This file contains everything related to particle storage. More...

#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <mpi.h>
#include "utils.h"
#include "particle_data.h"
#include "global.h"
#include "communication.h"
#include "grid.h"
#include "interaction_data.h"
#include "integrate.h"
#include "cells.h"
#include "rotation.h"
#include "virtual_sites.h"

Include dependency graph for particle_data.c:

Go to the source code of this file.

Defines
#define	PART_INCREMENT 8
	granularity of the particle buffers in particles
#define	REQ_SNDRCV_PART 0xaa
	my magic MPI code for send/recv_particles
Functions
int	try_delete_bond (Particle part, int bond)
	Remove bond from particle if possible.
void	try_delete_exclusion (Particle *part, int part2)
	Remove exclusion from particle if possible.
void	try_add_exclusion (Particle *part, int part2)
	Insert an exclusion if not already set.
void	auto_exclusion (int distance)
	Automatically add the next <distance> neighbors in each molecule to the exclusion list.
void	init_particle (Particle *part)
	Initialize a particle.
void	free_particle (Particle *part)
	Deallocate the dynamic storage of a particle.
void	updatePartCfg (int bonds_flag)
	Get the complete unsorted informations on all particles into partCfg if something's changed.
int	sortPartCfg ()
	sorts the partCfg array.
void	freePartCfg ()
	release the partCfg array.
void	realloc_local_particles (int part)
	resize local_particles.
static void	realloc_particle_node (int part)
	resize particle_node.
void	particle_invalidate_part_node ()
	Invalidate particle_node.
void	build_particle_node ()
	Rebuild particle_node from scratch.
void	init_particlelist (ParticleList *pList)
	Initialize a particle list.
int	realloc_particlelist (ParticleList *l, int size)
	Allocate storage for local particles and ghosts.
void	update_local_particles (ParticleList *pl)
	Update the entries in local_particles for all particles in the list pl.
Particle *	got_particle (ParticleList *l, int id)
	Search for a specific particle.
Particle *	append_unindexed_particle (ParticleList l, Particle part)
	Append a particle at the end of a particle List.
Particle *	append_indexed_particle (ParticleList l, Particle part)
	Append a particle at the end of a particle List.
Particle *	move_unindexed_particle (ParticleList dl, ParticleList sl, int i)
	Remove a particle from one particle List and append it to another.
Particle *	move_indexed_particle (ParticleList dl, ParticleList sl, int i)
	Remove a particle from one particle List and append it to another.
int	get_particle_data (int part, Particle *data)
	Get particle data.
int	place_particle (int part, double p[3])
	Call only on the master node.
int	set_particle_v (int part, double v[3])
	Call only on the master node: set particle velocity.
int	set_particle_f (int part, double F[3])
	Call only on the master node: set particle force.
int	set_particle_mass (int part, double mass)
	Call only on the master node: set particle mass.
int	set_particle_rotational_inertia (int part, double rinertia[3])
	Call only on the master node: set particle rotational inertia.
int	set_particle_rotation (int part, int rot)
	Call only on the master node: Specifies whether a particle's rotational degrees of freedom are integrated or not.
int	set_particle_dipm (int part, double dipm)
	Call only on the master node: set particle dipole moment (absolut value).
int	set_particle_dip (int part, double dip[3])
	Call only on the master node: set particle dipole orientation.
int	set_particle_virtual (int part, int isVirtual)
	Call only on the master node: set particle dipole moment (absolut value).
int	set_particle_vs_relative (int part, int vs_relative_to, double vs_distance)
int	set_particle_q (int part, double q)
	Call only on the master node: set particle charge.
int	set_particle_mu_E (int part, double mu_E[3])
	Call only on the master node: set particle electrophoretic mobility.
int	set_particle_type (int part, int type)
	Call only on the master node: set particle type.
int	set_particle_mol_id (int part, int mid)
	Call only on the master node: set particle's molecule id.
int	set_particle_quat (int part, double quat[4])
	Call only on the master node: set particle orientation using quaternions.
int	set_particle_omega_lab (int part, double omega_lab[3])
	Call only on the master node: set particle angular velocity from lab frame.
int	set_particle_omega_body (int part, double omega[3])
	Call only on the master node: set particle angular velocity in body frame.
int	set_particle_torque_lab (int part, double torque_lab[3])
	Call only on the master node: set particle torque from lab frame.
int	set_particle_torque_body (int part, double torque[3])
	Call only on the master node: set particle torque in body frame.
int	set_particle_temperature (int part, double T)
	Call only on the master node: set particle temperature.
int	set_particle_gamma (int part, double gamma)
	Call only on the master node: set particle frictional coefficient.
int	set_particle_ext_torque (int part, int flag, double torque[3])
	Call only on the master node: set particle external torque.
int	set_particle_ext_force (int part, int flag, double force[3])
	Call only on the master node: set particle external force.
int	set_particle_fix (int part, int flag)
	Call only on the master node: set coordinate axes for which the particles motion is fixed.
int	change_particle_bond (int part, int *bond, int delete)
	Call only on the master node: change particle bond.
void	remove_all_particles ()
	remove all particles.
int	remove_particle (int part)
	remove particle with a given identity.
void	local_remove_particle (int part)
	Used by mpi_remove_particle, should not be used elsewhere.
void	local_place_particle (int part, double p[3], int new)
	Used by mpi_place_particle, should not be used elsewhere.
void	local_remove_all_particles ()
	Used by mpi_remove_particle, should not be used elsewhere.
void	local_rescale_particles (int dir, double scale)
	Used by mpi_rescale_particles, should not be used elsewhere.
void	added_particle (int part)
	Used by mpi_place_particle, should not be used elsewhere.
int	local_change_bond (int part, int *bond, int delete)
	Used by mpi_send_bond, should not be used elsewhere.
void	remove_all_bonds_to (int identity)
	for all local particles, remove bonds incorporating the specified particle.
void	local_change_exclusion (int part1, int part2, int delete)
	Used for example by mpi_send_exclusion.
void	send_particles (ParticleList *particles, int node)
	Synchronous send of a particle buffer to another node.
void	recv_particles (ParticleList *particles, int node)
	Synchronous receive of a particle buffer from another node.
void	add_partner (IntList *il, int i, int j, int distance)
int	change_exclusion (int part1, int part2, int delete)
	Call only on the master node: change particle constraints.
void	remove_all_exclusions ()
	remove all exclusions.
int	init_gc (void)
	linked list for particles of a given type
int	init_type_array (int type)
	init particle lists
int	reallocate_type_array (int type)
	resize the array for the list of ids for a certain type
int	remove_id_type_array (int part_id, int type)
int	update_particle_array (int type)
int	reallocate_global_type_list (int size)
	make more type_arrays available
int	find_particle_type (int type, int *id)
int	find_particle_type_id (int type, int id, int in_id)
	return an array with real particle id and the corresponding index of typelist
int	delete_particle_of_type (int type)
	delete one randomly chosen particle of given type returns ES_OK if succesful or else ES_ERROR
int	add_particle_to_list (int part_id, int type)
int	gc_status (int type)
int	free_particle_lists (void)
	free particle lists
int	number_of_particles_with_type (int type, int *number)
Variables
int	max_seen_particle = -1
	Highest particle number seen so far.
int	n_total_particles = 0
	total number of particles on all nodes.
int	max_particle_node = 0
	Capacity of the particle_node / local_particles.
int *	particle_node = NULL
	Used only on master node: particle->node mapping.
int	max_local_particles = 0
Particle **	local_particles = NULL
	id->particle mapping on all nodes.
Particle *	partCfg = NULL
	Particles' current configuration.
int	partCfgSorted = 0
	if non zero, partCfg is sorted by particle order, and the particles are stored consecutively starting with 0.
IntList	partCfg_bl = { NULL, 0, 0 }
	bondlist for partCfg, if bonds are needed

