Sinp

Namespaces
namespace	sinp
	Functions for the d-SEAMS readers.

Functions
std::vector< std::string >	sinp::getInpFileList (std::string inputFolder)
	Get file list inside the input folder.
int	sinp::nLammpsFrames (const std::string &filename)
void	sinp::dropLammpsDumpIndex (const std::string &filename)
	Drop a cached dump session (tests that rewrite a path in place).
void	sinp::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 >	sinp::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 >	sinp::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 >	sinp::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 >	sinp::readXYZ (std::string filename)
	Function for reading in atom coordinates from an XYZ file.
std::vector< std::vector< int > >	sinp::readBonds (std::string filename)
	Reads bonds into a vector of vectors from a file with a specific format.
bool	sinp::atomInSlice (double x, double y, double z, std::array< double, 3 > coordLow, std::array< double, 3 > coordHigh)

Detailed Description

Function Documentation

atomInSlice()

bool sinp::atomInSlice ( double x, double y, double z, std::array< double, 3 > coordLow, std::array< double, 3 > coordHigh )

inline

True when each component lies in [lo, hi], or that axis has lo == hi (unconstrained). ([0,0,0], [50,0,0]) is x in [0, 50], y and z open.

If this is 3 then the particle is inside the volume slice

Definition at line 129 of file seams_input.hpp.

                                                       {
  int flag = 0; 
 
  if (((x >= coordLow[0]) && (x <= coordHigh[0])) ||
      coordLow[0] == coordHigh[0]) {
    flag++;
  }
  if (((y >= coordLow[1]) && (y <= coordHigh[1])) ||
      coordLow[1] == coordHigh[1]) {
    flag++;
  }
  if (((z >= coordLow[2]) && (z <= coordHigh[2])) ||
      coordLow[2] == coordHigh[2]) {
    flag++;
  }
 
  if (flag == 3) {
    return true;
  } else {
    return false;
  }
}

dropLammpsDumpIndex()

void sinp::dropLammpsDumpIndex

(

const std::string &

filename

)

Drop a cached dump session (tests that rewrite a path in place).

forEachLammpsFrame()

void sinp::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 )

Call fn(frame, cloud) for each frame in [first, last] (1-based, inclusive). last <= 0 means every ITEM: TIMESTEP. typeFilter <= 0 keeps every atom. nThreads <= 0 uses the OpenMP default; 1 is serial. Each worker opens its own handle and seeks the shared offset table. Incremental RingUpdater / AffiliationUpdater state cannot be shared across workers: use the batch classifiers.

getInpFileList()

std::vector< std::string > sinp::getInpFileList

(

std::string

inputFolder

)

Get file list inside the input folder.

nLammpsFrames()

int sinp::nLammpsFrames

(

const std::string &

filename

)

Number of ITEM: TIMESTEP frames in a LAMMPS dump, or 0 if the file cannot be read. The first full count per path walks the file once and later reads seek, matching chemfiles Trajectory::nsteps and readcon's frame-offset table. Sequential load_frame walks reuse a live cursor the way LAMMPS ReaderNative does on rerun.

readBonds()

std::vector< std::vector< int > > sinp::readBonds

(

std::string

filename

)

Reads bonds into a vector of vectors from a file with a specific format.

readLammpsTrj()

molSys::PointCloud< molSys::Point< double >, double > sinp::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} )

Function for reading in a specified frame (frame number and not timestep value)

readLammpsTrjO()

molSys::PointCloud< molSys::Point< double >, double > sinp::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} )

One LAMMPS dump frame, one atom type. The type argument is any LAMMPS type (the O in the name is historical). If isSlice is true, each kept point gets inSlice set; atoms outside the box stay in the cloud. nop is the type-filtered count.

readLammpsTrjreduced()

molSys::PointCloud< molSys::Point< double >, double > sinp::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} )

One LAMMPS dump frame, one atom type, dropping atoms outside the slice when isSlice is true. nop is the kept count. An axis with lo == hi is unconstrained.

readXYZ()

molSys::PointCloud< molSys::Point< double >, double > sinp::readXYZ

(

std::string

filename

)

Function for reading in atom coordinates from an XYZ file.