bop.hpp File Reference
File for the bond order parameter analysis. More...
#include <array>#include <boost/geometry.hpp>#include <boost/math/special_functions/spherical_harmonic.hpp>#include <cmath>#include <complex>#include <generic.hpp>#include <math.h>#include <mol_sys.hpp>#include <neighbours.hpp>#include <seams_output.hpp>
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Data Structures | |
| struct | chill::YlmAtom |
| This contains a complex vector of length \(2l+1\). More... | |
| struct | chill::QlmAtom |
| This is the local orientational bond order parameter \(q_{lm}\), of length \(2l+1\). More... | |
Namespaces | |
| chill | |
| CHILL and CHILL+ structure classification. This namespace contains functions that are used in the CHILL/CHILL+ classification scheme, as well as a yodaCloud struct to hold all the information. | |
| sph | |
| Functions used for spherical harmonics. | |
Functions | |
| molSys::PointCloud< molSys::Point< double >, double > | chill::getCorrel (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< std::vector< int >> nList, bool isSlice=false) |
| molSys::PointCloud< molSys::Point< double >, double > | chill::getIceTypeNoPrint (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< std::vector< int >> nList, bool isSlice=false) |
| Classifies each atom according to the CHILL algorithm without printing. More... | |
| molSys::PointCloud< molSys::Point< double >, double > | chill::getIceType (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< std::vector< int >> nList, std::string path, int firstFrame, bool isSlice=false, std::string outputFileName="chill.txt") |
| Classifies each atom according to the CHILL algorithm. More... | |
| molSys::PointCloud< molSys::Point< double >, double > | chill::getCorrelPlus (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< std::vector< int >> nList, bool isSlice=false) |
| Gets c_ij and then classifies bond types according to the CHILL+ algorithm. More... | |
| molSys::PointCloud< molSys::Point< double >, double > | chill::getIceTypePlus (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< std::vector< int >> nList, std::string path, int firstFrame, bool isSlice=false, std::string outputFileName="chillPlus.txt") |
| Classifies each atom according to the CHILL+ algorithm. More... | |
| std::vector< double > | chill::getq6 (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< std::vector< int >> nList, bool isSlice=false) |
| molSys::PointCloud< molSys::Point< double >, double > | chill::reclassifyWater (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< double > *q6) |
| int | chill::printIceType (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::string path, int firstFrame, bool isSlice=false, std::string outputFileName="superChill.txt") |
| Prints out the iceType for a particular frame onto the terminal. More... | |
| bool | chill::isInterfacial (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< std::vector< int >> nList, int iatom, int num_staggrd, int num_eclipsd) |
| int | chill::numStaggered (molSys::PointCloud< molSys::Point< double >, double > *yCloud, std::vector< std::vector< int >> nList, int jatom) |
| Finds the number of staggered bonds for a given atom of index jatom. More... | |
| std::vector< std::complex< double > > | sph::spheriHarmo (int orderL, std::array< double, 2 > radialCoord) |
| std::array< double, 2 > | sph::radialCoord (std::array< double, 3 > cartCoord) |
| std::vector< std::complex< double > > | sph::lookupTableQ3Vec (std::array< double, 2 > angles) |
| Lookup table for Q3. More... | |
| std::complex< double > | sph::lookupTableQ3 (int m, std::array< double, 2 > angles) |
| Lookup table for Q3 (m=0 to m=6) More... | |
| std::vector< std::complex< double > > | sph::lookupTableQ6Vec (std::array< double, 2 > angles) |
| Lookup table for Q6. More... | |
| std::complex< double > | sph::lookupTableQ6 (int m, std::array< double, 2 > angles) |
| Lookup table for Q6 (m=0 to m=12) More... | |
Detailed Description
File for the bond order parameter analysis.
Definition in file bop.hpp.