scatter.cpp File Reference

Functions for calculating electron scattering profiles. More...

#include "scatter.h"
#include "rwmodel_param.h"

Functions
double	signal_integrated (double emu, double imu, double ke, double ki, int ef)
double	signal_integrated_new (double emu, double imu, double k, int ef)
vector< string >	all_elements (map< string, Bcomptype > &types)
JSvalue	js_all_elements (map< string, Bcomptype > &types)
JSvalue	js_composition (vector< string > &vs)
JSvalue	js_composition (string s)
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...
vector< double >	calculate_potential_curve (Bcomptype &ct, double dr, double rmax)
	Calculates the atomic potential for elastic electron scattering for a component type. 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 > &types)
	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	ice_cross_section (map< string, Bcomptype > &types, double volt)
	Calculates the total cross section for ice up to the aperture cutoff. 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 > &materials, vector< double > fractions, CTFparam &ctf)
	Calculates the expected intensity given a thickness of vitreous ice. More...
double	ice_intensity (map< string, Bcomptype > &types, double thickness, 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...

Variables
int	verbose
auto	string_is_empty

Detailed Description

Functions for calculating electron scattering profiles.

Author

Bernard Heymann

Date

Created: 20190521

Modified: 20210514

Function Documentation

all_elements()

vector< string > all_elements

(

map< string, Bcomptype > &

types

)

calculate_potential_curve()

vector< double > calculate_potential_curve	(	Bcomptype &	ct,
		double	dr,
		double	rmax
	)

Calculates the atomic potential for elastic electron scattering for a component type.

Parameters

&ct	component type.
dr	radius increment.
rmax	maximum radius.

Returns

vector<double> array with potential profile.

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.

ice_cross_section()

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

Calculates the total cross section for ice up to the aperture cutoff.

Parameters

&types	component types.
volt	acceleration voltage.

Returns

double cross section.

ice_intensity()

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

Calculates the expected intensity given a thickness of vitreous ice.

Parameters

thickness	component types.
&types	component types.
ctf	microscope parameters.

Returns

double intensity.

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.

js_all_elements()

JSvalue js_all_elements

(

map< string, Bcomptype > &

types

)

js_composition() [1/2]

JSvalue js_composition

(

string

s

)

js_composition() [2/2]

JSvalue js_composition

(

vector< string > &

vs

)

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_integrated()

double signal_integrated	(	double	emu,
		double	imu,
		double	ke,
		double	ki,
		int	ef
	)

signal_integrated_new()

double signal_integrated_new	(	double	emu,
		double	imu,
		double	k,
		int	ef
	)

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.

Variable Documentation

string_is_empty

auto string_is_empty

Initial value:

= []( const std::string &s )
{
    return s.size() < 1;
}

verbose

int verbose

extern