10 Ways to Get the Energy and Other Properties

Most AMS calculations produce several output files:

  • the standard output (jobname.out file)

  • the logfile (jobname.logfile, or ams.log)

  • the binary ams.rkf file inside the jobname.results directory

  • the binary “engine.rkf” file inside the jobname.results directory. The name of the file depends on the calculation, and can be adf.rkf, band.rkf, dftb.rkf, reaxff.rkf, etc.

One important result from an AMS geometry optimization or single-point calculation is the final potential energy. AMS will print this number in hartree to the standard output, logfile, and engine.rkf file.

This tutorial shows you how to get this number with the

Most of these tools can also be used to extract many other properties, such as atom coordinates, bond lengths, orbital energies, excitation energies, density of states, etc.

Note

ADF and BAND give the energy with respect to fragments. The fragments are spherically symmetric nonspinpolarized atoms, by default. See also the FAQ.

This tutorial uses results from Getting started: Geometry optimization of ethanol.

Graphical User Interface

1. Standard output

  • Select the job in AMSjobs (SCM → Jobs)

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  • SCM → Output

  • Scroll down towards the end, or search for “CALCULATION RESULTS” with the search box at the bottom of the window.

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  • Under “CALCULATION RESULTS” is a line with the energy.

2. Logfile

  • Select the job in AMSjobs (SCM → Jobs)

  • SCM → Logfile

  • Scroll down towards the end. Depending on the engine and task, the energy is sometimes printed as “Bond Energy”, “ENERGY OF FORMATION”, “current energy”, etc.

../_images/2_1.png

3. KF browser

KF browser is a program for viewing the binary ams.rkf and engine.rkf files.

  • Select the job in AMSjobs (SCM → Jobs)

  • SCM → KF browser. This will show you the contents on the ams.rkf file.

  • File → Related files -> engine.rkf (here: adf.rkf)

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  • Click on the arrow next to Energies

../_images/3_2.png

To start kfbrowser from the command line, run $AMSBIN/kfbrowser engine.rkf.

See also: The difference between ams.rkf and engine.rkf.

Tip

If you select File → Expert Mode, you will see the raw structure of the binary file.

4. Spreadsheet (Excel) summary

  • Select the job in AMSJobs (SCM → Jobs)

  • Tools → Build spreadsheet…

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  • Choose your preferred units

../_images/4_2.png

  • Click “Do It”

This places a spreadsheet .xlsx file in the job.results folder and opens it in your default spreadsheet viewer. The energy is given under “Main results”.

../_images/4_3.png

See also: Documentation for spreadsheet export.

5. AMSjobs

  • Open AMSjobs (SCM → Jobs)

  • View → Comments

  • Select the job

  • Job → Edit Comments

  • In the Results dropdown menu choose Energy

  • Click Set as Default

  • Click Save

../_images/10ways_amsjobs.png

Command-line (bash, terminal)

Start a terminal window as follows:

  • Windows: Help → Command-line, type bash and hit Enter.

  • MacOS: Help → Terminal.

  • Linux : Open a terminal and run: source /path/to/ams/amsbashrc.sh

../_images/6_1.png

In the examples, replace /path/to/engine.rkf with the actual path to the file (the path can be absolute or relative).

6. Command-line: amsreport

$AMSBIN/amsreport /path/to/engine.rkf energy

Some engines calculate the energy by summing up contributions. See the contributions with

$AMSBIN/amsreport /path/to/engine.rkf energies

You can also read key-value pairs from engine.rkf directly. To find out which entry to read, first inspect the file with kfbrowser in Expert Mode (File → Expert Mode).

$AMSBIN/amsreport /path/to/engine.rkf "AMSResults%Energy" -r

amsreport can also extract many other properties. See the amsreport documentation.

7. Command-line: dmpkf

$AMSBIN/dmpkf /path/to/engine.rkf "AMSResults%Energy"

Python

amspython is the python interpreter included with the Amsterdam Modeling Suite. It gives you access to the PLAMS python library.

9. Python: Load an AMSJob

To get the final energy:

  • Save the below code snippet into a file filename.py

  • Run it from the command-line with: $AMSBIN/amspython filename.py.

from scm.plams import *
job = AMSJob.load_external('/path/to/jobname.results')
energy = job.results.get_energy()
print(energy)

To get all the energies from for example a geometry optimization:

from scm.plams import *
job = AMSJob.load_external('/path/to/jobname.results')
energies_list = job.results.get_history_property('Energy')
print(energies_list)

PLAMS has many different functions for extracting results. See the AMSResults API.

10. Python: Direct access to .rkf file

To find out which entry to read from a binary file, first inspect the file with kfbrowser in Expert Mode (File → Expert Mode).

To get the final energy with KFReader:

  • Save the below code snippet into a file filename.py

  • Run it from the command-line with: $AMSBIN/amspython filename.py.

from scm.plams import *
kf = KFReader('/path/to/jobname.results/engine.rkf')
energy = kf.read('AMSResults', 'Energy')
print(energy)

Alternatively, load an AMSJob and call the readrkf method on its results:

from scm.plams import *
job = AMSJob.load_external('/path/to/jobname.results')
energy = job.results.readrkf('AMSResults', 'Energy', file='engine')
print(energy)