mol_bonds.h File Reference

Header for molecular dynamics. More...

#include "rwmd.h"
#include "rwmolecule.h"
#include "mol_util.h"
#include "utilities.h"

Functions
Bbond *	md_generate_bond_list (Bmolgroup *molgroup, Bmd *md)
	Generates a distance-based bond list. More...
Bbond *	md_generate_molecular_bond_list (Bmolgroup *molgroup, Bmd *md)
	Generates an intramolecular distance-based bond list. More...
Bbond *	md_generate_bond_list_with_valence (Bmolgroup *molgroup, Bmd *md, int valence)
	Generates a bond list based on a single valence and the shortest current bond lengths. More...
double	md_bond_list_set_parameters (Bbond *bondlist, Bbondtype *bondtype)
	Assigns covalent bond lengths to bonds. More...
int	md_show_bonds (Bmolgroup *molgroup)
	Shows the bonds and bond lengths. More...
int	md_show_bond_stats (Bmolgroup *molgroup)
	Shows the number of bonds and the valency per atom. More...
double	md_find_bond_length (Batom *atom1, Batom *atom2, Bbondtype *bondtype)
	Finds the reference covalent bond length. More...
Bbondtype *	md_find_bond_type (Batom *atom1, Batom *atom2, Bbondtype *bondtype)
	Finds the bond type. More...
int	md_show_bond_types (Bmolgroup *molgroup, Bbondtype *bondtype)
	Shows the bond type composition. More...
double	md_angle (Batom *atom1, Batom *atom2, Batom *atom3)
	Calculates the angle between three atoms. More...
double	md_calculate_deviations (Bmolgroup *molgroup, int wrap)
	Calculates deviations from the reference bond lengths and angles. More...
int	md_calculate_radial_deviation (Bmolgroup *molgroup)
	Calculates the radial deviations from the center of the box. More...

Detailed Description

Header for molecular dynamics.

Author

Bernard Heymann

Date

Created: 20010828

Modified: 20180228

Function Documentation

md_angle()

double md_angle	(	Batom *	atom1,
		Batom *	atom2,
		Batom *	atom3
	)

Calculates the angle between three atoms.

Parameters

*atom1	first atom.
*atom2	second atom.
*atom3	third atom.

Returns

double angle.

The angle associated with the second atom and between the bonds linking
the first and third atoms is calculated.

md_bond_list_set_parameters()

double md_bond_list_set_parameters	(	Bbond *	bondlist,
		Bbondtype *	bondtype
	)

Assigns covalent bond lengths to bonds.

Parameters

*bondlist	list of bonds.
*bondtype	list of bond types.

Returns

double fraction of bond types found.

The bond lengths are taken from a bond type list.

md_calculate_deviations()

double md_calculate_deviations	(	Bmolgroup *	molgroup,
		int	wrap
	)

Calculates deviations from the reference bond lengths and angles.

Parameters

*molgroup	molecule group.
wrap	flag to wrap around periodic boundaries.

Returns

double angle.

md_calculate_radial_deviation()

int md_calculate_radial_deviation

(

Bmolgroup *

molgroup

)

Calculates the radial deviations from the center of the box.

Parameters

*molgroup

molecule group.

Returns

double angle.

md_find_bond_length()

double md_find_bond_length	(	Batom *	atom1,
		Batom *	atom2,
		Bbondtype *	bondtype
	)

Finds the reference covalent bond length.

Parameters

*atom1	first atom.
*atom2	second atom.
*bondtype	bond type list.

Returns

double bond length.

The bond type is found in the bond type list, and the bond length is
set from the bond type structure.

md_find_bond_type()

Bbondtype * md_find_bond_type	(	Batom *	atom1,
		Batom *	atom2,
		Bbondtype *	bondtype
	)

Finds the bond type.

Parameters

*atom1	first atom.
*atom2	second atom.
*bondtype	bond type list.

Returns

Bbondtype* bond type structure.

The bond type is found in the bond type list.

md_generate_bond_list()

Bbond * md_generate_bond_list	(	Bmolgroup *	molgroup,
		Bmd *	md
	)

Generates a distance-based bond list.

Parameters

*molgroup	molecule group structure.
*md	global molecular dynamics structure.

Returns

Bbond* new bond list.

This function assumes very little and defines bonds purely on distance.
This means that the bond distances must already have been defined well.
The bond length is defined in the molecular dynamics structure.
If the molecule group already has a bond list, no new bonds are generated. 

md_generate_bond_list_with_valence()

Bbond * md_generate_bond_list_with_valence	(	Bmolgroup *	molgroup,
		Bmd *	md,
		int	valence
	)

Generates a bond list based on a single valence and the shortest current bond lengths.

Parameters

*molgroup	molecule group structure.
*md	global molecular dynamics structure.
valence	atom valence.

Returns

Bbond* new bond list.

This function attempts to assign bonds based on atomic valence by
finding the top number of shortests bonds. The current bond length is
encoded in the bond strength variable, k, in the bond structure.

md_generate_molecular_bond_list()

Bbond * md_generate_molecular_bond_list	(	Bmolgroup *	molgroup,
		Bmd *	md
	)

Generates an intramolecular distance-based bond list.

Parameters

*molgroup	molecule group structure.
*md	global molecular dynamics structure.

Returns

Bbond* new bond list.

This function defines bonds on distance and within molecules.
This means that the bond distances must already have been defined well.
The bond length is defined in the molecular dynamics structure.
If the molecule group already has a bond list, no new bonds are generated. 

md_show_bond_stats()

int md_show_bond_stats

(

Bmolgroup *

molgroup

)

Shows the number of bonds and the valency per atom.

Parameters

*molgroup

molecule group.

Returns

int number of bonds.

Uses the bond list defined for the molecule group.

md_show_bond_types()

int md_show_bond_types	(	Bmolgroup *	molgroup,
		Bbondtype *	bondtype
	)

Shows the bond type composition.

Parameters

*molgroup	molecule group.
*bondtype	bond type list.

Returns

int 0.

For each bond, the bond type is found in the bond type list.
The number variable for each bond type is used for counting.

md_show_bonds()

int md_show_bonds

(

Bmolgroup *

molgroup

)

Shows the bonds and bond lengths.

Parameters

*molgroup

molecule group.

Returns

int number of bonds.

Uses the bond list defined for the molecule group.