Maxwell Equations Molecular Dynamics (MEMD) method for electrostatic interactions. More...

#include <mpi.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "ghosts.h"
#include "global.h"
#include "grid.h"
#include "integrate.h"
#include "initialize.h"
#include "interaction_data.h"
#include "particle_data.h"
#include "communication.h"
#include "maggs.h"
#include "thermostat.h"
#include "cells.h"
#include "domain_decomposition.h"
#include "errorhandling.h"

Include dependency graph for maggs.c:

Go to the source code of this file.

Defines
#define	REQ_MAGGS_SPREAD 300
#define	REQ_MAGGS_EQUIL 301
#define	SELF_FACTOR_1 1.57364595
#define	SELF_FACTOR_2 1.5078141
#define	SPACE_DIM 3
#define	NOWHERE -1
#define	NDIRS 6
#define	XPLUS 0
#define	YPLUS 1
#define	ZPLUS 2
#define	ZMINUS 3
#define	YMINUS 4
#define	XMINUS 5
#define	OPP_DIR(dir) (5-(dir))
#define	FOR3D(dir) for(dir=0; dir<SPACE_DIM; dir++)
#define	FORALL_INNER_SITES(i, j, k)
#define	FORALL_SITES(i, j, k)
Typedefs
typedef int	t_ivector [SPACE_DIM]
typedef double	t_dvector [SPACE_DIM]
typedef int	t_dirs [NDIRS]
Functions
int	maggs_get_linear_index (int x, int y, int z, int latticedim[SPACE_DIM])
	Turns the 3D index into a linear index.
int	maggs_count_charged_particles ()
	Counts the total number of charged particles on all processors.
int	maggs_get_offset (int index_shift, int index_base, int axes, int adim[3])
	Index shift is calculated for moving in various directions with the linear index.
void	maggs_calc_directions (int j, int dir1, int dir2)
	For any direction j, write the two other directions into the pointers in circular permutation.
double	maggs_calc_curl (int mue, int nue, double field, int Neighbor, int index)
	Calculates the finite differences rotation in real space in mue-nue plane: $\frac{\partial}{\partial t}{D} = \nabla \times B$ (and prefactors plus current) The given "double* field" should be a B-Field!!
double	maggs_calc_dual_curl (int mue, int nue, double field, int Neighbor, int index)
	Calculates the finite differences rotation in dual space in mue-nue plane: $\frac{\partial}{\partial t}{B} = - \nabla \times D / (\epsilon)$ The given "double* field" should be a D-Field!!
void	maggs_update_plaquette (int mue, int nue, int *Neighbor, int index, double delta)
	updates all D-fields on links of the plaquette and the surroundings.
int	maggs_sanity_checks ()
	Basic sanity checks to see if the code will run.
void	maggs_compute_dipole_correction ()
int	maggs_set_parameters (double bjerrum, double f_mass, int mesh, int finite_epsilon_flag, double epsilon_infty)
	called from: initialize.c
void	maggs_setup_neighbors ()
	sets up nearest neighbors for each site in linear index
void	maggs_setup_local_lattice ()
	Set up lattice, calculate dimensions and lattice parameters Allocate memory for lattice sites and fields.
void	maggs_calc_surface_patches (t_surf_patch *surface_patch)
	sets up surface patches for all domains.
void	maggs_prepare_surface_planes (int dim, MPI_Datatype xy, MPI_Datatype xz, MPI_Datatype yz, t_surf_patch surface_patch)
	sets up MPI communications for domain surfaces
void	maggs_exchange_surface_patch (double *field, int dim, int e_equil)
	MPI communication of surface region.
double	maggs_interpol1D (double x)
	Interpolation function in one dimension.
void	maggs_interpolate_charge (int first, double rel, double q)
	Does the actual interpolating calculation.
void	maggs_accumulate_charge_from_ghosts ()
	add charges from ghost cells to lattice sites.
void	maggs_distribute_particle_charges ()
	finds current lattice site of each particle.
void	maggs_calc_charge_gradients (double rel, double q, double grad)
	Does the actual calculation of the gradient.
void	maggs_update_charge_gradients (double *grad)
	finds correct lattice cube for particles.
void	calc_self_energy_coeffs ()
	Calculate the self energy coefficients for the system, if corrected with Lattice Green's function.
double	maggs_check_curl_E ()
	For energy minimization:
void	maggs_perform_rot_move_inplane (int i, int n)
	If curl(E) is not zero, update plaquette with corrections.
void	maggs_minimize_transverse_field ()
	For energy minimization: Relax B-fields in all directions.
void	maggs_calc_init_e_field ()
	calculates initial electric field configuration.
void	maggs_calc_charge_fluxes_1D (double q, double help, double flux, int dir)
	calculate the charge flux in direction "dir".
int	maggs_check_intersect_1D (double delta, double r_new, int dir, int first, double *t_step, int identity)
	Extend particle trajectories on the one time step and check if the trajectory intersects the cell boundary in direction dirx#.
void	maggs_calc_e_field_on_link_1D (int index, double *flux, double v, int dir)
	updates field on link coupling it with current.
void	maggs_add_current_on_segment (Particle *p, int ghost_cell)
	loop over all cells and call charge current functions
void	maggs_couple_current_to_Dfield ()
	Calculate fluxes and couple them with fields symplectically.
void	maggs_propagate_B_field (double dt)
	propagate the B-field via $\frac{\partial}{\partial t}{B} = \nabla\times D$ (and prefactor) CAREFUL: Usually this function is called twice, with dt/2 each time to ensure a time reversible integration scheme!
void	maggs_add_transverse_field (double dt)
	calculate D-field from B-field according to $\frac{\partial}{\partial t}{D} = \nabla\times B$ (and prefactors)
void	interpolate_part_charge_from_grad (double rel_x, double grad, double rho)
	interpolation function, solely for new self force correction.
void	calc_part_self_force (Particle *p)
	new self force correction with lattice Green's function.
void	maggs_calc_self_influence (Particle *P)
	For each particle P, calculates self energy influence with direct Greens function, assuming constant permittivity on each lattice site.
void	maggs_calc_part_link_forces (Particle p, int index, double grad)
	Calculate the actual force from the E-Field.
void	maggs_calc_forces ()
	Public function.
double	maggs_electric_energy ()
	integrates 0.5DE over the whole system public function!
double	maggs_magnetic_energy ()
	Public funxtion.
void	maggs_init ()
	Initialization function.
void	maggs_exit ()
	Frees the dynamically allocated memory Currently not called from anywhere.
Variables
MAGGS_struct	maggs = { 1, 1.0, 0. , 0. , 0. , 0. , 0. , 0 , 0. , 0. , {{0.},{0.}}}
static lattice_parameters	lparams
static t_site *	lattice
static double *	Dfield
static double *	Bfield
static t_dirs *	neighbor

