mod_nonbonded – openMMPol

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Variables

pair_allocation_chunk

Abstract Interfaces

vdw_term vdw_gterm

Derived Types

ommp_nonbonded_type

Functions

get_Rij0 get_eij get_Rij0_inter get_eij_inter

Subroutines

vdw_init vdw_set_cutoff vdw_terminate vdw_remove_potential vdw_set_pair vdw_lennard_jones vdw_lennard_jones_Rijgrad vdw_buffered_7_14 vdw_buffered_7_14_Rijgrad vdw_potential vdw_geomgrad vdw_potential_inter vdw_geomgrad_inter vdw_potential_inter_restricted vdw_geomgrad_inter_restricted

Variables

Type	Visibility	Attributes		Name		Initial
integer(kind=ip),	private,	parameter	::	pair_allocation_chunk	=	16

Abstract Interfaces

abstract interface

private subroutine vdw_term(Rij, Rij0, Eij, V)

Arguments

Type	Intent		Name
real(kind=rp),	intent(in)	::	Rij
real(kind=rp),	intent(in)	::	Rij0
real(kind=rp),	intent(in)	::	Eij
real(kind=rp),	intent(inout)	::	V

abstract interface

private subroutine vdw_gterm(Rij, Rij0, Eij, Rijgrad)

Arguments

Type	Intent		Name
real(kind=rp),	intent(in)	::	Rij
real(kind=rp),	intent(in)	::	Rij0
real(kind=rp),	intent(in)	::	Eij
real(kind=rp),	intent(out)	::	Rijgrad

Derived Types

type, public :: ommp_nonbonded_type

Derived type for storing the information relative to the calculation of non-bonding interactions

Components

Type	Visibility	Attributes		Name		Initial
type(ommp_topology_type),	public,	pointer	::	top			Data structure for topology
logical(kind=lp),	public		::	use_nl			Flag for using neighbors list
type(ommp_neigh_list),	public		::	nl			Neighbor list struture
real(kind=rp),	public,	allocatable, dimension(:)	::	vdw_r			VdW radii for the atoms of the system
real(kind=rp),	public,	allocatable, dimension(:)	::	vdw_e			Vdw energies for the atoms of fthe system
real(kind=rp),	public,	allocatable, dimension(:)	::	vdw_f			Scale factor for displacing the interaction center
integer(kind=ip),	public		::	npair	=	0	Number of nonbonded pair parameters
logical(kind=lp),	public,	allocatable	::	vdw_pair_mask_a(:,:)			Mask to apply a pair parameter to a pair of atoms dimension is Natoms x Nparams
logical(kind=lp),	public,	allocatable	::	vdw_pair_mask_b(:,:)			Mask to apply a pair parameter to a pair of atoms dimension is Natoms x Nparams
real(kind=rp),	public,	allocatable	::	vdw_pair_r(:)			Radii for the VdW atom pairs
real(kind=rp),	public,	allocatable	::	vdw_pair_e(:)			VdW energies for atom pairs
real(kind=rp),	public,	dimension(4)	::	vdw_screening	=	[0.0, 0.0, 1.0, 1.0]	Screening factors for 1,2 1,3 and 1,4 neighbours. Default vaules from tinker manual.
real(kind=rp),	public		::	radf	=	1.0	Scal factor for atomic radii/diameters (1.0 is used for diameters, 2.0 for radii)
integer(kind=ip),	public		::	radrule			Flag for the radius rule to be used
integer(kind=ip),	public		::	radtype			Flag for the radius type
integer(kind=ip),	public		::	vdwtype			Flag for the vdW type
integer(kind=ip),	public		::	epsrule			Flag for eps rule !!TODO

Functions

private pure function get_Rij0(vdw, i, j) result(Rij0)

Arguments

Type	Intent	Attributes		Name
type(ommp_nonbonded_type),	intent(in),	target	::	vdw	Nonbonded data structure
integer(kind=ip),	intent(in)		::	i	Indices of interacting atoms
integer(kind=ip),	intent(in)		::	j	Indices of interacting atoms

Return Value real(kind=rp)

private pure function get_eij(vdw, i, j) result(eij)

Arguments

Type	Intent		Name
type(ommp_nonbonded_type),	intent(in)	::	vdw	Nonbonded data structure
integer(kind=ip),	intent(in)	::	i	Indices of interacting atoms
integer(kind=ip),	intent(in)	::	j	Indices of interacting atoms

Return Value real(kind=rp)

private pure function get_Rij0_inter(vdw1, vdw2, i, j) result(Rij0)

Arguments

Type	Intent	Attributes		Name
type(ommp_nonbonded_type),	intent(in),	target	::	vdw1	Nonbonded data structure
type(ommp_nonbonded_type),	intent(in),	target	::	vdw2	Nonbonded data structure
integer(kind=ip),	intent(in)		::	i	Indices of interacting atoms
integer(kind=ip),	intent(in)		::	j	Indices of interacting atoms

