ofVec3f SteeringBehaviors::Cohesion(const std::vector<Vehicle*>&_neighbors)
{
ofVec3f _steeringForce(0.0, 0.0, 0.0);
ofVec3f CenterOfMass(0.0, 0.0, 0.0);
int NeighborCount = 0;
for (int a = 0; a < _neighbors.size(); ++a)
{
//make sure this agent isn't included in the calculations and that
//the agent being examined is close enough. ***also make sure it doesn't
//include the evade target ***
if ((_neighbors[a] != m_Vehicle) && (_neighbors[a]->IsTagged()) && (_neighbors[a] != m_Vehicle->Target()))
{
CenterOfMass += _neighbors[a]->Pos();
++NeighborCount;
}
}
if (NeighborCount > 0)
{
CenterOfMass /= NeighborCount;
_steeringForce = Seek(CenterOfMass);
}
return(_steeringForce.getNormalized());
}
ofVec3f SteeringBehaviors::CohesionPlus(const std::vector<Vehicle*>&_neighbors)
{
ofVec3f CenterOfMass(0.0,0.0,0.0);
ofVec3f _steeringForce(0.0, 0.0, 0.0);
int NeighborCount = 0;
//iterate through the neighbors and sum up all the position vectors
for (BaseEntity* pV = m_Vehicle->GameWorld()->CellSpace()->begin();
!m_Vehicle->GameWorld()->CellSpace()->end();
pV = m_Vehicle->GameWorld()->CellSpace()->next())
{
//make sure this agent isn't included in the caclulations and that the agent being examined is close enough
if (pV != m_Vehicle)
{
CenterOfMass += pV->Pos();
++NeighborCount;
}
}
if (NeighborCount > 0)
{
CenterOfMass /= NeighborCount;
_steeringForce = Seek(CenterOfMass);
}
return (_steeringForce.getNormalized());
}
void vtkKMeansClustering::EstimateClusterCenters(vtkPoints* data, vtkPoints* clusterCenters)
{
vtkSmartPointer<vtkPoints> oldCenters =
vtkSmartPointer<vtkPoints>::New();
oldCenters->ShallowCopy(clusterCenters);
clusterCenters->Reset();
clusterCenters->Squeeze();
for(unsigned int cluster = 0; cluster < this->K; cluster++)
{
vtkSmartPointer<vtkPoints> classPoints =
vtkSmartPointer<vtkPoints>::New();
for(unsigned int point = 0; point < data->GetNumberOfPoints(); point++)
{
if(this->Labels[point] == cluster)
{
classPoints->InsertNextPoint(data->GetPoint(point));
}
}
double center[3];
if(classPoints->GetNumberOfPoints() == 0)
{
//GetRandomPoint(data, center);
oldCenters->GetPoint(cluster, center);
}
else
{
CenterOfMass(classPoints, center);
}
clusterCenters->InsertNextPoint(center);
}
}
void sdgEngine::Explode(float factor)
{
double com[3]; //residue center-of-mass
CenterOfMass(_atoms, com);
MIAtom_const_iter i, e = _atoms.end();
for (i = _atoms.begin(); i != e; ++i)
{
(*i)->setPosition( (float)(com[0] + factor * ((*i)->x() - com[0])),
(float)(com[1] + factor * ((*i)->y() - com[1])),
(float)(com[2] + factor * ((*i)->z() - com[2])));
}
}
vnl_double_3x3 SampleCovarianceMatrix(const std::vector<vgl_point_3d<double> > &Points)
{
vgl_point_3d<double> u = CenterOfMass(Points);
vnl_double_3x3 S;
S.fill(0);
for(unsigned int i = 0; i < Points.size(); i++)
{
vgl_vector_3d<double> V = Points[i] - u;
vnl_double_3x3 OP = VXLHelpers::OuterProduct(V, V);
S += OP;
}
S /= Points.size();
return S;
}
vgl_plane_3d<double> BestPlane(const std::vector<vgl_point_3d<double> > &Points)
{
//this function finds the eigen vector corresponding to the smallest eigen value and places the plane's P0 at the center of mass of the points.
