CRYSTAL_COORDINATES
Coordinates of a 3D "Slab" of points

CRYSTAL_COORDINATES is a FORTRAN90 program which generates the coordinates of a set of 4 * NX * NY * NZ points in a rectangular block of NX * NY * NZ cells, with face-centered cubic symmetry.

The user is allowed to specify the width of a cell, and the maximum magnitude of a random displacement of each point.

The coordinate data is written to a file that can be used for visualization, or more likely as the initial condition for the coordinates of molecules in a molecular dynamics simulation.

If the initial line of the output file is removed, the remainder becomes an "XYZ" file which can be plotted by several programs.

Usage:

crystal_coordinates

begins the program.

Inputs:

a

the lattice spacing, or cell width, in Angstroms.

nx

the number of cells in the X direction.

ny

the number of cells in the Y direction.

nz

the number of cells in the Z direction.

displac

the maximum magnitude of a random displacement applied to every node coordinate.

file_name

the name of the file into which the coordinate data is to be stored.

The output file has a single initial line of the form

        % F n x-width y-width z-width
      

n

is the number of points.

x-width, y-width, z-width

are the total widths of the slab in the X, Y and Z directions.

Languages:

CRYSTAL_COORDINATES is available in a FORTRAN90 version.

Related Programs:

MD1, a FORTRAN90 program which is a molecular dynamics simulation program.

MD2, a FORTRAN90 program which is a molecular dynamics simulation program.

MD3, a FORTRAN90 program which is a molecular dynamics simulation program.

MD3GLUE, a FORTRAN90 program which is a molecular dynamics simulation program.

MDBNCH, a FORTRAN77 program which carries out a molecular dynamics benchmark.

XYZ_DISPLAY, a MATLAB program which reads XYZ information defining points in 3D, and displays an image in the MATLAB graphics window.

XYZ_DISPLAY_OPENGL, a C++ program which reads XYZ information defining points in 3D, and displays an image using OpenGL.

Reference:

1. Matthew Allen, DJ Tildesley,
   Computer Simulation of Liquids,
   Oxford University Press, 1987,
   ISBN: 0198556454,
   LC: QC145.2.
2. Furio Ercolessi,
   A Molecular Dynamics Primer,
   ercolessi.pdf
3. Dennis Rapaport,
   The Art of Molecular Dynamics Simulation,
   Cambridge University Press, 2004,
   ISBN: 0521825687.

Source Code:

• crystal_coordinates.f90, the source code.
• crystal_coordinates.sh, commands to compile the source code.

Examples and Tests:

• crystal_10_10_10_input.txt, input for a 10 x 10 x 10 slab.
• crystal_10_10_10.txt, the coordinate file.
• crystal_10_10_10_output.txt, the output from a run of the program.

List of Routines:

• MAIN is the main program for CRYSTAL_COORDINATES.
• GENERATE_CRYSTAL generates the atomic coordinates.
• GET_UNIT returns a free FORTRAN unit number.
• READ_PARAMETERS obtains the parameters from the user.
• TIMESTAMP prints the current YMDHMS date as a time stamp.

You can go up one level to the FORTRAN90 source codes.