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