Multiple molecules multiple methods
***********************************

Multiple jobs Multiple molecules

The AMS-GUI can handle multiple molecules, or multiple methods, or
both, with one relatively simple setup.


Multiple molecules
==================

With AMSinput you can set up a calculation, and then run your set up
for multiple molecules automatically. At run time the molecules are
then taken from an .sdf file that has the same name as your .ams file
(except for the extension obviously). This SDF file may come from
somewhere else, or you can actually create and edit multiple molecules
inside AMSinput.

After the calculation the result is a new .sdf file. That .sdf file is
a standard SDF file, with the calculated energy in the title for each
molecule. It also contains references to the calculation results for
the individual molecules. And it may contain some extra information
per molecule (depending on the calculation).

As an example, let's calculate the H-NMR spectra for methane and
ethane with one single set-up.


Set up methane and ethane in AMSinput
-------------------------------------

   Start AMSinput
   Create methane by copy-pasting the following coordinates into AMSinput

   C     0.00000000     0.00000000     0.00000000
   H     0.63290000    -0.63290000    -0.63290000
   H    -0.63290000     0.63290000    -0.63290000
   H     0.63290000     0.63290000     0.63290000
   H    -0.63290000    -0.63290000     0.63290000

Next we will add an extra molecule (ethane) to AMSinput:

   Use the **Edit → New Molecule** menu command
   Create ethane by copy-pasting the following coordinates into AMSinput

   C     0.00000000     0.00000000     0.76580000
   C     0.00000000     0.00000000    -0.76580000
   H    -0.88670000     0.51190000     1.16680000
   H     0.88670000     0.51190000     1.16680000
   H     0.00000000    -1.02390000     1.16680000
   H     0.00000000     1.02390000    -1.16680000
   H    -0.88670000    -0.51190000    -1.16680000
   H     0.88670000    -0.51190000    -1.16680000

   Switch between the two molecules using the arrows at the bottom
   Adjust the names of the molecules to methane and ethane (click on the name, it becomes editable)
 [image]


H-NMR calculation
-----------------

Next we will set up the calculation of an H-NMR:

   Go to the NMR panel (in the Properties section)
   Check the Shielding for all H atoms check box
   Use the **File → Run** menu, save your job as NMR
   When asked to run all 2 molecules, click Yes

In the AMSjobs window you should see the job running. Also note that
it gives you the information that the job uses the nmr.sdf file. When
you open the job you will see the results for two different molecules
in the .results folder:

   Wait for the calculation to finish
   Click on the triangle before the job name to see the files belonging to that job
 [image]

Note that the results of the calculated NMR spectra will depend on the
geometries for methane and ethane, on the used basis set, XC
functional, etcetera. See also ADF FAQ: What settings are recommended
for NMR calculations?

Use AMSspectra to see the calculated NMR spectra. When opening the
job, it will show an averaged spectrum. Use the View menu to adjust
what curves to see:

   **SCM → Spectra**
   In the AMSspectra window: **View → Average/All Curve**
   Change the width of peaks to 0.01
 [image]

You can also open the result files for the individual calculations:

   In AMSjobs click once on results/mol_1.results/adf.rkf to select it
   **SCM → Spectra**
   Change the width of peaks to 0.01
 [image]

   Close AMSinput and AMSspectra


Multiple Methods
================

You can also set up a series of calculations with different methods,
and run them automatically one after each other. The geometries will
automatically be passed from one job to the next.

As examples we first show how to set up a series like: DFTB
optimization, ADF optimization and ADF UV/Vis spectrum for the
optimized structure. We will then run this set up twice: once for the
specified molecule, and once for a set of molecules.


Set up a series of calculations
-------------------------------

The first step in the series is a DFTB calculation on a molecule, we
will use Acetone as an example:

   Start AMSinput
   Make (or find) an Acetone molecule
   Switch to DFTB mode
   Select the 'SCC-DFTB' model
   Select the 'Dresden' parameter directory
   Save as 'dftb'
   Close AMSinput

The second step in the series is an ADF geometry optimization of the
optimized structure from the first step:

   Start AMSinput
   Select the **Geometry Optimization** task
   Switch to the **Model→ Coordinates** panel
   Use Job Result
   Molecule from dftb.ams
 [image]

We now use the Job Result option in the Coordinates panel: this will
make sure that the selected job is run first, and that the resulting
geometry of that job will be used as input geometry for the current
calculation.

