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Adding pressure measurement via r dot f and temperature measurement and control including rotational energy. Adding random orientation on initialisation. Modifying constantProperties construction to detect point masses. Tidy up hitWallPatch function to remove commented out stochastic wall code.

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This commit is contained in:
graham 2009-01-12 17:35:57 +00:00
parent 7f9f091f42
commit fa8f316ecc
7 changed files with 114 additions and 92 deletions
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20
applications/solvers/molecularDynamics/mdFoam/mdFoam.C
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@ -46,20 +46,40 @@ int main(int argc, char *argv[])
# include "temperatureAndPressureVariables.H"
label nAveragingSteps = 0;
Info << "\nStarting time loop\n" << endl;
while (runTime.run())
{
runTime++;
nAveragingSteps++;
Info << "Time = " << runTime.timeName() << endl;
molecules.evolve();
# include "meanMomentumEnergyAndNMols.H"
# include "temperatureAndPressure.H"
if (runTime.outputTime())
{
molecules.applyConstraintsAndThermostats
(
485.4,
averageTemperature
);
}
runTime.write();
if (runTime.outputTime())
{
nAveragingSteps = 0;
}
Info << "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
<< " ClockTime = " << runTime.elapsedClockTime() << " s"
<< nl << endl;

20
src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H
View File

@ -33,11 +33,13 @@ Description
\*---------------------------------------------------------------------------*/
accumulatedTotalMomentum += singleStepTotalMomentum;
accumulatedTotalLinearMomentum += singleStepTotalLinearMomentum;
accumulatedTotalMass += singleStepTotalMass;
accumulatedTotalKE += singleStepTotalKE;
accumulatedTotalLinearKE += singleStepTotalLinearKE;
accumulatedTotalAngularKE += singleStepTotalAngularKE;
accumulatedTotalPE += singleStepTotalPE;
@ -55,12 +57,12 @@ if (runTime.outputTime())
averageTemperature =
(
2.0/(3.0 * moleculeCloud::kb * accumulatedNMols)
2.0/(6.0 * moleculeCloud::kb * accumulatedNMols)
*
(
accumulatedTotalKE
accumulatedTotalLinearKE + accumulatedTotalAngularKE
-
0.5*magSqr(accumulatedTotalMomentum)/accumulatedTotalMass
0.5*magSqr(accumulatedTotalLinearMomentum)/accumulatedTotalMass
)
);
@ -82,7 +84,7 @@ if (runTime.outputTime())
Info << "----------------------------------------" << nl
<< "Averaged properties" << nl
<< "Average |velocity| = "
<< mag(accumulatedTotalMomentum)/accumulatedTotalMass
<< mag(accumulatedTotalLinearMomentum)/accumulatedTotalMass
<< " m/s" << nl
<< "Average temperature = "
<< averageTemperature << " K" << nl
@ -98,11 +100,13 @@ if (runTime.outputTime())
// reset counters
accumulatedTotalMomentum = vector::zero;
accumulatedTotalLinearMomentum = vector::zero;
accumulatedTotalMass = 0.0;
accumulatedTotalKE = 0.0;
accumulatedTotalLinearKE = 0.0;
accumulatedTotalAngularKE = 0.0;
accumulatedTotalPE = 0.0;

6
src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressureVariables.H
View File

@ -30,11 +30,13 @@ Description
\*---------------------------------------------------------------------------*/
vector accumulatedTotalMomentum(vector::zero);
vector accumulatedTotalLinearMomentum(vector::zero);
scalar accumulatedTotalMass = 0.0;
scalar accumulatedTotalKE = 0.0;
scalar accumulatedTotalAngularKE = 0.0;
scalar accumulatedTotalLinearKE = 0.0;
scalar accumulatedTotalPE = 0.0;

