Using Avogadro Program

  1. Avogadro Molecular Modeling Program
  2. Using Avogadro Program For Dummies

BackgroundThe Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. ResultsThe work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself.

Using Avogadro Program

The application and library can each be extended by implementing a plugin module in C or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. ConclusionsAvogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from.

Many fields such as chemistry, materials science, physics, and biology, need efficient computer programs to both build and visualize molecular structures. The field of molecular graphics is dominated by viewers with little or no editing capabilities, such as RasMol , Jmol , PyMOL , VMD , QuteMol , BALLView , VESTA , and XCrySDen , , among many others. The aforementioned viewers are all freely available, and most of them are available under open-source licenses and work on the most common operating systems (Linux, Apple Mac OS X, Microsoft Windows, and BSD).The choice of software capable of building chemical structures in three dimensions is far smaller. There are existing commercial packages, such as CAChe/Scigress , ChemBio3D , GaussView , HyperChem , CrystalMaker , Materials Studio , and Spartan , which are polished and capable of constructing many different types of molecular structures.

Avogadro

They are, however, not available for all operating systems (most of them only run on Microsoft Windows), and are not easily extensible, customized, or integrated into automated workflows. Licensing costs can be prohibitive.

If the company were to change its direction or focus, this can lead to a loss of a significant research investment in a commercial product. Furthermore, in most cases, these programs use custom, proprietary file formats, and semantic and chemical data can be lost in conversion to other data formats.The selection of free, open-source, cross-platform, three-dimensional, molecular builders was quite limited when the Avogadro project was founded in late 2006. Ghemical was one of the only projects satisfying these needs at the time. Two of the authors (Hutchison and Curtis) contributed to Ghemical previously, but had found that it was not easily extensible. This led them to found a new project to address the issues they had observed in Ghemical and other packages. The Molden application was also available, able to build up small molecules and analyze output from several quantum codes. However, it suffers from a restrictive license and it uses an antiquated graphical toolkit, which is not native on most modern operating systems.Broad goals for the design of a molecular editor were identified following a case study of the available applications.

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One of the main issues with both commercial and open-source applications is a lack of extensibility; many of the applications also only work on one or two operating systems. The creation of an open and extensible framework that implements many of the necessary foundations for a molecular builder and visualizer would facilitate more effective research in this area. Further, the open, standardized Chemical Markup Language (CML) file format would be used, to secure semantic and chemical data and allow easy interoperability with other chemistry software.At the time of writing, it is apparent that other researchers have perceived similar needs. Several new applications are available today that focus on both building and visualizing molecular structure. These include CCP1GUI , Gabedit and some highly specific editors such as MacMolPlt which focus on particular computational packages (i.e., GAMESS-US for MacMolPlt).

Whilst offering many interesting and useful features, these projects suffer from the same issues centering around effective reuse of existing code, well commented and documented code, and easy extension to add new features and adapt for specialized areas. The Avogadro project was started in earnest in 2007, and over the first 5 years of development has been downloaded over 270,000 times , been translated into over 20 languages , and has over 20 contributors. So far, it has been cited over 100 times , including applications in spectroscopy, catalysis, materials chemistry, theoretical chemistry, biochemistry, and molecular dynamics, among many others –.From the beginning, the project has strived to make a robust, flexible framework for both building and visualizing molecular structures. Much of the initial focus has been placed on preparing input and analyzing output from quantum calculations. Other applications such as preparing input for MD simulations and visualizing periodic structures will also be presented, demonstrating the flexibility of the Avogadro platform. The development team has also been members of the Blue Obelisk movement, following the three pillars outlined by the group: Open Data, Open Standards, and Open Source ,.

Avogadro Molecular Modeling Program

Software architectureOne area that seems to suffer in many code bases in chemistry is software architecture. This can lead to less maintainable code, poor code reuse, and a much higher barrier to entry. Problems were identified in other projects with a view to minimize their impact when developing Avogadro. Modern software design processes were used in the initial planning stages of Avogadro, along with the choice of modern programming languages and libraries.Avogadro has close ties to several other free, cross-platform, open-source projects to reuse as much code as is practical.

These projects include Qt to provide a free, cross-platform graphical toolkit; Open Babel for chemical file input/output, geometry optimization, and other chemical perception; Eigen for matrix and vector mathematics; OpenGL/GLSL for real-time, three-dimensional rendering; and POV-Ray for ray-traced rendering.Based on the previous experience of the authors and a review of available programs at the time, several fundamental choices were made. The C programming language; the Qt graphical toolkit; OpenGL for 3D visualization; CMake as the build system; and Open Babel as the chemical library. Using this combination of languages and libraries requires the project to be licensed under the GNU GPLv2 license and made openly available to all.The core of Avogadro is written in portable C code with platform-specific differences abstracted away by Qt, OpenGL, and Open Babel.