Detailed Description

Maxwell Equations Molecular Dynamics (MEMD) method for electrostatic interactions.

We use a local update scheme to propagate artificial B-fields on a lattice in the system. In principal, the algorithm simulates full electrodynamics, but with a tunable speed of light.

The method is very usable for large particle numbers or highly parallel architectures, since it is local and scales linearly. It is not suited for high-precision calculation of forces, since the simple interpolation scheme produces errors in the order of 10^-5 in the force.

The chosen mesh should roughly be of the size of the particles.

Further reading on the algorithm: I. Pasichnyk and B. Dunweg, Coulomb interaction via local dynamics: a molecular-dynamics algorithm. J. Phys: Condens. Matter, 16 ,p. 1399-4020, (2004).

We use a local update scheme to propagate artificial B-fields on a lattice in the system. In principal, the algorithm simulates full electrodynamics, but with a tunable speed of light.

The method is very usable for large particle numbers or highly parallel architectures, since it is local and scales linearly. It is not suited for high-precision calculation of forces, since the simple interpolation scheme produces errors in the order of 10^-5 in the force.

The chosen mesh should roughly be of the size of the particles.

Define Documentation

#define FOR3D ( dir ) for(dir=0; dir<SPACE_DIM; dir++)

Definition at line 94 of file maggs.c.

