The Complete Introduction to LAMMPS from Udemy

What's inside

Learning objectives

Lammps
Molecular dynamics

Coding and modelling complex molecules, stressing crystal structures, deposition of atoms/molecules onto solid substrates and more

Lammps
Molecular dynamics
Coding and modelling complex molecules, stressing crystal structures, deposition of atoms/molecules onto solid substrates and more

Syllabus

Introduction

Learning Outcomes

Course Requirements

Who is this Course for?

Installation prt 01 - LAMMPS

Installation prt 02 - Ubuntu Terminal Emulator

Installation prt03 - Ovito

LAMMPS Installation Structure prt 01

LAMMPS Installation Structure prt 02

LAMMPS Case Directory Structure (prt 03)

LAMMPS Input Files - First Look (prt 04)

LAMMPS Installation Structure prt 05

LAMMPS Installation Structure prt 06

Case 1: LAMMPS Case Structure, Principles of Molecular Dynamics

Crack Propagation Case - Header and Periodic BCs

A Word on Units

Crack Propagation Case - Other Boundary Conditions f and s

Crack Propagation Case - Other BCs (m) and Crystal Lattices

Crack Propagation Case - Crystal Structures

Crack Propagation Case - Potentials

Crack Propagation Case - Fundamental Equation of Motion prt 01

Crack Propagation Case - Fundamental Equation of Motion prt 02

Crack Propagation Case - Fundamental Equation of Motion prt 03

Crack Propagation Case - Units prt 01

Crack Propagation Case - Units prt 02

Crack Propagation Case - Regions prt 01

Crack Propagation Case - Regions prt 02

Crack Propagation Case - Groups

Crack Propagation Case - Neighbor Lists prt 01

Crack Propagation Case - Neighbor Lists prt 02

Crack Propagation Case - Velocity prt 01

Crack Propagation Case - Velocity prt 02

Crack Propagation Case - Velocity prt 03

Crack Propagation Case - Fixes

Crack Propagation Case - Ensembles

Crack Propagation Case - Setforce

Crack Propagation Case - Output prt 01

Crack Propagation Case - Output prt 02

Crack Propagation Case - Output prt 03

Crack Propagation Case - Playing with the code prt 01

Crack Propagation Case - Playing with the code prt 02

Crack Propagation Case - Playing with the code prt 03

Case 2: Fluid Flow in LAMMPS

Flow Case prt 01

Flow Case prt 02

Case 3: Deposition and a First Look at Molecules

Deposition Case with Atoms prt 01

Deposition Case with Atoms prt 02

Deposition Case with Atoms prt 03

Deposition Case with Molecules prt 01

Deposition Case with Molecules prt 02

Deposition Case with Molecules prt 03

Deposition Case with Molecules and SHAKE prt 01

Deposition Case with Molecules and SHAKE prt 02

Deposition Case with Molecules and SHAKE prt 03

Deposition Case with Molecules and SHAKE prt 04

Deposition Case with Molecules and SHAKE prt 05

Final Case: Peptides and Defining Complex Molecules in LAMMPS

Peptide Case prt 01

Peptide Case prt 02

Peptide Case prt 03

Peptide Case prt 04

Peptide Case prt 05

Peptide Case prt 06

Course Conclusion

Good to know

Know what's good

, what to watch for

, and possible dealbreakers

Demystifies the fundamentals of molecular dynamics, making it straightforward and easily understood for those with a foundational knowledge of atomic science

Provides a solid grounding in LAMMPS simulation use and construction, enabling expansion into various areas of interest within molecular dynamics

Explores the coding and modeling of complex molecules, stressing crystal structures, and deposition of atoms/molecules onto solid substrates, which are relevant to materials science

Explains common LAMMPS functions that control simulations, giving the power to organize anything from stressing crystals to the folding of enzymes

Takes you through the structure of all LAMMPS cases, enabling navigation of any common LAMMPS case file and directory, which is essential for practical application

Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in The Complete Introduction to LAMMPS with these activities:

Review Classical Mechanics

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Reinforce your understanding of classical mechanics, which forms the basis of molecular dynamics simulations.

Browse courses on Classical Mechanics

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Review relevant chapters in a physics textbook.
Work through practice problems related to forces and motion.
Focus on concepts like potential energy and kinetic energy.

Read 'Understanding Molecular Simulation' by Frenkel and Smit

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Deepen your understanding of molecular simulation principles and algorithms.

View Understanding Molecular Simulation: From... on Amazon

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Obtain a copy of the book.
Read the chapters relevant to the course topics.
Work through the examples and exercises.

Practice LAMMPS Input Scripting

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Improve your ability to write and debug LAMMPS input scripts.

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Start with simple example scripts from the LAMMPS documentation.
Modify existing scripts to explore different simulation parameters.
Try to replicate the examples covered in the course.