Detailed Description

This file contains everything related to particle storage.

If you want to add a new property to the particles, it is probably a good idea to modify Particle to give scripts access to that property. You always have to modify two positions: first the print section, where you should add your new data at the end, and second the read section where you have to find a nice and short name for your property to appear in the Tcl code. Then you just parse your part out of argc and argv.

The corresponding header file is particle_data.h.

Definition in file particle_data.c.

Define Documentation

#define PART_INCREMENT 8

granularity of the particle buffers in particles

Definition at line 51 of file particle_data.c.

Referenced by realloc_local_particles(), realloc_particle_node(), and realloc_particlelist().

#define REQ_SNDRCV_PART 0xaa

my magic MPI code for send/recv_particles

Definition at line 54 of file particle_data.c.

Referenced by recv_particles(), and send_particles().

Function Documentation

int add_particle_to_list	(	int	part_id,
		int	type
	)

Definition at line 1883 of file particle_data.c.

References ES_ERROR, ES_OK, i, TypeList::id_list, TypeOfIndex::index, Index, max(), TypeOfIndex::max_entry, TypeList::max_entry, NOT_INDEXED, reallocate_type_array(), IndexOfType::type, Type, and type_array.

Referenced by set_particle_type().

void add_partner	(	IntList *	il,
		int	i,
		int	j,
		int	distance
	)

Definition at line 1510 of file particle_data.c.

References distance(), IntList::e, IntList::n, and realloc_intlist().

Referenced by auto_exclusion(), and tclcommand_part_print_bond_partners().

void added_particle ( int part )

Used by mpi_place_particle, should not be used elsewhere.

Called if on a different node a new particle was added.

Parameters:

part	the identity of the particle added

Definition at line 1231 of file particle_data.c.

References i, max_seen_particle, n_total_particles, part, and realloc_local_particles().

Referenced by mpi_place_new_particle(), and mpi_place_new_particle_slave().

Particle* append_indexed_particle	(	ParticleList *	plist,
		Particle *	part
	)

Append a particle at the end of a particle List.

reallocates particles if necessary! This procedure cares for local_particles.

Parameters:

plist	List to append the particle to.
part	Particle to append.

Returns:: Pointer to new location of the particle.

Definition at line 443 of file particle_data.c.

References ParticleProperties::identity, ParticleList::n, Particle::p, ParticleList::part, realloc_particlelist(), and update_local_particles().

Referenced by dd_append_particles().

Particle* append_unindexed_particle	(	ParticleList *	plist,
		Particle *	part
	)

Append a particle at the end of a particle List.

reallocates particles if necessary! This procedure does not care for local_particles.

Parameters:

plist	List to append the particle to.
part	Particle to append.

Returns:: Pointer to new location of the particle.

Definition at line 432 of file particle_data.c.

References ParticleList::n, ParticleList::part, and realloc_particlelist().

Referenced by dd_topology_init(), layered_topology_init(), and nsq_topology_init().

void auto_exclusion ( int distance )

Automatically add the next <distance> neighbors in each molecule to the exclusion list.

This uses the bond topology obtained directly from the particles, since only this contains the full topology, in contrast to topology::topology. To easily setup the bonds, all data should be on a single node, therefore the partCfg array is used. With large amounts of particles, you should avoid this function and setup exclusions manually.

Definition at line 1546 of file particle_data.c.

References add_partner(), Particle::bl, bonded_ia_params, change_exclusion(), distance(), IntList::e, free, i, ia_params, ParticleProperties::identity, init_intlist(), malloc, max_seen_particle, IntList::n, n_total_particles, Bonded_ia_parameters::num, Particle::p, realloc_intlist(), updatePartCfg(), and WITH_BONDS.

Referenced by tclcommand_part().

void build_particle_node ( )

Rebuild particle_node from scratch.

After a simulation step particle_node has to be rebuild since the particles might have gone to a different node.

Definition at line 374 of file particle_data.c.

