2 = dr*dr;
if (!open_faces[2]){
xp = c1 + del1*radius/r;
yp = c2 + del2*radius/r;
if (x[2] < lo) {
dx = lo-x[2];
zp = lo;
}
else if (x[2] > hi) {
dx = x[2]-hi;
zp = hi;
}
else {
dx = 0;
zp = x[2];
}
d2prev = dr2 + dx*dx;
}
// closest point on bottom cap
if (!open_faces[0]) {
dx = lo - x[2];
if (r < radius) d2 = dx*dx;
else d2 = dr2 + dx*dx;
if (d2 < d2prev) {
zp = lo;
if (r < radius) {
xp = x[0];
yp = x[1];
}
d2prev = d2;
}
}
// closest point on top cap
if (!open_faces[1]) {
dx = hi - x[2];
if (r < radius) d2 = dx*dx;
else d2 = dr2 + dx*dx;
if (d2 < d2prev) {
zp = hi;
if (r < radius) {
xp = x[0];
yp = x[1];
}
}
}
}
add_contact(0,x,xp,yp,zp);
contact[0].radius = crad;
contact[0].varflag = varflag;
contact[0].iwall = 0;
if (contact[0].r < cutoff) return 1;
return 0;
}
}
/* ----------------------------------------------------------------------
change region shape via variable evaluation
------------------------------------------------------------------------- */
void RegCylinder::shape_update()
{
radius = input->variable->compute_equal(rvar);
if (radius < 0.0)
error->one(FLERR,"Variable evaluation in region gave bad value");
if (axis == 'x') radius *= xscale;
else if (axis == 'y') radius*= yscale;
else radius *= zscale;
}
/* ----------------------------------------------------------------------
error check on existence of variable
------------------------------------------------------------------------- */
void RegCylinder::variable_check()
{
rvar = input->variable->find(rstr);
if (rvar < 0)
error->all(FLERR,"Variable name for region cylinder does not exist");
if (!input->variable->equalstyle(rvar))
error->all(FLERR,"Variable for region cylinder is invalid style");
}
/* ----------------------------------------------------------------------
Set values needed to calculate velocity due to shape changes.
These values do not depend on the contact, so this function is
called once per timestep by fix/wall/gran/region.
------------------------------------------------------------------------- */
void RegCylinder::set_velocity_shape()
{
if (axis == 'x'){
xcenter[0] = 0;
xcenter[1] = c1;
xcenter[2] = c2;
}
else if (axis == 'y'){
xcenter[0] = c1;
xcenter[1] = 0;
xcenter[2] = c2;
}
else{
xcenter[0] = c1;
xcenter[1] = c2;
xcenter[2] = 0;
}
forward_transform(xcenter[0], xcenter[1], xcenter[2]);
if (update->ntimestep > 0) rprev = prev[4];
else rprev = radius;
prev[4] = radius;
}
/* ----------------------------------------------------------------------
add velocity due to shape change to wall velocity
------------------------------------------------------------------------- */
void RegCylinder::velocity_contact_shape(double *vwall, double *xc)
{
double delx, dely, delz; // Displacement of contact point in x,y,z
if (axis == 'x'){
delx = 0;
dely = (xc[1] - xcenter[1])*(1 - rprev/radius);
delz = (xc[2] - xcenter[2])*(1 - rprev/radius);
}
else if (axis == 'y'){
delx = (xc[0] - xcenter[0])*(1 - rprev/radius);
dely = 0;
delz = (xc[2] - xcenter[2])*(1 - rprev/radius);
}
else{
delx = (xc[0] - xcenter[0])*(1 - rprev/radius);
dely = (xc[1] - xcenter[1])*(1 - rprev/radius);
delz = 0;
}
vwall[0] += delx/update->dt;
vwall[1] += dely/update->dt;
vwall[2] += delz/update->dt;
//printf ("R is %g, prev %g, velocity of wall at %g %g %g is %g %g %g\n",radius,rprev,xc[0],xc[1],xc[2],vwall[0],vwall[1],vwall[2]);
}
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