Return Value real(kind=rp)

private pure function get_eij_inter(vdw1, vdw2, i, j) result(eij)

Arguments

Type	Intent		Name
type(ommp_nonbonded_type),	intent(in)	::	vdw1	Nonbonded data structure
type(ommp_nonbonded_type),	intent(in)	::	vdw2	Nonbonded data structure
integer(kind=ip),	intent(in)	::	i	Indices of interacting atoms
integer(kind=ip),	intent(in)	::	j	Indices of interacting atoms

Return Value real(kind=rp)

Subroutines

public subroutine vdw_init(vdw, top, vdw_type, radius_rule, radius_size, radius_type, epsrule, cutoff)

Initialize the non-bonded object allocating the parameters vectors

Arguments

Type	Intent	Attributes		Name
type(ommp_nonbonded_type),	intent(inout)		::	vdw
type(ommp_topology_type),	intent(in),	target	::	top
character(len=*)			::	vdw_type
character(len=*)			::	radius_rule
character(len=*)			::	radius_size
character(len=*)			::	radius_type
character(len=*)			::	epsrule
real(kind=rp)			::	cutoff

public subroutine vdw_set_cutoff(vdw, cutoff, subdivision)

Arguments

Type	Intent		Name
type(ommp_nonbonded_type),	intent(inout)	::	vdw
real(kind=rp),	intent(in)	::	cutoff
integer(kind=ip),	intent(in)	::	subdivision

public subroutine vdw_terminate(vdw)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_nonbonded_type),	intent(inout)			::	vdw

public subroutine vdw_remove_potential(vdw, i)

Remove the VdW interaction from the specified atom the atom will not interact anymore with any other atom

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_nonbonded_type),	intent(inout)			::	vdw
integer(kind=ip),	intent(in)			::	i

public subroutine vdw_set_pair(vdw, mask_a, mask_b, r, e)

Arguments

Type	Intent		Name
type(ommp_nonbonded_type),	intent(inout)	::	vdw	Nonbonded data structure
logical(kind=lp),	intent(in)	::	mask_a(vdw%top%mm_atoms)
logical(kind=lp),	intent(in)	::	mask_b(vdw%top%mm_atoms)
real(kind=rp),	intent(in)	::	r	Equilibrium distance for the pair
real(kind=rp),	intent(in)	::	e	Depth of the potential

private subroutine vdw_lennard_jones(Rij, Rij0, Eij, V)

Arguments

Type	Intent		Name
real(kind=rp),	intent(in)	::	Rij
real(kind=rp),	intent(in)	::	Rij0
real(kind=rp),	intent(in)	::	Eij
real(kind=rp),	intent(inout)	::	V

private subroutine vdw_lennard_jones_Rijgrad(Rij, Rij0, Eij, Rijgrad)

Arguments

Type	Intent		Name
real(kind=rp),	intent(in)	::	Rij
real(kind=rp),	intent(in)	::	Rij0
real(kind=rp),	intent(in)	::	Eij
real(kind=rp),	intent(out)	::	Rijgrad

private subroutine vdw_buffered_7_14(Rij, Rij0, Eij, V)

Compute the dispersion-repulsion energy using the buffered 7-14 potential. Details can be found in ref: 10.1021/jp027815

Arguments

Type	Intent		Name
real(kind=rp),	intent(in)	::	Rij
real(kind=rp),	intent(in)	::	Rij0
real(kind=rp),	intent(in)	::	Eij
real(kind=rp),	intent(inout)	::	V

private subroutine vdw_buffered_7_14_Rijgrad(Rij, Rij0, Eij, Rijgrad)

Compute the gradient of vdw energy (using the buffered 7-14 potential ref: 10.1021/jp027815) with respect to the distance between the two atoms (Rij).

Arguments

Type	Intent		Name
real(kind=rp),	intent(in)	::	Rij
real(kind=rp),	intent(in)	::	Rij0
real(kind=rp),	intent(in)	::	Eij
real(kind=rp),	intent(out)	::	Rijgrad

public subroutine vdw_potential(vdw, V)

Compute the dispersion repulsion energy for the whole system using a double loop algorithm

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_nonbonded_type),	intent(in),		target	::	vdw	Nonbonded data structure
real(kind=rp),	intent(inout)			::	V	Potential, result will be added

public subroutine vdw_geomgrad(vdw, grad)

Compute the dispersion repulsion geometric gradients for the whole system using a double loop algorithm

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_nonbonded_type),	intent(in),		target	::	vdw	Nonbonded data structure
real(kind=rp),	intent(inout)			::	grad(3,vdw%top%mm_atoms)	Gradients, result will be added

public subroutine vdw_potential_inter(vdw1, vdw2, V)

Compute the dispersion repulsion energy for the whole system using a double loop algorithm

Arguments

Type	Intent	Attributes		Name
type(ommp_nonbonded_type),	intent(in),	target	::	vdw1	Nonbonded data structure
type(ommp_nonbonded_type),	intent(in),	target	::	vdw2	Nonbonded data structure
real(kind=rp),	intent(inout)		::	V	Potential, result will be added

public subroutine vdw_geomgrad_inter(vdw1, vdw2, grad1, grad2)

