Force_t Struct Reference

Definition of Force_t object. More...

#include <defn.h>

List of all members.

Public Attributes
ForceParam *	param
ForceSelect *	select
ForceDomain *	domain
int32 *	idmap
int32 *	mapnb
int32 *	atom_bond_sel
int32 *	atom_angle_sel
int32 *	atom_dihed_sel
int32 *	atom_impr_sel
int32 *	abset_sel
int32 *	total_sel
int32	atom_bond_sel_len
int32	atom_angle_sel_len
int32	atom_dihed_sel_len
int32	atom_impr_sel_len
int32	abset_sel_len
int32	total_sel_len
int32	is_alloc_sel
double	u_buffer
double *	e_buffer
MD_Dvec *	f_buffer
MD_Dvec *	trpos
MD_Dvec *	poswrap
double	elec_const
double	elec_cutoff2
double	inv_elec_cutoff2
double	ewald_grad_coef
double	vdw_cutoff2
double	switch_dist2
double	inv_denom_switch
ForceVdwparam *	vdwparam
ForceBucksafe *	bucksafe
MD_Dvec	v1
MD_Dvec	v2
MD_Dvec	v3
double	lv1
double	lv2
double	lv3
MD_Dvec	nv1
MD_Dvec	nv2
MD_Dvec	nv3
MD_Dvec	center
MD_Dvec	lowerc
MD_Dvec	ta1
MD_Dvec	ta2
MD_Dvec	ta3
MD_Dvec	offset_table [27]
double	volume
int32	is_periodic
int32	is_orthogonal
double	domain_len_frac
int32	max_steps
int32	cnt_steps
int32	is_domain_update
int32	is_minmax
MD_Dvec	smin
MD_Dvec	smax
int32	is_fixed_lattice
int32	k1
int32	k2
int32	k3
MD_Dvec	dv1
MD_Dvec	dv2
MD_Dvec	dv3
MD_Dvec	tb1
MD_Dvec	tb2
MD_Dvec	tb3
double	ucellsize
double	vcellsize
double	wcellsize
double	inv_ucellsize
double	inv_vcellsize
double	inv_wcellsize
MD_Dvec	lowcell
MD_Dvec	delta
MD_Dvec	gscale
ForceCell *	cell
int32	maxcells
int32	ncells
int32	nucells
int32	nvcells
int32	nwcells
int32 *	next
double	outer_cutoff2
double	delta_dis2
MD_Dvec *	pos_init
MD_Dvec *	wrap_save
ForcePairlist *	pairlist
int32	pairlist_set_id
int32	need_pairlist_regen
int32 **	excl_list
int32 **	scaled14_list
int32 **	exclx
int32 **	excl12
int32 **	excl13
int32 **	excl14
int32 **	scaled14
int32 *	lenx
int32 *	len12
int32 *	len13
int32 *	accum
int32 *	dest
int32	is_bres_term1
int32	is_bres_term2
double	sq_minradius
double	minlength

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Detailed Description

Definition of Force_t object.

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Member Data Documentation

int32* Force_t::abset_sel

combined sets A and B of selected pairs

int32 Force_t::abset_sel_len

length of abset_sel array

int32* Force_t::accum

for merging lists

int32* Force_t::atom_angle_sel

list of atoms involved in selected angles

int32 Force_t::atom_angle_sel_len

length of atom_angle_sel array

int32* Force_t::atom_bond_sel

list of atoms involved in selected bonds

int32 Force_t::atom_bond_sel_len

length of atom_bond_sel array

int32* Force_t::atom_dihed_sel

list of atoms involved in selected diheds

int32 Force_t::atom_dihed_sel_len

length of atom_dihed_sel array

int32* Force_t::atom_impr_sel

list of atoms involved in selected imprs

int32 Force_t::atom_impr_sel_len

length of atom_impr_sel array

ForceBucksafe* Force_t::bucksafe

square matrix of extra coefficients needed for safe extension to Buckingham, accessed by atom type numbers

MD_Dvec Force_t::center

center of cell

int32 Force_t::cnt_steps

count number of force_compute() calls, range 0..max_steps

MD_Dvec Force_t::delta

displacement of transformed lower corner from origin

int32* Force_t::dest

for merging lists

ForceDomain* Force_t::domain

points to user domain definition

double Force_t::domain_len_frac

Where do we place "walls" for nonperiodic domain? The walled region is mapped into the unit cube and used to determine gridcell hash. This parameter is fraction of length between furthest atoms. (try 0.9 for gridcell?)

