void Foam::displacementMotionSolver::updateMesh(const mapPolyMesh& mpm)
{
// pointMesh already updates pointFields
motionSolver::updateMesh(mpm);
// Map points0_. Bit special since we somehow have to come up with
// a sensible points0 position for introduced points.
// Find out scaling between points0 and current points
// Get the new points either from the map or the mesh
const pointgpuField& points =
(
mpm.hasMotionPoints()
? mpm.preMotionPoints()
: mesh().points()
);
// Note: boundBox does reduce
const vector span0 = boundBox(points0_).span();
const vector span = boundBox(points).span();
vector scaleFactors(cmptDivide(span0, span));
pointField newPoints0(mpm.pointMap().size());
forAll(newPoints0, pointI)
{
label oldPointI = mpm.pointMap()[pointI];
if (oldPointI >= 0)
{
label masterPointI = mpm.reversePointMap()[oldPointI];
if (masterPointI == pointI)
{
newPoints0[pointI] = points0_[oldPointI];
}
else
{
// New point - assume motion is scaling
newPoints0[pointI] = points0_[oldPointI] + cmptMultiply
(
scaleFactors,
points[pointI] - points[masterPointI]
);
}
}
else
{
FatalErrorIn
(
"displacementMotionSolver::updateMesh"
"(const mapPolyMesh&)"
) << "Cannot determine co-ordinates of introduced vertices."
<< " New vertex " << pointI << " at co-ordinate "
<< points[pointI] << exit(FatalError);
}
}
void Foam::displacementSBRStressFvMotionSolver::updateMesh
(
const mapPolyMesh& mpm
)
{
fvMotionSolver::updateMesh(mpm);
// Map points0_
// Map points0_. Bit special since we somehow have to come up with
// a sensible points0 position for introduced points.
// Find out scaling between points0 and current points
// Get the new points either from the map or the mesh
const pointField& points =
(
mpm.hasMotionPoints()
? mpm.preMotionPoints()
: fvMesh_.points()
);
// Note: boundBox does reduce
const boundBox bb0(points0_, true);
const vector span0(bb0.max()-bb0.min());
const boundBox bb(points, true);
const vector span(bb.max()-bb.min());
vector scaleFactors(cmptDivide(span0, span));
pointField newPoints0(mpm.pointMap().size());
forAll(newPoints0, pointI)
{
label oldPointI = mpm.pointMap()[pointI];
if (oldPointI >= 0)
{
label masterPointI = mpm.reversePointMap()[oldPointI];
if (masterPointI == pointI)
{
newPoints0[pointI] = points0_[oldPointI];
}
else
{
// New point. Assume motion is scaling.
newPoints0[pointI] =
points0_[oldPointI]
+ cmptMultiply
(
scaleFactors,
points[pointI]-points[masterPointI]
);
}
}
else
{
FatalErrorIn
(
"displacementSBRStressFvMotionSolver::updateMesh"
"(const mapPolyMesh& mpm)"
) << "Cannot work out coordinates of introduced vertices."
<< " New vertex " << pointI << " at coordinate "
<< points[pointI] << exit(FatalError);
}
}
int main(int argc, const char * argv[]) {
int numParticles = 24;
double charges_arr[] = {0.131300, 0.147300, 0.139400, 0.157400, 0.117000, 0.067800, 0.091200, 0.424900, 0.425600, 0.483500, 0.423600, -0.109800, -0.094800, -0.207900, -0.146800, -0.151000, 0.126300, 0.936500, -0.045900, -0.074300, -0.833000, -0.711000, -0.801600, -0.495800};
double atomicRadii_arr[] = {0.120000, 0.120000, 0.120000, 0.120000, 0.120000, 0.120000, 0.120000, 0.120000, 0.120000, 0.120000, 0.120000, 0.170000, 0.170000, 0.170000, 0.170000, 0.170000, 0.170000, 0.170000, 0.170000, 0.170000, 0.155000, 0.150000, 0.150000, 0.150000};
double scaleFactors_arr[] = {0.850000, 0.850000, 0.850000, 0.850000, 0.850000, 0.850000, 0.850000, 0.850000, 0.850000, 0.850000, 0.850000, 0.720000, 0.720000, 0.720000, 0.720000, 0.720000, 0.720000, 0.720000, 0.720000, 0.720000, 0.790000, 0.850000, 0.850000, 0.850000};
std::vector<double> charges(charges_arr, charges_arr + sizeof(charges_arr) / sizeof(double));
