File parameters.hpp

This file contains the parameters class which contains the settings and values used to adjust the program control flow to the user input files.

Author: Benjamin Lindner ben@benlabs.net
Version: See VERSION in CMakeLists.txt
Copyright: GNU General Public License

class SampleStructureParameters

#include <parameters.hpp>

Section which defines the structure

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

std::string file

std::string filepath

std::string format

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class SampleSelectionParameters

#include <parameters.hpp>

Section which defines a generic selection (used as parent by specific selections)

Subclassed by SampleFileSelectionParameters, SampleIndexSelectionParameters, SampleLexicalSelectionParameters, SampleRangeSelectionParameters

Public Functions

inline SampleSelectionParameters()

inline SampleSelectionParameters(std::string type)

inline std::string type()

inline std::string write_xml(int pad = 0)

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Private Members

std::string type_

Friends

friend class boost::serialization::access

class SampleIndexSelectionParameters : public SampleSelectionParameters

#include <parameters.hpp>

Section which defines a selection based on individual indexes

Public Functions

inline SampleIndexSelectionParameters()

inline SampleIndexSelectionParameters(std::vector<size_t> ids)

inline std::string write_xml(int pad = 0)

Public Members

std::vector<size_t> ids_

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class SampleRangeSelectionParameters : public SampleSelectionParameters

#include <parameters.hpp>

Section which defines a selection based on a given range

Public Functions

inline SampleRangeSelectionParameters()

inline SampleRangeSelectionParameters(size_t from, size_t to)

inline std::string write_xml(int pad = 0)

Public Members

size_t from_

size_t to_

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class SampleLexicalSelectionParameters : public SampleSelectionParameters

#include <parameters.hpp>

Section which defines a selection based on a lexical pattern (regular expression matching atom labels)

Public Functions

inline SampleLexicalSelectionParameters()

inline SampleLexicalSelectionParameters(std::string expression)

inline std::string write_xml(int pad = 0)

Public Members

std::string expression_

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class SampleFileSelectionParameters : public SampleSelectionParameters

#include <parameters.hpp>

Section which defines a file based selection

Public Functions

inline SampleFileSelectionParameters()

inline SampleFileSelectionParameters(std::string file, std::string format, std::string selector, std::string expression)

inline std::string write_xml(int pad = 0)

Public Members

std::string file_

std::string filepath_

std::string format_

std::string selector_

std::string expression_

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class SampleFramesetParameters

#include <parameters.hpp>

Section which defines a single trajectory file entry

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

size_t first

size_t last

size_t clones

bool last_set

size_t stride

std::string file

std::string filepath

std::string format

std::string index

std::string indexpath

bool index_default

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class SampleFramesetsParameters : public std::vector<SampleFramesetParameters>

#include <parameters.hpp>

Section which lists the used trajectory files

Public Functions

inline std::string write_xml(int pad = 0)

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class SampleMotionReferenceParameters

#include <parameters.hpp>

Section which stores reference information which may be required during some alignment procedures

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

std::string type

std::string selection

std::string file

std::string filepath

std::string format

size_t frame

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class SampleMotionParameters

#include <parameters.hpp>

Section which defines artificial motions

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

std::string type

double displace

double frequency

double radius

std::string selection

unsigned long seed

long sampling

CartesianCoor3D direction

SampleMotionReferenceParameters reference

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class SampleAlignmentReferenceParameters

#include <parameters.hpp>

Section which stores reference information which may be required during some alignment procedures

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

std::string type

std::string selection

std::string file

std::string filepath

std::string format

size_t frame

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class SampleAlignmentParameters

#include <parameters.hpp>

Section which stores alignment information, which is applied during the staging of the trajectory data

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

SampleAlignmentReferenceParameters reference

std::string type

std::string selection

std::string order

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class SampleParameters

#include <parameters.hpp>

Section which stores sample specific parameters

Public Functions

~SampleParameters()

inline std::string write_xml(int pad = 0)

Public Members

SampleStructureParameters structure

std::map<std::string, SampleSelectionParameters*> selections

SampleFramesetsParameters framesets

std::vector<SampleMotionParameters> motions

std::vector<SampleAlignmentParameters> alignments

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class ScatteringBackgroundFactor

#include <parameters.hpp>

Section which stores selection based scaling factors for background correction

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

std::string selection

double value

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version): Serialization allows sample transmission via MPI.

