void realign::realignPeriodically()
{
vector <baseType> along(vl->size());
baseType timeFirstRun;
in >> timeFirstRun;
// cout << "timeFirstRun: " << timeFirstRun << endl;
// cout << "time: " << dynNode::time << endl;
for (unsigned int i = 0; i < vl->size(); i++ )
in >>along[i];
meanVar dist = calculateDist(along);
if (counter==skip)
{
counter = 0;
out << dynNode::time << " " << setprecision(20) << dist.mean << " " << sqrt(dist.var) << endl;
cout << "vorher:" << setprecision(20) << dist.mean << " " << sqrt(dist.var) << endl;
realignNow(along, eps, dist);
meanVar newDist = calculateDist(along);
cout << "nachher:" << setprecision(20) << newDist.mean << " " << sqrt(newDist.var) << endl;
}
else
{
counter++;
out << "#" << setprecision(20) << dynNode::time << " " << dist.mean << " " << sqrt(dist.var) << endl;
}
}
void slice_torus (struct msscene *ms, struct surface *current_surface, double fine_pixel, double probe_radius, struct face *fac)
{
int k, j, i, nfocus, near1, naif;
double anginc, bigrad;
double focus[3], vect1[3], vect2[3], vect[3], qvect[3];
double dtq, tcv[3];
double *foci = (double *) NULL;
char message[MAXLINE];
struct leaf *lf;
struct circle *cir1, *cir2, *cir3;
struct circle *lfcir, *torcir;
struct variety *vty, *atm1, *atm2;
struct arc *a, *nxta;
struct arc *torarc;
struct vertex *torvtx[2];
struct vertex *qvtx;
struct vertex *conevtx;
struct cycle *cyc;
struct edge *edg;
struct cept *ex;
vty = fac -> vty;
if (vty -> type != TORUS) {
ex = new_cept (GEOMETRY_ERROR, INCONSISTENCY, FATAL_SEVERITY);
add_function (ex, "slice_torus");
add_source (ex, "msrender.c");
add_long (ex, "variety type", (long) vty -> type);
return;
}
if (vty -> tube) {
slice_elbow (ms, current_surface, fine_pixel, fac);
return;
}
if (debug >= 2) {
sprintf (message,"render saddle face for atoms %5d %5d",
vty -> atmnum[0], vty -> atmnum[1]);
inform(message);
}
/* get pointers to atom varieties */
atm1 = *(current_surface -> variety_handles + fac -> vty -> atmnum[0] - 1);
atm2 = *(current_surface -> variety_handles + fac -> vty -> atmnum[1] - 1);
/* check versus window */
bigrad = distance (atm1 -> center, atm2 -> center) +
atm1 -> radii[0] + atm2 -> radii[0];
for (k = 0; k < 3; k++) {
if (vty -> center[k] + bigrad < ms -> window[0][k]) return;
if (vty -> center[k] - bigrad > ms -> window[1][k]) return;
}
/* leaf circle */
lfcir = allocate_circle ();
if (error()) {
add_object (tail_cept, CIRCLE, "leaf circle");
add_function (tail_cept, "slice_torus");
return;
}
/* leaf */
lf = allocate_leaf ();
if (error()) {
add_object (tail_cept, LEAF, "leaf");
add_function (tail_cept, "slice_sphere");
return;
}
/* torus circle radius, center, axis */
torcir = new_circle (vty -> center, vty -> radii[0], vty -> axis);
if (torcir == NULL) {
add_object (tail_cept, CIRCLE, "torus circle");
add_function (tail_cept, "slice_circle");
return;
}
/* torus arc */
torarc = allocate_arc ();
if (error()) {
add_object (tail_cept, ARC, "torus arc");
add_function (tail_cept, "slice_torus");
add_source (tail_cept, "msrender.c");
return;
}
for (j = 0; j < 2; j++) {
torvtx[j] = allocate_vertex ();
if (error()) {
add_object (tail_cept, VERTEX, "torus vertex");
add_function (tail_cept, "slice_torus");
add_source (tail_cept, "msrender.c");
return;
}
}
torarc -> cir = torcir;
/* copy atom numbers from variety to leaf */
for (k = 0; k < MAXPA; k++)
lf -> atmnum[k] = fac -> vty -> atmnum[k];
/* set up leaf fields */
lf -> cir = lfcir;
lf -> shape = fac -> shape;
lf -> type = fac -> vty -> type;
lf -> fac = fac;
lf -> cep = 0;
lf -> clip_ep = 0;
lf -> side = OUTSIDE;
lf -> comp = fac -> comp;
lf -> input_hue = fac -> input_hue;
/* both endpoints of saddle face leaf are always accessible */
for (j = 0; j < 2; j++)
lf -> where[j] = ACCESSIBLE;
/* angular increment for rotation of leaf about torus axis */
anginc = fine_pixel / (vty -> radii[0]);
/* next we need endpoints for torus arc */
/* get them from concave arcs bounding saddle face */
/* intialization */
cir1 = NULL;
cir2 = NULL;
cir3 = NULL;
qvtx = NULL;
conevtx = NULL;
near1 = 0;
/* look for concave arcs */
naif = 0;
for (cyc = fac -> first_cycle; cyc != NULL; cyc = cyc -> next)
for (edg = cyc -> first_edge; edg != NULL; edg = edg -> next) {
naif++;
a = edg -> arcptr;
