ia_bond_m – BROWNPAK

This module contains routines to evaluate bond potentials and their derivative.

The following styles are available:

Style 0. None (only topology)
Style 1. Harmonic. See bond_harm_set.
Style 2. FENE. See bond_fene_set.
Style 3. Kremer-Grest. See bond_kg_set.
Style 4. Marko-Siggia. See bond_ms_set.

Uses

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Used by

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Nodes of different colours represent the following:

Solid arrows point from a submodule to the (sub)module which it is descended from. Dashed arrows point from a module or program unit to modules which it uses. Where possible, edges connecting nodes are given different colours to make them easier to distinguish in large graphs.

Subroutines

ia_bond_setup ia_get_bond_force bond_harm_set bond_harm bond_fene_set bond_fene bond_kg_set bond_kg bond_ms_set bond_ms

Subroutines

public subroutine ia_bond_setup(num_bond_types, bond_styles, bond_params)

Sets up parameters for bond potentials

Arguments

Type	Intent	Attributes		Name
integer,	intent(in)		::	num_bond_types	Number of bond types
integer,	intent(in),	dimension(:)	::	bond_styles	Styles for each type
real(kind=rp),	intent(inout),	dimension(:,:)	::	bond_params	Parameters for each type, depending on style

public subroutine ia_get_bond_force(rij_mag, sty, params, enrg, frc, ierr)

Calculates the energy & its derivative due to a bond.

Arguments

Type	Intent	Attributes		Name
real(kind=rp),	intent(in)		::	rij_mag	Distance between bonded atoms
integer,	intent(in)		::	sty	Style of the bond
real(kind=rp),	intent(in),	dimension(:)	::	params	Parameters for bonded interaction
real(kind=rp),	intent(out)		::	enrg	Bond energy
real(kind=rp),	intent(out)		::	frc	Derivative of the potential. This is the magnitude of the force due to this potential.
integer,	intent(out)		::	ierr	Error flag

private subroutine bond_harm_set(params, k, r0)

Setter for harmonic bond interaction.

Arguments

Type	Intent	Optional	Attributes		Name
real(kind=rp),	intent(inout),		dimension(:)	::	params
real(kind=rp),	intent(in),	optional		::	k
real(kind=rp),	intent(in),	optional		::	r0

private subroutine bond_harm(r, params, enrg, frc)

Calculates energy & its derivative for harmonic bond. See bond_harm_set.

Arguments

Type	Intent	Attributes		Name
real(kind=rp),	intent(in)		::	r
real(kind=rp),	intent(in),	dimension(:)	::	params
real(kind=rp),	intent(out)		::	enrg
real(kind=rp),	intent(out)		::	frc

private subroutine bond_fene_set(params, k, rmax, r0)

Setter for FENE bond.

Arguments

Type	Intent	Optional	Attributes		Name
real(kind=rp),	intent(inout),		dimension(:)	::	params
real(kind=rp),	intent(in),	optional		::	k
real(kind=rp),	intent(in),	optional		::	rmax
real(kind=rp),	intent(in),	optional		::	r0

private subroutine bond_fene(r, params, enrg, frc, ierr)

Calculates energy & its derivative for FENE bond. See bond_fene_set.

Arguments

Type	Intent	Attributes		Name
real(kind=rp),	intent(in)		::	r
real(kind=rp),	intent(in),	dimension(:)	::	params
real(kind=rp),	intent(out)		::	enrg
real(kind=rp),	intent(out)		::	frc
integer,	intent(out)		::	ierr

private subroutine bond_kg_set(params, k, rmax, eps, sigma)

Setter for FENE bond interaction.

Arguments

Type	Intent	Optional	Attributes		Name
real(kind=rp),	intent(inout),		dimension(:)	::	params
real(kind=rp),	intent(in),	optional		::	k
real(kind=rp),	intent(in),	optional		::	rmax
real(kind=rp),	intent(in),	optional		::	eps
real(kind=rp),	intent(in),	optional		::	sigma

private subroutine bond_kg(r, params, enrg, frc, ierr)

Calculates energy & its derivative for Kremer-Grest bond. See bond_kg_set.

Arguments

Type	Intent	Attributes		Name
real(kind=rp),	intent(in)		::	r
real(kind=rp),	intent(in),	dimension(:)	::	params
real(kind=rp),	intent(out)		::	enrg
real(kind=rp),	intent(out)		::	frc
integer,	intent(out)		::	ierr

private subroutine bond_ms_set(params, lp, rmax)

Setter for Marko-Siggia bond.

Arguments

Type	Intent	Optional	Attributes		Name
real(kind=rp),	intent(inout),		dimension(:)	::	params
real(kind=rp),	intent(in),	optional		::	lp
real(kind=rp),	intent(in),	optional		::	rmax

private subroutine bond_ms(r, params, enrg, frc, ierr)

Evaluates the potential & its derivative for Marko-Siggia bond. See bond_ms_set.

Arguments

Type	Intent	Attributes		Name
real(kind=rp),	intent(in)		::	r
real(kind=rp),	intent(in),	dimension(:)	::	params
real(kind=rp),	intent(out)		::	enrg
real(kind=rp),	intent(out)		::	frc
integer,	intent(out)		::	ierr

ia_bond_m Module

Contents

Subroutines

Uses

Used by

Contents

Subroutines

Subroutines

public subroutine ia_bond_setup(num_bond_types, bond_styles, bond_params)

Arguments

public subroutine ia_get_bond_force(rij_mag, sty, params, enrg, frc, ierr)

Arguments

private subroutine bond_harm_set(params, k, r0)

Arguments

private subroutine bond_harm(r, params, enrg, frc)

Arguments

private subroutine bond_fene_set(params, k, rmax, r0)

Arguments

private subroutine bond_fene(r, params, enrg, frc, ierr)

Arguments

private subroutine bond_kg_set(params, k, rmax, eps, sigma)

Arguments

private subroutine bond_kg(r, params, enrg, frc, ierr)

Arguments

private subroutine bond_ms_set(params, lp, rmax)

Arguments

private subroutine bond_ms(r, params, enrg, frc, ierr)

Arguments