rattle.c File Reference

#include <mpi.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "domain_decomposition.h"
#include "rattle.h"

Include dependency graph for rattle.c:

Go to the source code of this file.

Functions
void	save_old_pos ()
	Transfers the current particle positions from r.p[3] to r.p_pold[3] of the Particle structure.
void	init_correction_vector ()
	Initialize the correction vector.
void	correct_pos_shake ()
	Propagate velocity and position while using SHAKE algorithm for bond constraint.
void	correct_vel_shake ()
	Correction of current velocities using RATTLE algorithm.
int	rigid_bond_set_params (int bond_type, double d, double p_tol, double v_tol)
	set the parameter for a rigid, aka RATTLE bond
Private functions
void	compute_pos_corr_vec (int *repeat_)
	Calculates the corrections required for each of the particle coordinates according to the RATTLE algorithm.
void	app_pos_correction ()
	Positional Corrections are added to the current particle positions.
void	transfer_force_init_vel ()
	Transfers temporarily the current forces from f.f[3] of the Particle structure to r.p_old[3] location and also intializes velocity correction vector.
void	compute_vel_corr_vec (int *repeat_)
	Calculates corrections of the current particle velocities according to RATTLE algorithm.
void	apply_vel_corr ()
	Velocity corrections are added to the current particle velocities.
void	revert_force ()
	Invoked from correct_vel_shake().
void	print_bond_len ()
	For debugging purpose--prints the bond lengths between particles that have rigid_bonds.
Variables
int	n_rigidbonds = 0
	number of rigid bonds

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Function Documentation

void app_pos_correction

(

)

Positional Corrections are added to the current particle positions.

Apply corrections to each particle.

Invoked from correct_pos_shake()

Completed for one particle

Definition at line 185 of file rattle.c.

References CellPList::cell, ParticleForce::f, Particle::f, i, local_cells, Particle::m, CellPList::n, ParticleList::n, ParticlePosition::p, ParticleList::part, Particle::r, and ParticleMomentum::v.

Referenced by correct_pos_shake().

void apply_vel_corr

(

)

Velocity corrections are added to the current particle velocities.

Apply velocity corrections.

Invoked from correct_vel_shake()

Completed for one particle

Definition at line 336 of file rattle.c.

References CellPList::cell, ParticleForce::f, Particle::f, i, local_cells, Particle::m, CellPList::n, ParticleList::n, ParticleList::part, and ParticleMomentum::v.

Referenced by correct_vel_shake().

void compute_pos_corr_vec

(

int *

repeat_

)

Calculates the corrections required for each of the particle coordinates according to the RATTLE algorithm.

Compute positional corrections.

Invoked from correct_pos_shake()

Definition at line 129 of file rattle.c.

References Particle::bl, bonded_ia_params, BONDED_IA_RIGID_BOND, CellPList::cell, IntList::e, ERROR_SPRINTF, ES_INTEGER_SPACE, ParticleForce::f, Particle::f, get_mi_vector(), i, ia_params, ParticleProperties::identity, local_cells, local_particles, CellPList::n, ParticleList::n, Bonded_ia_parameters::num, ParticlePosition::p, Particle::p, Bonded_ia_parameters::p, ParticlePosition::p_old, ParticleList::part, PMASS, Particle::r, Bonded_ia_parameters::rigid_bond, runtime_error(), scalar(), sqrlen(), and Bonded_ia_parameters::type.

Referenced by correct_pos_shake().

void compute_vel_corr_vec

(

int *

repeat_

)

Calculates corrections of the current particle velocities according to RATTLE algorithm.

Velocity correction vectors are computed.

Invoked from correct_vel_shake()

Definition at line 280 of file rattle.c.

References Particle::bl, bonded_ia_params, BONDED_IA_RIGID_BOND, CellPList::cell, IntList::e, ERROR_SPRINTF, ES_INTEGER_SPACE, ParticleForce::f, Particle::f, get_mi_vector(), i, ia_params, ParticleProperties::identity, local_cells, local_particles, Particle::m, CellPList::n, ParticleList::n, Bonded_ia_parameters::num, ParticlePosition::p, Particle::p, Bonded_ia_parameters::p, ParticleList::part, PMASS, Particle::r, Bonded_ia_parameters::rigid_bond, runtime_error(), scalar(), Bonded_ia_parameters::type, ParticleMomentum::v, and vecsub().

Referenced by correct_vel_shake().

void correct_pos_shake

(

)

Propagate velocity and position while using SHAKE algorithm for bond constraint.

