Molecular Dynamics

General

This code supports the training on Modern Fortran, OpenMP and OpenACC that I teach for LSU and LONI HPC users. This code is not for learning Molecular Dynamics (though I might use it in the future). Can also be used for a tutorial on Makefiles.

Objective

Take the original code and rewrite using Modern Fortran concepts learned viz,

• spit code into smaller subunits: modules, functions and subroutines
• generalize code so that the following parameters are read as input
  • number of atoms or number of unit cells (you can't do both)
  • simulation/equilibration temperature
  • number of times steps
  • you will need to make use of allocatable arrays
• use object oriented concepts such as
  • derived type data types
  • generic procedures and operator overloading
• Extra exercise: add another potential e.g. Morse potential for the simulation

Parallelize the code using

1. OpenMP
2. OpenACC
3. CUDA Fortran (when I learn how to do it)

Code Description

• Original Code: md-orig.f90
  • This is the original code that students need to to work on. The Objective is to modify this code using as many features as you have grasped.
• Modified Code: md-v1.f90
  • This version splits the original code into many subprograms.
• Modified Code: md-v2.f90
  • This version generalizes the size of the program, reads input parameters and uses allocatable arrays. Arrays are passed as explicit shape arrays.
• Modified Code: md-v3.f90
  • In this version, arrays are passed as assumed shape arrays with intent attribute creating a need for interface.
  • A module for calculating the potential and force is added.
  • Morse potential is also added
  • If this is final version, the only thing left for you to learn is Object Oriented concepts. Congratulations!
• Modified Code: md-v4.f90
  • Derived Types for MD variables are introduced.
• Object Oriented Code : md-v5.f90
  • Adds generic procedures and operator overloading to the md-v4.f90 code.
  • If this is your final version, you have learned a lot of Modern Fortran Concepts. Congratulations!
• OpenMP Code : md-omp.f90
  • Parallelize the md.f90 code using OpenMP directives.
• OpenACC Code : md-acc.f90
  • Parallelize the md.f90 code using OpenACC directives. For this code to work, you need to have access to a machine with an accelerator such as NVIDIA GPUs and an OpenACC supported compiler such as Portland Group Compilers. It should work with Cray or CAPS Compilers but I don't have access to one.

Requires

Compilers:

• gfortran,
• intel fortran or
• portland group compilers

For OpenACC/CUDA, portland group compilers is required and a machine with NVIDIA GPUs (code is tested on NVIDIA Tesla M2090, don't have access to AMD GPUs)

Compiling

$ make [option] [COMP=compiler]

options:

• Serial : v{0-5}
• OpenMP : omp
• OpenACC : acc

compiler:

• gfortran : gcc
• intel : intel
• portland : pgi
• IBM XL : ibm (Makefile doesn't work on AIX)

Input Files

• md.inp : Input file for version 2-5, openmmp and openacc (default potential is lj)
• md.in : Input file for version 3-5, openmp and openacc

Running

Serial Code

$ ./md{0-5} [<input, needed for version 2-5>]

OpenMP Code

$ OMP_NUM_THREADS=x ./mdo <input>

where x is between 1 and number of processor cores

OpenACC Code

$ ./mda <input>

Output Files

The code will produce output to screen, you can redirect output to a file and analyze the simulation temperature and energy.

$ ./md0 > md.out

The code also produces a atom.xyz file with atomic coordinates at each time step.

Visualization of MD Simulation using VMD

The VMD script, atom.vmd will read in the atom.xyz file and enable one to view the simulation

$ vmd -e atom.vmd

Author

Alex Pacheco
Manager, Research Computing
XSEDE Campus Champion
Lehigh University

Material Developed as
HPC User Services Consultant,
Louisiana State University