Data Structures
struct	engine
struct	engine_set
struct	engine_comm
Defines
#define	engine_err_ok 0
#define	engine_err_null -1
#define	engine_err_malloc -2
#define	engine_err_space -3
#define	engine_err_pthread -4
#define	engine_err_runner -5
#define	engine_err_range -6
#define	engine_err_cell -7
#define	engine_err_domain -8
#define	engine_err_nompi -9
#define	engine_err_mpi -10
#define	engine_err_bond -11
#define	engine_err_angle -12
#define	engine_err_reader -13
#define	engine_err_psf -14
#define	engine_err_pdb -15
#define	engine_err_cpf -16
#define	engine_err_potential -17
#define	engine_err_exclusion -18
#define	engine_err_sets -19
#define	engine_err_dihedral -20
#define	engine_err_cuda -21
#define	engine_err_nocuda -22
#define	engine_err_cudasp -23
#define	engine_err_maxparts -24
#define	engine_err_queue -25
#define	engine_flag_none 0
#define	engine_flag_tuples 1
#define	engine_flag_static 2
#define	engine_flag_localparts 4
#define	engine_flag_cuda 8
#define	engine_flag_explepot 16
#define	engine_flag_verlet 32
#define	engine_flag_verlet_pairwise 64
#define	engine_flag_affinity 128
#define	engine_flag_prefetch 256
#define	engine_flag_verlet_pseudo 512
#define	engine_flag_unsorted 2048
#define	engine_flag_mpi 4096
#define	engine_flag_parbonded 8192
#define	engine_flag_async 16384
#define	engine_flag_sets 32768
#define	engine_flag_nullpart 65536
#define	engine_flag_dispatch 131072
#define	engine_bonds_chunk 100
#define	engine_angles_chunk 100
#define	engine_rigids_chunk 50
#define	engine_dihedrals_chunk 100
#define	engine_exclusions_chunk 100
#define	engine_bonded_maxnrthreads 16
#define	engine_bonded_nrthreads ((omp_get_num_threads()<engine_bonded_maxnrthreads)?omp_get_num_threads():engine_bonded_maxnrthreads)
Enumerations
enum	{ engine_timer_step = 0, engine_timer_prepare, engine_timer_verlet, engine_timer_exchange1, engine_timer_nonbond, engine_timer_bonded, engine_timer_bonded_sort, engine_timer_bonds, engine_timer_angles, engine_timer_dihedrals, engine_timer_exclusions, engine_timer_advance, engine_timer_rigid, engine_timer_exchange2, engine_timer_shuffle, engine_timer_cuda_load, engine_timer_cuda_unload, engine_timer_cuda_dopairs, engine_timer_last }
Functions
int	engine_addpot (struct engine e, struct potential p, int i, int j)
	Add an interaction potential.
int	engine_addtype (struct engine e, double mass, double charge, char name, char *name2)
	Add a type definition.
int	engine_advance (struct engine *e)
	Update the particle velocities and positions, re-shuffle if appropriate.
int	engine_angle_addpot (struct engine e, struct potential p)
	Add a angle potential.
int	engine_angle_add (struct engine *e, int i, int j, int k, int pid)
	Add a angle interaction to the engine.
int	engine_angle_eval (struct engine *e)
	Compute the angled interactions stored in this engine.
int	engine_barrier (struct engine *e)
	Barrier routine to hold the `runners` back.
int	engine_bond_addpot (struct engine e, struct potential p, int i, int j)
	Add a bond potential.
int	engine_bond_add (struct engine *e, int i, int j)
	Add a bonded interaction to the engine.
int	engine_bond_eval (struct engine *e)
	Compute the bonded interactions stored in this engine.
int	engine_bonded_eval (struct engine *e)
	Compute all bonded interactions stored in this engine.
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_dihedral_addpot (struct engine e, struct potential p)
	Add a dihedral potential.
int	engine_dihedral_eval (struct engine *e)
	Compute the dihedral interactions stored in this engine.
int	engine_dump_PSF (struct engine e, FILE psf, FILE pdb, char excl[], int nr_excl)
