CONNECTIVITY


Function

Connectivity contains procedures for determining lists of bonds, bond angles and dihedral angles.

This module is discussed in chapter 3 of the book A Practical Introduction to the Simulation of Molecular Systems.

Dependencies

Module Variables
DEFINITIONS DP
ELEMENTS RADII
IO_UNITS OUTPUT
SORT SORT_INTEGER
ATOMS Most of the public items in the module.
SEQUENCE NRESID, RESIND


Public Variables

None.

Public Procedures

There are three public subroutines in this module that the user is likely to need.

SubroutinePurpose
CONNECTIVITY_ANGLES Generate a bond angle connectivity list.
CONNECTIVITY_BONDS Generate a bond connectivity list.
CONNECTIVITY_DIHEDRALS Generate a dihedral angle connectivity list.


CONNECTIVITY_ANGLES

Argument Type Intent Optional Purpose
ANGLES Integer(:,:) Pointer No The angle lists to generate.
BONDS Integer(:,:) In No The bond lists to use in the generation.




CONNECTIVITY_BONDS

Argument Type Intent Optional Purpose
BONDS Integer(:,:) Pointer No The bond lists to generate.
BUFFER Real In No The buffer size to use in the list generation.




CONNECTIVITY_DIHEDRALS

Argument Type Intent Optional Purpose
DIHEDRALS Integer(:,:) Pointer No The dihedral angle lists to generate.
BONDS Integer(:,:) In No The bond lists to use in the generation.
ANGLES Integer(:,:) In No The bond angle lists to use in the generation.




Stability

It is likely that the algorithm in CONNECTIVITY_BONDS will be replaced by a better one that does not make use of the data in SEQUENCE. Otherwise, stable.



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