Spectroscopy and properties¶
Electronic structure of periodic systems¶
Periodic EffectiveMass Enabled Yes/No KPointCoord float_list NumAbove integer NumBelow integer StepSize float End BandStructure Automatic Yes/No DeltaK float Enabled Yes/No FatBands Yes/No UseSymmetry Yes/No End BZPath Path # Non-standard block. See details. ... End End DOS EMax float EMin float Enabled Yes/No NSteps integer End End
Type: Block Description: Block that sets various details of the calculation only relevant for periodic systems.
Type: Block Description: In a semi-conductor, the mobility of electrons and holes is related to the curvature of the bands at the top of the valence band and the bottom of the conduction band. With the effective mass option, this curvature is obtained by numerical differentiation. The estimation is done with the specified step size, and twice the specified step size, and both results are printed to give a hint on the accuracy. By far the most convenient way to use this key is without specifying any options.
Type: Bool Default value: No GUI name: Effective mass Description: In a semi-conductor, the mobility of electrons and holes is related to the curvature of the bands at the top of the valence band and the bottom of the conduction band. With the effective mass option, this curvature is obtained by numerical differentiation. The estimation is done with the specified step size, and twice the specified step size, and both results are printed to give a hint on the accuracy. By far the most convenient way to use this key is without specifying any options.
Type: Float List Unit: 1/Bohr Recurring: True GUI name: At K-point Description: Coordinate of the k-points for which you would like to compute the effective mass.
Type: Integer Default value: 1 GUI name: Include N bands above Description: Number of bands to take into account above the Fermi level.
Type: Integer Default value: 1 GUI name: Include N bands below Description: Number of bands to take into account below the Fermi level.
Type: Float Default value: 0.001 Description: Size of the step taken in reciprocal space to perform the numerical differentiation
Type: Block Description: Options for band structure plotting. This has no effect on the calculated energy. [Warning: The band structure is only computed in case of k-space sampling, i.e. it is not computed for Gamma-only calculations (see: Periodic%KSpace).]
Type: Bool Default value: Yes GUI name: Automatic generate path Description: Generate and use the standard path through the Brillouin zone. If not, use the user defined path (set via Custom path in the GUI, or with the Periodic%BZPath keyword in the run script).
Type: Float Default value: 0.1 Unit: 1/Bohr GUI name: Interpolation delta-K Description: Step size in reciprocal space for band structure interpolation. Using a smaller number will produce smoother band curves at an increased computational time.
Type: Bool Default value: Yes GUI name: Calculate band structure Description: Whether or not to calculate the band structure.
Type: Bool Default value: Yes GUI name: Calculate fatbands Description: Control the computation of the fat bands (only when the bandstructure is calculated). The fat bands are the periodic equivalent of the Mulliken population analysis. The definition of the fat bands can be found in the Band Documentation.
Type: Bool Default value: Yes Description: If set, only the irreducible wedge of the Wigner-Seitz cell is sampled. If not, the whole (inversion-unique) Wigner-Seitz cell is sampled.
Type: Block Description: If [BandStructure%Automatic] is disabled, DFTB will compute the band structure for the user-defined path in the [BZPath] block. You should define the vertices of your path in fractional coordinates (with respect to the reciprocal lattice vectors) in the [Path] sub-block. If you want to make a jump in your path, you need to specify a new [Path] sub-block.
Type: Non-standard block Recurring: True Description: A section of a k space path.
Type: Block Description: The subkeys of [DOS] allow to customize the calculation of the density of states.
Type: Float Default value: 0.75 Unit: Hartree Description: Upper end of the energy interval in which the density of states is calculated.
Type: Float Default value: -0.75 Unit: Hartree Description: Lower end of the energy interval in which the density of states is calculated.
Type: Bool Default value: Yes GUI name: Calculate DOS Description: Whether or not to calculate the DOS. Note that the DOS will always be calculated when also the band structure is calculated.
