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enable and apply clang-format

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This commit is contained in:
Axel Kohlmeyer
2023-04-03 21:41:09 -04:00
parent b53a47b192
commit 27127a46cc
5 changed files with 844 additions and 734 deletions
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339
src/region_prism.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -26,105 +25,126 @@
using namespace LAMMPS_NS;
#define BIG 1.0e20
static constexpr double BIG = 1.0e20;
/* ---------------------------------------------------------------------- */
RegPrism::RegPrism(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
{
options(narg-11,&arg[11]);
options(narg - 11, &arg[11]);
if (strcmp(arg[2],"INF") == 0 || strcmp(arg[2],"EDGE") == 0) {
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 xlo = domain->boxlo[0];
} else xlo = xscale*utils::numeric(FLERR,arg[2],false,lmp);
error->all(FLERR, "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 * utils::numeric(FLERR, arg[2], false, lmp);
if (strcmp(arg[3],"INF") == 0 || strcmp(arg[3],"EDGE") == 0) {
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 xhi = domain->boxhi[0];
} else xhi = xscale*utils::numeric(FLERR,arg[3],false,lmp);
error->all(FLERR, "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 * utils::numeric(FLERR, arg[3], false, lmp);
if (strcmp(arg[4],"INF") == 0 || strcmp(arg[4],"EDGE") == 0) {
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 ylo = domain->boxlo[1];
} else ylo = yscale*utils::numeric(FLERR,arg[4],false,lmp);
error->all(FLERR, "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 * utils::numeric(FLERR, arg[4], false, lmp);
if (strcmp(arg[5],"INF") == 0 || strcmp(arg[5],"EDGE") == 0) {
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 yhi = domain->boxhi[1];
} else yhi = yscale*utils::numeric(FLERR,arg[5],false,lmp);
error->all(FLERR, "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 * utils::numeric(FLERR, arg[5], false, lmp);
if (strcmp(arg[6],"INF") == 0 || strcmp(arg[6],"EDGE") == 0) {
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 zlo = domain->boxlo[2];
} else zlo = zscale*utils::numeric(FLERR,arg[6],false,lmp);
error->all(FLERR, "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 * utils::numeric(FLERR, arg[6], false, lmp);
if (strcmp(arg[7],"INF") == 0 || strcmp(arg[7],"EDGE") == 0) {
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 zhi = domain->boxhi[2];
} else zhi = zscale*utils::numeric(FLERR,arg[7],false,lmp);
error->all(FLERR, "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 * utils::numeric(FLERR, arg[7], false, lmp);
xy = xscale*utils::numeric(FLERR,arg[8],false,lmp);
xz = xscale*utils::numeric(FLERR,arg[9],false,lmp);
yz = yscale*utils::numeric(FLERR,arg[10],false,lmp);
xy = xscale * utils::numeric(FLERR, arg[8], false, lmp);
xz = xscale * utils::numeric(FLERR, arg[9], false, lmp);
yz = yscale * utils::numeric(FLERR, arg[10], false, lmp);
// 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) error->all(FLERR,"Illegal region prism xlo: {} >= xhi: {}", xlo, xhi);
if (ylo >= yhi) error->all(FLERR,"Illegal region prism ylo: {} >= yhi: {}", ylo, yhi);
if (zlo >= zhi) error->all(FLERR,"Illegal region prism zlo: {} >= zhi: {}", zlo ,zhi);
if (xlo >= xhi) error->all(FLERR, "Illegal region prism xlo: {} >= xhi: {}", xlo, xhi);
if (ylo >= yhi) error->all(FLERR, "Illegal region prism ylo: {} >= yhi: {}", ylo, yhi);
if (zlo >= zhi) error->all(FLERR, "Illegal region prism zlo: {} >= zhi: {}", zlo, zhi);
if (xy != 0.0 && xlo == -BIG && xhi == BIG)
error->all(FLERR,"Illegal region prism non-zero xy tilt with infinite x size");
error->all(FLERR, "Illegal region prism non-zero xy tilt with infinite x size");
if (xy != 0.0 && ylo == -BIG && yhi == BIG)
error->all(FLERR,"Illegal region prism non-zero xy tilt with infinite y size");
error->all(FLERR, "Illegal region prism non-zero xy tilt with infinite y size");
if (xz != 0.0 && xlo == -BIG && xhi == BIG)
error->all(FLERR,"Illegal region prism non-zero xz tilt with infinite x size");
error->all(FLERR, "Illegal region prism non-zero xz tilt with infinite x size");
if (xz != 0.0 && zlo == -BIG && zhi == BIG)
error->all(FLERR,"Illegal region prism non-zero xz tilt with infinite z size");
error->all(FLERR, "Illegal region prism non-zero xz tilt with infinite z size");
if (yz != 0.0 && ylo == -BIG && yhi == BIG)
error->all(FLERR,"Illegal region prism non-zero yz tilt with infinite y size");
error->all(FLERR, "Illegal region prism non-zero yz tilt with infinite y size");
if (yz != 0.0 && zlo == -BIG && zhi == BIG)
error->all(FLERR,"Illegal region prism non-zero yz tilt with infinite z size");
error->all(FLERR, "Illegal region prism non-zero yz tilt with infinite z size");
// 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_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_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;
} 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;
if (interior)
tmax = 3;
else
tmax = 1;
// h = transformation matrix from tilt coords (0-1) to box coords (xyz)
