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diff --git a/.doctrees/docs/LICENSE.doctree b/.doctrees/docs/LICENSE.doctree
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diff --git a/_sources/docs/LICENSE.md.txt b/_sources/docs/LICENSE.md.txt
diff --git a/_sources/docs/README.md.txt b/_sources/docs/README.md.txt
@@ -0,0 +1,6 @@
+# Avogadro: Molecular Editor and Visualization
+
+A markdown-formatted manual for Avogadro v2.0
+
+This manual is made available under the Creative Commons Attribution
+Share-Alike 4.0 license (CC-by-SA 4.0).
diff --git a/_sources/docs/SUMMARY.md.txt b/_sources/docs/SUMMARY.md.txt
@@ -0,0 +1,59 @@
+# Table of contents
+
+* [Preface](index.md)
+* [What's New in Avogadro 2](whats-new-in-avogadro-2/README.md)
+  * [Major New Features](whats-new-in-avogadro-2/major-new-features.md)
+  * [Interface Changes](whats-new-in-avogadro-2/interface-changes.md)
+* [Getting Started](getting-started/README.md)
+  * [Introduction](getting-started/introduction.md)
+  * [Drawing Molecules](getting-started/drawing-molecules.md)
+  * [Making Selections](getting-started/making-selections.md)
+* [Tools](tools/README.md)
+  * [Navigate Tool](tools/navigate-tool.md)
+  * [Draw Tool](tools/draw-tool.md)
+  * [Bond-Centric Manipulate Tool](tools/bond-centric-manipulate-tool.md)
+  * [Manipulate Tool](tools/manipulate-tool.md)
+  * [Selection Tool](tools/selection-tool.md)
+  * [Auto-Rotate Tool](tools/auto-rotate-tool.md)
+  * [Auto-Optimize Tool](tools/auto-optimize-tool.md)
+  * [Measure Tool](tools/measure-tool.md)
+  * [Align Tool](tools/align-tool.md)
+* [Menus](menus/README.md)
+  * [File Menu](menus/file-menu.md)
+  * [Edit Menu](menus/edit-menu.md)
+  * [View Menu](menus/view-menu.md)
+  * [Build Menu](menus/build-menu.md)
+  * [Select Menu](menus/select-menu.md)
+  * [Extension Menu](menus/extensions-menu.md)
+* [Building Molecules](building-molecules/README.md)
+  * [Importing Molecules by Name](building-molecules/importing-molecules-by-name.md)
+  * [Importing from the Protein Data Bank (PDB)](building-molecules/importing-from-the-pdb.md)
+  * [Building a Peptide](building-molecules/building-a-peptide.md)
+  * [Building DNA or RNA](building-molecules/building-dna-rna.md)
+  * [Building Carbon Nanotubes](building-molecules/building-carbon-nanotubes.md)
+  * [Insert Molecular Fragments](building-molecules/insert-fragments.md)
+  * [Building with SMILES](building-molecules/building-with-smiles.md)
+* [Building Materials](building-materials/README.md)
+  * [Building a Supercell](building-materials/supercell.md)
+  * [Making a Crystal Surface Slab](building-materials/building-a-crystal-slab.md)
+  * [Building a Polymer Unit Cell](building-materials/building-a-polymer-unit-cell.md)
+  * [Perceiving Crystall Symmetry](building-materials/crystal-symmetry-perception.md)
+  * [Reducing Crystals to a Primitive Unit Cell](building-materials/reducing-crystals-to-primitive-cells.md)
+  * [Scaling Crystal Cell Volume](building-materials/scaling-crystal-volumes.md)
+  * [Building Molecule-Surface Interactions](building-materials/molecule-surface-interactions.md)
+* [Optimizing Geometry](optimizing-geometry/README.md)
+  * [Introduction to Molecular Mechanics](optimizing-geometry/molecular-mechanics.md)
+  * [Finding Conformers of Molecules](optimizing-geometry/conformers.md)
+  * [Geometry Constraints](optimizing-geometry/constraints.md)
+* [Display Types](display-types/README.md)
+  * [Different Display Styles](display-types/display-types.md)
+  * [Coloring Part of a Molecules](display-types/coloring-part-of-a-molecule.md)
+* [Tutorials](tutorials/README.md)
+  * [Naming a Molecule](tutorials/naming-a-molecule.md)
+  * [Viewing Vibrations](tutorials/viewing-vibrations.md)
+  * [Viewing Molecular Orbitals](tutorials/viewing-molecular-orbitals.md)
+  * [Viewing Electrostatic Potential Maps](tutorials/viewing-electrostatic-potential.md)
+  * [Using QTAIM (Atoms in Molecules) Analysis](tutorials/using-qtaim-and-wfn.md)
+* [Extensions](extensions/README.md)
+  * [ABINIT Input Generator](extensions/abinit-generator.md)
+  * [LAMMPS Input](extensions/lammps-input-for-water.md)
diff --git a/_sources/docs/building-materials/building-a-crystal-slab.md.txt b/_sources/docs/building-materials/building-a-crystal-slab.md.txt
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+# Making a Crystal Surface Slab
+
+Build up a crystal surface, e.g., Pt  for a defined Miller Plane.