Compute the dispersion repulsion energy for the whole system using a double loop algorithm

Arguments

Type	Intent	Attributes		Name
type(ommp_nonbonded_type),	intent(in),	target	::	vdw1	Nonbonded data structure
type(ommp_nonbonded_type),	intent(in),	target	::	vdw2	Nonbonded data structure
real(kind=rp),	intent(inout)		::	grad1(3,vdw1%top%mm_atoms)	Potential, result will be added
real(kind=rp),	intent(inout)		::	grad2(3,vdw2%top%mm_atoms)	Potential, result will be added

public subroutine vdw_potential_inter_restricted(vdw1, vdw2, pairs, s, n, V)

Compute the dispersion repulsion energy between two systems vdw1 and vdw2 accounting only for the pairs pairs(1,i)--pairs(2,i) and scaling each interaction by s(i).

Arguments

Type	Intent	Attributes		Name
type(ommp_nonbonded_type),	intent(in),	target	::	vdw1	Nonbonded data structure
type(ommp_nonbonded_type),	intent(in),	target	::	vdw2	Nonbonded data structure
integer(kind=ip),	intent(in)		::	pairs(2,n)	pairs of atoms for which the interaction should be computed
real(kind=rp),	intent(in)		::	s(:)	scaling factors for each interaction
integer(kind=ip),	intent(in)		::	n	number of pairs for which the interaction should be computed
real(kind=rp),	intent(inout)		::	V	Potential, result will be added

public subroutine vdw_geomgrad_inter_restricted(vdw1, vdw2, pairs, s, n, grad1, grad2)

Compute the dispersion repulsion energy for the whole system using a double loop algorithm

Arguments

Type	Intent	Attributes		Name
type(ommp_nonbonded_type),	intent(in),	target	::	vdw1	Nonbonded data structure
type(ommp_nonbonded_type),	intent(in),	target	::	vdw2	Nonbonded data structure
integer(kind=ip),	intent(in)		::	pairs(2,n)	pairs of atoms for which the interaction should be computed
real(kind=rp),	intent(in)		::	s(:)	scaling factors for each interaction
integer(kind=ip),	intent(in)		::	n	number of pairs for which the interaction should be computed
real(kind=rp),	intent(inout)		::	grad1(3,vdw1%top%mm_atoms)	Potential, result will be added
real(kind=rp),	intent(inout)		::	grad2(3,vdw2%top%mm_atoms)	Potential, result will be added

mod_nonbonded Module

Contents

Uses

Used by

Contents

Variables

Abstract Interfaces

abstract interface

private subroutine vdw_term(Rij, Rij0, Eij, V)

Arguments

abstract interface

private subroutine vdw_gterm(Rij, Rij0, Eij, Rijgrad)

Arguments

Derived Types

type, public :: ommp_nonbonded_type

Components

Functions

private pure function get_Rij0(vdw, i, j) result(Rij0)

Arguments

Return Value real(kind=rp)

private pure function get_eij(vdw, i, j) result(eij)

Arguments

Return Value real(kind=rp)

private pure function get_Rij0_inter(vdw1, vdw2, i, j) result(Rij0)

Arguments

Return Value real(kind=rp)

private pure function get_eij_inter(vdw1, vdw2, i, j) result(eij)

Arguments

Return Value real(kind=rp)

Subroutines

public subroutine vdw_init(vdw, top, vdw_type, radius_rule, radius_size, radius_type, epsrule, cutoff)

Arguments

public subroutine vdw_set_cutoff(vdw, cutoff, subdivision)

Arguments

public subroutine vdw_terminate(vdw)

Arguments

public subroutine vdw_remove_potential(vdw, i)

Arguments

public subroutine vdw_set_pair(vdw, mask_a, mask_b, r, e)

Arguments

private subroutine vdw_lennard_jones(Rij, Rij0, Eij, V)

Arguments

private subroutine vdw_lennard_jones_Rijgrad(Rij, Rij0, Eij, Rijgrad)

Arguments

private subroutine vdw_buffered_7_14(Rij, Rij0, Eij, V)

Arguments

private subroutine vdw_buffered_7_14_Rijgrad(Rij, Rij0, Eij, Rijgrad)

Arguments

public subroutine vdw_potential(vdw, V)

Arguments

public subroutine vdw_geomgrad(vdw, grad)

Arguments

public subroutine vdw_potential_inter(vdw1, vdw2, V)

Arguments

public subroutine vdw_geomgrad_inter(vdw1, vdw2, grad1, grad2)

Arguments

public subroutine vdw_potential_inter_restricted(vdw1, vdw2, pairs, s, n, V)

Arguments

public subroutine vdw_geomgrad_inter_restricted(vdw1, vdw2, pairs, s, n, grad1, grad2)

Arguments