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Computational Materials Sciencece
Home
Curriculum Vitae
Software
pymatmc2
pypospack
1.0 Installation instructions
Developer's Guide
Process Documentation Standards
Documentation of pypospack
New potential development support
Organization of the Package
pyflamestk.eam
pyflamestk.pyposmat.py
pyflamestk.vvuq.py
pypospack unit testing
Desktop Setup
New Website
Topology Optimization
PETSc
TopOp
Firedrake
Helmholtz Filters
Method of Adjoints (MMA)
JAX
Density Functional Theory
Metallic Clusters.
VLE and metallic clusters
Computational Engineering
COMSOL
Molecular Dynamics
Thermodynamic Ensembles
Developing Interatomic Potentials
Conventional Approach for Developing Interatomic Potentials
MOO algorithms
Pareto Approach to Developing Potentials
PCA and Clustering
Explicit Dynamics
Project Koios
website
Cluster Installation Notes
Untitled page
Node specifications
os installation
Raspberry Pi 4B 8GB
NUC7i5BNH
NVIDIA Jetson Nano 4GB
Credential managment
blog notes
koios 2021.06.28
koios 2021.06.29
koios 2021.06.30
koios 2021.07.03
server management
freeIPA
ansible
openLDAP
Finance Projects
Software Development
Tools
Visual Studio Code
Agile Methodology
Project Management Tools
Programming Languages
Python Language
Software Code Standards
time in python
parallelization, mpi4py
Torque
Python
Building Python in a Home Directory
numpy
python IO
Python Packages
Visualiation in Python
Python Development
Code Development Environment
Introduction to numpy
Plotting using matplotlib
Testing with pytest
Python Packages
Julia Language
Software Design
UML: Sequence Diagrams
UML: Class Diagrams
UML: Activity Diagrams
Version Control (git)
Setting Up Git
Compiling git from source
Merging with git
Using Git
Continous Integration
Documentation Tools
LaTeX
Sphinx
Reading and writing to files
Workflow Tools
CompMatSci Bootcamp
0. Setting up your workstation
0.1 Installation on Mac OS
0.3 Windows Desktop Setup
0.3.1 Install CYGWIN
0.3.2 Ubuntu for Windows
0.3.3 MPI
0.4 Windows Linux System
1. Setting up your environment
1.1 Logging in to your environment.
1.2 Setting up your environment
1.3 Setting up python
setting up mpi4py
python_io
matplotlib
1.7.4 Python Virtual Environments
packages for pymatmc2
1.4.4 Windows
1.5 Setting up GULP
1.6 Setting up git for version control
1.7 Environment variables
1.8 Installing LaTeX
1.9 Setting up databases
2.0 Software Setup
1.4 Setting up VASP
1.4.1 pitzer.osc.edu
1.4.3 MacOSX
1.3 Setting up LAMMPS
1.3.1 Installation on Windows
1.3.2 Installation of OSU Clusters
1.3.3 Installation of UFRC (old)
2.3 ORCA
2. Job Submission
UF Hipergator Information
3. VASP Simulatons
3.1 INCAR
3.2 Calculating Free Atom Energies
4. LAMMPS Simulations
4.1 Moltemplate
5. Making Grain Boundaries
MexM Tutorials
VASP
Lesson 1
OSZICAR
k-Points Convergene
KPOINTS
Energy Cutoff Convergence
Polarization Calculations
vasp_inputscrpt
Pedagogical Approach to VVUQ
Defect Chemistry
Lattice Dynamics
