BALL::FDPB Class Reference
[Solvation methods]
#include <BALL/SOLVATION/poissonBoltzmann.h>
Detailed Description
Finite Difference Poisson Boltzmann Solver.
Member Typedef Documentation
typedef struct FastAtomStruct BALL::FDPB::FastAtom [read] |
Member Enumeration Documentation
Error codes: these are the possible error codes that can be produced by FDPB.
- Enumerator:
ERROR__NONE No error.
ERROR__UNKNOWN Unknown error.
ERROR__NOT_IMPLEMENTED Not implemented error. Someone has been too lazy to implement the this method. Wait for the next release...
ERROR__CANNOT_CREATE_ATOM_ARRAY Unable to create the atom array/out of memory. FDPB internally creates a dynamic array containing the atoms of the system. If FDPB::setupAtomArray() cannot create this array you normally ran out of virtual memory.
ERROR__CANNOT_CREATE_SAS_GRID Unable to create SAS grid/out of memory. FDPB uses a TRegularData3D<char> (FDPB::SAS_grid) to describe whether a point in space is inside the ion exclusion layer. This grid is created by FDPB::setupSASGrid(). On failure this error code is set. It usually indicates a lack of virtual memory.
ERROR__CANNOT_CREATE_EPSILON_GRID Unable to create dielectric grid/out of memory. FDPB uses a
TRegularData3D<float>( FDPB::eps_grid ) to describe the dielectric constant
as a function of space. This grid is created by calling FDPB::setupEpsGrid(). It contains the relative dielectric constant between neighbouring grid points. - If virtual memory is exhausted and the grid could not be created this error is set.
ERROR__CANNOT_CREATE_KAPPA_GRID Unable to create grid for the modified Debye Hueckel parameter/out of memory. The modified Debye Hueckel parameter
is also a function of space and therefore represented by a TRegularData3D<float> (FDPB::kappa_grid). The grid is created by FDPB::setupKappaGrid(). - If the creation of this grid fails due to a alack of virtual memory this error code is set.
ERROR__CANNOT_CREATE_CHARGE_GRID Unable to create charge grid/out of memory. FDPB::setupQGrid() distributes the charge of the atoms in a grid. This grid is named FDPB::q_grid.
- If the creation of this grid fails due to a lack of virtual memory, this error code is set.
ERROR__CANNOT_CREATE_PHI_GRID Unable to create electrostatic potential grid/out of memory. FDPB::setupPhiGrid() creates a TRegularData3D<float> (FDPB::phi_grid) containing the electrostatic potential as a function of space. If the creation of this grid fails due to a lack of virtual memory, this error code is set.
ERROR__SAS_GRID_REQUIRED Create solvent accessible surface grid first. This error code is set by FDPB::setupKappGrid() if it is called but the ion excluded surface has not been set (usually by calling FDPB::setupSASGrid).
- Solution: call FDPB::setupKappaGrid after calling FDPB::setupSASGrid.
ERROR__EPSILON_GRID_REQUIRED Create dielectric constant grid first. This error code is set by FDPB::setupQGrid(), FDPB::setupKappaGrid(), or FDPB::setupPhiGrid() if it was called, but FDPB::eps_grid was not defined yet (this is usually done by calling FDPB::setupEpsGrid ).
- Solution: call FDPB::setupEpsGrid first
ERROR__ATOM_ARRAY_REQUIRED Create atom array first. This error code is set by FDPB::setupQGrid() or FDPB::setupBoundary() if it was called but FDPB::atom_array was not yet defined (this is usually done by calling FDPB::setupAtomArray()).
- Solution: call FDPB::setupAtomArray() first
ERROR__PHI_GRID_REQUIRED Create electrostatic potential grid first. FDPB::phi_grid contains the electrostatic potential at each point in space. FDPB::setupBoundary() sets this error code if it is called but FDPB::phi_grid has not been set yet. Solution: call FDPB::setupPhiGrid() before calling FDPB::setupBoundary()
ERROR__OUT_OF_MEMORY Not enough virtual memory. This error code is set if FDPB::solve() ran out of virtual memory while creating some internal datastructures. Solution: reduce grid dimensions or increase grid spacing.
ERROR__UNKNOWN_DIELECTRIC_SMOOTHING_METHOD The specified method to smooth the dielectric constant grid is not allowed. FDPB::setupEpsGrid sets this error code, if it cannot identify the method given in FDPB::Option::dielectric_smoothing.
