ForceParam_t Struct Reference

Used to configure Force_t class. More...

#include <fparam.h>

List of all members.

Public Attributes
MD_AtomPrm *	atomprm
MD_BondPrm *	bondprm
MD_AnglePrm *	angleprm
MD_TorsPrm *	dihedprm
MD_TorsPrm *	imprprm
MD_NbfixPrm *	nbfixprm
int32	atomprm_len
int32	bondprm_len
int32	angleprm_len
int32	dihedprm_len
int32	imprprm_len
int32	nbfixprm_len
MD_Atom *	atom
MD_Bond *	bond
MD_Angle *	angle
MD_Tors *	dihed
MD_Tors *	impr
MD_Excl *	excl
int32	atom_len
int32	bond_len
int32	angle_len
int32	dihed_len
int32	impr_len
int32	excl_len
double	cutoff
double	elec_cutoff
double	vdw_cutoff
double	switchdist
double	elec_const
double	dielectric
double	scaling14
double	ewald_coef
double	radius1
double	radius2
double	length1
double	length2
double	konst1
double	konst2
int32	exp1
int32	exp2
int32	forcetypes
int32	exclpolicy
int32	elecopts
int32	vdwopts
int32	bresopts
int32	shell_width
double	cutoff_ratio
double	delta_dis
double	cell_margin

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Detailed Description

Used to configure Force_t class.

User sets the internal fields of this class in order to configure the evaluation performed by the Force_t class. The contents of the ForceParam_t container are intended to be setup once before constructing the Force_t object, then treated as read-only data.

The user provides and retains ownership of memory buffer space for all arrays. The force field parameter and topology arrays all follow the MDAPI guidelines as defined by mdtypes.h file. In particular, it is expected that the proper cross-indexing between topology and force field parameter arrays have been established. The best way to do this is to use the MDIO library for reading the relevant force field parameter and topology files.

The parameter ForceParam_t::atom_len indicates the number of atoms in the system, providing the expected array length of the ForceResult_t force arrays and the pos array passed to force_create() and force_compute().

The boundary restraint and nonbonded parameters follow the NAMD conventions, as described in its documentation.

The field ForceParam_t::forcetype specifies what parts of the force field are to be evaluated. It is assigned a bitwise ORed collection of ForceType_t constants.

The remaining fields ForceParam_t::excltype, ForceParam_t::electype, ForceParam_t::vdwtype, and ForceParam_t::brestype are each assigned a single value from respective enumerated types ForceExcltype_t, ForceElectype_t, ForceVdwtype_t, and ForceBrestype_t. These, respectively, indicate which type of interactions are to be excluded, the type and smoothing of electrostatic interactions, the type and switching of van der Waals interactions, and the type of boundary restraints.

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Member Data Documentation

MD_Angle* ForceParam_t::angle

Array of angles.

int32 ForceParam_t::angle_len

Length of angle array.

MD_AnglePrm* ForceParam_t::angleprm

Array of angle parameters.

int32 ForceParam_t::angleprm_len

Length of angle parameters array.

MD_Atom* ForceParam_t::atom

Array of atoms (contains mass and charge).

int32 ForceParam_t::atom_len

Length of atom array (number of atoms in system).

MD_AtomPrm* ForceParam_t::atomprm

Array of atom parameters.

int32 ForceParam_t::atomprm_len

Length of atom parameters array.

MD_Bond* ForceParam_t::bond

Array of bonds.

int32 ForceParam_t::bond_len

Length of bond array.

MD_BondPrm* ForceParam_t::bondprm

Array of bond parameters.

int32 ForceParam_t::bondprm_len

Length of bond parameters array.

int32 ForceParam_t::bresopts

Options for boundary restraints, generally intended for nonperiodic boundaries.

double ForceParam_t::cell_margin

Add to minimum cell size.

double ForceParam_t::cutoff

Cutoff distance used to define both electrostatics and van der Waals interactions.

double ForceParam_t::cutoff_ratio

Make minimum cell size at least this fraction of cutoff (typically 1/shell_width).

double ForceParam_t::delta_dis

Maximum allowable distance any atom can travel before pairlists must be regenerated (default is 1.5 Angstroms).

double ForceParam_t::dielectric

Dielectric constant, typically set to 1.0.

MD_Tors* ForceParam_t::dihed

Array of dihedrals.

int32 ForceParam_t::dihed_len

Length of dihedral array.

MD_TorsPrm* ForceParam_t::dihedprm

Array of dihedral parameters.

int32 ForceParam_t::dihedprm_len

Length of dihedral parameters array.

double ForceParam_t::elec_const

Constant for electrostatic interactions, typically should be defined using MD_COULOMB from MDAPI mdtypes.h file.

double ForceParam_t::elec_cutoff

Cutoff distance for electrostatics.

int32 ForceParam_t::elecopts

Options for electrostatic forces.

double ForceParam_t::ewald_coef

Ewald coefficient for real space part.

MD_Excl* ForceParam_t::excl

Array of nonbonded exclusions.

int32 ForceParam_t::excl_len

Length of nonbonded exclusion array.

int32 ForceParam_t::exclpolicy

Gives nonbonded exclusion policy.

int32 ForceParam_t::exp1

Exponent for first harmonic potential. Should be an even positive integer.

int32 ForceParam_t::exp2

Exponent for second harmonic potential. Should be an even positive integer.

int32 ForceParam_t::forcetypes

Indicates types of forces to be computed.

MD_Tors* ForceParam_t::impr

Array of impropers.

int32 ForceParam_t::impr_len

Length of improper array.

MD_TorsPrm* ForceParam_t::imprprm

Array of improper parameters.

int32 ForceParam_t::imprprm_len

Length of improper parameters array.

double ForceParam_t::konst1

Constant for first harmonic potential.

double ForceParam_t::konst2

Constant for second harmonic potential.

double ForceParam_t::length1

For cylindrical restraints: distance at which first potential takes effect along cylinder axis.

double ForceParam_t::length2

For cylindrical restraints: distance at which second potential takes effect along cylinder axis.

MD_NbfixPrm* ForceParam_t::nbfixprm

Array of nonbonded parameters to override the combined pairs of atom parameters.

int32 ForceParam_t::nbfixprm_len

Length of nonbonded parameters array.

double ForceParam_t::radius1

Distance at which first potential boundary takes effect, measured as radius from center.

double ForceParam_t::radius2

Distance at which second potential boundary takes effect, measured as radius from center.

double ForceParam_t::scaling14

Extra multiplicative constant for electrostatic interactions between 1-4 pairs, applied only if FORCE_EXCL_SCAL14 flag is set, typically set to 1.0.

int32 ForceParam_t::shell_width

Thickness of shell of grid cells to evaluate (must be at least 1, max and default is 3).

double ForceParam_t::switchdist

Switching distance for van der Waals (needs to be strictly less than the cutoff).

double ForceParam_t::vdw_cutoff

Cutoff distance for van der Waals.

int32 ForceParam_t::vdwopts

Options for van der Waals forces.

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The documentation for this struct was generated from the following file:

• force/fparam.h

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