Type: Integer Default value: 300 Description: The number of energy intervals between [EMin] and [EMax] for which the density of states is calculated.
Excited states with time-dependent DFTB¶
DFTB allows for excited state calculations on molecular systems by means of single orbital transitions as well as time-dependent DFTB as published by Niehaus et al. in Phys. Rev. B 63, 085108 (2001). Singlet-singlet as well as singlet-triplet excitations can be calculated. DFTB also supports the calculation of excited state gradients, which allows geometry optimizations and vibrational frequency calculations for excited states.
The TD-DFTB implementation uses the PRIMME library (PReconditioned Iterative MultiMethod Eigensolver) by Andreas Stathopoulos and James R. McCombs, PRIMME: PReconditioned Iterative MultiMethod Eigensolver: Methods and software description ACM Transaction on Mathematical Software Vol. 37, No. 2, (2010), 21:1–21:30.
DFTB excited state calculations are controlled by the following keywords:
Properties Excitations SingleOrbTrans Enabled Yes/No Filter OSMin float dEMax float dEMin float End PrintLowest integer End TDDFTB Calc [None | Singlet | Triplet] DavidsonConfig ATCharges [Precalc | OnTheFly] SafetyMargin integer Tolerance float End Diagonalization [Auto | Davidson | Exact] Lowest integer Print string ScaleKernel float UpTo float End TDDFTBGradients Eigenfollow Yes/No Excitation integer_list End End End
Type: Block Description: DFTB can calculate various properties of the simulated system. This block configures which properties will be calculated.
Type: Block Description: Contains all options related to the calculation of excited states, either as simple single orbitals transitions or from a TD-DFTB calculation.
Type: Block Description: The simplest approximation to the true excitations are the single orbital transitions (sometimes called Kohn-Sham transitions), that is transitions where a single electron is excited from an occupied Kohn-Sham orbital into a virtual orbital. The calculation of these transitions is configured in this section. Note that the SingleOrbTrans section is optional even though the single orbital transitions are also needed for TD-DFTB calculations. If the section is not present all single orbital transitions will still be calculated and used in a subsequent TD-DFTB calculation, but no output will be produced.
Type: Bool Default value: No GUI name: Single orbital transisitions: Calculate Description: Calculate the single orbital transitions.
Type: Block Description: This section allows to remove single orbital transitions based on certain criteria. All filters are disabled by default.
Type: Float GUI name: Minimum oscillator strength Description: Removes single orbital transitions with an oscillator strength smaller than this threshold. A typical value to start (if used at all) would be 1.0e-3.
Type: Float Unit: Hartree Description: Removes single orbital transitions with an orbital energy difference larger than this threshold.
Type: Float Unit: Hartree Description: Removes single orbital transitions with an orbital energy difference smaller than this threshold.
Type: Integer Default value: 10 Description: The number of single orbital transitions that are printed to the screen and written to disk. If not a TD-DFTB calculation, the default is to print the 10 lowest single orbital transitions. In case of a TD-DFTB calculation it is assumed that the single orbital transitions are only used as an input for TD-DFTB and nothing will be printed unless PrintLowest is specified explicitly.
Type: Block Description: Calculations with time-dependent DFTB can be configured in the TDDFTB section and should in general give better results than the raw single orbital transitions. TD-DFTB calculates the excitations in the basis of the single orbital transitions, whose calculation is configured in the SingleOrbTrans section. Using a filter in SingleOrbTrans can therefore be used to reduce the size of the basis for TD-DFTB. One possible application of this is to accelerate the calculation of electronic absorption spectra by removing single orbital transitions with small oscillator strengths from the basis. Note that the entire TDDFTB section is optional. If no TDDFTB section is found, the behavior depends on the existence of the SingleOrbTrans section: If no SingleOrbTrans section is found (the Excitations section is completely empty then) a TD-DFTB calculation with default parameters will be performed. If only the SingleOrbTrans section is present no TD-DFTB calculation will be done.
