//!Precompute relative rotations (and precompute ScGeom3D)
void ScGeom6D::precomputeRotations(const State& rbp1, const State& rbp2, bool isNew, bool creep){
if (isNew) {
initRotations(rbp1,rbp2);
} else {
Quaternionr delta((rbp1.ori * (initialOrientation1.conjugate())) * (initialOrientation2 * (rbp2.ori.conjugate())));
delta.normalize();
if (creep) delta = delta * twistCreep;
AngleAxisr aa(delta); // axis of rotation - this is the Moment direction UNIT vector; // angle represents the power of resistant ELASTIC moment
//Eigen::AngleAxisr(q) returns nan's when q close to identity, next tline fixes the pb.
// add -DYADE_SCGEOM_DEBUG to CXXFLAGS to enable this piece or just do
// #define YADE_SCGEOM_DEBUG //(but do not commit with that enabled in the code)
#ifdef YADE_SCGEOM_DEBUG
if (isnan(aa.angle())) {
cerr<<"NaN angle found in angleAxisr(q), for quaternion "<<delta<<", after quaternion product"<<endl;
cerr<<"rbp1.ori * (initialOrientation1.conjugate())) * (initialOrientation2 * (rbp2.ori.conjugate()) with quaternions :"<<endl;
cerr<<rbp1.ori<<" * "<<initialOrientation1<<" * "<<initialOrientation2<<" * "<<rbp2.ori<<endl<<" and sub-products :"<<endl<<rbp1.ori * (initialOrientation1.conjugate())<<" * "<<initialOrientation2 * (rbp2.ori.conjugate())<<endl;
cerr <<"q.w (before normalization) "<<delta.w();
delta.normalize();
cerr <<"q.w (after) "<<delta.w()<<endl;
AngleAxisr bb(delta);
cerr<<delta<<" "<<bb.angle()<<endl;
}
#else
if (isnan(aa.angle())) aa.angle()=0;
#endif
if (aa.angle() > Mathr::PI) aa.angle() -= Mathr::TWO_PI; // angle is between 0 and 2*pi, but should be between -pi and pi
twist = (aa.angle() * aa.axis().dot(normal));
bending = Vector3r(aa.angle()*aa.axis() - twist*normal);
}
}
int TorsionalMinimisation::runcore()
{
if( m_InitPickerSerial != getPickerSerial() )
{
initRotations(); // reinitialisation must occur, the atomic range definition has changed.
}
m_BestStore.store();
// Important to reinitialise these to ensure that we can call Run again without affecting the minimisation outcome.
for( size_t i = 0; i < ChiRotDefs.size(); i++ )
{
ChiRotDefs[i].Value = 0.0;
ChiRotDefs[i].PrevValue = 0.0;
}
for( size_t i = 0; i < PhiPsiRotDefs.size(); i++ )
{
PhiPsiRotDefs[i].Value = 0.0;
PhiPsiRotDefs[i].PrevValue = 0.0;
}
getWSpace().Step = Step = 0; // let WorkSpace know about the current Step #
// set the initial Step size
// should be 100% if we are not in steric clash!
AngleCap = IntendedMaxAngleCap * InitialCapFactor; //if require a gentle start - depends a bit on steric condition
SCAngleCap = IntendedMaxSCAngleCap * InitialCapFactor;
previous_epot = DBL_MAX;
PrevSquare = RESET_PREV_SQUARE;
Uphill = 0;
// Ene monitoring for grad cutoff
const size_t gradWindowSize = 20;
std::vector<double> xGradMarker(gradWindowSize);
std::vector<double> yGradMarker(gradWindowSize);
size_t currentGradMarker = 0;
Hamiltonian best_epot; // record the best energy, store the conformation when we beat it ...
best_epot.epot = DBL_MAX; // Big number, the first step of minimisation will beat this ...
