FDPB::Option Struct Reference

Symbolic names for option keys. More...

#include <poissonBoltzmann.h>

List of all members.

Static Public Attributes

const String VERBOSITY

The verbosity level.

const String PRINT_TIMING

Print the timing for each step.

const String SPACING

The grid spacing in Angstrom.

const String BORDER

The border of the system.

const String IONIC_STRENGTH

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.

const String SOLUTE_DC

The dielectric constant of the solute.

const String SOLVENT_DC

The dielectric constant of the solvent.

const String PROBE_RADIUS

The probe radius used for calculating the SAS of the molecule.

const String ION_RADIUS

The ion exclusion radius.

const String TEMPERATURE

The temperature of the system.

const String BOUNDARY

Boundary condition for solving the differential equation.

const String CHARGE_DISTRIBUTION

Charge distribution of the system.

const String DIELECTRIC_SMOOTHING

Smoothing the dielectric constant.

const String OFFSET

Use an offset.

const String RMS_CRITERION

Define the RMS criterion.

const String MAX_CRITERION

Define the MAX criterion.

const String CHECK_AFTER_ITERATIONS

Checking frequency.

const String MAX_ITERATIONS

The upper limit of iterations.

const String LOWER

The lower corner of the grid.

const String UPPER

The upper corner of the grid.

const String BOUNDING_BOX_LOWER

The lower corner of the bounding box of the solute molecule.

const String BOUNDING_BOX_UPPER

The upper corner of the bounding box of the solute molecule.

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.

Member Data Documentation

const String 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

const String 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

const String 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

const String 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

const String 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

const String 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

const String 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

const String FDPB::Option::ION_RADIUS [static]

The ion exclusion radius.

See also:
Default::ION_RADIUS

Parameters:

ion_radius float

const String 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

const String 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

const String 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

const String 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

const String 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

const String 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

const String 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

const String 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

const String 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

const String 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

const String 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

const String 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

const String FDPB::Option::UPPER [static]

The upper corner of the grid.
This is the analogous option to
See also:
LOWER.

Parameters:

upper Vector3

const String 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


Static Public Attributes
const String	VERBOSITY
	The verbosity level.
const String	PRINT_TIMING
	Print the timing for each step.
const String	SPACING
	The grid spacing in Angstrom.
const String	BORDER
	The border of the system.
const String	IONIC_STRENGTH
	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.
const String	SOLUTE_DC
	The dielectric constant of the solute.
const String	SOLVENT_DC
	The dielectric constant of the solvent.
const String	PROBE_RADIUS
	The probe radius used for calculating the SAS of the molecule.
const String	ION_RADIUS
	The ion exclusion radius.
const String	TEMPERATURE
	The temperature of the system.
const String	BOUNDARY
	Boundary condition for solving the differential equation.
const String	CHARGE_DISTRIBUTION
	Charge distribution of the system.
const String	DIELECTRIC_SMOOTHING
	Smoothing the dielectric constant.
const String	OFFSET
	Use an offset.
const String	RMS_CRITERION
	Define the RMS criterion.
const String	MAX_CRITERION
	Define the MAX criterion.
const String	CHECK_AFTER_ITERATIONS
	Checking frequency.
const String	MAX_ITERATIONS
	The upper limit of iterations.
const String	LOWER
	The lower corner of the grid.
const String	UPPER
	The upper corner of the grid.
const String	BOUNDING_BOX_LOWER
	The lower corner of the bounding box of the solute molecule.
const String	BOUNDING_BOX_UPPER
	The upper corner of the bounding box of the solute molecule.