mod_bonded – openMMPol

Module to handle the bonded part of the FF, it closely follows the AMOEBA functional form.

Uses

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Variables

OMMP_ANG_SIMPLE OMMP_ANG_H0 OMMP_ANG_H1 OMMP_ANG_H2 OMMP_ANG_INPLANE OMMP_ANG_INPLANE_H0 OMMP_ANG_INPLANE_H1

Subroutines

bond_init bond_potential bond_geomgrad angle_init angle_potential angle_geomgrad strbnd_init strbnd_potential strbnd_geomgrad urey_init urey_potential urey_geomgrad opb_init opb_potential opb_geomgrad pitors_init pitors_potential pitors_geomgrad torsion_init torsion_potential torsion_geomgrad imptorsion_potential imptorsion_geomgrad imptorsion_init angtor_init strtor_init angtor_potential angtor_geomgrad strtor_potential strtor_geomgrad tortor_init tortor_newmap tortor_potential tortor_geomgrad bonded_terminate bond_terminate angle_terminate strbnd_terminate urey_terminate opb_terminate pitors_terminate torsion_terminate imptorsion_terminate tortor_terminate angtor_terminate strtor_terminate

Variables

Type	Visibility	Attributes		Name		Initial
integer(kind=ip),	public,	parameter	::	OMMP_ANG_SIMPLE	=	0	Simple angle with no difference for hydrogen environments
integer(kind=ip),	public,	parameter	::	OMMP_ANG_H0	=	1	Simple angle with two different hydrogen environments
integer(kind=ip),	public,	parameter	::	OMMP_ANG_H1	=	2	Simple angle with three different hydrogen environments
integer(kind=ip),	public,	parameter	::	OMMP_ANG_H2	=	3	Simple angle with four different hydrogen environments
integer(kind=ip),	public,	parameter	::	OMMP_ANG_INPLANE	=	4	In-plane angle with no difference for hydrogen environments
integer(kind=ip),	public,	parameter	::	OMMP_ANG_INPLANE_H0	=	5	In-plane angle with two different hydrogen environments
integer(kind=ip),	public,	parameter	::	OMMP_ANG_INPLANE_H1	=	6	In-plane angle with three different hydrogen environments