	Dump the contents of the enginge to a PSF and PDB file.
int	engine_exclusion_add (struct engine *e, int i, int j)
	Add a exclusioned interaction to the engine.
int	engine_exclusion_eval (struct engine *e)
	Correct for the excluded interactions stored in this engine.
int	engine_exclusion_shrink (struct engine *e)
	Remove duplicate exclusions.
int	engine_finalize (struct engine *e)
	Initialize an engine with the given data and MPI enabled.
int	engine_flush_ghosts (struct engine *e)
	Clear all particles from this engine's ghost cells.
int	engine_flush (struct engine *e)
	Clear all particles from this engine.
int	engine_gettype (struct engine e, char name)
	Look for a given type by name.
int	engine_gettype2 (struct engine e, char name2)
	Look for a given type by its second name.
int	engine_init (struct engine e, const double origin, const double dim, double L, double cutoff, unsigned int period, int max_type, unsigned int flags)
	Initialize an engine with the given data.
int	engine_load_ghosts (struct engine e, double x, double v, int type, int pid, int vid, double q, unsigned int flags, int N)
	Load a set of particle data as ghosts.
int	engine_load (struct engine e, double x, double v, int type, int pid, int vid, double charge, unsigned int flags, int N)
	Load a set of particle data.
int	engine_nonbond_eval (struct engine *e)
	Compute the nonbonded interactions in the current step.
int	engine_read_cpf (struct engine e, FILE cpf, double kappa, double tol, int rigidH)
	Read the potentials from a CHARMM parameter file.
int	engine_read_psf (struct engine e, FILE psf, FILE *pdb)
	Read the simulation setup from a PSF and PDB file pair.
int	engine_read_xplor (struct engine e, FILE xplor, double kappa, double tol, int rigidH)
	Read the potentials from a XPLOR parameter file.
int	engine_rigid_add (struct engine *e, int pid, int pjd, double d)
	Add a rigid constraint to the engine.
int	engine_rigid_eval (struct engine *e)
	Resolve the constraints.
int	engine_rigid_sort (struct engine *e)
	Split the rigids into local, semilocal and non-local.
int	engine_rigid_unsort (struct engine *e)
	Shuffle the rigid constraints randomly.
int	engine_setexplepot (struct engine e, struct potential ep)
	Set the explicit electrostatic potential.
int	engine_shuffle (struct engine *e)
	Re-shuffle the particles in the engine.
int	engine_split_bisect (struct engine *e, int N)
	Split the computational domain over a number of nodes using bisection.
int	engine_split (struct engine *e)
	Set-up the engine for distributed-memory parallel operation.
int	engine_start_SPU (struct engine *e, int nr_runners)
	Start the SPU-associated runners in the given engine.
int	engine_start (struct engine *e, int nr_runners, int nr_queues)
	Start the runners in the given engine.
int	engine_step (struct engine *e)
	Run the engine for a single time step.
int	engine_timers_reset (struct engine *e)
	Set all the engine timers to 0.
int	engine_unload_marked (struct engine e, double x, double v, int type, int pid, int vid, double q, unsigned int flags, double *epot, int N)
	Unload a set of particle data from the marked cells of an engine.
int	engine_unload_strays (struct engine e, double x, double v, int type, int pid, int vid, double q, unsigned int flags, double *epot, int N)
	Unload real particles that may have wandered into a ghost cell.
int	engine_unload (struct engine e, double x, double v, int type, int pid, int vid, double charge, unsigned int flags, double *epot, int N)
	Unload a set of particle data from the engine.
int	engine_verlet_update (struct engine *e)
	Check if the Verlet-list needs to be updated.
Variables
int	engine_err
char *	engine_err_msg []

