doxygen/write__annotated__frame_8h_source.html

// -*-c++-*-

#ifndef STORMM_WRITE_SDF_H

#define STORMM_WRITE_SDF_H


#include <vector>

#include "copyright.h"

#include "FileManagement/file_util.h"

#include "Synthesis/phasespace_synthesis.h"

#include "coordinateframe.h"

#include "coordinate_series.h"

#include "coordinate_swap_plan.h"

#include "phasespace.h"


namespace stormm {

namespace trajectory {


using diskutil::PrintSituation;

using synthesis::PhaseSpaceSynthesis;

using synthesis::PsSynthesisReader;


void writeFrame(std::ofstream *foutp, const TextFile &tf);


void writeFrame(const std::string &filename, PrintSituation expectation, const TextFile &tf);


void writeFrame(std::ofstream *foutp, const TextFile &tf, const double* xcrd, const double* ycrd,

                const double* zcrd, const CoordinateSwapPlan &excision);


void writeFrame(const std::string &filename, PrintSituation expectation, const TextFile &tf,

                const double* xcrd, const double* ycrd, const double* zcrd,

                const CoordinateSwapPlan &excision);


void writeFrame(const std::string &filename, PrintSituation expectation, const TextFile &tf,

                const PhaseSpaceReader &psr, const CoordinateSwapPlan &excision);


void writeFrame(const std::string &filename, PrintSituation expectation, const TextFile &tf,

                const PhaseSpace &ps, const CoordinateSwapPlan &excision);


void writeFrame(const std::string &filename, PrintSituation expectation, const TextFile &tf,

                const PhaseSpace &ps, const CoordinateSwapPlan &excision,

                CoordinateCycle time_point = CoordinateCycle::WHITE);


void writeFrame(const std::string &filename, PrintSituation expectation, const TextFile &tf,

                const CoordinateFrameReader &cfr, const CoordinateSwapPlan &excision);


void writeFrame(const std::string &filename, PrintSituation expectation, const TextFile &tf,

                const CoordinateFrame &cf, const CoordinateSwapPlan &excision);


template <typename T>

void writeFrame(std::ofstream *foutp, PrintSituation expectation, const TextFile &tf,

                const CoordinateSeriesReader<T> &csr, const CoordinateSwapPlan &excision);


template <typename T>

void writeFrame(std::ofstream *foutp, const TextFile &tf, const CoordinateSeries<T> &cs,

                const CoordinateSwapPlan &excision);


template <typename T>

void writeFrame(const std::string &filename, PrintSituation expectation, const TextFile &tf,

                const CoordinateSeries<T> &cs, const CoordinateSwapPlan &excision);


void writeFrame(std::ofstream *foutp, const std::vector<TextFile> &tf_list,

                const PsSynthesisReader &poly_psr,

                const std::vector<CoordinateSwapPlan> &excision_list,

                const std::vector<int> &plan_indices);


void writeFrame(const std::string &filename, PrintSituation expectation,

                const std::vector<TextFile> &tf_list, const PhaseSpaceSynthesis &poly_ps,

                const std::vector<CoordinateSwapPlan> &excision_list,

                const std::vector<int> &plan_indices);


void writeFrame(const std::string &filename, PrintSituation expectation,

                const std::vector<TextFile> &tf_list, const PhaseSpaceSynthesis &poly_ps,

                const std::vector<CoordinateSwapPlan> &excision_list,

                const std::vector<int> &plan_indices,

                CoordinateCycle time_point = CoordinateCycle::WHITE);


} // namespace trajectory

} // namespace stormm


#include "write_annotated_frame.tpp"


#endif

stormm::parse::TextFile
Structure for translating a text file into a compact, rapidly parsable vector of characters in CPU RA...
Definition textfile.h:45

stormm::synthesis::PhaseSpaceSynthesis
A fixed-precision representation of coordinates, velocities, and forces to manage a set of simulation...
Definition phasespace_synthesis.h:325

stormm::trajectory::CoordinateFrame
Store the coordinates and box information for a frame, only. This abridged struct can serve when the ...
Definition coordinateframe.h:111

stormm::trajectory::CoordinateSeries
Store the coordinates and box information for a series of frames, in one of several levels of precisi...
Definition coordinate_series.h:137

stormm::trajectory::CoordinateSwapPlan
Collect the information needed to swap the coordinates (and, if applicable, the box information) in a...
Definition coordinate_swap_plan.h:14

stormm::trajectory::PhaseSpace
An object to complement a topology and hold positions, velocities, and forces of all particles in a s...
Definition phasespace.h:141

stormm::synthesis::PsSynthesisReader
The reader for a PhaseSpaceSynthesis object, containing all of the data relevant for propagating dyna...
Definition phasespace_synthesis.h:199

stormm::trajectory::CoordinateFrameReader
Collect C-style pointers for the elements of a read-only CoordinateFrame object.
Definition coordinateframe.h:65

stormm::trajectory::CoordinateSeriesReader
Collect C-style pointers and critical constants for a read-only CoordinateSeries object.
Definition coordinate_series.h:96

stormm::trajectory::PhaseSpaceReader
Collect constants and pointers to the components of a read-only PhaseSpace object.
Definition phasespace.h:81