vgl_point_3d<double> Centroid = CenterOfMass(Points);
vnl_double_3x3 S = SampleCovarianceMatrix(Points);
std::vector<vnl_double_3> evecs = VXLHelpers::EigenVectors(S);
std::vector<vgl_vector_3d<double> > EvecsVGL;
for(unsigned int i = 0; i < 3; i++)
EvecsVGL.push_back(VXLHelpers::vnl_vector_to_vgl_vector(evecs[i]));
//WriteEigenVectorVTP(Centroid, EvecsVGL, .3);
vgl_plane_3d<double> P(EvecsVGL[0], Centroid); //apparently these are sorted from smallest to largest?
return P;
}
int NS_DIM_PREFIX BalanceGridRCB (MULTIGRID *theMG, int level)
{
HEAP *theHeap = theMG->theHeap;
GRID *theGrid = GRID_ON_LEVEL(theMG,level); /* balance grid of level */
LB_INFO *lbinfo;
ELEMENT *e;
int i, son;
INT MarkKey;
/* distributed grids cannot be redistributed by this function */
if (me!=master && FIRSTELEMENT(theGrid) != NULL)
{
printf("Error: Redistributing distributed grids using recursive coordinate bisection is not implemented!\n");
return (1);
}
if (me==master)
{
if (NT(theGrid) == 0)
{
UserWriteF("WARNING in BalanceGridRCB: no elements in grid\n");
return (1);
}
Mark(theHeap,FROM_TOP,&MarkKey);
lbinfo = (LB_INFO *)
GetMemUsingKey(theHeap, NT(theGrid)*sizeof(LB_INFO), FROM_TOP, MarkKey);
if (lbinfo==NULL)
{
Release(theHeap,FROM_TOP,MarkKey);
UserWrite("ERROR in BalanceGridRCB: could not allocate memory from the MGHeap\n");
return (1);
}
/* construct LB_INFO list */
for (i=0, e=FIRSTELEMENT(theGrid); e!=NULL; i++, e=SUCCE(e))
{
lbinfo[i].elem = e;
CenterOfMass(e, lbinfo[i].center);
}
/* apply coordinate bisection strategy */
theRCB(lbinfo, NT(theGrid), 0, 0, DimX, DimY, 0);
IFDEBUG(dddif,1)
for (e=FIRSTELEMENT(theGrid); e!=NULL; e=SUCCE(e))
{
UserWriteF("elem %08x has dest=%d\n",
DDD_InfoGlobalId(PARHDRE(e)), PARTITION(e));
}
ENDDEBUG
for (i=0, e=FIRSTELEMENT(theGrid); e!=NULL; i++, e=SUCCE(e))
{
InheritPartition (e);
}
Release(theHeap,FROM_TOP,MarkKey);
}
return 0;
}
//
// LATER: remove printfs...
//
// main tracking function. Processes a given sequence of type YARPImageSequence.
int
YARPFlowTracker::Apply (YARPOutputPortOf<YARPGenericImage>& port)
{
printf ("ox %d oy %d\n", ox, oy);
// PROCESSING SEQUENCE.
int start = seq->GetStartPushing();
int stop = seq->GetStopPushing();
printf ("Processing from frame %d to %d\n", start, stop);
printf ("Sequence has %d frames\n", seq->GetNumElements());
assert (stop-start+1 <= m_maxsize);
// PREPARE SEQUENCE FOR PROCESSING.
