Todo List

Member AngledPeriodicBoundary::checkBoundaryAfterParticleMoved (BaseParticle *P, ParticleHandler &pH UNUSED)

TW: can't we do the shift in the createPeriodicParticles function only? We are checking the distance three times!

Member AngledPeriodicBoundary::set (Vec3D normalLeft, Vec3D normalRight, Vec3D origin)

TW: Note, I cannot calculate angular shift; this needs to be revisited when we complete quaternion implementation

Member AngledPeriodicBoundary::shiftPosition (BaseParticle *P)

add velocity, angular, springs shift

TW: not sure how to calculate the angular position in common_axis direction; this needs to be revisited when we complete quaternion implementation

Member AngledPeriodicBoundary::shiftPositions (Vec3D &P1, Vec3D &P2)

TW: this still doesn't shift all data

Member BaseHandler< T >::BaseHandler (const BaseHandler< T > &BH)

Should max objects be set to the number of objects after this constructor? Maybe in copyContentsFromOtherHandler?

Member BaseHandler< T >::setId (T *object, unsigned int id)

we should use this function only to set the id of particles, not BaseObject::setId; however, to block BaseObject::setId, I need to make this function a friend of BaseObject, and I don't know how to do that.

Class BaseInteractable

Check prescribed objects have infinite mass.

Member BaseInteractable::BaseInteractable ()

TW: why do some constructors (e.g. BaseInteractable, BaseParticle)not explicitly call the constructor from the inherited class?

Member BaseInteractable::getInteractionWith (BaseParticle *P, Mdouble timeStamp, InteractionHandler *interactionHandler)=0

TW make sure this function sets normal, distance, overlap, contact point

AT why is this a BaseParticle and not a BaseInteratable.

Member BaseInteractable::getOrientation () const

This is not full implemented and is related to quaterians.

Returns

Returns a reference to a Vec3D returns the position of the interactable.

Member BaseInteraction::copySwitchPointer (const BaseInteractable *original, BaseInteractable *ghost) const

Can this be simpler if we replace the particle with the ghost.

Parameters

[in]	original	BaseInteractable* to the original particles who periodic image is being created from.
[in]	ghost	BaseInteractble* to the new ghost (periodic partcles) that has just been created.

Member BaseInteraction::gatherContactStatistics ()

Thomas please document this; as this is the area you are currently rewriting.

Thomas please document.

TW centre is used just for backward compatibility; replace centre by contact law; we also have to correct it in StatisticsVector::gatherContactStatistics. There also seems to be an issue with the normal being defined differently for walls

Member BaseInteraction::getAbsoluteNormalForce () const

Ant: Check this comment.

Returns

Mdouble that contains the absolute norm (length) of the normal force.

Member BaseInteraction::getNormalRelativeVelocity () const

Ant: Check this comment.

Returns

Mdouble that contains the norm (length) of the relative velocity.

Member BaseInteraction::integrate (Mdouble timeStep)

Ant: When is this case; is there an examepl?

Member BaseInteraction::rotateHistory (Matrix3D &rotationMatrix)

some of these might be unneccesary

Member BaseInteraction::timeStamp_

TW it would be safer to use the integer timestep here, instead of the double

Member BaseInteraction::write (std::ostream &os) const

should we output id's here? os << " id " << getId() << " particleIds " << P_->getId() << " " << I_->getId();

Member BaseInteraction::writeToFStat (std::ostream &os) const

TW centre is used just for backward compatibility; replace centre by getContactPoint(); we also have to correct it in StatisticsVector::gatherContactStatistics.

note, here normal is used as branch vector!! There also seems to be an issue with the normal being defined differently for walls

the flip in normal/tangential direction for walls should not be done; this is an old bug

Member BaseObject::setId (const unsigned int id)

TW: here we should update BaseHandler::nextId_

Member BaseParticle::getDisplacement2 (Mdouble xmin, Mdouble xmax, Mdouble ymin, Mdouble ymax, Mdouble zmin, Mdouble zmax, Mdouble t) const

see .cc file.

Rewrite, redefine (TW). Is only used in StatisticsVector.hcc, consider moving to that class.