Define Documentation

#define engine_angles_chunk 100

#define engine_bonded_maxnrthreads 16

#define engine_bonded_nrthreads ((omp_get_num_threads()<engine_bonded_maxnrthreads)?omp_get_num_threads():engine_bonded_maxnrthreads)

#define engine_bonds_chunk 100

#define engine_dihedrals_chunk 100

#define engine_err_angle -12

#define engine_err_bond -11

#define engine_err_cell -7

#define engine_err_cpf -16

#define engine_err_cuda -21

#define engine_err_cudasp -23

#define engine_err_dihedral -20

#define engine_err_domain -8

#define engine_err_exclusion -18

#define engine_err_malloc -2

#define engine_err_maxparts -24

#define engine_err_mpi -10

#define engine_err_nocuda -22

#define engine_err_nompi -9

#define engine_err_null -1

#define engine_err_ok 0

#define engine_err_pdb -15

#define engine_err_potential -17

#define engine_err_psf -14

#define engine_err_pthread -4

#define engine_err_queue -25

#define engine_err_range -6

#define engine_err_reader -13

#define engine_err_runner -5

#define engine_err_sets -19

#define engine_err_space -3

#define engine_exclusions_chunk 100

#define engine_flag_affinity 128

#define engine_flag_async 16384

#define engine_flag_cuda 8

#define engine_flag_dispatch 131072

#define engine_flag_explepot 16

#define engine_flag_localparts 4

#define engine_flag_mpi 4096

#define engine_flag_none 0

#define engine_flag_nullpart 65536

#define engine_flag_parbonded 8192

#define engine_flag_prefetch 256

#define engine_flag_sets 32768

#define engine_flag_static 2

#define engine_flag_tuples 1

#define engine_flag_unsorted 2048

#define engine_flag_verlet 32

#define engine_flag_verlet_pairwise 64

#define engine_flag_verlet_pseudo 512

#define engine_rigids_chunk 50

Enumeration Type Documentation

anonymous enum

Timer IDs.

Enumerator:

engine_timer_step
engine_timer_prepare
engine_timer_verlet
engine_timer_exchange1
engine_timer_nonbond
engine_timer_bonded
engine_timer_bonded_sort
engine_timer_bonds
engine_timer_angles
engine_timer_dihedrals
engine_timer_exclusions
engine_timer_advance
engine_timer_rigid
engine_timer_exchange2
engine_timer_shuffle
engine_timer_cuda_load
engine_timer_cuda_unload
engine_timer_cuda_dopairs
engine_timer_last

Function Documentation

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

Add an interaction 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 potential for pairs of particles of type i and j, where i and j may be the same type ID.

int engine_addtype	(	struct engine *	e,
		double	mass,
		double	charge,
		char *	name,
		char *	name2
	)

Add a type definition.

Parameters:

e	The engine.
mass	The particle type mass.
charge	The particle type charge.
name	Particle name, can be `NULL`.
name2	Particle second name, can be `NULL`.

Returns:: The type ID or < 0 on error (see engine_err).

The particle type ID must be an integer greater or equal to 0 and less than the value max_type specified in engine_init.

int engine_advance ( struct engine * e )

Update the particle velocities and positions, re-shuffle if appropriate.

Parameters:

e	The engine on which to run.

Returns:: engine_err_ok or < 0 on error (see engine_err).

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_barrier ( struct engine * e )

Barrier routine to hold the runners back.

Parameters:

e	The engine to wait on.

Returns:: engine_err_ok or < 0 on error (see engine_err).

After being initialized, and after every timestep, every runner calls this routine which blocks until all the runners have returned and the engine signals the next timestep.

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_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_dump_PSF	(	struct engine *	e,
		FILE *	psf,
		FILE *	pdb,
		char *	excl[],
		int	nr_excl
	)

Dump the contents of the enginge to a PSF and PDB file.

Parameters:

e	The engine.
psf	A pointer to `FILE` to which to write the PSF file.
pdb	A pointer to `FILE` to which to write the PDB file.

If any of psf or pdb are NULL, the respective output will not be generated.

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).

int engine_finalize ( struct engine * e )

Initialize an engine with the given data and MPI enabled.

