- Motivation
Master's computational project to learn the basic knowledge of parallel computing applied to molecular dynamics. The main objectives of this project are:
- Develop a molecular dynamics program.
- Once the sequential program is done, develop programs where the tasks of each loop are distributed in different processors and check the optimization characteristics for each one.
- Analyze the speed-up and compare time execution with different number of particles in parallel program. The execution has been performed at the BSC Mare Nostrum where large number of CPUs where used; we worked almost with 400 processors.
- The system
We work with a Van der Waals gas, specifically helium gas, described by Lennard-Jones potential model to approach the interactions between pairs of particles. We consider a system of N particles in a canonical ensemble (NVT ensemble) under periodic boundary conditions. First, we create a FCC lattice taking care that there are no overlaps between particles. At this point, we can study the molecular dynamics of interest.
- Molecular dynamics
The integrator used to solve the Newton’s equations of motion is the velocity Verlet. The user can choose whether the system is in contact with a heat bath by activating the Andersen thermostat or not. During the simulation, we calculate the positions and the velocities of the system many times, obtaining its evolution.
Information to install and execute the programs.
Working environment:
Linux Shell and Bash
Sequential compilers:
ifort (Default)
gfortran (Must configure Makefile)
Parallel compilers:
intel openmpi (Default)
The programs are ready-to-use. The user has to download the repository in a local computer folder or computing cluster and configure the compiler and flags options in the Makefile.
Sequential program
Makefile: configure compiler and flags variables (ifort by default)
Parallel program (computing cluster)
Makefile: configure the compiler and flags variables (mpifort by default)
"run_sub.sh" (1): Check the execution order ( mpirun by default)
"run_sub.sh" (2): Configure the submit options ( BSC by default)
"run.sh" (1): Check Makefile flags for ifort or gfortran.
"run.sh" (2): Configure "run.sh" number of processors.
Sequential program
(1) Configure the simulation parameters (INPUT folder)
(2) Execute the "run.sh" script.
(3) Collect results in the OUTPUT folder.
The results folder name is the date-time when the task was submitted.
Parallel program (computing cluster)
(1) Configure the simulation parameters (INPUT folder)
(2) Execute the "run_sub.sh" script.
(3) Collect results in the OUTPUT folder.
The results folder name is the date-time when the task was executed.
In the OUTPUT folder is provided a run_check subfolder with input configuration parameters and graphs. Put the same parameters in the INPUT files, run the program and compare the graphs; they should be similar except for a random factor.
- Initial FCC structure in a cubic volume.
- Uniform distribution of initial velocities.
- Melting and equilibration at a customizable temperature.
- Velocity Verlet algorithm to integrate the equations.
- Andersen Thermostat to control the bath temperature.
- Pair interactions with Lennard-Johnes potential.
- Periodic boundary conditions.
- Thermodynamic results in real and reduced units.
- Fortran
- Open MPI subroutines
- Random numbers: CALL RANDOM_NUMBER(x) (no explicit seed)
- Gnuplot
- Bash shell scripts
- Computing Cluster
Outcome : 21 / 04 / 2020 (version 1.0)
Last moified: NONE (version --)
- Input parameters
- Speed up and running time recommendations
parameters.dat
particles # Number of particles (x^3 *4 ; with x natural and positive)
density # Density (reduced units)
time # Simulation time (reduced units)
h # Time step (reduced units)
sigma # Sigma of the gas (Angstroms)
epsilon # Epsilon of the gas (kJ/mol)
mass # Mass (g/mol)
(boolean) # To add a thermostat
temperature # If true, temperature of the thermostat (reduced units)
dx # Precision for the radial distribution function (reduced units)
config.dat
temperature # Temperature of the initial melting (reduced units)
iterations # Melting Velo Verlet Integration steps
(boolean) # Print thermodynamic magnitudes
iterations # Delta iterations to measure thermodynamic magnitudes
(boolean) # Compute the radial distribution function
iterations # Delta iterations to compute the Rad. Dist. Func.
(boolean) # Time-positions of the particles (.xyz file)
iterations # Delta iterations to save the positions
constants.dat
0.008314462 # Boltzman constant in kJ/molK
6.022d23 # Avogadro number
MDP-Double Work
- Same number of interactions for each processor.
- No symmetric reduction is made to compute the half of the matrix.
- Every processor has the same work.
MDP- Pair
- Same number of interactions for each processor.
- List of pairs distributed for each processor.
- Every processor has the same work.
MDP- Symmetric Matrix
- Different number of interactions for each processor.
- Use of the symmetry force to parallelize.
- Different distribution of work between processors.
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