Getting started: Geometry optimization of ethanol
*************************************************

ADF DFT Building structures Geometry optimization Orbital Energy
levels Electron density

This tutorial will help you to:

* create a simple molecule

* view the molecule from all sides and save a picture

* make a couple of changes to the molecule with different tools

* set up your ADF calculation

* perform the actual ADF calculation

* visualize some results: energy levels, geometry, electron density,
  orbitals, ...

See also:

  More detailed information on the features presented in this tutorial
  can be found in the AMS driver manual and ADF manual.


Step 1: Preparations
====================


Start AMSjobs
-------------

On a Unix-like system, enter the following command:

   cd
   amsjobs &

On Windows, one can start AMSjobs by double-clicking on the AMS-GUI
icon on the Desktop:

   Double click the AMS-GUI icon on the Desktop

On MacOS, use the AMS2025.xxx application to start AMSjobs:

   Double click on the AMS2025.xxx icon

   [image]

Note that the directory in which AMSjobs depends on how you start
AMSjobs, so your screen might look different.


Make a directory for the tutorial
---------------------------------

We prefer to run the tutorial in a new, clean, directory. That way we
will not interfere with other projects. AMSjobs not only manages your
jobs, but also has some file management options. In this case we use
AMSjobs to make the new directory:

   Select the **File → New Directory** command (the New Directory command from the File menu)
   Rename the new directory by typing 'Tutorial' and a Return

   [image]

   Change into that directory by clicking once on the folder icon in front of it

   [image]


Start AMSinput
--------------

Now we will start AMSinput in this directory using the SCM menu:

   Select the **SCM → New Input** menu command

The AMSinput module should start:

   [image]

The AMSinput window consists of the following main parts:

* the menu bar with the menu commands (SCM, File, Edit, ...). On a Mac
  the menu bar is at the top of the screen

* the drawing area of the molecule editor, on the middle left side

* the status field at the lower part of the drawing area (blank when
  AMSinput is empty as shown above)

* the molecule editor tools, below the drawing area

* many panels for input options, on the right side. Currently the
  'Main' panel for 'ADF' is visible

* Panel bar with menu commands to activate the module and options
  panel of choice

* a search tool [image: Search][image]


Undo
----

AMSinput has an Undo command (**Edit → Undo**), which works on your
molecule (thus not on your input options).

If you make a mistake while making changes to your molecule, just use
the **Edit → Undo** menu command to go back in time. You can Undo more
than one step, or Redo a step (with **Edit → Redo**) if you wish to do
so.


Step 2: Create your molecule
============================


Create a molecule
-----------------

The molecule we are going to create is ethanol.

First we will draw the two carbon atoms, next the oxygen atom, and
after that we will add all hydrogen atoms at once. Finally, we will
pre-optimize the geometry within AMSinput.


Create the first carbon atom
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

To create an atom, you need to select an atom tool.

   Select the C-tool by clicking on the button with the 'C'

Back glow is added to the 'C' button to indicate that you are using
the C-tool. Also, the status field in the left bottom corner shows 'C
tool' to indicate that you are using the C-tool.

Now create the first carbon atom:

   Click somewhere in the drawing area

   [image]

One carbon atom has been created.

Note that:

* if you move the mouse you will see a white line from that carbon
  atom to the current mouse pointer position: this shows you are in
  'bonding' mode, and that the bond will be made to the atom just
  created

* the 'C' button has back glow, indicating you are still using the
  C-tool

* the cyan halo around the carbon atom indicates that it is the
  current selection

* the status field contains information about the current selection:
  it is a Carbon, number 1, its coordinates and the current
  coordination number (number of bonds)

* the status field also shows the current tool (C), and that a single
  bond will be made


Create the second carbon atom
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

   Click somewhere in the drawing area to create a second carbon atom

   [image]

A second carbon atom has been created, bonded to the first atom.

The atom will be created along the 'bonding line', at a distance that
corresponds to a normal C-C single bond distance. That is, the bond
length is constrained while drawing.

The newly created atom becomes the new selection, still using the
C-tool in bonding mode. The next bond will be created to the last atom
added.


