Institute for Materials Science, Chair of Materials Science and Nanotechnology
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Computersimulation in der Materialwissenschaft
WS 2014-2015
Diplom Werkstoffwissenschaft + andere Interessenten
Arezoo Dianat und Leonardo Medrano Institut für Werkstoffwissenschaft
Professur Werkstoffwissenschaft und Nanotechnologie
ORT: SCH/A316/H
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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
Institute for Materials Science, Chair of Materials Science and Nanotechnology
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Molecular Dynamics
Basic concepts
Defects
What we can study with
MD?
Molecular Dynamics (MD) is a computational method to
predict the movement of an atom under a force contributed
by other atoms.
Heterostructures Low-dimensional
systems
2D materials 0D materials
Nanotubes and
nanowires
Institute for Materials Science, Chair of Materials Science and Nanotechnology
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Molecular Dynamics
Algorithm for MD
U: Interaction potential
among the atoms
(Force Field)
Second
Newton Law
Maximum
simulation time
Institute for Materials Science, Chair of Materials Science and Nanotechnology
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Molecular Dynamics
How could we perform
a MD simulation?
Private code
Open source code
We can develop our own
MD code employing:
C++
Python
Fortran
Java, etc.
Commercial code
You have to pay for it.
Free access.
Institute for Materials Science, Chair of Materials Science and Nanotechnology
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LAMMPS: Large-scale Atomic/Molecular Massively
Parallel Simulator
Institute for Materials Science, Chair of Materials Science and Nanotechnology
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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
LAMMPS code
Institute for Materials Science, Chair of Materials Science and Nanotechnology
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LAMMPS code
Overview
Self-assembled
monolayers
Electrochemical
absorption of OH
Electrocatalytic activity
of gold nanoparticles
Chemical vapor
deposition
Institute for Materials Science, Chair of Materials Science and Nanotechnology
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LAMMPS code
Overview
DNA base detection
Thermal
transport in
nanomaterials
Growth of
nanowires Electron beam
irradiation
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
How could I get this code?
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URL: lammps.sandia.gov
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
INPUT file
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Commands
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
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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.
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
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Example 1: energy minimization
“units metal”:
Options:
Options:
Options:
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
Example 1: energy minimization
Options:
Options:
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Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
Example 1: energy minimization
Options:
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Options:
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
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Example 1: energy minimization
Options:
Options:
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
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Example 1: energy minimization
Options:
Options:
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
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Example 1: energy minimization
Options:
Options:
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
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Example 1: energy minimization
Options:
Options: Options:
RUN LAMMPS: Open a console
and write,
$ lmp < lammps.inp
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
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XYZ file Number
of atoms
Chemical
symbol of
the atoms
Atomic
positions (x,y,z)
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
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VMD Visualizer
Open a console and
write: VMD.
It is also possible to do:
>$ vmd file.xyz
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
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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
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
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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.
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
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Example 2: thermal relaxation
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
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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
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
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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 case we take the average among the values corresponding to 100, 200, 300, 400, ……, 1000 timesteps.
This command defines the simulation time:
simulation time = timestep*#run
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
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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.
Total energy = -2396.25 eV
Institute for Materials Science, Chair of Materials Science and Nanotechnology
LAMMPS code
30
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.
Institute for Materials Science, Chair of Materials Science and Nanotechnology
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