MD1
Molecular Dynamics Simulation

MD1 is a FORTRAN90 program, using double precision arithmetic, which is the first of a series of programs that show a typical molecular dynamics simulation.

Usage:

md1 < input.txt > output.txt

reads the input file input.txt, and writes the output to output.txt. 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 Data and Programs:

CRYSTAL_COORDINATES is a FORTRAN90 program which generates suitable coordinates for a set of molecules in a rectangular slab.

GNUPLOT is a plotting 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 MD1 output file.

MD2 is a FORTRAN90 program which carries out a molecular dynamics simulation.

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

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

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

MDDISK is a C program which simulates 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. Philipp Janert,
   Gnuplot in Action: Understanding Data with Graphs,
   Manning, 2008,
   ISBN: 1-933988-39-8.
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:

• md1.f90, the source code.
• md1.csh, commands to compile the source code.

Examples and Tests:

STEP0 is the initial data:

• md1_sample0.txt, a file containing the initial point positions.

STEP1 reads the initial data from STEP0, runs for 100 steps, and writes the new data:

• md1_input1.txt, a short input file of user parameter values.
• md1_output1.txt, printed output from a run of the program, which can be fed directly into GNUPLOT for time evolution plots.
• md1_sample1.txt, a file containing the updated point positions, velocities and accelerations.

STEP2 reads the data from STEP1, runs for 100 more steps, and writes the new data:

• md1_input2.txt, a short input file of user parameter values.
• md1_output2.txt, printed output from a run of the program, which can be fed directly into GNUPLOT for time evolution plots.
• md1_sample2.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.