Ghost Positions Update

Definition at line 210 of file rattle.c.

References app_pos_correction(), cell_structure, check_resort_particles(), CellStructure::collect_ghost_force_comm, comm_cart, compute_pos_corr_vec(), ERROR_SPRINTF, ES_INTEGER_SPACE, ghost_communicator(), init_correction_vector(), MPI_Bcast(), MPI_INT, MPI_Reduce(), MPI_SUM, runtime_error(), SHAKE_MAX_ITERATIONS, this_node, and CellStructure::update_ghost_pos_comm.

Referenced by integrate_vv().

void correct_vel_shake

(

)

Correction of current velocities using RATTLE algorithm.

transfer the current forces to r.p_old of the particle structure so that velocity corrections can be stored temporarily at the f.f[3] of the particle structure

Puts back the forces from r.p_old to f.f[3]

Definition at line 393 of file rattle.c.

References apply_vel_corr(), cell_structure, CellStructure::collect_ghost_force_comm, comm_cart, compute_vel_corr_vec(), errexit(), ghost_communicator(), init_correction_vector(), MPI_Bcast(), MPI_INT, MPI_Reduce(), MPI_SUM, revert_force(), SHAKE_MAX_ITERATIONS, this_node, transfer_force_init_vel(), and CellStructure::update_ghost_pos_comm.

Referenced by integrate_vv().

void init_correction_vector

(

)

Initialize the correction vector.

The correction vector is stored in f.f of particle strcuture.

Definition at line 98 of file rattle.c.

References CellPList::cell, Particle::f, ghost_cells, i, local_cells, CellPList::n, ParticleList::n, and ParticleList::part.

Referenced by correct_pos_shake(), and correct_vel_shake().

void print_bond_len

(

)

For debugging purpose--prints the bond lengths between particles that have rigid_bonds.

Definition at line 426 of file rattle.c.

References Particle::bl, bonded_ia_params, BONDED_IA_RIGID_BOND, CellPList::cell, IntList::e, ERROR_SPRINTF, ES_INTEGER_SPACE, get_mi_vector(), i, ParticleProperties::identity, local_cells, local_particles, CellPList::n, ParticleList::n, Bonded_ia_parameters::num, ParticlePosition::p, Particle::p, ParticleList::part, Particle::r, runtime_error(), sqrlen(), this_node, and Bonded_ia_parameters::type.

void revert_force

(

)

Invoked from correct_vel_shake().

Put back the forces from r.p_old to f.f.

Put back the forces from r.p_old to f.f

Definition at line 362 of file rattle.c.

References CellPList::cell, Particle::f, ghost_cells, i, local_cells, CellPList::n, ParticleList::n, ParticlePosition::p_old, ParticleList::part, and Particle::r.

Referenced by correct_vel_shake().

int rigid_bond_set_params	(	int	bond_type,
		double	d,
		double	p_tol,
		double	v_tol
	)

set the parameter for a rigid, aka RATTLE bond

Definition at line 466 of file rattle.c.

References bonded_ia_params, BONDED_IA_RIGID_BOND, ES_ERROR, ES_OK, FIELD_RIGIDBONDS, make_bond_type_exist(), mpi_bcast_ia_params(), mpi_bcast_parameter(), n_rigidbonds, Bonded_ia_parameters::num, Bonded_ia_parameters::p, Bonded_ia_parameters::rigid_bond, time_step, and Bonded_ia_parameters::type.

Referenced by tclcommand_inter_parse_rigid_bond().

void save_old_pos

(

)

Transfers the current particle positions from r.p[3] to r.p_pold[3] of the Particle structure.

Invoked from correct_pos_shake()

Definition at line 69 of file rattle.c.

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

Referenced by integrate_vv().

void transfer_force_init_vel

(

)

Transfers temporarily the current forces from f.f[3] of the Particle structure to r.p_old[3] location and also intializes velocity correction vector.

The forces are transfered temporarily from f.f member of particle structure to r.p_old, which is idle now and initialize the velocity correction vector to zero at f.f[3] of Particle structure.

Invoked from correct_vel_shake()

Definition at line 243 of file rattle.c.

References CellPList::cell, ParticleForce::f, Particle::f, ghost_cells, i, local_cells, CellPList::n, ParticleList::n, ParticlePosition::p_old, ParticleList::part, and Particle::r.

Referenced by correct_vel_shake().

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Variable Documentation

int n_rigidbonds = 0

number of rigid bonds

Definition at line 30 of file rattle.c.

Referenced by on_ghost_flags_change(), and rigid_bond_set_params().