Referenced by calc_part_self_force(), maggs_accumulate_charge_from_ghosts(), maggs_add_current_on_segment(), maggs_calc_charge_gradients(), maggs_calc_forces(), maggs_calc_init_e_field(), maggs_calc_part_link_forces(), maggs_calc_self_influence(), maggs_couple_current_to_Dfield(), maggs_distribute_particle_charges(), maggs_electric_energy(), maggs_interpolate_charge(), maggs_minimize_transverse_field(), maggs_sanity_checks(), maggs_setup_local_lattice(), and maggs_update_charge_gradients().

#define FORALL_INNER_SITES	(	i,
		j,
		k
	)

Value:

for(i=lparams.inner_left_down[0];i<lparams.inner_up_right[0];i++)       \
    for(j=lparams.inner_left_down[1];j<lparams.inner_up_right[1];j++)   \
      for(k=lparams.inner_left_down[2];k<lparams.inner_up_right[2];k++)

Definition at line 96 of file maggs.c.

Referenced by maggs_calc_init_e_field(), maggs_check_curl_E(), maggs_electric_energy(), and maggs_magnetic_energy().

#define FORALL_SITES	(	i,
		j,
		k
	)

Value:

for(i=0;i<lparams.dim[0];i++)                   \
    for(j=0;j<lparams.dim[1];j++)               \
      for(k=0;k<lparams.dim[2];k++)

Definition at line 101 of file maggs.c.

Referenced by maggs_setup_local_lattice().

#define NDIRS 6

Definition at line 83 of file maggs.c.

#define NOWHERE -1

Definition at line 82 of file maggs.c.

Referenced by maggs_calc_e_field_on_link_1D(), and maggs_interpolate_charge().

#define OPP_DIR ( dir ) (5-(dir))

Definition at line 90 of file maggs.c.

Referenced by maggs_calc_curl().

#define REQ_MAGGS_EQUIL 301

Definition at line 70 of file maggs.c.

Referenced by maggs_calc_init_e_field().

#define REQ_MAGGS_SPREAD 300

Definition at line 69 of file maggs.c.

Referenced by maggs_exchange_surface_patch().

#define SELF_FACTOR_1 1.57364595

Definition at line 74 of file maggs.c.

Referenced by maggs_calc_self_influence().

#define SELF_FACTOR_2 1.5078141

Definition at line 75 of file maggs.c.

Referenced by maggs_calc_self_influence().

#define SPACE_DIM 3

Definition at line 81 of file maggs.c.

Referenced by calc_part_self_force(), calc_self_energy_coeffs(), maggs_accumulate_charge_from_ghosts(), maggs_add_current_on_segment(), maggs_calc_forces(), maggs_calc_init_e_field(), maggs_calc_part_link_forces(), maggs_calc_self_influence(), maggs_distribute_particle_charges(), maggs_interpolate_charge(), and maggs_update_charge_gradients().

#define XMINUS 5

Definition at line 89 of file maggs.c.

Referenced by maggs_calc_init_e_field(), and maggs_setup_neighbors().

#define XPLUS 0

Definition at line 84 of file maggs.c.

Referenced by maggs_calc_init_e_field(), and maggs_setup_neighbors().

#define YMINUS 4

Definition at line 88 of file maggs.c.

Referenced by maggs_calc_init_e_field(), and maggs_setup_neighbors().

#define YPLUS 1

Definition at line 85 of file maggs.c.

Referenced by maggs_calc_init_e_field(), maggs_get_linear_index(), and maggs_setup_neighbors().

#define ZMINUS 3

Definition at line 87 of file maggs.c.

Referenced by maggs_calc_init_e_field(), and maggs_setup_neighbors().

#define ZPLUS 2

Definition at line 86 of file maggs.c.

Referenced by maggs_calc_init_e_field(), maggs_get_linear_index(), and maggs_setup_neighbors().

Typedef Documentation

typedef int t_dirs[NDIRS]

Definition at line 113 of file maggs.c.

typedef double t_dvector[SPACE_DIM]

Definition at line 112 of file maggs.c.

typedef int t_ivector[SPACE_DIM]

Definition at line 111 of file maggs.c.

Function Documentation

void calc_part_self_force ( Particle * p )

new self force correction with lattice Green's function.

Parameters:

p	Particle pointer

Definition at line 2017 of file maggs.c.

