void KoulesSimulator::elasticCollision(unsigned int i, unsigned int j)
{
double *a = &qcur_[ind(i)], *b = &qcur_[ind(j)];
double d[2] = { b[0] - a[0], b[1] - a[1] };
normalize2(d);
double va = dot2(a + 2, d), vb = dot2(b + 2, d);
if (va - vb <= 0.)
return;
double ma = si_->getStateSpace()->as<KoulesStateSpace>()->getMass(i);
double mb = si_->getStateSpace()->as<KoulesStateSpace>()->getMass(j);
double vap = (va * (ma - mb) + 2. * mb * vb) / (ma + mb);
double vbp = (vb * (mb - ma) + 2. * ma * va) / (ma + mb);
double amag = vap - va, bmag = vbp - vb;
if (std::abs(amag) < eps)
amag = amag < 0. ? -eps : eps;
if (std::abs(bmag) < eps)
bmag = bmag < 0. ? -eps : eps;
#ifndef NDEBUG
double px = ma * a[2] + mb * b[2], py = ma * a[3] + mb * b[3];
double k = ma * (a[2] * a[2] + a[3] * a[3]) + mb * (b[2] * b[2] + b[3] * b[3]);
#endif
vadd2(a + 2, amag, d);
vadd2(b + 2, bmag, d);
#ifndef NDEBUG
// preservation of momemtum
assert(std::abs(ma * a[2] + mb * b[2] - px) < 1e-6);
assert(std::abs(ma * a[3] + mb * b[3] - py) < 1e-6);
// preservation of kinetic energy
assert(std::abs(ma * (a[2] * a[2] + a[3] * a[3]) + mb * (b[2] * b[2] + b[3] * b[3]) - k) < 1e-6);
#endif
}
void kalman_2D_prediction(kalman_filter_2D_t *kalman, vector_2_t control)
{
kalman->state = vadd2( mvmul2(kalman->system_model, kalman->state),
mvmul2(kalman->control_model, control));
kalman->covariance= madd2( mmul2( mmul2( kalman->system_model,
kalman->covariance),
trans2(kalman->system_model)),
kalman->noise_prediction);
}
void sl_entity_aabb( sl_box *result, const sl_entity *q )
{
v2 min_p1, max_p1;
v2 min_p2, max_p2, offset;
m22 m2;
min_p1 = vec2( -1.0f, -1.0f );
max_p1 = vec2( 1.0f, 1.0f );
m2 = mtruncate42( &q->world_matrix );
min_p2 = vmulm2( &m2, min_p1 );
max_p2 = vmulm2( &m2, max_p1 );
offset.x = q->world_matrix.A[ 12 ];
offset.y = q->world_matrix.A[ 13 ];
min_p1 = vadd2( min_p2, offset );
max_p1 = vadd2( max_p2, offset );
result->min_p = vmin2( min_p1, max_p1 );
result->max_p = vmax2( min_p1, max_p1 );
}
void kalman_2D_update(kalman_filter_2D_t *kalman, vector_2_t measurement)
{
vector_2_t innovation = vsub2( measurement,
mvmul2(kalman->observation_model, kalman->state));
matrix_2x2_t innovation_covariance = madd2( mmul2( mmul2(kalman->observation_model, kalman->covariance),
trans2(kalman->observation_model)),
kalman->noise_measurement);
matrix_2x2_t kalman_gain = mmul2( mmul2(kalman->covariance, trans2(kalman->observation_model)),
inv2(innovation_covariance));
kalman->state = vadd2(kalman->state, mvmul2(kalman_gain, innovation));
kalman->covariance = mmul2( msub2(ident_2x2, mmul2(kalman_gain, kalman->observation_model)),
kalman->covariance);
}
void
oneDynamicsFrame(struct part *part,
int iters,
struct xyz *averagePositions,
struct xyz **pOldPositions,
struct xyz **pNewPositions,
struct xyz **pPositions,
struct xyz *force)
{
int j;
int loop;
double deltaTframe;
struct xyz f;
struct xyz *tmp;
struct jig *jig;
struct xyz *oldPositions = *pOldPositions;
struct xyz *newPositions = *pNewPositions;
struct xyz *positions = *pPositions;
// wware 060109 python exception handling
NULLPTR(part);
NULLPTR(averagePositions);
NULLPTR(oldPositions);
NULLPTR(newPositions);
NULLPTR(positions);
iters = max(iters,1);
deltaTframe = 1.0/iters;
for (j=0; j<part->num_atoms; j++) {
vsetc(averagePositions[j],0.0);
}
// See http://www.nanoengineer-1.net/mediawiki/index.php?title=Verlet_integration
// for a discussion of how dynamics is done in the simulator.