References max_seen_particle, mpi_who_has(), and realloc_particle_node().

Referenced by change_exclusion(), change_particle_bond(), get_particle_data(), place_particle(), remove_particle(), set_particle_dip(), set_particle_dipm(), set_particle_ext_force(), set_particle_ext_torque(), set_particle_f(), set_particle_fix(), set_particle_gamma(), set_particle_mass(), set_particle_mol_id(), set_particle_mu_E(), set_particle_omega_body(), set_particle_omega_lab(), set_particle_q(), set_particle_quat(), set_particle_rotation(), set_particle_rotational_inertia(), set_particle_temperature(), set_particle_torque_body(), set_particle_torque_lab(), set_particle_type(), set_particle_v(), set_particle_virtual(), set_particle_vs_relative(), tclcommand_part_parse_bond(), tclcommand_part_parse_cmd(), tclcommand_part_parse_exclusion(), tclcommand_part_print_all(), tclcommand_readmd(), and tclcommand_writemd().

int change_exclusion	(	int	part,
		int	part2,
		int	delete
	)

Call only on the master node: change particle constraints.

Parameters:

part	identity of particle for which the exclusion is set.
part2	identity of particle for which the exclusion is set. If -1, delete all exclusions.
delete	if true, do not add the exclusion, rather delete it if found

Returns:: ES_OK on success or ES_ERROR if no success (e. g. particles do not exist / did not have exclusion set)

Definition at line 1524 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_exclusion(), and particle_node.

Referenced by auto_exclusion(), and tclcommand_part_parse_exclusion().

int change_particle_bond	(	int	part,
		int *	bond,
		int	delete
	)

Call only on the master node: change particle bond.

Parameters:

part	identity of principal atom of the bond.
bond	field containing the bond type number and the identity of all bond partners (secundary atoms of the bond). If NULL, delete all bonds.
delete	if true, do not add the bond, rather delete it if found

Returns:: ES_OK on success or ES_ERROR if no success (e. g. particle or bond to delete does not exist)

Definition at line 1040 of file particle_data.c.

References build_particle_node(), ERROR_SPRINTF, ES_ERROR, ES_INTEGER_SPACE, max_seen_particle, mpi_send_bond(), n_bonded_ia, part, particle_node, and runtime_error().

Referenced by crosslinkC(), diamondC(), icosaederC(), polymerC(), and tclcommand_part_parse_bond().

int delete_particle_of_type ( int type )

delete one randomly chosen particle of given type returns ES_OK if succesful or else ES_ERROR

Definition at line 1849 of file particle_data.c.

References ES_ERROR, ES_OK, find_particle_type_id(), Index, malloc, max(), TypeList::max_entry, remove_particle(), IndexOfType::type, and type_array.

Referenced by part_parse_gc().

int find_particle_type	(	int	type,
		int *	id
	)

Definition at line 1794 of file particle_data.c.

References ES_ERROR, ES_OK, i, i_random(), TypeList::id_list, TypeOfIndex::index, Index, TypeOfIndex::max_entry, TypeList::max_entry, IndexOfType::type, Type, and type_array.

Referenced by part_parse_gc().

int find_particle_type_id	(	int	type,
		int *	id,
		int *	in_id
	)

return an array with real particle id and the corresponding index of typelist

Definition at line 1815 of file particle_data.c.

References ES_ERROR, ES_OK, i, i_random(), TypeList::id_list, TypeOfIndex::index, Index, TypeOfIndex::max_entry, TypeList::max_entry, IndexOfType::type, Type, and type_array.

Referenced by delete_particle_of_type().

void free_particle ( Particle * part )

Deallocate the dynamic storage of a particle.

Definition at line 272 of file particle_data.c.

References Particle::bl, Particle::el, and realloc_intlist().

Referenced by local_remove_particle(), send_particles(), tclcommand_analyze_parse_reference_point(), tclcommand_part_parse_print(), tclcommand_writemd(), and tclprint_to_result_Particle().

int free_particle_lists ( void )

free particle lists

Definition at line 1965 of file particle_data.c.

References ES_OK, free, i, TypeOfIndex::index, Index, TypeOfIndex::max_entry, IndexOfType::type, Type, and type_array.

void freePartCfg ( )

release the partCfg array.

Use this function, since it also frees the bonds, if they are used.

Definition at line 332 of file particle_data.c.

References free, and realloc_intlist().

Referenced by on_integration_start(), on_particle_change(), tclcommand_analyze_parse_get_folded_positions(), and updatePartCfg().

int gc_status ( int type )

Definition at line 1945 of file particle_data.c.

References ES_ERROR, ES_OK, i, TypeOfIndex::index, Index, TypeOfIndex::max_entry, TypeList::max_entry, IndexOfType::type, Type, and type_array.

int get_particle_data	(	int	part,
		Particle *	data
	)

Get particle data.

Note that the bond intlist is allocated so that you are responsible to free it later.

Parameters:

part	the identity of the particle to fetch
data	where to store its contents.

Returns:: ES_OK if particle existed

Definition at line 505 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_recv_part(), part, and particle_node.

Referenced by remove_particle(), set_particle_omega_lab(), set_particle_torque_lab(), set_particle_type(), tclcommand_analyze_parse_and_print_check_mol(), tclcommand_analyze_parse_reference_point(), tclcommand_part_parse_print(), tclcommand_writemd(), tclprint_to_result_Particle(), and vs_relate_to().

Particle* got_particle	(	ParticleList *	plist,
		int	id
	)

Search for a specific particle.

Parameters:

plist	the list on which to operate
id	the identity of the particle to search

Returns:: a pointer to the particle structure or NULL if particle is not in this list

Definition at line 420 of file particle_data.c.

References i, ParticleProperties::identity, ParticleList::n, Particle::p, and ParticleList::part.

int init_gc ( void )

linked list for particles of a given type

vars and fields

Definition at line 1622 of file particle_data.c.