+
+## Import the appropriate crystal structure.
+
+![](../.gitbook/assets/import-the-appropriate-crystal-structure.png)
+
+Either open a CIF file with the crystal structure needed, or import one from the built-in Avogadro crystal library. The tutorial will assume you import a structure from the Avogadro library. Choose File &gt; Import &gt; Crystal to bring up the library.
+
+![](../.gitbook/assets/media_1332447195630.png)
+
+Either browse through the crystals, or type a filter -- by element or name. Click "Insert" to import the selected structure.
+
+![](../.gitbook/assets/media_1332447360825.png)
+
+Importing a crystal will show the asymmetric unit cell \(e.g., one atom for Silver here\).
+
+![](../.gitbook/assets/media_1332448938642.png)
+
+To build a specified surface \(e.g., Ag \) choose Crystallography &gt; Build &gt; Slab... to bring up the slab builder settings. Future crystal builders \(e.g., nanoparticles, supercells\) will also appear in this menu.
+
+![](../.gitbook/assets/3d1781c8-d8ba-45ce-af85-65625a1c4d24.png)
+
+Specify the indices of the Miller plane desired \(for hexagonal unit cells, all 4 indices will appear\), and choose the dimensions in either distances or repeating cells of the resulting surface. The generated surface is aligned in the XY plane, and a specified thickness will be cleaved in the z-axis below the XY plane. This feature allows easy alignment between a new surface and a molecule for surface interaction calculations. Click "Build" to start the surface generation.
+
+![](../.gitbook/assets/media_1332468285179.png)
+
+After clicking "Build," Avogadro will generate a large supercell, align, rotate, and cleave the designated surface. This may take some time, depending on the size of the crystal cell. Here translucent van der Waals spheres are used to illustrate the corrugation of the Ag  surface. The resulting surface is a 2x2 supercell, with a large spacing \(40 Å\) in the z-axis.
+
diff --git a/_sources/docs/building-materials/building-a-polymer-unit-cell.md.txt b/_sources/docs/building-materials/building-a-polymer-unit-cell.md.txt
@@ -0,0 +1,52 @@
+# 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 other programs can be performed similarly.
+
+![](../.gitbook/assets/media_1260118979959.png)
+
+Build out the molecule for the unit cell. Notice that while the repeat unit here is 2 rings, we have built 3 rings. This way, we will properly model the bond which spans two unit cells.
+
+![](../.gitbook/assets/media_1260119377141.png)
+
+Optimize the geometry of the molecule.
+
+![](../.gitbook/assets/media_1260119456591.png)
+
+Switch to the Align tool to translate and orient the unit cell coordinates.
+
+![](../.gitbook/assets/media_1260119601872.png)
+
+Make sure to open the Tool Settings window, which will allow you to work with the Align tool.
+
+![](../.gitbook/assets/media_1260119685502.png)
+
+First click on the "start" atom of the polythiophene. This atom will be translated to the origin \(0, 0, 0\). Then click on the corresponding atom in the "next" unit cell. The distance between these two atoms will define one axis in the unit cell.
+
+![](../.gitbook/assets/media_1260119852731.png)
+
+In the "Align Settings" window, define an axis for the unit cell. Then click the Align button. This will change the coordinate set to have atom \#1 at the origin, and atom \#2 \(from the step above\) projected onto the x-axis.
+
+![](../.gitbook/assets/media_1260120107101.png)
+
+Open the Cartesian Editor window to verify the results of the Align operation.
+
+![](../.gitbook/assets/Screen-shot-2009-12-06-at-12.23.01-PM.png)
+
+Notice that atom \#1 is at the origin, and atom \#11 is projected onto the X-axis. The size of the unit cell is 7.806Å -- the distance between atom \#1 and atom \#11.
