DCD_ANALYSIS


Function

DCD_Analysis contains procedures for calculating self-diffusion coefficients and radial distribution functions.

This module is a new one but it has the same functionality as the module TRAJECTORY_ANALYSIS which is described in detail in chapter 10 of the book A Practical Introduction to the Simulation of Molecular Systems.

Dependencies

Module Variables
CONSTANTS PI
DEFINITIONS DP
IO_UNITS OUTPUT
STATUS ERROR
DCD_IO Most of the public items in the module.


Public Variables

None.

Public Procedures

There are three public subroutines in this module.

SubroutinePurpose
DCD_DSELF Calculate a self-diffusion coefficient using an Einstein relation.
DCD_RDF_CROSS Calculate a radial distribution function between two sets of atoms.
DCD_RDF_SELF Calculate a radial distribution function for a single set of atoms.


DCD_DSELF

Argument Type Intent Optional Purpose
FILE Character ( Len = * ) In No The trajectory file name.
TSTOP Integer In No The number of frames for which the Einstein function is to be calculated.
TIME_STEP Real In Yes The time step.
SELECTION Logical(1:NATOMS) In Yes An atom selection array.


Error Meaning
The number of frames in the trajectory is too small for the input TSTOP value. The value of the argument TSTOP is greater than the number of frames on the trajectory.
The SELECTION array is incompatible with the trajectory. The number of atoms in the trajectory and the size of the selection array are not the same.




DCD_RDF_CROSS

Argument Type Intent Optional Purpose
FILE Character ( Len = * ) In No The trajectory file name.
NBINS Integer In No The number of bins to use in the analysis.
UPPER Real In No The maximum distance for which to calculate the RDF.
SELECTION1 Logical(1:NATOMS) In No The first atom selection array.
SELECTION2 Logical(1:NATOMS) In No The second atom selection array.
BOX_SIZE Real(1:3) In Yes The periodic box dimensions.


Error Meaning
There is trajectory crystal information and BOX_SIZE was specified. The trajectory file contains the information about the size of the periodic box and yet the argument BOX_SIZE was given.
There is no trajectory crystal information and BOX_SIZE was missing. The trajectory file does not contain information about the size of the periodic box and yet the argument BOX_SIZE was missing.
The SELECTION arrays are incompatible with the trajectory. The number of atoms in the trajectory and the sizes of the selection arrays are not the same.
The box size is too small for upper bound of g(r). The value of the argument UPPER is too big for the size of the periodic box.




DCD_RDF_SELF

Argument Type Intent Optional Purpose
FILE Character ( Len = * ) In No The trajectory file name.
NBINS Integer In No The number of bins to use in the analysis.
UPPER Real In No The maximum distance for which to calculate the RDF.
SELECTION Logical(1:NATOMS) In Yes The atom selection array.
BOX_SIZE Real(1:3) In Yes The periodic box dimensions.


Error Meaning
There is trajectory crystal information and BOX_SIZE was specified. The trajectory file contains the information about the size of the periodic box and yet the argument BOX_SIZE was given.
There is no trajectory crystal information and BOX_SIZE was missing. The trajectory file does not contain information about the size of the periodic box and yet the argument BOX_SIZE was missing.
The SELECTION array is incompatible with the trajectory. The number of atoms in the trajectory and the size of the selection array are not the same.
The box size is too small for upper bound of g(r). The value of the argument UPPER is too big for the size of the periodic box.




Stability

Optional arguments which return the calculated as arrays or write the results to a specific file will be added. Otherwise, stable.



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