processor.Reset ();
oseq.Reset ();
contact = 0;
contact_frame = 0;
howmanycontacts = 0;
lack_of_vectors = 0;
int i, frame;
for (frame = start; frame <= stop; frame++)
{
oseq.IncrementCounter ();
contact = processor.Apply (seq->GetImageRef (frame),
oseq.GetImageRef (frame-start));
oseq.GetImageRef (frame-start) = seq->GetImageRef (frame);
if (contact)
{
processor.GetPokeDirection (dirx, diry);
processor.GetSegmentedImage (segmentation_mask);
segmentation_mask_copy = segmentation_mask;
processor.GetFlipper(flipper_segmentation_mask);
flipper_segmentation_mask_copy = flipper_segmentation_mask;
ba.Apply(segmentation_mask_copy);
orientation = ba.GetAngle();
orientation_quality = ba.GetPointiness();
// enlarge it twice.
GrowMask (segmentation_mask, extended_segmentation);
segmentation_mask = extended_segmentation;
GrowMask (segmentation_mask, extended_segmentation);
CenterOfMass (extended_segmentation, com_x, com_y);
contact_frame = frame;
howmanycontacts++;
GenerateAndSend (port);
}
}
if (howmanycontacts == 0)
{
printf ("No poking detected... \n");
// nothing much to do.
return -1;
}
// OPTICFLOW.
int startopticflow = contact_frame - 5; //10;
if (startopticflow < start) startopticflow = start;
int endopticflow = contact_frame + FRAMES_TRACKED;
if (endopticflow > stop) endopticflow = stop;
// TRACK.
int endtracking = contact_frame+FRAMES_TRACKED;
if (endtracking > stop) endtracking = stop;
// optic flow mask, initialize optic flow and additional tracker.
mask.Zero();
YARPColorConverter::RGB2Grayscale (seq->GetImageRef(startopticflow), mono);
of.Initialize (mono);
bool trackvalid = false;
int sx = com_x, sy = com_y;
int sx2 = com_x, sy2 = com_y;
tracker.Initialize (seq->GetImageRef(startopticflow), com_x, com_y);
YarpPixelBGR green;
green.r = green.b = 0;
green.g = 0;
i = 0;
for (frame = startopticflow+1; frame <= endopticflow; frame++)
{
AddCircleOutline (oseq.GetImageRef(frame-start+1), green, sx, sy, 10);
if (tracker.IsTracking())
{
tracker.Apply (seq->GetImageRef(frame), true, sx2, sy2, trackvalid);
printf ("frame: %d, valid: %d, sx, sy: %d %d\n", frame, trackvalid, sx2, sy2);
}
YARPColorConverter::RGB2Grayscale (seq->GetImageRef(frame), mono);
if (frame < contact_frame)
of.Apply (mono, mask, sx2-sx, sy2-sy, outimage, vx[frame-start], vy[frame-start]);
else
of.Apply (mono, extended_segmentation, sx2-sx, sy2-sy, outimage, vx[frame-start], vy[frame-start]);
sx = sx2;
sy = sy2;
of.DrawFlow (oseq.GetImageRef (frame-start));
if (frame == contact_frame)
WriteMask (extended_segmentation, oseq.GetImageRef (frame-start));
if (frame >= contact_frame+1 && frame <= endtracking)
{
if (ComputeRotation (extended_segmentation,
vx[frame-start],
vy[frame-start],
ox,
oy,
trsf[i],
10) == -2)
lack_of_vectors++;
i++;
WriteMask (extended_segmentation, oseq.GetImageRef (frame-start));
}
}
CenterOfMass (extended_segmentation, final_x, final_y);
printf ("starting point: %d %d\n", com_x, com_y);
printf ("center of mass: %d %d\n", final_x, final_y);
dispframe = contact_frame - start - 10; // it was -5.
m_stepping = 2;
if (lack_of_vectors > 6)
{
printf ("optic flow is poor, skipping frames\n");
oseq.Reset ();
// adjust start frame parity.
int newstart = start;
if (((contact_frame % 2) == 0 && (newstart % 2) == 1) ||
((contact_frame % 2) == 1 && (newstart % 2) == 0)
)
newstart ++;
lack_of_vectors = 0;
printf ("re-processing from frame %d to %d\n", start, stop);
// RECOMPUTING INDEX ETC.
