Resources

Avogadro contains a nanotube builder extension (shown on the right). The extension generates a single-wall carbon nanotube from an (n,m) specification. More info can be found here.

So what new functionality does the extension add? The short answer: Everything I could think of. The long answer? Well, that needs a list or two:

• Customizable docking editors allow direct editing of:
• Cell parameters a, b, c, alpha, beta, and gamma
• The cell matrix, as either row or column vectors
• The atomic coordinates, in either cartesian or fractional units
• Customizable unit display:
• All lengths (parameters, cell matrix, cartesian coordinates) can be displayed in Angstrom, Bohr, nanometer, or picometer
• All angles can be displayed in degree or radian
• Immediate feedback on invalid entry: Text turns red when an invalid entry is made
• Plain text entry -- perfect for copy/pasting to/from input/output files.

• Some of the new tools in the Crystallography menu:
• Add / Remove unit cell Symmetry tools:
• Detect spacegroup
• Manually set spacegroup
• Symmetrize cell and coordinates to detected space group
• Fill unit cell using a few atoms and the current space group's symmetry operations
• Structure reductions:
• Reduce to primitive cell
• Reduce to Niggli cell
• Option to preserve either cartesian or fractional coordinates when the cell is modified
• Display fractionalization matrix
• Import POSCAR style data from clipboard (more formats to come)
• Copy POSCAR to clipboard
• Translate ("wrap") atoms to lie inside unit cell
• Rotate to standard orientation (i.e. A along x, B in x,y plane)
• Scale cell to a specified volume (isotropic scaling)
• On-screen display of crystallographic properties:
• Lattice type
• Space group
• Cell Volume

• The substrate (template) and matrix (monomer) molecules can be drawn and pre–optimized by Avogadro or imported into Avogadro from a file using one of the common chemical structure formats. The number of matrix and substrate molecules are specified in the GUI. Either isolated molecules or complexes (dimers, trimers etc.) may be employed.


• Conformers of the substrate and/or matrix molecules are generated and pre–optimized using one of the force field implementations in the OpenBabel library. Either an exhaustive search can be performed, or a specified number of conformers may be created. The latter option does not guarantee that the most stable conformers will be found, since the conformer­generating algorithm stops once the specified number has been reached.


• Conformers of the matrix and/or substrate molecules are chosen such that the probability \(p_i\) of selecting a given individual is calculated from its energy \(E_i\) (evaluated via the specified force field) as:
  
  

  \(p_{i}=N\left(1-\frac{E_{i}-E_\mathrm{min}}{E_\mathrm{max}-E_\mathrm{min}}\right)\)

  where \(E_\mathrm{min}\) and \(E_\mathrm{max}\) are the energies of the most stable and the least stable conformer, and \(N\) is a normalization factor ensuring that \(\Sigma p_i = 1\).