Functions for calculating electron scattering profiles. More...

#include "rwmodel.h"
#include "rwmodel_param.h"
#include "ctf.h"
#include "string_util.h"
#include "utilities.h"

Functions
vector< string >	all_elements (map< string, Bcomptype > &types)

vector< double >	calculate_scattering_curve (Bcomptype &ct, double ds, double scut)
	Calculates an elastic electron scattering profile for a component type. More...

map< string, vector< double > >	calculate_scattering_curves (JSvalue &el, map< string, Bcomptype > &types, double ds, double scut)
	Calculates elastic electron scattering profiles for a subset of component types. More...

map< string, vector< double > >	calculate_scattering_curves (map< string, Bcomptype > &types, double ds, double scut)

double	scatter_curve_integral (Bcomptype &ct)
	Calculates the integral of the whole curve. More...

map< string, vector< double > >	calculate_potential_curves (JSvalue &el, map< string, Bcomptype > &types, double dr, double rmax)
	Calculates potential profiles for a subset of component types. More...

double	elastic_cross_section (Bcomptype &ct, double volt)
	Calculates the full elastic cross section (no aperture). More...

double	elastic_cross_section_integrated (Bcomptype &ct, CTFparam &ctf)
	Integrates the elastic scattering curve up to the aperture cutoff. More...

double	elastic_cross_section (map< string, Bcomptype > &types, double volt)
	Calculates the combined elastic cross section for a defined composition. More...

double	elastic_cross_section_integrated (map< string, Bcomptype > &types, CTFparam &ctf)
	Calculates the combined elastic cross section for a defined composition. More...

double	inelastic_cross_section_langmore (long Z, double volt)
	Calculates the inelastic cross section for an component type. More...

double	inelastic_cross_section_langmore (map< string, Bcomptype > &types, double volt)
	Calculates the combined inelastic cross section for a defined composition. More...

double	cross_section (map< string, Bcomptype > &types, double volt)
	Calculates the combined total cross section for a defined composition. More...

double	cross_section_integrated (map< string, Bcomptype > &types, CTFparam &ctf)
	Calculates the combined total cross section for a defined composition. More...

double	cross_section_half_maximal_frequency (Bcomptype &ct)
	Calculates the half-maximal frequency for a component type. More...

double	cross_section_half_maximal_frequency (map< string, Bcomptype > &at)
	Calculates the half-maximal frequency for an component type. More...

Bmaterial	material_combine (vector< Bmaterial > &mlist, vector< double > fractions)
	Creates a newAssembles a component composition from a set of materials with fractional contributions. More...

Bmaterial	material_ice (map< string, Bcomptype > &types)
	Returns vitreous ice as material. More...

double	effective_mean_free_path (Bmaterial &material, CTFparam &ctf)
	Calculates the average effective mean free path. More...

double	effective_mean_free_path (vector< Bmaterial > &material, vector< double > fractions, CTFparam &ctf)
	Calculates the expected intensity given a thickness of vitreous ice. More...

double	signal_intensity (Bmaterial &material, double thickness, CTFparam &ctf)
	Calculates the expected intensity given a thickness of vitreous ice. More...

vector< double >	signal_intensity (Bmaterial &material, double thick_step, double thick_max, CTFparam &ctf)
	Calculates the expected intensity vs thickness of vitreous ice. More...

int	write_scattering_curves (Bstring &paramfile, Bstring &outfile, Bstring &selection, double resolution)
	Calculates and writes atomic scattering profiles to a file. More...

int	write_potential_curves (Bstring &paramfile, Bstring &outfile, Bstring &selection, double radius)
	Calculates and writes atomic scattering profiles to a file. More...

Detailed Description

Functions for calculating electron scattering profiles.

Author: Bernard Heymann

Date: Created: 20190521; Modified: 20210515

Function Documentation

◆ all_elements()

vector< string > all_elements ( map< string, Bcomptype > & types )

◆ calculate_potential_curves()

map< string, vector< double > > calculate_potential_curves	(	JSvalue &	el,
		map< string, Bcomptype > &	types,
		double	dr,
		double	rmax
	)

Calculates potential profiles for a subset of component types.

Parameters

&el	elements to calculate curves for.
&types	component type.
dr	radius increment.
rmax	maximum radius.

Returns: map<string, vector<double>> array with potential profile.

◆ calculate_scattering_curve()

vector< double > calculate_scattering_curve	(	Bcomptype &	ct,
		double	ds,
		double	scut
	)

Calculates an elastic electron scattering profile for a component type.

Parameters

&ct	component type.
ds	frequency space sampling increment.
scut	maximum spacial frequency.

Returns: vector<double> array with scattering profile.

◆ calculate_scattering_curves() [1/2]

map< string, vector< double > > calculate_scattering_curves	(	JSvalue &	el,
		map< string, Bcomptype > &	types,
		double	ds,
		double	scut
	)

Calculates elastic electron scattering profiles for a subset of component types.

Parameters

&el	elements to calculate curves for.
&types	component type.
ds	frequency space sampling increment.
scut	maximum spacial frequency.

Returns: map<string, vector<double>> array with scattering profile.

◆ calculate_scattering_curves() [2/2]

map< string, vector< double > > calculate_scattering_curves	(	map< string, Bcomptype > &	types,
		double	ds,
		double	scut
	)

◆ cross_section()

double cross_section	(	map< string, Bcomptype > &	types,
		double	volt
	)

Calculates the combined total cross section for a defined composition.

Parameters

&types	component types.
volt	acceleration voltage.

Returns: double integral.

