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Gamgi is a program to build, view, and analyze atomic strucures such as molecules, crystals, glasses, liquids, etc..

GAMGI (General Atomistic Modelling Graphic Interface) is a program to build, view, and analyze atomic strucures such as molecules, crystals, glasses, liquids, etc. It aims to be useful for: the scientific community working in Atomistic Modelling that needs a graphic interface to build input data and to view and analyse output data, calculated with Ab-Initio and Molecular Mechanics programs; the scientific community at large studying chemistry, physics, materials science, geology, etc., that needs a graphic interface to view and analyse atomic structural information and to prepare images for presentations in classes and seminars; teaching chemistry and physics in secondary schools and universities; science promotion in schools, exhibitions and science museums.

GAMGI aims to be useful for: 1) the scientific community working in atomistic modelling, who needs a graphic interface to build and analyse atomic structures; 2) the scientific community at large, who needs a graphic interface to study atomic structures and to prepare images for presentations; 3) teaching the atomic structure of matter in schools and universities, even inviting students to run GAMGI at home; 4) science promotion, in exhibitions and science museums.

GAMGI supports the following objects: Text, Orbital, Bond, Atom, Direction, Plane, Group, Molecule, Cluster, Cell, Arrow, Shape, Graph, Assembly, Light, Layer and Window.

Text
.

GAMGI supports both wired (stroked) and solid (extruded) 3D fonts.

Stroked fonts are needed to show information (as measurements and object identification) on the screen, which needs to be three-dimensional because it will be linked to molecules and other three-dimensional objects. Stroked fonts are relatively simple, so characters can be drawn fast. Measurements and object identification must work in both manual and automatic modes. In the automatic mode, measurements of distances and angles must be recalculated and the results updated in the text objects in real time, while the user manipulates the objects.

Extruded fonts are designed to provide the highest possible visual quality to text objects. These fonts work well with lights and can be relatively complex, so they are much slower than the stroked fonts.

Text objects can own other text objects only, so they are recursive objects. This gives the user maximum flexibility to manipulate different text fragments separately and compose them to obtain the final result. Text objects can be owned by any other GAMGI object except lights and windows.

Orbital.

Only the low-level engine infra-structure of orbital objects is implemented so far. The goal is to describe: 1) simple hydrogen-like orbitals, s, p, d, f, etc., and its hybridisations, sp, sp2, sp3, etc.; 2) complex representations of the electronic clouds surrounding the nucleus, commonly provided by combinations of Gaussian, Slater and plane wave analytic functions; 3) combinations of numerical functions usually described by spline line coefficients; 4) pseudo-potentials electronic descriptions.

The main difficulty with orbitals is to collect the data from files with completely different formats, provided by Gaussian, ADF, DSolid, Plana, etc. and build a common way to handle all this information. This problem must be correlated with the way GAMGI handles input/output data.

Orbitals can own text objects, so for example the name of the orbital can be attached to it.

Bond.

GAMGI handles bonds between atoms as objects owned by these atoms. Each atom can have an unlimited number of bonds. Each bond must have two parent atoms. Bonds can own orbitals and texts.

Atom
.

Atoms are the most important objects in GAMGI. They can own orbitals, texts and are the only objects that can own bonds.

Direction
.

Direction objects were designed primarily to handle crystallographic directions but they should provide useful functionality even in the absence of periodic cells. Currently, crystallographic directions can be viewed directly in space or represented as poles or traces in stereographic projections. Important properties such as the distance between nodes or the angles between directions and planes can be determined just clicking on the objects.

Futurely users should be able to choose directions of atoms in cells, clusters or molecules, automatically producing direction objects reproducing those directions, including the atoms and its child, bonds, orbitals and texts, and then handle these new direction objects as totally independent viewing and building tools.

Direction objects can own atoms, orbitals and texts.

Plane.

Plane objects were designed primarily to handle crystallographic planes but they should provide useful functionality even in the absence of periodic cells. Currently, crystallographic planes can be viewed directly in space, in the reciprocal lattice, or represented as poles or traces in stereographic projections. Important properties such as the distance between planes, the area per node or the angles between planes and directions can be determined just clicking on the objects.

Futurely users should be able to choose planes of atoms in cells, clusters or molecules, automatically producing plane objects reproducing those planes, including the atoms and its child, bonds, orbitals and texts, and then handle these new plane objects as totally independent viewing and building tools.

Implementing x-ray and electronic diffraction patterns, showing crystallographic planes as circular spots, represents a high priority project for the future.

Plane objects can own directions, atoms, orbitals and texts.

Group.