Derived Types

type, public :: ommp_bonded_type

Components

Type	Visibility	Attributes		Name		Initial
type(ommp_topology_type),	public,	pointer	::	top			Data structure for topology
integer(kind=ip),	public		::	nbond			Number of bond terms in the potential energy function
integer(kind=ip),	public,	allocatable	::	bondat(:,:)			Atoms involved in the ith bond term
real(kind=rp),	public		::	bond_cubic			3rd and 4th order terms coefficients, corresponding to $k^{(2)}$ and $k^{(3)}$
real(kind=rp),	public		::	bond_quartic			3rd and 4th order terms coefficients, corresponding to $k^{(2)}$ and $k^{(3)}$
real(kind=rp),	public,	allocatable	::	kbond(:)			Force constants for bond terms
real(kind=rp),	public,	allocatable	::	l0bond(:)			Equilibrium lengths for bonds
logical(kind=lp),	public		::	use_bond	=	.false.	Flag to enable the calculation of bond terms in potential energy function
integer(kind=ip),	public		::	nangle			Number of angle terms in the potential energy function
integer(kind=ip),	public,	allocatable	::	angleat(:,:)			Atoms involved in the ith angle term
integer(kind=ip),	public,	allocatable	::	anglety(:)			Type of function to be used for ith angle term
integer(kind=ip),	public,	allocatable	::	angauxat(:)			Auxiliary atom to be used in calculaton of ith angle term
real(kind=rp),	public		::	angle_cubic			Coefficients for 3rd to 6th order terms corresponding to $k^{(3)}$ ... $k^{(6)}$ .
real(kind=rp),	public		::	angle_quartic			Coefficients for 3rd to 6th order terms corresponding to $k^{(3)}$ ... $k^{(6)}$ .
real(kind=rp),	public		::	angle_pentic			Coefficients for 3rd to 6th order terms corresponding to $k^{(3)}$ ... $k^{(6)}$ .
real(kind=rp),	public		::	angle_sextic			Coefficients for 3rd to 6th order terms corresponding to $k^{(3)}$ ... $k^{(6)}$ .
real(kind=rp),	public,	allocatable	::	kangle(:)			Force constants for the ith angle term
real(kind=rp),	public,	allocatable	::	eqangle(:)			Equilibrium angle for the ith angle term
logical(kind=lp),	public		::	use_angle	=	.false.	Flag to enable the calculation of angle terms in potential energy function
integer(kind=ip),	public		::	nstrbnd			Number of stretching-bending coupling terms in potential energy function
integer(kind=ip),	public,	allocatable	::	strbndat(:,:)			Atoms involved in the ith stretching-bending term
real(kind=rp),	public,	allocatable	::	strbndk1(:)			Force constants for the ith stretching-bending term ( $k_1$ and $k_2$ )
real(kind=rp),	public,	allocatable	::	strbndk2(:)			Force constants for the ith stretching-bending term ( $k_1$ and $k_2$ )
real(kind=rp),	public,	allocatable	::	strbndthet0(:)			Equilibrium angle for the ith stretching-bending term
real(kind=rp),	public,	allocatable	::	strbndl10(:)			Equilibrium distances for the ith stretching-bending term
real(kind=rp),	public,	allocatable	::	strbndl20(:)			Equilibrium distances for the ith stretching-bending term
logical(kind=lp),	public		::	use_strbnd	=	.false.	Flag to enable calculation of stretching-bending coupling terms in potential energy function
integer(kind=ip),	public		::	nangtor
integer(kind=ip),	public,	allocatable	::	angtorat(:,:)
integer(kind=ip),	public,	allocatable	::	angtor_t(:)
integer(kind=ip),	public,	allocatable	::	angtor_a(:,:)
real(kind=rp),	public,	allocatable	::	angtork(:,:)
logical(kind=lp),	public		::	use_angtor	=	.false.
integer(kind=ip),	public		::	nstrtor
integer(kind=ip),	public,	allocatable	::	strtorat(:,:)
integer(kind=ip),	public,	allocatable	::	strtor_t(:)
integer(kind=ip),	public,	allocatable	::	strtor_b(:,:)
real(kind=rp),	public,	allocatable	::	strtork(:,:)
logical(kind=lp),	public		::	use_strtor	=	.false.
integer(kind=ip),	public		::	nurey			Number of Urey-Bradley terms in potential energy function
integer(kind=ip),	public,	allocatable	::	ureyat(:,:)			Atoms involved in ith Urey-Bradley term
real(kind=rp),	public		::	urey_cubic			3rd and 4th order constants for U-B potential ( $k^{(3)}$ and $k^{(4)}$ )
real(kind=rp),	public		::	urey_quartic			3rd and 4th order constants for U-B potential ( $k^{(3)}$ and $k^{(4)}$ )
real(kind=rp),	public,	allocatable	::	kurey(:)			Force constants for U-B terms
real(kind=rp),	public,	allocatable	::	l0urey(:)			Equilibrium distance for U-B potentials
logical(kind=lp),	public		::	use_urey	=	.false.	Flag to enable calculation of U-B terms in the potential energy function
integer(kind=ip),	public		::	nopb			Number of out-of-plane bending function in potential energy func.
integer(kind=ip),	public,	allocatable	::	opbat(:,:)			Atoms involved in ith oop bending function
real(kind=rp),	public		::	opb_cubic	=	0.0	Coefficients for 3rd to 6th order terms corresponding to $k^{(3)}$ ... $k^{(6)}$ for out-of-plane bending.
real(kind=rp),	public		::	opb_quartic	=	0.0	Coefficients for 3rd to 6th order terms corresponding to $k^{(3)}$ ... $k^{(6)}$ for out-of-plane bending.
real(kind=rp),	public		::	opb_pentic	=	0.0	Coefficients for 3rd to 6th order terms corresponding to $k^{(3)}$ ... $k^{(6)}$ for out-of-plane bending.
real(kind=rp),	public		::	opb_sextic	=	0.0	Coefficients for 3rd to 6th order terms corresponding to $k^{(3)}$ ... $k^{(6)}$ for out-of-plane bending.
real(kind=rp),	public,	allocatable	::	kopb(:)			Force constants for ith out-of plane bending
logical(kind=lp),	public		::	use_opb	=	.false.	Flag to enable out-of-plane bending calculation
integer(kind=ip),	public		::	npitors
integer(kind=ip),	public,	allocatable	::	pitorsat(:,:)
real(kind=rp),	public,	allocatable	::	kpitors(:)
logical(kind=lp),	public		::	use_pitors	=	.false.
integer(kind=ip),	public		::	ntorsion
integer(kind=ip),	public,	allocatable	::	torsionat(:,:)
integer(kind=ip),	public,	allocatable	::	torsn(:,:)
real(kind=rp),	public,	allocatable	::	torsamp(:,:)
real(kind=rp),	public,	allocatable	::	torsphase(:,:)
logical(kind=lp),	public		::	use_torsion	=	.false.
integer(kind=ip),	public		::	nimptorsion
integer(kind=ip),	public,	allocatable	::	imptorsionat(:,:)
integer(kind=ip),	public,	allocatable	::	imptorsn(:,:)
real(kind=rp),	public,	allocatable	::	imptorsamp(:,:)
real(kind=rp),	public,	allocatable	::	imptorsphase(:,:)
logical(kind=lp),	public		::	use_imptorsion	=	.false.
integer(kind=ip),	public		::	ntortor
integer(kind=ip),	public,	allocatable	::	tortorat(:,:)
integer(kind=ip),	public,	allocatable	::	tortorprm(:)
integer(kind=ip),	public,	allocatable	::	ttmap_shape(:,:)
real(kind=rp),	public,	allocatable	::	ttmap_ang1(:)
real(kind=rp),	public,	allocatable	::	ttmap_ang2(:)
real(kind=rp),	public,	allocatable	::	ttmap_v(:)
real(kind=rp),	public,	allocatable	::	ttmap_vx(:)
real(kind=rp),	public,	allocatable	::	ttmap_vy(:)
real(kind=rp),	public,	allocatable	::	ttmap_vxy(:)
logical(kind=lp),	public		::	use_tortor	=	.false.