References MAGGS_struct::alpha, ParticleForce::f, Particle::f, FOR3D, i, interpolate_part_charge_from_grad(), maggs_calc_charge_gradients(), maggs_calc_directions(), Particle::p, ParticleProperties::q, and SPACE_DIM.

void calc_self_energy_coeffs ( )

Calculate the self energy coefficients for the system, if corrected with Lattice Green's function.

Definition at line 1121 of file maggs.c.

References MAGGS_struct::alpha, i, MAGGS_struct::inva, M_PI, MAGGS_struct::mesh, MAGGS_struct::prefactor, SPACE_DIM, and SQR().

void interpolate_part_charge_from_grad	(	double	rel_x,
		double *	grad,
		double *	rho
	)

interpolation function, solely for new self force correction.

Definition at line 1975 of file maggs.c.

References i.

Referenced by calc_part_self_force().

void maggs_accumulate_charge_from_ghosts ( )

add charges from ghost cells to lattice sites.

loop over ghost cells

Definition at line 969 of file maggs.c.

References CellPList::cell, FOR3D, ghost_cells, i, MAGGS_struct::inva, lparams, maggs_interpolate_charge(), CellPList::n, ParticleList::n, ParticlePosition::p, Particle::p, ParticleList::part, Particle::r, and SPACE_DIM.

Referenced by maggs_distribute_particle_charges().

void maggs_add_current_on_segment	(	Particle *	p,
		int	ghost_cell
	)

loop over all cells and call charge current functions

Parameters:

p	Particle pointer
ghost_cell	flag if cell is ghost cell

Definition at line 1753 of file maggs.c.

References FOR3D, ParticleProperties::identity, MAGGS_struct::inva, lparams, Particle::m, maggs_calc_charge_fluxes_1D(), maggs_calc_e_field_on_link_1D(), maggs_check_intersect_1D(), maggs_get_linear_index(), ParticlePosition::p, Particle::p, ParticleProperties::q, Particle::r, SPACE_DIM, and ParticleMomentum::v.

Referenced by maggs_couple_current_to_Dfield().

void maggs_add_transverse_field ( double dt )

calculate D-field from B-field according to $\frac{\partial}{\partial t}{D} = \nabla\times B$ (and prefactors)

Parameters:

dt	MD time step

Definition at line 1939 of file maggs.c.

References Bfield, Dfield, i, MAGGS_struct::inva, MAGGS_struct::invsqrt_f_mass, lparams, maggs_calc_curl(), maggs_exchange_surface_patch(), maggs_get_linear_index(), neighbor, and SQR().

Referenced by maggs_calc_forces().

void maggs_calc_charge_fluxes_1D	(	double	q,
		double *	help,
		double *	flux,
		int	dir
	)

calculate the charge flux in direction "dir".

Parameters:

q	charge of the moving particle
help	the relative position in the cube to the opposite of left down front lattice site.
flux	flux variable to write into
dir	direction in which to calculate the flux

Definition at line 1633 of file maggs.c.

References MAGGS_struct::inva, maggs_calc_directions(), and MAGGS_struct::prefactor.

Referenced by maggs_add_current_on_segment().

void maggs_calc_charge_gradients	(	double *	rel,
		double	q,
		double *	grad
	)

Does the actual calculation of the gradient.

Parameters:

Parameters:

rel	3dim-array of relative position in cube,
q	charge,
grad	huge gradient array to write into

Definition at line 1046 of file maggs.c.

References FOR3D, i, and maggs_calc_directions().

Referenced by calc_part_self_force(), and maggs_update_charge_gradients().

double maggs_calc_curl	(	int	mue,
		int	nue,
		double *	field,
		int *	Neighbor,
		int	index
	)

Calculates the finite differences rotation in real space in mue-nue plane: $\frac{\partial}{\partial t}{D} = \nabla \times B$ (and prefactors plus current) The given "double* field" should be a B-Field!!

Returns:: rotation result

Parameters:

mue	direction 1 of plane to rotate in
nue	direction 2 of plane to rotate in
field	input B-field
Neighbor	neighbor lattice site
index	index of current lattice site

Definition at line 350 of file maggs.c.

References OPP_DIR.