Friends

friend class boost::serialization::access

class ScatteringBackgroundKappaParameters

#include <parameters.hpp>

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

std::string selection

double value

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class ScatteringBackgroundCutBoxParameters

#include <parameters.hpp>

Section added by arnab majumdar, hereon new option: under back ground cut - box - sld (double)

xlength (double)
ylength (double)
zlength (double)
midpoint (coor_3D) - x
- y
- z

Public Functions

inline ScatteringBackgroundCutBoxParameters()

inline std::string write_xml(int pad = 0)

Public Members

ImagNum sld

double xlength

double ylength

double zlength

CartesianCoor3D midpoint

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class ScatteringBackgroundCutParameters

#include <parameters.hpp>

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

ScatteringBackgroundCutBoxParameters box

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class ScatteringBackgroundParameters

#include <parameters.hpp>

new feature added by Arnab Majumdar, hereon ends here. There are other minor changes in the code. Section which stores background correction parameters

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

std::string type

ScatteringBackgroundFactor factor

std::vector<ScatteringBackgroundKappaParameters> kappas

ScatteringBackgroundCutParameters cut

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class ScatteringAverageOrientationVectorsParameters : public std::vector<CartesianCoor3D>

#include <parameters.hpp>

Section which is used when vector based orientational averaging is performed

Public Functions

void create()

inline std::string write_xml(int pad = 0)

Public Members

std::string type

std::string algorithm

std::string file

std::string filepath

size_t resolution

unsigned long seed

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class ScatteringAverageOrientationMultipoleMomentsParameters : public std::vector<std::pair<long, long>>

#include <parameters.hpp>

Section which is used to store the used multipole identifiers when multipole based orientational averaging is performed

Public Functions

void create()

inline std::string write_xml(int pad = 0)

Public Members

std::string type

long resolution

std::string file

std::string filepath

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class ScatteringAverageOrientationMultipoleParameters

#include <parameters.hpp>

Section which is used when multipole based orientational averaging is performed

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

std::string type

ScatteringAverageOrientationMultipoleMomentsParameters moments

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class ScatteringAverageOrientationExactParameters

#include <parameters.hpp>

Section which is used when exact orientational averaging is performed

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

std::string type

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class ScatteringAverageOrientationParameters

#include <parameters.hpp>

Section which defines orientational averaging procedures

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

std::string type

CartesianCoor3D axis

ScatteringAverageOrientationVectorsParameters vectors

ScatteringAverageOrientationMultipoleParameters multipole

ScatteringAverageOrientationExactParameters exact

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class ScatteringAverageParameters

#include <parameters.hpp>

Section which defines averaging procedures

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

ScatteringAverageOrientationParameters orientation

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class ScatteringDspParameters

#include <parameters.hpp>

Section which defines further processing of the scattering signal, e.g. autocorrelation

Public Types

enum class Type

Values:

enumerator Autocorrelate

enumerator Square

enumerator Plain

enum class Method

Values:

enumerator FFTW

enumerator Direct

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

std::string type

std::string method

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class ScatteringVectorsScanParameters

#include <parameters.hpp>

Section which describes a scan entry used to construct the scattering vectors

Public Functions

inline ScatteringVectorsScanParameters()

inline std::string write_xml(int pad = 0)

Public Members

double from

double to

size_t points

double exponent

CartesianCoor3D basevector

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class ScatteringVectorsParameters : public std::vector<CartesianCoor3D>

#include <parameters.hpp>

Section which defines the scattering vectors

Public Functions

void create_from_scans()

inline std::string write_xml(int pad = 0)

Public Members

std::vector<ScatteringVectorsScanParameters> scans

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class ScatteringSignalParameters

