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ENH: Using site lists in force calculation.

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This commit is contained in:
graham
2011-06-28 18:33:08 +01:00
parent 76b9524796
commit 7ffe4d83d7
6 changed files with 372 additions and 382 deletions
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5
applications/solvers/discreteMethods/molecularDynamics/mdFoam/Make/options
View File

@ -1,7 +1,6 @@
EXE_INC = \
-I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
-I$(LIB_SRC)/lagrangian/molecularDynamics/molecularMeasurements/lnInclude \
-I$(LIB_SRC)/finiteVolume/lnInclude \
-I$(LIB_SRC)/lagrangian/basic/lnInclude \
-I$(LIB_SRC)/meshTools/lnInclude
@ -11,6 +10,4 @@ EXE_LIBS = \
-lfiniteVolume \
-llagrangian \
-lmolecule \
-lpotential \
-lmolecularMeasurements
-lpotential

15
src/lagrangian/molecularDynamics/molecule/polyatomic/polyatomic/polyatomic.C
View File

@ -156,13 +156,15 @@ bool Foam::polyatomic::move(polyatomic::trackingData& td, const scalar trackTime
tau_ = vector::zero;
forAll(siteForces_, s)
forAll(siteForces_, sI)
{
const vector& f = siteForces_[s];
const vector& f = siteForces_[sI];
a_ += f/m;
tau_ += (constProps.siteReferencePositions()[s] ^ (Q_.T() & f));
tau_ +=
constProps.sites()[sI].siteReferencePosition()
^ (Q_.T() & f);
}
v_ += 0.5*trackTime*a_;
@ -231,7 +233,12 @@ void Foam::polyatomic::transformProperties(const vector& separation)
void Foam::polyatomic::setSitePositions(const constantProperties& constProps)
{
sitePositions_ = position_ + (Q_ & constProps.siteReferencePositions());
forAll(constProps.sites(), sI)
{
sitePositions_[sI] =
position_
+ (Q_ & constProps.sites()[sI].siteReferencePosition());
}
}

54
src/lagrangian/molecularDynamics/molecule/polyatomic/polyatomic/polyatomic.H
View File

@ -41,6 +41,7 @@ SourceFiles
#include "IOstream.H"
#include "autoPtr.H"
#include "diagTensor.H"
#include "constPropSite.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@ -78,18 +79,16 @@ public:
{
// Private data
Field<vector> siteReferencePositions_;
//- Sites of mass, charge or interaction
List<constPropSite> sites_;
List<scalar> siteMasses_;
//- Which sites require electrostatic interactions
List<label> electrostaticSites_;
List<scalar> siteCharges_;
List<label> siteIds_;
List<bool> pairPotentialSites_;
List<bool> electrostaticSites_;
//- Which sites require pair interactions
List<label> pairPotSites_;
//- Moment of intertia (in principal axis configiration)
diagTensor momentOfInertia_;
scalar mass_;
@ -97,8 +96,6 @@ public:
// Private Member Functions
void checkSiteListSizes() const;
void setInteracionSiteBools
(
const List<word>& siteIds,
@ -113,27 +110,19 @@ public:
inline constantProperties();
//- Construct from dictionary
inline constantProperties(const dictionary& dict);
inline constantProperties
(
const dictionary& dict,
const labelList& siteIds
);
// Member functions
inline const Field<vector>& siteReferencePositions() const;
inline const List<constPropSite>& sites() const;
inline const List<scalar>& siteMasses() const;
inline const List<label>& pairPotSites() const;
inline const List<scalar>& siteCharges() const;
inline const List<label>& siteIds() const;
inline List<label>& siteIds();
inline const List<bool>& pairPotentialSites() const;
inline bool pairPotentialSite(label sId) const;
inline const List<bool>& electrostaticSites() const;
inline bool electrostaticSite(label sId) const;
inline const List<label>& electrostaticSites() const;
inline const diagTensor& momentOfInertia() const;
@ -181,14 +170,22 @@ private:
// Private data
//- Orientation, stored as the rotation tensor to transform
// from the polyatomic to the global reference frame, i.e.:
// globalVector = Q_ & bodyLocalVector
// bodyLocalVector = Q_.T() & globalVector
tensor Q_;
// Linear velocity of polyatomic
vector v_;
// Total linear acceleration of polyatomic
vector a_;
//- Angular momentum of polyatomic, in body local reference frame
vector pi_;
//- Total torque on polyatomic, in body local reference frame
vector tau_;
vector specialPosition_;
@ -198,6 +195,9 @@ private:
// - r_ij f_ij, stress dyad
tensor rf_;
// // - r_ij outer product f_ij: virial contribution
// tensor rDotf_;
label special_;
label id_;

