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Molecular Dynamics of Liquid Argon

ICTP - CMP Diploma 2019-2020

Numerical methods II - Final Project

Jesus Andres Espinoza-Valverde

Folder Organization

Our package contains the following directories:

  • sources: This Folder contains the source code.
  • input: Here we store the input files.
  • results: Within this folder we store the raw output of the simulation.
  • executable: This folder is meant to contain our executable binary.
  • scripts: Here we have helper bash scripts.
  • data_analysis: This folder contains a python script that we used to analyze the simulation data.
  • documents: Here we find references and important documents.

Source Code Files

The source code is composed by the following files:

  • md.f90: The main program, it contains the main molecular dynamics loop.
  • physics.f90: This file contains physics-related modules and routines.
  • io.f90: This file contains input/output and file management modules and routines.
  • utils.f90: Here we find miscellaneous modules and routines.

Simulation Modules

MODULE Physical Constants (physconst)

Description: This module holds the needed physical constants used in the simulation.

MODULE Molecular Dynamics System (mdsys)

Description: This module holds the complete system information.

MODULE High precision kinds

Description: This module contains redefinitions for precision of floating point number and length file size names.

MODULE Utilities (utils)

Description: This module contains helper and miscellaneous routines.

Routines:

  • pbc routine (pbc): applies minimum image convention.
  • Box-Muller Method (box_muller_method): Generates Gaussian random numbers.

MODULE Physics

Description: This module contains all physically-related routines.

Routines:

  • Get kinetic energy routine (getekin): Computes total kinetic energy of the system.
  • Get temperature routine (gettemp): Computes the temperature of the system.
  • Force routine (force): Computes the temperature of the system.
  • Velocity Verlet routine (velverlet): Updates velocities and p via Verlet Algorithm.
  • Poors-man Thermostat routine (thermostat): Rescales temperature of the system.
  • Maxwell Bolzmann velocity initializator (MaxBoltz_Dist_vel_init): Initialize velocities according to MB velocity distribution at a given temperature.
  • FCC lattice positions iniatializator (fcc_lattice_positions_init): Initialize positions in a FCC lattice.
  • Force to Zero routine (force_to_zero): Resets Force values.
  • Get distances routine (get_distances): Computes distances between the particles in the system.

MODULE Input/Output

Description: This module is in charge of the reading and writing files with simulation data.

Routines:

  • ioopen routine (ioopen): Opens all the needed files.
  • ioclose routine (ioclose): Closes all the needed files.
  • output routine (output): Writes simulation data into files.
  • output temps routine (output_temps): writes temperature data only.

Animation

A cool video of this simulation using VMD software can be found here:

https://youtu.be/M-hA6Vg5Mno