Four other activities

Expand to see all activities and additional details

Show all seven activities

Explore 'The Art of Molecular Dynamics Simulation' by Rapaport

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Gain a deeper understanding of the practical aspects of molecular dynamics simulation.

View The Art of Molecular Dynamics Simulation on Amazon

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Obtain a copy of the book.
Focus on chapters related to force fields and integration methods.
Compare the techniques described in the book with those used in LAMMPS.

Create a LAMMPS Simulation Tutorial

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Solidify your knowledge by explaining a specific LAMMPS simulation setup to others.

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Choose a specific simulation topic covered in the course.
Write a step-by-step tutorial explaining the setup and execution.
Include clear explanations of the LAMMPS commands used.
Share your tutorial on a relevant online forum or blog.

Contribute to the LAMMPS Documentation

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Deepen your understanding of LAMMPS by improving its documentation.

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Identify areas in the LAMMPS documentation that are unclear or incomplete.
Write improved explanations or examples.
Submit your contributions to the LAMMPS developers.

Simulate a Novel Material Property

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Apply your LAMMPS skills to investigate a material property not covered in the course.

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Choose a material and a property to simulate (e.g., thermal conductivity of graphene).
Research existing literature on the simulation of that property.
Develop a LAMMPS input script to perform the simulation.
Analyze the results and compare them with literature values.

Career center

Learners who complete The Complete Introduction to LAMMPS will develop knowledge and skills that may be useful to these careers:

Molecular Modeler

A molecular modeler is responsible for creating and analyzing computational models of molecules to understand their properties and interactions. This course provides essential training in molecular dynamics simulations using LAMMPS, the key tool for this role. The course teaches students how to construct and interpret LAMMPS simulations of systems ranging from simple molecules to large peptides. A molecular modeler must know how to set up simulations, manage boundary conditions, apply different potentials, and analyze the outputs. The course, with emphasis on complex molecule construction and simulation, gives a distinct advantage. A molecular modeler uses these techniques regularly to drive forward research in drug discovery, materials science, and other areas. This course provides a solid foundation in the practical skills and fundamental knowledge required to succeed as a molecular modeler.

See salaries and explore the career path for Molecular Modeler

Computational Materials Scientist

A computational materials scientist uses simulations to study the properties of materials. This course helps build a foundation for performing molecular dynamics simulations, the primary technique used in this role. The course teaches how to use LAMMPS, a software package essential for this work, providing the practical skills to simulate material behavior at the atomic level. A computational materials scientist must understand how to set up and run these simulations, interpret results, and apply insights to materials design and discovery. The course provides experience in understanding LAMMPS case structure, commands, fixes, and functions. It also explores how to model complex molecules and crystal structures, which is vital for materials research. This knowledge is directly translatable to the daily work of a computational materials scientist, who will use these kinds of simulations to investigate materials at the atomic level.

See salaries and explore the career path for Computational Materials Scientist

Computational Chemist

A computational chemist uses computer simulations to study molecules and chemical reactions. This course helps introduce the practical side of molecular dynamics simulations, which are essential in a computational chemist's work. The course teaches students how to use LAMMPS to investigate a variety of systems, from small molecules to larger biomolecules. Computational chemists manipulate parameters to gain insight into chemical behavior and predict new properties. The course's detailed instruction on LAMMPS commands, fixes, and other functions provides a strong foundation for performing such work. This course explores how to model complex molecules and run various simulations, such as crystal stressing, which is directly relevant to a computational chemist's responsibilities.

See salaries and explore the career path for Computational Chemist

Simulation Engineer

A simulation engineer develops and implements computational models to simulate physical processes and systems. This course provides a practical understanding of how to use LAMMPS for molecular dynamics simulations, a core skill for this role. The course covers topics such as file structure, commands, fixes, and functions, which allow the simulation engineer to create and manage complex simulations. The ability to model molecules, crystal structures, and atomic deposition, as instructed in this course, is directly relevant to the work of a simulation engineer. The course's hands-on approach with different simulation cases helps a simulation engineer develop the problem-solving skills to tackle complex scenarios. A simulation engineer needs to construct, analyze, and interpret results of various simulations, often in the context of materials or biological systems, and this course helps build a foundation for that.

See salaries and explore the career path for Simulation Engineer

Biomolecular Engineer

A biomolecular engineer works on the design and development of biological systems and materials at the molecular level. This course may be a useful introduction to molecular dynamics, a computational method important in this field. The course specifically covers how to use LAMMPS to simulate molecular systems, which is a practical skill required of many biomolecular engineers. The course includes instruction on how to model peptides and other complex molecules, and how to apply boundary conditions and different potentials. A biomolecular engineer might rely on simulations to understand protein folding and interactions. This course is useful for anyone seeking to apply computational methods to biological systems.