306
src/lagrangian/molecularDynamics/molecule/polyatomic/polyatomic/polyatomicI.H
View File

@ -27,12 +27,9 @@ License
inline Foam::polyatomic::constantProperties::constantProperties()
:
siteReferencePositions_(Field<vector>(0)),
siteMasses_(List<scalar>(0)),
siteCharges_(List<scalar>(0)),
siteIds_(List<label>(0)),
pairPotentialSites_(List<bool>(false)),
electrostaticSites_(List<bool>(false)),
sites_(),
electrostaticSites_(),
pairPotSites_(),
momentOfInertia_(diagTensor(0, 0, 0)),
mass_(0)
{}
@ -40,47 +37,117 @@ inline Foam::polyatomic::constantProperties::constantProperties()
inline Foam::polyatomic::constantProperties::constantProperties
(
const dictionary& dict
const dictionary& dict,
const labelList& siteIds
)
:
siteReferencePositions_(dict.lookup("siteReferencePositions")),
siteMasses_(dict.lookup("siteMasses")),
siteCharges_(dict.lookup("siteCharges")),
siteIds_(List<word>(dict.lookup("siteIds")).size(), -1),
pairPotentialSites_(),
sites_(),
electrostaticSites_(),
pairPotSites_(),
momentOfInertia_(),
mass_()
mass_(0)
{
checkSiteListSizes();
List<word> siteIdNames = dict.lookup("siteIds");
setInteracionSiteBools
List<vector> siteReferencePositions(dict.lookup("siteReferencePositions"));
List<scalar> siteMasses(dict.lookup("siteMasses"));
List<scalar> siteCharges(dict.lookup("siteCharges"));
List<word> pairPotentialIds(dict.lookup("pairPotentialSiteIds"));
if
(
List<word>(dict.lookup("siteIds")),
List<word>(dict.lookup("pairPotentialSiteIds"))
( siteIdNames.size() != sites_.size() )
|| ( siteReferencePositions.size() != sites_.size() )
|| ( siteCharges.size() != sites_.size() )
)
{
FatalErrorIn
(
"Foam::polyatomic::constantProperties::constantProperties"
"("
"const dictionary& dict"
")"
)
<< "Sizes of site id, charge and "
<< "referencePositions are not the same: " << sites_.size()
<< nl << abort(FatalError);
}
sites_.setSize(siteIdNames.size());
electrostaticSites_.setSize(sites_.size(), -1);
pairPotSites_.setSize(sites_.size(), -1);
label pairI = 0;
label electrostaticI = 0;
forAll(sites_, sI)
{
sites_[sI] = constPropSite
(
siteReferencePositions[sI],
siteMasses[sI],
siteCharges[sI],
siteIds[sI],
siteIdNames[sI],
(findIndex(pairPotentialIds, siteIdNames[sI]) != -1), // pair
(mag(siteCharges[sI]) > VSMALL) // charge
);
mass_ = sum(siteMasses_);
if (sites_[sI].pairPotentialSite())
{
pairPotSites_[pairI++] = sI;
}
vector centreOfMass(vector::zero);
if (sites_[sI].electrostaticSite())
{
electrostaticSites_[electrostaticI++] = sI;
}
if (sites_[sI].pairPotentialSite() && !sites_[sI].electrostaticSite())
{
WarningIn
(
"Foam::polyatomic::constantProperties::constantProperties"
"("
"const dictionary& dict"
")"
)
<< siteIdNames[sI] << " is a non-interacting site." << endl;
}
}
pairPotSites_.setSize(pairI);
electrostaticSites_.setSize(electrostaticI);
// Calculate the centre of mass of the body and subtract it from each
// position
forAll(siteReferencePositions_, i)
vector centreOfMass(vector::zero);
forAll(sites_, sI)
{
centreOfMass += siteReferencePositions_[i]*siteMasses_[i];
mass_ += sites_[sI].siteMass();
centreOfMass +=
sites_[sI].siteReferencePosition()*sites_[sI].siteMass();
}
centreOfMass /= mass_;
siteReferencePositions_ -= centreOfMass;
forAll(sites_, sI)
{
sites_[sI].siteReferencePosition() -= centreOfMass;
}
if (siteIds_.size() == 1)
if (sites_.size() == 1)
{
// Single site polyatomic - no rotational motion.
siteReferencePositions_[0] = vector::zero;
sites_[0].siteReferencePosition() = vector::zero;
momentOfInertia_ = diagTensor(-1, -1, -1);
}
@ -90,36 +157,46 @@ inline Foam::polyatomic::constantProperties::constantProperties
