MD3
Molecular Dynamics Simulation

MD3 is a FORTRAN90 program which is the third of a series of programs that show a typical molecular dynamics simulation.

MD3 is a somewhat more sophisticated version of MD2. In particular, the program uses Verlet neighbor lists, with an automatic list update.

Usage:

md3 < md3.inp > md3.out

reads the input file md3.inp, and writes the output to md3.out. Also expects to read a file with a name like sample0.txt (specified in the input file) with initial point locations, and will write an output file with a name like sample1.txt containing the updated point locations.

Related Programs:

CRYSTAL_COORDINATES is an executable FORTRAN90 program which can be used to generate suitable coordinates for a set of molecules in a rectangular slab. This data can be used as the initial data by MD3.

GNUPLOT is a program which can be used to display the time evolution of temperature, kinetic energy, potential energy, total energy, or pressure, which are the individual columns of the MD3 output file.

MD_OPEN_MP is a FORTRAN90 program which carries out a molecular dynamics simulation using OpenMP.

MD1 is an executable FORTRAN90 program which is a simpler version of MD2.

MD2 is an executable FORTRAN90 program which is a molecular dynamics simulation program.

MD3GLUE is an executable FORTRAN90 program which is a molecular dynamics simulation program.

MDBNCH is an executable FORTRAN77 program which is a benchmark molecular simulation calculation.

MDDISK is a C program which is a simulation of a soft disk fluid.

Reference:

1. Matthew Allen, Dominic Tildesley,
   Computer Simulation of Liquids,
   Oxford University Press, 1987,
   ISBN: 0198556454,
   LC: QC145.2.
2. Furio Ercolessi,
   A Molecular Dynamics Primer,
   ercolessi.pdf
3. David Fincham, BJ Ralston,
   Molecular Dynamics Simulation Using the Cray-1 Vector Processing Computer,
   Computer Physics Communications,
   Volume 23, pages 127-134, 1981,
4. Dennis Rapaport,
   An Introduction to Interactive Molecular-Dynamics Simulation,
   Computers in Physics,
   Volume 11, Number 4, July/August 1997, pages 337-347.
5. Dennis Rapaport,
   The Art of Molecular Dynamics Simulation,
   Cambridge University Press, 2004,
   ISBN: 0521825687.

Source Code:

• md3.f90, the source code.
• md3.csh, commands to compile the source code.

Examples and Tests:

• md3_input.txt, a short input file of user parameter values.
• md3_output.txt, printed output from a run of the program.
• md3_sample0.txt, a file containing the initial point positions.
• md3_sample1.txt, a file containing the updated point positions, velocities and accelerations.

List of Routines:

• PARTICLES is a module for atom property data.
• SIMULATION_CONTROL is a module for simulation control data.
• POTENTIAL is a module with the parameters of the Lennard-Jones potential.
• STATISTICS is a module with statistical quantities.
• MAIN is the main program for the MD1 molecular dynamics program.
• INITIALIZE controls the initialization procedure.
• READ_SAMPLE reads the initial sample from file unit 1.
• READ_INPUT reads the parameters controlling the simulation.
• INITIAL_PRINTOUT prints information on the run parameters.
• EVOLVE_SAMPLE controls the time evolution of the system.
• REFOLD_POSITIONS folds exiting particles back into the box.
• COMPUTE_FORCES computes the forces on atoms.
• COMPUTE_TEMPERATURE updates the kinetic energy and computes temperature.
• TERMINATE carries out the termination procedures.
• PRINT_STATISTICS prints statistics from the calculation.
• TIMESTAMP prints the current YMDHMS date as a time stamp.
• WRITE_SAMPLE writes the final sample to file unit 2.

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