std::vector<double> atomicRadii(atomicRadii_arr, atomicRadii_arr + sizeof(atomicRadii_arr) / sizeof(double));
std::vector<double> scaleFactors(scaleFactors_arr, scaleFactors_arr + sizeof(scaleFactors_arr) / sizeof(double));
vector3 atomCoordinates[numParticles];
atomCoordinates[0][0] = 2.805550;
atomCoordinates[0][1] = 0.089450;
atomCoordinates[0][2] = 1.683500;
atomCoordinates[1][0] = 2.713690;
atomCoordinates[1][1] = 0.503260;
atomCoordinates[1][2] = 1.735420;
atomCoordinates[2][0] = 2.580450;
atomCoordinates[2][1] = 0.033700;
atomCoordinates[2][2] = 1.759150;
atomCoordinates[3][0] = 2.487860;
atomCoordinates[3][1] = 0.447340;
atomCoordinates[3][2] = 1.816930;
atomCoordinates[4][0] = 2.946940;
atomCoordinates[4][1] = 0.422240;
atomCoordinates[4][2] = 1.714860;
atomCoordinates[5][0] = 2.984070;
atomCoordinates[5][1] = 0.255700;
atomCoordinates[5][2] = 1.683920;
atomCoordinates[6][0] = 2.861380;
atomCoordinates[6][1] = 0.300150;
atomCoordinates[6][2] = 1.449780;
atomCoordinates[7][0] = 3.095920;
atomCoordinates[7][1] = 0.243650;
atomCoordinates[7][2] = 1.485840;
atomCoordinates[8][0] = 3.085850;
atomCoordinates[8][1] = 0.363430;
atomCoordinates[8][2] = 1.370570;
atomCoordinates[9][0] = 3.130310;
atomCoordinates[9][1] = 0.402180;
atomCoordinates[9][2] = 1.526820;
atomCoordinates[10][0] = 2.352870;
atomCoordinates[10][1] = 0.278670;
atomCoordinates[10][2] = 1.858320;
atomCoordinates[11][0] = 2.737170;
atomCoordinates[11][1] = 0.168810;
atomCoordinates[11][2] = 1.712970;
atomCoordinates[12][0] = 2.683540;
atomCoordinates[12][1] = 0.398830;
atomCoordinates[12][2] = 1.742020;
atomCoordinates[13][0] = 2.610740;
atomCoordinates[13][1] = 0.137850;
atomCoordinates[13][2] = 1.754950;
atomCoordinates[14][0] = 2.556960;
atomCoordinates[14][1] = 0.368490;
atomCoordinates[14][2] = 1.788380;
atomCoordinates[15][0] = 2.774370;
atomCoordinates[15][1] = 0.299610;
atomCoordinates[15][2] = 1.706940;
atomCoordinates[16][0] = 2.522120;
atomCoordinates[16][1] = 0.234120;
atomCoordinates[16][2] = 1.795440;
atomCoordinates[17][0] = 2.884280;
atomCoordinates[17][1] = 0.507750;
atomCoordinates[17][2] = 1.481190;
atomCoordinates[18][0] = 2.913600;
atomCoordinates[18][1] = 0.335030;
atomCoordinates[18][2] = 1.658250;
atomCoordinates[19][0] = 2.926150;
atomCoordinates[19][1] = 0.365170;
atomCoordinates[19][2] = 1.508870;
atomCoordinates[20][0] = 3.065150;
atomCoordinates[20][1] = 0.341270;
atomCoordinates[20][2] = 1.470230;
atomCoordinates[21][0] = 2.912950;
atomCoordinates[21][1] = 0.548670;
atomCoordinates[21][2] = 1.368890;
atomCoordinates[22][0] = 2.827210;
atomCoordinates[22][1] = 0.581440;
atomCoordinates[22][2] = 1.566630;
atomCoordinates[23][0] = 2.405610;
atomCoordinates[23][1] = 0.197730;
atomCoordinates[23][2] = 1.831700;
ObcParameters* obcParameters = new ObcParameters(numParticles,
ObcParameters::ObcTypeII);
obcParameters->setAtomicRadii(atomicRadii);
obcParameters->setScaledRadiusFactors(scaleFactors);
obcParameters->setSolventDielectric(static_cast<double>(78.5));
obcParameters->setSoluteDielectric(static_cast<double>(1.0));
obcParameters->setPi4Asolv(4*M_PI*2.25936);
obcParameters->setUseCutoff(static_cast<double>(1.5));
ReferenceObc *obc = new ReferenceObc(obcParameters);
obc->setIncludeAceApproximation(true);
vector3 inputForces[numParticles];
double obcEnergy;
obcEnergy = obc->computeBornEnergyForces(atomCoordinates, charges, inputForces);
// Energy is inconsistent with MMTK version
std::cout << "Obc energy: " << obcEnergy << std::endl;
for (int i = 0; i < numParticles; ++i)
std::cout << inputForces[i][0] << ' ' << inputForces[i][1] << ' ' << inputForces[i][2] << std::endl;
delete obcParameters;
return 0;
}
