SELF_AVOIDING_WALK


Function

Self_Avoiding_Walk has procedures for determining reaction paths. The algorithm was developed by R. Elber and co-workers.

The use of this module is fully explained in chapter 6 of the book A Practical Introduction to the Simulation of Molecular Systems.

Dependencies

Module Variables
DEFINITIONS DP
IO_UNITS OUTPUT
STATUS ERROR
CONJUGATE_GRADIENT CONJUGATE_GRADIENT_MINIMIZE
ATOMS ATMCRD, ATMFIX, NATOMS, NFIXED, NFREE
DCD_IO Many of the public items in the module.
POTENTIAL_ENERGY ATMDER, ENERGY, ETOTAL, GRADIENT
SUPERIMPOSE SUPERIMPOSE_KABSCH


Public Variables

None.

Public Procedures

There are three public subroutines in this module.

SubroutinePurpose
CHAIN_EXPAND Expand a chain of structures.
CHAIN_INITIALIZE Generate an initial chain of structures.
CHAIN_OPTIMIZE Optimize a chain of structures.


CHAIN_EXPAND

Argument Type Intent Optional Purpose
FILE_IN Character ( Len = * ) In No The name of the input trajectory file.
FILE_OUT Character ( Len = * ) In No The name of the output trajectory file.
NINSERT Integer In No The number of structures to insert between each existing structure in the chain.


Error Meaning
Invalid number of insertions. The value of the argument NINSERT is less than 1.
The number of trajectory points must be odd. The input trajectory file contains an even number of structures.




CHAIN_INITIALIZE

Argument Type Intent Optional Purpose
FILE Character ( Len = * ) In No The name of the output trajectory file.
NPOINTS Integer In No The number of structures in the chain.
REACTANTS Real(1:3,1:NATOMS) In No The reactant structure.
PRODUCTS Real(1:3,1:NATOMS) In No The product structure.


Error Meaning
Too few points in trajectory. The value of the argument NPOINTS is less than 3.
The number of trajectory points must be odd. The chain must contain an odd number of structures.
Fixed atom coordinate mismatch in reactant and product structures. Fixed atoms are defined but the values of at least one of the fixed atom's coordinates differs between the reactant and product structures.




CHAIN_OPTIMIZE

Argument Type Intent Optional Purpose
FILE_IN Character ( Len = * ) In No The name of the input trajectory file.
FILE_OUT Character ( Len = * ) In No The name of the output trajectory file.
GAMMA Real In Yes The self avoiding walk GAMMA parameter.
LAMBDA Real In Yes The self avoiding walk LAMBDA parameter.
RHO Real In Yes The self avoiding walk RHO parameter.
PRINT_FREQUENCY Integer In Yes The print frequency.
STEP_NUMBER Integer In Yes The maximum number of iterations.
GRADIENT_TOLERANCE Real In Yes The gradient tolerance convergence criterion.
STEP_SIZE Real In Yes The starting step size.


Error Meaning
The number of trajectory points must be odd. The input trajectory file contains an even number of structures.




Stability

Stable.



Back to the DYNAMO Home-Page.