KF output files¶
Accessing KF files¶
KF files are Direct Access binary files. KF stands for Keyed File: KF files are keyword oriented, which makes them easy to process by simple procedures. Internally all the data on KF files is organized into sections containing variables, so each datum on the file can be identified by the combination of section and variable.
All KF files can be opened using the KFbrowser GUI program:
$AMSBIN/kfbrowser path/to/ams.rkf
By default KFbrowser shows a just a curated summary of the results on the file, but you can make it show the raw section and variable structure by switching it to expert mode. To do this, click on File → Expert Mode or press ctrl/cmd + e.
KF files can be opened and read with Command line tools.
For working with the data from KF files, it is often useful to be able to read them from Python. Using the AMS Python Stack, this can easily be done with the AKFReader class:
>>> from scm.akfreader import AKFReader
>>> kf = AKFReader("path/to/ams.rkf")
>>> "Molecule%Coords" in kf
True
>>> kf.description("Molecule%Coords")
{
'_type': 'float_array',
'_shape': [3, 'nAtoms'],
'_comment': 'Coordinates of the nuclei (x,y,z)',
'_unit': 'Bohr'
}
>>> kf.read("Molecule%Coords")
array([[-11.7770694 , -4.19739597, 0.04934546],
[ -9.37471321, -2.63234227, -0.13448698],
...
[ 10.09508738, -1.06191208, 1.45286913],
[ 10.11689333, -1.5080196 , -1.87916127]])
Tip
For a full overview of the available methods in AKFReader, see the AKFReader API documentation.
Sections and variables on dftb.rkf¶
- AMSResults
Section content: Generic results of the DFTB evaluation.
AMSResults%AAT_Transpose- Type:
float_array
- Description:
VCD atomic axial tensors (AATs).
- Shape:
[3, 3, Molecule%nAtoms]
AMSResults%BondInfo- Type:
subsection
- Description:
FIXME: this section should include the file shared/ArchivedBondInfo.json, but there is a problem: the variable ‘BondInfo.LatticeDisplacements@dim’ is longer than 32 characters (the KF limit) and this messes up things. For now I’ll just ignore all the variables in here…
AMSResults%Bonds- Type:
subsection
- Description:
Bond info
AMSResults%Bonds%Atoms- Type:
archived_int_array
- Description:
?
AMSResults%Bonds%CellShifts- Type:
archived_int_array
- Description:
?
AMSResults%Bonds%description- Type:
string
- Description:
A string containing a description of how the bond orders were calculated / where they come from
AMSResults%Bonds%hasCellShifts- Type:
bool
- Description:
Whether there are cell shifts (relevant only in case of periodic boundary conditions)
AMSResults%Bonds%Index- Type:
archived_int_array
- Description:
index(i) points to the first element of Atoms, Orders, and CellShifts belonging to bonds from atom ‘i’. Index(1) is always 1, Index(nAtoms+1) is always nBonds + 1
AMSResults%Bonds%Orders- Type:
archived_float_array
- Description:
The bond orders.
AMSResults%BulkModulus- Type:
float
- Description:
The Bulk modulus (conversion factor from hartree/bohr^3 to GPa: 29421.026)
- Unit:
hartree/bohr^3
AMSResults%Charges- Type:
float_array
- Description:
Net atomic charges as computed by the engine (for example, the Charges for a water molecule might be [-0.6, 0.3, 0.3]). The method used to compute these atomic charges depends on the engine.
- Unit:
e
- Shape:
[Molecule%nAtoms]
AMSResults%DipoleGradients- Type:
float_array
- Description:
Derivative of the dipole moment with respect to nuclear displacements.
- Shape:
[3, 3, Molecule%nAtoms]
AMSResults%DipoleMoment- Type:
float_array
- Description:
Dipole moment vector (x,y,z)
- Unit:
e*bohr
- Shape:
[3]
AMSResults%ElasticTensor- Type:
float_array
- Description:
The elastic tensor in Voigt notation (6x6 matrix for 3D periodic systems, 3x3 matrix for 2D periodic systems, 1x1 matrix for 1D periodic systems).
- Unit:
hartree/bohr^nLatticeVectors
- Shape:
[:, :]
AMSResults%Energy- Type:
float
- Description:
The energy computed by the engine.
- Unit:
hartree
AMSResults%fractionalOccupation- Type:
bool
- Description:
Whether of not we have fractionally occupied orbitals (i.e. not all occupations are integer numbers).
AMSResults%Gradients- Type:
float_array
- Description:
The nuclear gradients.
- Unit:
hartree/bohr
- Shape:
[3, Molecule%nAtoms]
AMSResults%Hessian- Type:
float_array
- Description:
The Hessian matrix
- Unit:
hartree/bohr^2
- Shape:
[3*Molecule%nAtoms, 3*Molecule%nAtoms]
AMSResults%HOMOEnergy- Type:
float_array
- Description:
Molecular Orbital Info: energy of the HOMO.
- Unit:
hartree
- Shape:
[nSpin]
AMSResults%HOMOIndex- Type:
int_array
- Description:
Molecular Orbital Info: index in the arrays orbitalEnergies and orbitalOccupations corresponding to the HOMO.
- Shape:
[nSpin]
AMSResults%HOMOLUMOGap- Type:
float_array
- Description:
Molecular Orbital Info: HOMO-LUMO gap per spin.
- Unit:
hartree
- Shape:
[nSpin]
AMSResults%LUMOEnergy- Type:
float_array
- Description:
Molecular Orbital Info: energy of the LUMO.
- Unit:
hartree
- Shape:
[nSpin]
AMSResults%LUMOIndex- Type:
int_array
- Description:
Molecular Orbital Info: index in the arrays orbitalEnergies and orbitalOccupations corresponding to the LUMO.
- Shape:
[nSpin]
AMSResults%Molecules- Type:
subsection
- Description:
Molecules
AMSResults%Molecules%AtCount- Type:
archived_int_array
- Description:
shape=(nMolType), Summary: number of atoms per formula.
AMSResults%Molecules%Atoms- Type:
archived_int_array
- Description:
shape=(nAtoms), atoms(index(i):index(i+1)-1) = atom indices of molecule i
AMSResults%Molecules%Count- Type:
archived_int_array
- Description:
Mol count per formula.
AMSResults%Molecules%Formulas- Type:
string
- Description:
Summary: unique molecule formulas
AMSResults%Molecules%Index- Type:
archived_int_array
- Description:
shape=(nMol+1), index(i) = index of the first atom of molecule i in array atoms(:)
AMSResults%Molecules%Type- Type:
archived_int_array
- Description:
shape=(nMol), type of the molecule, reference to the summary arrays below
AMSResults%nOrbitals- Type:
int
- Description:
Molecular Orbital Info: number of orbitals.
AMSResults%nSpin- Type:
int
- Description:
Molecular Orbital Info: number spins (1: spin-restricted or spin-orbit coupling, 2: spin unrestricted).
AMSResults%orbitalEnergies- Type:
float_array
- Description:
Molecular Orbital Info: the orbital energies.
- Unit:
hartree
- Shape:
[nOrbitals, nSpin]
AMSResults%orbitalOccupations- Type:
float_array
- Description:
Molecular Orbital Info: the orbital occupation numbers. For spin restricted calculations, the value will be between 0 and 2. For spin unrestricted or spin-orbit coupling the values will be between 0 and 1.
- Shape:
[nOrbitals, nSpin]
AMSResults%PESPointCharacter- Type:
string
- Description:
The character of a PES point.
- Possible values:
[‘local minimum’, ‘transition state’, ‘stationary point with >1 negative frequencies’, ‘non-stationary point’]
AMSResults%PoissonRatio- Type:
float
- Description:
The Poisson ratio
AMSResults%ShearModulus- Type:
float
- Description:
The Shear modulus (conversion factor from hartree/bohr^3 to GPa: 29421.026)
- Unit:
hartree/bohr^3
AMSResults%SmallestHOMOLUMOGap- Type:
float
- Description:
Molecular Orbital Info: the smallest HOMO-LUMO gap irrespective of spin (i.e. min(LUMO) - max(HOMO)).
- Unit:
hartree
AMSResults%StressTensor- Type:
float_array
- Description:
The clamped-ion stress tensor in Cartesian notation.
- Unit:
hartree/bohr^nLatticeVectors
- Shape:
[:, :]
AMSResults%YoungModulus- Type:
float
- Description:
The Young modulus (conversion factor from hartree/bohr^3 to GPa: 29421.026)
- Unit:
hartree/bohr^3
- band_curves
Section content: Band dispersion curves.
band_curves%brav_type- Type:
string
- Description:
Type of the lattice.
band_curves%Edge_#_bands- Type:
float_array
- Description:
The band energies
- Shape:
[nBands, nSpin, :]
band_curves%Edge_#_direction- Type:
float_array
- Description:
Direction vector.