// we want:
// x(t+dt) = 2x(t) - x(t-dt) + A dt^2
// or:
// newPositions = 2 * positions - oldPositions + A dt^2
// wware 060110 don't handle Interrupted with the BAIL mechanism
for (loop=0; loop < iters && !Interrupted; loop++) {
_last_iteration = loop == iters - 1;
Iteration++;
// wware 060109 python exception handling
updateVanDerWaals(part, NULL, positions); BAIL();
calculateGradient(part, positions, force); BAIL();
/* first, for each atom, find non-accelerated new pos */
/* Atom moved from oldPositions to positions last time,
now we move it the same amount from positions to newPositions */
for (j=0; j<part->num_atoms; j++) {
// f = positions - oldPositions
vsub2(f,positions[j],oldPositions[j]);
// newPositions = positions + f
// or:
// newPositions = 2 * positions - oldPositions
vadd2(newPositions[j],positions[j],f);
// after this, we will need to add A dt^2 to newPositions
}
// pre-force jigs
for (j=0;j<part->num_jigs;j++) { /* for each jig */
jig = part->jigs[j];
// wware 060109 python exception handling
NULLPTR(jig);
switch (jig->type) {
case LinearMotor:
jigLinearMotor(jig, positions, newPositions, force, deltaTframe);
break;
default:
break;
}
}
/* convert forces to accelerations, giving new positions */
//FoundKE = 0.0; /* and add up total KE */
for (j=0; j<part->num_atoms; j++) {
// to complete Verlet integration, this needs to do:
// newPositions += A dt^2
//
// force[] is in pN, mass is in g, Dt in seconds, f in pm
vmul2c(f,force[j],part->atoms[j]->inverseMass); // inverseMass = Dt*Dt/mass
// XXX: 0.15 probably needs a scaling by Dt
// 0.15 = deltaX
// keMax = m v^2 / 2
// v^2 = 2 keMax / m
// v = deltaX / Dt = sqrt(2 keMax / m)
// deltaX = Dt sqrt(2 keMax / m)
// We probably don't want to do this, because a large raw
// velocity isn't a problem, it's just when that creates a
// high force between atoms that it becomes a problem. We
// check that elsewhere.
//if (!ExcessiveEnergyWarning && vlen(f)>0.15) { // 0.15 is just below H flyaway
// WARNING3("Excessive force %.6f in iteration %d on atom %d -- further warnings suppressed", vlen(f), Iteration, j+1);
// ExcessiveEnergyWarningThisFrame++;
//}
vadd(newPositions[j],f);
//vsub2(f, newPositions[j], positions[j]);
//ff = vdot(f, f);
//FoundKE += atom[j].energ * ff;
}
// Jigs are executed in the following order: motors,
// thermostats, grounds, measurements. Motions from each
// motor are added together, then thermostats operate on the
// motor output. Grounds override anything that moves atoms.
// Measurements happen after all things that could affect
// positions, including grounds.
// motors
for (j=0;j<part->num_jigs;j++) { /* for each jig */
jig = part->jigs[j];
if (jig->type == RotaryMotor) {
jigMotor(jig, deltaTframe, positions, newPositions, force);
}
// LinearMotor handled in preforce above
}
// thermostats
for (j=0;j<part->num_jigs;j++) { /* for each jig */
jig = part->jigs[j];
if (jig->type == Thermostat) {
jigThermostat(jig, deltaTframe, positions, newPositions);
}
}
// grounds
for (j=0;j<part->num_jigs;j++) { /* for each jig */
jig = part->jigs[j];
if (jig->type == Ground) {
jigGround(jig, deltaTframe, positions, newPositions, force);
}
}
// measurements
for (j=0;j<part->num_jigs;j++) { /* for each jig */
jig = part->jigs[j];
switch (jig->type) {
case Thermometer:
jigThermometer(jig, deltaTframe, positions, newPositions);
break;
case DihedralMeter:
jigDihedral(jig, newPositions);
break;
case AngleMeter:
jigAngle(jig, newPositions);
break;
case RadiusMeter:
jigRadius(jig, newPositions);
break;
default:
break;
}
}
for (j=0; j<part->num_atoms; j++) {
vadd(averagePositions[j],newPositions[j]);
}
tmp=oldPositions; oldPositions=positions; positions=newPositions; newPositions=tmp;
if (ExcessiveEnergyWarningThisFrame > 0) {
ExcessiveEnergyWarning = 1;
}
}
for (j=0; j<part->num_atoms; j++) {
vmulc(averagePositions[j],deltaTframe);
}
*pOldPositions = oldPositions;
*pNewPositions = newPositions;
*pPositions = positions;
}