Info<< nl << "Linear polyatomic." << endl;
vector dir = siteReferencePositions_[1] - siteReferencePositions_[0];
vector dir =
sites_[1].siteReferencePosition()
- sites_[0].siteReferencePosition();
dir /= mag(dir);
tensor Q = rotationTensor(dir, vector(1,0,0));
siteReferencePositions_ = (Q & siteReferencePositions_);
forAll(sites_, sI)
{
sites_[sI].siteReferencePosition() =
(Q & sites_[sI].siteReferencePosition());
}
// The rotation was around the centre of mass but remove any
// components that have crept in due to floating point errors
centreOfMass = vector::zero;
forAll(siteReferencePositions_, i)
forAll(sites_, sI)
{
centreOfMass += siteReferencePositions_[i]*siteMasses_[i];
centreOfMass +=
sites_[sI].siteReferencePosition()*sites_[sI].siteMass();
}
centreOfMass /= mass_;
siteReferencePositions_ -= centreOfMass;
forAll(sites_, sI)
{
sites_[sI].siteReferencePosition() -= centreOfMass;
}
diagTensor momOfInertia = diagTensor::zero;
forAll(siteReferencePositions_, i)
forAll(sites_, sI)
{
const vector& p(siteReferencePositions_[i]);
const vector& p(sites_[sI].siteReferencePosition());
momOfInertia +=
siteMasses_[i]*diagTensor(0, p.x()*p.x(), p.x()*p.x());
sites_[sI].siteMass()*diagTensor(0, p.x()*p.x(), p.x()*p.x());
}
momentOfInertia_ = diagTensor
@ -137,11 +214,11 @@ inline Foam::polyatomic::constantProperties::constantProperties
tensor momOfInertia(tensor::zero);
forAll(siteReferencePositions_, i)
forAll(sites_, sI)
{
const vector& p(siteReferencePositions_[i]);
const vector& p(sites_[sI].siteReferencePosition());
momOfInertia += siteMasses_[i]*tensor
momOfInertia += sites_[sI].siteMass()*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(),
@ -152,8 +229,8 @@ inline Foam::polyatomic::constantProperties::constantProperties
if (eigenValues(momOfInertia).x() < VSMALL)
{
FatalErrorIn("polyatomic::constantProperties::constantProperties")
<< "An eigenvalue of the inertia tensor is zero, the polyatomic "
<< dict.name() << " is not a valid 6DOF shape."
<< "An eigenvalue of the inertia tensor is zero, the "
<< "polyatomic " << dict.name() << " is not a valid 6DOF shape."
<< nl << abort(FatalError);
}
@ -172,7 +249,11 @@ inline Foam::polyatomic::constantProperties::constantProperties
// Transform the site positions
siteReferencePositions_ = (Q & siteReferencePositions_);
forAll(sites_, sI)
{
sites_[sI].siteReferencePosition() =
(Q & sites_[sI].siteReferencePosition());
}
// Recalculating the moment of inertia with the new site positions
@ -181,25 +262,29 @@ inline Foam::polyatomic::constantProperties::constantProperties
centreOfMass = vector::zero;
forAll(siteReferencePositions_, i)
forAll(sites_, sI)
{
centreOfMass += siteReferencePositions_[i]*siteMasses_[i];
centreOfMass +=
sites_[sI].siteReferencePosition()*sites_[sI].siteMass();
}
centreOfMass /= mass_;
siteReferencePositions_ -= centreOfMass;
forAll(sites_, sI)
{
sites_[sI].siteReferencePosition() -= centreOfMass;
}
// Calculate the moment of inertia in the principle component
// reference frame
momOfInertia = tensor::zero;
forAll(siteReferencePositions_, i)
forAll(sites_, sI)
{
const vector& p(siteReferencePositions_[i]);
const vector& p(sites_[sI].siteReferencePosition());
momOfInertia += siteMasses_[i]*tensor
momOfInertia += sites_[sI].siteMass()*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(),
@ -256,62 +341,29 @@ inline Foam::polyatomic::polyatomic
// * * * * * * * constantProperties Private Member Functions * * * * * * * * //
inline void Foam::polyatomic::constantProperties::checkSiteListSizes() const
{
if
(
siteIds_.size() != siteReferencePositions_.size()
|| siteIds_.size() != siteCharges_.size()