References ES_ERROR, ES_OK, GC_init, Index, malloc, IndexOfType::max_entry, TypeOfIndex::max_entry, number_of_type_lists, Type, type_array, and Type_array_init.

Referenced by init_type_array().

void init_particle ( Particle * part )

Initialize a particle.

This function just sets all values to the defaults (mostly zeros)! Do NOT use this without setting the values of the identity and position to reasonable values. Also make sure that you update local_particles.

Add here all initializations you need to be done !!! If dynamic memory allocation is involved, also look at free_particle.

Definition at line 96 of file particle_data.c.

Referenced by local_place_particle().

void init_particlelist ( ParticleList * pList )

Initialize a particle list.

Use with care and ONLY for initialization!

Definition at line 380 of file particle_data.c.

References ParticleList::max, ParticleList::n, and ParticleList::part.

Referenced by dd_exchange_and_sort_particles(), layered_exchange_and_sort_particles(), nsq_balance_particles(), and realloc_cells().

int init_type_array ( int type )

init particle lists

Definition at line 1640 of file particle_data.c.

References TypeList::cur_size, ES_ERROR, ES_OK, i, TypeList::id_list, ParticleProperties::identity, TypeOfIndex::index, Index, init_gc(), malloc, IndexOfType::max_entry, TypeOfIndex::max_entry, TypeList::max_entry, n_total_particles, number_of_type_lists, Particle::p, realloc, reallocate_global_type_list(), IndexOfType::type, Type, type_array, Type_array_init, updatePartCfg(), and WITHOUT_BONDS.

Referenced by number_of_particles_with_type(), and part_parse_gc().

int local_change_bond	(	int	part,
		int *	bond,
		int	delete
	)

Used by mpi_send_bond, should not be used elsewhere.

Modify a bond.

Parameters:

part	the identity of the particle to change
bond	the bond to do
delete	if true, delete the bond instead of add

Returns:: ES_OK for add or successful delete, ES_ERROR else

Definition at line 1246 of file particle_data.c.

References Particle::bl, bonded_ia_params, IntList::e, ES_OK, i, IntList::n, Bonded_ia_parameters::num, part, realloc_intlist(), and try_delete_bond().

Referenced by detect_collision(), handle_collisions(), mpi_send_bond(), and mpi_send_bond_slave().

void local_change_exclusion	(	int	part1,
		int	part2,
		int	delete
	)

Used for example by mpi_send_exclusion.

Locally add a exclusion to a particle.

Parameters:

part1	the identity of the first exclusion partner
part2	the identity of the second exclusion partner
delete	if true, delete the exclusion instead of add

Definition at line 1336 of file particle_data.c.

References CellPList::cell, local_cells, CellPList::n, ParticleList::n, part, ParticleList::part, realloc_intlist(), try_add_exclusion(), and try_delete_exclusion().

Referenced by mpi_send_exclusion(), and mpi_send_exclusion_slave().

void local_place_particle	(	int	part,
		double	p[3],
		int	new
	)

Used by mpi_place_particle, should not be used elsewhere.

Move a particle to a new position. If it does not exist, it is created. the position must be on the local node!

Parameters:

part	the identity of the particle to move
p	its new position
new	if true, the particle is allocated, else has to exists already

Definition at line 1145 of file particle_data.c.

References cell_structure, errexit(), fold_position(), i, ParticleLocal::i, ParticleProperties::identity, init_particle(), Particle::l, ParticleList::n, ParticlePosition::p, Particle::p, ParticlePosition::p_old, part, ParticleList::part, PART_TRACE, CellStructure::position_to_cell, Particle::r, realloc_particlelist(), this_node, and update_local_particles().

Referenced by mpi_place_new_particle(), mpi_place_new_particle_slave(), mpi_place_particle(), and mpi_place_particle_slave().

void local_remove_all_particles ( )

Used by mpi_remove_particle, should not be used elsewhere.

Locally remove all particles.

Definition at line 1191 of file particle_data.c.

References CellPList::cell, i, local_cells, max_seen_particle, CellPList::n, ParticleList::n, n_total_particles, ParticleList::part, and realloc_intlist().

Referenced by mpi_remove_particle_slave().

void local_remove_particle ( int part )

Used by mpi_remove_particle, should not be used elsewhere.

Remove a particle on this node.

Parameters:

part	the identity of the particle to remove

Definition at line 1107 of file particle_data.c.

References CellPList::cell, errexit(), free_particle(), ParticleProperties::identity, local_cells, CellPList::n, ParticleList::n, Particle::p, part, ParticleList::part, and this_node.

Referenced by mpi_remove_particle_slave().

void local_rescale_particles	(	int	dir,
		double	scale
	)

Used by mpi_rescale_particles, should not be used elsewhere.

Locally rescale all particles on current node.

Parameters:

dir	direction to scale (0/1/2 = x/y/z, 3 = x+y+z isotropically)
scale	factor by which to rescale (>1: stretch, <1: contract)

Definition at line 1209 of file particle_data.c.

References CellPList::cell, local_cells, CellPList::n, ParticleList::n, ParticlePosition::p, ParticleList::part, and Particle::r.

Referenced by mpi_rescale_particles(), and mpi_rescale_particles_slave().

Particle* move_indexed_particle	(	ParticleList *	destList,
		ParticleList *	sourceList,
		int	ind
	)

Remove a particle from one particle List and append it to another.

Refill the sourceList with last particle and update its entry in local_particles. Reallocates particles if necessary. This procedure cares for local_particles.

Parameters:

destList	List where the particle is appended.
sourceList	List where the particle will be removed.
ind	Index of the particle in the sourceList.

Returns:: Pointer to new location of the particle.

Definition at line 476 of file particle_data.c.

References i, ParticleProperties::identity, ParticleList::n, Particle::p, ParticleList::part, realloc_particlelist(), and update_local_particles().

