Single-point calculation

In this type of project, it is calculated the wave function and charge density, and hence the energy, of the particular arrangement of nuclei defined by the atomistic model.

We refer the user to section Structure Modeling in ASAP for further information on ASAP structure builder/viewer interface.

ASAP sets single-point calculation as the default project type.

Click on the Parameters icon to open the Single-point Parameter widget,

Please refet to the Variables section to know how to edit Atomic positions, Magnetic moments, Atomic masses and Velocities in ASAP.

When Single-point calculation is selected the user can decide to compute additional properties, please refer to the section Properties for a detailed explanation.

Click on the Calculator icon to select the computational engine to be used during the single point calculation.

We refer the user to chapter Calculators for further information on ASAP available calculators.

Click on the Run icon to open Run widget. Then click on the Run button to start the the single-point calculation.

We refer the user to chapter Configure ASAP runners for further information on computational resources configuration in ASAP.

After submitting a single-point calculation, the complete calculation output in real-time is shown in the Run widget.

Analysis

The information provided by the analysis widget also depends on the properties that were selected on the Parameters widget, see section Properties.

When the calculation is completed, press the Exit and analyse button to open the single-point analysis widget.

The following information extracted from the single-point calculation output is available:

Input

It shows the complete input file of the single-point calculation. This option is only available for SIESTA calculator.

Output

It shows the complete output file of the single-point calculation.

Energies

It shows the information on: Total energy, Fermi energy minimum, maximum and frontier orbital energies HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital). As well as energy gap and Eigenvalue energies.

Density of States

Density Of States describes the number of states per interval of energy, at each energy level, that are available to be occupied.

Check the SCF DOS tick box to visualise the density of states of the system originated from the single-particle (Kohn-Sham) eigenvalues computed during self-consistent field loop.

You can adjust the energy range (x-axis) by tuning the minimum and maximum energies (in eV) shown at the top of the figure.

You can also tune the following parameters:

• Smearing. Gaussian or Lorentzian representations of the Dirac delta function.

• Full width at half maximum (FWHM) The broadening is defined by the full-width-at-half-maximum in both representations (Gaussian and Lorentzian) of the Dirac delta function.

• Zero @ Fermi. Sets the origin of the DOS function at Fermi level.

  

Right-click on the density of states figure to make available the following options:

• Save figure as…. We support the following formats: pdf, png, jpg, jpeg, ps, eps, and svg.

• Open in Matplotlib… Open with Matplotlib the python script used to plot the figure.

• Save a Matplotlib script as… Save the python script used to plot the figure.

• Export data… Export the data from the density of states figure to a text file format.

Check the Post-SCF-DOS tick box to visualize the density of states computed after a self-consistent field loop with a custom BZ sampling.

You can adjust the energy range (x-axis) by tuning the minimum and maximum energies shown at the top of the widget, in units of eV, meV, kcal/mol, kJ/mol, Ha, mHa, Ry and mRy.

Check the Zero @ Fermi level tick box to set the origin of the post-SCF DOS function at the Fermi energy level.

The electronic band structure of a solid describes the range of energies that an electron within the solid may have (energy bands) and the ranges of energies it may not have (band gaps). Check the Band structure tick box to visualise the corresponding graph. Please note that this option is only available for infinite-sized systems.

Notice that you can adjust the band structure energy range (y-axis) by tuning the minimum and maximum energies shown at the top of the figure, in units of eV, meV, kcal/mol, kJ/mol, Ha, mHa, Ry and mRy.

Check the Zero @ Fermi level tick box to center the DOS at the Fermi energy level.

Right-click on the band structure figure to make available the following options:

• Save figure as…. We support the following formats: pdf, png, jpg, jpeg, ps, eps and svg.

• Open in Matplotlib…. Matplolib library allows the user an interactive visualisation of the figure (scale axis, zoom on speci1c X and Y values…).

• Save a Matplotlib script as…. Save the Matplotlib script used to plot the figure.

• Export band structure to JSON…

• Export band structure to .bands…

• Export DOS…. Export the data from the band structure figure to a text file format.

Partial DOS

Check the PDOS option to visualise the partial density of states of the system.

To visualise the projected DOS on specific atoms, select them by their chemical species or choose a range of atom indices.

You can also select the angular momenta of the atomic orbitals that will be included in the PDOS visualisation.

You can change the label at your convenience. Press the Add curve button to incorporate each of your selections.

You can change units on the top right side of the widget. The options are eV, meV, kcal/mol, kJ/mol, Ry, mRy, Ha and mHa.