The CMake build system makes the build process relatively simple on all supported platforms. Avogadro has been successfully built and tested on Linux, Apple Mac OS X, and Microsoft Windows in common 32 and 64 bit hardware architectures.The Avogadro framework uses the model, view, controller paradigm. The model is comprised of the core data classes such as Molecule, Atom, and Bond, views are made up of the engine/display plugins, and controllers are the tools (interactive mouse) and extensions (non-interactive, form based/menu based). Every plugin has full access to the core data model, but view and controller plugins are conceptually different; views are responsible for displaying data and controllers are responsible for modifying/changing data.Plugins rely on Avogadro’s set of programming interfaces and almost all functionality is implemented in self contained plugins that are loaded at runtime. The majority of plugins distributed with Avogadro are written in C, but the API is also available in the Python scripting language. This allows for a great deal of choice in how plugins are implemented. Each plugin is a singleton class that implements a particular set of functions–depending on the type of plugin–which allows for features to be implemented in a very modular way.Over the last few years Avogadro development has started to use nightly builds of the latest version of the code in order to automatically flag issues introduced in new commits.

Code review was also introduced in order to add a review step before new code is merged, along with softening the line between someone with commit rights and someone without (anyone can propose and upload a patch, but a small group can choose if/when the patch will be merged). Some automated testing has been added, but coverage at this point remains relatively low. API documentation is automatically generated from comments in the code using Doxygen. Plugin interfaceAvogadro plugins are divided into four different types corresponding to four main classes that derive from this common base class, specializing their interface for specific activities (Figure ).

The Avogadro::Color base class defines the virtual interface for applying colors to atoms, bonds, and other properties. Avogadro::Engine defines the common interface for all display types in Avogadro: simple ball and stick, Van der Waals visualizations, surfaces, and force visualizations. The Avogadro::Tool base class provides the interface for all interactive tools, focusing principally on mouse and keyboard interaction with Avogadro. Examples of tool plugins include the draw tool used to draw molecules atom by atom, and the navigation tool used to pan, rotate, and scale the view of the molecule. There are also several specialized tools such as the alignment tool.

Finally there is the Avogadro::Extension class, which defines the interface for dialog based plugins. These extensions can interact with the molecule, and are used for a variety of purposes from molecule properties dialogs to input file generation dialogs for many quantum codes including NWChem, Gaussian, GAMESS, and others. This class of plugin is also applied to file import, and network aware extensions querying web databases for structures given their common name for example.At start up, several standard directories, which may be customized, are searched for plugins. The Qt plugin framework is used to check that the plugins have a recent enough version to be loaded, and the plugin type can be deduced once loaded. The user interface is then populated with appropriate entries; tools are added to the main toolbar using their embedded icons, display types are added to the display type list, and menu entries are added for all loaded extensions.The tool and display type plugins can both (optionally) provide a dialog for configuring the plugin. Dialogs are specific to each plugin and integrated into the user interface. Display typesDisplay plugins are referred to as “engines” internally.

Their primary focus is rendering graphics to the screen. As is the case with most molecular graphics, a large portion of the geometric primitives are spheres and cylinders, typically used to represent atoms and bonds. There are many other properties that can be rendered using the display type plugins, for example, some of the engines also convey information about the underlying data the geometric primitives represent to allow for the molecule to be edited. Table shows a summary of the display plugins distributed with Avogadro. The navigation tool provides basic scene navigation, implementing rotation,panning, tilting, and zooming support.

The initial point of interaction (where the click occurs) changes the anchor point for navigation; navigation takes place about the center of molecule when clicking in empty space or about the center of any clicked atom. During interaction, the navigation tool provides visual cues to show what type of navigation is taking place. The navigation tool is also used as the default tool if the currently active tool does not handle the mouse event passed to it.One of the other central tools is the draw tool, which implements a free-hand molecule drawing input method supporting key.

Explanation:This question requires an understanding of what avogadro's number actually represents. Avogadro's number, 6.022. 10 23 is the number of things in one mole.

Using Avogadro Program For Dummies

The question indicates that there is 1 mole of H 2. Thus there are 6.022. 10 23 molecules of H 2. However the question is asking for the amount of atoms in 1 mole of H 2. Thus we must consider the makeup of an H 2 molecule, where we see that it is a diatomic molecule. Thus we must multiply 6.022.

10 23 by 2 to calculate the number of individual atoms present in 1 mole of H 2. We find our answer to be 1.2044.

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