Referenced by dd_exchange_and_sort_particles(), layered_append_particles(), and layered_exchange_and_sort_particles().

Particle* move_unindexed_particle	(	ParticleList *	destList,
		ParticleList *	sourceList,
		int	ind
	)

Remove a particle from one particle List and append it to another.

Refill the sourceList with last particle and update its entry in local_particles. reallocates particles if necessary. This procedure does not care for local_particles. NOT IN USE AT THE MOMENT.

Parameters:

destList	List where the particle is appended.
sourceList	List where the particle will be removed.
ind	Index of the particle in the sourceList.

Returns:: Pointer to new location of the particle.

Definition at line 460 of file particle_data.c.

References i, ParticleList::n, ParticleList::part, and realloc_particlelist().

int number_of_particles_with_type	(	int	type,
		int *	number
	)

Definition at line 1979 of file particle_data.c.

References ES_OK, i, TypeOfIndex::index, Index, init_type_array(), TypeOfIndex::max_entry, TypeList::max_entry, NOT_INDEXED, IndexOfType::type, Type, and type_array.

Referenced by part_parse_gc().

void particle_invalidate_part_node ( )

Invalidate particle_node.

This has to be done at the beginning of the integration.

Definition at line 364 of file particle_data.c.

References free, max_particle_node, and particle_node.

Referenced by cells_re_init(), and cells_resort_particles().

int place_particle	(	int	part,
		double	p[3]
	)

Call only on the master node.

Move a particle to a new position. If it does not exist, it is created.

Parameters:

part	the identity of the particle to move
p	its new position

Returns:: ES_PART_OK if particle existed, ES_PART_CREATED if created and ES_PART_ERROR if id is illegal

Definition at line 521 of file particle_data.c.

References build_particle_node(), cell_structure, ES_PART_CREATED, ES_PART_ERROR, ES_PART_OK, i, max_seen_particle, mpi_place_new_particle(), mpi_place_particle(), part, particle_node, CellStructure::position_to_node, and realloc_particle_node().

Referenced by analyze_activate(), counterionsC(), diamondC(), handle_collisions(), icosaederC(), polymerC(), saltC(), tclcommand_part_parse_pos(), and tclcommand_readmd().

void realloc_local_particles ( int part )

resize local_particles.

Parameters:

part	the highest existing particle

Definition at line 342 of file particle_data.c.

References max_local_particles, PART_INCREMENT, and realloc.

Referenced by added_particle().

static void realloc_particle_node ( int part ) [static]

resize particle_node.

This procedure is only used on the master node in Tcl mode.

Parameters:

part	the highest existing particle

Definition at line 355 of file particle_data.c.

References max_particle_node, PART_INCREMENT, particle_node, and realloc.

Referenced by build_particle_node(), place_particle(), and remove_all_particles().

int realloc_particlelist	(	ParticleList *	plist,
		int	size
	)

Allocate storage for local particles and ghosts.

This version does not care for the bond information to be freed if necessary.

Parameters:

plist	the list on which to operate
size	the size to provide at least. It is rounded up to multiples of PART_INCREMENT.

Returns:: true iff particle adresses have changed

Definition at line 387 of file particle_data.c.

References max(), ParticleList::max, ParticleList::n, ParticleList::part, PART_INCREMENT, PART_TRACE, realloc, and this_node.

Referenced by append_indexed_particle(), append_unindexed_particle(), cell_cell_transfer(), cells_re_init(), dd_exchange_and_sort_particles(), layered_exchange_and_sort_particles(), local_place_particle(), move_indexed_particle(), move_unindexed_particle(), nsq_balance_particles(), put_recv_buffer(), realloc_cells(), recv_particles(), and send_particles().

int reallocate_global_type_list ( int size )

make more type_arrays available

Definition at line 1783 of file particle_data.c.

References ES_ERROR, ES_OK, number_of_type_lists, realloc, and type_array.

Referenced by init_type_array().

int reallocate_type_array ( int type )

resize the array for the list of ids for a certain type

Definition at line 1708 of file particle_data.c.

References TypeList::cur_size, ES_ERROR, ES_OK, TypeList::id_list, Index, realloc, IndexOfType::type, and type_array.

Referenced by add_particle_to_list(), and update_particle_array().

void recv_particles	(	ParticleList *	particles,
		int	node
	)

Synchronous receive of a particle buffer from another node.

The other node MUST call send_particles when this is called. The particles are APPENDED to the list, so it has to be a valid one

Definition at line 1444 of file particle_data.c.

References alloc_intlist(), Particle::bl, comm_cart, IntList::e, Particle::el, errexit(), ParticleProperties::identity, init_intlist(), MPI_BYTE, MPI_INT, MPI_Recv(), MPI_STATUS_IGNORE, IntList::n, ParticleList::n, Particle::p, ParticleList::part, PART_TRACE, realloc_intlist(), realloc_particlelist(), REQ_SNDRCV_PART, this_node, and update_local_particles().

Referenced by dd_exchange_and_sort_particles(), layered_exchange_and_sort_particles(), and nsq_balance_particles().

void remove_all_bonds_to ( int part )

for all local particles, remove bonds incorporating the specified particle.

Parameters:

part	identity of the particle to free from bonds

Definition at line 1298 of file particle_data.c.

References Particle::bl, bonded_ia_params, CellPList::cell, IntList::e, errexit(), i, local_cells, IntList::n, CellPList::n, ParticleList::n, Bonded_ia_parameters::num, part, ParticleList::part, realloc_intlist(), and this_node.

Referenced by mpi_remove_particle_slave().

void remove_all_exclusions ( )

remove all exclusions.

Definition at line 1540 of file particle_data.c.

References mpi_send_exclusion().

Referenced by tclcommand_part().

void remove_all_particles ( )

remove all particles.

Definition at line 1065 of file particle_data.c.

References mpi_remove_particle(), and realloc_particle_node().

