avospglib and spglib have been moved into libavogadro

avospglib is a wrapper for SPGlib that uses
Avogadro::Molecule+OpenBabel::OBUnitCell as parameters

the crystallography extension has been updated to use the new
specification of avospglib

Change-Id: I3d4965c35fc80ce71b948584bb36ddab8df8e546
quantum espresso input generator

Espresso does not use point group symmetry, instead it relies on knowing
the Bravais lattice type or the primitive lattice and the atomic basis.

Now that avospglib is available to all extensions, the getPrimitive
method is used to generate the primitive lattice and basis atoms.

The three crystal structure options are

1. Displayed (default)
  Take the current specification of the cell matrix and displayed atoms as
  input.  It is probably best to use a "filled" unit cell here.  I am
  going to take the assumption that Avogadro will display a conventional
  unit cell.  I believe is it not appropriate to use ibrav with this
  option as the Quantum Espresso will find the wrong symmetry.

2. Generate Primitive
  Generate the primitive lattice vectors (CELL_PARAMETERS) and basis atoms
  from the displayed unit cell.  This uses avospglib.  This option has
  been verified to produce the correct symmetry for several example
  crystal structures.

3. Manual input
  Using the displayed coordinates, the user can choose the Bravais lattice
  and the lattice parameters.

The lattice parameter can be changed irrespective of what is displayed.
Since ATOMIC_POSITIONS and CELL_PARAMETERS are in relative coordinates
for options 1 and 2 above this is very safe and allows the user to change
the lattice parameter quickly and easily without having to mess around
in the displayed molecule.

I have used the pseudopotential file list from the full archive at
http://www.quantum-espresso.org/pseudo/espresso_pp.tar.gz.

Change-Id: I1560c2eca6f2b260dce2b07d26449ad5861a17d8
Fix "rogue" slab atoms bug.

Adds a small amount of floating-point slop
to comparisons when comparing atoms at
unit cell boundaries. Fixes the "rogue atom"
bug where edges of the slab weren't always
uniform.

Change-Id: I195601f786ef9a9e8cb2546a50edc0971d72bbbf
Allow manual translation or rotation.

Adds a settings widget to the manipulate tool.
This allows manual translation or rotation
around the origin or the center of geometry.
Also supports undo of manipulations.

Change-Id: I45a9e02dc6251dfc6f2f0f55d79ed6039ce88697
Add a new supercell builder tool.

Replaces the old supercell builder.
In addition to boxes (as previous), the new
interface allows building nanoparticles and
eventually nanorods. Elliptical nanoparticles
and nanorods are currently unimplemented.

Change-Id: I73f2350784b92de8f0cc405b4870ae8ea4f0ab0d
Modify the setOBMol method to fill crystal cells.

The existing code will import only the asymmetric
unit cell, which is surprising for most inorganic
crystals. (It works fine for molecular crystals.)
This patch adds a heuristic to fill the unit cell
when presented with a crystal < 4 carbon atoms.

This also removes similar code from the insert
crystal extension.

Change-Id: I07f613cebaa72bb6b51c7c6714f1e2d8533ab792
simple lammps input generator for water

This input generator along with the OpenBabel lmpdat format can be used
to create input files for MD simulations.

The SPC and SPC/E water models are programmed.

J. Phys. Chem. A, 2001, 105 (43), pp 9954–9960
DOI: 10.1021/jp003020w

Change-Id: Icf27536174cfa7a720ec3e625849310e71ff1bfd
Added a few more minor crystal structures.

Includes some molecules, like benzene.

Change-Id: I170fb8b88a2caee26a099fd20368dcc4fcbac5d3
Merge branch 'ENH-supercell-builder' into pettt-m4
Merge branch 'ENH_crystal-fill-cell-heuristic' into pettt-m4
Merge branch 'ENH_manual-manipulate' into pettt-m4
Merge branch 'fix-slab-rogue-atoms' into pettt-m4
Merge branch 'LammpsInput' into pettt-m4
Merge branch 'qEspressoInput' into pettt-m4
Added a simple polymer builder.

Includes a library of common polymers as SMILES.
Allows typing arbitrary custom SMILES in place of files.
Will integrate with an amorphous crystal builder later.

Change-Id: Ic82c726085accd9cb72c4d4f438e9730ec77461f
Merge branch 'ENH_insert-polymer' into pettt-m4