//
segmentation_mask = segmentation_mask_copy;
flipper_segmentation_mask = flipper_segmentation_mask_copy;
// enlarge it twice.
GrowMask (segmentation_mask, extended_segmentation);
segmentation_mask = extended_segmentation;
GrowMask (segmentation_mask, extended_segmentation);
// contact frame is ok.
// poke dir is ok.
// center of mass is ok.
// RECOMPUTE OPTIC FLOW.
int startopticflow = contact_frame - 10; //20;
if (startopticflow < newstart) startopticflow = newstart;
if (((contact_frame % 2) == 0 && (startopticflow % 2) == 1) ||
((contact_frame % 2) == 1 && (startopticflow % 2) == 0)
)
startopticflow ++;
int endopticflow = contact_frame + FRAMES_TRACKED*2;
if (endopticflow > stop) endopticflow = stop;
// TRACK.
int endtracking = contact_frame+FRAMES_TRACKED*2;
if (endtracking > stop) endtracking = stop;
YARPColorConverter::RGB2Grayscale (seq->GetImageRef(startopticflow), mono);
of.Initialize (mono);
bool trackvalid = false;
int sx = com_x, sy = com_y;
int sx2 = com_x, sy2 = com_y;
tracker.Initialize (seq->GetImageRef(startopticflow), com_x, com_y);
YarpPixelBGR green;
green.r = green.b = 0;
green.g = 0;
for (frame = start; frame <= stop; frame++)
{
oseq.IncrementCounter ();
oseq.GetImageRef (frame-start) = seq->GetImageRef (frame);
}
i = 0;
for (frame = startopticflow+2; frame <= endopticflow; frame+=2)
{
AddCircleOutline (oseq.GetImageRef(frame-start+2), green, sx, sy, 10);
if (tracker.IsTracking())
{
tracker.Apply (seq->GetImageRef(frame), true, sx2, sy2, trackvalid);
printf ("frame: %d, valid: %d, sx, sy: %d %d\n", frame, trackvalid, sx2, sy2);
}
YARPColorConverter::RGB2Grayscale (seq->GetImageRef(frame), mono);
if (frame < contact_frame)
of.Apply (mono, mask, sx2-sx, sy2-sy, outimage, vx[frame-start], vy[frame-start]);
else
of.Apply (mono, extended_segmentation, sx2-sx, sy2-sy, outimage, vx[frame-start], vy[frame-start]);
sx = sx2;
sy = sy2;
of.DrawFlow (oseq.GetImageRef (frame-start));
if (frame == contact_frame)
WriteMask (extended_segmentation, oseq.GetImageRef (frame-start));
if (frame >= contact_frame+2 && frame <= endtracking)
{
if (ComputeRotation (extended_segmentation,
vx[frame-start],
vy[frame-start],
ox,
oy,
trsf[i],
10) == -2)
lack_of_vectors++;
i++;
WriteMask (extended_segmentation, oseq.GetImageRef (frame-start));
}
}
CenterOfMass (extended_segmentation, final_x, final_y);
printf ("starting point: %d %d\n", com_x, com_y);
printf ("center of mass: %d %d\n", final_x, final_y);
printf ("improved? %d\n", lack_of_vectors);
//
//
//
m_stepping = 4;
dispframe = contact_frame - start - 10;
if (dispframe < 0) dispframe = 0;
if (lack_of_vectors > 6)
{
// bad sequence.