See salaries and explore the career path for Biomolecular Engineer

Research Scientist

A research scientist conducts investigations to advance knowledge in specific fields, often using computational methods. This course may be helpful for research scientists who need to use molecular dynamics simulations in their work. The course provides hands-on experience with LAMMPS, which is used to simulate a variety of physical systems. The course explores how to simulate complex molecules, crystal structures, and the interactions of atoms and molecules, skills that are helpful in many research areas. The course also introduces the fundamentals of molecular dynamics. A research scientist often needs to make their own simulation tools, so familiarity with a tool like LAMMPS is helpful. This course may be useful for a research scientist looking to expand the scope of their research into the field of molecular simulations.

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Drug Discovery Scientist

A drug discovery scientist identifies and develops new drug candidates, often using computational methods to analyze and model molecular interactions. This course introduces techniques of molecular dynamics simulation, which are essential to this work. The course provides an introduction to using LAMMPS, a tool used to simulate the behavior of molecular systems. The course covers essential concepts in model construction, including setting up boundary conditions, applying potentials, and running complex simulations. The course also covers the modeling of peptides and other molecules, which are central to drug development efforts. This course may be helpful to a drug discovery scientist looking to broaden their knowledge of computational tools.

See salaries and explore the career path for Drug Discovery Scientist

Nanoengineer

A nanoengineer designs and creates materials and devices at the nanoscale. This course helps introduce the fundamentals of simulating systems at the atomic level. As part of the job, a nanoengineer needs to understand how materials behave at these tiny scales. The course highlights a practical approach to setting up and running molecular dynamics simulations using LAMMPS, which allows a nanoengineer to examine system properties. The course's discussions of crystal structures, atom deposition, and complex molecule modeling are all important for the work of a nanoengineer. This course, introducing how to stress crystals, may be valuable to any nanoengineer. The course may be useful in preparing a nanoengineer for this work.

See salaries and explore the career path for Nanoengineer

Materials Engineer

A materials engineer develops, tests, and processes materials for various applications, and often needs to use computer simulations in order to do their work effectively. This course helps introduce methods of molecular dynamics simulation. The course provides an introduction to using LAMMPS, a software package used to simulate material behavior at the atomic level. The course walks participants though the setup of common simulation cases and discusses relevant commands, fixes, and functions. The modelling of crystal structures is an important part of what a materials engineer does, and this course may be useful in that regard. The course also discusses concepts such as atom deposition and complex molecule construction. This course may be broadly helpful for a material engineer.

See salaries and explore the career path for Materials Engineer

Process Engineer

A process engineer develops and optimizes industrial processes, often relying on simulations to understand system behavior and to improve efficiency. The course may be useful for process engineers who want to understand the behavior of systems at the molecular level. The course introduces the practical use of LAMMPS, a tool used to run simulations of this kind. The course provides instruction in setting up simulation files, using commands and fixes, and working with complex molecules, skills which can be helpful for a process engineer. The course also touches on fluid flow simulation, which can be relevant to a process engineer's work. This course may be useful for process engineers seeking to expand their simulation capabilities.

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Data Scientist

A data scientist uses statistical methods and data modeling techniques to analyze complex data sets. This course may be helpful for a data scientist who is interested in extending their skill-set to molecular simulation. The course emphasizes a practical approach to using LAMMPS for molecular dynamics simulation. The course's instruction on working with input files, defining simulation parameters, and analyzing outputs may be useful to a data scientist. A data scientist may want to apply their skills to analyzing simulations. This course may give a data scientist exposure to working with molecular simulations.

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Software Developer

A software developer designs, develops, and maintains software applications, and may wish to work on software used for scientific simulation. This course provides a practical introduction to LAMMPS, which is a software package used for molecular dynamics simulations. This course may be useful for a software developer looking to get familiar with the kinds of technical tools used in scientific computing. The course may provide direct experience writing scripts that interface with LAMMPS. The course provides instruction on setting up simulation files, using commands and fixes, and exploring simulation cases. This course may be relevant to a software developer in this field.

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Science Writer

A science writer communicates scientific information to a general audience. This course may be helpful for a science writer looking to build their background in molecular simulation. The course provides a practical introduction to molecular dynamics, including coverage of the use of tools like LAMMPS. The course touches on many simulation case studies. The course may provide a helpful introduction for a science writer who wishes to write about molecular simulation.

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Physics Teacher

A physics teacher educates students on physics concepts and principles. This course may be helpful for a physics teacher looking for a practical way to introduce concepts in molecular dynamics to students. The course includes hands-on instruction in setting up molecular dynamics simulations using LAMMPS. The course covers the structure of LAMMPS simulations. This course may help the teacher develop new and interesting content for their course.

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Laboratory Technician

A laboratory technician assists scientists or engineers in a laboratory setting. This course may be useful for a laboratory technician working in a materials or chemistry lab. The course introduces molecular dynamics simulations and how to use LAMMPS, a tool for simulation. The course may help a laboratory technician to prepare simulation files, manage calculations, and assist in the analysis of results. This course may help a lab technician learn about the computational techniques associated with their work.

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The Complete Introduction to LAMMPS

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