Create the oxygen atom
~~~~~~~~~~~~~~~~~~~~~~

To create the oxygen atom you need to switch to the O-tool:

   Select the O-tool by clicking on the button with the 'O'

With the O-tool, create an oxygen atom bonded to the second carbon;

   Click somewhere in the drawing area

   [image]

The oxygen atom has been added.

For now, we are done using atom tools, so go back to the select tool:

   Select the select-tool by clicking on the button with the arrow (or press the Esc key)


Add the hydrogens
~~~~~~~~~~~~~~~~~

Now many hydrogen atoms need to be added. You can do this using the
H-tool, but a much easier method is to use the **Atoms → Add
Hydrogens** menu command:

   [image]

The 'Add Hydrogen' menu command works on the selection only, when
present. Thus, only one hydrogen atom would be added to the oxygen
atom. This is not what you want. So first we make sure that nothing is
selected by clicking in empty space.

   Click in an empty part of the drawing area

Now no atoms are selected any more.

   Select the **Atoms → Add Hydrogens** command

Many menu commands have shortcuts. In this case you can also use the
shortcut (ctrl-E or cmd-E, depending on your platform) as an
alternative. The shortcuts are indicated in the menu commands.

   [image]

All atoms will be saturated with hydrogen atoms. And you have created
an ethanol molecule, though the geometry is still far from perfect.


Pre-optimize the geometry
~~~~~~~~~~~~~~~~~~~~~~~~~

Now use the optimizer that comes with AMSinput to pre-optimize the
geometry.

   Click on the pre-optimizer button [image: PreOptimTool][image]

   [image]

The geometry of the molecule will be pre-optimized, using the
Universal Force Field (UFF) by default.

Tip:

  You can change the default method for pre-optimization via **SCM →
  Preferences**, or use a different pre-optimizer by right-clicking on
  the cog wheel and selecting the method to use from the pop-up menu.

In the status field below the drawing area you can follow the pre-
optimization iteration number and the energy relatively to the
starting configuration.


Viewing the molecule
--------------------


Rotate, translate, or zoom
~~~~~~~~~~~~~~~~~~~~~~~~~~

You can rotate, translate, and zoom your molecule using the mouse.

You need to drag with the mouse: press a mouse button, and while
holding it down move it. Which mouse button, and which modifier key
you press at the same time, determines what will happen:

+----------------------------------------------------+----------------------------------------------------+
| Rotate                                             | Left                                               |
+----------------------------------------------------+----------------------------------------------------+
| Rotate in-plane                                    | ctrl-Left                                          |
+----------------------------------------------------+----------------------------------------------------+
| Translate                                          | Right                                              |
+----------------------------------------------------+----------------------------------------------------+
| Zoom                                               | Mouse wheel, or (not on windows) alt-Left (drag up |
|                                                    | or down)                                           |
+----------------------------------------------------+----------------------------------------------------+

The rotate, translate, and zoom operations change how you look at the
molecule, they do not change the coordinates.

This behavior is the default behavior, you can change what the right
mouse button does using the Preferences.

   Click once somewhere in empty space to make sure nothing is selected

   Click with the left mouse button, and drag:
   your molecule will rotate

   Click with the left mouse button with the ctrl-key, and drag:
   your molecule will rotate in-plane

   Click with the right mouse button, and drag:
   your molecule will be translated

   Click with the right Middle button (if available), and drag up and down:
   you will zoom closer to or away from your molecule

   (not on windows) Click with the left mouse button with the alt-key, and drag:
   you will zoom closer to or away from your molecule

   Use the mouse wheel, if you have one:
   you will zoom closer to or away from your molecule

   Using all these options, try to position the ethanol as in the following figure:

   [image]


Save picture
~~~~~~~~~~~~

You can save a picture of your molecule using the  'Save Picture ...'
command from the File menu.

   [image]

   Select the **File → Save Picture ...** command
   Enter the name for your picture: ethanol
   Click the 'Save' button

A picture will be saved to disk containing the figure of your
molecule. Only the  drawing area is saved in the picture, not all the
input.

Tip:

  The default format used is PNG. You can change this in **SCM →
  Preferences**. You can also change the resolution via **File →
  Picture Resolution**. A smaller resolution will result in a smaller
  file, but will reduce the quality.


Molecular conformation
----------------------


Rotate such that you look along the C-C axis
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

   Rotate your molecule into the following position:

   [image]


Select the top CH3 group
~~~~~~~~~~~~~~~~~~~~~~~~

   Click once on the top carbon atom
   Use the **Select → Select Connected** menu command

   [image]

As you will notice, all atoms directly connected to the selected atom
are added to the selection. Alternatively, you can also make a
selection by shift-clicking on the elements you want to select.