Referenced by tclcommand_part().

int remove_id_type_array	(	int	part_id,
		int	type
	)

Definition at line 1717 of file particle_data.c.

References ES_OK, i, TypeList::id_list, TypeOfIndex::index, Index, max(), TypeOfIndex::max_entry, TypeList::max_entry, IndexOfType::type, Type, and type_array.

Referenced by remove_particle(), and set_particle_type().

int remove_particle ( int part )

remove particle with a given identity.

Also removes all bonds to the particle.

Parameters:

part	identity of the particle to remove

Returns:: ES_OK on success or ES_ERROR if particle does not exist

Definition at line 1071 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, FIELD_MAXPART, free, get_particle_data(), malloc, max_seen_particle, mpi_bcast_parameter(), mpi_remove_particle(), Particle::p, part, particle_node, remove_id_type_array(), and ParticleProperties::type.

Referenced by delete_particle_of_type(), and tclcommand_part_parse_delete().

void send_particles	(	ParticleList *	particles,
		int	node
	)

Synchronous send of a particle buffer to another node.

The other node MUST call recv_particles when this is called. The particles data is freed.

Definition at line 1400 of file particle_data.c.

References Particle::bl, comm_cart, IntList::e, Particle::el, free_particle(), ParticleProperties::identity, init_intlist(), MPI_BYTE, MPI_INT, MPI_Send(), IntList::n, ParticleList::n, Particle::p, ParticleList::part, PART_TRACE, realloc_intlist(), realloc_particlelist(), REQ_SNDRCV_PART, and this_node.

Referenced by dd_exchange_and_sort_particles(), layered_exchange_and_sort_particles(), and nsq_balance_particles().

int set_particle_dip	(	int	part,
		double	dip[3]
	)

Call only on the master node: set particle dipole orientation.

Parameters:

part	the particle.
dip	its new dipole orientation.

Returns:: ES_OK if particle existed

Definition at line 669 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_dip(), part, and particle_node.

Referenced by tclcommand_part_parse_dip(), and tclcommand_readmd().

int set_particle_dipm	(	int	part,
		double	dipm
	)

Call only on the master node: set particle dipole moment (absolut value).

Parameters:

part	the particle.
dipm	its new dipole moment.

Returns:: ES_OK if particle existed

Definition at line 653 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_dipm(), part, and particle_node.

Referenced by tclcommand_part_parse_dipm().

int set_particle_ext_force	(	int	part,
		int	flag,
		double	force[3]
	)

Call only on the master node: set particle external force.

Parameters:

part	the particle.
flag	new value for ext_flag.
force	new value for ext_force.

Returns:: ES_OK if particle existed

Definition at line 1005 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_ext_force(), part, PARTICLE_EXT_FORCE, and particle_node.

Referenced by tclcommand_part_parse_ext_force().

int set_particle_ext_torque	(	int	part,
		int	flag,
		double	torque[3]
	)

Call only on the master node: set particle external torque.

Parameters:

part	the particle.
flag	new value for ext_flag.
torque	new value for ext_torque.

Returns:: ES_OK if particle existed

Definition at line 987 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_ext_torque(), part, PARTICLE_EXT_TORQUE, and particle_node.

Referenced by tclcommand_part_parse_ext_torque().

int set_particle_f	(	int	part,
		double	F[3]
	)

Call only on the master node: set particle force.

Parameters:

part	the particle.
F	its new force.

Returns:: ES_OK if particle existed

Definition at line 581 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_f(), part, and particle_node.

Referenced by tclcommand_part_parse_f(), and tclcommand_readmd().

int set_particle_fix	(	int	part,
		int	flag
	)

Call only on the master node: set coordinate axes for which the particles motion is fixed.

Parameters:

part	the particle.
flag	new value for flagged coordinate axes to be fixed

Returns:: ES_OK if particle existed

Definition at line 1022 of file particle_data.c.

References build_particle_node(), COORDS_FIX_MASK, ES_ERROR, ES_OK, max_seen_particle, mpi_send_ext_force(), part, and particle_node.

Referenced by tclcommand_part_parse_fix(), and tclcommand_part_parse_unfix().

int set_particle_gamma	(	int	part,
		double	gamma
	)

Call only on the master node: set particle frictional coefficient.

Parameters:

part	the particle.
gamma	its new frictional coefficient.

Returns:: ES_OK if particle existed

Definition at line 965 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_set_particle_gamma(), part, and particle_node.

Referenced by part_parse_gamma().

int set_particle_mass	(	int	part,
		double	mass
	)

Call only on the master node: set particle mass.

Parameters:

part	the particle.
mass	its new mass.

Returns:: ES_OK if particle existed

Definition at line 598 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_mass(), part, and particle_node.

Referenced by tclcommand_part_parse_mass(), and tclcommand_readmd().

int set_particle_mol_id	(	int	part,
		int	mid
	)

Call only on the master node: set particle's molecule id.

Parameters:

part	the particle.
mid	its new mol id.

Returns:: ES_OK if particle existed

Definition at line 810 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_mol_id(), part, and particle_node.

Referenced by tclcommand_part_parse_mol_id().

int set_particle_mu_E	(	int	part,
		double	mu_E[3]
	)

Call only on the master node: set particle electrophoretic mobility.

Parameters:

part	the particle.
mu_E	its new mobility.

Returns:: ES_OK if particle existed

Definition at line 745 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_mu_E(), part, and particle_node.

Referenced by tclcommand_part_parse_mu_E().

int set_particle_omega_body	(	int	part,
		double	omega[3]
	)

Call only on the master node: set particle angular velocity in body frame.

Parameters:

part	the particle.
omega	its new angular velocity.

Returns:: ES_OK if particle existed

Definition at line 875 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_omega(), part, and particle_node.

Referenced by tclcommand_part_parse_omega_body().

int set_particle_omega_lab	(	int	part,
		double	omega[3]
	)

Call only on the master node: set particle angular velocity from lab frame.

