History#

2026.10.21 – Bugfix: an MD without fixed charges is skipped, not an error

  • For an MD without fixed charges, as with a machine-learned forcefield, the step stopped the job with an error, so the analyses after it never ran. It now says there is no dipole to analyze and skips the analysis.

2026.10.19 – Scaled ion charges

  • In MD with the charges of the ions scaled (LAMMPS’s ‘Scale the charges of ions by’, e.g. 0.8), the ions were taken for molecules with broken charges. They are now recognized as ions, and left out of the dipole as before.

2026.10.18 – Bugfix: fluids without partial charges are skipped

  • For a fluid whose molecules have no partial charges, such as argon, the step printed a dielectric constant of 1, a dipole of 0 and a Kirkwood factor of nan, with a warning about the electrostatics. It now says there is no dipole and skips the analysis, as Ionic Conductivity does without ions, and checking the flowchart warns of it once the atoms are typed.

2026.10.17.1 – Analyze MD run before the step; more results; labelled errors

  • 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.

  • New results: the mean dipole of a molecule, the Kirkwood factor g_K, and the mean dipole of the cell, which should be near zero; a statement that the formula assumes conducting (tin-foil) Ewald boundaries.

  • For an isotropic run ε is one value, with a check that the diagonal components agree; otherwise the components are given too.

2026.10.17 – First release: the static dielectric constant

  • The static dielectric constant of liquids, and of the solvent of electrolytes, from the fluctuations of the dipole of the cell in MD with fixed charges, with errors from independent runs or blocks, the running estimate and the correlation time of the dipole.

  • 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.