Functions

private pure function cos_torsion(top, idx)

Compute the cosine of torsional angle between four atoms specified with indices idx

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_topology_type),	intent(in)			::	top
integer(kind=ip),	intent(in)			::	idx(4)

Return Value real(kind=rp)

private pure function ang_torsion(top, idx)

Compute the torsional angle between four atoms specified with indices idx; results are in range [-pi;pi]

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_topology_type),	intent(in)			::	top
integer(kind=ip),	intent(in)			::	idx(4)

Return Value real(kind=rp)

Subroutines

public subroutine bond_init(bds, n)

Initialize array used in calculation of bond stratching terms of potential energy

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type)				::	bds
integer(kind=ip)				::	n	Number of bond stretching functions in the potential energy of the system

public subroutine bond_potential(bds, V)

Compute the bond-stretching terms of the potential energy.
They are computed according to the general formula adopted in AMOEBA Force Field: $U_{bond} = \sum_i k_i \Delta l_i^2 \large(1 + k^{(3)}\Delta l_i + k^{(4)}\Delta l_i^2 \large)$ $\Delta l_i = l_i - l^{(eq)}_i$

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	V	Bond potential, result will be added to V

public subroutine bond_geomgrad(bds, grad)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds	Bonded potential data structure
real(kind=rp),	intent(inout)			::	grad(3,bds%top%mm_atoms)	Gradients of bond stretching terms of potential energy

public subroutine angle_init(bds, n)

Initialize arrays used in calculation of angle bending functions

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds
integer(kind=ip)				::	n	Number of angle bending functions in the potential energy of the system

public subroutine angle_potential(bds, V)

Compute angle-bending terms of the potential energy function.
Simple angle terms are computed according to the formula: $U_{angle} = \sum_i k_i \Delta \theta_i^2 \large(1 + \sum_{j=1}^4 k^{(j+2)} \Delta \theta_i^j \large)$ $\Delta \theta_i = \theta_i - \theta^{(eq)}_i$
Out-of plane angle are more complex. First, central atom has to be a trigonal center, the other two atoms together with the auxliary atom (that is the remaining one connected to the trigonal center) define the projection plane. During the first run the auxiliary atom is found and saved. Then, the trigonal center is projected on the plane defined by the other three atoms, and the angle is the one defined by the projection (which is the vertex, and the other two atoms -- the auxiliary is excluded). Then the same formula used for simple angle terms is used. Trigonal center Normal vector of the projection plane

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	V	Bond potential, result will be added to V

public subroutine angle_geomgrad(bds, grad)

Trigonal center

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds	Bonded potential data structure
real(kind=rp),	intent(inout)			::	grad(3,bds%top%mm_atoms)	Gradients of bond stretching terms of potential energy

public subroutine strbnd_init(bds, n)

Initialize arrays for calculation of stretch-bend cross term potential

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds
integer(kind=ip)				::	n	Number of stretch-bend functions in the potential energy of the system

public subroutine strbnd_potential(bds, V)

Compute the stretch-bend cross term potential.
Those terms are computed according the following formula: $U_{bond/angle} = (k_i \Delta l_i + k_j \Delta l_j) \Delta \theta_{ij}$ where $\theta_{ij}$ is the angle delimited by the bond $i$ and $j$ .
The force constants $k_i$ and $k_j$ are explicitely defined in the FF, while the equilibrium values are the same as for stretching and bending terms.