+
+![](../.gitbook/assets/media_1260120454671.png)
+
+Now delete "extra" atoms which should not be included in the unit cell calculations. This includes the third ring \(including atom 11\) and the "end" hydrogen atoms. For example, you can use the select tool and drag over the atoms to be deleted to pick them.
+
+![](../.gitbook/assets/media_1260120552391.png)
+
+Once selected, you can use the "Clear" menu command to delete the atoms.
+
+![](../.gitbook/assets/media_1260120773167.png)
+
+If you wish to submit the unit cell to Gaussian, pick the Gaussian input extension.
+
+![](../.gitbook/assets/Screen-shot-2009-12-06-at-12.36.05-PM.png)
+
+Set options as you desire. Make sure to add a "TV 7.806 0.0 0.0" line at the bottom of the preview text. This will enable the unit cell calculation by setting the translation vector for the unit cell.
+
diff --git a/_sources/docs/building-materials/crystal-symmetry-perception.md.txt b/_sources/docs/building-materials/crystal-symmetry-perception.md.txt
@@ -0,0 +1,30 @@
+# Perceiving Crystall Symmetry
+
+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 crystallographic coordinates.
+
+## Open a Crystal File
+
+![](../.gitbook/assets/open-a-crystal-file.png)
+
+Here we open an example VASP calculation by opening the POSCAR file.
+
+![](../.gitbook/assets/media_1340332954652.png)
+
+This example is triclinic, looking for Li / H structures. Note that VASP files do not specify a space group, so it is reported as "Unknown."
+
+![](../.gitbook/assets/media_1340332967365.png)
+
+We can either set the spacegroup manually, or here, perceive the space group, using the open source spglib code.
+
+![](../.gitbook/assets/media_1340332976902.png)
+
+We need to set the tolerance, since some atoms may be slightly out of place in Cartesian coordinates.
+
+![](../.gitbook/assets/media_1340332995909.png)
+
+Our example VASP file isn't very interesting -- the space group is P1.
+
+![](../.gitbook/assets/media_1340333044109.png)
+
+Here's another example, where the space group is P 1 21 1.
+
diff --git a/_sources/docs/building-materials/index.md.txt b/_sources/docs/building-materials/index.md.txt
@@ -0,0 +1,2 @@
+# Building Materials
+
diff --git a/_sources/docs/building-materials/molecule-surface-interactions.md.txt b/_sources/docs/building-materials/molecule-surface-interactions.md.txt
@@ -0,0 +1,56 @@
+# Building 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 "Building a Crystal Surface" lesson.
+
+## Start with a generated Crystal Surface
+
+![](../.gitbook/assets/start-with-a-generated-crystal-surface.png)
+
+Generate the desired crystal surface. Avogadro will center the surface cell, aligned in the XY plane, with slab atoms defined below Z = 0. The Slab Builder also leaves a large space along the z-axis to allow insertion of molecules for surface interaction calculations. You can control this padding as indicated above.
+
+## New Window: Create our Molecule
+
+![](../.gitbook/assets/new-window--create-our-molecule.png)
+
+In a new window, draw the desired molecule, or open a file. Here we consider ethanol.
+
+![](../.gitbook/assets/media_1332469166966.png)
+
+We will use the "Align Tool" to allow us to rotate and align the molecule with the OH group at the origin, and the molecule aligned along the z-axis.
+
+![](../.gitbook/assets/media_1332469324737.png)
+
+We will click on the terminal H atom \(which will be translated to the origin\) followed by the carbon atom \(which will define the z-axis of the molecule\).
+
+![](../.gitbook/assets/media_1332469442064.png)
+
+After defining the atoms \(they will show colored spheres and numbers once selected\), click on the "Align" button to translate and rotate the molecule.
+
+![](../.gitbook/assets/media_1332469725677.png)
+
+You may wish to alter the current camera view. Choosing View &gt; Align View to Axes will reset the view to project the z-axis of the molecule to point towards you.
+
+![](../.gitbook/assets/media_1332469784810.png)
+
+Perfect! Now we can copy our ethanol to the surface document.
+
+![](../.gitbook/assets/media_1332469837440.png)
+
+After copying, we can switch to our surface.
+
+![](../.gitbook/assets/media_1332470049992.png)
+
+Now we'll paste in the ethanol molecule.
+
+![](../.gitbook/assets/media_1332470085470.png)
+
+Note that the ethanol is now embedded in the surface, centered as desired. The Manipulate tool has been selected, allow us to translate the molecule as needed.
