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.

Languages:

MD3 is available in a FORTRAN90 version.

Related Programs:

CRYSTAL_COORDINATES, is a 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.

MD_OPENMP, a FORTRAN90 program which carries out a molecular dynamics simulation using OpenMP.

MD1, a FORTRAN90 program which is a simpler version of MD2.

MD2, 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 is a benchmark molecular simulation calculation.

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.
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.sh, commands to compile the source code.

Examples and Tests:

• md3_input.txt, a short input file of user parameter values.
• md3.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.