NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
POLARIZATION - BIREFRINGENCE AND HUYGEN'S THEORY OF DOUBLE REFRACTION Anuroop Ashok
SIMPLE AND ACCESSIBLE SLIDES ON POLARIZATION. IT INCLUDES SLIDES ON DOUBLE REFRACTION , CALCITE CRYSTALS, HUYGEN'S THEORY , NEGATIVE AND POSITIVE CRYSTALS,...
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
POLARIZATION - BIREFRINGENCE AND HUYGEN'S THEORY OF DOUBLE REFRACTION Anuroop Ashok
SIMPLE AND ACCESSIBLE SLIDES ON POLARIZATION. IT INCLUDES SLIDES ON DOUBLE REFRACTION , CALCITE CRYSTALS, HUYGEN'S THEORY , NEGATIVE AND POSITIVE CRYSTALS,...
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
This is the plenary talk given by Prof Shyue Ping Ong at the 57th Sanibel Symposium held on St Simon's Island in Georgia, USA.
Abstract: Powered by methodological breakthroughs and computing advances, electronic structure methods have today become an indispensable toolkit in the materials designer’s arsenal. In this talk, I will discuss two emerging trends that holds the promise to continue to push the envelope in computational design of materials. The first trend is the development of robust software and data frameworks for the automatic generation, storage and analysis of materials data sets. The second is the advent of reliable central materials data repositories, such as the Materials Project, which provides the research community with efficient access to large quantities of property information that can be mined for trends or new materials. I will show how we have leveraged on these new tools to accelerate discovery and design in energy and structural materials as well as our efforts in contributing back to the community through further tool or data development. I will also provide my perspective on future challenges in high-throughput computational materials design.
An Introduction to Crystallography, Elements of crystals crystal systems: Cubic (Isometric) System,Tetragonal System, Orthorhombic System, Hexagonal System; Trigonal System, Monoclinic System, Triclinic System
This presentation was part of the workshop on Materials Project Software infrastructure conducted for the Materials Virtual Lab in Nov 10 2014. It presents an introduction to the Python Materials Genomics (pymatgen) materials analysis library. Pymatgen is a robust, open-source Python library for materials analysis. It currently powers the public Materials Project (http://www.materialsproject.org), an initiative to make calculated properties of all known inorganic materials available to materials researchers. These are some of the main features:
1. Highly flexible classes for the representation of Element, Site, Molecule, Structure objects.
Extensive io capabilities to manipulate many VASP (http://cms.mpi.univie.ac.at/vasp/) and ABINIT (http://www.abinit.org/) input and output files and the crystallographic information file format. This includes generating Structure objects from vasp input and output. There is also support for Gaussian input files and XYZ file for molecules.
2. Comprehensive tool to generate and view compositional and grand canonical phase diagrams.
3. Electronic structure analyses (DOS and Bandstructure).
4. Integration with the Materials Project REST API.
This presentation was part of the workshop on Materials Project Software infrastructure conducted for the Materials Virtual Lab in Nov 10 2014. It presents an introduction to the pymatgen-db database plugin for the pymatge) materials analysis library, and the custodian error recovery framework.
Pymatgen-db enables the creation of Materials Project-style MongoDB databases for management of materials data. A query engine is also provided to enable the easy translation of MongoDB docs to useful pymatgen objects for analysis purposes.
Custodian is a simple, robust and flexible just-in-time (JIT) job management framework written in Python. Using custodian, you can create wrappers that perform error checking, job management and error recovery. It has a simple plugin framework that allows you to develop specific job management workflows for different applications. Error recovery is an important aspect of many high-throughput projects that generate data on a large scale. The specific use case for custodian is for long running jobs, with potentially random errors. For example, there may be a script that takes several days to run on a server, with a 1% chance of some IO error causing the job to fail. Using custodian, one can develop a mechanism to gracefully recover from the error, and restart the job with modified parameters if necessary. The current version of Custodian also comes with sub-packages for error handling for Vienna Ab Initio Simulation Package (VASP) and QChem calculations.
