Functions | |
int | rdf2::rdf2Danalysis_AA (std::string path, std::vector< double > *rdfValues, molSys::PointCloud< molSys::Point< double >, double > *yCloud, double cutoff, double binwidth, int firstFrame, int finalFrame) |
std::vector< int > | rdf2::sampleRDF_AA (molSys::PointCloud< molSys::Point< double >, double > *yCloud, double cutoff, double binwidth, int nbin) |
Samples the RDF histogram at every step. More... | |
int | rdf2::normalizeRDF (int nopA, std::vector< double > *rdfValues, std::vector< int > histogram, double binwidth, int nbin, std::vector< double > volumeLengths, int nIter) |
Normalize the histogram. More... | |
std::vector< double > | rdf2::getSystemLengths (molSys::PointCloud< molSys::Point< double >, double > *yCloud) |
Gets the lengths of the volume slice of the quasi-two-dimensional system. More... | |
double | rdf2::getPlaneArea (std::vector< double > volumeLengths) |
Gets the plane area from the volume lengths vector. More... | |
double rdf2::getPlaneArea | ( | std::vector< double > | volumeLengths | ) |
Gets the plane area from the volume lengths vector.
Calculates the plane area from the volume lengths. This is the product of the two largest dimensions of the quasi-two-dimensional system.
[in] | volumeLengths | A vector of the lengths of the volume slice or simulation box |
Definition at line 264 of file rdf2d.cpp.
std::vector< double > rdf2::getSystemLengths | ( | molSys::PointCloud< molSys::Point< double >, double > * | yCloud | ) |
Gets the lengths of the volume slice of the quasi-two-dimensional system.
Calculates the lengths of the quasi-two-dimensional system. The smallest length is the 'height'.
[in] | yCloud | The molSys::PointCloud struct for the system. |
Definition at line 212 of file rdf2d.cpp.
int rdf2::normalizeRDF | ( | int | nopA, |
std::vector< double > * | rdfValues, | ||
std::vector< int > | histogram, | ||
double | binwidth, | ||
int | nbin, | ||
std::vector< double > | volumeLengths, | ||
int | nIter | ||
) |
Normalize the histogram.
Normalizes the histogram and adds it to the RDF. The normalization requires the plane area and height.
[in] | nopA | The number of particles of type A. |
[in] | rdfValues | Radial distribution function values for all the frames, in the form of a vector. |
[in] | histogram | The histogram for the current frame. |
[in] | binwidth | The width of each bin for the RDF histogram. |
[in] | nbin | The number of bins for the RDF. |
[in] | volumeLengths | The confining dimensions of the quasi-two-dimensional system, which may be the slice dimensions or the dimensions of the box. |
[in] | nIter | The number of iterations for which the coordinates will be binned. This is basically equivalent to the number of frames over which the RDF will be calculated. |
Definition at line 162 of file rdf2d.cpp.
int rdf2::rdf2Danalysis_AA | ( | std::string | path, |
std::vector< double > * | rdfValues, | ||
molSys::PointCloud< molSys::Point< double >, double > * | yCloud, | ||
double | cutoff, | ||
double | binwidth, | ||
int | firstFrame, | ||
int | finalFrame | ||
) |
Main function for calculating the RDF for the same type of particle: calls other functions for initializing, sampling and normalizing the RDF
Calculates the in-plane RDF for quasi-two-dimensional water, when both the atoms are of the same type. The input PointCloud only has particles of type A in it. This is registered as a Lua function and is accessible to the user. Internally, this function calls the following functions:
[in] | path | The file path of the output directory to which output files will be written. |
[in] | rdfValues | Vector containing the RDF values. |
[in] | yCloud | The input PointCloud. |
[in] | cutoff | Cutoff for the RDF. This should not be greater than half the box length. |
[in] | binwidth | Width of the bin for histogramming. |
[in] | firstFrame | The first frame for RDF binning. |
[in] | finalFrame | The final frame for RDF binning. |
Definition at line 45 of file rdf2d.cpp.
std::vector< int > rdf2::sampleRDF_AA | ( | molSys::PointCloud< molSys::Point< double >, double > * | yCloud, |
double | cutoff, | ||
double | binwidth, | ||
int | nbin | ||
) |
Samples the RDF histogram at every step.
Samples the RDF for a particular frame The input PointCloud only has particles of type A in it.
[in] | yCloud | The input PointCloud. |
[in] | cutoff | Cutoff for the RDF calculation, which should be less than or equal to half the box length. |
[in] | binwidth | Width of the bin. |
[in] | nbin | Number of bins. |
Definition at line 115 of file rdf2d.cpp.