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sinp Namespace Reference
Sinp

Functions for the d-SEAMS readers. More...

Functions

std::vector< std::string > getInpFileList (std::string inputFolder)
 Get file list inside the input folder.
int nLammpsFrames (const std::string &filename)
void dropLammpsDumpIndex (const std::string &filename)
 Drop a cached dump session (tests that rewrite a path in place).
void forEachLammpsFrame (const std::string &filename, int first, int last, int typeFilter, const std::function< void(int, molSys::PointCloud< molSys::Point< double >, double > &)> &fn, int nThreads=0)
molSys::PointCloud< molSys::Point< double >, double > readLammpsTrj (std::string filename, int targetFrame, molSys::PointCloud< molSys::Point< double >, double > &yCloud, 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})
molSys::PointCloud< molSys::Point< double >, double > readLammpsTrjO (std::string filename, int targetFrame, molSys::PointCloud< molSys::Point< double >, double > &yCloud, int typeO, 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})
molSys::PointCloud< molSys::Point< double >, double > readLammpsTrjreduced (std::string filename, int targetFrame, molSys::PointCloud< molSys::Point< double >, double > &yCloud, int typeI, 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})
molSys::PointCloud< molSys::Point< double >, double > readXYZ (std::string filename)
 Function for reading in atom coordinates from an XYZ file.
std::vector< std::vector< int > > readBonds (std::string filename)
 Reads bonds into a vector of vectors from a file with a specific format.
bool atomInSlice (double x, double y, double z, std::array< double, 3 > coordLow, std::array< double, 3 > coordHigh)

Detailed Description

Functions for the d-SEAMS readers.

This namespace contains functions that are used for reading in the formats supported by d-SEAMS. LAMMPS trajectory files and XYZ files are currently supported, though it is recommended to use LAMMPS trajectory files, since the simulation box size etc. are not normally present in XYZ files, and many analyses may fail without the correct box dimensions.

Changelog