The Complete Introduction to LAMMPS

Investigate crack propagation in a two-dimensional LAMMPS simulation, using the Leonard Jones six 12 potential and boundary setups, including periodic BCs, to understand how the case is structured.

Explore how units work in LAMMPS, including Leonard Jones dimensionless units (LJ), alternative conventions, and the meaning of sigma as the distance where the potential energy is zero.

Explore how crack propagation models handle boundary conditions in LAMMPS, including fixed, periodic, reflect, and shrinkwrap boundaries, and how atoms interact with domain edges.

Explore crack propagation under shrink-wrapped boundaries with a minimum domain size in a two-dimensional LAMMPS setup, using atomic style, a neighbor list, and a hexagonal lattice and unit cell.

Explore crack propagation in crystal structures with a lammps setup that illustrates simple cubic instability and transition to hexagonal lattices, including region definitions, atom types, and lennard jones potentials.

Explore the Leonard Jones potential for a two-atom system, where the potential energy varies with their distance, defining an equilibrium separation and the forces via the negative gradient.

Describe how the Lennard-Jones potential in LAMMPS encodes attraction and repulsion with epsilon and sigma, and shows how distance governs forces, the minimum, and zero-crossings.

Explore setting up a two-dimensional material under stress to study crack propagation in LAMMPS, using Lennard-Jones with epsilon=1, sigma=1, a 2.5 cutoff, wildcard atom types, and periodic boundaries.

Explore how a finite cut-off simplifies lammps simulations by ignoring distant interactions, focusing on nearby neighbor pairs in a hexagonal lattice and defining domains, boundary conditions, and neighbor lists.

Understand Leonard Jones units as a dimensionless scale for crack propagation simulations, and learn to set mass, sigma, and epsilon to one to compare relative energies and temperature.

Learn how Leonard Jones units express time, length, energy, and mass as non dimensional fractions of characteristic quantities, simplifying dynamics in molecular simulations while noting conversion challenges for literature comparisons.

Define and assign simulation regions and groups in LAMMPS, using block regions, coordinates, and group operations like union and subtract to prepare atom initialization.

In this LAMMPS crack propagation case, define a fixed boundary and a movable group, create left upper and left lower regions with notch to nucleate cracks and manage inter-group interactions.

Describe setting lammps groups and atom types, assigning left upper to type two and left lower to types three through five, with mass definitions to distinguish types.

Explore how cutoff lengths and neighbor lists in LAMMPS reduce Lennard Jones force calculations by zeroing distant interactions, while predicting atom movement to boost computational efficiency.

Understand how to build and update neighbor lists to limit distance checks within a cutoff, boosting molecular dynamics efficiency while noting the need to recalculate lists and benchmark accuracy.

Learn how LAMMPS uses compute commands to measure temperature from atomic energy, and how velocity and fix commands interact within a crack propagation case.

Apply the velocity command to assign random velocities to atoms in a group to reach a target temperature, and ensure distinct seeds for pseudo random generation.

Learn how a compute supplies temperature to a velocity command, then set and ramp the upper mobile group's velocities from 0 to 0.3 in the y direction.

Explore how the fixed command applies to all atoms using the N.V. (micro canonical) ensemble, and contrast extrinsic vs intrinsic properties in crack propagation simulations.

Define how fixing two variables in an ensemble—such as N, V, and E—controls the system’s thermodynamics, with microcanonical as the simplest case and NPT, grand canonical, and others possible.

The lecture shows how the fix set force applies boundary forces in x, y, z to a boundary group; zeroing y and z forces constrains motion and stops crack propagation.

Set up shows how run controls simulation duration, output frequency, and time steps in a Lennard-Jones crack propagation case, stressing small steps to avoid nonphysical results.

Balance simulation, analytical results, and experiments in crack propagation, and validate molecular dynamics results against theory and lab data; tune time steps and use thermo and neighbor-list controls.