)
{
FatalErrorIn("polyatomic::constantProperties::checkSiteListSizes")
<< "Sizes of site id, charge and "
<< "referencePositions are not the same. "
<< nl << abort(FatalError);
}
}
inline void Foam::polyatomic::constantProperties::setInteracionSiteBools
(
const List<word>& siteIds,
const List<word>& pairPotSiteIds
)
{
pairPotentialSites_.setSize(siteIds_.size());
electrostaticSites_.setSize(siteIds_.size());
forAll(siteIds_, i)
{
const word& id(siteIds[i]);
pairPotentialSites_[i] = (findIndex(pairPotSiteIds, id) > -1);
electrostaticSites_[i] = (mag(siteCharges_[i]) > VSMALL);
}
}
inline bool Foam::polyatomic::constantProperties::linearMoleculeTest() const
{
if (siteIds_.size() == 2)
if (sites_.size() == 2)
{
return true;
}
vector refDir = siteReferencePositions_[1] - siteReferencePositions_[0];
vector refDir =
sites_[1].siteReferencePosition()
- sites_[0].siteReferencePosition();
refDir /= mag(refDir);
for
(
label i = 2;
i < siteReferencePositions_.size();
i < sites_.size();
i++
)
{
vector dir = siteReferencePositions_[i] - siteReferencePositions_[i-1];
vector dir =
sites_[i].siteReferencePosition()
- sites_[i - 1].siteReferencePosition();
dir /= mag(dir);
@ -327,93 +379,27 @@ inline bool Foam::polyatomic::constantProperties::linearMoleculeTest() const
// * * * * * * * constantProperties Member Functions * * * * * * * * * * * * //
inline const Foam::Field<Foam::vector>&
Foam::polyatomic::constantProperties::siteReferencePositions() const
inline const Foam::List<Foam::constPropSite>&
Foam::polyatomic::constantProperties::sites() const
{
return siteReferencePositions_;
}
inline const Foam::List<Foam::scalar>&
Foam::polyatomic::constantProperties::siteMasses() const
{
return siteMasses_;
}
inline const Foam::List<Foam::scalar>&
Foam::polyatomic::constantProperties::siteCharges() const
{
return siteCharges_;
return sites_;
}
inline const Foam::List<Foam::label>&
Foam::polyatomic::constantProperties::siteIds() const
Foam::polyatomic::constantProperties::pairPotSites() const
{
return siteIds_;
return pairPotSites_;
}
inline Foam::List<Foam::label>&
Foam::polyatomic::constantProperties::siteIds()
{
return siteIds_;
}
inline const Foam::List<bool>&
Foam::polyatomic::constantProperties::pairPotentialSites() const
{
return pairPotentialSites_;
}
inline bool Foam::polyatomic::constantProperties::pairPotentialSite
(
label sId
) const
{
label s = findIndex(siteIds_, sId);
if (s == -1)
{
FatalErrorIn("polyatomicI.H") << nl
<< sId << " site not found."
<< nl << abort(FatalError);
}
return pairPotentialSites_[s];
}
inline const Foam::List<bool>&
inline const Foam::List<Foam::label>&
Foam::polyatomic::constantProperties::electrostaticSites() const
{
return electrostaticSites_;
}
inline bool Foam::polyatomic::constantProperties::electrostaticSite
(
label sId
) const
{
label s = findIndex(siteIds_, sId);
if (s == -1)
{
FatalErrorIn
(
"polyatomic::constantProperties::electrostaticSite(label)"
) << sId << " site not found."
<< nl << abort(FatalError);
}
return electrostaticSites_[s];
}
inline const Foam::diagTensor&
Foam::polyatomic::constantProperties::momentOfInertia() const
{
@ -433,7 +419,8 @@ inline bool Foam::polyatomic::constantProperties::pointMolecule() const
}
inline Foam::label Foam::polyatomic::constantProperties::degreesOfFreedom() const
inline Foam::label
Foam::polyatomic::constantProperties::degreesOfFreedom() const
{
if (linearMolecule())
{
@ -458,8 +445,7 @@ inline Foam::scalar Foam::polyatomic::constantProperties::mass() const
inline Foam::label Foam::polyatomic::constantProperties::nSites() const
{
return siteIds_.size();
return sites_.size();
}

