Small generic functions that are shared by all namespaces. More...
Functions | |
| double | radDeg (double angle) |
| 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. More... | |
| double | getAverageWithoutOutliers (std::vector< double > inpVec) |
| Get the average, after excluding the outliers, using quartiles. More... | |
| double | calcMedian (std::vector< double > *input) |
| Inline generic function for calculating the median given a vector of the values. More... | |
| double | periodicDist (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. More... | |
| double | unWrappedDistFromPoint (molSys::PointCloud< molSys::Point< double >, double > *yCloud, int iatom, std::vector< double > singlePoint) |
| double | distance (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. More... | |
| std::array< double, 3 > | relDist (molSys::PointCloud< molSys::Point< double >, double > *yCloud, int iatom, int jatom) |
| bool | compareByAtomID (const molSys::Point< double > &a, const molSys::Point< double > &b) |
| int | prettyPrintYoda (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::string outFile) |
| Generic function for printing all the struct information. More... | |
| int | unwrappedCoordShift (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) More... | |
| 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. This returns a vector with the words in it. More... | |
| std::vector< double > | tokenizerDouble (std::string line) |
| Function for tokenizing line strings into a vector of doubles. More... | |
| std::vector< int > | tokenizerInt (std::string line) |
| Function for tokenizing line strings into a vector of ints. More... | |
| bool | file_exists (const std::string &name) |
| Function for checking if a file exists or not. More... | |
| std::vector< std::complex< double > > | avgVector (std::vector< std::complex< double >> v, int l, int neigh) |
| 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, std::unordered_multimap< int, int > molIDAtomIDmap, int molID, bool inSliceValue=true) |
Variables | |
| const double | pi = boost::math::constants::pi<double>() |
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.