- Shape:
[nDimK]
band_curves%Edge_#_fatBands- Type:
float_array
- Description:
Fat band split up of the bands
- Shape:
[nBas, nBands, nSpin, :]
band_curves%Edge_#_kPoints- Type:
float_array
- Description:
Coordinates for points along the edge.
- Shape:
[nDimK, :]
band_curves%Edge_#_labels- Type:
lchar_string_array
- Description:
Labels for begin and end point of the edge.
- Shape:
[2]
band_curves%Edge_#_lGamma- Type:
bool
- Description:
Is gamma point?
band_curves%Edge_#_nKPoints- Type:
int
- Description:
The nr. of k points along the edge.
band_curves%Edge_#_vertices- Type:
float_array
- Description:
Begin and end point of the edge.
- Shape:
[nDimK, 2]
band_curves%Edge_#_xFor1DPlotting- Type:
float_array
- Description:
x Coordinate for points along the edge.
- Shape:
[:]
band_curves%indexLowestBand- Type:
int
- Description:
?
band_curves%nBands- Type:
int
- Description:
Number of bands.
band_curves%nBas- Type:
int
- Description:
Number of basis functions.
band_curves%nDimK- Type:
int
- Description:
Dimension of the reciprocal space.
band_curves%nEdges- Type:
int
- Description:
The number of edges. An edge is a line-segment through k-space. It has a begin and end point and possibly points in between.
band_curves%nEdgesInPath- Type:
int
- Description:
A path is built up from a number of edges.
band_curves%nSpin- Type:
int
- Description:
Number of spin components.
- Possible values:
[1, 2]
band_curves%path- Type:
int_array
- Description:
If the (edge) index is negative it means that the vertices of the edge abs(index) are swapped e.g. path = (1,2,3,0,-3,-2,-1) goes though edges 1,2,3, then there’s a jump, and then it goes back.
- Shape:
[nEdgesInPath]
band_curves%path_type- Type:
string
- Description:
?
- BandStructure
Section content: Info regarding the band structure…
BandStructure%BandGap- Type:
float
- Description:
The band gap. For molecules this is the HOMO-LUMO gap.
- Unit:
hartree
BandStructure%BandGap(FromPath)- Type:
float
- Description:
Band gap obtained along the path (if any). This is more accurate compared to the BandGap variable in this section if both TopValenceBand and BottomConductionBand are on the path. Only calculated when the band structure is requested.
- Unit:
hartree
BandStructure%bandsEnergyRange- Type:
float_array
- Description:
The energy ranges (min/max) of the bands
- Unit:
hartree
- Shape:
[2, nBand, nSpin]
BandStructure%BottomConductionBand- Type:
float
- Description:
The bottom of the conduction band
- Unit:
hartree
BandStructure%CoordsBottomConductionBand- Type:
float_array
- Description:
The coordinates in k-space of the bottom of the conduction band
- Unit:
1/bohr
- Shape:
[nDimK]
BandStructure%CoordsTopValenceBand- Type:
float_array
- Description:
The coordinates in k-space of the top of the valence band
- Unit:
1/bohr
- Shape:
[nDimK]
BandStructure%DerivativeDiscontinuity- Type:
float
- Description:
Correction to be added to the band gap to get the fundamental gap. (band only)
- Unit:
hartree
BandStructure%FermiEnergy- Type:
float
- Description:
Fermi level
- Unit:
hartree
BandStructure%HasGap- Type:
bool
- Description:
Whether the system has a gap.
BandStructure%HomoBandIndex- Type:
int
- Description:
The index of the highest occupied band
BandStructure%HomoDegeneracy- Type:
int
- Description:
How many states are exactly at the HOMO level
BandStructure%HomoSpinIndex- Type:
int
- Description:
In case of an unrestricted calculation: which of the two spins has the HOMO?
BandStructure%LumoBandIndex- Type:
int
- Description:
The index of the lowest unoccupied band
BandStructure%LumoDegeneracy- Type:
int
- Description:
How many states are exactly at the LUMO level
BandStructure%LumoSpinIndex- Type:
int
- Description:
In case of an unrestricted calculation: which of the two spins has the LUMO?
BandStructure%nBand- Type:
int
- Description:
The number of bands for which the band ranges are stored.
BandStructure%nDimK- Type:
int
- Description:
The number of dimensions for the k-coordinates for CoordsTopValenceBand and CoordsBottomConductionBand.
BandStructure%nSpin- Type:
int
- Description:
If 1: spin restricted calculation. For unrestricted results it has the value of 2.
- Possible values:
[1, 2]
BandStructure%TopValenceBand- Type:
float
- Description:
The top of the valence band
- Unit:
hartree
- BZcell(primitive cell)
Section content: The Brillouin zone of the primitive cell.
BZcell(primitive cell)%boundaries- Type:
float_array
- Description:
Normal vectors for the boundaries.
- Shape:
[ndim, nboundaries]
BZcell(primitive cell)%distances- Type:
float_array
- Description:
Distance to the boundaries.
- Shape:
[nboundaries]
BZcell(primitive cell)%idVerticesPerBound- Type:
int_array
- Description:
The indices of the vertices per bound.
- Shape:
[nvertices, nboundaries]
BZcell(primitive cell)%latticeVectors- Type:
float_array
- Description:
The lattice vectors.
- Shape:
[3, :]
BZcell(primitive cell)%nboundaries- Type:
int
- Description:
The nr. of boundaries for the cell.
BZcell(primitive cell)%ndim- Type:
int
- Description:
The nr. of lattice vectors spanning the Wigner-Seitz cell.
BZcell(primitive cell)%numVerticesPerBound- Type:
int_array
- Description:
The nr. of vertices per bound.
- Shape:
[nboundaries]
BZcell(primitive cell)%nvertices- Type:
int
- Description:
The nr. of vertices of the cell.
BZcell(primitive cell)%vertices- Type:
float_array
- Description:
The vertices of the bounds.
- Unit:
a.u.
- Shape:
[ndim, nvertices]
- DFTBEngineRestart
Section content: Stuff needed for restarting the DFTB engine
- DOS
Section content: Info regarding the DOS
DOS%Atom per basis function- Type:
int_array
- Description:
Atom index per basis function.
DOS%COOP per basis pair- Type:
float_array
- Description:
COOP per basis pair.
- Shape:
[nEnergies, nSpin, :, :]
DOS%DeltaE- Type:
float
- Description:
The energy difference between sampled DOS energies. When there is no DOS at all a certain energy range can be skipped.
- Unit:
hartree
DOS%DOS per basis function- Type:
float_array
- Description:
DOS contributions per basis function, based on Mulliken analysis.
- Shape:
[nEnergies, nSpin, :]
DOS%Energies- Type:
float_array
- Description:
The energies at which the DOS is sampled.
- Unit:
hartree
- Shape:
[nEnergies]
DOS%Fermi Energy- Type:
float
- Description:
The fermi energy.
- Unit:
hartree
DOS%IntegrateDeltaE- Type:
bool
- Description:
If enabled it means that the DOS is integrated over intervals of DeltaE. Sharp delta function like peaks cannot be missed this way.
DOS%L-value per basis function- Type:
int_array
- Description:
quantum number l for all basis functions.
DOS%M-value per basis function- Type:
int_array
- Description:
quantum number m for all basis functions.
DOS%nEnergies- Type:
int
- Description:
The nr. of energies to use to sample the DOS.
DOS%nSpin- Type:
int
- Description:
The number of spin components for the DOS.
- Possible values:
[1, 2]
DOS%Overlap population per basis pai- Type:
float_array
- Description:
? note that the word ‘pair’ is cut of due to the finite length of the kf variables name…
DOS%Population per basis function- Type:
float_array
- Description:
?
DOS%Symmetry per basis function- Type:
int_array
- Description:
?
DOS%Total DOS- Type:
float_array
- Description:
The total DOS.
- Shape:
[nEnergies, nSpin]
- DOS_Phonons
Section content: Phonon Density of States
DOS_Phonons%DeltaE- Type:
float
- Description:
The energy difference between sampled DOS energies. When there is no DOS at all a certain energy range can be skipped.
- Unit:
hartree
DOS_Phonons%Energies- Type:
float_array
- Description:
The energies at which the DOS is sampled.
- Unit:
hartree
- Shape:
[nEnergies]
DOS_Phonons%Fermi Energy- Type:
float
- Description:
The fermi energy.
- Unit:
hartree
DOS_Phonons%IntegrateDeltaE- Type:
bool
- Description:
If enabled it means that the DOS is integrated over intervals of DeltaE. Sharp delta function like peaks cannot be missed this way.
DOS_Phonons%nEnergies- Type:
int
- Description:
The nr. of energies to use to sample the DOS.
DOS_Phonons%nSpin- Type:
int
- Description:
The number of spin components for the DOS.
- Possible values:
[1, 2]
DOS_Phonons%Total DOS- Type:
float_array
- Description:
The total DOS.
- Shape:
[nEnergies, nSpin]
- Dynamical Polarizability
Section content: ?
