rwmodel_param.cpp File Reference

Library routines to read and write model dynamics parameters in STAR format. More...

#include "rwmodel_param.h"
#include "rwmodel_star.h"
#include "star.h"
#include "json.h"
#include "model_tags.h"
#include "mol_tags.h"
#include "linked_list.h"
#include "string_util.h"
#include "utilities.h"

Functions
Bmodparam	model_param_generate (Bmodel *model)
	Generates a model parameter file from a model. More...
int	model_param_generate (Bmodparam &md, Bmodel *model)
int	model_param_set_type_indices (Bmodel *model, Bmodparam &md)
	Sets the component type indices from the model parameters. More...
Bstar	read_parameter_file (Bstring &filename)
map< string, Bcomptype >	read_atom_properties (Bstar &star)
map< string, Bcomptype >	read_atom_properties (Bstring &filename)
map< string, Bmaterial >	read_material_star (Bstring &filename)
map< string, Bmaterial >	read_material_json (Bstring &filename)
map< string, Bmaterial >	read_material_properties (Bstring &filename)
int	write_material_star (Bstring &filename, map< string, Bmaterial > material)
int	write_material_json (Bstring &filename, map< string, Bmaterial > material)
int	write_material_properties (Bstring &filename, map< string, Bmaterial > material)
Bmodparam	read_dynamics_parameters (Bstring &filename)
	Reads a model parameter file. More...
int	update_dynamics_parameters (Bmodparam &md, Bstring &filename)
	Updates model parameters from a parameter file. More...
int	write_dynamics_parameters (Bstring &filename, Bmodparam &md)
	Writes a model parameter file. More...

Variables
int	verbose

Detailed Description

Library routines to read and write model dynamics parameters in STAR format.

Author

Bernard Heymann

Date

Created: 20100305

Modified: 20210326

Function Documentation

model_param_generate() [1/2]

Bmodparam model_param_generate

(

Bmodel *

model

)

Generates a model parameter file from a model.

Parameters

*model

linked list of models.

Returns

Bmodparam* new model parameter structure.

All the types in a list of models are collated into a string list of
types for a new model parameter structure.
The distances between component types in the matrix is set to the
smallest such distance between components of the relevant types.
The distance constant is set to 1.
The distance potential type is set to 2 (soft sphere).

model_param_generate() [2/2]

int model_param_generate	(	Bmodparam &	md,
		Bmodel *	model
	)

model_param_set_type_indices()

int model_param_set_type_indices	(	Bmodel *	model,
		Bmodparam &	md
	)

Sets the component type indices from the model parameters.

Parameters

*model	linked list of models.
&md	model parameter structure.

Returns

int 0.

The position of a type in the distance matrix type list determines
the type index within the distance matrix itself.
The indices of the component types within each model is then set
to the corresponding index for the distance matrix.
If the type is not represented in the distance matrix, its index
is set to -1.

read_atom_properties() [1/2]

map< string, Bcomptype > read_atom_properties

(

Bstar &

star

)

read_atom_properties() [2/2]

map< string, Bcomptype > read_atom_properties

(

Bstring &

filename

)

read_dynamics_parameters()

Bmodparam read_dynamics_parameters

(

Bstring &

filename

)

Reads a model parameter file.

Parameters

&filename

file name.

Returns

Bmodparam new model parameter structure.

The only format supported is a STAR format.

read_material_json()

map< string, Bmaterial > read_material_json

(

Bstring &

filename

)

read_material_properties()

map< string, Bmaterial > read_material_properties

(

Bstring &

filename

)

read_material_star()

map< string, Bmaterial > read_material_star

(

Bstring &

filename

)

read_parameter_file()

Bstar read_parameter_file

(

Bstring &

filename

)

update_dynamics_parameters()

int update_dynamics_parameters	(	Bmodparam &	md,
		Bstring &	filename
	)

Updates model parameters from a parameter file.

Parameters

&md	model parameters.
&filename	file name.

Returns

int 0.

The only format supported is a STAR format.

write_dynamics_parameters()

int write_dynamics_parameters	(	Bstring &	filename,
		Bmodparam &	md
	)

Writes a model parameter file.

Parameters

&filename	file name.
&md	model parameter structure.

Returns

int 0.

The only format supported is a STAR format.

write_material_json()

int write_material_json	(	Bstring &	filename,
		map< string, Bmaterial >	material
	)

write_material_properties()

int write_material_properties	(	Bstring &	filename,
		map< string, Bmaterial >	material
	)

write_material_star()

int write_material_star	(	Bstring &	filename,
		map< string, Bmaterial >	material
	)

Variable Documentation

verbose

int verbose

extern