SEAMM Ionic Conductivity Plug-in

A SEAMM plug-in for the ionic conductivity of electrolytes from MD.

• Free software: BSD-3-Clause

• Documentation: https://molssi-seamm.github.io/ionic_conductivity_step/index.html

• Code: https://github.com/molssi-seamm/ionic_conductivity_step

History

2026.10.17.1 – Analyze MD run before the step; labelled errors; no ions skipped

• The step analyzes MD run before it in the flowchart – the runs of a Loop around the MD, as independent replicas (“the last MD run of each loop iteration”, the default) – or md.h5md files; it no longer runs its own MD in a sub-flowchart. Older flowcharts that stored its settings for that can still be read; the check before the job runs says what replaces them.

• The check before the job runs also warns when the analysis is inside the loop holding its MD, when the loop changes the temperature or pressure, and when the thermostat does not suit the analysis, with fixes; the step warns before the MD when the system is small.

• Errors are the 95% confidence interval, Student’s t for the number of runs or blocks, and the output says so; stored errors are standard errors.

• The state of the runs – temperature, pressure, volume and density with their errors, and the equilibrium density where an NPT run before them gives the bulk modulus – is reported and stored. The values of each run or block are in step.out.

• Bugfix: a system without ions stopped the job; it is now reported and skipped.

• A warning before the MD runs when there are fewer than about 10 ion pairs.

• σ and the ions’ diffusion coefficients are averages of their x, y and z components, with a check that they agree; with the Yeh-Hummer correction, the values in the box and corrected are both given, with the viscosity used.

2026.10.17 – First release: the ionic conductivity

• The ionic conductivity of electrolytes from MD with fixed charges, by Einstein-Helfand from the collective displacement of the ions’ charges and by Nernst-Einstein from their self-diffusion, and the ionicity; errors from independent runs or blocks; the Yeh-Hummer correction of the self-diffusion with the viscosity from a Viscosity step.

• Runs its own MD or analyzes the MD earlier in the flowchart, and checks before the job runs that the MD samples the positions often enough.