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region.cpp
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Sat, Jun 8, 11:49

region.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.h"
#include "update.h"
#include "domain.h"
#include "lattice.h"
#include "input.h"
#include "variable.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
Region::Region(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
{
int n = strlen(arg[0]) + 1;
id = new char[n];
strcpy(id,arg[0]);
n = strlen(arg[1]) + 1;
style = new char[n];
strcpy(style,arg[1]);
varshape = 0;
xstr = ystr = zstr = tstr = NULL;
dx = dy = dz = 0.0;
copymode = 0;
}
/* ---------------------------------------------------------------------- */
Region::~Region()
{
if (copymode) return;
delete [] id;
delete [] style;
delete [] xstr;
delete [] ystr;
delete [] zstr;
delete [] tstr;
}
/* ---------------------------------------------------------------------- */
void Region::init()
{
if (xstr) {
xvar = input->variable->find(xstr);
if (xvar < 0) error->all(FLERR,"Variable name for region does not exist");
if (!input->variable->equalstyle(xvar))
error->all(FLERR,"Variable for region is invalid style");
}
if (ystr) {
yvar = input->variable->find(ystr);
if (yvar < 0) error->all(FLERR,"Variable name for region does not exist");
if (!input->variable->equalstyle(yvar))
error->all(FLERR,"Variable for region is not equal style");
}
if (zstr) {
zvar = input->variable->find(zstr);
if (zvar < 0) error->all(FLERR,"Variable name for region does not exist");
if (!input->variable->equalstyle(zvar))
error->all(FLERR,"Variable for region is not equal style");
}
if (tstr) {
tvar = input->variable->find(tstr);
if (tvar < 0) error->all(FLERR,"Variable name for region does not exist");
if (!input->variable->equalstyle(tvar))
error->all(FLERR,"Variable for region is not equal style");
}
}
/* ----------------------------------------------------------------------
return 1 if region is dynamic (moves/rotates) or has variable shape
else return 0 if static
------------------------------------------------------------------------- */
int Region::dynamic_check()
{
if (dynamic || varshape) return 1;
return 0;
}
/* ----------------------------------------------------------------------
called before looping over atoms with match() or surface()
this insures any variables used by region are invoked once per timestep
also insures variables are invoked by all procs even those w/out atoms
necessary if equal-style variable invokes global operation
with MPI_Allreduce, e.g. xcm() or count()
------------------------------------------------------------------------- */
void Region::prematch()
{
if (varshape) shape_update();
if (dynamic) pretransform();
}
/* ----------------------------------------------------------------------
determine if point x,y,z is a match to region volume
XOR computes 0 if 2 args are the same, 1 if different
note that inside() returns 1 for points on surface of region
thus point on surface of exterior region will not match
if region has variable shape, invoke shape_update() once per timestep
if region is dynamic, apply inverse transform to x,y,z
unmove first, then unrotate, so don't have to change rotation point
caller is responsible for wrapping this call with
modify->clearstep_compute() and modify->addstep_compute() if needed
------------------------------------------------------------------------- */
int Region::match(double x, double y, double z)
{
if (dynamic) inverse_transform(x,y,z);
return !(inside(x,y,z) ^ interior);
}
/* ----------------------------------------------------------------------
generate error if Kokkos function defaults to base class
------------------------------------------------------------------------- */
void Region::match_all_kokkos(int, DAT::t_int_1d)
{
error->all(FLERR,"Can only use Kokkos supported regions with Kokkos package");