#include <parameters.hpp>

Section which stores parameters used during the writing of the signal file

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

std::string file

std::string filepath

bool fqt

bool fq

bool fq0

bool fq2

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class ScatteringParameters

#include <parameters.hpp>

Section which stores parameters used during the scattering calculation

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

std::string type

ScatteringDspParameters dsp

ScatteringVectorsParameters qvectors

ScatteringAverageParameters average

ScatteringBackgroundParameters background

ScatteringSignalParameters signal

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class StagerParameters

#include <parameters.hpp>

Section which stores parameters used during data staging

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

bool dump

std::string file

std::string filepath

std::string format

std::string target

std::string mode

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class LimitsServicesSignalMemoryParameters

#include <parameters.hpp>

Section which stores parameters affecting the memory limitations of the file writer service

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

size_t server

size_t client

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class LimitsServicesSignalTimesParameters

#include <parameters.hpp>

Section which stores parameters affecting the timing of the file writer service

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

size_t serverflush

size_t clientflush

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class LimitsServicesSignalParameters

#include <parameters.hpp>

Section which stores parameters affecting the file writer service, which writes results to the signal file

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

LimitsServicesSignalMemoryParameters memory

LimitsServicesSignalTimesParameters times

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class LimitsServicesMonitorParameters

#include <parameters.hpp>

Section which stores parameters affecting the monitoring service, which reports progress to the console

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

size_t delay

size_t sampling

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class LimitsServicesParameters

#include <parameters.hpp>

Section which stores parameters affecting the services

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

LimitsServicesSignalParameters signal

LimitsServicesMonitorParameters monitor

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class LimitsComputationMemoryParameters

#include <parameters.hpp>

Section which stores memory limits during the computation

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

size_t result_buffer

size_t alignpad_buffer

size_t exchange_buffer

size_t signal_buffer

size_t scale

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class LimitsComputationParameters

#include <parameters.hpp>

Section which stores parameters used during the computation

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

size_t threads

size_t processes

size_t cores

LimitsComputationMemoryParameters memory

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class LimitsDecompositionPartitionsParameters

#include <parameters.hpp>

Section which stores parameters determining the computational partition size

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

bool automatic

size_t size

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class LimitsDecompositionParameters

#include <parameters.hpp>

Section which stores parameters used for partitioning the computation among the available compute nodes

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

double utilization

LimitsDecompositionPartitionsParameters partitions

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class LimitsSignalParameters

#include <parameters.hpp>

Section which stores parameters used during the writing of the signal output file

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

size_t chunksize

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class LimitsStageMemoryParameters

#include <parameters.hpp>

Section which stores memory limits during the data staging process.

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

size_t data

size_t buffer

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class LimitsStageParameters

#include <parameters.hpp>

Section which stores limits regarding the data staging process.

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

LimitsStageMemoryParameters memory

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class LimitsParameters

#include <parameters.hpp>

Section which stores computational limitations and performance characteristics.

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

LimitsStageParameters stage

LimitsSignalParameters signal

LimitsServicesParameters services

LimitsComputationParameters computation

LimitsDecompositionParameters decomposition

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class DebugMonitorParameters

#include <parameters.hpp>

Section which stores parameters influencing the progress monitoring

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

bool update

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class DebugPrintParameters

#include <parameters.hpp>

Section which stores switches for dumping information to console output.

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

bool orientations

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class DebugIowriteParameters

#include <parameters.hpp>

Section which stores IO write specific debug parameters. Used to tune the frequency by which the results are written to the signal file. Can also be used to avoid writing to the signal file.

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

bool write

bool buffer

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class DebugParameters

#include <parameters.hpp>

Section which stores debug parameters

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

bool timer

bool barriers

DebugIowriteParameters iowrite

DebugPrintParameters print

DebugMonitorParameters monitor

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class DatabaseParameters

#include <parameters.hpp>

Section which stores a reference to the used database

Public Functions

inline std::string write_xml(int pad = 0)

Public Members

std::string type

std::string file

std::string filepath

std::string format

Private Functions

template<class Archive> inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access