Dynamical Polarizability%frequency #- Type:
float
- Description:
?
Dynamical Polarizability%imagPolar #- Type:
float_array
- Description:
?
Dynamical Polarizability%nr of frequencies- Type:
int
- Description:
?
Dynamical Polarizability%realPolar #- Type:
float_array
- Description:
?
- EffectiveMass
Section content: In the effective mass approximation the curvature of the bands is a measure of the charge mobility. The curvature is obtained by numerical differentiation. The mass is the inverse of the curvature.
EffectiveMass%EffectiveMasses- Type:
float_array
- Description:
Inverse curvatures at the extrema. Several bands may be sampled at once. The shape is [ndimk,ndimk,:,nKPoints,nspin].
- Unit:
a.u.
EffectiveMass%ErrorEffectiveMasses- Type:
float_array
- Description:
Estimated errors from using two different step sizes for finite difference calculations.
- Unit:
a.u.
EffectiveMass%kCoordinates- Type:
float_array
- Description:
The coordinates in k-space of the top of the valence band(s) or bottom of conduction band(s).
- Unit:
1/bohr
- Shape:
[kspace%ndimk, nKPoints]
EffectiveMass%nKPoints- Type:
int
- Description:
The number of k points for which the effective mass is calculated. These should always be extrema (minimum or maximum) of the bands.
- Excitations SOT A
Section content: Single oribtal transitions. Ask Robert about this.
Excitations SOT A%contr #- Type:
float_array
- Description:
Contributions to excitation #.
- Shape:
[:]
Excitations SOT A%contr index #- Type:
int_array
- Description:
Indices (org/new) for contributions to excitation #.
- Shape:
[:, 2]
Excitations SOT A%contr irep index #- Type:
int_array
- Description:
Irrep indices (org/new) for contributions to excitation #.
- Shape:
[:, 2]
Excitations SOT A%contr transdip #- Type:
float_array
- Description:
Contributions to transition dipole #.
- Shape:
[3, :]
Excitations SOT A%eigenvec #- Type:
float_array
- Description:
Eigenvectors for excitation #.
- Shape:
[:]
Excitations SOT A%excenergies- Type:
float_array
- Description:
Excitation energies.
- Shape:
[:]
Excitations SOT A%gradient #- Type:
float_array
- Description:
Gradient for excitation #.
- Shape:
[3, Molecule%nAtoms]
Excitations SOT A%nr of contributions #- Type:
int
- Description:
Number of contributions for excitation #.
Excitations SOT A%nr of excenergies- Type:
int
- Description:
Number of excitation energies.
Excitations SOT A%oscillator strengths- Type:
float_array
- Description:
Oscillator strengths.
- Shape:
[nr of excenergies]
Excitations SOT A%transition dipole moments- Type:
float_array
- Description:
Transition dipole moments.
- Shape:
[3, nr of excenergies]
- Excitations SS A
Section content: Singlet-singlet.
Excitations SS A%contr #- Type:
float_array
- Description:
Contributions to excitation #.
- Shape:
[:]
Excitations SS A%contr index #- Type:
int_array
- Description:
Indices (org/new) for contributions to excitation #.
- Shape:
[:, 2]
Excitations SS A%contr irep index #- Type:
int_array
- Description:
Irrep indices (org/new) for contributions to excitation #.
- Shape:
[:, 2]
Excitations SS A%contr transdip #- Type:
float_array
- Description:
Contributions to transition dipole #.
- Shape:
[3, :]
Excitations SS A%eigenvec #- Type:
float_array
- Description:
Eigenvectors for excitation #.
- Shape:
[nTransUse]
Excitations SS A%excenergies- Type:
float_array
- Description:
Excitation energies.
- Shape:
[nr of excenergies]
Excitations SS A%gradient #- Type:
float_array
- Description:
Gradient for excitation #.
- Shape:
[3, Molecule%nAtoms]
Excitations SS A%nr of contributions #- Type:
int
- Description:
Number of contributions for excitation #.
Excitations SS A%nr of excenergies- Type:
int
- Description:
Number of excitation energies.
Excitations SS A%nTransUse- Type:
int
- Description:
Number of single orbital transitions.
Excitations SS A%oscillator strengths- Type:
float_array
- Description:
Oscillator strengths.
- Shape:
[nr of excenergies]
Excitations SS A%transition dipole moments- Type:
float_array
- Description:
Transition dipole moments.
- Shape:
[3, nr of excenergies]
- Excitations ST A
Section content: Singlet-triplet.
Excitations ST A%contr #- Type:
float_array
- Description:
Contributions to excitation #.
- Shape:
[:]
Excitations ST A%contr index #- Type:
int_array
- Description:
Indices (org/new) for contributions to excitation #.
- Shape:
[:, 2]
Excitations ST A%contr irep index #- Type:
int_array
- Description:
Irrep indices (org/new) for contributions to excitation #.
- Shape:
[:, 2]
Excitations ST A%contr transdip #- Type:
float_array
- Description:
Contributions to transition dipole #.
- Shape:
[3, :]
Excitations ST A%eigenvec #- Type:
float_array
- Description:
Eigenvectors for excitation #.
- Shape:
[nTransUse]
Excitations ST A%excenergies- Type:
float_array
- Description:
Excitation energies.
- Shape:
[nr of excenergies]
Excitations ST A%gradient #- Type:
float_array
- Description:
Gradient for excitation #.
- Shape:
[3, Molecule%nAtoms]
Excitations ST A%nr of contributions #- Type:
int
- Description:
Number of contributions for excitation #.
Excitations ST A%nr of excenergies- Type:
int
- Description:
Number of excitation energies.
Excitations ST A%nTransUse- Type:
int
- Description:
Number of single orbital transitions.
Excitations ST A%oscillator strengths- Type:
float_array
- Description:
Oscillator strengths.
- Shape:
[nr of excenergies]
Excitations ST A%transition dipole moments- Type:
float_array
- Description:
Transition dipole moments.
- Shape:
[3, nr of excenergies]
- FOPopulations
Section content: ?
FOPopulations%fo_grosspop(#)- Type:
float_array
- Description:
Gross population of fragment orbitals in full system.
- Shape:
[FragmentOrbitals%nOrbitals]
FOPopulations%fo_index(#)- Type:
int_array
- Description:
Fragment orbital number for each stored fragment orbital contribution per molecular orbital.
FOPopulations%fo_pop(#)- Type:
float_array
- Description:
Stored fragment orbital contribution per molecular orbital.
FOPopulations%nEntries- Type:
int
- Description:
The number of sets. At the moment it should be 1, only nSpin=1 and nKpoints=1 supported.
FOPopulations%number of contributions(#)- Type:
int_array
- Description:
Number of stored fragment orbital contributions per molecular orbital
- Shape:
[FragmentOrbitals%nOrbitals]
- FragmentOrbitals
Section content: ?
FragmentOrbitals%AtomicFragmentOrbitals- Type:
bool
- Description:
Whether atomic fragment orbitals are used.
FragmentOrbitals%BaseNameFragFile- Type:
lchar_string_array
- Description:
Not used if AtomicFragmentOrbitals is true. Guess for reasonable fragment names in case of the AMS-GUI.
- Shape:
[nFragments]
FragmentOrbitals%Coefficients(#)- Type:
float_array
- Description:
Fragment orbital coefficients in the basis of all fragment basis functions.
- Shape:
[nBasisFunctions, nOrbitals]
FragmentOrbitals%Energies(#)- Type:
float_array
- Description:
Fragment orbital energies.
- Shape:
[nOrbitals]
FragmentOrbitals%Fragment- Type:
int_array
- Description:
On which fragment is a fragment orbital.
- Shape:
[nOrbitals]
FragmentOrbitals%FragmentSymbols- Type:
lchar_string_array
- Description:
Unique name of the fragments, typically name includes the chemical formula and a number.
- Shape:
[nFragments]
FragmentOrbitals%iFO- Type:
int_array
- Description:
Orbital number of the fragment orbital in the fragment on which the fragment orbital is located.
- Shape:
[nOrbitals]
FragmentOrbitals%MOinFO(#)- Type:
float_array
- Description:
Molecular orbital (MO) coefficients in the basis of fragment orbitals (FO).
- Shape:
[nOrbitals, nOrbitals]
FragmentOrbitals%nBasisFunctions- Type:
int
- Description:
Total number of basis functions (summed over fragments). At the moment nBasisFunctions equals nOrbitals.
FragmentOrbitals%nEntries- Type:
int
- Description:
The number of sets. At the moment it should be 1, only nSpin=1 and nKpoints=1 supported.
FragmentOrbitals%nFragments- Type:
int
- Description:
Number of fragments
FragmentOrbitals%nOrbitals- Type:
int
- Description:
Total number of orbitals (summed over fragments).
FragmentOrbitals%Occupations(#)- Type:
float_array
- Description:
Fragment orbital occupation numbers.
