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eonc::Matter Member List

This is the complete list of members for eonc::Matter, including all inherited members.

applyPeriodicBoundary()eonc::Matterprivate
applyPeriodicBoundary(double &component, int axis)eonc::Matterprivate
applyPeriodicBoundary(AtomMatrix &diff)eonc::Matterprivate
applyPeriodicBoundaryIfEnabled()eonc::Matterinline
assertIsolatedMoleculeLayoutSafe() consteonc::Matterprivate
atomicNrseonc::Matterprivate
atomIndexeonc::Matterprivate
biasForceseonc::Matterprivate
biasPotentialeonc::Matterprivate
celleonc::Matterprivate
cellInverseeonc::Matterprivate
clearMovieFrames()eonc::Matterinline
compare(const Matter &matter, bool indistinguishable=false)eonc::Matter
computePotential() consteonc::Matterprivate
con2matter(std::string filename)eonc::Matterinline
con2matter(const readcon::ConFrame &frame, io::ConFrameMetadata *out_metadata=nullptr)eonc::Matterinline
convel2matter(std::string filename)eonc::Matterinline
distance(long index1, long index2) consteonc::Matter
distance(const Matter &matter, long index) consteonc::Matter
distanceTo(const Matter &matter)eonc::Matter
energyVarianceeonc::Mattermutableprivate
forceCallseonc::Mattermutableprivate
forceseonc::Mattermutableprivate
forcesData()eonc::Matterinline
freeIndiceseonc::Mattermutableprivate
freeMaskeonc::Mattermutableprivate
getAccelerations()eonc::Matter
getAtomicNr(long int atom) consteonc::Matter
getAtomicNrs() consteonc::Matter
getAtomicNrsFree() consteonc::Matter
getAtomIndex(long int atom) consteonc::Matterinline
getBiasForces()eonc::Matter
getCell() consteonc::Matter
getEnergyVariance() consteonc::Matter
getFixed(long int atom) consteonc::Matter
getFixed(long int atom, int axis) consteonc::Matter
getFixedMask(long int atom) consteonc::Matter
getForceCalls() consteonc::Matter
getForces() consteonc::Matter
getForcesFree() consteonc::Matter
getForcesFreeV() consteonc::Matter
getForcesRaw() consteonc::Matter
getForcesV() consteonc::Matter
getFree() consteonc::Matter
getFreeV() consteonc::Matter
getHeaderCon() consteonc::Matterinline
getKineticEnergy() consteonc::Matter
getMass(long int atom) consteonc::Matter
getMasses() consteonc::Matter
getMechanicalEnergy() consteonc::Matter
getPbcConvention() consteonc::Matterinline
getPeriodic() const noexcepteonc::Matterinline
getPosition(long int atom, int axis) consteonc::Matter
getPositions() consteonc::Matter
getPositionsCopy() consteonc::Matter
getPositionsFree() consteonc::Matter
getPositionsFreeV() consteonc::Matter
getPositionsV() consteonc::Matter
getPotential()eonc::Matter
getPotentialCalls() consteonc::Matter
getPotentialEnergy() consteonc::Matter
getVelocities() consteonc::Matter
getWriteConForces() const noexcepteonc::Matterinline
headerConeonc::Matterprivate
io::con2matter(Matter &, const readcon::ConFrame &, io::ConFrameMetadata *)eonc::Matterfriend
isFixedeonc::Matterprivate
m_logeonc::Matterprivate
maskedForceseonc::Mattermutableprivate
masseseonc::Matterprivate
Matter(std::shared_ptr< Potential > pot, const Parameters &params)eonc::Matterinline
Matter(const Matter &matter)eonc::Matter
Matter(Matter &&other) noexcepteonc::Matter
matter2con(std::string filename, bool append=false, const io::ConFrameMetadata *metadata=nullptr)eonc::Matterinline
matter2convel(std::string filename)eonc::Matterinline
matter2xyz(std::string filename, bool append=false)eonc::Matterinline
maxForce(void) consteonc::Matter
movie_frames_eonc::Matterprivate
movieFrames() consteonc::Matterinline
nAtomseonc::Matterprivate
needsForceUpdate() consteonc::Matterinline
numberOfAtoms() consteonc::Matter
numberOfFixedAtoms() consteonc::Matter
numberOfFreeAtoms() consteonc::Matter
operator=(const Matter &matter)eonc::Matter
operator=(Matter &&other) noexcepteonc::Matter
parameterseonc::Matterprivate
pbc(const AtomMatrix &diff) consteonc::Matterinline
pbcConventioneonc::Matterprivate
pbcV(const VectorXd &diff) consteonc::Matterinline
pdistance(long index1, long index2, int axis) consteonc::Matter
perAtomNorm(const Matter &matter)eonc::Matter
positionseonc::Matterprivate
potentialeonc::Matterprivate
potentialEnergyeonc::Mattermutableprivate
recomputeFreeMaskeonc::Mattermutableprivate
recomputeMaskedForceseonc::Mattermutableprivate
recomputePotentialeonc::Mattermutableprivate
relax(bool quiet=false, bool writeMovie=false, bool checkpoint=false, std::string prefixMovie=std::string(), std::string prefixCheckpoint=std::string(), bool retainMovieFrames=false)eonc::Matter
removeNetForceeonc::Matterprivate
resetForceCalls()eonc::Matter
resize(long int nAtoms)eonc::Matter
setAtomicNr(long int atom, long atomicNr)eonc::Matter
setAtomicNrs(const VectorXi &atmnrs)eonc::Matter
setAtomIndex(long int atom, std::int64_t index)eonc::Matterinline
setBiasForces(const AtomMatrix &bf)eonc::Matter
setBiasPotential(BondBoost *bondBoost)eonc::Matter
setCell(const Matrix3d &newCell)eonc::Matter
setComputedPotential(double energy, double variance)eonc::Matter
setFixed(long int atom, int isFixed)eonc::Matter
setFixed(long int atom, int axis, int isFixed)eonc::Matter
setFixedMask(long int atom, std::array< bool, 3 > mask)eonc::Matter
setForces(const AtomMatrix &f)eonc::Matter
setHeaderCon(const std::array< std::string, 5 > &headers)eonc::Matterinline
setHeaderConLine(size_t i, std::string line)eonc::Matterinline
setMass(long int atom, double mass)eonc::Matter
setMasses(const VectorXd &massesIn)eonc::Matter
setPbcConvention(PbcConvention convention)eonc::Matterinline
setPeriodic(bool periodic)eonc::Matterinline
setPosition(long int atom, int axis, double position)eonc::Matter
setPositions(const AtomMatrix &pos)eonc::Matter
setPositionsFree(const AtomMatrix &pos)eonc::Matter
setPositionsFreeV(const VectorXd &pos)eonc::Matter
setPositionsV(const VectorXd &pos)eonc::Matter
setPotential(std::shared_ptr< Potential > pot)eonc::Matter
setVelocities(const AtomMatrix &v)eonc::Matter
setVelocity(long int atom, int axis, double velocity)eonc::Matter
structCompeonc::Matterprivate
takeMovieFrames()eonc::Matterinline
usePeriodicBoundarieseonc::Matterprivate
velocitieseonc::Matterprivate
writeTibble(std::string filename)eonc::Matterinline
~Matter()=defaulteonc::Matter