/home/pedro/work/mdcore/src/engine_bonded.c File Reference

#include <stdlib.h>
#include <stdio.h>
#include <pthread.h>
#include <math.h>
#include <float.h>
#include <string.h>
#include "../config.h"
#include <omp.h>
#include "cycle.h"
#include "errs.h"
#include "fptype.h"
#include "lock.h"
#include "part.h"
#include "cell.h"
#include "fifo.h"
#include "space.h"
#include "potential.h"
#include "runner.h"
#include "bond.h"
#include "rigid.h"
#include "angle.h"
#include "dihedral.h"
#include "exclusion.h"
#include "reader.h"
#include "engine.h"

Defines
#define	error(id)   ( engine_err = errs_register( id , engine_err_msg[-(id)] , __LINE__ , __FUNCTION__ , __FILE__ ) )
Functions
int	engine_bonded_eval_sets (struct engine *e)
	Compute all bonded interactions stored in this engine.
int	engine_bonded_sets (struct engine *e, int max_sets)
	Assemble non-conflicting sets of bonded interactions.
int	engine_dihedral_add (struct engine *e, int i, int j, int k, int l, int pid)
	Add a dihedral interaction to the engine.
int	engine_angle_add (struct engine *e, int i, int j, int k, int pid)
	Add a angle interaction to the engine.
int	engine_exclusion_shrink (struct engine *e)
	Remove duplicate exclusions.
int	engine_exclusion_add (struct engine *e, int i, int j)
	Add a exclusioned interaction to the engine.
int	engine_bond_add (struct engine *e, int i, int j)
	Add a bonded interaction to the engine.
int	engine_bonded_eval (struct engine *e)
	Compute all bonded interactions stored in this engine.
int	engine_bonded_eval_alt (struct engine *e)
	Compute all bonded interactions stored in this engine.
int	engine_dihedral_eval (struct engine *e)
	Compute the dihedral interactions stored in this engine.
int	engine_angle_eval (struct engine *e)
	Compute the angled interactions stored in this engine.
int	engine_exclusion_eval (struct engine *e)
	Correct for the excluded interactions stored in this engine.
int	engine_bond_eval (struct engine *e)
	Compute the bonded interactions stored in this engine.
int	engine_bond_addpot (struct engine *e, struct potential *p, int i, int j)
	Add a bond potential.
int	engine_dihedral_addpot (struct engine *e, struct potential *p)
	Add a dihedral potential.
int	engine_angle_addpot (struct engine *e, struct potential *p)
	Add a angle potential.

---

Define Documentation

#define error

(

id

)

( engine_err = errs_register( id , engine_err_msg[-(id)] , __LINE__ , __FUNCTION__ , __FILE__ ) )

---

Function Documentation

int engine_angle_add	(	struct engine *	e,
		int	i,
		int	j,
		int	k,
		int	pid
	)

Add a angle interaction to the engine.

Parameters:

e	The engine.
i	The ID of the first part.
j	The ID of the second part.
k	The ID of the third part.
pid	Index of the potential for this bond.

Returns:

engine_err_ok or < 0 on error (see engine_err).

int engine_angle_addpot	(	struct engine *	e,
		struct potential *	p
	)

Add a angle potential.

Parameters:

e	The engine.
p	The potential to add to the engine.

Returns:

The ID of the added angle potential or < 0 on error (see engine_err).

int engine_angle_eval

(

struct engine *

e

)

Compute the angled interactions stored in this engine.

Parameters:

e	The engine.

Returns:

engine_err_ok or < 0 on error (see engine_err).

int engine_bond_add	(	struct engine *	e,
		int	i,
		int	j
	)

Add a bonded interaction to the engine.

Parameters:

e	The engine.
i	The ID of the first part.
j	The ID of the second part.

Returns:

engine_err_ok or < 0 on error (see engine_err).

int engine_bond_addpot	(	struct engine *	e,
		struct potential *	p,
		int	i,
		int	j
	)

Add a bond potential.

Parameters:

e	The engine.
p	The potential to add to the engine.
i	ID of particle type for this interaction.
j	ID of second particle type for this interaction.

Returns:

engine_err_ok or < 0 on error (see engine_err).

Adds the given bonded potential for pairs of particles of type i and j, where i and j may be the same type ID.

int engine_bond_eval

(

struct engine *

e

)

Compute the bonded interactions stored in this engine.

Parameters:

e	The engine.

Returns:

engine_err_ok or < 0 on error (see engine_err).

int engine_bonded_eval

(

struct engine *

e

)

Compute all bonded interactions stored in this engine.

Parameters:

e	The engine.

Returns:

engine_err_ok or < 0 on error (see engine_err).

Does the same as engine_bond_eval, engine_angle_eval and #engine_dihedral eval, yet all in one go to avoid excessive updates of the particle forces.

int engine_bonded_eval_alt

(

struct engine *

e

)

Compute all bonded interactions stored in this engine.

Parameters:

e	The engine.

Returns:

engine_err_ok or < 0 on error (see engine_err).

Does the same as engine_bond_eval, engine_angle_eval and #engine_dihedral eval, yet all in one go to avoid excessive updates of the particle forces.

int engine_bonded_eval_sets

(

struct engine *

e

)

Compute all bonded interactions stored in this engine.

Parameters:

e	The engine.

Returns:

engine_err_ok or < 0 on error (see engine_err).

Does the same as engine_bond_eval, engine_angle_eval and #engine_dihedral eval, yet all in one go to avoid excessive updates of the particle forces.

int engine_bonded_sets	(	struct engine *	e,
		int	max_sets
	)

Assemble non-conflicting sets of bonded interactions.

Parameters:

e	The engine.

Returns:

engine_err_ok or < 0 on error (see engine_err).

int engine_dihedral_add	(	struct engine *	e,
		int	i,
		int	j,
		int	k,
		int	l,
		int	pid
	)

Add a dihedral interaction to the engine.

Parameters:

e	The engine.
i	The ID of the first part.
j	The ID of the second part.
k	The ID of the third part.
l	The ID of the fourth part.
pid	Index of the potential for this bond.

Returns:

engine_err_ok or < 0 on error (see engine_err).

int engine_dihedral_addpot	(	struct engine *	e,
		struct potential *	p
	)

Add a dihedral potential.

Parameters:

e	The engine.
p	The potential to add to the engine.

Returns:

The ID of the added dihedral potential or < 0 on error (see engine_err).

int engine_dihedral_eval

(

struct engine *

e

)

Compute the dihedral interactions stored in this engine.

Parameters:

e	The engine.

Returns:

engine_err_ok or < 0 on error (see engine_err).

int engine_exclusion_add	(	struct engine *	e,
		int	i,
		int	j
	)

Add a exclusioned interaction to the engine.

Parameters:

e	The engine.
i	The ID of the first part.
j	The ID of the second part.

Returns:

engine_err_ok or < 0 on error (see engine_err).

int engine_exclusion_eval

(

struct engine *

e

)

Correct for the excluded interactions stored in this engine.

Parameters:

e	The engine.

Returns:

engine_err_ok or < 0 on error (see engine_err).

int engine_exclusion_shrink

(

struct engine *

e

)

Remove duplicate exclusions.

Parameters:

e	The engine.

Returns:

The number of unique exclusions or < 0 on error (see engine_err).