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8fb28ae020eab4fe61dc5af0f3b3aae2faf94409
lammps/src/region.cpp

383 lines
12 KiB
C++
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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"
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]);
xstr = ystr = zstr = tstr = NULL;
dx = dy = dz = 0.0;
laststep = -1;
}
/* ---------------------------------------------------------------------- */
Region::~Region()
{
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, 0 if static
only primitive regions define it here
union/intersect regions have their own dynamic_check()
------------------------------------------------------------------------- */
int Region::dynamic_check()
{
return dynamic;
}
/* ----------------------------------------------------------------------
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 is dynamic, apply inverse transform to x,y,z
unmove first, then unrotate, so don't have to change rotation point
------------------------------------------------------------------------- */
int Region::match(double x, double y, double z)
{
if (dynamic) inverse_transform(x,y,z);
return !(inside(x,y,z) ^ interior);
}
/* ----------------------------------------------------------------------
generate list of contact points for interior or exterior regions
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
------------------------------------------------------------------------- */
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;
}
/* ----------------------------------------------------------------------
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) {
if (update->ntimestep != laststep)
theta = input->variable->compute_equal(tvar);
rotate(x,y,z,theta);
}
if (moveflag) {
if (update->ntimestep != laststep) {
if (xstr) dx = input->variable->compute_equal(xvar);
if (ystr) dy = input->variable->compute_equal(yvar);
if (zstr) dz = input->variable->compute_equal(zvar);
}
x += dx;
y += dy;
z += dz;
}
laststep = update->ntimestep;
}
/* ----------------------------------------------------------------------
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) {
if (update->ntimestep != laststep) {
if (xstr) dx = input->variable->compute_equal(xvar);
if (ystr) dy = input->variable->compute_equal(yvar);
if (zstr) dz = input->variable->compute_equal(zvar);
}
x -= dx;
y -= dy;
z -= dz;
}
if (rotateflag) {
if (update->ntimestep != laststep)
theta = input->variable->compute_equal(tvar);
rotate(x,y,z,-theta);
}
laststep = update->ntimestep;
}
/* ----------------------------------------------------------------------
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
P = point = vector = point of rotation
R = vector = axis of rotation
w = omega of rotation (from period)
X0 = x,y,z = initial coord of atom
R0 = runit = unit vector for R
C = (X0 dot R0) R0 = projection of atom coord onto R
D = X0 - P = vector from P to X0
A = D - C = vector from R line to X0
B = R0 cross A = vector perp to A in plane of rotation
A,B define plane of circular rotation around R line
x,y,z = P + C + A cos(w*dt) + B sin(w*dt)
------------------------------------------------------------------------- */
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);
double x0dotr = x*runit[0] + y*runit[1] + z*runit[2];
c[0] = x0dotr * runit[0];
c[1] = x0dotr * runit[1];
c[2] = x0dotr * runit[2];
d[0] = x - point[0];
d[1] = y - point[1];
d[2] = z - point[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] = atof(arg[iarg+2]);
point[1] = atof(arg[iarg+3]);
point[2] = atof(arg[iarg+4]);
axis[0] = atof(arg[iarg+5]);
axis[1] = atof(arg[iarg+6]);
axis[2] = atof(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 && domain->lattice == NULL)
error->all(FLERR,"Use of region with undefined lattice");
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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