MexM-NN
encoder
ATAT
machine learning primers
Computational Materials
1.0 Introduction to Crystallography
1.1 Introduction to Crystal Structures
2.0 Density Functional Theory
Calculating Enthalpy of Formation
Gaussian
Untitled page
3.0 Molecular Dynamics
Buckingham Potential
EAM DYNAMO setfl
EAM Functional Forms
LAMMPS
Building Lammps
LAMMPS structure files
Making LAMMPS structures
MEAM
MD Thermostats
Neighbor Lists
Running a Molecular Dynamics Simulation
QEQ
Calculating Surface Energies
gnuplot
Ionic Relaxation
Lattice Dynamics
Mesoscale Modelling
MOOSE
Desktop installation of MOOSE
Nudged Elastic Band
Numerics
Uncertainty Quantification and Provenance in Computational Materials
VVUQ
pedagogical examples
CompMatSci
FLAMES - hermes cluster
hipergator
MPI
Introduction to MPI
Introduction to MPI
Introduction to MPI4py
Oracle VM VirtuaBox
AbInit
Research Notes
Machine Learning
Clustering Algorithms
Bayesian Inference
Material Systems
Magnesium Oxide
Uranium Dioxide (UO2)
Silicon Carbide
Gallium Nitride (GaN)
Brillouin Scattering
Brillouin Zones
Interatomic Potentials
Molybdenum Disulfide (MoS2)
Raman Spectroscopy
Computing Resources
Amazon AWS MPI Cluster
Integration with Materials Project
Setting up WordPress on AWS
Continuum Mechanics
Elastic Properties
Material System
fcc_crystal
Fe-C
MgO
Nickel
Niobium Carbide
Si-C
Computational Materials Sciencece
Home
Curriculum Vitae
Software
pymatmc2
pypospack
1.0 Installation instructions
Developer's Guide
Process Documentation Standards
Documentation of pypospack
New potential development support
Organization of the Package
pyflamestk.eam
pyflamestk.pyposmat.py
pyflamestk.vvuq.py
pypospack unit testing
Desktop Setup
New Website
Topology Optimization
PETSc
TopOp
Firedrake
Helmholtz Filters
Method of Adjoints (MMA)
JAX
Density Functional Theory
Metallic Clusters.
VLE and metallic clusters
Computational Engineering
COMSOL
Molecular Dynamics
Thermodynamic Ensembles
Developing Interatomic Potentials
Conventional Approach for Developing Interatomic Potentials
MOO algorithms
Pareto Approach to Developing Potentials
PCA and Clustering
Explicit Dynamics
Project Koios
website
Cluster Installation Notes
Untitled page
Node specifications
os installation
Raspberry Pi 4B 8GB
NUC7i5BNH
NVIDIA Jetson Nano 4GB
Credential managment
blog notes
koios 2021.06.28
koios 2021.06.29
koios 2021.06.30
koios 2021.07.03
server management
freeIPA
ansible
openLDAP
Finance Projects
Software Development
Tools
Visual Studio Code
Agile Methodology
Project Management Tools
Programming Languages
Python Language
Software Code Standards
time in python
parallelization, mpi4py
Torque
Python
Building Python in a Home Directory
numpy
python IO
Python Packages
Visualiation in Python
Python Development
Code Development Environment
Introduction to numpy
Plotting using matplotlib
Testing with pytest
Python Packages
Julia Language
Software Design
UML: Sequence Diagrams
UML: Class Diagrams
UML: Activity Diagrams
Version Control (git)
