Molecular Dynamics Simulations

Transcription

1 Molecular Dynamics Simulations Dr. Kasra Momeni

2 Outline LAMMPS AdHiMad Lab 2

3 What is LAMMPS? LMMPS = Large-scale Atomic/Molecular Massively Parallel Simulator Open-Source ( Running classic MD (although other codes have implemented in LAMMPS as it evolved, such as quasi-continuum methods) It utilizes parallelization algorithms to speed up the simulations Different feature: MD, non-equilibrium MD, energy minimization Ability to run on different parallelization platforms ( Graphic Processing Units (GPU), MPI, OpenMP) Ability to connect to other scales: quantum mechanics, kinetic Monte Carlo, Finite Element,... AdHiMad Lab 3

4 LAMMPS Feature Extendible Extensive documents/tutorials Strong user community (mailing list: Extensive examples Workshops Text based (using a scripting language to setup the simulations) - No graphics - Not interactive - Line by line run AdHiMad Lab 4

5 Structure of LAMMPS Scripts Define the Units and atom attributes Create simulation cell and position atoms in the cell Define groups of atoms (that have the same property) Set properties of atoms (velocity and mass) Define atomic interactions Define the system constraints Define the properties of interest (You need to define the analysis you interested before running simulations, there is limited post processing) Set the output periods of the simulation Performing the simulation AdHiMad Lab 5

6 Flow Chart of Running LAMMPS Command for running LAMMPS Single processor run: LAMMPS executable < input file Multiple processor (parallel) run: mpirun -np 8 LAMMPS executable < input file Preparing Input File(s) Running LAMMPS (Passing the script file) lmp < input_file.in Collecting Output File(s) Analyzing Output File(s) using in-house codes or others (OVITO, VMD) AdHiMad Lab 6

7 LAMMPS Common Commands Initialization Please take a look at online documentation of each command for more details clear clears all memory units units that will be used for the simulation dimension Dimension of the simulation cell boundary Periodic or non-periodic boundary conditions atom_style Determines attributes associated with the atoms. atom_modify Modify certain attributes of atoms defined and stored within LAMMPS (other than what is specified by the atom_style ) AdHiMad Lab 7

8 LAMMPS Common Commands Initialization lattice Type of lattice (fcc, bcc, hcp, etc. ) region Specifies the simulation cell dimension/geometry create_box Creates the simulation box using the dimensions of region create_atoms Creates atoms (or molecules) on a lattice replicate replicate the periodic cell in each direction AdHiMad Lab 8

9 LAMMPS Common Commands Initialization pair_style Specifies the interatomic potential pair_coeff Specify the pairwise force field coefficients neighbor sets parameters that affect the building of pairwise neighbor lists neigh_modify Sets the parameters of pairwise neighbor lists compute Define variables to store certain calculations AdHiMad Lab 9

10 LAMMPS Common Commands Running reset_timestep Resets timestep fix Sets system constrains thermo specifies the output during the run thermo_style specifies what type of output min_style specifies minimization technique minimize starts the minimization AdHiMad Lab 10

11 LAMMPS Common Commands Post Process variable Defines variables print Print text or value of a variabel AdHiMad Lab 11

12 Practice Problem Perform the simulations of Homework 2 using LAMMPS AdHiMad Lab 12

13 Useful Links LAMMPS Tutorials pdf Many more are available online AdHiMad Lab 13

14 Questions AdHiMad Lab 14