Member BaseParticle::getInteractionWith (BaseParticle *P, Mdouble timeStamp, InteractionHandler *interactionHandler)

We should consider setting the contact point to

Author

weinhartt

Member BaseParticle::integrateBeforeForceComputation (double time, double timeStep)

TW: add sum sum fi Wi (the stress gradient) to the statistics

If the position is described by the used, one should also call BaseInteractabld::integrateBeforeForceComputation. To check if it works correctly, remove the p0.fixParticle() line from the DrivenParticleUnitTest

Author

irana

Member BaseParticle::invMass_

TW: why do we need to store mass and inertia; we already have invMass and invInertia; can we take it out?

Member BaseParticle::oldRead (std::istream &is)

{fix this function} IFCD: what is broken about it?

Member BaseParticle::ParticleSpecies

Is it possible to only make the function ParticleSpecies::computeMass a friend?

Member BaseParticle::setIndSpecies (unsigned int indSpecies)

TW do we have to update the species stored in the interactions here?

Member BaseParticle::setSpecies (const ParticleSpecies *species)

TW: this function should also check if the particle is the correct particle for the species type

TW should we chaeck here if we have the right kind of species for the right kind of particle?

Member BaseWall::clear ()

TW Why is this function deprecated? How else do I reset the wall properties e.g. of an intersection of walls

Member BaseWall::getInteractionWith (BaseParticle *p, Mdouble timeStamp, InteractionHandler *interactionHandler)

{DK: What is the contact point for interactions with walls}

Member BaseWall::setSpecies (const ParticleSpecies *species)

TW: this function should also check if the particle is the correct particle for the species type.

Member BondedInteraction::BondedInteraction (const BondedInteraction &p)

tw check if the parameters are valid when inserting the species into the handler

Member ChargedBondedInteraction::ChargedBondedInteraction (BaseInteractable *P, BaseInteractable *I, Mdouble timeStamp)

Clean up this file by using the logger instead of cout, //cout, cerr and assert, and by motivating why the commented out code needs to be here.

Complete the documentation of these methods

Member Chute::Chute (const Chute &other)

Check if this should indeed be a shallow copy.

Member Chute::createBottom ()

Does the bottom we always has to be this particle? Maybe add a BaseParticle* argument, and add a default value with particle radius < 1e-12.

Member Chute::getNCreated () const

This method is not implemented.

Member Chute::increaseNCreated ()

This method is not implemented.

Member Chute::printTime () const

currently, this is going to cout. Do we want to make it a logger message?

Member Chute::setChuteAngle (Mdouble chuteAngle)

would a check on the angle be beneficial to check if it is indeed in degrees?

Member Chute::setRoughBottomType (std::string roughBottomTypeString)

: logger::Fatal seems very strong here, maybe set a default instead?

Member ChuteBottom::ChuteBottom (const ChuteBottom &other)

IFCD: why are the name and file-stuff not set here, in contrast to constructor()?

Member ChuteBottom::makeRoughBottom (Chute &chute)

IFCD: Only a warning, or an error?

Dinant is not a fan of this algorithm (i.e. popping back stuff while in iterator) Consider copying all (moved) valid particles directly to the chute handler instead, and apply the iterator in the for-loop initiation

after copying a particle handler, you have to set the species pointers to the species of the chute problem; a) do you need to set other things? b) this should probably be done in ParticleHandler::operator=() => YES INDEED, the operator=() should create a DEEP copy!

Member ChuteBottom::setupInitialConditions ()

The createBottom() function also creates some walls and boundaries, but at slightly different locations. In this version they are removed and reset, but this is (in my opinion (Dinant)) not the correct way.

Particles are created without insertion boundary... this reeks of double work (see also Dinant's todo in this same function (ChuteBottom::setupInitialConditions()). (BvdH)

Member ChuteWithHopper::addHopper ()

Waarom had ik deze ook al weer gecomment? IFCD: this was probably BvdH

Why shift A by arbitrary number of 40, when isHopperCentred_ = True? NB: this is probably the same shift of 40 as happens in HopperInsertionBoundary::generateParticle(RNG) with the calculation of 'point A'. NB2: seems to be just generating a nice 'view' of the hopper (in the center of the viewer...?)

Member ChuteWithHopper::getChuteLength () const

this hides the non-virtual function Chute::getChuteLength

Member ChuteWithHopper::getTimeStepRatio () const

Consider generalising this method by implementing it in the MercuryBase class.