- Shape:
[nOrbitals]
FragmentOrbitals%Overlaps(#)- Type:
float_array
- Description:
Overlap fragment orbitals
- Shape:
[nOrbitals, nOrbitals]
FragmentOrbitals%SiteEnergies(#)- Type:
float_array
- Description:
The Site energy of a fragment orbital (FO) is defined as the diagonal Fock matrix element of the Fock matrix of the full system in FO representation.
- Shape:
[nOrbitals]
FragmentOrbitals%SubSpecies- Type:
lchar_string_array
- Description:
Symmetry labels of fragment orbitals. In case of AtomicFragmentOrbitals the subspecies are atomic like S, P:x, etcetera. Otherwise symmetry NOSYM is used and the subspecies are all A.
- Shape:
[nOrbitals]
- General
Section content: General information about the DFTB calculation.
General%account- Type:
string
- Description:
Name of the account from the license
General%engine input- Type:
string
- Description:
The text input of the engine.
General%engine messages- Type:
string
- Description:
Message from the engine. In case the engine fails to solves, this may contains extra information on why.
General%file-ident- Type:
string
- Description:
The file type identifier, e.g. RKF, RUNKF, TAPE21…
General%jobid- Type:
int
- Description:
Unique identifier for the job.
General%program- Type:
string
- Description:
The name of the program/engine that generated this kf file.
General%release- Type:
string
- Description:
The version of the program that generated this kf file (including svn revision number and date).
General%termination status- Type:
string
- Description:
The termination status. Possible values: ‘NORMAL TERMINATION’, ‘NORMAL TERMINATION with warnings’, ‘NORMAL TERMINATION with errors’, ‘ERROR’, ‘IN PROGRESS’.
General%title- Type:
string
- Description:
Title of the calculation.
General%uid- Type:
string
- Description:
SCM User ID
General%version- Type:
int
- Description:
Version number?
- KFDefinitions
Section content: The definitions of the data on this file
KFDefinitions%json- Type:
string
- Description:
The definitions of the data on this file in json.
- kspace
Section content: Info regarding the k-space integration…
kspace%avec- Type:
float_array
- Description:
The lattice stored as a 3xnLatticeVectors matrix. Only the ndimk,ndimk part has meaning.
- Unit:
bohr
- Shape:
[3, :]
kspace%bvec- Type:
float_array
- Description:
The inverse lattice stored as a 3x3 matrix. Only the ndimk,ndimk part has meaning.
- Unit:
1/bohr
- Shape:
[ndim, ndim]
kspace%bzvol- Type:
float
- Description:
The volume of the BZ zone. In 2D it is the surface and in 1D it is the length. The unit is bohr raised to the power ndim.
kspace%iDimkEffective- Type:
int_array
- Description:
Which latttice vectors are really used for the k-space integration.
- Shape:
[nDimkEffective]
kspace%isKunComplex- Type:
bool_array
- Description:
Whether or not the Hamiltonian matrix is complex for a unique k-point.
- Shape:
[kuniqu]
kspace%kequiv- Type:
int_array
- Description:
When kequiv(i)=i the k-point is unique.
- Shape:
[kt]
kspace%kequn- Type:
int_array
- Description:
When looping over all k-points, the unique index is kun=kequn(k).
- Shape:
[kt]
kspace%kinteg- Type:
int
- Description:
In case a symmetric grid is used this is the parameter used to create it.
kspace%klbl- Type:
lchar_string_array
- Description:
labels describing the k-points
- Shape:
[kt]
kspace%klblun- Type:
lchar_string_array
- Description:
labels describing the unique k-points
- Shape:
[kuniqu]
kspace%klnear- Type:
bool
- Description:
Whether or not linear k-space integration is used (symmetric method with even kinteg).
kspace%ksimpl- Type:
int_array
- Description:
Index array defining the simplices, referring to the xyzpt array.
- Shape:
[nvertk, nsimpl]
kspace%kt- Type:
int
- Description:
The total number of k-points used by the k-space to sample the unique wedge of the Brillouin zone.
kspace%ktBoltz- Type:
float
- Description:
band only?.
kspace%kuniqu- Type:
int
- Description:
The number of symmetry unique k-points where an explicit diagonalization is needed. Smaller or equal to kt.
kspace%ndim- Type:
int
- Description:
The nr. of lattice vectors.
kspace%ndimk- Type:
int
- Description:
The nr. of dimensions used in the k-space integration.
kspace%nDimkEffective- Type:
int
- Description:
Normally ndimk is equal to the number of lattice vectors. For very large lattice vectors the k-space dispersion is ignored, leading to a lower dimensional band structure.
kspace%noperk- Type:
int
- Description:
The nr. of operators in k-space. band only?
kspace%nsimpl- Type:
int
- Description:
The number of simplices constructed from the k-points to span the IBZ.
kspace%numBoltz- Type:
int
- Description:
Number of energies to sample around the fermi energy. band only?
kspace%numEquivSimplices- Type:
int_array
- Description:
Simplices may be equivalent due to symmetry operations..
- Shape:
[nsimpl]
kspace%nvertk- Type:
int
- Description:
The number of vertices that each simplex has.
kspace%operk- Type:
float_array
- Description:
Symmetry operators in k-space. band only?
- Unit:
bohr
- Shape:
[ndim, ndim, noperk]
kspace%xyzpt- Type:
float_array
- Description:
The coordinates of the k-points.
- Unit:
1/bohr
- Shape:
[ndimk, kt]
- kspace(primitive cell)
Section content: should not be here!!!
kspace(primitive cell)%avec- Type:
float_array
- Description:
The lattice stored as a 3xnLatticeVectors matrix. Only the ndimk,ndimk part has meaning.
- Unit:
bohr
- Shape:
[3, :]
kspace(primitive cell)%bvec- Type:
float_array
- Description:
The inverse lattice stored as a 3x3 matrix. Only the ndimk,ndimk part has meaning.
- Unit:
1/bohr
- Shape:
[ndim, ndim]
kspace(primitive cell)%kt- Type:
int
- Description:
The total number of k-points used by the k-space to sample the unique wedge of the Brillouin zone.
kspace(primitive cell)%kuniqu- Type:
int
- Description:
The number of symmetry unique k-points where an explicit diagonalization is needed. Smaller or equal to kt.
kspace(primitive cell)%ndim- Type:
int
- Description:
The nr. of lattice vectors.
kspace(primitive cell)%ndimk- Type:
int
- Description:
The nr. of dimensions used in the k-space integration.
kspace(primitive cell)%xyzpt- Type:
float_array
- Description:
The coordinates of the k-points.
- Unit:
1/bohr
- Shape:
[ndimk, kt]
- Low Frequency Correction
Section content: Configuration for the Head-Gordon Dampener-powered Free Rotor Interpolation.
Low Frequency Correction%Alpha- Type:
float
- Description:
Exponent term for the Head-Gordon dampener.
Low Frequency Correction%Frequency- Type:
float
- Description:
Frequency around which interpolation happens, in 1/cm.
Low Frequency Correction%Moment of Inertia- Type:
float
- Description:
Used to make sure frequencies of less than ca. 1 1/cm don’t overestimate entropy, in kg m^2.
- Matrices
Section content: Section that can contain any number of real matrices
Matrices%Data(#)- Type:
float_array
- Description:
The array, rank and dimensions as specified by Dimensions.
Matrices%Dimensions(#)- Type:
int_array
- Description:
The dimensions of the array
Matrices%Name(#)- Type:
string
- Description:
The name of the matrix.
Matrices%nEntries- Type:
int
- Description:
The number of matrices
Matrices%Type(#)- Type:
string
- Description:
The type such as Real, and perhaps Complex?
- Mobile Block Hessian
Section content: Mobile Block Hessian.
Mobile Block Hessian%Coordinates Internal- Type:
float_array
- Description:
?
Mobile Block Hessian%Free Atom Indexes Input- Type:
int_array
- Description:
?
Mobile Block Hessian%Frequencies in atomic units- Type:
float_array
- Description:
?
Mobile Block Hessian%Frequencies in wavenumbers- Type:
float_array
- Description:
?
Mobile Block Hessian%Input Cartesian Normal Modes- Type:
float_array
- Description:
?
Mobile Block Hessian%Input Indexes of Block #- Type:
int_array
- Description:
?
Mobile Block Hessian%Intensities in km/mol- Type:
float_array
- Description:
?
Mobile Block Hessian%MBH Curvatures- Type:
float_array
- Description:
?
Mobile Block Hessian%Number of Blocks- Type:
int
- Description:
Number of blocks.
Mobile Block Hessian%Sizes of Blocks- Type:
int_array
- Description:
Sizes of the blocks.
- Shape:
[Number of Blocks]
- Molecule
Section content: The input molecule of the calculation.
Molecule%AtomicNumbers- Type:
int_array
- Description:
Atomic number ‘Z’ of the atoms in the system
- Shape:
[nAtoms]
Molecule%AtomMasses- Type:
float_array
- Description:
Masses of the atoms
- Unit:
a.u.