The study of crystal geometry helps to understand the behaviour of solids and their
mechanical,
electrical,
magnetic
optical and
Metallurgical properties
Prof Ong gave a webinar talk on the AI Revolution in Materials Science for the Singapore Agency of Science Technology and Research (A*STAR). In this talk, he discussed the big challenges in materials science where AI can potentially make a huge impact towards addressing as well as outstanding challenges and opportunities to bringing forth the AI revolution to the materials domain.
NANO281 is the University of California San Diego NanoEngineering Department's first course on the application of data science in materials science. It is taught by Professor Shyue Ping Ong of the Materials Virtual Lab (http://www.materialsvirtuallab.org).
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
In this talk at the CECAM 2015 Workshop on Future Technologies in Automated Atomistic Simulations, I will discuss the Materials Project Ecosystem, an initiative to develop a comprehensive set of open-source software and data tools for materials informatics. The Materials Project is a US Department of Energy-funded initiative to make the computed properties of all known inorganic materials publicly available to all materials researchers to accelerate materials innovation. Today, the Materials Project database boasts more than 58,000 materials, covering a broad range of properties, including energetic properties (e.g., phase and aqueous stability, reaction energies), electronic structure (bandstructures, DOSs) and structural and mechanical properties (e.g., elastic constants).
A linchpin of the Materials Project is its robust data and software infrastructure, built on best open-source software development practices such as continuous testing and integration, and comprehensive documentation. I will provide an overview of the open-source software modules that have been developed for materials analysis (Python Materials Genomics), error handling (Custodian) and scientific workflow management (FireWorks), as well as the Materials API, a first-of-its-kind interface for accessing materials data based on REpresentational State Transfer (REST) principles. I will show a materials researcher may use and build on these software and data tools for materials informatics as well as to accelerate his own research.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
UCSD NANO 266 Quantum Mechanical Modelling of Materials and Nanostructures is a graduate class that provides students with a highly practical introduction to the application of first principles quantum mechanical simulations to model, understand and predict the properties of materials and nano-structures. The syllabus includes: a brief introduction to quantum mechanics and the Hartree-Fock and density functional theory (DFT) formulations; practical simulation considerations such as convergence, selection of the appropriate functional and parameters; interpretation of the results from simulations, including the limits of accuracy of each method. Several lab sessions provide students with hands-on experience in the conduct of simulations. A key aspect of the course is in the use of programming to facilitate calculations and analysis.
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2. Readings
¡Chapter 3 of Structure of Materials
NANO 106 - Crystallography of Materials by Shyue Ping Ong - Lecture 1
3. What is a crystal?
¡A crystal is a time-invariant, 3D arrangement of
atoms or molecules on a lattice.
NANO 106 - Crystallography of Materials by Shyue Ping Ong - Lecture 1
Perovskite SrTiO3
The “motif”
repeated on each point in the cubic
lattice below…
4. Nets and Lattices
¡A lattice (3D) or net (2D) is an abstract concept of
an infinite array of discrete points generated by a
set of translation operations.
NANO 106 - Crystallography of Materials by Shyue Ping Ong - Lecture 1
The motif
Repeated
infinitely in all
directions
5. Concept of Symmetry
¡You have just encountered
your first symmetry concept
– translational symmetry.
¡A symmetry operation is a
permutation of atoms such
that the molecule or crystal
is indistinguishable before
and after the operation.
¡It also means that all lattice
points have exactly the
same “environment”.
NANO 106 - Crystallography of Materials by Shyue Ping Ong - Lecture 1
6. Identify the nets in the following
patterns
NANO 106 - Crystallography of Materials by Shyue Ping Ong - Lecture 1
7. Identify the nets in the following
patterns
NANO 106 - Crystallography of Materials by Shyue Ping Ong - Lecture 1
8. Basis and translation vectors
¡ How are points in a lattice related to one another (e.g.
how do we get from point A to point B)?
NANO 106 - Crystallography of Materials by Shyue Ping Ong - Lecture 1
A
B
b
a
Let us define basis vectors a and b.
