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devel

API Documentation

The trunk version of the Avogadro documentation is available at http://avogadro.cc/api/dev/.

Best Practices

This page is a guide for newcomers to the project. It should gain some insight on how the project has been designed code-wise and save you time in the long r...

Compiling on Windows

These instructions are to allow users to build Avogadro from the very latest code. Be aware that Avogadro may fail to build or work properly at any given tim...

Compiling on Linux and Mac OS X

These instructions are intended to help users and contributors build Avogadro from the latest code. Be aware that Avogadro may fail to build or work properly...

Getting Involved

Avogadro has a very open and active development community. Currently there are more than 10 active developers and other various contributers.

Creating a Third Party Plugin

Choose plugin type

Design

Avogadro started with a single idea. All great editors are improved by plugins.

Developer:Guidelines

Developer Guidelines

Links

The following are a set of links and bookmarks for developers on a range of useful topics. This includes galleries of example molecular rendering programs,

Localization

Launchpad

Refactoring Ideas

This page contains some ideas about future refactorization of libavogadro. They may seriously break ABI (and possibly API), and should be discussed

Release Checklist

Create a draft of the release notes on the wiki. Grab the latest i18n files from Launchpad translations. Make sure to update CMakeLists.txt and Doxyfi...

Standards

When in doubt about standards, consider the policies which KDE has set (see [\

To Do for 1.1

The upcoming development series 1.1.x will be a series of unstable/beta releases, leading up to the 1.2.0 release. This process will be similar to the 0.9.x ...

Working With Git

In December 2008 Avogadro moved its version control system over to Git, hosted at GitHub. Git is quite different to traditional, centralized version control ...

docs

Building a Crystal Surface (Slab)

Build up a crystal surface, e.g., Pt <111> for a defined Miller Plane.

Building a Polymer Unit Cell

A walk-through on creating a unit cell (of a polymer) using Avogadro and the Align tool. This specific example uses Gaussian, but translation vectors for oth...

Crystal Symmetry Perception

Calculation results often specify all atoms and translation vectors, but not the space group. Here we see how to perceive the space group from a set of cryst...

Molecule-Surface Interactions

Beyond building a crystal surface, new features in Avogadro make it easy to consider molecule-surface interactions. The lesson picks up at the end of the “Bu...

Reducing Crystals to Primitive Unit Cells

Some simulations use “supercells” – larger periodic boundary systems than the primitive unit cell. Here is a walk-through on reducing a large supercell to th...

Scaling Crystal Volumes

Avogadro 1.1 allows you to adjust the volume or spacing of a unit cell.

Super Cell Builder

Once a crystal surface has been built, the Super Cell Builder can expand atoms within a space group, replicate the unit cell, and perform simple bonding.

Building a Peptide

A walkthrough on how to create a custom peptide model in Avogadro.

Building Carbon Nanotubes

Avogadro 1.1 includes a new nanotube builder, based on the well-known TubeGen code and website from the Doren group at U. Delaware. (http://turin.nss.udel.ed...

Building DNA/RNA

Avogadro now has a builder for nucleic acid sequences and this walk-through will show you how to use it.

Building with SMILES

SMILES (Simplified molecular-input line-entry system) allows you to build molecules through a string of text. If you have a SMILES string (e.g., copied from ...

Importing from the Protein Data Bank (PDB)

You can read PDB files that you download yourself from http://www.rcsb.org/ or access the PDB code yourself.

Importing Molecules by Name

Select the “File” menu.

Insert Fragments

Avogadro includes over 300 common molecules and molecular fragments to make building larger structures easy.

Coloring Part of a Molecule

Coloring various parts of a molecule can provide a more visually stimulating way to display qualitative information.

Different Display Types in Avogadro

ABINIT Generator

Avogadro has a new interface to the open source solid-state code ABINIT, provided by one of the ABINIT developers, Prof. Matthieu Verstraete

LAMMPS input for water

Prepare initial geometry

Drawing Molecules

Molecules are built and edited with the draw tool.

Introduction

Avogadro is a “molecular editor,” designed to be easy to use to construct and view molecules and materials in 3D. It runs on Windows, Linux, and Mac.

Making Selections

The selection tool is also a useful feature to master when beginning to learn Avogadro. Generally, the selection tool allows for the individual selection of ...

Preface

Avogadro: Molecular Editor and Visualization

Build Menu

Edit Menu

Extensions Menu

File Menu

Select Menu

View Menu

Conformer Search

How to search for low-energy conformations

Constraints & Optimizations

Avogadro allows for the optimization of an object, with respect to a variable(s). Below is one example of how constraints can be applied while optimizing a m...

Molecular Mechanics & Force Fields

Avogadro comes equipped with multiple different force fields. Below is general information regarding the force fields to help you select the best optimizatio...

Align Tool

The align tool rotates, and translates a molecule(s) into a specific reference frame.

Auto Optimize Tool

The Auto Optimize tool continuously optimizes molecular geometry through molecular mechanics. This tool provides an interactive interface, allowing you to ma...

Auto Rotate Tool

The auto rotate tool allows for the continuous rotation of a molecule.

Bond Centric Manipulate Tool

The Bond-Centric Manipulate tool alters angles, bonds, and torsions of a molecule.

Draw Tool

1. Creating a Molecule

Manipulate Tool

The manipulate tool allows you to move atoms and selected fragments.

Measure Tool

The measure tool determines bond lengths, angles, and dihedrals.

Navigate Tool

The navigation tool is used to pan, rotate, and scale the view of a molecule.

Selection Tool

The selection tool allows the indiviual selection of atoms, bonds, or fragments.

Naming a molecule with PubChem

Avogadro 1.1 and later includes support for naming compounds using the NIH Chemical Resolver system and the PubChem database.

Using Atoms-In-Molecules (Bader) Analysis - QTAIM and WFN

Avogadro now includes support for the QTAIM analysis developed by Prof. Richard Bader and his group. This technique allows Avogadro to determine bond connect...

Viewing Electrostatic Potential Maps

The electrostatic potential maps help to visualize charge distribution, and other charge related properties of molecules.

Viewing Molecular Orbitals

This feature requires a “checkpoint” or “formatted checkpoint” from quantum chemistry codes

Viewing Spectral Properties

This tutorial covers plotting vibrational spectra, but other types of spectra are possible with the output files from quantum chemical programs

Viewing Vibrations

This feature allows visualizing vibrations from a “frequency” calculation with quantum chemistry codes (e.g., Gaussian, Q-Chem, etc.)

install

DebianUbuntuPackages

Debian

Distribution Packages

Debian

Get Avogadro

The latest and greatest release of Avogadro is Avogadro 1.2.0 as of 15 June, 2016, and release notes are available.

OpenSUSEPackages

OpenSUSE 11.0

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