Referenced by maggs_add_transverse_field().

void maggs_calc_directions	(	int	j,
		int *	dir1,
		int *	dir2
	)

For any direction j, write the two other directions into the pointers in circular permutation.

Parameters:

j	given first direction
dir1	write second direction into
dir2	write third direction into

Definition at line 321 of file maggs.c.

Referenced by calc_part_self_force(), maggs_calc_charge_fluxes_1D(), maggs_calc_charge_gradients(), maggs_calc_e_field_on_link_1D(), and maggs_calc_part_link_forces().

double maggs_calc_dual_curl	(	int	mue,
		int	nue,
		double *	field,
		int *	Neighbor,
		int	index
	)

Calculates the finite differences rotation in dual space in mue-nue plane: $\frac{\partial}{\partial t}{B} = - \nabla \times D / (\epsilon)$ The given "double* field" should be a D-Field!!

Returns:: rotation result

Parameters:

mue	direction 1 of plane to rotate in
nue	direction 2 of plane to rotate in
field	input D-field
Neighbor	neighbor lattice site
index	index of current lattice site

Definition at line 370 of file maggs.c.

Referenced by maggs_propagate_B_field().

void maggs_calc_e_field_on_link_1D	(	int	index,
		double *	flux,
		double	v,
		int	dir
	)

updates field on link coupling it with current.

Force is multiplied by the time_step

Parameters:

index	index of lattice site
flux	charge flux in lattice site
v	speed of particle
dir	first direction of flux calculation

Definition at line 1707 of file maggs.c.

References Dfield, lattice, lparams, maggs_calc_directions(), maggs_get_offset(), neighbor, and NOWHERE.

Referenced by maggs_add_current_on_segment().

void maggs_calc_forces ( )

Public function.

Calculate the forces on all particles.

Calculates the actual force on each particle by calling all other needed functions (except for maggs_propagate_B_field)

Definition at line 2195 of file maggs.c.

References CellPList::cell, cells_get_n_particles(), MAGGS_struct::finite_epsilon_flag, FOR3D, i, MAGGS_struct::inva, local_cells, lparams, maggs_add_transverse_field(), maggs_calc_part_link_forces(), maggs_calc_self_influence(), maggs_compute_dipole_correction(), maggs_couple_current_to_Dfield(), maggs_get_linear_index(), MAGGS_TRACE, maggs_update_charge_gradients(), CellPList::n, ParticleList::n, ParticlePosition::p, Particle::p, ParticleList::part, ParticleProperties::q, Particle::r, realloc, SPACE_DIM, and time_step.

Referenced by calc_long_range_forces().

void maggs_calc_init_e_field ( )

calculates initial electric field configuration.

currently uses simple and slow method of plaquettes and links. energy minimization takes up lots of time.

Definition at line 1324 of file maggs.c.

References CELL_GLOBAL_EXCHANGE, cells_resort_particles(), comm_cart, Dfield, FOR3D, FORALL_INNER_SITES, i, MAGGS_struct::inva, iy, lattice, lparams, maggs_check_curl_E(), maggs_distribute_particle_charges(), maggs_exchange_surface_patch(), maggs_get_linear_index(), maggs_minimize_transverse_field(), MAGGS_TRACE, MAGGS_struct::mesh, MPI_Allreduce(), MPI_Comm_free(), MPI_Comm_split(), MPI_DOUBLE, MPI_Recv(), MPI_Send(), MPI_SUM, n_nodes, neighbor, node_grid, node_neighbors, node_pos, MAGGS_struct::prefactor, REQ_MAGGS_EQUIL, ROUND_ERROR_PREC, SPACE_DIM, SQR(), this_node, XMINUS, XPLUS, YMINUS, YPLUS, ZMINUS, and ZPLUS.

Referenced by maggs_init().

void maggs_calc_part_link_forces	(	Particle *	p,
		int	index,
		double *	grad
	)

Calculate the actual force from the E-Field.

Parameters:

p	Particle pointer
index	index of the lattice site
grad	charge gradient

Definition at line 2144 of file maggs.c.

References Dfield, ParticleForce::f, Particle::f, FOR3D, lattice, lparams, maggs_calc_directions(), maggs_get_offset(), neighbor, MAGGS_struct::prefactor, and SPACE_DIM.

