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.
Module | Variables |
---|---|
DEFINITIONS | DP |
ELEMENTS | RADII |
IO_UNITS | OUTPUT |
SORT | SORT_INTEGER |
ATOMS | Most of the public items in the module. |
SEQUENCE | NRESID, RESIND |
None.
There are three public subroutines in this module that the user is likely to need.
Subroutine | Purpose |
---|---|
CONNECTIVITY_ANGLES | Generate a bond angle connectivity list. |
CONNECTIVITY_BONDS | Generate a bond connectivity list. |
CONNECTIVITY_DIHEDRALS | Generate a dihedral angle connectivity list. |
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. |
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. |
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. |
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.