Qmd Plmd

Workflow Map

Summarize recalculation ranges for one ZONE

• ZONE_recal_plumed_info.sh is the main helper.
• Run it from a ZONE directory.
• It scans */pre/recal/*/OUTCAR, extracts the last TOTEN, first cell volume, target temperature, and external pressure, then writes a plumed.info summary file.
• This is the script to use when CV or bias ranges need to reflect the recalculation data inside one zone.

Summarize a flat recal directory

• recal_plumed_info.sh is the simpler sibling for flatter layouts where recalculation folders are numeric children of the current directory.
• It writes the same kind of plumed.info, but assumes a simpler directory structure.

Plot COLVAR

• plot_plmd_COLVAR.py is the current general-purpose plotter.
• It strips the #! FIELDS header into a temporary COLVAR.plot, reads the result with pandas, and plots the first N variables after time or all variables if -n 0 is given.
• It also applies percentile-based y-limits to avoid single outliers destroying the plot scale.

Plot older special-case COLVAR channels

• plot_plmd__XRD_V_E_vs_t.py is an older, narrower plotter that expects specific columns such as xrd, vol, and energy.
• Use it only when the local COLVAR file really follows that schema.

Practical Guidance

• These scripts are tightly tied to VASP-style recalculation folders and OUTCAR parsing, not generic PLUMED-only trajectories.
• Numeric child-folder assumptions are common; preserve them unless you are intentionally broadening the scripts.
• For ALCHEMY tasks, use this folder for post-processing and use qmd/ALCHEMY plus ALCHEMY__dev for setup-generation logic.
• For official PLUMED syntax and COLVAR semantics, read references/external_docs.md.