See https://www.youtube.com/watch?v=3LsRYnRDSRA for a bizarre example where a custom struct Tpair { const Particle &first, second; }; outperforms std::pair due to missed compiler optimization.

Class Faunus::Energy::Ewald

energy() currently has the responsibility to update k-vectors.

Class Faunus::Energy::ExternalAkesson

Split this into two classes; one with a static rho, and a derived that updates rho

Class Faunus::Energy::ExternalPotential

The dN check is inefficient as it calculates the external potential on all particles.

Member Faunus::Energy::Hamiltonian::Hamiltonian (Space &spc, const json &j)

Move addEwald to Nonbonded as it now has access to Hamiltonian and can add

Member Faunus::Energy::Nonbonded< TPairEnergy, TPairingPolicy >::force (std::vector< Point > &forces) override

A stub. Change to reflect only active particle, see Space::activeParticles().

Member Faunus::Energy::Penalty::sync (EnergyTerm *other, const Change &change) override

: this doubles the MPI communication

Member Faunus::Energy::Penalty::~Penalty () override

Foul to let constructor be responsible for i/o...

Member Faunus::Energy::PolicyIonIon::updateComplex (EwaldData &data, const Space::GroupVector &groups) const override

Add OpenMP pragma to first loop

Class Faunus::Geometry::Chameleon

Implement unit tests

Member Faunus::Geometry::rotate (iterator begin, iterator end, const Eigen::Quaterniond &quaternion, BoundaryFunction apply_boundary=[](auto &) {}, const Point &shift=Point::Zero())

Currently both quaternion and rotation matrix are passed, but one of them should be enough

Class Faunus::Legendre< T, max_order, use_table >

Benchmark use_table

Class Faunus::MetropolisMonteCarlo

The class has too many responsibilities, particularly in setting up the system.

Member Faunus::MetropolisMonteCarlo::restore (const json &j)

Too many responsibilities; tidy up!

Member Faunus::MetropolisMonteCarlo::sweep ()

using weight to mark as move as static is ugly

Class Faunus::move::ConformationSwap

Add feature to align molecule on top of an exiting one

Class Faunus::move::FindCluster

This is a break-out from Cluster and further separation of functionality could be made

Member Faunus::move::LangevinVelocityVerlet::step (PointVector &velocities, PointVector &forces) override

Splitting scheme still hard-coded to 'BAOAB'

Class Faunus::move::Move

Privatize and rename members

Class Faunus::move::SpeciationMove

Split atom-swap functionality to separate helper class

Member Faunus::move::SpeciationMove::swapParticleProperties (Particle &particle, int new_atomid)

This could make use of policies to customize how particles should be updated. Split to helper class.

Class Faunus::move::TranslateRotate

under construction

Class Faunus::ordered_pair< T >

Add std::pair copy operator

Class Faunus::pairpotential::BondData

Memory inefficient to store energy and force functors. Virtual functions?

Class Faunus::pairpotential::CigarWithCigar< PatchPotential, CylinderPotential >

Energy calculation badly needs refactoring!

Member Faunus::pairpotential::CosAttract::operator() (const Particle &, const Particle &, double squared_distance, const Point &) const override

The function x(c,r2,rc) defined herein could be approximated by a series expansion for r2=rcwc2.

Class Faunus::pairpotential::FunctorPotential

to_json should retrieve info from potentials instead of merely passing input

Class Faunus::pairpotential::Multipole

Only dipole-dipole interactions are currently enabled

Class Faunus::pairpotential::PairPotential

Self-energies should be handled by a separate interaction class and is stored here only to be able to retrieve them later on. The main reason for this is convenience as we in this way can register the self energy during processing of the pair potential input.

Class Faunus::pairpotential::SplinedPotential

Add force

Class Faunus::Particle

: memory model for extended properties not optimal

Member Faunus::Particle::rotate (const Eigen::Quaterniond &quaternion, const Eigen::Matrix3d &rotation_matrix)

Only one of the above should be enough

Class Faunus::ParticlePropertyBase

Is this really needed?

Member Faunus::ParticlePropertyBase::rotate (const Eigen::Quaterniond &q, const Eigen::Matrix3d &)

Inefficient to pass both Quaternion and rotation matrix.

Class Faunus::QuaternionRotate

Get rotate tensors using quaternion

Class Faunus::ReactionCoordinate::MoleculeProperty

Refactor so that each scheme is a derived class implementing a virtual energy function instead of the std::function object

Class Faunus::ReactionData

[x] Enable canonic and reservoir_size
[ ] Enable reservoir size to be given as molarity and number
[ ] Merge products and reactant structures using signed stoichiometric numbers
[x] reservoir_size should ideally be associated with an implicit molecule
[ ] direction should be a member of ReactionData due to possible data races

Class Faunus::RowMajorOffset< dim, Tindices >

this can be used to construct an N-dimensional matrix class

Class Faunus::SASA::SASACellList< CellList >

update function does perhaps unnecessary containsMember(Member&) checks

create a wrapper class for cell_list so that the Space dependence is in there and not here

Class Faunus::SingleUseJSON

This class should be retired and handled by JSON schema instead

Member Faunus::Space::updateInternalState (const Change &change)

Under construction and currently not in use

Member Faunus::Space::updateParticles (const iterator begin, const iterator end, ParticleVector::iterator destination, copy_operation copy_function=[](const Particle &src, Particle &dst) { dst=src;})

Since Space::groups is ordered, binary search could be used to filter

Namespace Faunus::SpheroCylinder

cleanup and split into smaller functions.

Member Faunus::SpheroCylinder::psc_intersect (const Cigar &particle1, const Cigar &particle2, const Point &r_cm, std::array< double, 5 > &intersections, double cutoff_squared)

Add documentation and split into smaller parts(!)

Member Faunus::Table2D< Tx, Ty >::load (const std::string &filename)

Implement end bin compensation as in the save() function when loading HISTOGRAMs

Class Faunus::Table< Tcoeff, base >

This really needs documentation and general refactoring!

Class Faunus::Tabulate::Andrea< T >

Hide data and functions; clean up r vs r2 mess.

Class Faunus::Tensor

add documentation

Member Faunus::Tensor::Tensor (double, double, double, double, double, double)

explain input

Class Faunus::TranslationalEntropy

[ ] Move to Energy namespace?
[ ] Verify with volume fluctuations which would make Energy::Isobaric redundant