if (a -> shape == CONVEX) {
cir3 = a -> cir;
continue;
}
if (edg -> next == NULL)
nxta = cyc -> first_edge -> arcptr;
else
nxta = edg -> next -> arcptr;
if (along (edg, vty -> axis))
cir2 = a -> cir;
else
cir1 = a -> cir;
/* check for cusp vertex */
if (a -> shape == CONCAVE && nxta -> shape == CONCAVE) {
/* cusp point joints two concave arcs */
qvtx = a -> vtx[1-edg->orn];
}
}
dtq = probe_radius * probe_radius - vty -> radii[0] * vty -> radii[0];
/* later: note: check PI in bubbles */
if (naif == 1) {
if (dtq <= 0.0) {
ex = new_cept (GEOMETRY_ERROR, INCONSISTENCY, FATAL_SEVERITY);
add_function (ex, "slice_torus");
add_source (ex, "msrender.c");
add_message(ex, "toroidal face with only one arc, but not cone");
return;
}
if (cir3 == NULL) {
ex = new_cept (GEOMETRY_ERROR, INCONSISTENCY, FATAL_SEVERITY);
add_function (ex, "slice_torus");
add_source (ex, "msrender.c");
add_message(ex, "toroidal face with only one arc, but no contact circle");
return;
}
/* cone */
qvtx = allocate_vertex ();
if (error()) {
add_object (tail_cept, VERTEX, "CUSP VERTEX");
add_function (tail_cept, "slice_torus");
add_source (tail_cept, "msrender.c");
return;
}
conevtx = qvtx;
dtq = sqrt (dtq);
for (k = 0; k < 3; k++)
tcv[k] = cir3 -> center[k] - torcir -> center[k];
normalize (tcv);
for (k = 0; k < 3; k++)
qvtx -> center[k] = torcir -> center[k] + dtq * tcv[k];
/* hope this is enough */
}
if (cir1 == NULL) informd2 ("cir1 null");
if (cir2 == NULL) informd2 ("cir2 null");
if (qvtx != NULL) informd2 ("cusp present");
/* check for cusp vertex */
if (qvtx != NULL) {
for (k = 0; k < 3; k++)
qvect[k] = qvtx -> center[k] - vty -> center[k];
near1 = (dot_product (qvect, vty -> axis) < 0.0);
}
/* check for hoop saddle face */
if (cir1 == NULL || cir2 == NULL) {
for (j = 0; j < 2; j++)
torarc -> vtx[j] = NULL;
informd2 ("complete toroidal hoop");
}
else {
/* concave arc circle centers are endpoints of sphere rolling */
for (k = 0; k < 3; k++) {
torvtx[0] -> center[k] = cir1 -> center[k];
torvtx[1] -> center[k] = cir2 -> center[k];
}
for (j = 0; j < 2; j++)
torarc -> vtx[j] = torvtx[j];
sprintf (message, "saddle rendering (from): %8.3f %8.3f %8.3f",
cir1 -> center[0], cir1 -> center[1], cir1 -> center[2]);
informd2 (message);
sprintf (message, "saddle rendering (to) : %8.3f %8.3f %8.3f",
cir2 -> center[0], cir2 -> center[1], cir2 -> center[2]);
informd2 (message);
}
/* the probe sphere centers are the foci of the leaves */
nfocus = render_sub_arc (torarc, &foci, anginc);
if (nfocus < 2) {
ex = new_cept (LOGIC_ERROR, MSUNDERFLOW, FATAL_SEVERITY);
add_function (ex, "slice_torus");
add_source (ex, "msrender.c");
add_long (ex, "number of foci", (long) nfocus);
return;
}
sprintf (message, "nfocus = %d", nfocus);
informd2 (message);
/* create leaves */
for (i = 0; i < nfocus; i++) {
for (k = 0; k < 3; k++) {
focus[k] = (*(foci + 3 * i + k));
lfcir -> center[k] = focus[k];
lf -> focus[k] = focus[k];
}
/* unit vectors from focus toward atoms */
for (k = 0; k < 3; k++) {
vect1[k] = atm1 -> center[k] - focus[k];
vect2[k] = atm2 -> center[k] - focus[k];
}
/* correct for cusp vertex */
if (qvtx != NULL) {
if (near1)
for (k = 0; k < 3; k++)
vect2[k] = qvtx -> center[k] - focus[k];
else
for (k = 0; k < 3; k++)
vect1[k] = qvtx -> center[k] - focus[k];
}
/* normalize vectors to unit length */
normalize (vect1);
normalize (vect2);
/* leaf circle radius is probe radius */
lfcir -> radius = probe_radius;
/* set up endpoints of leaf */
for (k = 0; k < 3; k++) {
lf -> ends[0][k] = focus[k] + lfcir -> radius * vect1[k];
lf -> ends[1][k] = focus[k] + lfcir -> radius * vect2[k];
}
/* compute leaf circle axis */
for (k = 0; k < 3; k++)
vect[k] = focus[k] - vty -> center[k];
cross (vty -> axis, vect, lfcir -> axis);
normalize (lfcir -> axis);
/* clip and render leaf */
clip_leaf (ms, current_surface, fine_pixel, lf);
if (error()) return;
}
/* return temporary memory */
if (!free_doubles (foci, 0, VERTS)) {
ex = new_cept (MEMORY_ERROR, FREEING, FATAL_SEVERITY);
add_variable (ex, VERTS, "foci");
add_function (ex, "slice_torus");
add_source (ex, "msrender.c");
return;
}
free_leaf (lf);
free_arc (torarc);
free_circle (torcir);
free_circle (lfcir);
for (j = 0; j < 2; j++)
free_vertex (torvtx[j]);
if (conevtx != NULL) free_vertex (conevtx);
return;
}