◆ cross_section_half_maximal_frequency() [1/2]

double cross_section_half_maximal_frequency ( Bcomptype & ct )

Calculates the half-maximal frequency for a component type.

Parameters

&ct	component type.

Returns: double half-maximal frequency.

◆ cross_section_half_maximal_frequency() [2/2]

double cross_section_half_maximal_frequency ( map< string, Bcomptype > & types )

Calculates the half-maximal frequency for an component type.

Parameters

&types component types.

Returns: double half-maximal frequency.

◆ cross_section_integrated()

double cross_section_integrated	(	map< string, Bcomptype > &	types,
		CTFparam &	ctf
	)

Calculates the combined total cross section for a defined composition.

Parameters

&types	component types.
&ctf	CTF and microscope parameters.

Returns

double integral.

If the slit width is specified, the energy filter is assumed to be used
and only the elastic cross section is returned.

◆ effective_mean_free_path() [1/2]

double effective_mean_free_path	(	Bmaterial &	material,
		CTFparam &	ctf
	)

Calculates the average effective mean free path.

Parameters

&material	material with types.
&ctf	microscope parameters.

Returns: double EMFP average.

◆ effective_mean_free_path() [2/2]

double effective_mean_free_path	(	vector< Bmaterial > &	materials,
		vector< double >	fractions,
		CTFparam &	ctf
	)

Calculates the expected intensity given a thickness of vitreous ice.

Parameters

&materials	list of materials with types.
&fractions	fractional contributions.
&ctf	microscope parameters.

Returns: double effective mean free path.

◆ elastic_cross_section() [1/2]

double elastic_cross_section	(	Bcomptype &	ct,
		double	volt
	)

Calculates the full elastic cross section (no aperture).

Parameters

&ct	component type.
volt	acceleration voltage.

Returns: double integral.

◆ elastic_cross_section() [2/2]

double elastic_cross_section	(	map< string, Bcomptype > &	types,
		double	volt
	)

Calculates the combined elastic cross section for a defined composition.

Parameters

&types	component types.
volt	acceleration voltage.

Returns: double integral.

◆ elastic_cross_section_integrated() [1/2]

double elastic_cross_section_integrated	(	Bcomptype &	ct,
		CTFparam &	ctf
	)

Integrates the elastic scattering curve up to the aperture cutoff.

Parameters

&ct	component type.
ctf	CTF and microscope parameters.

Returns: double integral.

◆ elastic_cross_section_integrated() [2/2]

double elastic_cross_section_integrated	(	map< string, Bcomptype > &	types,
		CTFparam &	ctf
	)

Calculates the combined elastic cross section for a defined composition.

Parameters

&types	component types.
ctf	CTF and microscope parameters.

Returns: double integral.

◆ inelastic_cross_section_langmore() [1/2]

double inelastic_cross_section_langmore	(	long	Z,
		double	volt
	)

Calculates the inelastic cross section for an component type.

Parameters

Z	atomic number.
volt	acceleration voltage.

Returns: double integral.

◆ inelastic_cross_section_langmore() [2/2]

double inelastic_cross_section_langmore	(	map< string, Bcomptype > &	types,
		double	volt
	)

Calculates the combined inelastic cross section for a defined composition.

Parameters

&types	component types.
volt	acceleration voltage.

Returns: double integral.

◆ material_combine()

Bmaterial material_combine	(	vector< Bmaterial > &	mlist,
		vector< double >	fractions
	)

Creates a newAssembles a component composition from a set of materials with fractional contributions.

Parameters

&mlist	list of materials.
&fractions	fractional contributions.

Returns: Bmaterial new combined material.

◆ material_ice()

Bmaterial material_ice ( map< string, Bcomptype > & types )

Returns vitreous ice as material.

Parameters

types reference parameters.

Returns: double density in molecules/A3.

◆ scatter_curve_integral()

double scatter_curve_integral ( Bcomptype & ct )

Calculates the integral of the whole curve.

Parameters

&ct	component type.

Returns

double integral.

Burge & Smith (1962) formula

◆ signal_intensity() [1/2]

vector< double > signal_intensity	(	Bmaterial &	material,
		double	thick_step,
		double	thick_max,
		CTFparam &	ctf
	)

Calculates the expected intensity vs thickness of vitreous ice.

Parameters

&material	material with types.
thick_step	specimen tickness step size (angstrom).
thick_max	maximum specimen thickness (angstrom).
&ctf	microscope parameters.

Returns: vector<double> array of intensities.

◆ signal_intensity() [2/2]

double signal_intensity	(	Bmaterial &	material,
		double	thickness,
		CTFparam &	ctf
	)

Calculates the expected intensity given a thickness of vitreous ice.

Parameters

&material	material with types.
thickness	specimen thickness.
ctf	microscope parameters.

Returns: double intensity.

◆ write_potential_curves()

int write_potential_curves	(	Bstring &	paramfile,
		Bstring &	outfile,
		Bstring &	selection,
		double	radius
	)

Calculates and writes atomic scattering profiles to a file.

Parameters

&paramfile	file with scattering coefficients.
&outfile	file to write curves to.
&selection	element selection.
radius	maximum radius.

Returns

int 0.

The scattering coefficients are obtained from an input parameter file.

◆ write_scattering_curves()

int write_scattering_curves	(	Bstring &	paramfile,
		Bstring &	outfile,
		Bstring &	selection,
		double	resolution
	)

Calculates and writes atomic scattering profiles to a file.

Parameters

&paramfile	file with scattering coefficients.
&outfile	file to write curves to.
&selection	element selection.
resolution	resolution limit.

Returns

int 0.

The scattering coefficients are obtained from an input parameter file.