Post-processing CONQUEST output


The utility PostProcessCQ allows users to post-process the output of a CONQUEST calculation, to produce structure files, densities of states, and charge density, band densities and STM images as CUBE files (which can be read by the freely available VESTA code).

There are a number of different analyses which can be performed: coordinate conversion (to formats which can be plotted); conversion of total charge density to CUBE file format; production of band-resolved (optionally k-point resolved) densities in CUBE file format; simple Tersoff-Hamann STM simulation; and calculation of densities of states, including projected DOS. You should ensure that all the files produced during the CONQUEST run are available for the post-processing (including eigenvalues.dat, chden.NNN, make_blk.dat or hilbert_make_blk.dat and ProcessNNNNNNNWF.dat and ProcessSijNNNNNNNWF.dat as applicable) as well as the input files.

Note that the utility reads the Conquest_input file, taking some flags from the CONQUEST run that generated the output, and some utility-specific flags that are detailed below.

Note also that projected DOS, band density and STM simulation are not at present compatible with multi-site support functions (MSSF), though we hope to implement this soon.

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Coordinate conversion

Set Process.Job coo to output a coordinate file for further processing or plotting. The utility will read the file specified by Process.Coordinates (which defaults to the file specified by IO.Coordinates). The output format is selected by specifying the Process.CoordFormat tag. The default output format is XYZ (which adds a .xyz suffix to the file name) using xyz. The CASTEP .cell output format can also be selected using cell. We plan to expand this conversion to other formats in the future.

Note that for a structural relaxation or molecular dynamics calculation, if you do not specify Process.Coordinates then the IO.Coordinates file, which will be converted, will be the input structure, not the output structure. Parameters that can be set are:

Process.Coordinates string (default: IO.Coordinates value)
Process.CoordFormat string (default: xyz; options: xyz, cell)

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Charge density

Setting Process.Job to cha, chg or den will convert the files chden.NNN which are written by CONQUEST to a cube file. The processing will use the files chden.NNN, Conquest_input and hilbert_make_blk.dat or raster_make_blk.dat. Parameters that can be set include:

Process.ChargeStub string (default: chden)

The ChargeStub simply defines the filename which will be read, and used for output.

Note that to output the chden.NNN files from CONQUEST, you must set the flag IO.DumpChargeDensity T in the CONQUEST run.

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Band density

Setting Process.Job to ban produces band densities from wave function coefficients output by CONQUEST. The CONQUEST run must have the following tags set:

IO.outputWF T

A set of bands whose coefficients are output are specified either with an energy range (the default is to produce all bands):

IO.WFRangeRelative T/F
IO.min_wf_E real (Ha)
IO.max_wf_E real (Ha)

or with a list of bands:

IO.maxnoWF n

%block WaveFunctionsOut
n entries, each a band number

The wavefunction range can be relative to the Fermi level (IO.WFRangeRelative T) otherwise it is absolute. Either of these will produce a file containing all eigenvalues at all k-points (eigenvalues.dat) and a series of files containing the wavefunction expansion coefficients for the selected bands (ProcessNNNNNNNWF.dat). These files are output as binary (unformatted) by default (this can be changed by setting IO.MatrixFile.BinaryFormat F before the CONQUEST run) and will be read using the same format (it is important to check this!).

From these wavefunction coefficient files, band densities can be produced in post-processing, using similar tags; either a range:

Process.min_wf_E real (Ha)
Process.max_wf_E real (Ha)
Process.WFRangeRelative T/F

or an explicit list of bands:

Process.noWF n

%block WaveFunctionsProcess
n entries, each a band number

Note that the bands to be processed must be a subset of the bands output by CONQUEST. The bands can be output summed over k-points, or at individual k-points, by setting Process.outputWF_by_kpoint to F or T respectively.

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Tersoff-Hamann STM simulation

Setting Process.Job ter will use a very simple Tersoff-Hamann approach to STM simulation, summing over band densities between the Fermi level and the bias voltage (this is often surprisingly accurate). The following parameters can be set:

STM.BiasVoltage    real (eV)
STM.FermiOffset    real (eV)
Process.MinZ       real (Bohr)
Process.MaxZ       real (Bohr)
Process.RootFile   string (default: STM)

The FermiOffset tag allows the user to shift the Fermi level (to simulate charging or an external field). The height of the simulation cell in which the STM image is calculated is set by the MinZ and MaxZ tags, and the filename by the RootFile tag.

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Density of states (DOS)

Setting Process.Job dos will produce a total density of states (DOS) for the system, using the eigenvalues output by CONQUEST. The following parameters can be set:

Process.min_DOS_E real    (Ha, default lowest eigenvalue)
Process.max_DOS_E real    (Ha, default highest eigenvalue)
Process.sigma_DOS real    (Ha, default 0.001)
Process.n_DOS     integer (default 1001)

The limits for the DOS are set by the first two parameters (note that CONQUEST will output all eigenvalues, so the limits on these are set by the eigenspectrum). The broadening applied to each state is set by sigma_DOS, while the number of bins is set by n_DOS. The integrated DOS is also calculated; the user can choose whether this is the total integrated DOS (i.e. from the lowest eigenvalue, regardless of the lower limit for DOS) or just the local integrated DOS (i.e. over the interval specified for the DOS) by setting Process.TotalIntegratedDOS to T or F, respectively.