36
src/lagrangian/molecularDynamics/molecule/molecule/molecule.C
View File

@ -246,38 +246,12 @@ void Foam::molecule::hitWallPatch
nw /= mag(nw);
scalar vn = v_ & nw;
// vector vt = v_ - vn*nw;
// Random rand(clock::getTime());
// scalar tmac = 0.8;
// scalar wallTemp = 2.5;
// if (rand.scalar01() < tmac)
// {
// // Diffuse reflection
//
// vector tw1 = vt/mag(vt);
//
// vector tw2 = nw ^ tw1;
//
// V_ = sqrt(wallTemp/mass_)*rand.GaussNormal()*tw1
// + sqrt(wallTemp/mass_)*rand.GaussNormal()*tw2
// - mag(sqrt(wallTemp/mass_)*rand.GaussNormal())*nw;
// }
// else
// {
// Specular reflection
if (vn > 0)
{
v_ -= 2*vn*nw;
}
// }
// Specular reflection
if (vn > 0)
{
v_ -= 2*vn*nw;
}
}

81
src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H
View File

@ -63,46 +63,47 @@ inline Foam::molecule::constantProperties::constantProperties
mass_ = sum(siteMasses);
// Calculate the centre of mass of the body and subtract it from each
// position
vector centreOfMass(vector::zero);
forAll(siteReferencePositions_, i)
{
// Calculate the centre of mass of the body and subtract it from each
// position
centreOfMass += siteReferencePositions_[i]*siteMasses[i];
}
vector centreOfMass(vector::zero);
centreOfMass /= mass_;
forAll(siteReferencePositions_, i)
{
centreOfMass += siteReferencePositions_[i]*siteMasses[i];
}
siteReferencePositions_ -= centreOfMass;
centreOfMass /= mass_;
// Calculate the inertia tensor in the current orientation
siteReferencePositions_ -= centreOfMass;
tensor momOfInertia(tensor::zero);
// Calculate the inertia tensor in the current orientation
forAll(siteReferencePositions_, i)
{
const vector& p(siteReferencePositions_[i]);
tensor I(tensor::zero);
forAll(siteReferencePositions_, i)
{
const vector& p(siteReferencePositions_[i]);
I += siteMasses[i]*tensor
(
p.y()*p.y() + p.z()*p.z(), -p.x()*p.y(), -p.x()*p.z(),
-p.y()*p.x(), p.x()*p.x() + p.z()*p.z(), -p.y()*p.z(),
-p.z()*p.x(), -p.z()*p.y(), p.x()*p.x() + p.y()*p.y()
);
}
momOfInertia += siteMasses[i]*tensor
(
p.y()*p.y() + p.z()*p.z(), -p.x()*p.y(), -p.x()*p.z(),
-p.y()*p.x(), p.x()*p.x() + p.z()*p.z(), -p.y()*p.z(),
-p.z()*p.x(), -p.z()*p.y(), p.x()*p.x() + p.y()*p.y()
);
}
if(eigenValues(momOfInertia).z() > VSMALL)
{
// Normalise the inertia tensor magnitude to avoid SMALL numbers in the
// components causing problems
I /= eigenValues(I).z();
momOfInertia /= eigenValues(momOfInertia).z();
tensor e = eigenVectors(I);
tensor e = eigenVectors(momOfInertia);
// Calculate the transformation between the principle axes to the global
// axes
// Calculate the transformation between the principle axes to the
// global axes
tensor Q =
vector(1,0,0)*e.x() + vector(0,1,0)*e.y() + vector(0,0,1)*e.z();
@ -110,13 +111,11 @@ inline Foam::molecule::constantProperties::constantProperties
// Transform the site positions
siteReferencePositions_ = (Q & siteReferencePositions_);
}
{
// Recalculating the moment of inertia with the new site positions
// The rotation was around the centre of mass but remove any components
// that have crept in due to floating point errors
// The rotation was around the centre of mass but remove any
// components that have crept in due to floating point errors
vector centreOfMass(vector::zero);
@ -129,16 +128,16 @@ inline Foam::molecule::constantProperties::constantProperties
siteReferencePositions_ -= centreOfMass;
// Calculate the moment of inertia in the principle component reference
// frame
// Calculate the moment of inertia in the principle component
// reference frame
tensor I(tensor::zero);
tensor momOfInertia(tensor::zero);
forAll(siteReferencePositions_, i)
{
const vector& p(siteReferencePositions_[i]);
I += siteMasses[i]*tensor
momOfInertia += siteMasses[i]*tensor
(
p.y()*p.y() + p.z()*p.z(), -p.x()*p.y(), -p.x()*p.z(),
-p.y()*p.x(), p.x()*p.x() + p.z()*p.z(), -p.y()*p.z(),
@ -146,9 +145,19 @@ inline Foam::molecule::constantProperties::constantProperties
);
}
momentOfInertia_ = diagTensor(I.xx(), I.yy(), I.zz());
momentOfInertia_ = diagTensor
(
momOfInertia.xx(),
momOfInertia.yy(),
momOfInertia.zz()
);
}
else
{
Info<< nl << "Molecule " << dict.name() << " is a point mass." << endl;
momentOfInertia_ = diagTensor(0, 0, 0);
}
}