- Values range:
[0, ‘\infinity’]
- Shape:
[nAtoms]
Molecule%AtomSymbols- Type:
string
- Description:
The atom’s symbols (e.g. ‘C’ for carbon)
- Shape:
[nAtoms]
Molecule%bondOrders- Type:
float_array
- Description:
The bond orders for the bonds in the system. The indices of the two atoms participating in the bond are defined in the arrays ‘fromAtoms’ and ‘toAtoms’. e.g. bondOrders[1]=2, fromAtoms[1]=4 and toAtoms[1]=7 means that there is a double bond between atom number 4 and atom number 7
Molecule%Charge- Type:
float
- Description:
Net charge of the system
- Unit:
e
Molecule%Coords- Type:
float_array
- Description:
Coordinates of the nuclei (x,y,z)
- Unit:
bohr
- Shape:
[3, nAtoms]
Molecule%eeAttachTo- Type:
int_array
- Description:
A multipole may be attached to an atom. This influences the energy gradient.
Molecule%eeChargeWidth- Type:
float
- Description:
If charge broadening was used for external charges, this represents the width of the charge distribution.
Molecule%eeEField- Type:
float_array
- Description:
The external homogeneous electric field.
- Unit:
hartree/(e*bohr)
- Shape:
[3]
Molecule%eeLatticeVectors- Type:
float_array
- Description:
The lattice vectors used for the external point- or multipole- charges.
- Unit:
bohr
- Shape:
[3, eeNLatticeVectors]
Molecule%eeMulti- Type:
float_array
- Description:
The values of the external point- or multipole- charges.
- Unit:
a.u.
- Shape:
[eeNZlm, eeNMulti]
Molecule%eeNLatticeVectors- Type:
int
- Description:
The number of lattice vectors for the external point- or multipole- charges.
Molecule%eeNMulti- Type:
int
- Description:
The number of external point- or multipole- charges.
Molecule%eeNZlm- Type:
int
- Description:
When external point- or multipole- charges are used, this represents the number of spherical harmonic components. E.g. if only point charges were used, eeNZlm=1 (s-component only). If point charges and dipole moments were used, eeNZlm=4 (s, px, py and pz).
Molecule%eeUseChargeBroadening- Type:
bool
- Description:
Whether or not the external charges are point-like or broadened.
Molecule%eeXYZ- Type:
float_array
- Description:
The position of the external point- or multipole- charges.
- Unit:
bohr
- Shape:
[3, eeNMulti]
Molecule%EngineAtomicInfo- Type:
string_fixed_length
- Description:
Atom-wise info possibly used by the engine.
Molecule%fromAtoms- Type:
int_array
- Description:
Index of the first atom in a bond. See the bondOrders array
Molecule%latticeDisplacements- Type:
int_array
- Description:
The integer lattice translations for the bonds defined in the variables bondOrders, fromAtoms and toAtoms.
Molecule%LatticeVectors- Type:
float_array
- Description:
Lattice vectors
- Unit:
bohr
- Shape:
[3, nLatticeVectors]
Molecule%nAtoms- Type:
int
- Description:
The number of atoms in the system
Molecule%nAtomsTypes- Type:
int
- Description:
The number different of atoms types
Molecule%nLatticeVectors- Type:
int
- Description:
Number of lattice vectors (i.e. number of periodic boundary conditions)
- Possible values:
[0, 1, 2, 3]
Molecule%toAtoms- Type:
int_array
- Description:
Index of the second atom in a bond. See the bondOrders array
- MoleculeSuperCell
Section content: The system used for the numerical phonon super cell calculation.
MoleculeSuperCell%AtomicNumbers- Type:
int_array
- Description:
Atomic number ‘Z’ of the atoms in the system
- Shape:
[nAtoms]
MoleculeSuperCell%AtomMasses- Type:
float_array
- Description:
Masses of the atoms
- Unit:
a.u.
- Values range:
[0, ‘\infinity’]
- Shape:
[nAtoms]
MoleculeSuperCell%AtomSymbols- Type:
string
- Description:
The atom’s symbols (e.g. ‘C’ for carbon)
- Shape:
[nAtoms]
MoleculeSuperCell%bondOrders- Type:
float_array
- Description:
The bond orders for the bonds in the system. The indices of the two atoms participating in the bond are defined in the arrays ‘fromAtoms’ and ‘toAtoms’. e.g. bondOrders[1]=2, fromAtoms[1]=4 and toAtoms[1]=7 means that there is a double bond between atom number 4 and atom number 7
MoleculeSuperCell%Charge- Type:
float
- Description:
Net charge of the system
- Unit:
e
MoleculeSuperCell%Coords- Type:
float_array
- Description:
Coordinates of the nuclei (x,y,z)
- Unit:
bohr
- Shape:
[3, nAtoms]
MoleculeSuperCell%eeAttachTo- Type:
int_array
- Description:
A multipole may be attached to an atom. This influences the energy gradient.
MoleculeSuperCell%eeChargeWidth- Type:
float
- Description:
If charge broadening was used for external charges, this represents the width of the charge distribution.
MoleculeSuperCell%eeEField- Type:
float_array
- Description:
The external homogeneous electric field.
- Unit:
hartree/(e*bohr)
- Shape:
[3]
MoleculeSuperCell%eeLatticeVectors- Type:
float_array
- Description:
The lattice vectors used for the external point- or multipole- charges.
- Unit:
bohr
- Shape:
[3, eeNLatticeVectors]
MoleculeSuperCell%eeMulti- Type:
float_array
- Description:
The values of the external point- or multipole- charges.
- Unit:
a.u.
- Shape:
[eeNZlm, eeNMulti]
MoleculeSuperCell%eeNLatticeVectors- Type:
int
- Description:
The number of lattice vectors for the external point- or multipole- charges.
MoleculeSuperCell%eeNMulti- Type:
int
- Description:
The number of external point- or multipole- charges.
MoleculeSuperCell%eeNZlm- Type:
int
- Description:
When external point- or multipole- charges are used, this represents the number of spherical harmonic components. E.g. if only point charges were used, eeNZlm=1 (s-component only). If point charges and dipole moments were used, eeNZlm=4 (s, px, py and pz).
MoleculeSuperCell%eeUseChargeBroadening- Type:
bool
- Description:
Whether or not the external charges are point-like or broadened.
MoleculeSuperCell%eeXYZ- Type:
float_array
- Description:
The position of the external point- or multipole- charges.
- Unit:
bohr
- Shape:
[3, eeNMulti]
MoleculeSuperCell%EngineAtomicInfo- Type:
string_fixed_length
- Description:
Atom-wise info possibly used by the engine.
MoleculeSuperCell%fromAtoms- Type:
int_array
- Description:
Index of the first atom in a bond. See the bondOrders array
MoleculeSuperCell%latticeDisplacements- Type:
int_array
- Description:
The integer lattice translations for the bonds defined in the variables bondOrders, fromAtoms and toAtoms.
MoleculeSuperCell%LatticeVectors- Type:
float_array
- Description:
Lattice vectors
- Unit:
bohr
- Shape:
[3, nLatticeVectors]
MoleculeSuperCell%nAtoms- Type:
int
- Description:
The number of atoms in the system
MoleculeSuperCell%nAtomsTypes- Type:
int
- Description:
The number different of atoms types
MoleculeSuperCell%nLatticeVectors- Type:
int
- Description:
Number of lattice vectors (i.e. number of periodic boundary conditions)
- Possible values:
[0, 1, 2, 3]
MoleculeSuperCell%toAtoms- Type:
int_array
- Description:
Index of the second atom in a bond. See the bondOrders array
- NAOSetCells
Section content: For periodic systems neighboring cells need to be considered. More cells are needed for more diffuse basis sets.
NAOSetCells%Coords(#{entry})- Type:
float_array
- Description:
Cell coordinates for a basis set.
- Shape:
[3, nCells(#{entry})]
NAOSetCells%Name(#{entry})- Type:
string
- Description:
The name of the basis set.
NAOSetCells%nAtoms(#{entry})- Type:
int
- Description:
Number of atoms for a basis set.
NAOSetCells%nCells(#{entry})- Type:
int
- Description:
Number of cells needed for a basis set.
NAOSetCells%nEntries- Type:
int
- Description:
The number of entries (basis sets), for basis sets like valence and core, fit, etc..
NAOSetCells%SkipAtom(#{entry})- Type:
bool_array
- Description:
Sometimes the functions of an atom do not require a cell at all.
- Shape:
[nAtoms(#{entry}), nCells(#{entry})]
- NumericalBasisSets
Section content: Specification of numerical atomic basis sets, consisting of a numerical radial table and a spherical harmonic: R_{nl} Y_{lm}.
NumericalBasisSets%BasisType(#{set},#{type})- Type:
string
- Description:
Something like valence or core for (type,set). Will not depend on type.