Group is an object container designed to handle a fragment of a molecule, a residue of a protein, a mero of a polymer chain, or other chemical species. Group objects can own an unlimited number of other chemical species as groups, atoms, and related objects as texts, orbitals, directions and planes. A group is therefore a recursive object, with unlimited nested levels, and its properties should reflect the child chemical features. For example, an amino-acid has amino NH2 and carboxylic acid COOH groups, the later in turn contains an hydroxyl group OH. Currently Group objects can be created only from XML files. Mechanisms to measure length, angle and torsion measurements in groups of atoms are already in place and tested. Algorithms and tools to modify length, angle and torsion values, in both open and cyclic structures have been implemented and fully tested. Everything else is not done yet.

Molecule
.

Molecule objects are essentially containers, objects whose primary purpose is to own other objects, as atoms and bonds. Molecules can own groups, planes, directions, atoms, orbitals and texts. Currently Group objects can be created only from XML files. Mechanisms to measure the point symmetry in molecules are already in place and tested. Everything else is not done yet.

Cluster
.

Cluster is an object container, designed to contain an unlimited number of chemical species as child objects, including other clusters, molecules, groups, atoms and related objects such as texts, orbitals, directions and planes. A cluster is therefore a recursive object, with unlimited nested levels, and its properties should reflect the child chemical features.

Clusters are currently used in the Voronoi tesselation of an arbitrary set of atoms.

Cell.

All the GAMGI functionality related with atomic structures with periodic boundary conditions is handled by cell objects. Crystalline structures can be created indicating either a crystalline lattice and a motif or a space group and the asymmetric unit atoms. The 14 Bravais lattices can be represented by Conventional, Primitive and Wigner-Seitz cells, plus Rhombus and Sphere volumes. Users can choose the number of cells, the volume size, the cell positioning, the type of cell borders, solid or wired cell representations, and the cell color. Any Cluster, Molecule, Group, Atom or even Orbital, Text object can be used as a valid motif to construct a periodic structure. GAMGI provides powerful yet simple pattern rules to indicate which lattice nodes should be filled, this way allowing users to create complex mixed structures that can be used to study liquids and other non-periodic systems. In particular, these pattern rules can be used to build 2D and 1D periodic and non-periodic structures.

Arrow
.

Arrow objects include different types of 2D and 3D arrows, which are not text objects but are very useful to prepare images containing atomic structures, graphs, text, etc., for presentations at seminars or school teaching, or for producing printed images for articles or books. Arrow objects can own text objects (only). This is useful for example to add an equilibrium constant over a double arrow symbolising a chemical equilibrium. The low-level engine infra-structure required to handle arrow objects is fully implemented but everything else is not done yet.

Shape


Shape objects describe backgrounds, boxes, circles, ellipses, diamonds, etc. designed to make an image for a presentation more clear and pretty. The aim is therefore to fill the gap between text and arrow objects. Shape objects can own text objects only. This is useful, for example to include a message in a box. Nice functionality to have in GAMGI shape objects includes: 1) several styles should be provided for shape objects, including solid, contour, partially transparent, etc.; 2) mechanisms should be provided to allow users to choose and apply OpenGL textures, in 2D and 3D shape objects; 3) mechanisms should be provided to allow users to make textures, namely profile gradients, as in the GIMP. The low-level engine infra-structure required to handle shape objects is fully implemented but everything else is not done yet.

Graph


Graph objects will be used to describe all sort of graphic information usually related with atomic structures, including for example radial distribution functions and electron density maps. In particular, graphs will be used to represent the copious amount of data often provided by ab-initio and molecular mechanics calculations. Graphs can own text objects only, which will be used for captions, titles, labels, etc. The low-level engine infra-structure required to handle Graph objects is fully implemented but everything else is not done yet.
Assembly


Assembly is an object container, designed to be fully flexible. An assembly can own any GAMGI objects, including other assembly objects, except lights, layers and windows. An assembly object is therefore a recursive object, with unlimited nested levels. For example, an assembly can be used to associate a graph with a molecule and a cell, to manipulate all of them at once. Currently Assembly objects can be created only from XML files. The graphic interfaces to properly link Assembly objects are not done yet.

Light

Everything related with lightning in GAMGI is handled by light objects. GAMGI lights implement all the functionality provided by the OpenGL specification. This includes directional, positional and spot lights, ambient, diffuse and specular light components, and axial and radial light attenuations. The maximum number of lights that each layer can own is fixed by the graphics library used with GAMGI. In Mesa this number is currently 8, the minimum required by the OpenGL specification. However, as the number of layers that each window can own is unlimited, the same is true for the total number of lights per image. Lights are the only objects in GAMGI that cannot own other objects.

Layer
.

GAMGI supports multiple, unlimited, layers for each window, allowing users to move and copy objects between different layers and see multiple layers simultaneously. A layer can own all kinds of GAMGI objects, except bonds, windows and layers. In particular, layers are the only GAMGI objects that can own lights.