   Save as 'adf-geo'
   Close AMSinput

The third step in the series is an ADF UV/Vis calculation for the ADF-
optimized structures:

   Start AMSinput
   Set up a UV/Vis calculation in the **Properties → Excitations(UV/Vis), CD**
 [image]

   Switch to the Coordinates panel
   Use Job Result
   Molecule from adf-geo.ams
 [image]

   Save as 'adf-uvvis'
   Close AMSinput


Run a series of calculations for a single molecule
--------------------------------------------------

To run the just created series of calculation all we need to do is to
start the final job (adf-uvvis). AMSjobs will detect that it uses
results of other jobs, and start those jobs automatically:

   Start AMSjobs (or make it active if it is still running)
   Select the adf-uvvis job

In the AMSjobs window you can see on which jobs the selected job
depends:

[image]

   Run the job

In AMSjobs you should now see all the jobs in the job series running,
one by one, in the proper order. If you wish you can examine the
results of each job step as you would for normal independent jobs.

Lets now just check the final UV/Vis spectrum:

   Select the adf-uvvis job in AMSjobs
   **SCM → Spectra**
 [image]

Remember that in the adf-uvvis job no molecule was specified, the
geometry has been imported from the result of the adf-geo job. And
that job in turn got the geometry from the dftb job.


Create an SDF file, and Run a series of calculations for a set of molecules
---------------------------------------------------------------------------

The series of calculations in the previous steps can also be run with
molecules from a .sdf file as input. Any SDF file can be used, for
example the earlier sdf files from this tutorial.

In this case we will make a new SDF file just to show how to do that
as well. First we make two .ams files, one for benzene and one for
water:

   Start AMSinput
   Make benzene
   Save as benzene.ams

   **File → New**
   Make water
   Save as water.ams
   Close AMSinput

Next we make an SDF file containing the two molecules we just made:

   Go to AMSjobs
   Select the benzene and water jobs you just made (use control click to select multiple items)
   **Tools → Add To SDF...**
 [image]

   In the Append to file option select a name for the .sdf file to create: mols.sdf
   Click OK

A new SDF file with the specified name will be created, containing the
structures you selected. You can also add extra molecules to the .sdf
file using the same method (just select an existing .sdf file instead
of a new one). You can also include structures resulting from
calculation results you have (.t21, .rkf files etc), or even from
simple .xyz or .mol files and so on.

Next we want to run the series of jobs (DFTB - ADF geometry
optimization - ADF UV/Vis) for all molecules in the mols.sdf file. In
the first job of the series (DFTB) specify to use molecules from the
.sdf file:

   Open the dftb.ams file in AMSinput again (click No when asked to update coordinates)
   Go to the coordinates panel
   Use Selected File
   Molecule From: select the mols.sdf file just created
 [image]

   **File → Save**
   In AMSjobs select the last job in the series (adf-uvvis)
   **Job → Run**

You should see all jobs running again in AMSjobs, but now multiple
times. In the .results directories you will find the results for the
individual jobs, and the final geometries are always collected in new
.sdf files.

   In AMSjobs show the details of the adf-uvvis job (click on the triangle)
 [image]

You can see the average or individual spectra via AMSspectra, or the
geometries using AMSmovie:

   **SCM → Spectra** (with the adf-uvvis job selected)
   In the AMSspectra window: **View → Average/All Curve**
 [image]

Such a multi molecule job can also be inspected with amsmovie

   **SCM → Movie** (with the adf-uvvis job selected)
 [image]

Here each frame corresponds to the final energy of the optimized
molecules (two in this example). Comparing energies of different
molecules is not very useful, but this feature makes sense when
considering conformers.