Author

BvdH NB: this method is used in ChuteWithHopper::setupInitialConditions().

Member ChuteWithHopper::setHopper (Mdouble exitLength, Mdouble exitHeight, Mdouble angle, Mdouble length, Mdouble height)

: check whether hopperCornerHeight >=0, if not change hopperangle, line 105, I do not yet understand what the criteria is...

Member CircularPeriodicBoundary::checkBoundaryAfterParticleMoved (BaseParticle *P, ParticleHandler &pH)

TW: Dinant, please confirm that i and oldI should be integer

Class Coil

IFCD: Can someone look at the details of the documentation of class Coil? I can't make sense of them.

Coil is now fixed in Z-direction, centered around the Z-axis. Consider converting to more general parameters, with direction of choise and central axis of choice.

Member Coil::getDistanceAndNormal (const BaseParticle &P, Mdouble &distance, Vec3D &normal_return) const override

Make this function readable and explain the steps in the details.

Page Directory Structure

TW What happened to the Template directory?

TW Anthony, please add information about your new output file here.

Member DPMBase::checkParticleForInteractionLocal (const BaseParticle &P)

tw check against periodic copies (see ShearCell3DInitialConditions.cpp)

Member DPMBase::checkParticleForInteractionLocalPeriodic (const BaseParticle &P)

TW the implementation of this function is not very efficient and should be improved

Parameters

p

Returns

Member DPMBase::computeExternalForces (BaseParticle *PI)

take out computeWalls() from compute External Forces method.

Parameters

[in]

CI

Member DPMBase::computeForcesDueToWalls (BaseParticle *PI)

TW: I think this torque has the wrong sign

Member DPMBase::getDoCGAlways () const

This method is not implemented

Member DPMBase::initialiseTangentialSprings ()

This method is not implemented and never used.

Member DPMBase::read (std::istream &is)

warning: hides non-virtual function from the class 'Files'.

Member DPMBase::setDoCGAlways (bool newDoCGFlag)

This method is not implemented

Member DPMBase::setRotation (bool newRotFlag)

{these functions should also update the mixed species}

Member DPMBase::setupInitialConditions ()

I (Anthony) wants to change this to be an external function. This has a lot of advantages especially when using copy-constructors. This is a major change and will break other codes, so therefore has to be done carefully.

Member DPMBase::solve ()

Is it neccesarry to reset initial conditions here and in setTimeStepByParticle (i.e. should it be in constructor) Thomas: I agree, setTimeStepByParticle should be rewritten to work without calling setupInitialConditions

Is it neccesarry to reset initial conditions here and in setTimeStepByParticle (i.e. should it be in constructor)? Thomas: I agree, setTimeStepByParticle should be rewritten to work without calling setupInitialConditions

Member DPMBase::write (std::ostream &os, bool writeAllParticles=true) const

what to do with statisticsFromRestartData?

TW: random number seed is not stored

TW: xBalls arguments are not stored

Member DPMBase::writeRestartFile ()

DPMBase::writeRestartFile should check if restartFIle is open or not

Member DPMBase::writeXBallsScript () const

Implement or make pure virtual

Member File::open ()

tw: DEBUG_OUTPUT is currently only defined in DPMBase.h

Member File::write (std::ostream &os) const

TW: openMode_ is not saved, maybe it should not even be stored but set every time you open a file

Member FileReader::read ()

taking this line of of the for loop gives a huge speed improvement; why?

Member FrictionInteraction::computeFrictionForce ()

TW: Why do we not use the corrected diameter here, as in the rolling case? And check if Stefan uses radius or diameter

Class FrictionSpecies

TW: should this class be renamed SlidingRollingTorsionFrictionSpecies?

Member helpers::computeCollisionTimeFromKAndDispAndEffectiveMass (Mdouble k, Mdouble disp, Mdouble mass)

This does not result in the same value as the given alternative.

Member helpers::computeDisptFromCollisionTimeAndRestitutionCoefficientAndTangentialRestitutionCoefficientAndEffectiveMass (Mdouble tc, Mdouble r, Mdouble beta, Mdouble mass)

what should be used instead of this function?

Member helpers::getMaximumVelocity (Mdouble k, Mdouble disp, Mdouble radius, Mdouble mass)

what should be used instead of this function?