printf ("Still bad flow after post-processing\n");
return -2;
}
}
return 0;
}
//酸素の位置を読みこむ。
sLattIce* load_LattIce( FILE* file, real hposition )
{
char buf[1000];
sLattIce* ice;
bool coord=False, network=False;
real rhb=0;
ice = calloc( 1, sizeof( sLattIce ) );
ice->periodic = False;
//ice->dryrun = False;
/*プロトンの場所は不明*/
ice->currentBond = -1;
ice->currentPotential = 0;
while( NULL != fgets( buf, sizeof( buf ), file ) ){
if ( strncmp( buf, "@BOX3",5 ) == 0 ){
fgets( buf, sizeof( buf ), file );
ice->periodic = True;
#ifdef SINGLEPRECISION
sscanf( buf, "%f %f %f", &ice->bx, &ice->by, &ice->bz );
#else
sscanf( buf, "%lf %lf %lf", &ice->bx, &ice->by, &ice->bz );
#endif
}
else if ( strncmp( buf, "@BXLA",5 ) == 0 ){
fgets( buf, sizeof( buf ), file );
ice->periodic = True;
#ifdef SINGLEPRECISION
sscanf( buf, "%f", &ice->bx );
#else
sscanf( buf, "%lf", &ice->bx );
#endif
ice->by = ice->bz = ice->bx;
}
else if ( strncmp( buf, "@NGPH", 5 ) == 0 ){
int o1,o2;
int no;
int nhb=0;
network = True;
fgets( buf, sizeof( buf ), file );
no = atoi( buf );
if ( ice->nOxygen == 0 ){
ice->nOxygen = no;
ice->comx = ice->comy = ice->comz = 0;
ice->oxygens = calloc( ice->nOxygen, sizeof( sOxygen ) );
ice->bonds = calloc( ice->nOxygen * 2, sizeof( sHydrogenBond ) );
}
else if ( ice->nOxygen != no ){
fprintf( stderr, "Error: number of sites differ: %d != %d\n",
ice->nOxygen, no );
exit(1);
}
/*ネットワークを読みこむ。一応有向グラフと考える。*/
while ( NULL != fgets( buf, sizeof( buf ), file ) ){
sOxygen* oxy1;
sOxygen* oxy2;
sHydrogenBond* hb;
sscanf( buf, "%d %d", &o1, &o2 );
if ( o1 < 0 ) break;
oxy1 = &ice->oxygens[ o1 ];
oxy2 = &ice->oxygens[ o2 ];
hb = &ice->bonds[ nhb ];
oxy1->hydrogenBond[ oxy1->nAdj ] = nhb;
oxy1->oxygen[ oxy1->nAdj ] = o2;
oxy2->hydrogenBond[ oxy2->nAdj ] = nhb;
oxy2->oxygen[ oxy2->nAdj ] = o1;
if ( o1 < o2 ){
hb->oxygen[0] = o1;
hb->oxygen[1] = o2;
hb->direction = +1;
}
else {
hb->oxygen[0] = o2;
hb->oxygen[1] = o1;
hb->direction = -1;
}
oxy1->outgo ++;
oxy1->nAdj ++;
oxy2->nAdj ++;
nhb ++;
}
ice->nBond = nhb;
}
else if ( strncmp( buf, "@PPOS", 5 ) == 0 ){
int o1,o2;
int no;
int nhb;
sOxygen* oxy1;
sOxygen* oxy2;
sHydrogenBond* hb;
/*@PPOSより前に@NGPHを読みこんでいる必要がある。*/
if ( ! network ){
fprintf( stderr, "Network topology must be read before proton position.\n" );
exit(1);
}
fgets( buf, sizeof( buf ), file );
no = atoi( buf );
/*ネットワークを読みこむ。一応有向グラフと考える。*/
nhb = ice->nBond;
/*最初のプロトンしか読まない。*/