We recommend that, for accurate DOS, CONQUEST should be run non-self-consistently with a very high k-point density, after reading in a well-converged input charge density: set minE.SelfConsistent F and General.LoadRho T (which will require that the converged charge density is written out by CONQUEST by setting IO.DumpChargeDensity T).

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Atom-projected DOS

Setting Process.Job pdos will produce a total density of states as above, as well as the density of states projected onto the individual atoms. Given support functions \(\phi_{i\alpha}(\mathbf{r})\) which are the basis functions of the Kohn-Sham eigenstates \(\psi_{n}(\mathbf{r}) = \sum_{i\alpha} c^{n}_{i\alpha}\phi_{i\alpha}(\mathbf{r})\), then the projection of a given state, \(n\), onto an atom \(i\) can be written as \(\sum_{\alpha j\beta} c^{n}_{i\alpha} S_{i\alpha,j\beta}c^{n\mathbf{k}}_{j\beta}\). The projected DOS is constructed using these projections.

If using pseudo-atomic orbitals (PAOs) as the basis set, then the atom-projected DOS can be further resolved by angular momentum (either just \(l\) or both \(l\) and \(m\)). If using pseudo-atomic orbitals (PAOs) with multi-site support functions or blip functions then it is not possible to decompose the DOS any further (in future, it may be possible to resolve the MSSF coefficients into the individual PAOs, and hence decompose pDOS by angular momentum). To output the necessary coefficients to produce atom-projected DOS, a CONQUEST run must be performed with the following parameters set:

IO.writeDOS T
IO.write_proj_DOS T

As for the DOS, very high Brillouin zone sampling is required for accurate projected DOS, which is most efficiently generated using a converged charge density and a non-self-consistent calculation with much higher k-point density. CONQUEST will produce the wavefunction files (ProcessNNNNNNNWF.dat and ProcessSijNNNNNNNWF.dat) as binary (unformatted) by default (change using the flag IO.MatrixFile.BinaryFormat F).

Once the files have been generated by CONQUEST, the output can be processed by setting the output tag:

Process.Job pdos

This is all that is needed for the simplest output. The number of bins and smearing of the peaks can be set using:

Process.sigma_DOS 0.002
Process.n_DOS 10001

To resolve the DOS by angular momentum as well as by atom, then the following flags can be set:

Process.pDOS_l_resolved T
Process.pDOS_lm_resolved T

Note that only one of these is needed, depending on what level of resolution is required. At present, angular momentum resolution is only available for the PAO basis set (not MSSF or blips) though it is under development for the MSSF basis (by projection onto the underlying PAO basis).

The energy range for the projected DOS can also be specified:

Process.min_DOS_E -0.35
Process.max_DOS_E  0.35
Process.WFRangeRelative T

where the final tag sets the minimum and maximum values relative to the Fermi level.

If you only want to produce pDOS for a few atoms, then you can set the variable Process.n_atoms_pDOS and list the atoms you want in the block pDOS_atoms:

Process.n_atoms_pDOS 2
%block pDOS_atoms

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Band structure

The band structure of a material can be generated by CONQUEST by performing a non-self-consistent calculation, after reading a well-converged charge density: set minE.SelfConsistent F and General.LoadRho T (remember that to write a converged charge density from CONQUEST you set IO.DumpChargeDensity T). The k-points required can be specified as lines of points in k-space; setting Diag.KspaceLines T enables this (replacing the usual MP mesh), while the number of lines (e.g. Gamma to L; L to X; would be two lines) is set with Diag.NumKptLines and the number of points along a line with Diag.NumKpts. The k-point lines themselves are set with a block labelled Diag.KpointLines which should have two entries (starting and finishing k-points) for each k-point line. (In constructing the k-point list, CONQUEST will automatically remove any duplicate points, so that the output can be plotted smoothly.) So to create a bandstructure from X-\(\Gamma\)-L-X (3 lines: X-\(\Gamma\); \(\Gamma\)-L; L-X) with 11 points in each line, you would use the following input:

Diag.KspaceLines T
Diag.NumKptLines 3
Diag.NumKpts 11
%block Diag.KpointLines
0.5 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.5 0.5 0.5
0.5 0.5 0.5
0.5 0.0 0.0

After running CONQUEST, setting Process.Job bst and running the post-processing will read the resulting eigenvalues.dat file, and produce a file BandStructure.dat. The x-axis will be the k-point index by default, but specifying Process.BandStrucAxis (taking value n for index, x, y or z for a single direction in k-space, or a to give all k-point coordinates) will allow you to control this. Limits on the energies to select the bands produced can be set with Process.min_DOS_E and Process.max_DOS_E.

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