Member helpers::readOptionalVariable (std::istream &is, std::string name, T &variable)

checkAndRead should check if the next variable in the ifstream is equal to the string nam, and only read in this case; otherwise continue, but I don't know how to put the location in the ifstream back.

Member HertzianSinterInteraction::getElasticEnergy () const

TW this is not correct; we should count the return energy

Member HertzianViscoelasticInteraction::computeNormalForce ()

check for superquadrics

Member HertzianViscoelasticInteraction::getElasticEnergy () const

TW This is not correct

Member HGrid::info () const

use logger everywhere

Member HGrid::Initialize_inv_size ()

TW: Where is this function defined??

Class HGridOptimiser

Find out what this class does and document it.

Class HopperInsertionBoundary

(BvdH) Better graphical diagrams are needed for further clarification, as well as some property renaming.

Member HopperInsertionBoundary::generateParticle (RNG &random)

(BvdH) make a nice (InkScape) diagram with all useful properties in one image, and some angles explaining the definitions of AB and AC directions, the P->setPosition operation and the calculation of the Z-direction of the Vec3D A position.

Thomas, could you check if this bug is still valid? (BvdH)

Member InfiniteWallWithHole::move_time (Mdouble dt)

TW: generalize the move function for all walls Allows the wall to be moved with time

Member InfiniteWallWithHole::set (Vec3D normal, Mdouble position, Mdouble holeRadius)

Since InfiniteWall:set is deprecated, should we deprecate this format as well (and similar formats in other walls)?

Author

weinhartt

Class InsertionBoundary

IFCD: Should operator= be implemented here and in the derived classes?

Member InsertionBoundary::checkBoundaryBeforeTimeStep (DPMBase *md)

rename to something like "insertUntilMaxFailed"?

Member InsertionBoundary::generateParticle (RNG &random)=0

(AT) think about implementation of this method here instead of in the children, since the checkBoundaryBeforeTimeStep (i.e., the actual insertion of particles) is also defined here. Current problem with this: boundary dimensions, which are needed for the particle placement, are now defined in the children, and depend heavily on its shape.

Member InsertionBoundary::getParticleToCopy () const

make this a debug check

Member InteractionHandler::eraseOldInteractions (Mdouble lastTimeStep)

TW: this function has to be sped up with sth like this: erase(remove_if(begin(), end(), bind2nd(checkSpringTime(), lastTimeStep)), end());

Member InteractionHandler::getInteraction (BaseInteractable *P, BaseInteractable *I, Mdouble timeStamp)

TW this can bet set earlier

Member InteractionHandler::InteractionHandler (const InteractionHandler &IH UNUSED)

Please check if interactions indeed don't need to be copied.

Member InteractionHandler::readObject (std::istream &is)

TW: Change identifier in restart file from id to index; is there any reason the id should be kept after restarting, once this is done? (Note, the id is set to the old one in the particle handler because interactions store id, not indices; also note id's are slow

Member InteractionHandler::removeObjectKeepingPeriodics (unsigned const int id)

TW The code assumes in a few places that P->getIndex()<I->getIndex(), but the copySwitchPointer function does not obey that rule; we have to check if this is valid behaviour.

this function will create an error if the timeStamp is in the future! This should not happen (ever), but who knows.

Member InteractionHandler::writeVTK () const

Check if this should indeed be a WARN

Member IntersectionOfWalls::move (const Vec3D &move) override

We should use the position_ and orientation_ of the IntersectionOfWalls; that way, IntersectionOfWalls can be moved with the standard BaseInteractable::move function, getting rid of an anomaly in the code and removing the virtual from the move function.

Author

weinhartt

Member IrreversibleAdhesiveInteraction::IrreversibleAdhesiveInteraction (const IrreversibleAdhesiveInteraction &p)

tw check if the parameters are valid when inserting the species into the handler

Class LeesEdwardsBoundary

Add link to paper by Lees-Edwards in the documentation of this class.

Is implemented for 2D only now. Needs extension to 3D.

Member LinearPlasticViscoelasticInteraction::getElasticEnergy () const

TW this is not correct; we should count the return energy

Member LinearPlasticViscoelasticNormalSpecies::setCollisionTimeAndRestitutionCoefficient (Mdouble tc, Mdouble eps, Mdouble mass)

TW: check that the masses are described correctly here (m_eff or m_p?))