Setting Up Git
Compiling git from source
Merging with git
Using Git
Continous Integration
Documentation Tools
LaTeX
Sphinx
Reading and writing to files
Workflow Tools
CompMatSci Bootcamp
0. Setting up your workstation
0.1 Installation on Mac OS
0.3 Windows Desktop Setup
0.3.1 Install CYGWIN
0.3.2 Ubuntu for Windows
0.3.3 MPI
0.4 Windows Linux System
1. Setting up your environment
1.1 Logging in to your environment.
1.2 Setting up your environment
1.3 Setting up python
setting up mpi4py
python_io
matplotlib
1.7.4 Python Virtual Environments
packages for pymatmc2
1.4.4 Windows
1.5 Setting up GULP
1.6 Setting up git for version control
1.7 Environment variables
1.8 Installing LaTeX
1.9 Setting up databases
2.0 Software Setup
1.4 Setting up VASP
1.4.1 pitzer.osc.edu
1.4.3 MacOSX
1.3 Setting up LAMMPS
1.3.1 Installation on Windows
1.3.2 Installation of OSU Clusters
1.3.3 Installation of UFRC (old)
2.3 ORCA
2. Job Submission
UF Hipergator Information
3. VASP Simulatons
3.1 INCAR
3.2 Calculating Free Atom Energies
4. LAMMPS Simulations
4.1 Moltemplate
5. Making Grain Boundaries
MexM Tutorials
VASP
Lesson 1
OSZICAR
k-Points Convergene
KPOINTS
Energy Cutoff Convergence
Polarization Calculations
vasp_inputscrpt
Pedagogical Approach to VVUQ
Defect Chemistry
Lattice Dynamics
MexM-NN
encoder
ATAT
machine learning primers
Computational Materials
1.0 Introduction to Crystallography
1.1 Introduction to Crystal Structures
2.0 Density Functional Theory
Calculating Enthalpy of Formation
Gaussian
Untitled page
3.0 Molecular Dynamics
Buckingham Potential
EAM DYNAMO setfl
EAM Functional Forms
LAMMPS
Building Lammps
LAMMPS structure files
Making LAMMPS structures
MEAM
MD Thermostats
Neighbor Lists
Running a Molecular Dynamics Simulation
QEQ
Calculating Surface Energies
gnuplot
Ionic Relaxation
Lattice Dynamics
Mesoscale Modelling
MOOSE
Desktop installation of MOOSE
Nudged Elastic Band
Numerics
Uncertainty Quantification and Provenance in Computational Materials
VVUQ
pedagogical examples
CompMatSci
FLAMES - hermes cluster
hipergator
MPI
Introduction to MPI
Introduction to MPI
Introduction to MPI4py
Oracle VM VirtuaBox
AbInit
Research Notes
Machine Learning
Clustering Algorithms
Bayesian Inference
Material Systems
Magnesium Oxide
Uranium Dioxide (UO2)
Silicon Carbide
Gallium Nitride (GaN)
Brillouin Scattering
Brillouin Zones
Interatomic Potentials
Molybdenum Disulfide (MoS2)
Raman Spectroscopy
Computing Resources
Amazon AWS MPI Cluster
Integration with Materials Project
Setting up WordPress on AWS
Continuum Mechanics
Elastic Properties
Material System
fcc_crystal
Fe-C
MgO
Nickel
Niobium Carbide
Si-C
More
Home
Curriculum Vitae
Software
pymatmc2
pypospack
1.0 Installation instructions
Developer's Guide
Process Documentation Standards
Documentation of pypospack
New potential development support
Organization of the Package
pyflamestk.eam
pyflamestk.pyposmat.py
pyflamestk.vvuq.py
pypospack unit testing
Desktop Setup
New Website
Topology Optimization
PETSc
TopOp
Firedrake
Helmholtz Filters
Method of Adjoints (MMA)
JAX
Density Functional Theory
Metallic Clusters.