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	V	Stretch-bend cross term potential, result will be added to V

public subroutine strbnd_geomgrad(bds, grad)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	grad(3,bds%top%mm_atoms)	Gradients of bond stretching terms of potential energy

public subroutine urey_init(bds, n)

Initialize Urey-Bradley potential arrays

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds
integer(kind=ip)				::	n	Number of Urey-Bradley functions in the potential energy of the system

public subroutine urey_potential(bds, V)

Compute the Urey-Bradley potential.
This is basically a virtual bond, with its stretching harminic potential that connect two otherwise un-connected bonds. The same potential formula used for normal stretching is used.

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	V	Urey-Bradley potential, result will be added to V

public subroutine urey_geomgrad(bds, grad)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds	Bonded potential data structure
real(kind=rp),	intent(inout)			::	grad(3,bds%top%mm_atoms)	Gradients of bond stretching terms of potential energy

public subroutine opb_init(bds, n, opbtype)

Initialize arrays for out-of-plane bending potential calculation.

Arguments

Type	Intent		Name
type(ommp_bonded_type),	intent(inout)	::	bds
integer(kind=ip)		::	n	Number of out of plane Bending functions in the potential energy of the system
character(len=*)		::	opbtype

public subroutine opb_potential(bds, V)

Computes the out-of-plane bending potential.
With Allinger formula: similarly to in plane angles, here we are considering a trigonal center, where D is the central atom and A, B, C are connected to D. Allinger formula consider the angle between vector $\vec{AD}$ and the normal vector of plane ABC, using $\frac{\pi}{2}$ as implicit equilibrium value. The formula for this potential term is: $U_{out-of-plane} = \sum_i k_i \chi_i^2 \large(1 + \sum_{j=1}^4 k^{(j+2)} \chi_i^j \large)$

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	V	out-of-plane potential, result will be added to V

public subroutine opb_geomgrad(bds, grad)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	grad(3,bds%top%mm_atoms)	Gradients of bond stretching terms of potential energy

public subroutine pitors_init(bds, n)

Initialize arrays needed to compute pi-torsion potential

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds
integer(kind=ip)				::	n	Number of out of plane pi-torsion functions in the potential enerpgy of the system

public subroutine pitors_potential(bds, V)

Compute pi-torsion terms of the potential.
This potential is defined on a $\pi$ -system, and uses the coordinates of six atoms A...F the central "double" bond is A-B, then C and D are connected to A while E and F are connected to B. So two plane ACD and BEF are defined. The potential is computed using the dihedral angle of the normal vector of those two planes, connected by segment A-B ( $\theta$ ).
The formula used is: $U_{\pi-torsion} = \sum_i k_i \large(1 + cos(2\theta-\pi) \large)$

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	V	pi-torsion potential, result will be added to V

public subroutine pitors_geomgrad(bds, grad)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	grad(3,bds%top%mm_atoms)	improper torsion potential, result will be added to V

public subroutine torsion_init(bds, n)

Initialize torsion potential arrays

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds
integer(kind=ip)				::	n	Number of torsion functions in the potential energy of the system

public subroutine torsion_potential(bds, V)

Compute torsion potential

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	V	torsion potential, result will be added to V

public subroutine torsion_geomgrad(bds, grad)

Compute torsion potential

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	grad(3,bds%top%mm_atoms)	Gradients of bond stretching terms of potential energy

public subroutine imptorsion_potential(bds, V)

Compute torsion potential

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	V	improper torsion potential, result will be added to V

public subroutine imptorsion_geomgrad(bds, grad)

Compute torsion potential

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	grad(3,bds%top%mm_atoms)	improper torsion potential, result will be added to V

public subroutine imptorsion_init(bds, n)

Initialize improper torsion potential arrays

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds
integer(kind=ip)				::	n	Number of improper torsion functions in the potential energy of the system

public subroutine angtor_init(bds, n)