- Solution: specify a valid smoothing method in FDPB::options
- See also:
FDPB::Option::dielectric_smoothing
ERROR__UNKNOWN_CHARGE_DISTRIBUTION_METHOD The specified charge distribution is not allowed. FDPB::setupQGrid() sets this error code, if it cannot identify the method given in FDPB::Option::charge_distribution.
- Solution: specify a valid charge distribution method in FDPB::options
- See also:
FDPB::Option::charge_distribution
ERROR__UNKNOWN_BOUNDARY_CONDITION_TYPE The specified boundary condition type is not allowed. FDPB::setupBoundary() sets this error code, if it cannot identify the boundary condition given in FDPB::Option::boundary.
- Solution: specify a valid boundary condition in FDPB::options
- See also:
FDPB::Option::boundary
ERROR__NOT_A_VECTOR_IN_UPPER_LOWER Upper or lower grid coordinates were specified in an incorrect format. This error code is set by FDPB::setupEpsGrid if the string given in FDPB::options (key FDPB::Option::LOWER or FDPB::Option::UPPER) were not in vector format.
- Solution: specify upper/lower coordinates in the correct format
- See also:
- Options::isVector
ERROR__ILLEGAL_VALUE_FOR_LOWER_UPPER Lower and upper corner of the grid were set to wrong values. Lower and upper corners of the grid given in FDPB::options (key FDPB::Option::LOWER and FDPB::Option::UPPER) must fulfill just one condition: every coordinate of lower hast to be less (not equal!) to the corresponding coordinate of upper.
- Solution: specify a reasonable non-degenerate grid
ERROR__SETUP_REQUIRED Call setup first. This error code is set by FDPB::solve() if FDPB::q_grid or FDPB::phi_grid or FDPB::eps_grid are undefined.
- Solution: define each of the above mentioned grids or call FDPB::setup()
NUMBER_OF_ERRORS Total number of errors defined.
Constructor & Destructor Documentation
| BALL::FDPB::FDPB | ( | System & | system | ) |
Constructor. Creates an instance of FDPB and calls setup(system). The options used are the default options.
- See also:
- setup(system)
| BALL::FDPB::FDPB | ( | Options & | new_options | ) |
| virtual BALL::FDPB::~FDPB | ( | ) | [virtual] |
Destructor.
Member Function Documentation
| double BALL::FDPB::calculateReactionFieldEnergy | ( | ) | const |
Calculate the reaction field energy.
- Returns:
- reaction field energy in kJ/mol
| void BALL::FDPB::destroy | ( | ) |
Frees all allocated memory and destroys the options and results.
| void BALL::FDPB::destroyGrids | ( | ) |
Destroys all allocated grids and the atom array. This method reverts the FDPB object to the state it had prior to a call to setup. Especially it frees all memory intensive datastructures.
- destroyGrids deletes eps_grid, kappa_grid, q_grid, phi_grid, and SAS_grid. Contrary to destroy, it doesnt't clear options and results.
| double BALL::FDPB::getEnergy | ( | ) | const |
Returns the energy of the last calculation. The total electrostatic energy of the FDPB object after the last iteration (even if no convergence was reached!) is returned in units of kJ/mol.
- See also:
- getNumberOfIterations
- Returns:
- energy in kJ/mol
| Index BALL::FDPB::getErrorCode | ( | ) | const |
Return the last error code. If a method fails, an internal error code is set in FDPB. This error code can be queried by calling this method. If no error occured it should return FDPB::ERROR__NONE.
- See also:
-
ErrorCodes
Return the last error message.
- See also:
-
ErrorCodes
| Size BALL::FDPB::getNumberOfIterations | ( | ) | const |
Returns the number of iterations needed to converge. Returns the number of iterations taken in the last call to FDPB::solve(). If convergence could not be reached (i.e., the convergence criterions defined in options could not be met), -1 is returned.
- Returns:
- int number of iterations
- See also:
Option::max_iterations
Default::max_iterations
| double BALL::FDPB::getReactionFieldEnergy | ( | ) | const |
Return the reaction field energy.
- Returns:
- reaction field energy in kJ/mol
Setup with assignment of options. This method copies the options given by options into the options variable of the FDPB object and invokes setup(system) afterwards.
