说明： 支持Fortran、OpenMP和OpenACC编程和Makefile训练的分子动力学代码 (Molecular Dynamics code to support training on Fortran, OpenMP and OpenACC programming and Makefile)
# 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} []
```
OpenMP Code
```
$ OMP_NUM_THREADS=x ./mdo
```
where x is between 1 and number of processor cores
OpenACC Code
```
$ ./mda
```
## 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