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.
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 |
None.
There are three public subroutines in this module.
Subroutine | Purpose |
---|---|
CHAIN_EXPAND | Expand a chain of structures. |
CHAIN_INITIALIZE | Generate an initial chain of structures. |
CHAIN_OPTIMIZE | Optimize a chain of structures. |
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. |
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. |
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. |
Stable.