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.
Module | Variables |
---|---|
CONSTANTS | PI |
DEFINITIONS | DP |
IO_UNITS | OUTPUT |
STATUS | ERROR |
DCD_IO | Most of the public items in the module. |
None.
There are three public subroutines in this module.
Subroutine | Purpose |
---|---|
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. |
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. |
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. |
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. |
Optional arguments which return the calculated as arrays or write the results to a specific file will be added. Otherwise, stable.