MD_Dvec Force_t::dv3

lattice vector "deltas," i.e. v1=k1*dv1, v2=k2*dv2, v3=k3*dv3

double* Force_t::e_buffer

alternate buffer for atom/bond potentials, might need to be as long as max{ atom_len, bond_len, angle_len, dihed_len, impr_len }

double Force_t::elec_const

electrostatic constant

double Force_t::elec_cutoff2

square of electrostatic cutoff distance

double Force_t::ewald_grad_coef

coefficient for Ewald real space gradient

int32** Force_t::excl12

lists for 1-2 exclusions (from MD_Bond)

int32** Force_t::excl13

lists for 1-3 exclusions

int32** Force_t::excl14

lists for 1-4 exclusions

int32** Force_t::excl_list

nonbonded exclusion list

int32** Force_t::exclx

explicit exclusions (from MD_Excl)

MD_Dvec* Force_t::f_buffer

alternate buffer for atomic forces

MD_Dvec Force_t::gscale

grid cell hashing scale factor for transformed coordinates

int32* Force_t::idmap

identity mapping for atom/bond selection, might need to be as long as max{ atom_len, bond_len, angle_len, dihed_len, impr_len }

double Force_t::inv_denom_switch

inverse of denominator for switching

double Force_t::inv_elec_cutoff2

multiplicative inverse of elec_cutoff2

int32 Force_t::is_alloc_sel

bit mask showing which arrays allocated

int32 Force_t::is_bres_term1

first term for boundary restraint is active

int32 Force_t::is_bres_term2

second term for boundary restraint is active

int32 Force_t::is_domain_update

flag set to "true" (nonzero) to indicate that the domain needs to be updated using force_setup_domain()

int32 Force_t::is_fixed_lattice

flag set to indicate use of fixed lattice

int32 Force_t::is_orthogonal

Boolean indicating that: v1=(|v1|,0,0); v2=(0,|v2|,0); v3=(0,0,|v3|)

int32 Force_t::is_periodic

bit-flag indicating periodicity of cell

int32 Force_t::k3

positive integer subdivisions of cell basis vectors

int32* Force_t::len12

counters for excl12 lists

int32* Force_t::len13

counters for excl13 lists

int32* Force_t::lenx

counters for exclx lists

MD_Dvec Force_t::lowcell

lower corner of grid cells (for nonperiodic systems, grid cells might cover larger area than domain)

MD_Dvec Force_t::lowerc

lower corner of cell

double Force_t::lv3

lengths of cell basis vectors

int32* Force_t::mapnb

pairwise set membership for each atom, FORCE_INDEX_ASET indicates atom in set A, FORCE_INDEX_BSET indicates atom in set B, both indicates there is no atom selection

int32 Force_t::max_steps

for nonperiodic systems, maximum number of force_compute() calls before domain update

double Force_t::minlength

minimum length

MD_Dvec Force_t::nv3

normalized basis vectors

MD_Dvec Force_t::offset_table[27]

gives quick lookup of 1-away periodic offsets that map back into domain

ForceParam* Force_t::param

points to user fundamental parameters

MD_Dvec* Force_t::poswrap

offset for periodic wrapping of atoms back into cell domain; each element is an integer linear combination of v1, v2, v3

int32** Force_t::scaled14

lists for scaled 1-4 exclusions

int32** Force_t::scaled14_list

list of scaled 1-4 interactions

ForceSelect* Force_t::select

points to user atom/bond selection

double Force_t::sq_minradius

square of minimum radius

double Force_t::switch_dist2

square of van der Waals switch distance

MD_Dvec Force_t::ta3

rows of transformation defined by: v1 -> (1,0,0); v2 -> (0,1,0); v3 -> (0,0,1)

MD_Dvec Force_t::tb3

rows of transformation defined by: dv1->(1,0,0); dv2->(0,1,0); dv3->(0,0,1)

int32* Force_t::total_sel

list of atoms to accumulate into total

int32 Force_t::total_sel_len

length of total_sel array

MD_Dvec* Force_t::trpos

transformed positions into the unit periodic cell [0,1)^3; nonperiodic directions might extend beyond the unit cell

double Force_t::u_buffer

alternate buffer for potential energy

MD_Dvec Force_t::v3

cell basis vectors

double Force_t::vdw_cutoff2

square of van der Waals cutoff distance

ForceVdwparam* Force_t::vdwparam

square matrix of van der Waals parameters accessed by atom type numbers

double Force_t::volume

computed volume of domain

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

• force/defn.h

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