Parameters:

e	The engine to initialize.
origin	An array of three doubles containing the cartesian origin of the space.
dim	An array of three doubles containing the size of the space.
L	The minimum cell edge length, should be at least `cutoff`.
cutoff	The maximum interaction cutoff to use.
period	A bitmask describing the periodicity of the domain (see space_periodic_full).
max_type	The maximum number of particle types that will be used by this engine.
flags	Bit-mask containing the flags for this engine.
comm	The MPI comm to use.
rank	The ID of this node.

Returns:: engine_err_ok or < 0 on error (see engine_err). Kill all runners and de-allocate the data of an engine.

Parameters:

e	the engine to finalize.

Returns:: engine_err_ok or < 0 on error (see engine_err).

int engine_flush ( struct engine * e )

Clear all particles from this engine.

Parameters:

e	The engine to flush.

Returns:: engine_err_ok or < 0 on error (see engine_err).

int engine_flush_ghosts ( struct engine * e )

Clear all particles from this engine's ghost cells.

Parameters:

e	The engine to flush.

Returns:: engine_err_ok or < 0 on error (see engine_err).

int engine_gettype	(	struct engine *	e,
		char *	name
	)

Look for a given type by name.

Parameters:

e	The engine.
name	The type name.

Returns:: The type ID or < 0 on error (see engine_err).

int engine_gettype2	(	struct engine *	e,
		char *	name2
	)

Look for a given type by its second name.

Parameters:

e	The engine.
name2	The type name2.

Returns:: The type ID or < 0 on error (see engine_err).

int engine_init	(	struct engine *	e,
		const double *	origin,
		const double *	dim,
		double *	L,
		double	cutoff,
		unsigned int	period,
		int	max_type,
		unsigned int	flags
	)

Initialize an engine with the given data.

Parameters:

e	The engine to initialize.
origin	An array of three doubles containing the cartesian origin of the space.
dim	An array of three doubles containing the size of the space.
L	The minimum cell edge length in each dimension.
cutoff	The maximum interaction cutoff to use.
period	A bitmask describing the periodicity of the domain (see space_periodic_full).
max_type	The maximum number of particle types that will be used by this engine.
flags	Bit-mask containing the flags for this engine.

Returns:: engine_err_ok or < 0 on error (see engine_err).

int engine_load	(	struct engine *	e,
		double *	x,
		double *	v,
		int *	type,
		int *	pid,
		int *	vid,
		double *	q,
		unsigned int *	flags,
		int	N
	)

Load a set of particle data.

Parameters:

e	The engine.
x	An `N` times 3 array of the particle positions.
v	An `N` times 3 array of the particle velocities.
type	A vector of length `N` of the particle type IDs.
pid	A vector of length `N` of the particle IDs.
vid	A vector of length `N` of the particle virtual IDs.
q	A vector of length `N` of the individual particle charges.
flags	A vector of length `N` of the particle flags.
N	the number of particles to load.

Returns:: engine_err_ok or < 0 on error (see engine_err).

If the parameters v, flags, vid or q are NULL, then these values are set to zero.

int engine_load_ghosts	(	struct engine *	e,
		double *	x,
		double *	v,
		int *	type,
		int *	pid,
		int *	vid,
		double *	q,
		unsigned int *	flags,
		int	N
	)

Load a set of particle data as ghosts.

Parameters:

e	The engine.
x	An `N` times 3 array of the particle positions.
v	An `N` times 3 array of the particle velocities.
type	A vector of length `N` of the particle type IDs.
pid	A vector of length `N` of the particle IDs.
vid	A vector of length `N` of the particle virtual IDs.
q	A vector of length `N` of the individual particle charges.
flags	A vector of length `N` of the particle flags.
N	the number of particles to load.

Returns:: engine_err_ok or < 0 on error (see engine_err).

If the parameters v, flags, vid or q are NULL, then these values are set to zero.

int engine_nonbond_eval ( struct engine * e )

Compute the nonbonded interactions in the current step.

Parameters:

e	The engine on which to run.

Returns:: engine_err_ok or < 0 on error (see engine_err).