+
+![](../.gitbook/assets/media_1340332629038.png)
+
+New in version 1.1 is an option to specify the exact amount to translate or rotate the selection \(i.e., the molecule we just pasted\). Here, we've specified that we want to move the molecule +2.5Å along the z-axis, above the surface, and then we click "Apply" to complete. We could also rotate around the z-axis if the positioning isn't as desired.
+
+![](../.gitbook/assets/media_1332470208253.png)
+
+Here we have translated the ethanol 2.5 Å above the Ag  surface and are ready to submit for a calculation.
+
diff --git a/_sources/docs/building-materials/reducing-crystals-to-primitive-cells.md.txt b/_sources/docs/building-materials/reducing-crystals-to-primitive-cells.md.txt
@@ -0,0 +1,24 @@
+# Reducing Crystals to a Primitive Unit Cell
+
+Some simulations use "supercells" -- larger periodic boundary systems than the primitive unit cell. Here is a walk-through on reducing a large supercell to the primitive unit cell.
+
+![](../.gitbook/assets/media_1340336029160.png)
+
+Open or import the file with the supercell -- here, CaCO3. Note that the space group is unknown, since the file came from VASP, which does not specify a space group with the coordinates.
+
+![](../.gitbook/assets/media_1340336076337.png)
+
+After perceiving the space group, we see correctly that the system is R -3 c. Now we can reduce the supercell to a primitive cell of CaCO3.
+
+![](../.gitbook/assets/media_1340336318568.png)
+
+Avogadro provides two algorithms for reducing the unit cell to a primitive or Niggli cell. Here, pick "Primitive." Note that the volume of this supercell was over 4,000 Å3.
+
+![](../.gitbook/assets/media_1340336361329.png)
+
+You will need to set a tolerance for the Cartesian coordinates \(here, in Å\).
+
+![](../.gitbook/assets/media_1340336453963.png)
+
+After reduction, note that the space group is retained, the lattice is properly Rhombohedral, and the unit cell volume is 36 times smaller.
+
diff --git a/_sources/docs/building-materials/scaling-crystal-volumes.md.txt b/_sources/docs/building-materials/scaling-crystal-volumes.md.txt
@@ -0,0 +1,32 @@
+# Scaling Crystal Cell Volume
+
+Avogadro 1.1 allows you to adjust the volume or spacing of a unit cell.
+
+![](../.gitbook/assets/media_1340337013909.png)
+
+After creating or opening the crystal \(here ice\), we see the normal unit cell and lattice information. We will now adjust the cell volume.
+
+![](../.gitbook/assets/media_1340336935090.png)
+
+Before we scale volume, we can either choose to preseve Cartesian coordinates \(which will add empty space to the edges of the unit cell\) or preserve fractional coordinates \(which will symmetrically scale the entire unit cell\). This walk-through will show both.
+
+![](../.gitbook/assets/media_1340336917161.png)
+
+First we'll scale the cell while preserving Cartesian coordinates.
+
+![](../.gitbook/assets/media_1340337222403.png)
+
+The units of the volume are determined by your settings \(here Å\). We adjust the volume from the original 389.78Å3, and click "OK."
+
+![](../.gitbook/assets/media_1340337322190.png)
+
+Here, we've greatly exaggerated the volume, to show the empty space \(arrows\) around the outside of the unit cell boundaries, when preserving Cartesian coordinates. The space group has also changed \(to C 1 m 1\).
+
+![](../.gitbook/assets/media_1340337494733.png)
+
+If you preserve fractional coordinates, you can scale the unit cell symmetrically.
+
+![](../.gitbook/assets/media_1340337575679.png)
+
+Note that while the volume is significantly expanded, the space group \(and fractional coordinates\) are retained.
+
diff --git a/_sources/docs/building-materials/supercell.md.txt b/_sources/docs/building-materials/supercell.md.txt
@@ -0,0 +1,22 @@
+# Building a Supercell
+
+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.
+
+When "Super Cell Builder..." is selected under the "Build" menu, the dialog box below pops up. This dialog box will allow you to replicate a unit cell that has already been created \(if need be, a unit cell can be created by selecting "Add Unit Cell" under the "Crystallography" menu\).
+
+![](../.gitbook/assets/8ffd03c7-52fb-443c-a2a3-e6e7605c113e.png)
+
+## Creating a Surface
+
+One way supercell can be utilized is by creating a surface. Below is an elemental unit cell comprised of silver. This cell was imported through the "File" menu, under "Import", "Crystal...". When the dialog box appears follow the procedure displayed below.