fgets( buf, sizeof( buf ), file );
sscanf( buf, "%d %d", &o1, &o2 );
oxy1 = &ice->oxygens[ o1 ];
oxy2 = &ice->oxygens[ o2 ];
hb = &ice->bonds[ nhb ];
oxy1->hydrogenBond[ oxy1->nAdj ] = nhb;
oxy1->oxygen[ oxy1->nAdj ] = o2;
oxy2->hydrogenBond[ oxy2->nAdj ] = nhb;
oxy2->oxygen[ oxy2->nAdj ] = o1;
hb->oxygen[0] = o1;
hb->oxygen[1] = o2;
hb->direction = 0;
oxy1->nAdj ++;
oxy2->nAdj ++;
ice->currentBond = nhb;
nhb ++;
ice->nBond = nhb;
}
else if ( strncmp( buf, "@RCOO", 5 ) == 0 ){
/*結合しているとみなすO-O間距離の閾値*/
fgets( buf, sizeof( buf ), file );
rhb = atof( buf );
}
else if ( strncmp( buf, "@NX4A", 5 ) == 0 ||
strncmp( buf, "@AR3A", 5 ) == 0 ||
strncmp( buf, "@NX3A", 5 ) == 0 ){
int o1;
int no;
coord = True;
fgets( buf, sizeof( buf ), file );
no = atoi( buf );
if ( ice->nOxygen == 0 ){
ice->nOxygen = no;
ice->comx = ice->comy = ice->comz = 0;
ice->oxygens = calloc( ice->nOxygen, sizeof( sOxygen ) );
ice->bonds = calloc( ice->nOxygen * 2, sizeof( sHydrogenBond ) );
}
else if ( ice->nOxygen != no ){
fprintf( stderr, "Error: number of sites differ: %d != %d\n",
ice->nOxygen, no );
exit(1);
}
/*座標を読みこむ。*/
for( o1=0; o1< ice->nOxygen; o1++ ){
fgets( buf, sizeof( buf ), file );
#ifdef SINGLEPRECISION
sscanf( buf, "%f %f %f",
&ice->oxygens[o1].x,
&ice->oxygens[o1].y,
&ice->oxygens[o1].z );
#elif real == double
sscanf( buf, "%lf %lf %lf",
&ice->oxygens[o1].x,
&ice->oxygens[o1].y,
&ice->oxygens[o1].z );
#else
#error
#endif
/*ファイルから読む場合はとりあえずダミーサイトではないと考える。→平成16年2月18日(水)変更。結合数によってダミーかどうかを決める。*/
ice->oxygens[o1].charge = -2;
}
#ifdef DEBUG
fprintf( stderr, "CoM: %f %f %f\n", ice->comx, ice->comy, ice->comz );
#endif
}
//if ( coord && network ) break;
}
if ( ! network && 0.0 < rhb ) {
DetermineBonds( ice, rhb );
}
CenterOfMass( ice );
/*O-O間のプロトンのとりうる位置3つの座標を計算する。*/
SetHBins( ice, hposition );
return ice;
//fprintf( stderr, "Error: No inputs.\n" );
//exit(1);
}
/*create N x N x N cubic ice */
sLattIce* CubicIce( int n, real hposition )
{
int x,y,z;
int nhb;
int o1;
sLattIce* ice;
ice = malloc( sizeof(sLattIce) );
ice->oxygens = calloc( n*n*n, sizeof( sOxygen ) );
ice->bonds = calloc( n*n*n*2, sizeof( sHydrogenBond ) );
ice->nOxygen = n*n*n;
ice->periodic = False;
//ice->dryrun = False;
for ( x=0; x<2*n; x+=2 ){
for ( y=0; y<2*n; y+=2 ){
for ( z=0; z<2*n; z+=2 ){
if ( ( ( x+y+z ) % 4 ) == 0 ){
int xi,yi,zi;
//位置から酸素IDを得る
int self = Coordinate2OxygenID( n, x, y, z );