NumericalBasisSets%bField for GIAO(#{set},#{type})- Type:
float_array
- Description:
Band only. Finite magnetic field strength for GIAOs.
- Shape:
[3]
NumericalBasisSets%d2RadialFuncs(#{set},#{type})- Type:
float_array
- Description:
The second derivative of the radial functions (for a type,set).
- Shape:
[NumRad(#{type}), nRadialFuncs(#{set},#{type})]
NumericalBasisSets%dRadialFuncs(#{set},#{type})- Type:
float_array
- Description:
The derivative of the radial functions (for a type,set).
- Shape:
[NumRad(#{type}), nRadialFuncs(#{set},#{type})]
NumericalBasisSets%Element(#{type})- Type:
string
- Description:
The chemical element (H,He,Li) for a type.
NumericalBasisSets%GridType(#{type})- Type:
string
- Description:
What kind of radial grid is used. Currently this is always logarithmic.
NumericalBasisSets%ljValues(#{set},#{type})- Type:
int_array
- Description:
Normally for each radial function the l value. In case of spin-orbit there is also a j value (for a type,set).
- Shape:
[2, nRadialFuncs(#{set},#{type})]
NumericalBasisSets%MaxRad(#{type})- Type:
float
- Description:
Maximum value of the radial grid (for a type).
NumericalBasisSets%MinRad(#{type})- Type:
float
- Description:
Minimum value of the radial grid (for a type).
NumericalBasisSets%nRadialFuncs(#{set},#{type})- Type:
int
- Description:
The number of radial functions (for a type,set).
NumericalBasisSets%nSets- Type:
int
- Description:
The number of basis sets stored for each type. For instance if you store core and the valence basis sets it is two.
NumericalBasisSets%nTypes- Type:
int
- Description:
The number of types: elements with a different basis set. Normally this is just the number of distinct elements in the system.
NumericalBasisSets%NumRad(#{type})- Type:
int
- Description:
The number of radial points (for a type).
NumericalBasisSets%RadialFuncs(#{set},#{type})- Type:
float_array
- Description:
The radial functions (for a type,set).
- Shape:
[NumRad(#{type}), nRadialFuncs(#{set},#{type})]
NumericalBasisSets%RadialMetaInfo(#{set},#{type})- Type:
float_array
- Description:
Info about the radial functions. Whether it is a NAO or STO. For instance for an STO the alpha value. All encoded in a real array of fixed size.
- Shape:
[:, nRadialFuncs(#{set},#{type})]
NumericalBasisSets%SpherHarmonicType(#{set},#{type})- Type:
string
- Description:
Either zlm or spinor (type,set). Will not depend on type.
- Orbitals
Section content: Info regarding the orbitals…
Orbitals%Coefficients(#)- Type:
float_array
- Description:
for each entry the orbital expansion coefficients.
- Shape:
[nBasisFunctions, nOrbitals]
Orbitals%CoefficientsImag(#)- Type:
float_array
- Description:
for each entry the imaginary part of the orbital expansion coefficients.
- Shape:
[nBasisFunctions, nOrbitals]
Orbitals%CoefficientsReal(#)- Type:
float_array
- Description:
for each entry the real part of the orbital expansion coefficients.
- Shape:
[nBasisFunctions, nOrbitals]
Orbitals%Energies(#)- Type:
float_array
- Description:
for each entry the eigen values.
- Shape:
[nOrbitals]
Orbitals%nBasisFunctions- Type:
int
- Description:
Total number of basis functions.
Orbitals%nEntries- Type:
int
- Description:
The number of sets. For a molecule this is nSpin, for a solid it is nKpoints*nSpin.
Orbitals%nOrbitals- Type:
int
- Description:
The number of orbitals stored for an entry. This can be equal or less than nBasisFunctions
Orbitals%Occupations(#)- Type:
float_array
- Description:
for each entry the Occupations.
- Shape:
[nOrbitals]
- phonon_curves
Section content: Phonon dispersion curves.
phonon_curves%brav_type- Type:
string
- Description:
Type of the lattice.
phonon_curves%Edge_#_bands- Type:
float_array
- Description:
The band energies
- Shape:
[nBands, nSpin, :]
phonon_curves%Edge_#_direction- Type:
float_array
- Description:
Direction vector.
- Shape:
[nDimK]
phonon_curves%Edge_#_kPoints- Type:
float_array
- Description:
Coordinates for points along the edge.
- Shape:
[nDimK, :]
phonon_curves%Edge_#_labels- Type:
lchar_string_array
- Description:
Labels for begin and end point of the edge.
- Shape:
[2]
phonon_curves%Edge_#_lGamma- Type:
bool
- Description:
Is gamma point?
phonon_curves%Edge_#_nKPoints- Type:
int
- Description:
The nr. of k points along the edge.
phonon_curves%Edge_#_vertices- Type:
float_array
- Description:
Begin and end point of the edge.
- Shape:
[nDimK, 2]
phonon_curves%Edge_#_xFor1DPlotting- Type:
float_array
- Description:
x Coordinate for points along the edge.
- Shape:
[:]
phonon_curves%indexLowestBand- Type:
int
- Description:
?
phonon_curves%nBands- Type:
int
- Description:
Number of bands.
phonon_curves%nBas- Type:
int
- Description:
Number of basis functions.
phonon_curves%nDimK- Type:
int
- Description:
Dimension of the reciprocal space.
phonon_curves%nEdges- Type:
int
- Description:
The number of edges. An edge is a line-segment through k-space. It has a begin and end point and possibly points in between.
phonon_curves%nEdgesInPath- Type:
int
- Description:
A path is built up from a number of edges.
phonon_curves%nSpin- Type:
int
- Description:
Number of spin components.
- Possible values:
[1, 2]
phonon_curves%path- Type:
int_array
- Description:
If the (edge) index is negative it means that the vertices of the edge abs(index) are swapped e.g. path = (1,2,3,0,-3,-2,-1) goes though edges 1,2,3, then there’s a jump, and then it goes back.
- Shape:
[nEdgesInPath]
phonon_curves%path_type- Type:
string
- Description:
?
- Phonons
Section content: Information on the numerical phonons (super cell) setup. NB: the reciprocal cell of the super cell is smaller than the reciprocal primitive cell.
Phonons%Modes- Type:
float_array
- Description:
The normal modes with the translational symmetry of the super cell.
- Shape:
[3, nAtoms, 3, NumAtomsPrim, nK]
Phonons%nAtoms- Type:
int
- Description:
Number of atoms in the super cell.
Phonons%nK- Type:
int
- Description:
Number of gamma-points (of the super cell) that fit into the primitive reciprocal cell.
Phonons%NumAtomsPrim- Type:
int
- Description:
Number of atoms in the primitive cell.
Phonons%xyzKSuper- Type:
float_array
- Description:
The coordinates of the gamma points that fit into the primitive reciprocal cell.
- Shape:
[3, nK]
- Plot
Section content: Generic section to store x-y plots.
Plot%numPlots- Type:
int
- Description:
Number of plots.
Plot%NumPoints(#)- Type:
int
- Description:
Number of x points for plot #.
Plot%NumYSeries(#)- Type:
int
- Description:
Number of y series for plot #.
Plot%Title(#)- Type:
string
- Description:
Title of plot #
Plot%XLabel(#)- Type:
string
- Description:
X label for plot #.
Plot%XUnit(#)- Type:
string
- Description:
X unit for plot #.
Plot%XValues(#)- Type:
float_array
- Description:
X values for plot #.
- Shape:
[:]
Plot%YLabel(#)- Type:
string
- Description:
Y label for plot #.
Plot%YUnit(#)- Type:
string
- Description:
Y unit for plot #.
Plot%YValues(#)- Type:
float_array
- Description:
Y values for plot #. Array has extra column NumYSeries.
- Properties
Section content: Generic container for properties.
- QMFQ
Section content: Why is this in the ams.rkf file and not in the adf.rkf file?
QMFQ%atoms to index- Type:
int_array
- Description:
?
QMFQ%atoms to mol label- Type:
int_array
- Description:
?
QMFQ%charge constraints- Type:
float_array
- Description:
?
QMFQ%external xyz- Type:
float_array
- Description:
?
QMFQ%fde atoms to index- Type:
int_array
- Description:
?
QMFQ%fde atoms to mol label- Type:
int_array
- Description:
?
QMFQ%fde charge constraints- Type:
float_array
- Description:
?
QMFQ%fde external xyz- Type:
float_array
- Description:
?
QMFQ%fde index to mol label- Type:
int_array
- Description:
?
QMFQ%fde type index- Type:
int_array
- Description:
?
QMFQ%index to mol label- Type:
int_array
- Description:
?
QMFQ%type alpha- Type:
float_array
- Description:
?
QMFQ%type chi- Type:
float_array
- Description:
?
QMFQ%type eta- Type:
float_array
- Description:
?
QMFQ%type index- Type:
int_array
- Description:
?
QMFQ%type name- Type:
string
- Description:
?
QMFQ%type rmu- Type:
float_array
- Description:
?