Member LinearViscoelasticInteraction::getSpecies () const

you can remove this by adding the species to the Interaction instead of the base interaction

Member LiquidBridgeWilletInteraction::getElasticEnergy () const

TW

Member LiquidMigrationWilletInteraction::form ()

: maybe we need to check ghost particles?

Member LiquidMigrationWilletInteraction::getElasticEnergy () const

TW

Member Logger< L, ASSERTS >::onWarn (module, msgstream.str())

The two functions below are MercuryDPM loggers, however the commented functions underneath are the hpGEM ones, I can't seem to get those working

Member logWriteAndDie (std::string module, std::string message)

Why is this here, and not in the logger?

Member main (int argc UNUSED, char *argv[] UNUSED)

TW maybe this should be part of readRestartFile

Member MaserBoundary::checkBoundaryAfterParticleMoved (BaseParticle *p, ParticleHandler &pH)

Apparently, somewhere in the ages past, at some time, there has existed a piece of code which prevents the particles crossing the periodic boundary on the left side from reappearing on the right. This was taken out somewhere between the dark ages an the current one (feb. 2015) and should be put back in. Only causes errors very rarely, and not in the compiler but rather in the actual physics going on (So its not detected by the MaserSelfTest). The current arrangement mainly causes problems with particles which oscillate on the boundary, continuously crossing from left to right and back. A visual consideration of this problem can be found in Documentation/Images/Maser_unperiodic_behaviour.jpg, which, granted, is appalling in its own right, but has yet to suffice in awaitance of a better (i.e. clearer) drawing. Therefore:

Create a new diagram explaining the problems with the previous (NOW: CURRENT!) implementation, and the exact differences between the two. I.e., an improved version of Documentation/Images/Maser_unperiodic_behaviour.jpg. (BvdH)

Member MaserBoundary::createPeriodicParticles (BaseParticle *p, ParticleHandler &pH)

The code has not implemented the actual outflow of 'normal' particles from the right boundary wall. I.e., the maser now is 'simply' a normal Periodic Boundary, with a lot of potential ;). I think the 'original author' planned to implement the outflow below, which is still left to be done. (BvdH) NB: a better place would be in the MaserBoundary::shiftPosition() or MaserBoundary::checkBoundaryAfterParticleMoved() method, which are called when the particles actually cross either of the boundary walls.

Member MaserBoundary::shiftPosition (BaseParticle *p)

Reconsider the way in which the shifting of particles is done. Now, the procedure is as follows: > PARTICLE's distance to either of the two walls is gotten by MaserBoundary::getDistance > Which of the two walls the particle is closest to, is saved in the BOUNDARY's boolean data member closestToLeftBoundary_ > PARTICLE's position is then shifted based on the BOUNDARY's closestToLeftBoundary_ data member and shift vector What might go wrong, is that it is allowed now to do a shift operation on the particle without being forced to first have the closestToLeftBoundary_ boolean set based on the same particle. Suggestion: get rid of the closestToLeftBoundary_ data member all together (it is a property of the particle after all, rather than one of the boundary), and implement the obtaining of which boundary to shift relatively to directly into the shift function. (NB: The PeriodicBoundary class contains the same TODO).

Member mathsFunc::log (Mdouble Power)

check if this function works

Member mathsFunc::tan (T x)

should be properly computed

Member MERCURY_ASSERTS

decide if this monologue of Chris should be moved elsewhere

Class MercuryBase

Discuss if we want to remove Mercury2D and Mercury3D and template MercuryBase as the interface for the user.

Member MercuryBase::checkParticleForInteraction (const BaseParticle &P) override

IFCD: I think it might be better if it returns true if there is an interaction.

Member MercuryBase::checkParticleForInteractionLocal (const BaseParticle &P) override

IFCD: I think it might be better if it returns true if there is an interaction.

Member MercuryBase::hGridActionsBeforeTimeStep () override

IFCD Look up if stepsBeforeUpdate is actually used.

TW: I believe the following two steps should be in hGridRebuild

Member MercuryBase::hGridInfo () const

IFCD: I don't know how to apply std::boolalpha to needsUpdate and updateEachTimeStep

Member MercuryBase::setHGridCellOverSizeRatio (Mdouble cellOverSizeRatio)

IFCD: I changed the if unequal to if equal, can someone check this is correct?