   Click in empty space
   Click on the top carbon atom
   Shift-Click once (without dragging) on each of the top hydrogen atoms

This has almost the same effect (in this case you have not selected
the second carbon atom).


Rotate the selection
~~~~~~~~~~~~~~~~~~~~

We are now trying to make an eclipsed geometry.

   ctrl-Click with the left mouse button **in one of the selected hydrogens**, and drag around to rotate the selection in-plane
   Rotate the hydrogen atoms in an almost eclipsed position. You have to click and start dragging at a selected item. If you click and drag in space you will move the entire molecule.

   [image]

You can move the selection by clicking in a selected object, and
dragging with the mouse. All usual operations are possible: rotate,
rotate in-plane, translate and zoom. Zoom in this case means moving
the selection perpendicular to the screen. If you click in empty
space, instead of in a selection, you will manipulate the whole
molecule instead of the selection.

In the status field you see the current rotation angle.


Back to Staggered Geometry
~~~~~~~~~~~~~~~~~~~~~~~~~~

   Click in empty space to clear the selection
   Click on the pre-optimize button [image: PreOptimTool][image]

The optimizer will bring the structure back to the original staggered
geometry. If it does not complete, repeat this step until it does.


Getting and setting geometry parameters
---------------------------------------


Bond length
~~~~~~~~~~~

First select the oxygen atom and the connected hydrogen atom.

This time we make the selection by dragging a rectangle around all
objects that we want to select.

   Using the left mouse button together with the shift key, drag a rectangle around the oxygen and hydrogen atom

   [image]

   Release the mouse button (and the shift key)

The oxygen atom and the hydrogen atom are selected.

   [image]

In the status area you see the distance between the selected atoms,
information about the bond, and a slider.

You can set the distance to any value you wish by editing it in the
rectangle showing the current value, or by using the slider.

   Use the slider to move the H atom

Tip:

  The order in which you have selected the atoms is shown with
  numbers. By default, the last atom selected will will be in the
  group of atoms to move.Press the **control key while using the
  slider**, and the **smallest group of atoms** will move.


Bond angle
~~~~~~~~~~

   Select first one of the top hydrogens by clicking on it
   Next, extend the selection (shift key) by clicking on the top carbon atom
   Finally, extend the selection (shift key) by clicking on another top hydrogen atom

   [image]

In the status area information about the bond angle of the selected
three atoms is given, and the slider is again visible. You can change
this value to a value you like by editing the value field or using the
slider.


Dihedral angle
~~~~~~~~~~~~~~

By selecting four atoms we get information about the dihedral angle.
And of course you can also change it, most conveniently using the
slider.

   Move the molecule such that you can see all atoms
   Select first one of the top hydrogens by clicking on it
   Next, extend the selection (shift key) by clicking on the top carbon atom
   Next, extend the selection (shift key) by clicking on the next carbon atom
   Finally, extend the selection (shift key) by clicking on the oxygen atom

   [image]


Coordinates
~~~~~~~~~~~

To view the coordinates we have to go to a different input panel. The
input panels can be selected using the panel bar on the top of the
input panels, the right half of the window.

   In the right side of the AMSinput window:
   Click on the **Model** tab in the panel bar
   Select the **Coordinates** command

   [image]

You get a list of all Cartesian coordinates. They will be updated in
real time when you make changes to the molecule, and you can also edit
the values yourself. In that case, the picture of the molecule will be
updated automatically.

Note that some atoms are highlighted. These are the currently selected
atoms.

The Move Atom(s) buttons (the arrows) will move the selected atoms up
or down. In this way you can re-order the atoms.


Extending and changing your molecule
------------------------------------

Before making some changes, let's re-optimize. We first select the
'Main' panel so the coordinates will not be visible during the pre-
optimization. Otherwise this may slow down the pre-optimization.

   Click on the "Main" tab
   Click in empty space to make sure nothing is selected
   Click on the pre-optimize button [image: PreOptimTool][image]

Let's try to change the CH2OH group in a COOH group.