23
src/lagrangian/molecularDynamics/molecule/polyatomic/polyatomicCloud/polyatomicCloud.C
View File

@ -64,7 +64,8 @@ void Foam::polyatomicCloud::buildConstProps()
forAll(idList, i)
{
const word& id = idList[i];
const dictionary& molDict = polyatomicPropertiesDict.subDict(id);
const dictionary& molDict(polyatomicPropertiesDict.subDict(id));
List<word> siteIdNames = molDict.lookup("siteIds");
@ -78,17 +79,23 @@ void Foam::polyatomicCloud::buildConstProps()
if (siteIds[sI] == -1)
{
FatalErrorIn("polyatomicCloud::buildConstProps()")
FatalErrorIn
(
"Foam::polyatomic::constantProperties::constantProperties"
"("
"const dictionary& dict"
")"
)
<< siteId << " site not found."
<< nl << abort(FatalError);
}
}
polyatomic::constantProperties& constProp = constPropList_[i];
constProp = polyatomic::constantProperties(molDict);
constProp.siteIds() = siteIds;
constPropList_[i] = polyatomic::constantProperties
(
molDict,
siteIds
);
}
}
@ -1237,7 +1244,7 @@ void Foam::polyatomicCloud::writeXYZ(const fileName& fName) const
{
const point& sP = mol().sitePositions()[i];
os << pot_.siteIdList()[cP.siteIds()[i]]
os << pot_.siteIdList()[cP.sites()[i].siteId()]
<< ' ' << sP.x()*1e10
<< ' ' << sP.y()*1e10
<< ' ' << sP.z()*1e10

81
src/lagrangian/molecularDynamics/molecule/polyatomic/polyatomicCloud/polyatomicCloudI.H
View File