Parameters:

part	the particle.
omega	its new angular velocity.

Returns:: ES_OK if particle existed

Definition at line 844 of file particle_data.c.

References build_particle_node(), define_rotation_matrix(), ES_ERROR, ES_OK, get_particle_data(), max_seen_particle, mpi_send_omega(), part, and particle_node.

Referenced by tclcommand_part_parse_omega_lab().

int set_particle_q	(	int	part,
		double	q
	)

Call only on the master node: set particle charge.

Parameters:

part	the particle.
q	its new charge.

Returns:: ES_OK if particle existed

Definition at line 728 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_q(), part, and particle_node.

Referenced by counterionsC(), diamondC(), icosaederC(), polymerC(), saltC(), tclcommand_part_parse_q(), and tclcommand_readmd().

int set_particle_quat	(	int	part,
		double	quat[4]
	)

Call only on the master node: set particle orientation using quaternions.

Parameters:

part	the particle.
quat	its new value for quaternions.

Returns:: ES_OK if particle existed

Definition at line 828 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_quat(), part, and particle_node.

Referenced by tclcommand_part_parse_quat(), and vs_relate_to().

int set_particle_rotation	(	int	part,
		int	rot
	)

Call only on the master node: Specifies whether a particle's rotational degrees of freedom are integrated or not.

If set to zero, the content of the torque and omega variables are meaningless

Parameters:

part	the particle.
rot	the degrees of freedom flag.

Returns:: ES_OK if particle existed

Definition at line 635 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_rotation(), part, and particle_node.

Referenced by tclcommand_part_parse_rotation().

int set_particle_rotational_inertia	(	int	part,
		double	rinertia[3]
	)

Call only on the master node: set particle rotational inertia.

Parameters:

part	the particle.
rinertia	its new inertia.

Returns:: ES_OK if particle existed

Definition at line 616 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_rotational_inertia(), part, and particle_node.

Referenced by tclcommand_part_parse_rotational_inertia().

int set_particle_temperature	(	int	part,
		double	T
	)

Call only on the master node: set particle temperature.

Parameters:

part	the particle.
T	its new temperature.

Returns:: ES_OK if particle existed

Definition at line 947 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_set_particle_temperature(), part, and particle_node.

Referenced by part_parse_temp().

int set_particle_torque_body	(	int	part,
		double	torque[3]
	)

Call only on the master node: set particle torque in body frame.

Parameters:

part	the particle.
torque	its new torque.

Returns:: ES_OK if particle existed

Definition at line 925 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_torque(), part, and particle_node.

Referenced by tclcommand_part_parse_torque_body().

int set_particle_torque_lab	(	int	part,
		double	torque[3]
	)

Call only on the master node: set particle torque from lab frame.

Parameters:

part	the particle.
torque	its new torque.

Returns:: ES_OK if particle existed

Definition at line 894 of file particle_data.c.

References build_particle_node(), define_rotation_matrix(), ES_ERROR, ES_OK, get_particle_data(), max_seen_particle, mpi_send_torque(), part, and particle_node.

Referenced by tclcommand_part_parse_torque_lab().

int set_particle_type	(	int	part,
		int	type
	)

Call only on the master node: set particle type.

Parameters:

part	the particle.
type	its new type.

Returns:: ES_OK if particle existed

Definition at line 762 of file particle_data.c.

References add_particle_to_list(), build_particle_node(), ES_ERROR, ES_OK, free, get_particle_data(), make_particle_type_exist(), malloc, max_seen_particle, mpi_send_type(), Particle::p, part, particle_node, remove_id_type_array(), ParticleProperties::type, and Type_array_init.

Referenced by counterionsC(), diamondC(), icosaederC(), polymerC(), saltC(), tclcommand_part_parse_type(), and tclcommand_readmd().

int set_particle_v	(	int	part,
		double	v[3]
	)

Call only on the master node: set particle velocity.

Parameters:

part	the particle.
v	its new velocity.

Returns:: ES_OK if particle existed

Definition at line 565 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_v(), part, and particle_node.

Referenced by maxwell_velocitiesC(), tclcommand_part_parse_v(), tclcommand_readmd(), and velocitiesC().

int set_particle_virtual	(	int	part,
		int	isVirtual
	)

Call only on the master node: set particle dipole moment (absolut value).

Parameters:

part	the particle.
isVirtual	its new dipole moment.

Returns:: ES_OK if particle existed

Definition at line 690 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_virtual(), part, and particle_node.

Referenced by tclcommand_part_parse_virtual().

int set_particle_vs_relative	(	int	part,
		int	vs_relative_to,
		double	vs_distance
	)

Definition at line 708 of file particle_data.c.

References build_particle_node(), ES_ERROR, ES_OK, max_seen_particle, mpi_send_vs_relative(), part, and particle_node.

Referenced by part_parse_vs_relative(), and vs_relate_to().

int sortPartCfg ( )

sorts the partCfg array.

This is indicated by setting partCfgSorted to 1. Note that for this to work the particles have to be stored consecutively starting with 0. This function is lazy.

Returns:: 1 iff sorting was possible, i. e. the particles were stored consecutively.

Definition at line 307 of file particle_data.c.

References free, i, malloc, max_seen_particle, n_total_particles, partCfgSorted, updatePartCfg(), and WITHOUT_BONDS.

void try_add_exclusion	(	Particle *	part,
		int	part2
	)

Insert an exclusion if not already set.

Definition at line 1373 of file particle_data.c.

References IntList::e, Particle::el, i, IntList::n, and realloc_intlist().

Referenced by local_change_exclusion().

int try_delete_bond	(	Particle *	part,
		int *	bond
	)

Remove bond from particle if possible.

Definition at line 1265 of file particle_data.c.

References Particle::bl, bonded_ia_params, IntList::e, ES_ERROR, ES_OK, i, IntList::n, Bonded_ia_parameters::num, and realloc_intlist().