Thus, we need to:

* remove one hydrogen

* change one hydrogen into an oxygen

* change a single bond into a double bond

After this, we will revert to the ethanol molecule.


Delete an atom
~~~~~~~~~~~~~~

First: delete one hydrogen

   Click in empty space to clear the selection
   Click once on the hydrogen to delete, it will be selected

   [image]

   Press the backspace key

   [image]

The selected atom is removed.


Change the type of an atom
~~~~~~~~~~~~~~~~~~~~~~~~~~

Next, we will change a hydrogen into an oxygen atom.

Tip:

  You can quickly select a tool using the C, O, H, N, S, P, or F
  keys.Or use X, type one or two letters, and Return, for any element.

   Select the O-tool (or press the 'O' key)
   Double-click on the hydrogen that should change into an oxygen

   [image]


Change the bond type of an existing bond
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Now the oxygen atom is singly bonded to the carbon, we need to change
this into a double bond.

   Click on the bond between the carbon and the new oxygen
   Use the **Bonds → Bond Order → Double** menu command (or just press the '2' key)

   [image]

The single bond has changed into a double bond.

Another way to modify a bond type is to click on the bond once which
will select this bond.  Then click on the bond tool in the molecule
editor panel ('ball and stick' logo to the right of the start), and
select the proper bond type.

Tip:

  Use the keyboard shortcuts: select a bond, press 1 for a single
  bond, 2 for a double bond, 3 for a triple bond and 4 for an aromatic
  bond.

To get a reasonable geometry optimize the structure:

   Click in empty space to deselect the bond
   Click on the pre-optimize button [image: PreOptimTool][image]
   If not converged, press pre-optimize again

   [image]