Member MercuryTimeStep< NDIMS >::dataFile_

Chris, please check if this parameter is needed; it causes a warning with [-Wunused-private-field]

Author

weinhartt

Member MindlinInteraction::getAbsoluteNormalForcePrevious () const

Ant: Check this comment.

Returns

Mdouble that contains the absolute norm (length) of the normal force.

Member MindlinInteraction::getTangentialOverlap () const override

TWnow this should be positive

Member MindlinRollingTorsionInteraction::computeFrictionForce ()

TW: Why do we not use the corrected diameter here, as in the rolling case? And check if Stefan uses radius or diameter

Class MindlinRollingTorsionSpecies

TW: should this class be renamed SlidingRollingTorsionMindlinRollingTorsionSpecies?

Member MindlinSpecies::mix (MindlinSpecies *const S, MindlinSpecies *const T)

KWY: Add a 'mix' property for shear modulus

Member ParhamiMcMeekingSinterInteraction::getElasticEnergy () const

TW

Returns

Mdouble

Member ParhamiMcMeekingSinterSpecies::ParhamiMcMeekingSinterSpecies ()

: implement initial/read/write values

Member ParticleHandler::largestParticle_

TW: note that checkExtrema gets called if a particle gets created and its Species and Radius gets set, even if it's not yet included in the particleHandler! This is necessary to check a not included particle for overlaps before inserting it into the handler. Not sure if this is a sensible structure; to be discussed.

Member ParticleHandler::readObject (std::istream &is)

make sure setting the id doesn't break the id setter :)

make sure setting the id doesn't break the id setter :)

make sure setting the id doesn't break the id setter :)

{Remove for final version}

Member ParticleHandler::writeVTK () const

Check if this should indeed be a WARN

Member ParticleSpecies::getMassFromRadius (const Mdouble radius) const

TW: should getMassFromRadius be removed? IFCD: it is used in at least one driver (AxisymmetricHopper).

Member ParticleSpecies::getVolumeFromRadius (const Mdouble radius) const

this should depend on the particle shape; thus, it should be a static function of BaseParticle

Member ParticleSpecies::setDensity (Mdouble density)

recalculate masses when setting dim_particle or rho

Member PeriodicBoundary::shiftPositions (Vec3D &postition1, Vec3D &postion2) const

(AT) see toDo of PeriodicBoundary::shiftPosition().

Class PossibleContact

Change the names so that they follow the code guidelines.

Class PossibleContactList

Look at the memory management of PossibleContactList. Maybe a destructor that takes out all remaining PossibleContact? Or is there a Handler that calls remove_ParticlePosibleContacts for all particles?

Restart-tests are not working with CONTACT_LIST_HGRID turned on, so either finish the ContactList-related code, or get rid of it. If we keep it, clean up the code, in particular the naming-convention.

Member Quarternion::integrate (const Vec3D &omega, double timeStep)

Are we sure this works? *this = deltaQ * *this

Author

weinhartt

Member RestrictedWall::getInteractionWith (BaseParticle *p, Mdouble timeStamp, InteractionHandler *interactionHandler) override

Shouldn't this function be defined in BaseWall?

{setting the index of the wall is necessary to get the right index reported in fstat; however, the better way would be to make setIndex virtual.}

Member RestrictedWall::set (BaseWall *wall, InfiniteWall *restriction)

TW maybe the Restricted wall should be templated with the wall type such that we don't need to use new and delete.

Member ReversibleAdhesiveInteraction::getElasticEnergy () const

TW

Returns

Mdouble

Class RNG

(AT) implement new C++-standard RNG instead of this one (Kudos on the hard work done here though ;). NB: maybe something for Mercury 2?

Member RNG::RNG ()

{Thomas: This code does sth. when min>max; I would prefer to throw an error.}

{the random seed should be stored in restart}

Member RoughBottomType

consider converting to an enum class.

consider changing to just 'bottomType' and add 'FLAT' (or something similar) as an option so that from ALL bottom types can be chosen with just ONE enumerator IFCD: I did add FLAT, but since there are multiple users using RoughBottomType, it might be a bad idea to change the interface with BottomType. Please also check if I have forgotten places to add "FLAT" to make this a complete interface.

Class Screw

IFCD: Can these details about class Screw be made more clear? I don't understand them.

