Spreadsheets (.xlsx)ΒΆ

Export AMS results to spreadsheet formatΒΆ

Starting from AMS2021.1, you can export the results of an AMS calculation to spreadsheet (.xlsx) format.

You can

  • convert a single AMS results folder to spreadsheet format
  • compare multiple AMS results in a single table

Create a .xlsx file for a single AMS resultΒΆ

In AMSjobs, select a finished job and go to Tools β†’ 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.

Note

Your spreadsheet viewer must be able to evaluate formulas. We recommend that you use Microsoft Excel (for Windows, Mac) or LibreOffice Calc (for Windows, Mac, Linux). Other spreadsheet programs (such as Apple’s Numbers, Google Docs, and Gnumeric) may not be able to calculate all formulas, or may lack some features like conditional formatting.

You can also choose to generate the spreadsheet when setting up the job in AMSinput. Select Details β†’ 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 jobsΒΆ

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

  • select SCM β†’ New Input,
  • select Details β†’ Summary as Spreadsheet (.xlsx),
  • set Output to job.results/job.xlsx to place the spreadsheet in the AMS results folder, or job.xlsx to place the spreadsheet in the same folder as the input file.
  • select the units that you prefer
  • select File β†’ Preset β†’ Save as preset
  • save it with the name Defaults
  • restart AMSinput

This will place a line creating the spreadsheet at the end of the .run file.

Compare multiple AMS calculations in a spreadsheetΒΆ

Graphical user interface: Select multiple jobs in AMSjobs, by holding Shift while clicking on the job names. Select Tools β†’ 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.

UnitsΒΆ

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.

Unit Comment
Angles degrees; cannot be changed
Dipole moment Β 
Electronic energy Orbital energies, excitation energies, band gaps, …
Energy Potential energy, kinetic energy, …
Entropy expressed in energy_unit/K
Frequency cm⁻¹; cannot be changed
Gradients (forces) Β 
Heat capacity expressed in energy_unit/K
Hessian, 2D stress Β 
Length Β 
Mass Β 
Pressure, 3D stress Β 
Quadrupole moment atomic units; cannot be changed
Temperature Kelvin; cannot be changed
Time ps; cannot be changed

Distributions and spectraΒΆ

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 LibreOfficeΒΆ

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.

Results available in spreadsheet formatΒΆ

The Amsterdam Modeling Suite can calculate thousands of different types of results. Only the most common ones are exported to spreadsheet format (see the below tables).

If you cannot find a result in the spreadsheet file, open the output file or use KFbrowser to inspect the binary .rkf results files.

EnginesΒΆ

ADF βœ”
BAND βœ”
COSMO-RS ❌
DFTB βœ”
ForceField βœ”
ReaxFF βœ”
ML Potential βœ”
Hybrid βœ”
Quantum ESPRESSO ❌
VASP via AMS βœ” (partial)

TasksΒΆ

COSMO-RS Compound ❌
Conformers ❌
GCMC ❌
Geometry optimization βœ”
IRC βœ”
Molecular Dynamics βœ”
NEGF ❌
Nudged elastic band (NEB) βœ”
PES Exploration βœ”
PES Scan βœ”
Single point βœ”
Transition state search βœ”
Vibrational Analysis ❌

Single-point propertiesΒΆ

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.

Property Β 
Atomic charges βœ”
Bader analysis, QTAIM ❌
Band gap βœ”
Band structure ❌
Bonds and bond orders ❌
Bulk modulus βœ”
Density of states (DOS) βœ”
Diffusion coefficient ❌
Dipole moment βœ”
Distance matrix βœ” (color-coded)
Eigenvalues and occupations per k-point ❌
Elastic tensor βœ”
Electron density at nuclei βœ” (ADF only)
Electrostatic potential at nuclei βœ” (ADF only)
Energy βœ”
Enthalpy βœ”
Entropy βœ”
Excitations (UV/VIS) βœ” (types, energies, spectrum)
Fermi energy βœ”
Gibbs free energy βœ”
Heat capacity βœ”
Hessian ❌
HOMO βœ”
HOMO-LUMO gap βœ”
Internal energy βœ”
k-point coordinates βœ”
LUMO βœ”
MDC-d charges and spins βœ”
MDC-m charges and spins βœ”
MDC-q charges and spins βœ”
Molecules ❌
Mulliken charges and spins βœ”
NMR ❌
Normal modes (IR spectrum) βœ” (symmetries, frequencies, spectrum)
Nuclear gradients (forces) βœ”
Orbitals βœ” (symmetries, energies, occupations)
Partial energies (Coulomb, …) βœ”
PES point character βœ”
Partial DOS (PDOS) ❌
Phonon DOS βœ”
Pressure βœ”
Quadrupole moment βœ”
Radial distribution function (RDF) ❌
Raman ❌
Shear modulus βœ”
Statistical thermal analysis (thermodynamics) βœ”
Stress tensor βœ”
Velocity autocorrelation function ❌
Young’s modulus βœ”
Zero point energy (ZPE) βœ”

Geometry optimization propertiesΒΆ

Geometry optimization summary

Convergence βœ” (see Termination status)
Final maxGrad βœ”
Final maxStressEnergyPerAtom βœ”
Final rmsGrad βœ”
Number of iterations βœ”

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.

Energy βœ”
Frame number βœ”
Lattice parameters (a, b, c) βœ”
maxGrad βœ”
maxStressEnergyPerAtom βœ”
Relative energy βœ”
rmsGrad βœ”

NEB propertiesΒΆ

Left barrier βœ”
Number of images βœ”
Number of iterations βœ”
Plot of energy vs. image βœ”
Right barrier βœ”

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

MD propertiesΒΆ

Timestep βœ”
Number of steps βœ”
Simulation time βœ”
Start and end step βœ”
Start and end time βœ”

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.

Cell volume βœ”
Conserved energy βœ”
Kinetic energy βœ”
Lattice parameters (a, b, c) βœ”
Number of atoms βœ”
Potential energy βœ”
Pressure βœ”
Step βœ”
Temperature βœ”
Time βœ”
Total energy βœ”

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.

SystemΒΆ

Atomic masses βœ”
Atomic positions (xyz coordinates) βœ”
Cell volume βœ”
Charge βœ”
Chemical formula βœ”
Density βœ”
Job name βœ”
Lattice parameters (a, b, c, Ξ±, Ξ², Ξ³) βœ”
Lattice vectors βœ”
Net spin ❌
Number of atoms βœ”
Mass βœ”
Periodicity βœ”
Picture βœ” [1]
Reciprocal lattice vectors ❌
Symmetry βœ” (only for ADF)
Velocities βœ”
[1]A picture is generated if it is possible to start the AMS GUI.

GeneralΒΆ

AMS version βœ”
CPU time βœ”
Elapsed time βœ”
Errors βœ”
Names of compute nodes ❌
Number of compute nodes ❌
Start and end time ❌
Text input βœ”
Termination status βœ”
Warnings βœ”