BALL::FDPB::Option Struct Reference

#include <BALL/SOLVATION/poissonBoltzmann.h>

Static Public Attributes
static const String	VERBOSITY
static const String	PRINT_TIMING
static const String	SPACING
static const String	BORDER
static const String	IONIC_STRENGTH
static const String	SOLUTE_DC
static const String	SOLVENT_DC
static const String	PROBE_RADIUS
static const String	ION_RADIUS
static const String	TEMPERATURE
static const String	BOUNDARY
static const String	CHARGE_DISTRIBUTION
static const String	DIELECTRIC_SMOOTHING
static const String	OFFSET
static const String	RMS_CRITERION
static const String	MAX_CRITERION
static const String	CHECK_AFTER_ITERATIONS
static const String	MAX_ITERATIONS
static const String	LOWER
static const String	UPPER
static const String	BOUNDING_BOX_LOWER
static const String	BOUNDING_BOX_UPPER

Detailed Description

Symbolic names for option keys. This struct contains a symbolic name for each recognized key in FDPB::options.

For each symbol the required type is given under parameters.

Definition at line 216 of file poissonBoltzmann.h.

Member Data Documentation

const String BALL::FDPB::Option::BORDER

static

The border of the system. Use this option to define the aumount of space left between the bounding box of the solute and the border of the cubic grid in every direction. Use units of Angstrom with this option. The default is 4 A.

See also

Default::BORDER

Parameters

border

float

Definition at line 255 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::BOUNDARY

static

Boundary condition for solving the differential equation. This parameter defines the type of boundary condition will be used for initializing the equation solver. Possible options are: zero, Debye, Coulomb, dipole and focusing. Default is dipole.

See also

Default::BOUNDARY

Parameters

boundary_condition

String

Definition at line 308 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::BOUNDING_BOX_LOWER

static

The lower corner of the bounding box of the solute molecule. This option works like

See also

LOWER for the bounding box of the solvent molecule.

Parameters

bounding_box_lower

Vector3

Definition at line 398 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::BOUNDING_BOX_UPPER

static

The upper corner of the bounding box of the solute molecule. This is the analogous option to

See also

BOUNDING_BOX_LOWER.

Parameters

bounding_box_upper

Vector3

Definition at line 404 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::CHARGE_DISTRIBUTION

static

Charge distribution of the system. This parameter chooses the method used for distributing charges oiver grid points. Possible methods are: trilinear and uniform. The default is uniform.

See also

Default::BORDER

Parameters

border

float

Definition at line 317 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::CHECK_AFTER_ITERATIONS

static

Checking frequency. This option defines the number of iterations which will be performed without checking the criterions. The default is 10.

See also

Default::CHECK_AFTER_ITERATIONS

Parameters

check_after_iterations

int

Definition at line 365 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::DIELECTRIC_SMOOTHING

static

Smoothing the dielectric constant. With this option you can choose a smoothing function for the dielectric thus permitting a smooth transition from the inside of the molecule (usually dc = 2.0) to the surrounding solvent (78.5). You have the followin options: none, uniform and harmonic. Default is none. different dielectric constant

See also

Default::DIELECTRIC_SMOOTHING

Parameters

dielectric_smoothing

String

Definition at line 329 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::ION_RADIUS

static

The ion exclusion radius.

See also

Default::ION_RADIUS

Parameters

ion_radius

float

Definition at line 292 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::IONIC_STRENGTH

static

The ionic strength of the salt solution This parameter defines the ionic strength of the salt solution in which the Poisson-Boltzmann calculation takes place. This parameter is given in units of mol/l. The default is 0, i. e. only a Poisson equation will be calculated.

See also

Default::IONIC_STRENGTH

Parameters

ionic_strength

float

Definition at line 265 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::LOWER

static

The lower corner of the grid. This option contains the lower corner of the grid. It can be used to fix it before setting up the solver. If this option was not used for initializing the solver gtrid it contains the automatically computed lower corner after the calculation. Use a vector of Angstroms with this option.

Parameters

lower

Vector3

Definition at line 385 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::MAX_CRITERION

static

Define the MAX criterion. This option defines the upper limit for the residuals. If the maximum residuals are below this value and the RMS lies below rms_criterion, the iteration terminates. The default is 1e-4.

See also

Default::MAX_CRITERION

Parameters

max_criterion

float

Definition at line 357 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::MAX_ITERATIONS

static

The upper limit of iterations. Use this option to define the maximum number of iterations to be performed. If the solver does not terminate when this number of iterations is reached, the calculation did not converge. The default is 500 interations.

See also

Default::MAX_ITERATIONS

Parameters

max_iterations

int

Definition at line 375 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::OFFSET

static

Use an offset. This option allows to offset the wohle system by the vector defined in thos option. The calculation does not use an offset by default. Use threedimensional vectors in units of Angstrom with this option.

Parameters

offset

Vector3

Definition at line 338 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::PRINT_TIMING

static

Print the timing for each step.

This prints the timing (if Option::verbosity > 1) of each setup routine and the time needed to solve the equations.

Results are also included in FDPB::results.

See also

Default::PRINT_TIMING

Parameters

print_timing

bool

Definition at line 236 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::PROBE_RADIUS

static

The probe radius used for calculating the SAS of the molecule. This parameter defaults to 1.4 A (water).

See also

Default::PROBE_RADIUS

Parameters

probe_radius

float

Definition at line 286 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::RMS_CRITERION

static

Define the RMS criterion. This option defines the RMS criterion in Angstrom used for terminating the iteration of the solver. If the RMS lies below rms_criterion and the maximum residuals are below max_criterion, the iteration terminates. The default is 1e-5 Angstrom.

See also

Default::RMS_CRITERION

Parameters

rms_criterion

float

Definition at line 348 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::SOLUTE_DC

static

The dielectric constant of the solute. This parameter derfaults to 2.0.

See also

Default::SOLUTE_DC

Parameters

solute_dielectric_constant

float

Definition at line 272 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::SOLVENT_DC

static

The dielectric constant of the solvent. This parameter defaults to 78.0.

See also

Default::SOLVENT_DC

Parameters

solvent_dielectric_constant

float

Definition at line 279 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::SPACING

static

The grid spacing in Angstrom. Use this option to define the distance between a grid point and its closest neighbour in units o Angstrom. The default spacing is 0.6 A.

See also

Default::SPACING

Parameters

spacing

float

Definition at line 245 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::TEMPERATURE

static

The temperature of the system. This parameter needs values in units of K. The default temperature is 298.15 K = 25.15 deg C.

See also

Default::TEMPERATURE

Parameters

temperature

float

Definition at line 299 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::UPPER

static

The upper corner of the grid. This is the analogous option to

See also

LOWER.

Parameters

upper

Vector3

Definition at line 391 of file poissonBoltzmann.h.

const String BALL::FDPB::Option::VERBOSITY

static

The verbosity level. Use integer values with this option. 0 = terse

99 = tell me everything

See also

Default::VERBOSITY

Parameters

verbosity

integer

Definition at line 225 of file poissonBoltzmann.h.