Examples
********


Geometry optimization
=====================

* Example: Simple geometry optimization

* Example: Two-stage geometry optimization with initial Hessian

* Example: Periodic lattice optimization under pressure

* Example: Phase Transition Due To External Nonuniform Stress

* Example: Boron nitride optimization under external stress

* Example: Graphene optimization under external stress

* Example: Constrained optimizations


Transition state search
=======================

* Example: TS search starting from initial Hessian

* Example: PES scan and TS search for H2 on graphene


Nudged Elastic Band (NEB)
=========================

* Nudged Elastic Band (NEB) Examples


Intrinsic reaction coordinate (IRC)
===================================

* Example: IRC for HCN

* Example: TS and IRC for Claisen reaction


PES scan
========

* Example: Linear transit

* Example: 2D PES scan

* Example: PES scan for lattice degrees of freedom


PES Exploration
===============

* Example: Basin Hopping for Ar 13 cluster

* Example: PES Exploration, Process Search for alanine with PLAMS

* Example: PES Exploration, Binding Sites for O on Pt 111

* Example: Importing conformers into PES explorations


Molecular dynamics
==================

* Example: Simple MD for H2

* Example: MD for a box of water

* Example: Lattice deformations in MD

* Example: PLUMED spherical constraint on Ion-Water cluster

* Example: MM/MM with constrained ion-water cluster in periodic water
  box

* Example: Measuring the friction coefficient using NEMD

* Example: Measuring the viscosity using NEMD

* Example: Two QM/MM calculations with only MM interactions across
  periodic boundaries


Trajectory replay
=================

* Example: Trajectory replays for PES scans, NEB and MD calculations


Vibrational analysis
====================

* Example: Mode Refinement

* Example: Mode Tracking

* Example: Vibronic-Structure Tracking


PES point properties
====================

* Example: Phonons for graphene

* Example: Phonons with isotopes

* Example: User-defined Brillouin zone for phonon dispersion

* Example: Elastic tensor


Pipe interface
==============

* Example: ASE calculator as a pipe worker

* Example: AMS as a pipe worker