All points in the lattice can therefore be
reached by integer linear combinations of the
basis vectors, i.e.,
By inspection, we can see that
If we choose A to be the arbitrary origin with
coordinates (0, 0), all other lattice points can
be represented as (u, v). For example,B = (2,
1). t is then known as the translation vector.
t
t = ua + vb, u,v ∈ Z
B- A = 2a + b
9. Basis and translation vectors
¡ For 3D lattices, there are three basis vectors instead of
two. Notationally,
¡ And each lattice point/node can be represented by
coordinates (u, v, w)
NANO 106 - Crystallography of Materials by Shyue Ping Ong - Lecture 1
t = ua + vb+ wc, u,v,w ∈ Z
10. Net and Lattice parameters
NANO 106 - Crystallography of Materials by Shyue Ping Ong - Lecture 1
a = Length of a
b = Length of b
c = Length of c
α = Angle between b and c
β = Angle between a and c
γ = Angle between a and b
a,b,c,α,β,γ{ }
a = Length of a
b = Length of b
γ = Angle between a and b
a,b,γ{ }
11. Lattice math example
¡A lattice is given by the following vectors in
Cartesian space:
¡ Calculate the lattice parameters a, b, c, α, β, γ.
¡ If a lattice node is given by coordinates (3, 2, 1) in
crystal coordinates, what are its coordinates in Cartesian
coordinates?
NANO 106 - Crystallography of Materials by Shyue Ping Ong - Lecture 1
a =
1
0
0
!
"
#
#
#
$
%
&
&
&
, b=
−1/ 2
3 / 2
0
!
"
#
#
##
$
%
&
&
&&
, c =
0
0
3
!
"
#
#
#
$
%
&
&
&
Blackboard
12. Deriving the 2D Crystal Systems
¡ What values can take? Or phrased in another way,
what special values of would result in additional
symmetry?
NANO 106 - Crystallography of Materials by Shyue Ping Ong - Lecture 1
a,b,γ{ }
a,b,γ{ }
Consider arbitrary
a,b,γ{ }
What are the symmetry
elements in this net?
The oblique net (and all 2D nets) has two-fold rotational symmetry.
13. Higher symmetry nets
NANO 106 - Crystallography of Materials by Shyue Ping Ong - Lecture 1
a ≠ b,γ = 90°
a = b,γ = 90°
Rectangular net Square net
a = b,γ =120°
Hexagonal net
14. Adding new nodes
¡Can we get a new distinct net by adding more
lattice points to existing nets?
NANO 106 - Crystallography of Materials by Shyue Ping Ong - Lecture 1
New centered rectangular
net, all nodes have the
same environment.
No new net!
If we reorient the lattice by 45
deg, we see that what we have
is simply a square net with
shorter vectors.
Not a net at all. All nodes
do not have the same
environment.
15. Rectangular
Five 2D nets
NANO 106 - Crystallography of Materials by Shyue Ping Ong - Lecture 1
p: primitive
c: centered
(lower case for 2D)
International symbols for 2D nets
Oblique Square Hexagonal
Four 2D crystal systems
m: monoclinic
o: orthorhombic
t: tetragonal
h: hexagonal
16. Unit Cells
NANO 106 - Crystallography of Materials by Shyue Ping Ong - Lecture 1
¡ A unit cell is simply a geometric unit that can be stacked
infinitely to reproduce the entire lattice.
¡ Primitive unit cells – only 1 lattice point in the cell
¡ Non-primitive cells – more than 1 lattice point in the cell
• Which of these cells are
primitive?
• How many lattice points
are there in each cell?
• Which cell(s) reflect the
full symmetry of the net?
17. The Wigner-Seitz Cell
¡ The Wigner-Seitz (WS) cell around a lattice point is
defined as the locus of points in space that are closer to
that lattice point than to any of the other lattice points.
NANO 106 - Crystallography of Materials by Shyue Ping Ong - Lecture 1
The WS cell
• is a unit cell, i.e., tiles
space to reproduce the
lattice;
• can have more than 4
sides in 2D and more
than 6 sides in 3D;
• Preserves symmetry of
net/lattice.