Add new (bonded) atoms
~~~~~~~~~~~~~~~~~~~~~~

Now, to revert to the ethanol molecule, we first remove the new
doubly-bonded oxygen atom, and then add one hydrogen atom.

   Click once on the doubly-bonded oxygen atom to select it
   Press the backspace key to delete it

   Select the H-tool (or press the 'H' key)
   Click once on the carbon atom connected to the oxygen

   [image]

Note that this way you started bonding mode again, as indicated by the
bond to the mouse position.

   Click once in empty space to make a hydrogen atom (connected to the carbon!)
   Click once **on the just created** atom to stop bonding

   Repeat this to add a second hydrogen to the carbon atom

   Pre-optimize the molecule

For the next step, we want to find the optimal geometry of a local
minimum, for this

   While holding shift select the top carbon, next carbon, oxygen, and its hydrogen in that order

   Use the slider or value field at the bottom to set the dihedral to 180.

   Deselect all atoms.

   Pre-optimize with the gear button

Make sure the O-H bond remains parallel to the C-C bond, or repeat
this process.

Warning:

  The results in the next section may look slightly different for
  other energy minima.

   [image]

Once again you have created an ethanol molecule.

Tip:

  When all atoms or none are selected, the pre-optimizer will be
  applied to the entire system. You can also choose to optimize part
  of your system by selecting a subset and applying the pre-optimizer
  only to that selection when prompted.


Step 3: Select calculation options
==================================


Task
----

AMS has many different modes of operation, or tasks.

See also: Tasks section  of the AMS driver manual.

To optimize the geometry of the ethanol molecule we choose the
geometry optimization task:

   Select **Geometry Optimization** from the 'Task' menu

   [image]

After selecting a task the AMS-GUI loads a preset that adjusts input
fields needed for this particular task. You can easily see what fields
have been updated by a preset: they are colored green.

Check the GUI presets documentation for more information about
presets.


XC functional
-------------

An important input option is the XC functional to use.

For this tutorial the default functional during the SCF is sufficient.
So just leave this at the default value.

Tip:

  You should select a good XC functional and basis set to get accurate
  results. Numerical quality will also play a role. There often is a
  trade-off between speed and accuracy. Different job types could have
  different recommendations. E.g. for geometry optimizations, GGAs
  with dispersion correction and a DZP basis may be good enough, while
  for NMR you may want to use a hybrid functional with a TZ2P basis.


Basis set
---------

With the Basis Set pull-down menu you select the basis set you want to
use.

The menu gives access to the Basis Sets regularly used.

For this tutorial we will choose a very small basis set. This will
yield less accurate results, but the calculation runs much faster.
Obviously, if you want more accurate results you should use a better
quality basis set. Thus:

   Select 'SZ' from the 'Basis Set' pull-down menu

   [image]

Tip:

  Colors of input field: changed by preset (green), by user (yellow),
  by both (red)


Numerical quality
-----------------

The ADF engine uses a numerical integration scheme for virtually
everything it may calculate. A numerical integration scheme generates
a grid and corresponding weights. The default integration method in
ADF and BAND is the Becke grid.

Another technical detail is that a density fitting method is used, for
computational efficiency. The spline Zlm fit is the default fit method
(the old Slater type fit is still available).

With the Numerical quality option you can select the quality of both
the Becke integration and the spline Zlm fit at the same time.

Increasing the quality makes the results more accurate, but will
require substantially more computation time.

Similarly, decreasing the quality will result in less accurate
results, but you may get results faster.

The default value will in most cases be fine, certainly for this
tutorial. If you go to the Details section you can set details of the
integration scheme and fit method. However, the Numerical quality
option in the main panel is the most convenient way to select the
quality.


Geometry Convergence
--------------------

   Click on the [image: MoreBtn][image] button next to the Task

   [image]

In this panel you can see the details of the geometry optimization,
such as the maximum number of iterations and the convergence
thresholds.

Tip:

  Click on a unit to change the unit, your choice will be
  remembered.Use the GUI Preferences to reset all units to the default
  values.

As the current set up is fine, go back to the main panel:

   Click the 'Main' button in the panel bar


Other input options
-------------------

The panels on the right side contain many more input options. You
select a panel with the menus in the panel bar, or by searching for a
particular option. When searching for an option, any text in the
panels will match, as well as from the help balloons. Also the
corresponding AMS input keys will match.

   [image]

The menu items use a color coding to show you which panels have been
affected by a preset (green), by the user (yellow), or both (red).

As we will not do anything special right now, you do not need to
change anything in other panels.


Step 4: Run your calculation
============================


Save your input and create a job script
---------------------------------------

Finally you will want to save your input.

   Select the **File → Save** command
   Make sure you select the Tutorial directory that we made
   Enter the name 'ethanol' in the Filename field

   [image]

   Click on Save

Now you have saved your current options and molecule information. The
file will automatically get the extension '.ams'.

AMSinput has also created a corresponding script file. This script
file has the same name, but with an extension '.run' instead of
'.ams'.

In the AMSjobs module you can see what files have been created:

   Click once in the AMSjobs window to activate it
   Click once on the triangle in front of the name of the job (ethanol)

You will see the .ams and .run files, and a .pid file that AMSjobs
uses to store information. You might also see the picture that you
saved, if you used the name 'ethanol' for it. Only the extensions are
listed, so the real filenames are ethanol.ams, ethanol.run and
ethanol.pid. Notice the job status icon (the open circle on the right)
that AMSjobs uses to indicate a new job.

   [image]


Run your calculation
--------------------

To actually perform the calculation (the geometry optimization of the
ethanol molecule), use the **Job → Run** menu command in AMSjobs:

   Make sure the ethanol job is selected in AMSjobs (it is if you followed the tutorial)
   Select the **Job → Run** command

This will execute the run script that has just been created. If you
have never made changes in the AMSjobs setup, the default behavior is
to run the job in the background on your local computer, using the
Sequential queue. This queue will make sure that if you try to run
more then one job at the same time, they will be run one after
another.

Once your job starts running, AMSjobs will show the progress of the
calculation: the last few lines of the logfile:

   [image]

Note that while running, the job status symbol in AMSjobs changes.

If you wish to see the full logfile while the calculation is running,
just click on the logfile lines displayed in the AMSjobs window:

   Click on the logfile lines in the AMSjobs window

Now the logfile is showing in the AMStail window:

   [image]


Step 5: Results of your calculation
===================================


Logfile: AMStail
----------------

The logfile is saved and extended by AMS as it is running. Normally it
is most convenient to view it only in the AMSjobs window to prevent
screen clutter.

Right now it is already showing in the AMStail window, and in the
AMSjobs window, but you could have used any text editor.

Wait for the calculation to finish:

   Wait until AMStail shows 'Job ... has finished' as last line
   Click the 'Update molecule' button that appears in the AMSinput window to update the geometry

   [image]

Close the AMStail window by using the **File → Close** menu command:

   In the window showing the logfile (the AMStail window):
   Select the **File → Close** command

In the AMSjobs window, note that the job status icon has changed to
indicate that the job is ready:

   [image]


Files
-----

AMS has created a couple of data files and a couple of text files.
You can check this in the AMSjobs window:

   Click on the AMSjobs window

   [image]

Note that the Local files are visible because earlier in the tutorial
you already clicked on the triangle opening the details for this job.

The .ams file is the input as saved by AMSinput.

The .run file is the run script, also saved by AMSinput.

Tip:

  To change the .run file, if necessary, use the 'Run Script' panel in
  AMSinput (in the Details section). Your changes will be saved in the
  .ams file. If you make changes to the .run file itself they will be
  overwritten next time you save the job with AMSinput.

The .pid file is a file that contains your job status and
configuration. It is used by AMSjobs.

The other files are produced by AMS. The .err file contains error
messages, the .logfile shows the progress of the calculation, the .out
file is the main (text) output file, and the other files are binary
files that store results of the calculation.


Geometry changes: AMSmovie
--------------------------

AMS has optimized the geometry, and we can use the AMSmovie module to
visualize the progress of the optimization. So let's start AMSmovie
using the SCM menu in your AMSinput window:

   [image]

   Select the **SCM → Movie** command in AMSinput
   Press the Play button (the right pointing arrow)

Tip:

  Press the space bar to start/stop playing in AMSmovie

The AMSmovie module will display a movie of the geometry optimization.

   [image]

Tip:

  Use the slider to quickly move through the frames.Use the left and
  right arrow keys to single step through the frames.

You control playing with the buttons. When your mouse pointer is above
any of the buttons, and not moving, a balloon, or tooltip, will pop up
showing what that particular button will do.

The graph on the right-hand side shows the energy and forces as
function of the geometry step.

You can show several graphs for different properties at the same time:

   Use the **Graph → Add Graph** menu command
   Select two carbon atoms by shift-clicking on them
   Use the **Graph → Distance, Angle, Dihedral** menu command

   [image]

Now you have two graphs. One of them is the 'active' graph. When you
make a new graph it will always be the active graph. You can also make
a graph active by clicking on it.

When you select a property from the Graph menu (Energy, Distance and
so on) that property will be plotted in the active graph.

You can also have multiple curves in one graph, if possible: one
property per Y-axis. You may have several curves on the same Y axes if
they are using the same unit (all Angstroms for example):

   Select two carbon atoms and one oxygen atom by shift-clicking on them
   Use the **Graph → Distance, Angle, Dihedral** menu command

   [image]

Another feature is that you can click on a point in one of the graphs.
It will be marked, the movie will jump to that particular step, and if
you have more then one graph the corresponding point(s) will also be
marked in the other graphs.

To rotate, translate, or zoom the picture, use your mouse, just as in
AMSinput.

   Use the slider to go to a frame in the middle of the optimization

Selecting atoms provides information about atoms, bonds, etc. in the
information field below the molecule editor pane. The information will
be updated when you go to another point in the movie (a different
geometry). You can see examples of these in the pictures above.

You can also show this information in the 3D window:

   Use the **Properties → Geometric Info → Angle** menu command

   [image]

The angle will be visually added to your molecule :