Referenced by maggs_calc_forces().

void maggs_calc_self_influence ( Particle * P )

For each particle P, calculates self energy influence with direct Greens function, assuming constant permittivity on each lattice site.

Parameters:

P	Particle pointer

Definition at line 2080 of file maggs.c.

References MAGGS_struct::bjerrum, ParticleForce::f, Particle::f, FOR3D, MAGGS_struct::inva, lparams, ParticlePosition::p, Particle::p, ParticleProperties::q, Particle::r, SELF_FACTOR_1, SELF_FACTOR_2, and SPACE_DIM.

Referenced by maggs_calc_forces().

void maggs_calc_surface_patches ( t_surf_patch * surface_patch )

sets up surface patches for all domains.

Parameters:

surface_patch the local surface patch

Definition at line 697 of file maggs.c.

References lparams.

Referenced by maggs_exchange_surface_patch().

double maggs_check_curl_E ( )

For energy minimization:

Returns:: maximum of curl(E) from all sites. May also be used to verify constraint surface condition.

Definition at line 1195 of file maggs.c.

References comm_cart, Dfield, FORALL_INNER_SITES, i, MAGGS_struct::inva, iy, lparams, maggs_get_linear_index(), MPI_Allreduce(), MPI_DOUBLE, MPI_MAX, and neighbor.

Referenced by maggs_calc_init_e_field().

int maggs_check_intersect_1D	(	double	delta,
		double	r_new,
		int	dir,
		int	first,
		double *	t_step,
		int	identity
	)

Extend particle trajectories on the one time step and check if the trajectory intersects the cell boundary in direction dirx#.

Returns:: zero if no particle crosses intersection

Parameters:

delta	amount by which the particle moves
r_new	current position of particle
dir	direction in which to check for intersection
first	position of particle within lattice cube
t_step	time step
identity	particle ID

Definition at line 1667 of file maggs.c.

References MAGGS_struct::a, MAGGS_TRACE, and sim_time.

Referenced by maggs_add_current_on_segment().

void maggs_compute_dipole_correction ( )

Definition at line 479 of file maggs.c.

References box_l, CellPList::cell, comm_cart, MAGGS_struct::epsilon_infty, Particle::f, i, local_cells, M_PI, MPI_Allreduce(), MPI_DOUBLE, MPI_SUM, CellPList::n, ParticleList::n, Particle::p, ParticleList::part, and ParticleProperties::q.

Referenced by maggs_calc_forces().

int maggs_count_charged_particles ( )

Counts the total number of charged particles on all processors.

Count the number of charges in the whole system.

Returns:: total number of charged particles in the system

Definition at line 272 of file maggs.c.

References CellPList::cell, comm_cart, i, local_cells, MPI_DOUBLE, MPI_Reduce(), MPI_SUM, CellPList::n, ParticleList::n, part, and ParticleList::part.

Referenced by mpi_bcast_event_slave().

void maggs_couple_current_to_Dfield ( )

Calculate fluxes and couple them with fields symplectically.

It is assumed that the particle can not cross more than one cell boundary per direction

loop over real particles

loop over ghost particles

Definition at line 1843 of file maggs.c.

References CellPList::cell, FOR3D, ghost_cells, i, local_cells, lparams, Particle::m, maggs_add_current_on_segment(), CellPList::n, ParticleList::n, ParticlePosition::p, ParticleList::part, Particle::r, and ParticleMomentum::v.

Referenced by maggs_calc_forces().

void maggs_distribute_particle_charges ( )

finds current lattice site of each particle.

calculates charge interpolation on cube.

=== charge assignment ===

loop over inner cells

Definition at line 1010 of file maggs.c.

References CellPList::cell, FOR3D, i, MAGGS_struct::inva, lattice, local_cells, lparams, maggs_accumulate_charge_from_ghosts(), maggs_interpolate_charge(), CellPList::n, ParticleList::n, ParticlePosition::p, ParticleList::part, Particle::r, and SPACE_DIM.

Referenced by maggs_calc_init_e_field().

double maggs_electric_energy ( )

integrates 0.5*D*E over the whole system public function!