Type: Multiple Choice Default value: None Options: [None, Singlet, Triplet] GUI name: Type of excitations Description: Specifies the multiplicity of the excitations to be calculated.
Type: Block Description: This section contains a number of keywords that can be used to override various internals of the Davidson eigensolver. The default values should generally be fine.
Type: Multiple Choice Default value: Precalc Options: [Precalc, OnTheFly] GUI name: Transition charges Description: Select whether the atomic transition charges are precalculated in advance or reevaluated during the iterations of the Davidson solver. Precalculating the charges will improve the performance, but requires additional storage. The default is to precalculate the atomic transition charges, but the precalculation may be disabled if not not enough memory is available.
Type: Integer Default value: 4 Description: The number of eigenvectors the Davidson method will calculate in addition to the ones requested by the user. With the Davidson eigensolver it is generally a good idea to calculate a few more eigenvectors than needed, as depending on the initial guess for the eigenvectors it can happen that the found ones are not exactly the lowest ones. This problem is especially prominent if one wants to calculate only a small number of excitations for a symmetric molecule, where the initial guesses for the eigenvectors might have the wrong symmetry. Note that the additionally calculated excitations will neither be written to the result file nor be visible in the output.
Type: Float Default value: 1e-09 Description: Convergence criterion for the norm of the residual.
Type: Multiple Choice Default value: Auto Options: [Auto, Davidson, Exact] GUI name: Method Description: Select the method used to solve the TD-DFTB eigenvalue equation. The most straightforward procedure is a direct diagonalization of the matrix from which the excitation energies and oscillator strengths are obtained. Since the matrix grows quickly with system size (number of used single orbital transitions squared), this option is possible only for small molecules. The alternative is the iterative Davidson method, which finds a few of the lowest excitations within an error tolerance without ever storing the full matrix. The default is to make this decision automatically based on the system size and the requested number of excitations.
Type: Integer Default value: 10 GUI name: Number of excitations Description: Specifies the number of excitations that are calculated. Note that in case of the exact diagonalization all excitations are calculated, but only the lowest ones are printed to screen and written to the output file. Also note that if limited both by number and by energy, (lowest and upto), DFTB will always use whatever results in the smaller number of calculated excitations. Type: String Description: Specifies whether to print details on the contribution of the individual single orbital transitions to the calculated excitations.
Type: Float Default value: 1.0 Unit: None Description: Set the scaling parameter of the response kernel. A scaling approach can be used to identify plasmons in molecules. While single-particle excitations are only slightly affected by scaling of the response kernel, plasmonic excitations are sensitive to variations in the scaling parameter. Default no scaling is used (scaling parameter = 1.0)
Type: Float Unit: Hartree GUI name: Excitations up to Description: Set the maximum excitation energy. Attempts to calculate all excitations up to a given energy by calculating a number of excitations equal to the number of single orbital transitions in this window. This is only approximately correct, so one should always add some safety margin. Note that if limited both by number and by energy, (lowest and upto), DFTB will always use whatever results in the smaller number of calculated excitations.
Type: Block Description: This block configures the calculation of analytical gradients for the TD-DFTB excitation energies, which allows the optimization of excited state geometries and the calculation of vibrational frequencies in excited states (see J. Comput. Chem., 28: 2589-2601). If the gradients are calculated, they will automatically be used for geometry optimizations or vibrational frequency calculations, if the corresponding Task is selected and only 1 excitation is selected. Vibrationally resolved UV/Vis spectroscopy (Franck-Condon Factors) can be calculated in combination with the FCF program or using the Vibrational Analysis Tools in AMS. See the ADF documentation on Vibrationally resolved electronic spectra or the AMS documentation for the Vibrational Analysis Tools.
