External tools

Post-processing for charge density, band density, DOS, STM

The utility PostProcessCQ allows users to post-process the output of a CONQUEST calculation, to produce the charge density, band densities, DOS and STM images in useful forms. It is described fully here.

Molecular-dynamics analysis

The consolidated md_analysis.py utility is located in src/utilities. It can plot the thermodynamic statistics written by CONQUEST and analyse trajectories for radial distribution functions (RDFs), velocity autocorrelation functions (VACFs), mean-squared displacements (MSDs) and stress. It can also compare the statistics from several calculations and calculate heat-flux autocorrelation functions (HFACFs).

The utility requires Python 3, NumPy, SciPy and Matplotlib. Run it from the calculation directory, giving the path to the copy in the CONQUEST source tree, for example:

python3 /path/to/CONQUEST/src/utilities/md_analysis.py [options]

The utility reads Conquest_input and the coordinate file named there. By default, the MD data are read from md.stats, md.frames and, for an HFACF, md.heatflux. A different statistics or frames file can be selected with --stats FILE or --frames FILE. CONQUEST controls how often frames are written to md.frames with AtomMove.OutputFreq; statistics are written to md.stats at every MD step.

Plotting statistics

With no analysis option, the utility plots the energy contributions, conserved quantity, temperature and pressure from md.stats and writes stats.pdf. For an NPT calculation it also plots the volume. For example,

python3 /path/to/CONQUEST/src/utilities/md_analysis.py --skip 200

omits the first 200 MD steps from the plots. --equil N independently sets the initial part omitted when calculating averages, while --landscape uses a two-by-two plot layout.

Statistics from calculations in several directories can be compared with --compare. Supply the directories with --dirs and, optionally, one legend label per directory with --description:

python3 /path/to/CONQUEST/src/utilities/md_analysis.py \
    --compare --dirs dir1 dir2 \
    --description "first calculation" "second calculation"

Trajectory analysis

The options --rdf, --vacf, --msd and --stress select analyses of md.frames. --stride N uses every Nth frame, --skip N ignores the initial part of the trajectory and --stop N sets the final MD step to analyse. --dump writes the numerical data used for RDF, VACF and MSD plots in addition to the PDF output.

For example,

python3 /path/to/CONQUEST/src/utilities/md_analysis.py \
    --rdf --stride 20 --rdfcut 8.0 --rdfwidth 0.08 \
    --dump --skip 200 --stop 400

calculates an RDF with an 8 Angstrom cutoff and 0.08 Angstrom bin width, using every twentieth selected frame. The results are written to rdf.pdf and, because --dump is present, rdf.dat.

The VACF and MSD analyses similarly write vacf.pdf and msd.pdf, with vacf.dat and msd.dat requested by --dump. --stress writes stress.pdf; for an NPT trajectory the cell dimensions are plotted with the stress.

For heat-flux analysis, enable MD.HeatFlux in the CONQUEST calculation and use --hfacf --acfwindow T, where T is the autocorrelation-window length in femtoseconds. The utility reads md.heatflux and writes hfacf.pdf.

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Atomic Simulation Environment (ASE)

ASE is a set of Python tools for setting up, manipulating, running, visualizing and analyzing atomistic simulations. ASE contains a CONQUEST interface, also called Calculator so that it can be used to calculate energies, forces and stresses as inputs to other calculations such as Phonon or NEB that are not implemented in CONQUEST. ASE is a versatile tool to manage CONQUEST calculations without pain either:

in a direct way where pre-processing, calculation and post-processing are managed on-the-fly by ASE,
or in an indirect way where the calculation step is performed outside the workflow, ie. on a supercomputer.

The ASE repository containing the Conquest calculator can be found here. Detailed documentation on how to manage Conquest calculations with ASE is available here.

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