Explore how LAMMPS outputs data via dumps, including atomic positions and velocities, every 500 time steps, and how image and movie dumps visualize atom configurations; tune thermo and log outputs.

Explore crack propagation in LAMMPS by tweaking the neighbor modify command to create or remove interfaces between atom types two and three, and observe crack nucleation and domain-wide failure.

Adjust velocity to raise temperature, observe diffusion and evaporation, and study shrink wrapping and fixed boundary effects on crack propagation in LAMMPS.

Learn how to use LAMMPS with ensembles to drive atom dynamics by exploring fixes, applying the NV ensemble to the mobile group, and observing boundary behavior.

Explore the obstacle flow case in LAMMPS, a two-dimensional, periodic setup using boundary regions, sphere obstacles, delete atom, and indent fixes to drive flow from left to right.

Explore how fix six pushes red atoms to create flow in the x direction, while average force stabilizes the upper boundary in LAMMPS.

Examine how the deposit case models atom and molecule deposition onto a 3D substrate in LAMMPS, highlighting interactions, boundary conditions, and the progression from atom-only to molecular simulations.

Run a deposition LAMMPS case with a local serial executable when the package manager version is out of date, and observe red and blue atoms forming a mixed region.

The lecture shows why fixed, reflective boundaries at the top and bottom are used with periodic boundaries in x and y, avoiding non-physical particle exchange and shrink-wrapping pitfalls.

Explore how fcc and bcc lattices differ, visualize offset square sheets and stacking in crystal structures, and grasp unit cells and packing density at angstrom scales.

Build FCC unit cells from gaps between atoms, adjust domain size and sigma to model equilibrium spacing, and explore stacking to reveal packing density differences with BCC and simple cubic.

Simulate deposition of two atom types raining onto a substrate using Lennard Jones potentials with distinct cutoffs, and define a mobile region governed by N.V. ensemble and Langevin fixes.

Explore how the Langevin thermostat in LAMMPS simulates Brownian motion for a group, using damping, seed, and temperature settings in Lennard-Jones units. Also see how the deposit fix adds atoms.

Simulate deposition in LAMMPS with fix deposit using PN, type, N, region, and velocity, detailing how atoms insert and why a reflect fix is needed to keep atoms from disappearing.

Explore a deposition case with molecules by defining three atom types, bond types, and harmonic bonds, using the deposit.molecule input and Lennard-Jones interactions with substrate regions.

Explores how to set up harmonic bonds in LAMMPS, interpreting bond coefficients, molecule and deposit commands, and reading the molecule dot dimer file to build two-atom molecules.

Explore how to specify special bond counts and bonds between neighbors for diatomic molecules, import complex molecules from databases, and deposit molecules with random orientations using LAMMPS and SHAKE fixes.

This lecture explains simulating the dynamics of a salivated peptide chain in water using Lammps, with real units, a data file, and coulomb and lennard-jones interactions with cutoffs.

Explore modeling a peptide in LAMMPS by importing a peptide data file, defining bonds and angles, and applying shake constraints.

Explore the peptide data file in a LAMMPS workflow, detailing atoms, bonds, angles, and masses. Explain harmonic bonds and angles, dihedral and improper terms, and LJ coefficients shaping molecular mechanics.

Identify unique atom identifiers and atom types in a lammps peptide data file. Understand how coordinates, charges, and periodic boundary conditions shape the simulated water environment and thermodynamic properties.

Explore how LAMMPS organizes atoms, bonds, and angles, with bond and angle coefficients to enforce geometry in a peptide and water system, including radians and degree conversions.

Specify peptide bond and angle details, four-atom connections, and use groups and dumps to manage water versus peptide, then explore temperature changes and the shake algorithm.

Explore how to apply LAMMPS fundamentals with Python scripting to access thermo outputs—energy, temperature, and pressure—from the terminal and log file, and model biomolecules using modular building blocks.