+
+![](../.gitbook/assets/creating-a-surface-.png)
+
+A unit cell can then be replicated to make a _slab_ or a surface. For this example, the parameters were edited as shown in the image below. After editing the parameters, clicking "Generate Cell" will expand your surface.
+
+![](../.gitbook/assets/ec31d9a6-90a0-43ca-85f1-de1d800a9495.png)
+
+A surface can then be _modified_ by introducing impurities. Here, copper impurities were added to the silver surface. This file can now be exported to another program to determine, through calculations, how the impurities will impact the surface.
+
+![](../.gitbook/assets/86d36773-eb7f-4cce-9269-40feb6993009.png)
+
diff --git a/_sources/docs/building-molecules/building-a-peptide.md.txt b/_sources/docs/building-molecules/building-a-peptide.md.txt
@@ -0,0 +1,32 @@
+# Building a Peptide
+
+A walkthrough on how to create a custom peptide model in Avogadro.
+
+![](../.gitbook/assets/Picture-2-1.png)
+
+Select the “Build” menu.
+
+![](../.gitbook/assets/Picture-1.png)
+
+![](../.gitbook/assets/media_1244841742875.png)
+
+Bring up the peptide builder window. You can select amino acids to insert into the new peptide.
+
+![](../.gitbook/assets/media_1244843543134.png)
+
+As you click on particular amino acids, they will be added to the sequence on the right. The peptide will build up as a sequence, starting from the N terminus. Of course you can also type the residues directly or paste from an online database.
+
+![](../.gitbook/assets/media_1244842311139.png)
+
+You can pick the secondary structure
+
+![](../.gitbook/assets/media_1244843607484.png)
+
+Click to insert the sequence into the main window. The new oligopeptide will be selected automatically, and the manipulate tool will allow you to translate and rotate the chain into the position you want.
+
+![](../.gitbook/assets/media_1244842953032.png)
+
+![](../.gitbook/assets/media_1244842940490.png)
+
+You may wish to re-center the view, since the new peptide may be large.
+
diff --git a/_sources/docs/building-molecules/building-carbon-nanotubes.md.txt b/_sources/docs/building-molecules/building-carbon-nanotubes.md.txt
@@ -0,0 +1,36 @@
+# 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. \([http://turin.nss.udel.edu/research/tubegenonline.html](http://turin.nss.udel.edu/research/tubegenonline.html)\)
+
+![](../.gitbook/assets/media_1340334543445.png)
+
+Under the Build menu, there’s a new option for the nanotube builder. At the moment only single-walled nanotubes \(SWNT\) can be built in one step, although it’s easy to generate several nested tubes for multi-walled \(MWNT\) as shown here.
+
+![](../.gitbook/assets/media_1340334581991.png)
+
+The builder will show up at the bottom of the Avogadro window. You can set the n,m indexes to determine the type of nanotube \(1\) the length of the tube \(2\), in Angstrom, bohr, picometers, nanometers, or periodic unit cells \(e.g., if you wish to do a calculation with periodic boundar conditions\), and how to terminate the nanotube \(3\). **NOTE**: determining double bonds can be time-consuming on large nanotubes.
+
+![](../.gitbook/assets/media_1340334958508.png)
+
+The nanotube will be generated aligned along the z-axis, so you may want to re-center the view.
+
+![](../.gitbook/assets/media_1340335027391.png)
+
+Here, we've added a 6,6 nanotube after inserting our 4,4 nanotube. We'll need to re-center the tube to produce a more accurate double-walled system.
+
+![](../.gitbook/assets/media_1340335238130.png)
+
+Here, we use the manual translation options, new in Avogadro 1.1, to “nudge” the 6,6 nanotube in the XY plane to properly center around the 4,4 nanotube.
+
+![](../.gitbook/assets/media_1340335304968.png)
+
+Here we’ve nudged the 6,6 tube into an approximately correct position. We’ll now use Avogadro’s built-in force fields and the Auto-Optimize tool to relax the structure.
+
+![](../.gitbook/assets/media_1340335406817.png)
+
+We \(1\) select the Auto-Optimize tool to allow interactive minimization of the nanotubes, and \(2\) select the MMFF94 force field. Other forcefields would also likely work well. Finally \(3\) start the optimization.
+
+![](../.gitbook/assets/media_1340335353244.png)
+
+After a few steps, you can see a nicely relaxed double-walled nanotube. You could repeat the process as desired.
+