}
/* ----------------------------------------------------------------------
generate list of contact points for interior or exterior regions
if region has variable shape, invoke shape_update() once per timestep
if region is dynamic:
before: inverse transform x,y,z (unmove, then unrotate)
after: forward transform contact point xs,yx,zs (rotate, then move),
then reset contact delx,dely,delz based on new contact point
no need to do this if no rotation since delxyz doesn't change
caller is responsible for wrapping this call with
modify->clearstep_compute() and modify->addstep_compute() if needed
------------------------------------------------------------------------- */
int Region::surface(double x, double y, double z, double cutoff)
{
int ncontact;
double xs,ys,zs;
double xnear[3],xorig[3];
if (dynamic) {
xorig[0] = x;
xorig[1] = y;
xorig[2] = z;
inverse_transform(x,y,z);
}
xnear[0] = x;
xnear[1] = y;
xnear[2] = z;
if (interior) ncontact = surface_interior(xnear,cutoff);
else ncontact = surface_exterior(xnear,cutoff);
if (rotateflag && ncontact) {
for (int i = 0; i < ncontact; i++) {
xs = xnear[0] - contact[i].delx;
ys = xnear[1] - contact[i].dely;
zs = xnear[2] - contact[i].delz;
forward_transform(xs,ys,zs);
contact[i].delx = xorig[0] - xs;
contact[i].dely = xorig[1] - ys;
contact[i].delz = xorig[2] - zs;
}
}
return ncontact;
}
/* ----------------------------------------------------------------------
add a single contact at Nth location in contact array
x = particle position
xp,yp,zp = region surface point
------------------------------------------------------------------------- */
void Region::add_contact(int n, double *x, double xp, double yp, double zp)
{
double delx = x[0] - xp;
double dely = x[1] - yp;
double delz = x[2] - zp;
contact[n].r = sqrt(delx*delx + dely*dely + delz*delz);
contact[n].delx = delx;
contact[n].dely = dely;
contact[n].delz = delz;
}
/* ----------------------------------------------------------------------
pre-compute dx,dy,dz and theta for a moving/rotating region
called once for the region before per-atom loop, via prematch()
------------------------------------------------------------------------- */
void Region::pretransform()
{
if (moveflag) {
if (xstr) dx = input->variable->compute_equal(xvar);
if (ystr) dy = input->variable->compute_equal(yvar);
if (zstr) dz = input->variable->compute_equal(zvar);
}
if (rotateflag) theta = input->variable->compute_equal(tvar);
}
/* ----------------------------------------------------------------------
transform a point x,y,z in region space to moved space
rotate first (around original P), then displace
------------------------------------------------------------------------- */
void Region::forward_transform(double &x, double &y, double &z)
{
if (rotateflag) rotate(x,y,z,theta);
if (moveflag) {
x += dx;
y += dy;
z += dz;
}
}
/* ----------------------------------------------------------------------
transform a point x,y,z in moved space back to region space
undisplace first, then unrotate (around original P)
------------------------------------------------------------------------- */
void Region::inverse_transform(double &x, double &y, double &z)
{
if (moveflag) {
x -= dx;
y -= dy;
z -= dz;
}
if (rotateflag) rotate(x,y,z,-theta);
}
/* ----------------------------------------------------------------------
rotate x,y,z by angle via right-hand rule around point and runit normal
sign of angle determines whether rotating forward/backward in time
return updated x,y,z
R = vector axis of rotation
P = point = point to rotate around
R0 = runit = unit vector for R
X0 = x,y,z = initial coord of atom
D = X0 - P = vector from P to X0
C = (D dot R0) R0 = projection of D onto R, i.e. Dparallel
A = D - C = vector from R line to X0, i.e. Dperp
B = R0 cross A = vector perp to A in plane of rotation, same len as A
A,B define plane of circular rotation around R line
