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Computersimulation in der

Institute for Materials Science, Chair of Materials Science and Nanotechnology

Materialwissenschaft
WS 2014-2015
Diplom Werkstoffwissenschaft + andere Interessenten

Arezoo Dianat und Leonardo Medrano


Institut für Werkstoffwissenschaft
Professur Werkstoffwissenschaft und Nanotechnologie

ORT: SCH/A316/H


  2
 v    
d r 1 H

/kBT
  ( v . ) v    p   v  f j

 t  m 2
  U (r ) A je
  dt Z j 1
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Topic:
Molecular Dynamics Simulations
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Outline:

Part I. Molecular Dynamics and LAMMPS code

Part II. Application 1: Melting and cooling of nanostructures

Part III. Application 2: Mechanical stress and Electron beam


irradiation

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Institute for Materials Science, Chair of Materials Science and Nanotechnology

Part I:

Molecular Dynamics
and LAMMPS code
Molecular Dynamics
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Basic concepts

Molecular Dynamics (MD) is a computational method to


predict the movement of an atom under a force contributed
by other atoms.

What we can study with


MD?

0D materials 2D materials

Nanotubes
and
nanowires
Low-dimensional
Heterostructures Defects 5
systems
Molecular Dynamics
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Algorithm for MD
U: Interaction potential
among the atoms
(Force Field)

Second
Newton Law

Maximum
simulation time

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Molecular Dynamics
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Open source code


How could we perform Free access.
a MD simulation?

Private code
We can develop our own
MD code employing:
Commercial code
 C++ You have to pay for it.
 Python
 Fortran
 Java, etc.

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Institute for Materials Science, Chair of Materials Science and Nanotechnology

LAMMPS: Large-scale Atomic/Molecular Massively


Parallel Simulator

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Scope:

 Classical molecular dynamics (MD) code.

 Open source, highly portable C++.

 Run in serial or parallel.

 Easy to download, install and run !!!

 Atomistic, mesoscale and coarse-grain simulations.

 Three primary communities are supported by force fields,


boundary conditions and diagnostics:
- Biomolecules and polymers (soft materials)
- Solids materials science
- Mesoscale to continuum
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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Overview Chemical vapor


deposition
Electrochemical Electrocatalytic activity
absorption of OH of gold nanoparticles

Self-assembled
monolayers

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Overview Growth of
Electron beam
nanowires
irradiation
DNA base detection

Thermal
transport in
nanomaterials
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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

How could I get this code?


URL: lammps.sandia.gov

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

INPUT file
Commands

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Example 1: energy minimization

Generate a perfect graphene flake and found the configuration


with minimal energy. Perform the same process for a defected
graphene flake.

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Example 1: energy minimization


Options:

“units metal”:
Options:

Options:

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Example 1: energy minimization

Options:

Options:

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Example 1: energy minimization

Options:

Options:

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Example 1: energy minimization

Options:

Options:

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Example 1: energy minimization

Options:

Options:

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Example 1: energy minimization

Options:

Options:

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Example 1: energy minimization

Options:

Options:
Options:

RUN LAMMPS: Open a console


and write,
$ lmp < lammps.inp 21
LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

XYZ file
Number
of atoms
Atomic
positions (x,y,z)

Chemical
symbol of
the atoms

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

VMD Visualizer
Open a console and
write: VMD.

It is also possible to do:

>$ vmd file.xyz

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Example 1: energy minimization


Generate a perfect graphene flake and found the configuration
with minimal energy. Perform the same process for a defected
graphene flake.
Without defects With defects

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Example 2: thermal relaxation

Generate a perfect silver bulk structure (fcc structure, L=2.5 nm).


Then, perform the following tasks:

 Thermal relaxation at 300 K for 20 ps and calculate the total


energy of the system.
 Make a plot of the temperature dependence of the total energy.
Temperature range: 300 – 1500 K and simulation time = 500 ps.

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Example 2: thermal relaxation

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Example 2: thermal relaxation

We use this command to control the temperature of the


system under a NVT ensemble.

fix ID ID-group nvt temp Tstart TFinal TDamp


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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Example 2: thermal relaxation

We define new variables that we want to


analyze and save them in the file
“data.out”. The data is saved over an
specific range of time (average). In this This command defines the simulation
case we take the average among the time:
values corresponding to 100, 200, 300,
400, ……, 1000 timesteps. simulation time = timestep*#run

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Example 2: thermal relaxation


Generate a perfect silver bulk Total energy = -2396.25 eV
structure (fcc structure, L=2.5
nm). Then, perform the
following tasks:

 Thermal relaxation at 300 K


for 20 ps and calculate the
total energy of the system.

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LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology

Example 2: thermal relaxation


Generate a perfect silver bulk
structure (fcc structure, L=2.5
nm). Then, perform the
following tasks:

 Thermal relaxation at 300 K


for 20 ps and calculate the
total energy of the system.
 Make a plot of the
temperature dependence of
the total energy. Temperature
range: 300 – 1500 K and
simulation time = 500 ps.
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Institute for Materials Science, Chair of Materials Science and Nanotechnology

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