Spreadsheets (.xlsx)¶

Create a .xlsx file for a single AMS result¶

In AMSjobs, select a finished job and go to Tools → Build spreadsheet. This will create a file called jobname.xlsx in the jobname.results folder, and open it in your default spreadsheet viewer.

You can also double-click on the file in AMSjobs to open it.

You can also choose to generate the spreadsheet when setting up the job in AMSinput. Select Details → Summary as Spreadsheet (.xlsx), and set the output and unit options to your preferences.

To generate a spreadsheet file from the command line, run

"$AMSBIN/amspython" "$AMSHOME/scripting/scm/xlsx/amsresults2xlsx.py" /path/to/jobname.results

You can also pass a --help flag to the above script to see some customization options.

Generate spreadsheet by default for all jobs¶

To automatically generate a spreadsheet at the end of every job that you set up via AMSinput,

• set the Output option on the Details → Summary as Spreadsheet (.xlsx) panel to either job.results/job.xlsx or job.xlsx,

• Follow the instructions for Presets and Defaults

Compare multiple AMS calculations in a spreadsheet¶

Graphical user interface: Select multiple jobs in AMSjobs, by holding Shift while clicking on the job names. Select Tools → Build spreadsheet.

This creates a spreadsheet containing a table that you can filter or sort based on a number of properties, for example

• Job name

• Engine, task

• Elapsed time, termination status

• Energy, zero-point energy

• HOMO, LUMO, band gap

• Dipole moments

• Excitation energies, oscillator strengths

• Lattice vectors and parameters

• Reaction energies and barriers

Command-line:

"$AMSBIN/amspython" "$AMSHOME/scripting/scm/xlsx/amsresults2xlsx.py" --multi \
   jobname1.results jobname2.results [jobname3.results...]

Pass the --help flag to the script to see more options.

Units¶

The generated spreadsheet contains a worksheet called Units. Under the heading Current units, you can see and change the units used throughout the spreadsheet. By clicking on one of the yellow cells, a drop-down list appears with the available options.

Distributions and spectra¶

A spectrum (e.g. the IR spectrum) is calculated in the spreadsheet using Gaussian broadening. If you prefer a different type of broadening (e.g. Lorentzian), you can do this in the GUI module AMSspectra.

Evaluate formulas with LibreOffice¶

The LibreOffice Calc spreadsheet program does not by default recalculate formulas in .xlsx files. If you use LibreOffice Calc, we recommend that you (in LibreOffice Calc) go to Tools -> Options -> LibreOffice calc -> Formulas and set Excel 2007 and newer to Always recalculate.

Engines¶

Tasks¶

Single-point properties¶

These properties are also given for the final frame of a geometry optimization or molecular dynamics simulation, or for the highest-energy image in an NEB calculation.

Geometry optimization properties¶

Geometry optimization summary

Per-frame information: These are plotted vs. the frame number. For some of the properties, the plots only show data near the end of the optimization.

NEB properties¶

Per-frame information: See geometry optimization per-frame information.

MD properties¶

Per-frame information: These (except for Step) are plotted vs. time.

If the trajectory file contains more than 2000 structures, two worksheets are created:

• The first contains data for the first 2000 frames

• The second gives 2000 evenly spaced data points spanning the entire trajectory. Example: The trajectory contains 10000 frames, data is then given for frames 1, 6, 11, …, 9991, 9996.

This is done to limit the size of the .xlsx file if the trajectory is very long.

Block averages: The total trajectory is divided into 5 equally sized blocks, and for each block the mean and standard deviation of all per-frame quantities are reported. Currently you cannot change the number of blocks.

System¶

1

A picture is generated if it is possible to start the AMS GUI.

General¶