Initialize angle-torsion coupling potential arrays

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds
integer(kind=ip)				::	n	Number of angle torsion coupling functions in the potential energy of the system

public subroutine strtor_init(bds, n)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds
integer(kind=ip)				::	n

public subroutine angtor_potential(bds, V)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	V

public subroutine angtor_geomgrad(bds, grad)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	grad(3,bds%top%mm_atoms)	improper torsion potential, result will be added to V

public subroutine strtor_potential(bds, V)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	V

public subroutine strtor_geomgrad(bds, grad)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	grad(3,bds%top%mm_atoms)	improper torsion potential, result will be added to V

public subroutine tortor_init(bds, n)

Initialize torsion-torsion correction potential arrays

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds
integer(kind=ip)				::	n	Number of torsion-torsion 'map' functions in the potential energy of the system

public subroutine tortor_newmap(bds, d1, d2, ang1, ang2, v)

Store in module memory the data describing a new torsion-torsion map

Arguments

Type	Intent		Name
type(ommp_bonded_type),	intent(inout)	::	bds
integer(kind=ip),	intent(in)	::	d1	Dimensions of the new map to be saved
integer(kind=ip),	intent(in)	::	d2	Dimensions of the new map to be saved
real(kind=rp),	intent(in)	::	ang1(:)	Value of torsion1 for the new map
real(kind=rp),	intent(in)	::	ang2(:)	Value of torsion2 for the new map
real(kind=rp),	intent(in)	::	v(:)	Value of potential for the new map

public subroutine tortor_potential(bds, V)

Compute torsion potential

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	V	torsion potential, result will be added to V

public subroutine tortor_geomgrad(bds, grad)

Compute torsion potential

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(in)			::	bds
real(kind=rp),	intent(inout)			::	grad(3,bds%top%mm_atoms)	improper torsion potential, result will be added to V

public subroutine bonded_terminate(bds)

Just terminate every "submodule" in bonded, deallocating arrays and disabling the potential terms

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds

public subroutine bond_terminate(bds)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds

public subroutine angle_terminate(bds)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds

public subroutine strbnd_terminate(bds)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds

public subroutine urey_terminate(bds)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds

public subroutine opb_terminate(bds)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds

public subroutine pitors_terminate(bds)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds

public subroutine torsion_terminate(bds)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds

public subroutine imptorsion_terminate(bds)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds

public subroutine tortor_terminate(bds)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds

public subroutine angtor_terminate(bds)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds

public subroutine strtor_terminate(bds)

Arguments

Type	Intent	Optional	Attributes		Name
type(ommp_bonded_type),	intent(inout)			::	bds

mod_bonded Module

Contents

Uses

Used by

Contents

Variables

Derived Types

type, public :: ommp_bonded_type

Components

Functions

private pure function cos_torsion(top, idx)

Arguments

Return Value real(kind=rp)

private pure function ang_torsion(top, idx)

Arguments

Return Value real(kind=rp)

Subroutines

public subroutine bond_init(bds, n)

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public subroutine bond_potential(bds, V)

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public subroutine bond_geomgrad(bds, grad)

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public subroutine angle_init(bds, n)

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public subroutine angle_potential(bds, V)

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public subroutine angle_geomgrad(bds, grad)

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public subroutine strbnd_init(bds, n)

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public subroutine strbnd_potential(bds, V)

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public subroutine strbnd_geomgrad(bds, grad)

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public subroutine urey_init(bds, n)

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public subroutine urey_potential(bds, V)

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public subroutine urey_geomgrad(bds, grad)

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public subroutine opb_init(bds, n, opbtype)

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public subroutine opb_potential(bds, V)

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public subroutine opb_geomgrad(bds, grad)

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public subroutine pitors_init(bds, n)

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public subroutine pitors_potential(bds, V)

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public subroutine pitors_geomgrad(bds, grad)

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public subroutine torsion_init(bds, n)

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public subroutine torsion_potential(bds, V)

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public subroutine torsion_geomgrad(bds, grad)

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public subroutine imptorsion_potential(bds, V)

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public subroutine imptorsion_geomgrad(bds, grad)

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public subroutine imptorsion_init(bds, n)

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public subroutine angtor_init(bds, n)

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public subroutine strtor_init(bds, n)

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public subroutine angtor_potential(bds, V)

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public subroutine angtor_geomgrad(bds, grad)

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public subroutine strtor_potential(bds, V)

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public subroutine strtor_geomgrad(bds, grad)

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public subroutine tortor_init(bds, n)

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public subroutine tortor_newmap(bds, d1, d2, ang1, ang2, v)