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

Several scripts that may be helpful with postprocessing molecular dynamics are included with CONQUEST. The can be found in the tools directory, and the executables are plot_stats.py, md_analysis.py and heat_flux.py. They have the following dependencies:

  • Python 3

  • Scipy/Numpy

  • Matplotlib

If Python 3 is installed the modules can be added easily using pip3 install scipy etc.

These scripts should be run in the calculation directory, and will automatically parse the necessary files, namely Conquest_input, input.log, md.stats and md.frames assuming they have the default names. They will also read the CONQUEST input flags to determine, for example, what ensemble is used, and process the results accordingly.

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Plotting statistics

usage: plot_stats.py [-h] [-c] [-d DIRS [DIRS ...]]
                    [--description DESC [DESC ...]] [--skip NSKIP]
                    [--stop NSTOP] [--equil NEQUIL] [--landscape]
                    [--mser MSER_VAR]

Plot statistics for a CONQUEST MD trajectory

optional arguments:
  -h, --help            show this help message and exit
  -c, --compare         Compare statistics of trajectories in directories
                        specified by -d (default: False)
  -d DIRS [DIRS ...], --dirs DIRS [DIRS ...]
                        Directories to compare (default: .)
  --description DESC [DESC ...]
                        Description of graph for legend (only if using
                        --compare) (default: )
  --skip NSKIP          Number of equilibration steps to skip (default: 0)
  --stop NSTOP          Number of last frame in analysis (default: -1)
  --equil NEQUIL        Number of equilibration steps (default: 0)
  --landscape           Generate plot with landscape orientation (default:
  --mser MSER_VAR       Compute MSER for the given property (default: None)

Running plot_stats.py --skip 200 in your calculation will generate a plot which should resemble the example below, skipping the first 200 steps. This example is a molecular dynamics simulation of 1000 atoms of bulk silicon in the NPT ensemble, at 300 K and 0.1 GPa.


The four plots are respectively the breakdown of energy contributions, the conserved quantity, the temperature and the pressure, the last of which is only included for NPT molecular dynamics. Several calculations in different directories can be compared using plot_stats.py --compare -d dir1 dir2 --description "dir1 description" "dir2 description". The following example compares the effect of changing the L tolerance in the above simulation. Note that the contents of the description field will be in the legend of the plot.


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MD analysis

usage: md_analysis.py [-h] [-d DIRS [DIRS ...]] [--skip NSKIP]
                      [--stride STRIDE] [--snap SNAP] [--stop NSTOP]
                      [--equil NEQUIL] [--vacf] [--msd] [--rdf] [--stress]
                      [--nbins NBINS] [--rdfwidth RDFWIDTH] [--rdfcut RDFCUT]
                      [--window WINDOW] [--fitstart FITSTART] [--dump]

Analyse a CONQUEST MD trajectory

optional arguments:
  -h, --help            show this help message and exit
  -d DIRS [DIRS ...], --dirs DIRS [DIRS ...]
                        Directories to compare (default: .)
  --skip NSKIP          Number of equilibration steps to skip (default: 0)
  --stride STRIDE       Only analyse every nth step of frames file (default:
  --snap SNAP           Analyse Frame of a single snapshot (default: -1)
  --stop NSTOP          Number of last frame in analysis (default: -1)
  --equil NEQUIL        Number of equilibration steps (default: 0)
  --vacf                Plot velocity autocorrelation function (default:
  --msd                 Plot mean squared deviation (default: False)
  --rdf                 Plot radial distribution function (default: False)
  --stress              Plot stress (default: False)
  --nbins NBINS         Number of histogram bins (default: 100)
  --rdfwidth RDFWIDTH   RDF histogram bin width (A) (default: 0.05)
  --rdfcut RDFCUT       Distance cutoff for RDF in Angstrom (default: 8.0)
  --window WINDOW       Window for autocorrelation functions in fs (default:
  --fitstart FITSTART   Start time for curve fit (default: -1.0)
  --dump                Dump secondary data used to generate plots (default:

The script md_analysis.py script performs various analyses of the trajectory by parsing the md.frames` file. So far, these include the radial distribution function, the velocity autocorrelation function, the mean squared deviation, and plotting the stress. For example, the command,

md_analysis.py --rdf --stride 20 --rdfcut 8.0 --nbins 100 --dump --skip 200 --stop 400

computes the radial distribution function of the simulation in the first example from every 20th time step (every 10 fs in this case), stopping after 400 steps, with a cutoff of 8.0 A, and the histogram is divided into 100 bins.


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CONQUEST structure file analysis

usage: structure.py [-h] [-i INFILE] [--bonds] [--density] [--nbins NBINS]
                    [-c CUTOFF [CUTOFF ...]] [--printall]

Analyse a CONQUEST-formatted structure

optional arguments:
  -h, --help            show this help message and exit
  -i INFILE, --infile INFILE
                        CONQUEST format structure file (default:
  --bonds               Compute average and minimum bond lengths (default:
  --density             Compute density (default: False)
  --nbins NBINS         Number of histogram bins (default: 100)
  -c CUTOFF [CUTOFF ...], --cutoff CUTOFF [CUTOFF ...]
                        Bond length cutoff matrix (upper triangular part, in
                        rows (default: None)
  --printall            Print all bond lengths (default: False)

The script structure.py can be used to analyse a CONQUEST-formatted structure file. This is useful to sanity-check the bond lengths or density, since an unphysical structure is so often the cause of a crash. For example, the bond lengths can be computed with

structure.py --bonds -c 2.0 3.0 3.0

where the -c flag specifies the bond cutoffs for the bonds 1-1, 1-2 and 2-2, where 1 is species 1 as specified in Conquest_input and 2 is species 2. The output will look something like this:

Mean bond lengths:
O-Si:   1.6535 +/-   0.0041 (24 bonds)
Minimum bond lengths:
O-Si:   1.6493

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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 versatil 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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