VLE and metallic clusters
Computational Engineering
COMSOL
Molecular Dynamics
Thermodynamic Ensembles
Developing Interatomic Potentials
Conventional Approach for Developing Interatomic Potentials
MOO algorithms
Pareto Approach to Developing Potentials
PCA and Clustering
Explicit Dynamics
Project Koios
website
Cluster Installation Notes
Untitled page
Node specifications
os installation
Raspberry Pi 4B 8GB
NUC7i5BNH
NVIDIA Jetson Nano 4GB
Credential managment
blog notes
koios 2021.06.28
koios 2021.06.29
koios 2021.06.30
koios 2021.07.03
server management
freeIPA
ansible
openLDAP
Finance Projects
Software Development
Tools
Visual Studio Code
Agile Methodology
Project Management Tools
Programming Languages
Python Language
Software Code Standards
time in python
parallelization, mpi4py
Torque
Python
Building Python in a Home Directory
numpy
python IO
Python Packages
Visualiation in Python
Python Development
Code Development Environment
Introduction to numpy
Plotting using matplotlib
Testing with pytest
Python Packages
Julia Language
Software Design
UML: Sequence Diagrams
UML: Class Diagrams
UML: Activity Diagrams
Version Control (git)
Setting Up Git
Compiling git from source
Merging with git
Using Git
Continous Integration
Documentation Tools
LaTeX
Sphinx
Reading and writing to files
Workflow Tools
CompMatSci Bootcamp
0. Setting up your workstation
0.1 Installation on Mac OS
0.3 Windows Desktop Setup
0.3.1 Install CYGWIN
0.3.2 Ubuntu for Windows
0.3.3 MPI
0.4 Windows Linux System
1. Setting up your environment
1.1 Logging in to your environment.
1.2 Setting up your environment
1.3 Setting up python
setting up mpi4py
python_io
matplotlib
1.7.4 Python Virtual Environments
packages for pymatmc2
1.4.4 Windows
1.5 Setting up GULP
1.6 Setting up git for version control
1.7 Environment variables
1.8 Installing LaTeX
1.9 Setting up databases
2.0 Software Setup
1.4 Setting up VASP
1.4.1 pitzer.osc.edu
1.4.3 MacOSX
1.3 Setting up LAMMPS
1.3.1 Installation on Windows
1.3.2 Installation of OSU Clusters
1.3.3 Installation of UFRC (old)
2.3 ORCA
2. Job Submission
UF Hipergator Information
3. VASP Simulatons
3.1 INCAR
3.2 Calculating Free Atom Energies
4. LAMMPS Simulations
4.1 Moltemplate
5. Making Grain Boundaries
MexM Tutorials
VASP
Lesson 1
OSZICAR
k-Points Convergene
KPOINTS
Energy Cutoff Convergence
Polarization Calculations
vasp_inputscrpt
Pedagogical Approach to VVUQ
Defect Chemistry
Lattice Dynamics
MexM-NN
encoder
ATAT
machine learning primers
Computational Materials
1.0 Introduction to Crystallography
1.1 Introduction to Crystal Structures
2.0 Density Functional Theory
Calculating Enthalpy of Formation
Gaussian
Untitled page
3.0 Molecular Dynamics
Buckingham Potential
EAM DYNAMO setfl
EAM Functional Forms
LAMMPS
Building Lammps
LAMMPS structure files
Making LAMMPS structures
MEAM
MD Thermostats
Neighbor Lists
Running a Molecular Dynamics Simulation
QEQ
Calculating Surface Energies
gnuplot
Ionic Relaxation
Lattice Dynamics
Mesoscale Modelling
MOOSE
Desktop installation of MOOSE
Nudged Elastic Band
Numerics
Uncertainty Quantification and Provenance in Computational Materials
VVUQ
pedagogical examples
CompMatSci
FLAMES - hermes cluster
hipergator
MPI
Introduction to MPI
Introduction to MPI
Introduction to MPI4py
Oracle VM VirtuaBox
AbInit
Research Notes
Machine Learning
Clustering Algorithms
Bayesian Inference
Material Systems
Magnesium Oxide
Uranium Dioxide (UO2)
Silicon Carbide
Gallium Nitride (GaN)
Brillouin Scattering
Brillouin Zones
Interatomic Potentials
Molybdenum Disulfide (MoS2)
Raman Spectroscopy
Computing Resources
Amazon AWS MPI Cluster
Integration with Materials Project
Setting up WordPress on AWS
Continuum Mechanics
Elastic Properties
Material System
fcc_crystal
Fe-C
MgO
Nickel
Niobium Carbide
Si-C
Uranium Dioxide (UO2)
Crystal Structure: Flourite (cubic) cF12
LAMMPS script
http://math.digi2.jp/math/lammps/examples/simple/
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