MD2
Molecular Dynamics Simulation

MD2 is a FORTRAN90 program which is the second of a series of programs that show a typical molecular dynamics simulation.

MD2 is a somewhat more sophisticated version of MD1. In particular, the potential is stored in numerical tables during the initialization phase. In the force loop, simple table lookup is performed. For the Lennard-Jones potential, the speed improvement is not very great, but for other potentials, this method may be preferred.

Usage:

md2 < md2.inp > md2.out

reads the input file md2.inp, and writes the output to md2.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 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 MD2.

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 MD2 output file.

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

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

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

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

MDBNCH is a 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. Dennis Rapaport,
   An Introduction to Interactive Molecular-Dynamics Simulation,
   Computers in Physics,
   Volume 11, Number 4, July/August 1997, pages 337-347.
4. Dennis Rapaport,
   The Art of Molecular Dynamics Simulation,
   Cambridge University Press, 2004,
   ISBN: 0521825687.

Source Code:

• md2.f90, the source code.
• md2.csh, commands to compile the source code.

Examples and Tests:

• md2_input.txt, a short input file of user parameter values.
• md2_output.txt, printed output from a run of the program.
• md2_sample0.txt, a file containing the initial point positions.
• md2_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.