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]])

Sections and variables on gfnff.rkf¶

AMSResults

Section content: Generic results of the ForceField Engine evaluation.

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%Config

Type:

subsection

Description:

Configuration of the GFNFF engine.

AMSResults%Config%accuracy

Type:

float

Description:

Accuracy parameter of GFNFF.

AMSResults%Config%includeBend

Type:

bool

Description:

Whether the following forcefield term was included: bending.

AMSResults%Config%includeBondedATM

Type:

bool

Description:

Whether the following forcefield term was included: bonded ATM

AMSResults%Config%includeBonding

Type:

bool

Description:

Whether the following forcefield term was included: bond potentials.

AMSResults%Config%includeDispersion

Type:

bool

Description:

Whether the following forcefield term was included: dispersion.

AMSResults%Config%includeEField

Type:

bool

Description:

Whether the following forcefield term was included: E field.

AMSResults%Config%includeElstat

Type:

bool

Description:

Whether the following forcefield term was included: electrostatic.

AMSResults%Config%includeHBonding

Type:

bool

Description:

Whether the following forcefield term was included: HB.

AMSResults%Config%includeRepulsion

Type:

bool

Description:

Whether the following forcefield term was included: bonded repulsion.

AMSResults%Config%includeSolvation

Type:

bool

Description:

Whether the following forcefield term was included: solvation.

AMSResults%Config%includeTors

Type:

bool

Description:

Whether the following forcefield term was included: torsions.

AMSResults%Config%includeXBonding

Type:

bool

Description:

Whether the following forcefield term was included: XB.

AMSResults%Config%version

Type:

int

Description:

Number indicating the version of the gfnff parameters used.

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%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%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%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%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

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]

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]

General

Section content: General information about the GFNFF 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(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.

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

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]

Properties

Section content: Generic container for properties. The program band uses different rules for Types and Subtypes.

Properties%nEntries

Type:

int

Description:

Number of properties.

Properties%Subtype(#)

Type:

string_fixed_length

Description:

Extra detail about the property. For a charge property this could be Mulliken.

Properties%Type(#)

Type:

string

Description:

Type of the property, like energy, gradients, charges, etc.

Properties%Value(#)

Type:

float_array

Description:

The value(s) of the property.

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]

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