@ -47,28 +47,18 @@ inline void Foam::polyatomicCloud::evaluatePair
const polyatomic::constantProperties& constPropJ(constProps(idJ));
List<label> siteIdsI = constPropI.siteIds();
List<label> siteIdsJ = constPropJ.siteIds();
List<bool> pairPotentialSitesI = constPropI.pairPotentialSites();
List<bool> electrostaticSitesI = constPropI.electrostaticSites();
List<bool> pairPotentialSitesJ = constPropJ.pairPotentialSites();
List<bool> electrostaticSitesJ = constPropJ.electrostaticSites();
forAll(siteIdsI, sI)
forAll(constPropI.pairPotSites(), pI)
{
label idsI(siteIdsI[sI]);
label sI = constPropI.pairPotSites()[pI];
forAll(siteIdsJ, sJ)
{
label idsJ(siteIdsJ[sJ]);
label idsI = constPropI.sites()[sI].siteId();
if (pairPotentialSitesI[sI] && pairPotentialSitesJ[sJ])
forAll(constPropJ.pairPotSites(), pJ)
{
label sJ = constPropJ.pairPotSites()[pJ];
label idsJ = constPropJ.sites()[sJ].siteId();
vector rsIsJ =
molI.sitePositions()[sI] - molJ.sitePositions()[sJ];
@ -105,9 +95,17 @@ inline void Foam::polyatomicCloud::evaluatePair
molJ.rf() += virialContribution;
}
}
}
if (electrostaticSitesI[sI] && electrostaticSitesJ[sJ])
forAll(constPropI.electrostaticSites(), pI)
{
label sI = constPropI.electrostaticSites()[pI];
forAll(constPropJ.electrostaticSites(), pJ)
{
label sJ = constPropJ.electrostaticSites()[pJ];
vector rsIsJ =
molI.sitePositions()[sI] - molJ.sitePositions()[sJ];
@ -117,9 +115,9 @@ inline void Foam::polyatomicCloud::evaluatePair
{
scalar rsIsJMag = mag(rsIsJ);
scalar chargeI = constPropI.siteCharges()[sI];
scalar chargeI = constPropI.sites()[sI].siteCharge();
scalar chargeJ = constPropJ.siteCharges()[sJ];
scalar chargeJ = constPropJ.sites()[sJ].siteCharge();
vector fsIsJ =
(rsIsJ/rsIsJMag)
@ -148,7 +146,6 @@ inline void Foam::polyatomicCloud::evaluatePair
}
}
}
}
}
@ -170,28 +167,18 @@ inline bool Foam::polyatomicCloud::evaluatePotentialLimit
const polyatomic::constantProperties& constPropJ(constProps(idJ));
List<label> siteIdsI = constPropI.siteIds();
List<label> siteIdsJ = constPropJ.siteIds();
List<bool> pairPotentialSitesI = constPropI.pairPotentialSites();
List<bool> electrostaticSitesI = constPropI.electrostaticSites();
List<bool> pairPotentialSitesJ = constPropJ.pairPotentialSites();
List<bool> electrostaticSitesJ = constPropJ.electrostaticSites();
forAll(siteIdsI, sI)
forAll(constPropI.pairPotSites(), pI)
{
label idsI(siteIdsI[sI]);
label sI = constPropI.pairPotSites()[pI];
forAll(siteIdsJ, sJ)
{
label idsJ(siteIdsJ[sJ]);
label idsI = constPropI.sites()[sI].siteId();
if (pairPotentialSitesI[sI] && pairPotentialSitesJ[sJ])
forAll(constPropJ.pairPotSites(), pJ)
{
label sJ = constPropJ.pairPotSites()[pJ];
label idsJ = constPropJ.sites()[sJ].siteId();
vector rsIsJ =
molI.sitePositions()[sI] - molJ.sitePositions()[sJ];
@ -238,9 +225,16 @@ inline bool Foam::polyatomicCloud::evaluatePotentialLimit
};
}
}
}
if (electrostaticSitesI[sI] && electrostaticSitesJ[sJ])
forAll(constPropI.electrostaticSites(), pI)
{
label sI = constPropI.electrostaticSites()[pI];
forAll(constPropJ.electrostaticSites(), pJ)
{
label sJ = constPropJ.electrostaticSites()[pJ];
vector rsIsJ =
molI.sitePositions()[sI] - molJ.sitePositions()[sJ];
@ -274,9 +268,9 @@ inline bool Foam::polyatomicCloud::evaluatePotentialLimit
return true;
}
scalar chargeI = constPropI.siteCharges()[sI];
scalar chargeI = constPropI.sites()[sI].siteCharge();
scalar chargeJ = constPropJ.siteCharges()[sJ];
scalar chargeJ = constPropJ.sites()[sJ].siteCharge();
if
(
@ -289,7 +283,6 @@ inline bool Foam::polyatomicCloud::evaluatePotentialLimit
}
}
}
}
return false;
}