Type: Bool Default value: No GUI name: Follow initial excitation Description: If this option is set, DFTB uses the transition density in atomic orbital basis to follow the initially selected excited state during a geometry optimization. This is useful if excited state potential energy surfaces cross each other and you want to follow the surface you started on.
Type: Integer List GUI name: Excitation number Description: Select which excited states to calculate the gradients for. Gradients can only be calculated for an excited states that has been calculated using TD-DFTB. Make sure that enough excitations are calculated.
Excited state gradients¶
Excited state gradients can be calculated with TD-DFTB, see the section Excited states with time-dependent DFTB.
Frequencies, phonons, VCD¶
Frequencies, phonons, and VCD and can be computed via numerical differentiation by the AMS driver. Several thermodynamic properties, such as zero-point energy, internal energy, entropy, free energy and specific heat are computed by default when calculating phonons.
Vibrationally resolved electronic spectra¶
Stress tensor, Elasticity¶
The stress tensor and elastic tensor (and related elastic properties such as bulk modulus, shear modulus and young modulus) can be computed via numerical differentiation by AMS.
Charges, Bond Orders, Dipole Moment, Polarizability¶
Charges, Mayer bond orders, Dipole Moment, and Polarizability can be requested to the DFTB engine in the AMS driver’s input:
Fragment orbital analysis¶
The fragment orbital analysis is not available for periodic systems calculated with multiple K-points.
A Mulliken population analysis based on the elementary atomic basis functions can be calculated with
Properties Fragments End End
For an atomic Mulliken population one should not specify any subkey
File in Properties%Fragments.
A Mulliken population analysis based on orbitals coming from larger fragments, that may consist of more than 1 atom, can be calculated if one includes the binary dftb.rkf result files of the calculated fragments in the input, for example, like:
Properties Fragments File frag1.results/dftb.rkf File frag2.results/dftb.rkf End End
Note that the nuclear coordinates of the atoms in the fragments should be at the exact same position as in the whole system. In addition, each atom of the whole system should be present exactly once in one of the fragment dftb.rkf files.
Properties Fragments Analysis Yes/No EMax float Emin float File string TIDegeneracyThreshold float TransferIntegrals Yes/No End End
Type: Block Description: Fragment files
Type: Bool Default value: Yes GUI name: Fragment analysis Description: Mulliken population analysis in terms of fragment orbitals.
Type: Float Default value: 0.25 Unit: Hartree Description: Upper end of the energy interval for which the orbitals are analyzed.
Type: Float Default value: -0.75 Unit: Hartree Description: Lower end of the energy interval for which the orbitals are analyzed.
Type: String Recurring: True Description: Path (either absolute or relative) of fragment file
Type: Float Default value: 0.1 Unit: eV Description: If the orbital energy of the fragment MO is within this threshold with fragment HOMO or LUMO energy, then this fragment MO is included in the calculation of the transfer integrals. Relevant in case there is (near) degeneracy.
Type: Bool Default value: No GUI name: Charge transfer integrals Description: Calculate the charge transfer integrals, spatial overlap integrals and site energies. Charge transfer integrals can be used in models that calculate transport properties.
An input for the GENNBO program of Prof. Weinholds Natural Bond Orbital (NBO) package, by E. Glendening et al. can be made, using the key Properties%NBOInput. Not available for periodic systems.
Properties NBOInput Yes/No End
Type: Bool Default value: No Description: Whether or not an input file for the NBO program is written to disk as nboInput.FILE47. The input file follows the FILE47 format as described in the NBO6 manual available on nbo6.chem.wisc.edu. By default, only the calculation of the natural bond orbitals and the natural localized molecular orbitals is enabled, but the nboInput.FILE47 file can be edited by hand to enable other analysis models. Please refer to the NBO6 manual for details.
The GENNBO executable is included in the AMS distribution. The GENNBO program can be called with:
#!/bin/sh $AMSBIN/gennbo6 ams.results/dftb-nboInput.FILE47