if(OutputLevel) infoLineHeader();
// Main simulation inner-loop
for( Step = 0; Step < Steps; Step++ )
{
if( AngleCap < 0.00001 )
{
// The minimisation has stalled, there is no point in doing more steps
break;
}
getWSpace().Step = Step;// let particle system know about the current Step #
//getWSpace().nlist().calcNewList();
refreshNeighborList();
ff->calcForces();
if(!isNumber(getWSpace().ene.epot))
{
if(OutputLevel)
{
printf("Torsional CG Minimisation Unstable. Terminating... \n");
}
return -1;
}
if( getWSpace().ene.epot < best_epot.epot )
{
best_epot = getWSpace().ene;
m_BestStore.store(); // record the best over the minimisation
}
ApplyXYZAbsoluteDotVector(); // 1. calculate the required torsional magnitudes.
ActionConjugateGradient(); // 2. Normalise the magnitudes to give required changes in radians and apply.
if(Step > 2) // until you have had 2 rounds, you cant assess "up-hill" or "down-hill"
{
if (getWSpace().ene.epot <= previous_epot)
{
Uphill = 0; // we are going "downhill"
AngleCap *= CapRise; // if move was downhill then increase Step size (1.2 is an empiricly "good" weighting)
SCAngleCap *= CapRise;
if(AngleCap > IntendedMaxAngleCap) AngleCap = IntendedMaxAngleCap;
if(SCAngleCap > IntendedMaxSCAngleCap) SCAngleCap = IntendedMaxSCAngleCap;
//previous_epot = getWSpace().ene.epot; // : if Enabled here, disable after if(Step > 2)...
}
else
{
if( Uphill > 20 ) // The minimisation has stalled, there is no point in doing more steps
{
break;
}
Uphill++; // if move was uphill then halve Step size
AngleCap *= CapDrop;
SCAngleCap *= CapDrop;
// reinitialise these
for( size_t i = 0; i < ChiRotDefs.size(); i++ )
{
ChiRotDefs[i].PrevValue = 0.0;
}
for( size_t i = 0; i < PhiPsiRotDefs.size(); i++ )
{
PhiPsiRotDefs[i].PrevValue = 0.0;
}
PrevSquare = RESET_PREV_SQUARE;
}
}
previous_epot = getWSpace().ene.epot; // : if Enabled here, disable in if(getWSpace().ene.epot <= previous_epot)...
// Energy change over a number of Steps.
// If no improvement over a gradient Cutoff then quit, our work is done...
if( SlopeCutoff > 0.0 )
{
if( currentGradMarker < gradWindowSize )
{
xGradMarker[currentGradMarker] = (double)Step;
yGradMarker[currentGradMarker++] = getWSpace().ene.epot;
}
else
{
double b = TMleastSquaresFit( xGradMarker, yGradMarker );
if( SlopeCutoff > -b )
{
break;
}
xGradMarker[currentGradMarker % gradWindowSize] = (double)Step;
yGradMarker[currentGradMarker % gradWindowSize] = getWSpace().ene.epot;
currentGradMarker++;
}
}
runmonitors();
// Save the coordinates in the trajectory as required
if((UpdateTra > 0) && ((Step % UpdateTra) == 0) )
{
getWSpace().outtra.append();
}
// Display any information as required
if( OutputLevel && (UpdateScr > 0) && ((Step % UpdateScr) == 0) )
{
// now print info line
infoLine();
ff->infoLine();
printf("\n");
}
}
m_BestStore.revert();
getWSpace().ene = best_epot; // its quicker to memcpy the energies than to ff->calcForces() ...
return Step; // success
} // end procedure
TorsionalMinimisation::TorsionalMinimisation( Physics::Forcefield &_ff, const PickAtomRanges& _newRange ):
RangesProtocolBase( _ff, _newRange )
{
settodefault();
initRotations(); // initialise the rotations that will be used during simulation
}
void CylScGeom6D::precomputeRotations(const State& rbp1, const State& rbp2, bool isNew, bool creep) {
initRotations(rbp1,rbp2);
}