// columns of h are edge vectors of tilted box
@ -140,26 +160,26 @@ RegPrism::RegPrism(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
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];
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[0] = xhi - xlo;
a[1] = 0.0;
a[2] = 0.0;
b[0] = xy;
b[1] = yhi-ylo;
b[1] = yhi - ylo;
b[2] = 0.0;
c[0] = xz;
c[1] = yz;
c[2] = zhi-zlo;
c[2] = zhi - zlo;
clo[0] = corners[0][0] = xlo;
clo[1] = corners[0][1] = ylo;
@ -196,19 +216,18 @@ RegPrism::RegPrism(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
// face = 6 inward-facing unit normals to prism faces
// order = xy plane, xz plane, yz plane
MathExtra::cross3(a,b,face[0]);
MathExtra::cross3(b,a,face[1]);
MathExtra::cross3(c,a,face[2]);
MathExtra::cross3(a,c,face[3]);
MathExtra::cross3(b,c,face[4]);
MathExtra::cross3(c,b,face[5]);
MathExtra::cross3(a, b, face[0]);
MathExtra::cross3(b, a, face[1]);
MathExtra::cross3(c, a, face[2]);
MathExtra::cross3(a, c, face[3]);
MathExtra::cross3(b, c, face[4]);
MathExtra::cross3(c, b, face[5]);
// remap open face indices to be consistent
if (openflag) {
int temp[6];
for (int i = 0; i < 6; i++)
temp[i] = open_faces[i];
for (int i = 0; i < 6; i++) temp[i] = open_faces[i];
open_faces[0] = temp[4];
open_faces[1] = temp[5];
open_faces[2] = temp[2];
@ -223,27 +242,51 @@ RegPrism::RegPrism(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg)
// 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[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[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;
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;
delete[] contact;
}
/* ----------------------------------------------------------------------
@ -258,12 +301,11 @@ RegPrism::~RegPrism()
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);
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;
if (a >= 0.0 && a <= 1.0 && b >= 0.0 && b <= 1.0 && c >= 0.0 && c <= 1.0) return 1;
return 0;
}
@ -283,10 +325,12 @@ int RegPrism::surface_interior(double *x, double cutoff)
// 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 (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;
}
@ -296,15 +340,17 @@ int RegPrism::surface_interior(double *x, double cutoff)
for (i = 0; i < 6; i++) {
if (open_faces[i]) continue;
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 (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];
contact[n].delx = dot * face[i][0];
contact[n].dely = dot * face[i][1];
contact[n].delz = dot * face[i][2];
contact[n].radius = 0;
contact[n].iwall = i;
n++;
@ -325,25 +371,29 @@ int RegPrism::surface_exterior(double *x, double cutoff)
int i;
double dot;
double *corner;
double xp,yp,zp;
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 (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 (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;
}
@ -354,8 +404,8 @@ int RegPrism::surface_exterior(double *x, double cutoff)
// 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);
find_nearest(x, xp, yp, zp);
add_contact(0, x, xp, yp, zp);
contact[0].radius = 0;
contact[0].iwall = 0;
if (contact[0].r < cutoff) return 1;
@ -369,8 +419,8 @@ int RegPrism::surface_exterior(double *x, double cutoff)
void RegPrism::find_nearest(double *x, double &xp, double &yp, double &zp)
{
int i,j,k,iface;
double xproj[3],xline[3],nearest[3];
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)
@ -384,27 +434,25 @@ void RegPrism::find_nearest(double *x, double &xp, double &yp, double &zp)
double distsq = BIG;
for (int itri = 0; itri < 12; itri++) {
iface = itri/2;
iface = itri / 2;
if (open_faces[iface]) continue;
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);
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);
}
}
@ -422,25 +470,24 @@ void RegPrism::find_nearest(double *x, double &xp, double &yp, double &zp)
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)
int RegPrism::inside_tri(double *x, double *v1, double *v2, double *v3, double *norm)
{
double edge[3],pvec[3],xproduct[3];
double edge[3], pvec[3], xproduct[3];
MathExtra::sub3(v2,v1,edge);
MathExtra::sub3(x,v1,pvec);
MathExtra::cross3(edge,pvec,xproduct);
if (MathExtra::dot3(xproduct,norm) < 0.0) return 0;
MathExtra::sub3(v2, v1, edge);
MathExtra::sub3(x, v1, pvec);
MathExtra::cross3(edge, pvec, xproduct);
if (MathExtra::dot3(xproduct, norm) < 0.0) return 0;
MathExtra::sub3(v3,v2,edge);
MathExtra::sub3(x,v2,pvec);
MathExtra::cross3(edge,pvec,xproduct);
if (MathExtra::dot3(xproduct,norm) < 0.0) return 0;
MathExtra::sub3(v3, v2, edge);
MathExtra::sub3(x, v2, pvec);
MathExtra::cross3(edge, pvec, xproduct);
if (MathExtra::dot3(xproduct, norm) < 0.0) return 0;
MathExtra::sub3(v1,v3,edge);
MathExtra::sub3(x,v3,pvec);
MathExtra::cross3(edge,pvec,xproduct);
if (MathExtra::dot3(xproduct,norm) < 0.0) return 0;
MathExtra::sub3(v1, v3, edge);
MathExtra::sub3(x, v3, pvec);
MathExtra::cross3(edge, pvec, xproduct);
if (MathExtra::dot3(xproduct, norm) < 0.0) return 0;
return 1;
}
@ -452,7 +499,7 @@ 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;
double rsq = delx * delx + dely * dely + delz * delz;
if (rsq >= dsq) return dsq;
nearest[0] = near[0];