Spreadsheets (.xlsx)

Export AMS results to spreadsheet format

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 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.

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 → 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,

  • select SCM → New Input,
  • select Details → 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 → Preset → 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 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.

Unit Comment
Angles degrees; cannot be changed
Dipole moment  
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)  
Heat capacity expressed in energy_unit/K
Hessian, 2D stress  
Length  
Mass  
Pressure, 3D stress  
Quadrupole moment atomic units; cannot be changed
Temperature Kelvin; cannot be changed
Time ps; cannot be changed

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.

Results available in spreadsheet format

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.

Engines

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

Tasks

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

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.

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

Geometry optimization properties

Geometry optimization summary

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

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

NEB properties

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

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

MD properties

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

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

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

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

General

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