   [image]

   In the AMSmovie window: select **File → Close Job**.
   If you are prompted to save changes, choose 'No'.


Orbital energy levels: AMSlevels
--------------------------------

   Select your job in the AMSjobs window by clicking on the job name
   Select the **SCM → Levels** command

Tip:

  In AMSjobs right-click on a job name to go quickly select it **and**
  show the SCM menu

AMSlevels will start and show a diagram of the energy levels of the
ethanol molecule.

   [image]

In the diagram you can see from what fragment types the molecular
levels are composed.

   Move the mouse around, above different levels, without clicking

Balloons will pop up with information about the level at the mouse
position: The MO number, eigenvalue, occupation, and how it is
composed of SFOs (symmetrized fragment orbitals).

   Click and hold on the HOMO level of the molecule

   [image]

   In the pop-up that appears, select 'Show Labels'
   Click and hold on the HOMO of the O fragment type
   In the pop-up, select 'Show Labels'

   [image]

The labels of the orbitals may be different as they depend on the
symmetry of your molecule.

To actually see the orbital, select the orbital from the top of the
pop-up menu:

   Click and hold on the HOMO level of ethanol
   Select the '10A' command (or similar depending on the symmetry)

A window with a picture of the orbital should appear.

   [image]

You can move (rotate, translate and zoom) the orbital with your mouse.

   Close the window showing the orbital: **File → Close Job** (in the window displaying the orbital)


Electron density, potential and orbitals: AMSview
-------------------------------------------------

   Select **SCM → View**

AMSview will start up and show a picture of your molecule and a panel
where calculated properties will be listed:

   [image]

You can use AMSview to visualize all kinds of 'field' related
properties: densities, orbitals, potentials, etc. You actually have
already used it before: the picture of the orbital that was created
using AMSlevels was shown by AMSview.

Use the mouse to rotate, translate or zoom, as in AMSinput.

In the Properties menu there are some pre-defined things to visualize:
density, spin-density, HOMO, LUMO and more. If you select one of
these, you will see the corresponding item immediately. However,
AMSview can do much more and gives you lots of control.

For example, lets show a density isosurface, colored by the
electrostatic potential:

   Select the **Add → Isosurface: Colored** command

At the right side extra controls will be created. AMSview creates such
controls for all visual items and special fields (surfaces, planes,
calculated fields, etc.) that you add.

   [image]

In this particular case the controls contains two pull-down menus that
you use to select the fields that you want to visualize.

   From the first pull-down menu in the controls, select **Density → Density SCF**

   [image]

   From the second pull-down menu in the controls, select **Potential → Coulomb Potential SCF**

   [image]

To demonstrate some other possibilities of AMSview, do the following:

   Select the **Properties → HOMO** command
   Un-Check (click on it) the **show** check box in the controls for the Density to hide the density
   Rotate the molecule to get a good view

   [image]

   Select the **Add → Plane: Colored** command
   In the new controls, from the 'Select Field ...' pull-down menu and select **Density → Density SCF**
   Hide the HOMO using the **Show** check button in the 'Isosurface: With Phase' controls
   Select the two carbon and the oxygen atoms (three atoms)
   Click on the Use selection button in the Point on plane row to align the plane with the three atoms
   Show the HOMO using the 'Isosurface: With Phase' controls
   Select the **Fields → Grid → Medium** command
   Click Yes to recalculate the fields
   Rotate your molecule to get a good view

   [image]

You can save the picture you create using the Save Picture menu
command:

   Select **File → Save Picture ...**
   Enter the name (without extension) of the file you want to create
   Click Save

A picture with the (file)name you specified has been created.

You might want to explore some more of the possibilities of AMSview on
your own. Many different properties can be visualized as you probably
have noticed in the pull-down menus.


Browsing the Output: AMSoutput
------------------------------

The output file (tutorial.out) is a plain text file. You can view it
with your favorite text editor (or text viewer). You can also use the
AMSoutput GUI module which provides a convenient way to check the
results:

   Select the **SCM → Output** command
   Select the **Properties → Bonding Energy Decomposition** command

The AMSoutput program will start showing the results of your
calculation, and via the menu you jumped to the section with bonding
energy decomposition details:

   [image]

You can use the menus to go to different parts of the output file, or
you can just use the scroll bar. If a menu option is shaded, this
means that no corresponding section of the output is available.

Tip:

  Click text highlighted in blue to jump to the next section with the
  same title, if present.

Tip:

  Use the search box at the bottom of the AMSoutput window
  (cmd/ctrl-F)


Convert results to spreadsheet (.xlsx)
--------------------------------------

You can also export the results of a finished calculation to
spreadsheet (.xlsx) format, that you can open in e.g., Microsoft Excel
or LibreOffice Calc.

   In AMSjobs select your job and choose **Tools → Build Spreadsheet**. Click the Do It button.

Only the most common types of results are exported to the spreadsheet.
For example, general information about the system, the orbital
energies, and the atomic positions and atomic charges. For a full
list, the spreadsheets documentation.

   [image]

   [image]


Close all open GUI windows
--------------------------

As we are now done with tutorial 1, close all windows that belong to
this tutorial:

   Select the **SCM → Quit All** command in any AMS-GUI window

All open windows from the AMS-GUI will be closed.
