https://github.com/juliamolsim/geometryoptimization.jl

Geometry optimization for molecular simulation
https://github.com/juliamolsim/geometryoptimization.jl

Last synced: about 1 month ago
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Geometry optimization for molecular simulation

• Host: GitHub
• URL: https://github.com/juliamolsim/geometryoptimization.jl
• Owner: JuliaMolSim
• License: mit
• Created: 2023-09-26T17:50:18.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2025-01-02T21:39:24.000Z (4 months ago)
• Last Synced: 2025-02-23T14:16:46.040Z (2 months ago)
• Language: Julia
• Homepage: https://juliamolsim.github.io/GeometryOptimization.jl/
• Size: 509 KB
• Stars: 7
• Watchers: 6
• Forks: 0
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# GeometryOptimization

[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://JuliaMolSim.github.io/GeometryOptimization.jl/stable/)

[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://JuliaMolSim.github.io/GeometryOptimization.jl/dev/)

[![Build Status](https://github.com/JuliaMolSim/GeometryOptimization.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/JuliaMolSim/GeometryOptimization.jl/actions/workflows/CI.yml?query=branch%3Amain)

[![Coverage](https://codecov.io/gh/JuliaMolSim/GeometryOptimization.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/JuliaMolSim/GeometryOptimization.jl)

A package for optimising the structural parameters of an atomistic system,

i.e. the step usually referred to as

**geometry optimisation** or **structural relaxation**

in electronic structure theory and atomistic modelling.

The package is generic in the datastructures used to represent the geometry,

the calculator used to evaluate energies and forces as well as the solver algorithm.

Generally all

[AtomsBase structures](https://github.com/JuliaMolSim/AtomsBase.jl)

and [AtomsCalculator calculators](https://github.com/JuliaMolSim/AtomsCalculators.jl)

should work out of the box.

See the [documentation](https://JuliaMolSim.github.io/GeometryOptimization.jl/stable/)

for examples and further details.

## Motivating example

We consider the optimisation of the bondlength of a hydrogen

molecule using a simple Lennard Jones potential:

```julia

using AtomsBase

using EmpiricalPotentials

using GeometryOptimization

using LinearAlgebra

using Unitful

using UnitfulAtomic

# Setup system and calculator

cell_vectors = ([10.0, 0.0, 0.0]u"Å", [0.0, 10.0, 0.0]u"Å", [0.0, 0.0, 10.0]u"Å")

system = periodic_system([:H => [0, 0, 0.0]u"bohr",

                          :H => [0, 0, 1.9]u"bohr"],

                         cell_vectors)

zH = 1

emins = Dict((zH, zH) => -1.17u"hartree", )

rmins = Dict((zH, zH) =>  0.743u"Å",      )

calc = LennardJones(emins, rmins, 5.0u"Å")

# Run the geometry optimisation

results = minimize_energy!(system, calc)

# Inspect the results

optsystem = results.system

optimised_bondlength = norm(position(optsystem[1]) - position(optsystem[2]))

```