QMFQ%type rq- Type:
float_array
- Description:
?
- QTAIM
Section content: Bader analysis (Atoms In Molecule): critical points and bond paths.
QTAIM%CoordinatesAlongBPs- Type:
float_array
- Description:
The position of each step point. (bond path index, step index, 3)
- Unit:
bohr
- Shape:
[nBondPaths, :, 3]
QTAIM%CoordinatesCPs- Type:
float_array
- Description:
Coordinates of the critical points.
- Unit:
bohr
- Shape:
[nCriticalPoints, 3]
QTAIM%DensityAlongBPs- Type:
float_array
- Description:
The density at that point along the bond path. (bond path index, step index)
- Shape:
[nBondPaths, :]
QTAIM%DensityAtCPs- Type:
float_array
- Description:
Density at the critical points.
- Shape:
[nCriticalPoints]
QTAIM%GradientAlongBPs- Type:
float_array
- Description:
The gradient at that point along the bond path. (bond path index, step index, 3)
- Shape:
[nBondPaths, :, 3]
QTAIM%GradientAtCPs- Type:
float_array
- Description:
Density gradients at the critical points.
- Shape:
[nCriticalPoints, 3]
QTAIM%HessianAlongBPs- Type:
float_array
- Description:
The gradient at that point along the bond path. (bond path index, step index, 6)
- Shape:
[nBondPaths, :, 6]
QTAIM%HessianAtCPs- Type:
float_array
- Description:
Density Hessian at the critical points (6 values, being the upper triangle of the Hessian).
- Shape:
[nCriticalPoints, 6]
QTAIM%nBondPaths- Type:
int
- Description:
Number of bond paths.
QTAIM%nCriticalPoints- Type:
int
- Description:
Number of critical points.
QTAIM%nStepsBondPaths- Type:
int_array
- Description:
The number of steps each bond path is made of.
- Shape:
[nBondPaths]
QTAIM%RankSignatureCPs- Type:
lchar_string_array
- Description:
Type of critical points. Possible values are: Atom, Cage, Bond, Ring.
- Shape:
[nCriticalPoints]
- RadialAtomicFunctions
Section content: Info regarding spherical atom centered functions.
RadialAtomicFunctions%d2RadialFunc(#{func},#{type})- Type:
float_array
- Description:
Second derivative of the radial function.
- Shape:
[NumericalBasisSets%NumRad(#{type})]
RadialAtomicFunctions%dRadialFunc(#{func},#{type})- Type:
float_array
- Description:
Derivative of the radial function.
- Shape:
[NumericalBasisSets%NumRad(#{type})]
RadialAtomicFunctions%FunctionType(#{func},#{type})- Type:
string
- Description:
FunctionType(a,b) gives the name of function a for type b. It could have a value like core density.
RadialAtomicFunctions%nFunctions- Type:
int
- Description:
The number of radial functions stored for each type. For instance if you store the core and the valence density it is two.
RadialAtomicFunctions%nTypes- Type:
int
- Description:
The number of types: elements with a different basis set. Normally this is just the number of distinct elements in the system.
RadialAtomicFunctions%RadialFunc(#{func},#{type})- Type:
float_array
- Description:
RadialFunc(a,b) gives the radial table for function a for type b
- Shape:
[NumericalBasisSets%NumRad(#{type})]
- SCCLogger
Section content: Details on the SCC logger.
- Symmetry
Section content: Info regarding the symmetry of the system.
Symmetry%nOperators- Type:
int
- Description:
The number of symmetry operations.
Symmetry%nsym excitations- Type:
int
- Description:
The number of symmetries for excitations..
Symmetry%PointGroupOperators- Type:
float_array
- Description:
The Point group part of the operators.
- Shape:
[3, 3, nOperators]
Symmetry%symlab excitations- Type:
lchar_string_array
- Description:
labels.
- Shape:
[nsym excitations]
Symmetry%Translations- Type:
float_array
- Description:
The (fractional lattice) translations part of the operators.
- Shape:
[3, nOperators]
- Thermodynamics
Section content: Thermodynamic properties computed from normal modes.
Thermodynamics%Enthalpy- Type:
float_array
- Description:
Enthalpy.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%Entropy rotational- Type:
float_array
- Description:
Rotational contribution to the entropy.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%Entropy total- Type:
float_array
- Description:
Total entropy.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%Entropy translational- Type:
float_array
- Description:
Translational contribution to the entropy.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%Entropy vibrational- Type:
float_array
- Description:
Vibrational contribution to the entropy.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%Gibbs free Energy- Type:
float_array
- Description:
Gibbs free energy.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%Heat Capacity rotational- Type:
float_array
- Description:
Rotational contribution to the heat capacity.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%Heat Capacity total- Type:
float_array
- Description:
Total heat capacity.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%Heat Capacity translational- Type:
float_array
- Description:
Translational contribution to the heat capacity.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%Heat Capacity vibrational- Type:
float_array
- Description:
Vibrational contribution to the heat capacity.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%Inertia direction vectors- Type:
float_array
- Description:
Inertia direction vectors.
- Shape:
[3, 3]
Thermodynamics%Internal Energy rotational- Type:
float_array
- Description:
Rotational contribution to the internal energy.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%Internal Energy total- Type:
float_array
- Description:
Total internal energy.
- Unit:
a.u.
Thermodynamics%Internal Energy translational- Type:
float_array
- Description:
Translational contribution to the internal energy.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%Internal Energy vibrational- Type:
float_array
- Description:
Vibrational contribution to the internal energy.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%lowFreqEntropy- Type:
float_array
- Description:
Entropy contributions from low frequencies (see ‘lowFrequencies’).
- Unit:
a.u.
- Shape:
[nLowFrequencies]
Thermodynamics%lowFreqHeatCapacity- Type:
float_array
- Description:
Heat capacity contributions from low frequencies (see ‘lowFrequencies’).
- Unit:
a.u.
- Shape:
[nLowFrequencies]
Thermodynamics%lowFreqInternalEnergy- Type:
float_array
- Description:
Internal energy contributions from low frequencies (see ‘lowFrequencies’).
- Unit:
a.u.
- Shape:
[nLowFrequencies]
Thermodynamics%lowFrequencies- Type:
float_array
- Description:
Frequencies below 20 cm^-1 (contributions from frequencies below 20 cm^-1 are not included in vibrational sums, and are saved separately to ‘lowFreqEntropy’, ‘lowFreqInternalEnergy’ and ‘lowFreqInternalEnergy’). Note: this does not apply to RRHO-corrected quantities.
- Unit:
cm^-1
- Shape:
[nLowFrequencies]
Thermodynamics%Moments of inertia- Type:
float_array
- Description:
Moments of inertia.
- Unit:
a.u.
- Shape:
[3]
Thermodynamics%nLowFrequencies- Type:
int
- Description:
Number of elements in the array lowFrequencies.
Thermodynamics%nTemperatures- Type:
int
- Description:
Number of temperatures.
Thermodynamics%Pressure- Type:
float
- Description:
Pressure used.
- Unit:
atm
Thermodynamics%RRHOCorrectedHeatCapacity- Type:
float_array
- Description:
Heat capacity T*S corrected using the ‘low vibrational frequency free rotor interpolation corrections’.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%RRHOCorrectedInternalEnergy- Type:
float_array
- Description:
Internal energy T*S corrected using the ‘low vibrational frequency free rotor interpolation corrections’.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%RRHOCorrectedTS- Type:
float_array
- Description:
T*S corrected using the ‘low vibrational frequency free rotor interpolation corrections’.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%Temperature- Type:
float_array
- Description:
List of temperatures at which properties are calculated.
- Unit:
a.u.
- Shape:
[nTemperatures]
Thermodynamics%TS- Type:
float_array
- Description:
T*S, i.e. temperature times entropy.
- Unit:
a.u.
- Shape:
[nTemperatures]
- TransferIntegrals
Section content: Charge transfer integrals relevant for hole or electron mobility calculations. Electronic coupling V (also known as effective (generalized) transfer integrals J_eff) V = (J-S(e1+e2)/2)/(1-S^2). For electron mobility calculations the fragment LUMOs are considered. For hole mobility calculations the fragment HOMOs are considered.
TransferIntegrals%Determinant- Type:
float
- Description:
Determinant related to overlap integrals used in ADF FOCDFT%electrontransfer.
TransferIntegrals%e1(electron)- Type:
float
- Description:
Site energy LUMO fragment 1.
- Unit:
hartree
TransferIntegrals%e1(hole)- Type:
float
- Description:
Site energy HOMO fragment 1.
- Unit:
hartree
TransferIntegrals%e2(electron)- Type:
float
- Description:
Site energy LUMO fragment 2.
- Unit:
hartree
TransferIntegrals%e2(hole)- Type:
float
- Description:
Site energy HOMO fragment 2.
- Unit:
hartree
TransferIntegrals%Electronic coupling- Type:
float
- Description:
Electronic coupling calculated by ADF FOCDFT%electrontransfer.
