MD1
Molecular Dynamics Simulation

MD1 is a FORTRAN90 program which carries out a molecular dynamics simulation, and which writes graphics files for processing by gnuplot.

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.

Languages:

MD1 is available in a FORTRAN90 version.

Related Data and Programs:

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

GNUPLOT, FORTRAN90 programs which illustrate how a program can write data and command files so that gnuplot can create plots of the program results.

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

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

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

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

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. 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.sh, 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.
• md11.txt, the output file.
• md1_data.txt, graphics data.
• md1_commands.txt, graphics commands.
• kinetic.png, a plot of kinetic energy.
• potential.png, a plot of potential energy.
• pressure.png, a plot of pressure.
• temperature.png, a plot of temperature.
• 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.
• md12.txt, printed output from a run of the program.
• 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.
• 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.