Get the electric energy of the system as return value.

Returns:: returns electric energy

Definition at line 2269 of file maggs.c.

References MAGGS_struct::a, comm_cart, Dfield, FOR3D, FORALL_INNER_SITES, i, lattice, lparams, maggs_get_linear_index(), MPI_Allreduce(), MPI_DOUBLE, MPI_SUM, and SQR().

Referenced by calc_long_range_energies().

void maggs_exchange_surface_patch	(	double *	field,
		int	dim,
		int	e_equil
	)

MPI communication of surface region.

works for D- and B-fields.

Parameters:

field	Field to communicate. Can be B- or D-field.
dim	Dimension in which to communicate
e_equil	Flag if field is already equilibated

surface_patch

direction loop

pack send halo-plane data

communication

copy locally

Definition at line 791 of file maggs.c.

References comm_cart, maggs_calc_surface_patches(), maggs_prepare_surface_planes(), MPI_BYTE, MPI_DOUBLE, MPI_Irecv(), MPI_Isend(), MPI_REQUEST_NULL, MPI_Type_commit(), MPI_Type_contiguous(), MPI_Type_hvector(), MPI_Type_vector(), MPI_Waitall(), node_neighbors, REQ_MAGGS_SPREAD, request, and this_node.

Referenced by maggs_add_transverse_field(), maggs_calc_init_e_field(), maggs_minimize_transverse_field(), and maggs_propagate_B_field().

void maggs_exit ( )

Frees the dynamically allocated memory Currently not called from anywhere.

Clean up, free memory.

Definition at line 2341 of file maggs.c.

References Bfield, Dfield, free, lattice, and neighbor.

int maggs_get_linear_index	(	int	x,
		int	y,
		int	z,
		int	latticedim[SPACE_DIM]
	)

Turns the 3D index into a linear index.

adim contains the dimensions of the lattice in the 3 directions: adim[0] = x_max, ..., adim[2] = z_max z is the first index!!!

Returns:: linear index

Parameters:

x	index in x direction
y	index in y direction
z	index in z direction
latticedim	dimensions of the lattice

Definition at line 263 of file maggs.c.

References YPLUS, and ZPLUS.

Referenced by maggs_add_current_on_segment(), maggs_add_transverse_field(), maggs_calc_forces(), maggs_calc_init_e_field(), maggs_check_curl_E(), maggs_electric_energy(), maggs_interpolate_charge(), maggs_magnetic_energy(), maggs_minimize_transverse_field(), maggs_propagate_B_field(), maggs_setup_local_lattice(), and maggs_setup_neighbors().

int maggs_get_offset	(	int	index_shift,
		int	index_base,
		int	axes,
		int	adim[3]
	)

Index shift is calculated for moving in various directions with the linear index.

Returns:: Offset of current node from base

Parameters:

index_shift	amount to move in direction
index_base	index of base on current processor
axes	in which direction to move
adim	dimensions of the local lattice

Definition at line 304 of file maggs.c.

Referenced by maggs_calc_e_field_on_link_1D(), maggs_calc_part_link_forces(), and maggs_interpolate_charge().

void maggs_init ( )

Initialization function.

initialization function, parse command and set parameters.

Sets maggs structure variables. Calls calculation of initial D-field.

Definition at line 2314 of file maggs.c.

References MAGGS_struct::a, MAGGS_struct::bjerrum, Coulomb_parameters::bjerrum, box_l, coulomb, MAGGS_struct::inva, M_PI, maggs_calc_init_e_field(), maggs_sanity_checks(), maggs_setup_local_lattice(), MAGGS_struct::mesh, MAGGS_struct::pref2, MAGGS_struct::prefactor, and temperature.

Referenced by on_boxl_change(), on_cell_structure_change(), on_coulomb_change(), and on_observable_calc().

double maggs_interpol1D ( double x )

Interpolation function in one dimension.

Currently only linear interpolation conserves charge.

Returns:: interpolation value

Parameters:

x	relative position of particle

Definition at line 911 of file maggs.c.

Referenced by maggs_interpolate_charge().

void maggs_interpolate_charge	(	int *	first,
		double *	rel,
		double	q
	)

Does the actual interpolating calculation.