You can adjust the energy range (x-axis) by tuning the minimum and maximum energies shown at the top of the figure.

Click on the Zero at Fermi level check box to center DOS at the fermi level.

You can change the colors of the curves by tuning the value on the Color column in the table on the bottom left of the widget. Please note that you must use Hexadecimal code.

Additionally, you can change the style of the lines by tuning the value on the column Style on the bottom left of the widget. Supported values are ‘-’, ‘–’, ‘-.’, ‘:’, ‘None’, ‘ ‘ , , ‘solid’, ‘dashed’, ‘dashdot’, ‘dotted’.

Charge

Option only available if at least one Charge Analysis method has been selected.

Click on the Charge Analysis… button to visualise the atomic charge.

You can visualise the charge of each atom of the project calculated by the selected methods. These charges are given in units of electrons.

Bader analysis

When the project is successfully completed, click the Exit & analyse button.

Then select Bader analysis in the Analysis widget.

Click the View in 3D button to view the structure in the advanced 3D viewer. You can see the equipotential surface induced by the charge distribution for a determined isovalue. See section Advanced 3D viewer for further information on the 3D advanced viewer.

In the previous figure you can see the structure of the project in 3D and the Bader charge isosurface.

Press the Export to cube button to export the volumetric data of the Bader analysis to a cube file.

Electrostatic potential

When the calculation is completed, select Exit and analyse… to open the analysis widget.

Check the tick-box Potential to visualise the electrostatic potential as a function of the distance. By default, the widget shows the average electrostatic potential (in eV units) in cross-section (z direction in Å).

The planar averaged electrostatic potential (\(V(z)\)) is calculated across the system as:

\[V(z)=1/S_{xy}\int \int V(x, y, z) dx dy,\]

where \(S_{xy}\) is the cross-section of the system.

In this example, we have computed the electrostatic potential for the frozen bulk geometry of freestanding PbZrTiO\(_3\)(001). It presents a tetragonal phase characterised by alternating columnar arrangement of Ti and Zr cations along the polar axis, \(z\).

The planar averaged of the electrostatic potential (red curve in the figure above) exhibits fast oscillations correlated with the atomic arrangement in the material. (Massimiliano Stengel and Nicola A. Spaldin, Phys. Rev. B 75, 20512, 2007). On the other hand, you can observe that the potential is flat at the vacuum region (0-18 Å  and 34 to 50 Å).

The potential drop observed at 0 Å  is due to the fact that “Slab.DipoleCorrection True” was requested to compensate for the electric field across the whole system.

Check the tick-box Macroaverage to visualise the macroscopically averaged potential. It is a convenient approach to evaluate information related to the variation of the electrostatic potential but discarding its fast oscillation related to atomic arrangement. (Massimiliano Stengel and Nicola A. Spaldin, Phys. Rev. B 75, 20512, 2007)

When Macroaverage is activated, you can modify two related parameters: the Length for averaging (in Units of Å, Bohr or nm) and the damping (dimensionless). The damping factor controls the local oscillations. The selection of a damping factor that is close to the lattice parameter smoothens local oscillations and makes the slope of the electrostatic potential easier to analyse.

You can also tune the following settings in the analysis widget:

• Axis: The axis (X, Y or Z) in which the electrostatic potential is evaluated.

• Potential: The units of the electrostatic potential: eV, meV, Rydberg or Hartree.

• Range: The range used as the x-axis. The units can be Å, Bohr and nm.

In this second example, we have computed the electrostatic potential of the tetracyanoquinodimethane molecule (TCNQ). TCNQ has a planar structure that consists of a central quinoid ring (C6H4) and four cyano groups (CN) attached to the corners.

The planar averaged of the electrostatic potential (red curve in the figure above) exhibits the variation of the electrostatic potential along the X axis correlated with the atomic arrangement in the material.

The analysis widget also offers the possibility of visualising the electrostatic potential by selecting View in 3D.

The cyano groups draw electron density away from the quinoid ring. Consequently it becomes electron-defficient, leading to a negative electrostatic potential around the carbon atoms of the ring.

On the other hand, nitrogen atoms in the cyano groups are electron-rich since they have they have lone pairs of electrons that are not shared with other atoms in the molecule. As a consecuence, the regions around the nitrogen atoms present positive electrostatic potential, approximately in [0,5.4] Ang and [14.5,20] Ang intervals.

Press the Export to cube button to export the volumetric data of the computed electrostatic potential to a cube file.