TransferIntegrals%J(charge recombination 12)- Type:
float
- Description:
Charge transfer integral HOMO fragment 1 - LUMO fragment 2 for charge recombination 1-2.
- Unit:
hartree
TransferIntegrals%J(charge recombination 21)- Type:
float
- Description:
Charge transfer integral LUMO fragment 1 - HOMO fragment 2 for charge recombination 2-1.
- Unit:
hartree
TransferIntegrals%J(electron)- Type:
float
- Description:
Charge transfer integral LUMO fragment 1 - LUMO fragment 2 for electron transfer.
- Unit:
hartree
TransferIntegrals%J(hole)- Type:
float
- Description:
Charge transfer integral HOMO fragment 1 - HOMO fragment 2 for hole transfer.
- Unit:
hartree
TransferIntegrals%S(charge recombination 12)- Type:
float
- Description:
Overlap integral HOMO fragment 1 - LUMO fragment 2 for charge recombination 1-2.
TransferIntegrals%S(charge recombination 21)- Type:
float
- Description:
Overlap integral LUMO fragment 1 - HOMO fragment 2 for charge recombination 2-1.
TransferIntegrals%S(electron)- Type:
float
- Description:
Overlap integral LUMO fragment 1 - LUMO fragment 2.
TransferIntegrals%S(hole)- Type:
float
- Description:
Overlap integral HOMO fragment 1 - HOMO fragment 2.
TransferIntegrals%V(charge recombination 12)- Type:
float
- Description:
Effective charge transfer integral HOMO fragment 1 - LUMO fragment 2 for charge recombination 1-2.
- Unit:
hartree
TransferIntegrals%V(charge recombination 21)- Type:
float
- Description:
Effective charge transfer integral LUMO fragment 1 - HOMO fragment 2 for charge recombination 2-1.
- Unit:
hartree
TransferIntegrals%V(electron)- Type:
float
- Description:
Effective transfer integral LUMO fragment 1 - LUMO fragment 2 for electron transfer.
- Unit:
hartree
TransferIntegrals%V(hole)- Type:
float
- Description:
Effective transfer integral HOMO fragment 1 - HOMO fragment 2 for hole transfer.
- Unit:
hartree
TransferIntegrals%Vtot(charge recombination 12)- Type:
float
- Description:
Total electronic coupling for charge recombination 1-2.
- Unit:
hartree
TransferIntegrals%Vtot(charge recombination 21)- Type:
float
- Description:
Total electronic coupling for charge recombination 2-1.
- Unit:
hartree
TransferIntegrals%Vtot(electron)- Type:
float
- Description:
Total electronic coupling for electron transfer.
- Unit:
hartree
TransferIntegrals%Vtot(hole)- Type:
float
- Description:
Total electronic coupling for hole transfer.
- Unit:
hartree
- Vibrations
Section content: Information related to molecular vibrations.
Vibrations%ExcitedStateLifetime- Type:
float
- Description:
Raman excited state lifetime.
- Unit:
hartree
Vibrations%ForceConstants- Type:
float_array
- Description:
The force constants of the vibrations.
- Unit:
hartree/bohr^2
- Shape:
[nNormalModes]
Vibrations%Frequencies[cm-1]- Type:
float_array
- Description:
The vibrational frequencies of the normal modes.
- Unit:
cm^-1
- Shape:
[nNormalModes]
Vibrations%Intensities[km/mol]- Type:
float_array
- Description:
The intensity of the normal modes.
- Unit:
km/mol
- Shape:
[nNormalModes]
Vibrations%IrReps- Type:
lchar_string_array
- Description:
Symmetry symbol of the normal mode.
- Shape:
[nNormalModes]
Vibrations%ModesNorm2- Type:
float_array
- Description:
Norms of the rigid motions.
- Shape:
[nNormalModes+nRigidModes]
Vibrations%ModesNorm2*- Type:
float_array
- Description:
Norms of the rigid motions (for a given irrep…?).
- Shape:
[nNormalModes+nRigidModes]
Vibrations%nNormalModes- Type:
int
- Description:
Number of normal modes.
Vibrations%NoWeightNormalMode(#)- Type:
float_array
- Description:
?.
- Shape:
[3, Molecule%nAtoms]
Vibrations%NoWeightRigidMode(#)- Type:
float_array
- Description:
?
- Shape:
[3, Molecule%nAtoms]
Vibrations%nRigidModes- Type:
int
- Description:
Number of rigid modes.
Vibrations%nSemiRigidModes- Type:
int
- Description:
Number of semi-rigid modes.
Vibrations%PVDOS- Type:
float_array
- Description:
Partial vibrational density of states.
- Values range:
[0.0, 1.0]
- Shape:
[nNormalModes, Molecule%nAtoms]
Vibrations%RamanDepolRatioLin- Type:
float_array
- Description:
Raman depol ratio (lin).
- Shape:
[nNormalModes]
Vibrations%RamanDepolRatioNat- Type:
float_array
- Description:
Raman depol ratio (nat).
- Shape:
[nNormalModes]
Vibrations%RamanIncidentFreq- Type:
float
- Description:
Raman incident light frequency.
- Unit:
hartree
Vibrations%RamanIntens[A^4/amu]- Type:
float_array
- Description:
Raman intensities
- Unit:
A^4/amu
- Shape:
[nNormalModes]
Vibrations%ReducedMasses- Type:
float_array
- Description:
The reduced masses of the normal modes.
- Unit:
a.u.
- Values range:
[0, ‘\infinity’]
- Shape:
[nNormalModes]
Vibrations%RotationalStrength- Type:
float_array
- Description:
The rotational strength of the normal modes.
- Shape:
[nNormalModes]
Vibrations%TransformationMatrix- Type:
float_array
- Description:
?
- Shape:
[3, Molecule%nAtoms, nNormalModes]
Vibrations%VROACIDBackward- Type:
float_array
- Description:
VROA Circular Intensity Differential: Backward scattering.
- Unit:
10⁻3
- Shape:
[nNormalModes]
Vibrations%VROACIDDePolarized- Type:
float_array
- Description:
VROA Circular Intensity Differential: Depolarized scattering.
- Unit:
10⁻3
- Shape:
[nNormalModes]
Vibrations%VROACIDForward- Type:
float_array
- Description:
VROA Circular Intensity Differential: Forward scattering.
- Unit:
10⁻3
- Shape:
[nNormalModes]
Vibrations%VROACIDPolarized- Type:
float_array
- Description:
VROA Circular Intensity Differential: Polarized scattering.
- Unit:
10⁻3
- Shape:
[nNormalModes]
Vibrations%VROADeltaBackward- Type:
float_array
- Description:
VROA Intensity: Backward scattering.
- Unit:
10⁻3 A^4/amu
- Shape:
[nNormalModes]
Vibrations%VROADeltaDePolarized- Type:
float_array
- Description:
VROA Intensity: Depolarized scattering.
- Unit:
10⁻3 A^4/amu
- Shape:
[nNormalModes]
Vibrations%VROADeltaForward- Type:
float_array
- Description:
VROA Intensity: Forward scattering.
- Unit:
10⁻3 A^4/amu
- Shape:
[nNormalModes]
Vibrations%VROADeltaPolarized- Type:
float_array
- Description:
VROA Intensity: Polarized scattering.
- Unit:
10⁻3 A^4/amu
- Shape:
[nNormalModes]
Vibrations%ZeroPointEnergy- Type:
float
- Description:
Vibrational zero-point energy.
- Unit:
hartree
- WScell(reciprocal_space)
Section content: The Wigner Seitz cell of reciprocal space, i.e. the Brillouin zone.
WScell(reciprocal_space)%boundaries- Type:
float_array
- Description:
Normal vectors for the boundaries.
- Shape:
[ndim, nboundaries]
WScell(reciprocal_space)%distances- Type:
float_array
- Description:
Distance to the boundaries.
- Shape:
[nboundaries]
WScell(reciprocal_space)%idVerticesPerBound- Type:
int_array
- Description:
The indices of the vertices per bound.
- Shape:
[nvertices, nboundaries]
WScell(reciprocal_space)%latticeVectors- Type:
float_array
- Description:
The lattice vectors.
- Shape:
[3, :]
WScell(reciprocal_space)%nboundaries- Type:
int
- Description:
The nr. of boundaries for the cell.
WScell(reciprocal_space)%ndim- Type:
int
- Description:
The nr. of lattice vectors spanning the Wigner-Seitz cell.
WScell(reciprocal_space)%numVerticesPerBound- Type:
int_array
- Description:
The nr. of vertices per bound.
- Shape:
[nboundaries]
WScell(reciprocal_space)%nvertices- Type:
int
- Description:
The nr. of vertices of the cell.
WScell(reciprocal_space)%vertices- Type:
float_array
- Description:
The vertices of the bounds.
- Unit:
a.u.
- Shape:
[ndim, nvertices]