This routine advances the timestep counter by one, prepares the space for a timestep, releases the runner's associated with the engine and waits for them to finnish.

int engine_read_cpf	(	struct engine *	e,
		FILE *	cpf,
		double	kappa,
		double	tol,
		int	rigidH
	)

Read the potentials from a CHARMM parameter file.

Parameters:

e	The engine.
cpf	The open CHARMM parameter file.
kappa	The PME screening width.
tol	The absolute tolerance for interpolation.
rigidH	Convert all bonds over a type starting with 'H' to a rigid constraint.

If kappa is zero, truncated Coulomb electrostatic interactions are assumed. If kappa is less than zero, no electrostatic interactions are computed.

Returns:: engine_err_ok or < 0 on error (see engine_err).

int engine_read_psf	(	struct engine *	e,
		FILE *	psf,
		FILE *	pdb
	)

Read the simulation setup from a PSF and PDB file pair.

Parameters:

e	The engine.
psf	The open PSF file.
pdb	The open PDB file.

Returns:: engine_err_ok or < 0 on error (see engine_err).

int engine_read_xplor	(	struct engine *	e,
		FILE *	xplor,
		double	kappa,
		double	tol,
		int	rigidH
	)

Read the potentials from a XPLOR parameter file.

Parameters:

e	The engine.
xplor	The open XPLOR parameter file.
kappa	The PME screening width.
tol	The absolute tolerance for interpolation.
rigidH	Convert all bonds over a type starting with 'H' to a rigid constraint.

If kappa is zero, truncated Coulomb electrostatic interactions are assumed. If kappa is less than zero, no electrostatic interactions are computed.

Returns:: engine_err_ok or < 0 on error (see engine_err).

int engine_rigid_add	(	struct engine *	e,
		int	pid,
		int	pjd,
		double	d
	)

Add a rigid constraint to the engine.

Parameters:

e	The engine.
pid	The ID of the first part.
pjd	The ID of the second part.

Returns:: The index of the rigid constraint or < 0 on error (see engine_err).

Beware that currently all particles have to have been inserted before the rigid constraints are added!

int engine_rigid_eval ( struct engine * e )

Resolve the constraints.

Parameters:

e	The engine.

Returns:: engine_err_ok or < 0 on error (see engine_err).

Note that if in parallel, engine_rigid_sort should be called before this routine.

int engine_rigid_sort ( struct engine * e )

Split the rigids into local, semilocal and non-local.

Parameters:

e	The engine.

Returns:: engine_err_ok or < 0 on error (see engine_err).

int engine_rigid_unsort ( struct engine * e )

Shuffle the rigid constraints randomly.

Parameters:

e	The engine.

Returns:: engine_err_ok or < 0 on error (see engine_err).

int engine_setexplepot	(	struct engine *	e,
		struct potential *	ep
	)

Set the explicit electrostatic potential.

Parameters:

e	The engine.
ep	The electrostatic potential.

Returns:: engine_err_ok or < 0 on error (see engine_err).

If ep is not NULL, the flag engine_flag_explepot is set, otherwise it is cleared.

int engine_shuffle ( struct engine * e )

Re-shuffle the particles in the engine.

Parameters:

e	The engine on which to run.

Returns:: engine_err_ok or < 0 on error (see engine_err).

int engine_split ( struct engine * e )

Set-up the engine for distributed-memory parallel operation.

Parameters:

e	The engine to set-up.

Returns:: engine_err_ok or < 0 on error (see engine_err).

This function assumes that engine_split_bisect or some similar function has already been called and that #nodeID, #nr_nodes as well as the cell nodeIDs have been set.

int engine_split_bisect	(	struct engine *	e,
		int	N
	)

Split the computational domain over a number of nodes using bisection.

Parameters:

e	The engine to split up.
N	The number of computational nodes.

Returns:: engine_err_ok or < 0 on error (see engine_err).

int engine_start	(	struct engine *	e,
		int	nr_runners,
		int	nr_queues
	)

Start the runners in the given engine.

Parameters:

e	The engine to start.
nr_runners	The number of runners start.

Returns:: engine_err_ok or < 0 on error (see engine_err).