- See also:
- setup(System& system)
- Parameters:
-
options the new options system the molecular system to be evaluated
- Returns:
- bool true on success, call getErrorCode otherwise
General setup method. Setup calls (in this order!)
- setupAtomArray
- setupEpsGrid
- setupSASGrid
- setupKappaGrid
- setupPhiGrid
- setupQGrid
- setupBoundary
If any of theses method invocations fail, it terminates at this point and returns false.
- On successful execution it returns true and the FDPB object is ready to solve the Poisson Boltzmann equation by calling solve().
- Parameters:
-
system the molecular system to be examined.
- Returns:
- bool true on success, call getErrorCode otherwise
Setup an compact datastructure containing all charged atoms. This method creates a dynamic array containing all charged atoms.
- The method may set the error code to ERROR__CANNOT_CREATE_ATOM_ARRAY and terminate with false if insufficient virtual memory is available to create the array.
- Parameters:
-
system the system to be evaluated
- Returns:
- bool true on success, call getErrorCode otherwise
- See also:
| bool BALL::FDPB::setupBoundary | ( | ) |
Setup boundary conditions for the electrostatic potential.
Setup the dielectric grid. The Finite Difference Poisson Boltzmann Method is based on the assumption that one can determine which points on a given grid are inside a given solute (with low dielectric constant) and which points are outside (i.e., they are in the high dielectric constant solvent).
setupEpsGridcreates a grid containing the dielectric constant between any two neighbouring grid points (i.e., it contains 3 N values). Points inside the molecule (i.i, inside the radius of any atom) are set to the solute dielectric constant, all other points are set to the solvent dielectric constant.
- This method also sets the coordinates and dimensions of the grid (extracted from either options or system) and the grid spacing.
- Normally this method is not called by the user, but automatically by setup. If you consider to call it by yourself, be sure to call the single setup methods in the correct order (as described for setup).
- This method may set one of the following error codes and return false afterwards:
- ERROR__NOT_A_VECTOR_IN_UPPER_LOWER
- ERROR__ILLEGAL_VALUE_FOR_LOWER_UPPER
- Parameters:
-
system the system to be evaluated
- Returns:
- true on success, call getErrorCode otherwise
| bool BALL::FDPB::setupKappaGrid | ( | ) |
Setup the Debye Hueckel parameter grid.
| bool BALL::FDPB::setupPhiGrid | ( | ) |
Setup electrostatic potential grid
| bool BALL::FDPB::setupQGrid | ( | ) |
Setup charge grid.
Setup the ion accessible grid. Not yet implemented!
| bool BALL::FDPB::solve | ( | ) |
Solves the linearized Poisson-Boltzmann equation.
Member Data Documentation
| vector<FDPB::FastAtom>* BALL::FDPB::atom_array |
An array containing a fast representation of all atoms in the system.
- See also:
- FastAtom
vector<Position> BALL::FDPB::boundary_points_ [protected] |
double BALL::FDPB::energy_ [protected] |
The grid containing the spatial dependent dielectric constant. The (relative) dielectric constant is unitless.
- See also:
- setupEpsGrid
int BALL::FDPB::error_code_ [protected] |
const char* BALL::FDPB::error_message_[] [static, protected] |
The grid containing the modified Debye Hueckel parameter.
- See also:
- setupKappaGrid
Vector3 BALL::FDPB::lower_ [protected] |
Size BALL::FDPB::number_of_iterations_ [protected] |
Vector3 BALL::FDPB::offset_ [protected] |
The options for the FDPB calculation.
The grid containing the electrostatic potential. Before a calculation this is grid is initialized with the boundary condition. After the calculation (i.e. after a call to solve()) it contains the electrostatic potential in units of J/C resulting from the Poisson-Boltzmann equation).
- See also:
The grid containing the atom charges (distributed). Each atom's charge is distributed on the grid by setupQGrid, according to the charge distribution method specified in options.
- q_grid contains these partial charges. Units are elementary charges, if the atom charges were given in multiples of the elementary charge (Atom::setCharge).
- See also:
BALL_ELEMENTARY_CHARGE
double BALL::FDPB::reaction_field_energy_ [protected] |
The results of the last calculation.
The grid describing the solvent accessible surface of the system.
float BALL::FDPB::spacing_ [protected] |
Vector3 BALL::FDPB::upper_ [protected] |
bool BALL::FDPB::use_offset_ [protected] |