23
src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
View File

@ -982,6 +982,25 @@ void Foam::moleculeCloud::createMolecule
cP.momentOfInertia()
);
scalar phi(rndGen_.scalar01()*mathematicalConstant::twoPi);
scalar theta(rndGen_.scalar01()*mathematicalConstant::twoPi);
scalar psi(rndGen_.scalar01()*mathematicalConstant::twoPi);
const tensor Q
(
cos(psi)*cos(phi) - cos(theta)*sin(phi)*sin(psi),
cos(psi)*sin(phi) + cos(theta)*cos(phi)*sin(psi),
sin(psi)*sin(theta),
- sin(psi)*cos(phi) - cos(theta)*sin(phi)*cos(psi),
- sin(psi)*sin(phi) + cos(theta)*cos(phi)*cos(psi),
cos(psi)*sin(theta),
sin(theta)*sin(phi),
- sin(theta)*cos(phi),
cos(theta)
);
addParticle
(
new molecule
@ -989,7 +1008,7 @@ void Foam::moleculeCloud::createMolecule
cloud,
position,
cell,
I,
Q,
v,
vector::zero,
pi,
@ -1124,6 +1143,8 @@ void Foam::moleculeCloud::applyConstraintsAndThermostats
for (mol = this->begin(); mol != this->end(); ++mol)
{
mol().v() *= temperatureCorrectionFactor;
mol().pi() *= temperatureCorrectionFactor;
}
}

20
src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H
View File

@ -91,11 +91,9 @@ inline void Foam::moleculeCloud::evaluatePair
molJ->potentialEnergy() += 0.5*potentialEnergy;
// What to do here?
molI->rf() += rsIsJ * fsIsJ;
// molI->rf() += rIJ * fIJ;
// molJ->rf() += rIJ * fIJ;
molJ->rf() += rsIsJ * fsIsJ;
}
}
@ -128,11 +126,9 @@ inline void Foam::moleculeCloud::evaluatePair
molJ->potentialEnergy() += 0.5*potentialEnergy;
// What to do here?
molI->rf() += rsIsJ * fsIsJ;
// molI->rf() += rIJ * fIJ;
// molJ->rf() += rIJ * fIJ;
molJ->rf() += rsIsJ * fsIsJ;
}
}
}
@ -200,9 +196,7 @@ inline void Foam::moleculeCloud::evaluatePair
molReal->potentialEnergy() += 0.5*potentialEnergy;
// What to do here?
// molReal->rf() += rRealRef * fRealRef;
molReal->rf() += rsRealsRef * fsRealsRef;
}
}
@ -233,9 +227,7 @@ inline void Foam::moleculeCloud::evaluatePair
molReal->potentialEnergy() += 0.5*potentialEnergy;
// What to do here?
// molReal->rf() += rRealRef * fRealRef;
molReal->rf() += rsRealsRef * fsRealsRef;
}
}
}