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gen Namespace Reference
Gen

Small generic functions that are shared by all namespaces. More...

Functions

double radDeg (double angle)
 Inline function for converting radians->degrees.
double eigenVecAngle (std::vector< double > OO, std::vector< double > OH)
 Eigen function for getting the angle (in radians) between the O–O and O-H vectors.
double getAverageWithoutOutliers (std::vector< double > inpVec)
 Get the average, after excluding the outliers, using quartiles.
double calcMedian (std::vector< double > *input)
 Inline generic function for calculating the median given a vector of the values.
std::array< double, 3 > triclinicMinImage (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, double xi, double yi, double zi, double xj, double yj, double zj)
double periodicDistSq (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, int iatom, int jatom)
 Inline generic function for obtaining the unwrapped periodic distance between two particles, whose indices (not IDs) have been given.
double periodicDist (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, int iatom, int jatom)
 Inline generic function for obtaining the unwrapped periodic distance between two particles, whose indices (not IDs) have been given.
void batchPeriodicDistSq (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, int iatom, const int *jatom, std::size_t n, double *distSq)
std::string formatDumpBox (const std::vector< double > &box)
void writeDumpBoxBounds (std::ostream &os, const molSys::PointCloud< molSys::Point< double >, double > &yCloud)
std::array< double, 3 > relDistFromPoint (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, int iatom, double xj, double yj, double zj)
 Inline generic function for obtaining the unwrapped periodic distance between one particle and another point, whose index has been given.
double unWrappedDistFromPoint (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, int iatom, const std::vector< double > &singlePoint)
double distance (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, int iatom, int jatom)
 Inline generic function for obtaining the wrapped distance between two particles WITHOUT applying PBCs, whose indices (not IDs) have been given.
std::array< double, 3 > relDist (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, int iatom, int jatom)
 Inline generic function for getting the relative unwrapped distance between two particles for each dimension.
bool compareByAtomID (const molSys::Point< double > &a, const molSys::Point< double > &b)
 Inline generic function for sorting or comparing two particles, according to the atom ID when the entire Point objects have been passed.
int prettyPrintYoda (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, std::string outFile)
 Generic function for printing all the struct information.
int unwrappedCoordShift (const molSys::PointCloud< molSys::Point< double >, double > &yCloud, int iatomIndex, int jatomIndex, double *x_i, double *y_i, double *z_i, double *x_j, double *y_j, double *z_j)
 Shift particles (unwrapped coordinates).
double angDistDegQuaternions (std::vector< double > quat1, std::vector< double > quat2)
std::vector< std::string > tokenizer (std::string line)
 Function for tokenizing line strings into words (strings) delimited by whitespace.
std::vector< double > tokenizerDouble (std::string line)
 Function for tokenizing line strings into a vector of doubles.
std::vector< int > tokenizerInt (std::string line)
 Function for tokenizing line strings into a vector of ints.
bool file_exists (const std::string &name)
 Function for checking if a file exists or not.
std::vector< std::complex< double > > avgVector (std::vector< std::complex< double > > v, int l, int neigh)
 Calculates the complex vector, normalized by the number of nearest neighbours, of length \(2l+1\).
molSys::PointCloud< molSys::Point< double >, double > getPointCloudOneAtomType (molSys::PointCloud< molSys::Point< double >, double > &yCloud, molSys::PointCloud< molSys::Point< double >, double > &outCloud, int atomTypeI, bool isSlice=false, std::array< double, 3 > coordLow=std::array< double, 3 >{0, 0, 0}, std::array< double, 3 > coordHigh=std::array< double, 3 >{0, 0, 0})
void moleculesInSingleSlice (molSys::PointCloud< molSys::Point< double >, double > &yCloud, bool clearPreviousSliceSelection=true, std::array< double, 3 > coordLow=std::array< double, 3 >{0, 0, 0}, std::array< double, 3 > coordHigh=std::array< double, 3 >{0, 0, 0})
void atomsInSingleSlice (molSys::PointCloud< molSys::Point< double >, double > &yCloud, bool clearPreviousSliceSelection=true, std::array< double, 3 > coordLow=std::array< double, 3 >{0, 0, 0}, std::array< double, 3 > coordHigh=std::array< double, 3 >{0, 0, 0})
void setAtomsWithSameMolID (molSys::PointCloud< molSys::Point< double >, double > &yCloud, const std::unordered_multimap< int, int > &molIDAtomIDmap, int molID, bool inSliceValue=true)

Variables

constexpr double pi = std::numbers::pi
 Uses Boost to get the value of pi.

Detailed Description

Small generic functions that are shared by all namespaces.

These are general functions (eg. for finding the periodic distance) which are required by several namespaces.

Changelog