Functionality currently implemented includes perspective and orthographic projections, full control over projection and model view (like a photographic camera) parameters, inside and outside visibility, background color, plus undo and save history mechanisms to keep and recover the whole contents of each layer, for as many levels as previously defined.

Perspective projection is better to simulate realistic views but the orthographic projection (mostly used in architecture) is usually preferred for most work related with building and viewing structures, because these are not distorted by perspective. The projection parameters, that control the matrix transformations related with the projection of the 3D space on the screen, are fully controlled by the users.


GAMGI supports multiple, unlimited, windows, which allow users to easily move and copy objects between them. Window objects are truely independent, so they can be opened and closed in any order. Windows can own layer objects only, which can be moved or copied between different windows.

Mission.

GAMGI at work
Our goal is to provide a free package to construct, view and analyse atomic structures, as powerful and simple to use as possible.

GAMGI aims to be useful for: 1) the scientific community working in atomistic modelling, who needs a graphic interface to build and analyse atomic structures; 2) the scientific community at large, who needs a graphic interface to study atomic structures and to prepare images for presentations; 3) teaching the atomic structure of matter in schools and universities, even inviting students to run GAMGI at home; 4) science promotion, in exhibitions and science museums.

Achievements.

GAMGI at work
GAMGI can determine any point group of symmetry, can build crystals for any space group of symmetry, can build Random Close Packing structures, Voronoi and coordination polyhedra for arbitrary structures. GAMGI comes with comprehensive atomic data, including ionic radius and isotopic data. GAMGI can handle an arbitrary number of independent windows, layers (with different referentials, projections, viewports and visibilities), lights (directional, positional and spot), 3D text fonts (extruded and stroked). Actions can be performed in a single object or in a list of objects previously selected. GAMGI comes with detailed but concise documentation, just one click away for each task.
Shortcomings.

GAMGI at work
Currently GAMGI cannot handle alpha helix or beta sheet protein secondary structures, cannot calculate struture factors or diffraction patterns, cannot calculate orbitals, cannot show data graphics, cannot handle .pdb, .jmol and .cif files, cannot export or import coordination or Voronoi polyhedra. Support to build molecular structures is sketchy.

Requirements.

GAMGI at work
GAMGI can be installed on any computer running Linux/Unix with the standard X Window System. GAMGI requires the following libraries: Gtk, Mesa, Gtkglext, Expat and Freetype. GAMGI 0.14.8 or above requires GTK 2.18 to compile. To run properly, GAMGI requires a graphics environment with at least 16 bits per pixel, plus a 3-button mouse.


Screenshots.

Image showing Zinc Blende with coordination polyhedra
Structure of Zinc Blende, with each S2- surrounded by four Zn2+. Tetrahedral coordination polyhedra are shown in Solid and Wired styles, with autonomy All and None, to ilustrate the new Polytope functionality. The Layer is represented with white background, often the best option when preparing a picture for publication. Gnome on Fedora 8. Size: 51,963 bytes.

Image showing convex hull from 50,000 atoms inside a cube

Coordination polyhedron obtained from 50,000 atoms randomly distributed inside a cube. This is exactly the same code used to obtain small coordination polyhedra as above for Zinc Blenda. Technically this is an implementation of a 3D convex hull incremental algorithm, with conflict lists to achieve NlogN scaling. It takes just 3-5 seconds to complete, because most atoms are deep inside the cube and can be efficiently discarded. Gnome on Ubuntu 9.04. Size: 32,761 bytes.

Image showing convex hull from 50,000 atoms on a sphere

Coordination polyhedron obtained from 50,000 atoms (almost) randomly distributed on the external surface of a sphere. This case takes much more time to calculate (about 30 seconds) because all atoms contribute to the final polygonal surface. As atoms are added one at a time (3D convex hull incremental algorithm), the polygonal surface must be recalculated 50,000 times. Gnome on Ubuntu 9.04. Size: 41,309 bytes.

Image showing YBa2Cu3O7 superconductor with 2D and 3D polytopes

A 3x3x2 convencional cell volume of orthorhombic (group 47) YBa2Cu3O7 superconductor, shown here with 2D squares and 3D square piramids to emphasize the oxygen coordination around copper. Outer atoms were removed to improve readability. Wyckoff coordinates were taken from Ira Burshtein Crystal Structures site. Gnome on Ubuntu 9.04. Size: 35,468 bytes.

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About Hugo Repetto

Ubuntu is a Linux distribution that offers an operating system predominantly focused on desktop computers but also provides support for servers. Based on Debian GNU / Linux, Ubuntu focuses on ease of use, freedom in usage restriction, regular releases (every 6 months) and ease of installation.
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