new x,y,z = P + C + A cos(angle) + B sin(angle)
------------------------------------------------------------------------- */
void Region::rotate(double &x, double &y, double &z, double angle)
{
double a[3],b[3],c[3],d[3],disp[3];
double sine = sin(angle);
double cosine = cos(angle);
d[0] = x - point[0];
d[1] = y - point[1];
d[2] = z - point[2];
double x0dotr = d[0]*runit[0] + d[1]*runit[1] + d[2]*runit[2];
c[0] = x0dotr * runit[0];
c[1] = x0dotr * runit[1];
c[2] = x0dotr * runit[2];
a[0] = d[0] - c[0];
a[1] = d[1] - c[1];
a[2] = d[2] - c[2];
b[0] = runit[1]*a[2] - runit[2]*a[1];
b[1] = runit[2]*a[0] - runit[0]*a[2];
b[2] = runit[0]*a[1] - runit[1]*a[0];
disp[0] = a[0]*cosine + b[0]*sine;
disp[1] = a[1]*cosine + b[1]*sine;
disp[2] = a[2]*cosine + b[2]*sine;
x = point[0] + c[0] + disp[0];
y = point[1] + c[1] + disp[1];
z = point[2] + c[2] + disp[2];
}
/* ----------------------------------------------------------------------
parse optional parameters at end of region input line
------------------------------------------------------------------------- */
void Region::options(int narg, char **arg)
{
if (narg < 0) error->all(FLERR,"Illegal region command");
// option defaults
interior = 1;
scaleflag = 1;
moveflag = rotateflag = 0;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal region command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all(FLERR,"Illegal region command");
iarg += 2;
} else if (strcmp(arg[iarg],"side") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal region command");
if (strcmp(arg[iarg+1],"in") == 0) interior = 1;
else if (strcmp(arg[iarg+1],"out") == 0) interior = 0;
else error->all(FLERR,"Illegal region command");
iarg += 2;
} else if (strcmp(arg[iarg],"move") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal region command");
if (strcmp(arg[iarg+1],"NULL") != 0) {
if (strstr(arg[iarg+1],"v_") != arg[iarg+1])
error->all(FLERR,"Illegal region command");
int n = strlen(&arg[iarg+1][2]) + 1;
xstr = new char[n];
strcpy(xstr,&arg[iarg+1][2]);
}
if (strcmp(arg[iarg+2],"NULL") != 0) {
if (strstr(arg[iarg+2],"v_") != arg[iarg+2])
error->all(FLERR,"Illegal region command");
int n = strlen(&arg[iarg+2][2]) + 1;
ystr = new char[n];
strcpy(ystr,&arg[iarg+2][2]);
}
if (strcmp(arg[iarg+3],"NULL") != 0) {
if (strstr(arg[iarg+3],"v_") != arg[iarg+3])
error->all(FLERR,"Illegal region command");
int n = strlen(&arg[iarg+3][2]) + 1;
zstr = new char[n];
strcpy(zstr,&arg[iarg+3][2]);
}
moveflag = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"rotate") == 0) {
if (iarg+8 > narg) error->all(FLERR,"Illegal region command");
if (strstr(arg[iarg+1],"v_") != arg[iarg+1])
error->all(FLERR,"Illegal region command");
int n = strlen(&arg[iarg+1][2]) + 1;
tstr = new char[n];
strcpy(tstr,&arg[iarg+1][2]);
point[0] = force->numeric(FLERR,arg[iarg+2]);
point[1] = force->numeric(FLERR,arg[iarg+3]);
point[2] = force->numeric(FLERR,arg[iarg+4]);
axis[0] = force->numeric(FLERR,arg[iarg+5]);
axis[1] = force->numeric(FLERR,arg[iarg+6]);
axis[2] = force->numeric(FLERR,arg[iarg+7]);
rotateflag = 1;
iarg += 8;
} else error->all(FLERR,"Illegal region command");
}
// error check
if ((moveflag || rotateflag) &&
(strcmp(style,"union") == 0 || strcmp(style,"intersect") == 0))
error->all(FLERR,"Region union or intersect cannot be dynamic");
// setup scaling
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
if (rotateflag) {
point[0] *= xscale;
point[1] *= yscale;
point[2] *= zscale;
}
// runit = unit vector along rotation axis
if (rotateflag) {
double len = sqrt(axis[0]*axis[0] + axis[1]*axis[1] + axis[2]*axis[2]);
if (len == 0.0)
error->all(FLERR,"Region cannot have 0 length rotation vector");
runit[0] = axis[0]/len;
runit[1] = axis[1]/len;
runit[2] = axis[2]/len;
}
if (moveflag || rotateflag) dynamic = 1;
else dynamic = 0;
}

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