Referenced by local_change_bond().

void try_delete_exclusion	(	Particle *	part,
		int	part2
	)

Remove exclusion from particle if possible.

Definition at line 1384 of file particle_data.c.

References IntList::e, Particle::el, i, IntList::n, and realloc_intlist().

Referenced by local_change_exclusion().

void update_local_particles ( ParticleList * pl )

Update the entries in local_particles for all particles in the list pl.

Parameters:

pl	the list to put in.

Definition at line 412 of file particle_data.c.

References i, ParticleList::n, and ParticleList::part.

Referenced by append_indexed_particle(), dd_topology_init(), layered_topology_init(), local_place_particle(), move_indexed_particle(), nsq_balance_particles(), nsq_topology_init(), and recv_particles().

int update_particle_array ( int type )

Definition at line 1761 of file particle_data.c.

References TypeList::cur_size, ES_ERROR, ES_OK, i, TypeList::id_list, ParticleProperties::identity, Index, TypeList::max_entry, n_total_particles, Particle::p, reallocate_type_array(), IndexOfType::type, type_array, updatePartCfg(), and WITHOUT_BONDS.

void updatePartCfg ( int bonds_flag )

Get the complete unsorted informations on all particles into partCfg if something's changed.

This is a severe performance drawback and might even fail for lack of memory for large systems. If you need the particle info sorted, call sortPartCfg instead. This function is lazy. If you would like the bonding information in partCfg to be valid you should set the value of to WITH_BONDS.

Definition at line 284 of file particle_data.c.

References freePartCfg(), ParticleLocal::i, Particle::l, malloc, mpi_get_particles(), n_total_particles, Particle::p, partCfgSorted, sortPartCfg(), unfold_position(), update_mol_pos_cfg(), and WITH_BONDS.

Variable Documentation

Particle** local_particles = NULL

id->particle mapping on all nodes.

This is used to find partners of bonded interactions.

Definition at line 65 of file particle_data.c.

Referenced by add_area_global_force(), add_bonded_energy(), add_bonded_force(), add_bonded_virials(), add_ljangle_pair_force(), add_three_body_bonded_stress(), add_volume_force(), calc_area_global(), calc_mol_pos(), calc_mol_vel(), calc_volume(), check_particle_consistency(), check_particles(), compute_pos_corr_vec(), compute_vel_corr_vec(), dd_exchange_and_sort_particles(), detect_collision(), force_and_velocity_display(), get_mol_com_particle(), handle_collisions(), init_local_particle_force(), invalidate_ghosts(), ljangle_pair_energy(), local_stress_tensor_calc(), mpi_recv_part(), mpi_recv_part_slave(), mpi_send_dip(), mpi_send_dip_slave(), mpi_send_dipm(), mpi_send_dipm_slave(), mpi_send_ext_force(), mpi_send_ext_force_slave(), mpi_send_ext_torque(), mpi_send_ext_torque_slave(), mpi_send_f(), mpi_send_f_slave(), mpi_send_mass(), mpi_send_mass_slave(), mpi_send_mol_id(), mpi_send_mol_id_slave(), mpi_send_mu_E(), mpi_send_mu_E_slave(), mpi_send_omega(), mpi_send_omega_slave(), mpi_send_q(), mpi_send_q_slave(), mpi_send_quat(), mpi_send_quat_slave(), mpi_send_rotation(), mpi_send_rotation_slave(), mpi_send_rotational_inertia(), mpi_send_rotational_inertia_slave(), mpi_send_torque(), mpi_send_torque_slave(), mpi_send_type(), mpi_send_type_slave(), mpi_send_v(), mpi_send_v_slave(), mpi_send_virtual(), mpi_send_virtual_slave(), mpi_send_vs_relative(), mpi_send_vs_relative_slave(), mpi_set_particle_gamma(), mpi_set_particle_gamma_slave(), mpi_set_particle_temperature(), mpi_set_particle_temperature_slave(), nemd_change_momentum(), nemd_get_velocity(), print_bond_len(), put_mol_force_on_parts(), put_recv_buffer(), sync_topo_part_info(), and vs_relative_get_real_particle().

int max_local_particles = 0

Definition at line 64 of file particle_data.c.

Referenced by realloc_local_particles().

int max_particle_node = 0

Capacity of the particle_node / local_particles.

Definition at line 62 of file particle_data.c.

Referenced by particle_invalidate_part_node(), and realloc_particle_node().

int max_seen_particle = -1

Highest particle number seen so far.

If you leave out some particle numbers, this number might be higher than the true number of particles. On the other hand, if you start your particle numbers at 0, the total number of particles is larger by 1.

Definition at line 60 of file particle_data.c.

Referenced by added_particle(), auto_exclusion(), build_particle_node(), change_exclusion(), change_particle_bond(), check_particle_consistency(), check_particles(), get_particle_data(), handle_collisions(), local_remove_all_particles(), mpi_who_has(), place_particle(), remove_particle(), set_particle_dip(), set_particle_dipm(), set_particle_ext_force(), set_particle_ext_torque(), set_particle_f(), set_particle_fix(), set_particle_gamma(), set_particle_mass(), set_particle_mol_id(), set_particle_mu_E(), set_particle_omega_body(), set_particle_omega_lab(), set_particle_q(), set_particle_quat(), set_particle_rotation(), set_particle_rotational_inertia(), set_particle_temperature(), set_particle_torque_body(), set_particle_torque_lab(), set_particle_type(), set_particle_v(), set_particle_virtual(), set_particle_vs_relative(), sortPartCfg(), tclcommand_imd_parse_pos(), tclcommand_metadynamics_parse_distance(), tclcommand_metadynamics_parse_relative_z(), tclcommand_part_parse_bond(), tclcommand_part_parse_print(), tclcommand_part_print_all(), tclcommand_part_print_bond_partners(), tclcommand_readmd(), and tclcommand_writemd().