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Matter Member List

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

applyPeriodicBoundary()Matterprivate
applyPeriodicBoundary(double &component, int axis)Matterprivate
applyPeriodicBoundary(AtomMatrix &diff)Matterprivate
applyPeriodicBoundaryIfEnabled()Matterinline
assertIsolatedMoleculeLayoutSafe() constMatterprivate
assignKeepingBias(const Matter &other)Matter
biasPotentialMatterprivate
cachedHostEpoch_Mattermutableprivate
cachedPotEpoch_Mattermutableprivate
cancel_token_Matterprivate
cancelToken() constMatterinline
captureStress() constMatterprivate
cauchyStress()Matter
clearMovieFrames()Matterinline
compare(const Matter &matter, bool indistinguishable=false)Matter
computePotential() constMatterprivate
con2matter(std::string filename)Matterinline
con2matter(const readcon::ConFrame &frame, io::ConFrameMetadata *out_metadata=nullptr)Matterinline
convel2matter(std::string filename)Matterinline
distance(long index1, long index2) constMatter
distance(const Matter &matter, long index) constMatter
distanceTo(const Matter &matter)Matter
energyVarianceMattermutableprivate
epochDirty() constMatterprivate
fileToMatterMatterprivate
forceCallsMattermutableprivate
forcesData()Matter
freeIndicesMattermutableprivate
getAccelerations()Matter
getAtomicNr(long int atom) constMatter
getAtomicNrs() constMatter
getAtomicNrsFree() constMatter
getAtomIndex(long int atom) constMatter
getBiasForces()Matter
getBiasPotential() constMatter
getCell() constMatter
getEnergyVariance() constMatter
getFixed(long int atom) constMatter
getFixed(long int atom, int axis) constMatter
getFixedMask(long int atom) constMatter
getForceCalls() constMatter
getForces() constMatter
getForcesFree() constMatter
getForcesFreeV() constMatter
getForcesRaw() constMatter
getForcesV() constMatter
getFree() constMatter
getFreeV() constMatter
getHeaderCon() constMatterinline
getKineticEnergy() constMatter
getMass(long int atom) constMatter
getMasses() constMatter
getMechanicalEnergy() constMatter
getPbcConvention() constMatterinline
getPeriodic() const noexceptMatterinline
getPosition(long int atom, int axis) constMatter
getPositions() constMatter
getPositionsCopy() constMatter
getPositionsFree() constMatter
getPositionsFreeV() constMatter
getPositionsV() constMatter
getPotential()Matter
getPotentialCalls() constMatter
getPotentialEnergy() constMatter
getSurfaceEpoch() const noexceptMatterinline
getVelocities() constMatter
getWriteConForces() const noexceptMatter
headerConMatterprivate
holdsExclusivePotential() constMatter
impl_Matterprivate
inp2matter(const std::string &filename)Matterinline
io::con2matter(Matter &, const readcon::ConFrame &, io::ConFrameMetadata *)Matterfriend
livePotential() constMatterprivate
m_logMatterprivate
mapFileRow(long file_row) constMatterinline
Matter(std::shared_ptr< Potential > pot, const Parameters &params)Matter
Matter(std::unique_ptr< Potential > pot, const Parameters &params)Matter
Matter(const Matter &matter)Matter
Matter(Matter &&other) noexceptMatter
matter2con(std::string filename, bool append=false, const io::ConFrameMetadata *metadata=nullptr)Matterinline
matter2convel(std::string filename)Matterinline
matter2xyz(std::string filename, bool append=false)Matterinline
maxForce(void) constMatter
maxFreeAtomForce(const AtomMatrix &rows) constMatter
movie_frames_Matterprivate
movieFrames() constMatterinline
nAtomsMatterprivate
needsForceUpdate() constMatterinline
numberOfAtoms() constMatter
numberOfFixedAtoms() constMatter
numberOfFreeAtoms() constMatter
operator=(const Matter &matter)Matter
operator=(Matter &&other) noexceptMatter
ownedPotentialMattermutableprivate
parametersMatterprivate
pbc(const AtomMatrix &diff) constMatter
pbcConventionMatterprivate
pbcV(const VectorXd &diff) constMatter
pdistance(long index1, long index2, int axis) constMatter
perAtomNorm(const Matter &matter)Matter
pollCancel(const char *site) constMatterinline
potentialMattermutableprivate
potentialEnergyMattermutableprivate
recomputeFreeMaskMattermutableprivate
recomputeMaskedForcesMattermutableprivate
recomputePotentialMattermutableprivate
relax(bool quiet=false, bool writeMovie=false, bool checkpoint=false, std::string prefixMovie=std::string(), std::string prefixCheckpoint=std::string(), bool retainMovieFrames=false)Matter
removeNetForceMatterprivate
resetForceCalls()Matter
resize(long int nAtoms)Matter
restoreFileForces(const AtomMatrix &fileForces, bool trustEnergy, double energy)Matterprivate
setAtomicNr(long int atom, long atomicNr)Matter
setAtomicNrs(const VectorXi &atmnrs)Matter
setAtomIndex(long int atom, std::int64_t index)Matter
setBiasForces(const AtomMatrix &bf)Matter
setBiasPotential(BondBoost *bondBoost)Matter
setCancelToken(CancelToken token)Matterinline
setCell(const Matrix3d &newCell)Matter
setComputedPotential(double energy, double variance)Matter
setEvaluation(const AtomMatrix &forces, double energy)Matterinline
setFileToMatter(std::vector< long > map)Matterinline
setFixed(long int atom, int isFixed)Matter
setFixed(long int atom, int axis, int isFixed)Matter
setFixedMask(long int atom, std::array< bool, 3 > mask)Matter
setForces(const AtomMatrix &f)Matter
setHeaderCon(const std::array< std::string, 5 > &headers)Matterinline
setHeaderConLine(size_t i, std::string line)Matterinline
setMass(long int atom, double mass)Matter
setMasses(const VectorXd &massesIn)Matter
setPbcConvention(PbcConvention convention)Matterinline
setPeriodic(bool periodic)Matterinline
setPosition(long int atom, int axis, double position)Matter
setPositions(const AtomMatrix &pos)Matter
setPositionsFree(const AtomMatrix &pos)Matter
setPositionsFreeV(const VectorXd &pos)Matter
setPositionsV(const VectorXd &pos)Matter
setPotential(std::shared_ptr< Potential > pot)Matter
setSurfaceEpoch(unsigned long long epoch)Matter
setVelocities(const AtomMatrix &v)Matter
setVelocity(long int atom, int axis, double velocity)Matter
shareOwnedPotential() constMatterprivate
stampSurfaceEpoch() constMatterprivate
structCompMatterprivate
surfaceEpoch_Matterprivate
takeMovieFrames()Matterinline
usePeriodicBoundariesMatterprivate
writeTibble(std::string filename)Matterinline
~Matter()Matter