if ( ice->oxygens[self].x != 0 || ice->oxygens[self].y != 0
|| ice->oxygens[self].z != 0 ){
printf("%d %d %d %d is used\n", self,x,y,z);
}
//位置を保存する
ice->oxygens[self].x = x;
ice->oxygens[self].y = y;
ice->oxygens[self].z = z;
//立方体表面にあるなら
if ( x == 0 || x == 2*n-2 ||
y == 0 || y == 2*n-2 ||
z == 0 || z == 2*n-2 )
//ダミーサイトである。
ice->oxygens[self].charge = 0;
else{
//水素の電荷の-2倍。
ice->oxygens[self].charge = -2;
ice->oxygens[self].oxygen[0] =
Coordinate2OxygenID( n, x+1, y+1, z+1 );
ice->oxygens[self].oxygen[1] =
Coordinate2OxygenID( n, x+1, y-1, z-1 );
ice->oxygens[self].oxygen[2] =
Coordinate2OxygenID( n, x-1, y+1, z-1 );
ice->oxygens[self].oxygen[3] =
Coordinate2OxygenID( n, x-1, y-1, z+1 );
ice->oxygens[self].nAdj = 4;
}
xi = x + 1;
yi = y + 1;
zi = z + 1;
self = Coordinate2OxygenID( n, xi, yi, zi );
ice->oxygens[self].x = xi;
ice->oxygens[self].y = yi;
ice->oxygens[self].z = zi;
if ( xi == 2*n-1 ||
yi == 2*n-1 ||
zi == 2*n-1 )
ice->oxygens[self].charge = 0;
else{
ice->oxygens[self].charge = -2;
ice->oxygens[self].oxygen[0] =
Coordinate2OxygenID( n, xi-1, yi-1, zi-1 );
ice->oxygens[self].oxygen[1] =
Coordinate2OxygenID( n, xi-1, yi+1, zi+1 );
ice->oxygens[self].oxygen[2] =
Coordinate2OxygenID( n, xi+1, yi-1, zi+1 );
ice->oxygens[self].oxygen[3] =
Coordinate2OxygenID( n, xi+1, yi+1, zi-1 );
ice->oxygens[self].nAdj = 4;
}
}
}
}
}
CenterOfMass( ice );
/*つぎに水素結合を定義する。*/
nhb = 0;
/*すべての酸素原子について*/
for ( o1=0; o1<n*n*n; o1++ ){
/*もしダミーサイト(表面サイト)でなければ*/
if ( ice->oxygens[o1].charge != 0 ){
int j;
/*4つの隣接酸素について*/
for( j=0; j<ice->oxygens[o1].nAdj; j++ ){
int o2;
o2 = ice->oxygens[o1].oxygen[j];
/*o1<o2なら、ボンドを登録する(重複登録をさけるため)*/
if ( o1 < o2 ) {
/*bondの2つの端点を登録する*/
ice->bonds[nhb].oxygen[0] = o1;
ice->bonds[nhb].oxygen[1] = o2;
/*この結合をo2への結合として登録する。*/
ice->oxygens[o1].hydrogenBond[j] = nhb;
/*隣接酸素がダミーサイトでないなら*/
if ( ice->oxygens[o2].charge != 0 ){
int k;
/*隣接酸素の隣接酸素について*/
for ( k=0; k<ice->oxygens[o2].nAdj; k++ )
/*それがo1なら*/
if ( ice->oxygens[o2].oxygen[k] == o1 )
/*この結合をo2からo1への結合として登録する*/
ice->oxygens[o2].hydrogenBond[k] = nhb;
}
/*登録結合数を増やす*/
nhb ++;
}
/*隣接酸素がダミーサイトなら*/
else if ( ice->oxygens[o2].charge == 0 ) {
/*o2 < o1でもボンドを登録する。*/
ice->bonds[nhb].oxygen[1] = o1;
ice->bonds[nhb].oxygen[0] = o2;
ice->oxygens[o1].hydrogenBond[j] = nhb;
nhb ++;
}
}
}
}
//結合総数には、ダミーボンドへの結合が含まれるので、酸素(電荷あり)の総数の2倍よりも大きいはず。
ice->nBond = nhb;
SetHBins( ice, hposition );
return ice;
}