Parameters:

first	3dim-array lattice position,
rel	3dim-array relative position in cube,
q	charge to interpolate

relative pos. w.r.t. first

calculate charges at each vertex

Definition at line 924 of file maggs.c.

References FOR3D, i, lattice, lparams, maggs_get_linear_index(), maggs_get_offset(), maggs_interpol1D(), neighbor, NOWHERE, and SPACE_DIM.

Referenced by maggs_accumulate_charge_from_ghosts(), and maggs_distribute_particle_charges().

double maggs_magnetic_energy ( )

Public funxtion.

Get the magnetic energy of the artificial transversal field component as return value.

Integrates the B-field over the whole system to get the energy of the magnetic field.

Returns:: returns magnetic energy

Definition at line 2292 of file maggs.c.

References MAGGS_struct::a, Bfield, FORALL_INNER_SITES, i, lparams, maggs_get_linear_index(), and SQR().

void maggs_minimize_transverse_field ( )

For energy minimization: Relax B-fields in all directions.

Definition at line 1265 of file maggs.c.

References Dfield, FOR3D, i, lparams, maggs_exchange_surface_patch(), maggs_get_linear_index(), and maggs_perform_rot_move_inplane().

Referenced by maggs_calc_init_e_field().

void maggs_perform_rot_move_inplane	(	int	i,
		int	n
	)

If curl(E) is not zero, update plaquette with corrections.

Parameters:

i	index of the current lattice site
n	coordinate, is the normal direction to the plaquette

Definition at line 1227 of file maggs.c.

References Dfield, i, maggs_update_plaquette(), neighbor, and ROUND_ERROR_PREC.

Referenced by maggs_minimize_transverse_field().

void maggs_prepare_surface_planes	(	int	dim,
		MPI_Datatype *	xy,
		MPI_Datatype *	xz,
		MPI_Datatype *	yz,
		t_surf_patch *	surface_patch
	)

sets up MPI communications for domain surfaces

Definition at line 762 of file maggs.c.

References MPI_BYTE, MPI_DOUBLE, MPI_Type_commit(), MPI_Type_contiguous(), and MPI_Type_vector().

Referenced by maggs_exchange_surface_patch().

void maggs_propagate_B_field ( double dt )

propagate the B-field via $\frac{\partial}{\partial t}{B} = \nabla\times D$ (and prefactor) CAREFUL: Usually this function is called twice, with dt/2 each time to ensure a time reversible integration scheme!

Propagate the B-field in the system.

Parameters:

dt	time step for update. Should be half the MD time step

Definition at line 1906 of file maggs.c.

References Bfield, Dfield, i, MAGGS_struct::invsqrt_f_mass, lparams, maggs_calc_dual_curl(), maggs_exchange_surface_patch(), maggs_get_linear_index(), and neighbor.

Referenced by integrate_vv().

int maggs_sanity_checks ( )

Basic sanity checks to see if the code will run.

Returns:: zero if everything is fine. -1 otherwise.

check if speed of light parameter makes sense

check for fixed particles

Definition at line 403 of file maggs.c.

References MAGGS_struct::a, MAGGS_struct::bjerrum, box_l, CellPList::cell, cell_structure, CELL_STRUCTURE_DOMDEC, COORDS_FIX_MASK, dd, ERROR_SPRINTF, ParticleLocal::ext_flag, MAGGS_struct::f_mass, FOR3D, i, Particle::l, local_cells, MAGGS_struct::mesh, CellPList::n, ParticleList::n, node_grid, ParticleList::part, PERIODIC, runtime_error(), skin, time_step, CellStructure::type, and DomainDecomposition::use_vList.

Referenced by maggs_init().

int maggs_set_parameters	(	double	bjerrum,
		double	f_mass,
		int	mesh,
		int	finite_epsilon_flag,
		double	epsilon_infty
	)

called from: initialize.c

set the main parameters for the algorithm.

Parameters:

bjerrum	Bjerrum length for the system
f_mass	parameter to tune the speed of light (1/c^2)
mesh	Mesh size in one dimension
finite_epsilon_flag	whether to do epsilon-at-infinity-correction
epsilon_infty	epsilon-at-infinity