History#

2026.10.21.1 – Onsager coefficients and transference numbers

  • The step now also gives the Onsager transport coefficients L_ab of the ionic species and the transference number of each ion (Fong et al. 2020), from the collective displacements of the ions’ centres of mass, with their errors. Both are given in the frame of the MD and relative to the mean motion of the solvent, the frame of the usual measurements. For a single cation, its transference number t+ can be stored as a property.

2026.10.21 – The ionic conductivity with a machine-learned forcefield

  • An MD without fixed charges, as with a machine-learned forcefield, stopped the step with an error. The conductivity needs only the ions’ net charges, so the ions are now found from, and carry, the formal charges of the structure. With no formal charges either, the step says so and skips the analysis.

2026.10.19 – Scaled ion charges

  • The ions of MD with scaled charges (LAMMPS’s ‘Scale the charges of ions by’, e.g. 0.8) were not recognized, since their charges are not integers. They are now found from their formal charges, and the Nernst-Einstein conductivity uses the charges the ions carried in the MD, like the Einstein-Helfand one, so that the ionicity compares like with like.

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.