Praktikum 4 18122014

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
Topic:
Molecular Dynamics Simulations
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
3
Part I:
Molecular Dynamics
and LAMMPS code
Molecular Dynamics
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
Algorithm for MD
U: Interaction potential
among the atoms
(Force Field)
Second
Newton Law
Maximum
simulation time
6
Molecular Dynamics
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.
7
LAMMPS: Large-scale Atomic/Molecular Massively

Parallel Simulator
8
LAMMPS code
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
9
LAMMPS code
Overview Chemical vapor

deposition
Electrochemical Electrocatalytic activity
absorption of OH of gold nanoparticles
Self-assembled
monolayers
10
LAMMPS code
Overview Growth of
Electron beam
nanowires
irradiation
DNA base detection
Thermal
transport in
nanomaterials
11
LAMMPS code
How could I get this code?

URL: lammps.sandia.gov
12
LAMMPS code
INPUT file
Commands
13
LAMMPS code
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.
14
LAMMPS code

Options:
“units metal”:
Options:
Options:
15
LAMMPS code
Options:
Options:
16
LAMMPS code
Options:
Options:
17
LAMMPS code
Options:
Options:
18
LAMMPS code
Options:
Options:
19
LAMMPS code
Options:
Options:
20
LAMMPS code
Options:
Options:
Options:
RUN LAMMPS: Open a console

and write,
$ lmp < lammps.inp 21
LAMMPS code
XYZ file
Number
of atoms
Atomic
positions (x,y,z)
Chemical
symbol of
the atoms
22
LAMMPS code
VMD Visualizer
Open a console and
write: VMD.
It is also possible to do:
>$ vmd file.xyz
23
LAMMPS code

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
24
LAMMPS code
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.
25
LAMMPS code
26
LAMMPS code
We use this command to control the temperature of the

system under a NVT ensemble.
fix ID ID-group nvt temp Tstart TFinal TDamp

27
LAMMPS code
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
28
LAMMPS code

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.
29
LAMMPS code

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.
30
31

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Computersimulation in der

Institute for Materials Science, Chair of Materials Science and Nanotechnology

Arezoo Dianat und Leonardo Medrano

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

Molecular Dynamics (MD) is a computational method to

What we can study with

Open source code

LAMMPS: Large-scale Atomic/Molecular Massively

 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,

Overview Chemical vapor

How could I get this code?

Example 1: energy minimization

Generate a perfect graphene flake and found the configuration

Example 1: energy minimization

Example 1: energy minimization

Example 1: energy minimization

Example 1: energy minimization

Example 1: energy minimization

Example 1: energy minimization

Example 1: energy minimization

RUN LAMMPS: Open a console

It is also possible to do:

>$ vmd file.xyz

Example 1: energy minimization

Example 2: thermal relaxation

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

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

Example 2: thermal relaxation

Example 2: thermal relaxation

We use this command to control the temperature of the

fix ID ID-group nvt temp Tstart TFinal TDamp

Example 2: thermal relaxation

We define new variables that we want to

Example 2: thermal relaxation

 Thermal relaxation at 300 K

Example 2: thermal relaxation

 Thermal relaxation at 300 K

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