Member Screw::getDistanceAndNormal (const BaseParticle &P, Mdouble &distance, Vec3D &normal_return) const final

Make this function readable and explain the steps in the details.

Class ShearBoxBoundary

Add link to paper by Lees-Edwards in the documentation of this class.

Is implemented for 2D only now. Needs extension to 3D.

Member SinterInteraction::computeNormalForce ()

basing the stiffness increase on the plastic overlap does not work: k2*(d-d0)=k1*d, k2=k1*(1+dk*d0) (1+dk*d0)*(d-d0)=d d+dk*d*d0-d0-dk*d0*d0=d -dk*d0^2+(dk*d-1)*d0+d=d d0=(dk*d-1)/dk

adhesive force only, or add normalForce?

Member SinterInteraction::getElasticEnergy () const

TW this is not correct; we should count the return energy

Member SinterNormalSpecies::setCollisionTimeAndRestitutionCoefficient (Mdouble tc, Mdouble eps, Mdouble mass)

TW: check that the masses are described correctly here (m_eff or m_p?))

Member SinterNormalSpecies::setSinterForceAndTime (Mdouble adhesionForce, Mdouble sinterTime, Mdouble radius)

fix

Member SlidingFrictionInteraction::getTangentialOverlap () const

TWnow this should be positive

Member SpeciesHandler::addObject (ParticleSpecies *const S)

TW don't put logger messages that only make sense for one application!

Member SpeciesHandler::getMixedObject (const unsigned int id1, const unsigned int id2)

This function should probably be made private. The user should use the function SpeciesHandler::getMixedObject(const U* S, const U* T), which deals with pointers.

Member SpeciesHandler::readObject (std::istream &is)

TW why does deleting these objects create a segmentation fault How do you create the segmentation fault?

Author

weinhartt

IFCD how does the numbering of mixedSpecies_ work? the numbering of mixed species is 01, 02, 12, 03, 13, 23, 04, 14, 24, 34, i.e. if you add the n-th ParticleSpecies, then you have to add n-1 MixedSpecies. So here I remove the last n-1 MixedSpecies and add n-1 new ones.

Author

weinhartt

Member StatisticsPoint< T >::CG_gradient (const Vec3D &P, const Mdouble phi)

{Only implemented for Gaussian}

Member StatisticsPoint< T >::CG_integral_gradient (Vec3D &P1, Vec3D &P2, Vec3D &P1_P2_normal, Mdouble P1_P2_distance)

{Only implemented for Gaussian and statavg Z}

Member StatisticsPoint< T >::CollisionalHeatFlux

{Heat flux calculations have not been checked, only implemented}

Member StatisticsPoint< T >::Dissipation

{Dissipation calculations have not been checked, only implemented}

Member StatisticsPoint< T >::Potential

{Potential calculations have not been checked, only implemented; fstat file does not include the torsional and rolling spring and hence cannot account for their potential}

Member StatisticsVector< T >::periodicWalls

{Thomas: the case periodicWalls=true seems to mess up some statistics. Needs to be checked or removed}

Member StatisticsVector< T >::rmin

Thomas: maybe this fixed condition should be replaced by a condition function, bool include_statistics_if()

Member to_string_padded (unsigned int value)

TW: I am not able to define the operator >> for enum class type (the implementation works fine for the old enum)

Member TriangulatedWall::Face::getDistanceAndNormal (const BaseParticle &p, Mdouble &distance, Vec3D &normal_return) const

make the triangle work from both sides

Member TriangulatedWall::move (const Vec3D &move) override

We should use the position_ and orientation_ of the TriangulatedWall; that way, TriangulatedWall can be moved with the standard BaseInteractable::move function, getting rid of an anomaly in the code and removing the virtual from the move function.

Author

weinhartt

Member TriangulatedWall::read (std::istream &is) override

Class Vec3D

Need to generalize this to n-dimensional vectors of any type

Member WallHandler::WallHandler (const WallHandler &BH)

why is this being done?

Member WallHandler::WallHandler ()

why is this being done?

Member WallHandler::writeVTK () const

Check if the documentation is correct

Member WallHandler::writeVTKBoundingBox () const

Check that this should indeed be WARN

Member WallHandler::writeVTKFile (const VTKContainer vtk) const

Check if this should indeed be a WARN