Allocates and starts the specified number of runner. Also initializes the Verlet lists.

int engine_start_SPU	(	struct engine *	e,
		int	nr_runners
	)

Start the SPU-associated runners in the given engine.

Parameters:

e	The engine to start.
nr_runners	The number of runners start.

Returns:: engine_err_ok or < 0 on error (see engine_err).

Allocates and starts the specified number of runner.

int engine_step ( struct engine * e )

Run the engine for a single time step.

Parameters:

e	The engine on which to run.

Returns:: engine_err_ok or < 0 on error (see engine_err).

This routine advances the timestep counter by one, prepares the space for a timestep, releases the runner's associated with the engine and waits for them to finnish.

Once all the runner's are done, the particle velocities and positions are updated and the particles are re-sorted in the space.

int engine_timers_reset ( struct engine * e )

Set all the engine timers to 0.

Parameters:

e	The engine.

Returns:: engine_err_ok or < 0 on error (see engine_err).

int engine_unload	(	struct engine *	e,
		double *	x,
		double *	v,
		int *	type,
		int *	pid,
		int *	vid,
		double *	q,
		unsigned int *	flags,
		double *	epot,
		int	N
	)

Unload a set of particle data from the engine.

Parameters:

e	The engine.
x	An `N` times 3 array of the particle positions.
v	An `N` times 3 array of the particle velocities.
type	A vector of length `N` of the particle type IDs.
pid	A vector of length `N` of the particle IDs.
vid	A vector of length `N` of the particle virtual IDs.
q	A vector of length `N` of the individual particle charges.
flags	A vector of length `N` of the particle flags.
epot	A pointer to a #double in which to store the total potential energy.
N	the maximum number of particles.

Returns:: The number of particles unloaded or < 0 on error (see engine_err).

The fields x, v, type, pid, vid, q, epot and/or flags may be NULL.

int engine_unload_marked	(	struct engine *	e,
		double *	x,
		double *	v,
		int *	type,
		int *	pid,
		int *	vid,
		double *	q,
		unsigned int *	flags,
		double *	epot,
		int	N
	)

Unload a set of particle data from the marked cells of an engine.

Parameters:

e	The engine.
x	An `N` times 3 array of the particle positions.
v	An `N` times 3 array of the particle velocities.
type	A vector of length `N` of the particle type IDs.
pid	A vector of length `N` of the particle IDs.
vid	A vector of length `N` of the particle virtual IDs.
q	A vector of length `N` of the individual particle charges.
flags	A vector of length `N` of the particle flags.
epot	A pointer to a #double in which to store the total potential energy.
N	the maximum number of particles.

Returns:: The number of particles unloaded or < 0 on error (see engine_err).

The fields x, v, type, pid, vid, q, epot and/or flags may be NULL.

int engine_unload_strays	(	struct engine *	e,
		double *	x,
		double *	v,
		int *	type,
		int *	pid,
		int *	vid,
		double *	q,
		unsigned int *	flags,
		double *	epot,
		int	N
	)

Unload real particles that may have wandered into a ghost cell.

Parameters:

e	The engine.
x	An `N` times 3 array of the particle positions.
v	An `N` times 3 array of the particle velocities.
type	A vector of length `N` of the particle type IDs.
pid	A vector of length `N` of the particle IDs.
vid	A vector of length `N` of the particle virtual IDs.
q	A vector of length `N` of the individual particle charges.
flags	A vector of length `N` of the particle flags.
epot	A pointer to a #double in which to store the total potential energy.
N	the maximum number of particles.

Returns:: The number of particles unloaded or < 0 on error (see engine_err).

The fields x, v, type, vid, pid, q, epot and/or flags may be NULL.

int engine_verlet_update ( struct engine * e )

Check if the Verlet-list needs to be updated.

Parameters:

e	The engine.

Returns:: engine_err_ok or < 0 on error (see engine_err).

Variable Documentation

int engine_err

ID of the last error.

char* engine_err_msg[]

List of error messages.

Data Structures

Defines

Enumerations

Functions

Variables

Define Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation