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 ams.rkf¶
Note
The AMS driver creates an entire directory full of result files.
Often there are multiple .rkf files in that directory.
This page only documents the sections and variables in the ams.rkf file.
- BindingSites
Section content: Information on binding sites for a adsorbate.
BindingSites%AdsorbateLabel- Type
string
- Description
Label for the adsorbate.
BindingSites%AverEnergy- Type
float_array
- Description
The average energy per site. The energy of all stationary states that at least has an atom attached to the given site contributes to this average.
- Unit
hartree
- Shape
[nSites]
BindingSites%Coords- Type
float_array
- Description
The coordinates of the sites.
- Unit
bohr
- Shape
[3, nSites]
BindingSites%CoordsFrac- Type
float_array
- Description
The fractional coordinates of the sites.
- Shape
[3, nSites]
BindingSites%FromSites- Type
int_array
- Description
Sites from where the connections start.
- Shape
[nConnections]
BindingSites%Labels- Type
lchar_string_array
- Description
Arbitrary labels for the binding sites. They are assigned according to the number of atom neighbors.
BindingSites%LatticeDisplacements- Type
int_array
- Description
Links between neighboring sites across the periodic boundary conditions.
- Shape
[:, nConnections]
BindingSites%nConnections- Type
int
- Description
The number of connections between sites.
BindingSites%nParentStates- Type
int_array
- Description
The number of stationary states contributing to the average and standard deviation of the energy. See AverEnergy and StdevEnergy.
- Shape
[nSites]
BindingSites%nSites- Type
int
- Description
The number of sites.
BindingSites%ParentAtoms- Type
int_array
- Description
Atom id that is attached to the site in the corresponding parent state. See ParentStates.
- Shape
[:]
BindingSites%ParentStates- Type
int_array
- Description
Stationary states ids contributing to the average and standard deviation of the energy. See AverEnergy and StdevEnergy.
- Shape
[:]
BindingSites%ReferenceRegionLabel- Type
string
- Description
Label for the reference region.
BindingSites%StdevEnergy- Type
float_array
- Description
Std. deviation for energy per site. The energy of all stationary states that at least has an atom attached to the given site contributes to this std. deviation.
- Unit
hartree
- Shape
[nSites]
BindingSites%ToSites- Type
int_array
- Description
Sites to where the connections end up.
- Shape
[nConnections]
- BinLog
Section content:
BinLog%Area(#)- Type
float_array
- Description
The area of the cell (only for 2D PBC). This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
bohr^2
BinLog%BiasEnergy(#)- Type
float_array
- Description
? This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
hartree
BinLog%blockSize- Type
int
- Description
Explain the block-system… ?
BinLog%BoostFactor(#)- Type
float_array
- Description
The boost factor for hyper-dynamics. Expand? This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
BinLog%ConservedEnergy(#)- Type
float_array
- Description
The conserved energy…? Some MD person, please fix. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
hartree
BinLog%currentEntryOpen- Type
bool
- Description
?
BinLog%Density(#)- Type
float_array
- Description
The density of the system (mass/simulation_cell_volume). Only for 3D PBC. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
dalton/bohr^3
BinLog%DipoleMoment_*(#)- Type
float_array
- Description
The dipolemoment of the full system. For periodic systems this value will often not make sense, because molecules are not mapped together
BinLog%Hypertime(#)- Type
float_array
- Description
Hyper time for hyper-dynamics. Expand? This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
femtosecond
BinLog%ItemName(#)- Type
string
- Description
?
BinLog%KineticEnergy(#)- Type
float_array
- Description
The kinetic energy of the system. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
hartree
BinLog%Length(#)- Type
float_array
- Description
The length of the cell (only for 1D PBC). This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
bohr
BinLog%MaxBiasEnergy(#)- Type
float_array
- Description
? This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
hartree
BinLog%MaxBoostFactor(#)- Type
float_array
- Description
The maximum boost factor for hyper-dynamics. Expand? This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
BinLog%nBlocks- Type
int
- Description
Explain the block-system… ?
BinLog%nEntries- Type
int
- Description
Number of MD history entries.
BinLog%PotentialEnergy(#)- Type
float_array
- Description
The potential energy, i.e. the energy as computed by the engine. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
hartree
BinLog%Pressure(#)- Type
float_array
- Description
The pressure of the system (only for 3D PBC). This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
hartree/bohr^3
BinLog%PressureTensor_*(#)- Type
float_array
- Description
?
BinLog%Step(#)- Type
int_array
- Description
The step number of the MD calculation. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
BinLog%Temperature(#)- Type
float_array
- Description
The temperature of the system, computed from the kinetic energy?. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
kelvin
BinLog%Time(#)- Type
float_array
- Description
The MD simulation time. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
femtosecond
BinLog%TotalEnergy(#)- Type
float_array
- Description
The total energy of the system: potential energy (as computed by the engine) + kinetic energy. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
hartree
BinLog%Volume(#)- Type
float_array
- Description
The volume of the cell (only for 3D PBC). This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
bohr^3
- ChemicalSystem(#)
Section content: Various ‘versions’ of the chemical system. See also the ‘SystemVersionHistory’ section.
ChemicalSystem(#)%AtomicNumbers- Type
int_array
- Description
Atomic number ‘Z’ of the atoms in the system
- Shape
[nAtoms]
ChemicalSystem(#)%AtomMasses- Type
float_array
- Description
Masses of the atoms
- Unit
a.u.
- Values range
[0, ‘\infinity’]
- Shape
[nAtoms]
ChemicalSystem(#)%AtomSymbols- Type
string
- Description
The atom’s symbols (e.g. ‘C’ for carbon)
- Shape
[nAtoms]
ChemicalSystem(#)%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
ChemicalSystem(#)%Charge- Type
float
- Description
Net charge of the system
- Unit
e
ChemicalSystem(#)%Coords- Type
float_array
- Description
Coordinates of the nuclei (x,y,z)
- Unit
bohr
- Shape
[3, nAtoms]
ChemicalSystem(#)%eeAttachTo- Type
int_array
- Description
A multipole may be attached to an atom. This influences the energy gradient.
ChemicalSystem(#)%eeChargeWidth- Type
float
- Description
If charge broadening was used for external charges, this represents the width of the charge distribution.
ChemicalSystem(#)%eeEField- Type
float_array
- Description
The external homogeneous electric field.
- Unit
hartree/(e*bohr)
- Shape
[3]
ChemicalSystem(#)%eeLatticeVectors- Type
float_array
- Description
The lattice vectors used for the external point- or multipole- charges.
- Unit
bohr
- Shape
[3, eeNLatticeVectors]
ChemicalSystem(#)%eeMulti- Type
float_array
- Description
The values of the external point- or multipole- charges.
- Unit
a.u.
- Shape
[eeNZlm, eeNMulti]
ChemicalSystem(#)%eeNLatticeVectors- Type
int
- Description
The number of lattice vectors for the external point- or multipole- charges.
ChemicalSystem(#)%eeNMulti- Type
int
- Description
The number of external point- or multipole- charges.
ChemicalSystem(#)%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).
ChemicalSystem(#)%eeUseChargeBroadening- Type
bool
- Description
Whether or not the external charges are point-like or broadened.
ChemicalSystem(#)%eeXYZ- Type
float_array
- Description
The position of the external point- or multipole- charges.
- Unit
bohr
- Shape
[3, eeNMulti]
ChemicalSystem(#)%EngineAtomicInfo- Type
string_fixed_length
- Description
Atom-wise info possibly used by the engine.
ChemicalSystem(#)%fromAtoms- Type
int_array
- Description
Index of the first atom in a bond. See the bondOrders array
ChemicalSystem(#)%latticeDisplacements- Type
int_array
- Description
The integer lattice translations for the bonds defined in the variables bondOrders, fromAtoms and toAtoms.
ChemicalSystem(#)%LatticeVectors- Type
float_array
- Description
Lattice vectors
- Unit
bohr
- Shape
[3, nLatticeVectors]
ChemicalSystem(#)%nAtoms- Type
int
- Description
The number of atoms in the system
ChemicalSystem(#)%nAtomsTypes- Type
int
- Description
The number different of atoms types
ChemicalSystem(#)%nLatticeVectors- Type
int
- Description
Number of lattice vectors (i.e. number of periodic boundary conditions)
- Possible values
[0, 1, 2, 3]
ChemicalSystem(#)%toAtoms- Type
int_array
- Description
Index of the second atom in a bond. See the bondOrders array
- CrestMTDHistory
Section content: Data related to Crest MD.
- CVHDBiasHistory
Section content: ?
CVHDBiasHistory%blockSize- Type
int
- Description
Explain the block-system… ?
CVHDBiasHistory%currentEntryOpen- Type
bool
- Description
?
CVHDBiasHistory%CVValue(#)- Type
float_array
- Description
?
CVHDBiasHistory%Height(#)- Type
float_array
- Description
?
CVHDBiasHistory%ItemName(#)- Type
string
- Description
?
CVHDBiasHistory%nBlocks- Type
int
- Description
Explain the block-system… ?
CVHDBiasHistory%nEntries- Type
int
- Description
Number of MD history entries.
CVHDBiasHistory%Step(#)- Type
int_array
- Description
The step number of the MD calculation. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- EnergyLandscape
Section content: Information on PES exploration.
EnergyLandscape%counts- Type
int_array
- Description
Number of times that the exploration job found each state.
- Shape
[nStates]
EnergyLandscape%Edge(#)- Type
subsection
- Description
From acerxn ?
EnergyLandscape%Edge(#)%brokenAtomsFrom- Type
int_array
- Description
From acerxn ?
EnergyLandscape%Edge(#)%brokenAtomsTo- Type
int_array
- Description
From acerxn ?
EnergyLandscape%Edge(#)%formedAtomsFrom- Type
int_array
- Description
From acerxn ?
EnergyLandscape%Edge(#)%formedAtomsTo- Type
int_array
- Description
From acerxn ?
EnergyLandscape%edgesBegin- Type
int_array
- Description
From acerxn ?
EnergyLandscape%edgesEnd- Type
int_array
- Description
From acerxn ?
EnergyLandscape%energies- Type
float_array
- Description
Energies of the stationary states.
- Unit
hartree
- Shape
[nStates]
EnergyLandscape%energyReferenceLabels- Type
string
- Description
?
EnergyLandscape%energyReferenceValues- Type
float_array
- Description
?
EnergyLandscape%fileNames- Type
ftl_string_array
- Description
Filenames for the stationary state calculations.
- Shape
[nStates]
EnergyLandscape%fragmentsEnergies- Type
float_array
- Description
?
EnergyLandscape%fragmentsFileNames- Type
string
- Description
?
EnergyLandscape%fragmentsRegions- Type
string
- Description
?
EnergyLandscape%fStatesAdsorptionPrefactors(#)- Type
float_array
- Description
?
EnergyLandscape%fStatesComposition(#)- Type
int_array
- Description
?
EnergyLandscape%fStatesConnections(#)- Type
int_array
- Description
?
EnergyLandscape%fStatesDesorptionPrefactors(#)- Type
float_array
- Description
?
EnergyLandscape%fStatesEnergy(#)- Type
float
- Description
?
EnergyLandscape%fStatesNConnections(#)- Type
int
- Description
?
EnergyLandscape%fStatesNFragments(#)- Type
int
- Description
?
EnergyLandscape%historyIndices- Type
int_array
- Description
Indices of the corresponding entries in the History section.
- Shape
[nStates]
EnergyLandscape%isTS- Type
bool_array
- Description
Whether a state is a transition state or a minimum.
- Shape
[nStates]
EnergyLandscape%names- Type
string
- Description
From acerxn ?
EnergyLandscape%nEdges- Type
int
- Description
From acerxn ?
EnergyLandscape%nFragments- Type
int
- Description
?
EnergyLandscape%nFStates- Type
int
- Description
?
EnergyLandscape%nStates- Type
int
- Description
The number of stationary states (points with vanishing gradient).
EnergyLandscape%prefactorsFromProduct- Type
float_array
- Description
?
EnergyLandscape%prefactorsFromReactant- Type
float_array
- Description
?
EnergyLandscape%prefactorsTemperature- Type
float
- Description
?
EnergyLandscape%products- Type
int_array
- Description
For stationary states that are a TS state this is the connected product.
- Shape
[nStates]
EnergyLandscape%reactants- Type
int_array
- Description
For stationary states that are a TS state this is the connected reactant.
- Shape
[nStates]
EnergyLandscape%referenceRegionLabel- Type
string
- Description
?
- EngineResults
Section content: Description and names of engine result files.
EngineResults%Description(#)- Type
string
- Description
Description of the results.
EngineResults%Files(#)- Type
string
- Description
Filenames of the result files from the engine
EngineResults%nEntries- Type
int
- Description
Number of engine results files.
EngineResults%Title(#)- Type
string
- Description
Title of engine calculations.
- GCMC
Section content: Data related to the Gran Canonical Monte Carlo procedure
GCMC%AccessibleVolume- Type
float
- Description
input accessible volume
GCMC%AtomicNumbers- Type
int_array
- Description
Atomic number ‘Z’ of the atoms in the system
- Shape
[nAtoms]
GCMC%AtomMasses- Type
float_array
- Description
Masses of the atoms
- Unit
a.u.
- Values range
[0, ‘\infinity’]
- Shape
[nAtoms]
GCMC%AtomSymbols- Type
string
- Description
The atom’s symbols (e.g. ‘C’ for carbon)
- Shape
[nAtoms]
GCMC%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
GCMC%Box- Type
float_array
- Description
Range of cell coordinates where atoms are allowed to be added (x,y,z min,max?)
- Unit
bohr
- Shape
[3, 2]
GCMC%ChangeVolume- Type
bool
- Description
Allow volume changes
GCMC%Charge- Type
float
- Description
Net charge of the system
- Unit
e
GCMC%Coords- Type
float_array
- Description
Coordinates of the nuclei (x,y,z)
- Unit
bohr
- Shape
[3, nAtoms]
GCMC%eeAttachTo- Type
int_array
- Description
A multipole may be attached to an atom. This influences the energy gradient.
GCMC%eeChargeWidth- Type
float
- Description
If charge broadening was used for external charges, this represents the width of the charge distribution.
GCMC%eeEField- Type
float_array
- Description
The external homogeneous electric field.
- Unit
hartree/(e*bohr)
- Shape
[3]
GCMC%eeLatticeVectors- Type
float_array
- Description
The lattice vectors used for the external point- or multipole- charges.
- Unit
bohr
- Shape
[3, eeNLatticeVectors]
GCMC%eeMulti- Type
float_array
- Description
The values of the external point- or multipole- charges.
- Unit
a.u.
- Shape
[eeNZlm, eeNMulti]
GCMC%eeNLatticeVectors- Type
int
- Description
The number of lattice vectors for the external point- or multipole- charges.
GCMC%eeNMulti- Type
int
- Description
The number of external point- or multipole- charges.
GCMC%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).
GCMC%eeUseChargeBroadening- Type
bool
- Description
Whether or not the external charges are point-like or broadened.
GCMC%eeXYZ- Type
float_array
- Description
The position of the external point- or multipole- charges.
- Unit
bohr
- Shape
[3, eeNMulti]
GCMC%EngineAtomicInfo- Type
string_fixed_length
- Description
Atom-wise info possibly used by the engine.
GCMC%fromAtoms- Type
int_array
- Description
Index of the first atom in a bond. See the bondOrders array
GCMC%HistoryAccepted- Type
int_array
- Description
result (1-accepted, 0-rejected)
- Shape
[NIterMCtried]
GCMC%HistoryAMSEnergy- Type
float_array
- Description
energy (AMSEnergy)
- Shape
[NIterMCtried]
GCMC%HistoryMCEnergy- Type
float_array
- Description
corrected MC energy (AMSEnergy - sum(ChemicalPotential))
- Shape
[NIterMCtried]
GCMC%HistoryMoleculeIndex- Type
int_array
- Description
molecule index of the type
- Shape
[NIterMCtried]
GCMC%HistoryMoleculeType- Type
int_array
- Description
molecule type
- Shape
[NIterMCtried]
GCMC%HistoryMoveType- Type
int_array
- Description
action type
- Shape
[NIterMCtried]
GCMC%HistoryVolume- Type
float_array
- Description
?
- Shape
[NIterMCtried]
GCMC%InitialEnergy- Type
float
- Description
?
- Unit
hartree
GCMC%Iterations- Type
int
- Description
Number of MC iterations before stopping
GCMC%latticeDisplacements- Type
int_array
- Description
The integer lattice translations for the bonds defined in the variables bondOrders, fromAtoms and toAtoms.
GCMC%LatticeVectors- Type
float_array
- Description
Lattice vectors
- Unit
bohr
- Shape
[3, nLatticeVectors]
GCMC%MapToOriginalCell- Type
bool
- Description
map atoms back to the original cell?
GCMC%MaxDistance- Type
float
- Description
Max radius for atom placement
- Unit
bohr
GCMC%MinDistance- Type
float
- Description
Min radius for atom placement
- Unit
bohr
GCMC%Mol#- Type
subsection
- Description
?
GCMC%Mol#%addedAtoms- Type
archived_int_array
- Description
Atom species indices
GCMC%Mol#%AtomicInfo- Type
archived_string_array
- Description
GCMC%Mol#%BondOrders- Type
archived_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
GCMC%Mol#%Charge- Type
float
- Description
Net charge of the system
- Unit
e
GCMC%Mol#%chemPot- Type
float
- Description
?
GCMC%Mol#%eeAttachTo- Type
archived_int_array
- Description
A multipole may be attached to an atom. This influences the energy gradient.
GCMC%Mol#%eeChargeWidth- Type
float
- Description
If charge broadening was used for external charges, this represents the width of the charge distribution
GCMC%Mol#%eeEField- Type
float_array
- Description
The external homogeneous electric field
- Unit
hartree/(e*bohr)
- Shape
[3]
GCMC%Mol#%eeLatticeVectors- Type
archived_float_array
- Description
The lattice vectors used for the external point- or multipole- charges
- Unit
bohr
GCMC%Mol#%eeMultipoles- Type
archived_float_array
- Description
The multiple charges.
- Unit
bohr
GCMC%Mol#%eenMulti- Type
int
- Description
The number of multipoles.
GCMC%Mol#%eeUseChargeBroadening- Type
bool
- Description
Whether or not the external charges are point-like or broadened
GCMC%Mol#%eeXYZ- Type
archived_float_array
- Description
The position of the external point- or multipole- charges
- Unit
bohr
GCMC%Mol#%FromAtoms- Type
archived_int_array
- Description
Index of the first atom in a bond. See the bondOrders array
GCMC%Mol#%hasLatticeDisplacements- Type
bool
- Description
The integer lattice translations for the bonds defined in the variables bondOrders, fromAtoms and toAtoms.
GCMC%Mol#%inserted- Type
int_array
- Description
?
GCMC%Mol#%kVectors- Type
float_array
- Description
Reciprocal lattice vectors (corresponding to the strained lattice vectors)
- Unit
1/bohr
- Shape
[3, 3]
GCMC%Mol#%LatticeDisplacements- Type
archived_int_array
- Description
The integer lattice translations for the bonds defined in the variables bondOrders, fromAtoms and toAtoms.
GCMC%Mol#%name- Type
string
- Description
?
GCMC%Mol#%nAtoms- Type
int
- Description
The number of atoms in the system
GCMC%Mol#%nInsert- Type
int
- Description
?
GCMC%Mol#%noAR- Type
bool
- Description
?
GCMC%Mol#%nSpecies- Type
int
- Description
The number different of atoms types
GCMC%Mol#%nVectors- Type
int
- Description
Number of lattice vectors (0:molecule, 1:chain, 2:slab, 3:bulk).
GCMC%Mol#%removedAtoms- Type
archived_int_array
- Description
Atom species indices
GCMC%Mol#%sp#inputSymbol- Type
string
- Description
Symbol as specified in the input
GCMC%Mol#%sp#mass- Type
float
- Description
mass
GCMC%Mol#%sp#regions- Type
archived_string_array
- Description
regions
GCMC%Mol#%sp#symbol- Type
string
- Description
Element symbol
GCMC%Mol#%sp#Z- Type
int
- Description
Atomic number
GCMC%Mol#%SpIndices- Type
archived_int_array
- Description
Atom species indices
GCMC%Mol#%SPlen- Type
int
- Description
Number of species
GCMC%Mol#%strain- Type
float_array
- Description
The strain matrix.
- Shape
[3, 3]
GCMC%Mol#%strainedVectors- Type
float_array
- Description
Strained real space lattice vectors
- Unit
bohr
- Shape
[3, 3]
GCMC%Mol#%ToAtoms- Type
archived_int_array
- Description
Index of the second atom in a bond. See the bondOrders array
GCMC%Mol#%unstrainedVectors- Type
float_array
- Description
Real space lattice vectors (unstrained).
- Unit
bohr
- Shape
[3, 3]
GCMC%Mol#%version- Type
int
- Description
GCMC%Mol#%xyzAtoms- Type
archived_float_array
- Description
Coordinates of the nuclei (x,y,z)
- Unit
bohr
GCMC%MoleculeName(#)- Type
string
- Description
?
GCMC%MoveType(#)- Type
string
- Description
?
GCMC%nAtoms- Type
int
- Description
The number of atoms in the system
GCMC%nAtomsTypes- Type
int
- Description
The number different of atoms types
GCMC%NIterMCaccept- Type
int
- Description
Number of moves accepted
GCMC%NIterMCreject- Type
int
- Description
Number of moves rejected
GCMC%NIterMCtried- Type
int
- Description
Number of moves tried, aka iteration number
GCMC%nLatticeVectors- Type
int
- Description
Number of lattice vectors (i.e. number of periodic boundary conditions)
- Possible values
[0, 1, 2, 3]
GCMC%NMCacceptAdd- Type
int
- Description
statistics about success rates of MC
GCMC%NMCacceptMove- Type
int
- Description
?
GCMC%NMCacceptRemove- Type
int
- Description
?
GCMC%NMCacceptVolume- Type
int
- Description
?
GCMC%NMCrejectAdd- Type
int
- Description
?
GCMC%NMCrejectMove- Type
int
- Description
?
GCMC%NMCrejectRemove- Type
int
- Description
?
GCMC%NMCrejectVolume- Type
int
- Description
?
GCMC%NMols- Type
int
- Description
?
GCMC%NonAccessibleVolume- Type
float
- Description
input non-accessible (vacuum) volume
GCMC%NumAttempts- Type
int
- Description
Maximum number of trial steps when inserting/moving a molecule
GCMC%Pressure- Type
float
- Description
NPT pressure
- Unit
a.u.
GCMC%Temperature- Type
float
- Description
system temperature
- Unit
kelvin
GCMC%toAtoms- Type
int_array
- Description
Index of the second atom in a bond. See the bondOrders array
GCMC%UseGCPreFactor- Type
bool
- Description
include GCE factors in probability?
GCMC%VolumeChangeMax- Type
float
- Description
input max volume change factor for NPT MC
GCMC%VolumeOption- Type
int
- Description
input accessible volume? 0=no (use total cell volume) 1=yes 2=bulk
- General
Section content: General information about the AMS driver calculation.
General%account- Type
string
- Description
Name of the account from the license
General%CPUTime- Type
float
- Description
CPU time of the AMS calculation.
- Unit
second
General%ElapsedTime- Type
float
- Description
Elapsed time of the AMS calculation.
- Unit
second
General%engine- Type
string
- Description
The main engine of the calculation.
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%SysTime- Type
float
- Description
System time of the AMS calculation.
- Unit
second
General%task- Type
string
- Description
The Task of the AMS driver (e.g. singlepoint, geometryoptimization, moleculardynamics…).
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%user input- Type
string
- Description
The text input of the AMS calculation.
General%version- Type
int
- Description
Version number?
- History
Section content: History of the system during the AMS calculation. What is stored here depends on the task of the AMS calculation. For example, for a GeometryOptimization this will contain the intermediate steps of the GO, while for a MoleculeDynamics calculation it will contain the MD frames.
History%Angle(#)- Type
float
- Description
IRC (Intrinsic Reaction Coordinate) angle((pivot->start),(pivot->coords)), indication of the path curvature.
- Unit
degrees
History%ArcLength(#)- Type
float
- Description
IRC (Intrinsic Reaction Coordinate): length of arc(start->pivot->coords).
- Unit
angstrom
History%Bonds- Type
subsection
- Description
?
History%Bonds%Atoms(#)- Type
int_array
- Description
?
History%Bonds%CellShifts(#)- Type
int_array
- Description
?
History%Bonds%Index(#)- Type
int_array
- Description
?
History%Bonds%Orders(#)- Type
float_array
- Description
?
History%Converged(#)- Type
bool
- Description
Whether the entry corresponds to a converged structure. The meaning of ‘converged’ depends on the Task.
History%Coords(#)- Type
float_array
- Description
Coordinates of the systems of a given entry.
- Shape
[3, :]
History%currentEntryOpen- Type
bool
- Description
Currently open entry?
History%Energy(#)- Type
float
- Description
Energy of the system of a given entry.
- Unit
hartree
History%EnergySubtype- Type
string
- Description
?
History%EngineEnergy(#)- Type
float
- Description
The energy as computed by the engine of a given entry.
- Unit
hartree
History%EngineEnergyU(#)- Type
float
- Description
The uncertainty of the energy as computed by the engine of a given entry.
- Unit
hartree
History%EngineGradients(#)- Type
float_array
- Description
The gradients as computed by the engine of a given entry.
- Unit
hartree/bohr
- Shape
[3, :]
History%EngineGradientsNormU(#)- Type
float_array
- Description
The uncertainty of the norm of the gradients (using the variance formula) as computed by the engine of a given entry.
- Unit
hartree/bohr
- Shape
[3, :]
History%EngineGradientsU(#)- Type
float_array
- Description
The uncertainty of the gradients as computed by the engine of a given entry.
- Unit
hartree/bohr
- Shape
[3, :]
History%ExitConditionMsg- Type
string
- Description
Message from the exit condition on what condition was met.
History%Gradients(#)- Type
float_array
- Description
Nuclear gradients of a given entry
- Unit
hartree/bohr
- Shape
[3, :]
History%IRCDirection(#)- Type
int
- Description
IRC (Intrinsic Reaction Coordinate) direction of a given entry (1=forward, 2=backwards).
History%IRCGradMax(#)- Type
float
- Description
IRC (Intrinsic Reaction Coordinate) Max of the gradient determining the step in the inner loop.
- Unit
hartree/bohr
History%IRCGradRms(#)- Type
float
- Description
IRC (Intrinsic Reaction Coordinate) Root mean square of the gradient determining the step in the inner loop.
- Unit
hartree/bohr
History%IRCIteration(#)- Type
int
- Description
IRC (Intrinsic Reaction Coordinate) outer loop iteration number.
History%ItemName(#)- Type
string
- Description
Name of generic item on this section?
History%LatticeVectors(#)- Type
float_array
- Description
The lattice vectors of a given entry.
- Unit
bohr
- Shape
[3, :]
History%maxGrad(#)- Type
float
- Description
Maximum Cartesian component of the nuclear gradients of a given entry. This is generally used as a convergence criterion in geometry optimizations and similar tasks.
- Unit
hartree/bohr
History%maxStep(#)- Type
float
- Description
Maximum difference in the Cartesian nuclear coordinates from the previous step. This is generally used as a convergence criterion in geometry optimizations and similar tasks.
- Unit
bohr
History%MaxStressEnergyPerAtom(#)- Type
float
- Description
Maximum value of stress_tensor * cell_volume / number_of_atoms (for 2D and 1D systems, the cell_volume is replaced by the cell_area and cell_length respectively). This is the quantity used for determining whether a lattice optimization has converged.
History%MCMolecule(#)- Type
int
- Description
Index of the randomly selected molecule/atom type to MCMove?
History%MCMove(#)- Type
int
- Description
Index of monte carlo move of a given entry.
History%MCMoveType(#)- Type
string
- Description
The type of monte carlo move. Can be one of the following: ‘Insert’, ‘Delete’, ‘Displace’, ‘ChangeVolume’
History%Mols- Type
subsection
- Description
Molecule detection info at various steps.
History%Mols%Atoms(#)- Type
int_array
- Description
atoms(index(i):index(i+1)-1) = atom indices of molecule i
History%Mols%Index(#)- Type
int_array
- Description
Size: Molecules%Num molecules. index(i) = index of the first atom of molecule i in array atoms(:)
History%Mols%Type(#)- Type
int_array
- Description
Index indicating the type of the molecule (‘Molecules%Molecule name #’’)
History%nEntries- Type
int
- Description
Number of history entries.
History%nLatticeVectors(#)- Type
int
- Description
The number of lattice vectors (i.e. the number of periodic boundary conditions) of a given entry.
History%OptIteration(#)- Type
int
- Description
IRC (Intrinsic Reaction Coordinate) inner loop iteration number.
History%OrigStep(#)- Type
int
- Description
Index of the original step for the Replay task.
History%PathLength(#)- Type
float
- Description
IRC (Intrinsic Reaction Coordinate): sum of the arc lengths up to the latest point.
- Unit
angstrom
History%rmsGrad(#)- Type
float
- Description
Root mean square of the nuclear gradients of a given entry. This is generally used as a convergence criterion in geometry optimizations and similar tasks.
- Unit
hartree/bohr
History%rmsStep(#)- Type
float
- Description
Root mean square of the difference between the nuclear coordinates at this step and at the previous step. This is generally used as a convergence criterion in geometry optimizations and similar tasks.
History%Step(#)- Type
int
- Description
The step number in a Molecular Dynamics calculation.
History%StressTensor(#)- Type
float_array
- Description
The stress tensor of a given entry.
- Unit
hartree/bohr^nLatticeVectors
- Shape
[:, :]
History%SystemVersion(#)- Type
int
- Description
Index of the versioned-chemical system of a given frame.
- IMDHORaman
Section content: Resonance raman spectra using IMDHO
IMDHORaman%nspectrum- Type
int
- Description
?
IMDHORaman%overtones- Type
int_array
- Description
?
IMDHORaman%ramanorder- Type
int
- Description
Maximum order of raman final state
IMDHORaman%spectrum- Type
float_array
- Description
?
- InputMolecule
Section content: The main input molecule of the calculation.
InputMolecule%AtomicNumbers- Type
int_array
- Description
Atomic number ‘Z’ of the atoms in the system
- Shape
[nAtoms]
InputMolecule%AtomMasses- Type
float_array
- Description
Masses of the atoms
- Unit
a.u.
- Values range
[0, ‘\infinity’]
- Shape
[nAtoms]
InputMolecule%AtomSymbols- Type
string
- Description
The atom’s symbols (e.g. ‘C’ for carbon)
- Shape
[nAtoms]
InputMolecule%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
InputMolecule%Charge- Type
float
- Description
Net charge of the system
- Unit
e
InputMolecule%Coords- Type
float_array
- Description
Coordinates of the nuclei (x,y,z)
- Unit
bohr
- Shape
[3, nAtoms]
InputMolecule%eeAttachTo- Type
int_array
- Description
A multipole may be attached to an atom. This influences the energy gradient.
InputMolecule%eeChargeWidth- Type
float
- Description
If charge broadening was used for external charges, this represents the width of the charge distribution.
InputMolecule%eeEField- Type
float_array
- Description
The external homogeneous electric field.
- Unit
hartree/(e*bohr)
- Shape
[3]
InputMolecule%eeLatticeVectors- Type
float_array
- Description
The lattice vectors used for the external point- or multipole- charges.
- Unit
bohr
- Shape
[3, eeNLatticeVectors]
InputMolecule%eeMulti- Type
float_array
- Description
The values of the external point- or multipole- charges.
- Unit
a.u.
- Shape
[eeNZlm, eeNMulti]
InputMolecule%eeNLatticeVectors- Type
int
- Description
The number of lattice vectors for the external point- or multipole- charges.
InputMolecule%eeNMulti- Type
int
- Description
The number of external point- or multipole- charges.
InputMolecule%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).
InputMolecule%eeUseChargeBroadening- Type
bool
- Description
Whether or not the external charges are point-like or broadened.
InputMolecule%eeXYZ- Type
float_array
- Description
The position of the external point- or multipole- charges.
- Unit
bohr
- Shape
[3, eeNMulti]
InputMolecule%EngineAtomicInfo- Type
string_fixed_length
- Description
Atom-wise info possibly used by the engine.
InputMolecule%fromAtoms- Type
int_array
- Description
Index of the first atom in a bond. See the bondOrders array
InputMolecule%latticeDisplacements- Type
int_array
- Description
The integer lattice translations for the bonds defined in the variables bondOrders, fromAtoms and toAtoms.
InputMolecule%LatticeVectors- Type
float_array
- Description
Lattice vectors
- Unit
bohr
- Shape
[3, nLatticeVectors]
InputMolecule%nAtoms- Type
int
- Description
The number of atoms in the system
InputMolecule%nAtomsTypes- Type
int
- Description
The number different of atoms types
InputMolecule%nLatticeVectors- Type
int
- Description
Number of lattice vectors (i.e. number of periodic boundary conditions)
- Possible values
[0, 1, 2, 3]
InputMolecule%toAtoms- Type
int_array
- Description
Index of the second atom in a bond. See the bondOrders array
- InputMolecule(#)
Section content: Any auxiliary, named input molecules of the calculation.
InputMolecule(#)%AtomicNumbers- Type
int_array
- Description
Atomic number ‘Z’ of the atoms in the system
- Shape
[nAtoms]
InputMolecule(#)%AtomMasses- Type
float_array
- Description
Masses of the atoms
- Unit
a.u.
- Values range
[0, ‘\infinity’]
- Shape
[nAtoms]
InputMolecule(#)%AtomSymbols- Type
string
- Description
The atom’s symbols (e.g. ‘C’ for carbon)
- Shape
[nAtoms]
InputMolecule(#)%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
InputMolecule(#)%Charge- Type
float
- Description
Net charge of the system
- Unit
e
InputMolecule(#)%Coords- Type
float_array
- Description
Coordinates of the nuclei (x,y,z)
- Unit
bohr
- Shape
[3, nAtoms]
InputMolecule(#)%eeAttachTo- Type
int_array
- Description
A multipole may be attached to an atom. This influences the energy gradient.
InputMolecule(#)%eeChargeWidth- Type
float
- Description
If charge broadening was used for external charges, this represents the width of the charge distribution.
InputMolecule(#)%eeEField- Type
float_array
- Description
The external homogeneous electric field.
- Unit
hartree/(e*bohr)
- Shape
[3]
InputMolecule(#)%eeLatticeVectors- Type
float_array
- Description
The lattice vectors used for the external point- or multipole- charges.
- Unit
bohr
- Shape
[3, eeNLatticeVectors]
InputMolecule(#)%eeMulti- Type
float_array
- Description
The values of the external point- or multipole- charges.
- Unit
a.u.
- Shape
[eeNZlm, eeNMulti]
InputMolecule(#)%eeNLatticeVectors- Type
int
- Description
The number of lattice vectors for the external point- or multipole- charges.
InputMolecule(#)%eeNMulti- Type
int
- Description
The number of external point- or multipole- charges.
InputMolecule(#)%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).
InputMolecule(#)%eeUseChargeBroadening- Type
bool
- Description
Whether or not the external charges are point-like or broadened.
InputMolecule(#)%eeXYZ- Type
float_array
- Description
The position of the external point- or multipole- charges.
- Unit
bohr
- Shape
[3, eeNMulti]
InputMolecule(#)%EngineAtomicInfo- Type
string_fixed_length
- Description
Atom-wise info possibly used by the engine.
InputMolecule(#)%fromAtoms- Type
int_array
- Description
Index of the first atom in a bond. See the bondOrders array
InputMolecule(#)%latticeDisplacements- Type
int_array
- Description
The integer lattice translations for the bonds defined in the variables bondOrders, fromAtoms and toAtoms.
InputMolecule(#)%LatticeVectors- Type
float_array
- Description
Lattice vectors
- Unit
bohr
- Shape
[3, nLatticeVectors]
InputMolecule(#)%nAtoms- Type
int
- Description
The number of atoms in the system
InputMolecule(#)%nAtomsTypes- Type
int
- Description
The number different of atoms types
InputMolecule(#)%nLatticeVectors- Type
int
- Description
Number of lattice vectors (i.e. number of periodic boundary conditions)
- Possible values
[0, 1, 2, 3]
InputMolecule(#)%toAtoms- Type
int_array
- Description
Index of the second atom in a bond. See the bondOrders array
- InputMolecules
Section content: Section to store additional information about the auxiliary, named input molecules.
InputMolecules%Name(#)- Type
string
- Description
The name that was given to the molecule stored in the corresponding InputMolecule(*) section. The name comes from the System block header in the AMS input file.
InputMolecules%numNamedMolecules- Type
int
- Description
The number of auxiliary, named input molecules.
- IRC
Section content: Data regarding the IRC calculation.
IRC%AtomicNumbers- Type
int_array
- Description
Atomic number ‘Z’ of the atoms in the system
- Shape
[nAtoms]
IRC%AtomMasses- Type
float_array
- Description
Masses of the atoms
- Unit
a.u.
- Values range
[0, ‘\infinity’]
- Shape
[nAtoms]
IRC%AtomSymbols- Type
string
- Description
The atom’s symbols (e.g. ‘C’ for carbon)
- Shape
[nAtoms]
IRC%barriers- Type
float_array
- Description
TS barrier energies (forward and backward?)
- Unit
hartree
- Shape
[2]
IRC%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
IRC%cen- Type
subsection
- Description
?
IRC%cen%addedAtoms- Type
archived_int_array
- Description
Atom species indices
IRC%cen%AtomicInfo- Type
archived_string_array
- Description
IRC%cen%BondOrders- Type
archived_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
IRC%cen%Charge- Type
float
- Description
Net charge of the system
- Unit
e
IRC%cen%eeAttachTo- Type
archived_int_array
- Description
A multipole may be attached to an atom. This influences the energy gradient.
IRC%cen%eeChargeWidth- Type
float
- Description
If charge broadening was used for external charges, this represents the width of the charge distribution
IRC%cen%eeEField- Type
float_array
- Description
The external homogeneous electric field
- Unit
hartree/(e*bohr)
- Shape
[3]
IRC%cen%eeLatticeVectors- Type
archived_float_array
- Description
The lattice vectors used for the external point- or multipole- charges
- Unit
bohr
IRC%cen%eeMultipoles- Type
archived_float_array
- Description
The multiple charges.
- Unit
bohr
IRC%cen%eenMulti- Type
int
- Description
The number of multipoles.
IRC%cen%eeUseChargeBroadening- Type
bool
- Description
Whether or not the external charges are point-like or broadened
IRC%cen%eeXYZ- Type
archived_float_array
- Description
The position of the external point- or multipole- charges
- Unit
bohr
IRC%cen%FromAtoms- Type
archived_int_array
- Description
Index of the first atom in a bond. See the bondOrders array
IRC%cen%hasLatticeDisplacements- Type
bool
- Description
The integer lattice translations for the bonds defined in the variables bondOrders, fromAtoms and toAtoms.
IRC%cen%kVectors- Type
float_array
- Description
Reciprocal lattice vectors (corresponding to the strained lattice vectors)
- Unit
1/bohr
- Shape
[3, 3]
IRC%cen%LatticeDisplacements- Type
archived_int_array
- Description
The integer lattice translations for the bonds defined in the variables bondOrders, fromAtoms and toAtoms.
IRC%cen%nAtoms- Type
int
- Description
The number of atoms in the system
IRC%cen%nSpecies- Type
int
- Description
The number different of atoms types
IRC%cen%nVectors- Type
int
- Description
Number of lattice vectors (0:molecule, 1:chain, 2:slab, 3:bulk).
IRC%cen%removedAtoms- Type
archived_int_array
- Description
Atom species indices
IRC%cen%sp#inputSymbol- Type
string
- Description
Symbol as specified in the input
IRC%cen%sp#mass- Type
float
- Description
mass
IRC%cen%sp#regions- Type
archived_string_array
- Description
regions
IRC%cen%sp#symbol- Type
string
- Description
Element symbol
IRC%cen%sp#Z- Type
int
- Description
Atomic number
IRC%cen%SpIndices- Type
archived_int_array
- Description
Atom species indices
IRC%cen%SPlen- Type
int
- Description
Number of species
IRC%cen%strain- Type
float_array
- Description
The strain matrix.
- Shape
[3, 3]
IRC%cen%strainedVectors- Type
float_array
- Description
Strained real space lattice vectors
- Unit
bohr
- Shape
[3, 3]
IRC%cen%ToAtoms- Type
archived_int_array
- Description
Index of the second atom in a bond. See the bondOrders array
IRC%cen%unstrainedVectors- Type
float_array
- Description
Real space lattice vectors (unstrained).
- Unit
bohr
- Shape
[3, 3]
IRC%cen%version- Type
int
- Description
IRC%cen%xyzAtoms- Type
archived_float_array
- Description
Coordinates of the nuclei (x,y,z)
- Unit
bohr
IRC%Charge- Type
float
- Description
Net charge of the system
- Unit
e
IRC%conf- Type
subsection
- Description
Configuration data for the IRC procedure.
IRC%conf%ConvGrad- Type
float
- Description
Convergence criterion for gradient
- Unit
hartree/bohr
IRC%conf%ConvStep- Type
float
- Description
Convergence criterion for step in optim coords
- Unit
bohr
IRC%conf%CoordType- Type
int
- Description
0, 1 or 2, see IRC_OPTIM_COORDS
IRC%conf%Directions- Type
int
- Description
one of IRC_DIRECTION_* constants
IRC%conf%HessFile- Type
string
- Description
File to get the Hessian from if hessianType==’fromfile’
IRC%conf%HessType- Type
string
- Description
The hessian type used in the IRC calculation: ‘calculate’, ‘fromfile’ or ‘restart’
IRC%conf%IrcStep- Type
float
- Description
Step size
- Unit
bohr
IRC%conf%keepResult- Type
bool
- Description
Keep rkf files from single point calculations for each converged path point
IRC%conf%MaxIRCStps- Type
int
- Description
Max number of IRC points before switching to energy minimization
IRC%conf%MaxIter- Type
int
- Description
Max num steps in each geometry optimization (inner IRC loop)
IRC%conf%MaxPoints- Type
int
- Description
Max number of IRC points before switching to the next direction
IRC%conf%MinEnProf- Type
bool
- Description
! Minimum energy profile (i.e. no mass-weighting) instead of IRC?
IRC%Coords- Type
float_array
- Description
Coordinates of the nuclei (x,y,z)
- Unit
bohr
- Shape
[3, nAtoms]
IRC%curIRCStep- Type
float
- Description
ircConfig%ircStep, possibly reduced for a curved path
IRC%direction- Type
int
- Description
Current direction: 1 - forward, 2 - backward
IRC%directionDone- Type
bool_array
- Description
Flag to see which direction has been already done (for restart)
- Shape
[2]
IRC%eeAttachTo- Type
int_array
- Description
A multipole may be attached to an atom. This influences the energy gradient.
IRC%eeChargeWidth- Type
float
- Description
If charge broadening was used for external charges, this represents the width of the charge distribution.
IRC%eeEField- Type
float_array
- Description
The external homogeneous electric field.
- Unit
hartree/(e*bohr)
- Shape
[3]
IRC%eeLatticeVectors- Type
float_array
- Description
The lattice vectors used for the external point- or multipole- charges.
- Unit
bohr
- Shape
[3, eeNLatticeVectors]
IRC%eeMulti- Type
float_array
- Description
The values of the external point- or multipole- charges.
- Unit
a.u.
- Shape
[eeNZlm, eeNMulti]
IRC%eeNLatticeVectors- Type
int
- Description
The number of lattice vectors for the external point- or multipole- charges.
IRC%eeNMulti- Type
int
- Description
The number of external point- or multipole- charges.
IRC%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).
IRC%eeUseChargeBroadening- Type
bool
- Description
Whether or not the external charges are point-like or broadened.
IRC%eeXYZ- Type
float_array
- Description
The position of the external point- or multipole- charges.
- Unit
bohr
- Shape
[3, eeNMulti]
IRC%EngineAtomicInfo- Type
string_fixed_length
- Description
Atom-wise info possibly used by the engine.
IRC%fromAtoms- Type
int_array
- Description
Index of the first atom in a bond. See the bondOrders array
IRC%gradCart- Type
archived_float_array
- Description
Cartesian gradients
- Unit
hartree/bohr
IRC%hessCart- Type
archived_float_array
- Description
Current Hessian in Cartesian coords
- Unit
hartree/bohr^2
IRC%hessInit- Type
archived_float_array
- Description
Initial Hessian in Cartesian coords
- Unit
hartree/bohr^2
IRC%histEnergy- Type
archived_float_array
- Description
Energy history
- Unit
hartree
IRC%histGradRms- Type
archived_float_array
- Description
Gradients RMS history
- Unit
hartree/bohr
IRC%histPathLength- Type
archived_float_array
- Description
Path length history
IRC%histStatus- Type
archived_int_array
- Description
Status history
IRC%histXYZ- Type
archived_float_array
- Description
XYZ history
IRC%initialEnergy- Type
float
- Description
TS energy
- Unit
hartree
IRC%initialGradRms- Type
float
- Description
TS RMS gradient
- Unit
hartree/bohr
IRC%ircIteration- Type
int
- Description
outer loop iteration number
IRC%latticeDisplacements- Type
int_array
- Description
The integer lattice translations for the bonds defined in the variables bondOrders, fromAtoms and toAtoms.
IRC%LatticeVectors- Type
float_array
- Description
Lattice vectors
- Unit
bohr
- Shape
[3, nLatticeVectors]
IRC%nAtoms- Type
int
- Description
The number of atoms in the system
IRC%nAtomsTypes- Type
int
- Description
The number different of atoms types
IRC%nLatticeVectors- Type
int
- Description
Number of lattice vectors (i.e. number of periodic boundary conditions)
- Possible values
[0, 1, 2, 3]
IRC%optIteration- Type
int
- Description
inner loop iteration number
IRC%pathLength- Type
float
- Description
Sum of the arc lengths up to the latest point
IRC%sys- Type
subsection
- Description
?
IRC%sys%addedAtoms- Type
archived_int_array
- Description
Atom species indices
IRC%sys%AtomicInfo- Type
archived_string_array
- Description
IRC%sys%BondOrders- Type
archived_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
IRC%sys%Charge- Type
float
- Description
Net charge of the system
- Unit
e
IRC%sys%eeAttachTo- Type
archived_int_array
- Description
A multipole may be attached to an atom. This influences the energy gradient.
IRC%sys%eeChargeWidth- Type
float
- Description
If charge broadening was used for external charges, this represents the width of the charge distribution
IRC%sys%eeEField- Type
float_array
- Description
The external homogeneous electric field
- Unit
hartree/(e*bohr)
- Shape
[3]
IRC%sys%eeLatticeVectors- Type
archived_float_array
- Description
The lattice vectors used for the external point- or multipole- charges
- Unit
bohr
IRC%sys%eeMultipoles- Type
archived_float_array
- Description
The multiple charges.
- Unit
bohr
IRC%sys%eenMulti- Type
int
- Description
The number of multipoles.
IRC%sys%eeUseChargeBroadening- Type
bool
- Description
Whether or not the external charges are point-like or broadened
IRC%sys%eeXYZ- Type
archived_float_array
- Description
The position of the external point- or multipole- charges
- Unit
bohr
IRC%sys%FromAtoms- Type
archived_int_array
- Description
Index of the first atom in a bond. See the bondOrders array
IRC%sys%hasLatticeDisplacements- Type
bool
- Description
The integer lattice translations for the bonds defined in the variables bondOrders, fromAtoms and toAtoms.
IRC%sys%kVectors- Type
float_array
- Description
Reciprocal lattice vectors (corresponding to the strained lattice vectors)
- Unit
1/bohr
- Shape
[3, 3]
IRC%sys%LatticeDisplacements- Type
archived_int_array
- Description
The integer lattice translations for the bonds defined in the variables bondOrders, fromAtoms and toAtoms.
IRC%sys%nAtoms- Type
int
- Description
The number of atoms in the system
IRC%sys%nSpecies- Type
int
- Description
The number different of atoms types
IRC%sys%nVectors- Type
int
- Description
Number of lattice vectors (0:molecule, 1:chain, 2:slab, 3:bulk).
IRC%sys%removedAtoms- Type
archived_int_array
- Description
Atom species indices
IRC%sys%sp#inputSymbol- Type
string
- Description
Symbol as specified in the input
IRC%sys%sp#mass- Type
float
- Description
mass
IRC%sys%sp#regions- Type
archived_string_array
- Description
regions
IRC%sys%sp#symbol- Type
string
- Description
Element symbol
IRC%sys%sp#Z- Type
int
- Description
Atomic number
IRC%sys%SpIndices- Type
archived_int_array
- Description
Atom species indices
IRC%sys%SPlen- Type
int
- Description
Number of species
IRC%sys%strain- Type
float_array
- Description
The strain matrix.
- Shape
[3, 3]
IRC%sys%strainedVectors- Type
float_array
- Description
Strained real space lattice vectors
- Unit
bohr
- Shape
[3, 3]
IRC%sys%ToAtoms- Type
archived_int_array
- Description
Index of the second atom in a bond. See the bondOrders array
IRC%sys%unstrainedVectors- Type
float_array
- Description
Real space lattice vectors (unstrained).
- Unit
bohr
- Shape
[3, 3]
IRC%sys%version- Type
int
- Description
IRC%sys%xyzAtoms- Type
archived_float_array
- Description
Coordinates of the nuclei (x,y,z)
- Unit
bohr
IRC%toAtoms- Type
int_array
- Description
Index of the second atom in a bond. See the bondOrders array
- 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.
- MDHistory
Section content: History of a Molecular dynamics simulation.
MDHistory%Area(#)- Type
float_array
- Description
The area of the cell (only for 2D PBC). This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
bohr^2
MDHistory%BerBstatEnergy(#)- Type
float_array
- Description
?
- Unit
hartree
MDHistory%BerTstat#Energy(#)- Type
float_array
- Description
?
- Unit
hartree
MDHistory%BerTstat#Temperature(#)- Type
float_array
- Description
Local temperature of the thermostat region
- Unit
kelvin
MDHistory%BiasEnergy(#)- Type
float_array
- Description
? This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
hartree
MDHistory%blockSize- Type
int
- Description
Explain the block-system… ?
MDHistory%BondBoostEnergy(#)- Type
float_array
- Description
BondBoost energy, part of the potential energy
- Unit
hartree
MDHistory%BoostFactor(#)- Type
float_array
- Description
The boost factor for hyper-dynamics. Expand? This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
MDHistory%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]).
- Unit
e
MDHistory%ConservedEnergy(#)- Type
float_array
- Description
The conserved energy…? Some MD person, please fix. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
hartree
MDHistory%CosineShearVelocity(#)- Type
float_array
- Description
?
MDHistory%currentEntryOpen- Type
bool
- Description
?
MDHistory%Density(#)- Type
float_array
- Description
The density of the system (mass/simulation_cell_volume). Only for 3D PBC. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
dalton/bohr^3
MDHistory%Eng*FrcRgn*(#)- Type
float_array
- Description
?
MDHistory%Engine*ForceRegion*(#)- Type
float_array
- Description
?
MDHistory%Hypertime(#)- Type
float_array
- Description
Hyper time for hyper-dynamics. Expand? This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
femtosecond
MDHistory%ItemName(#)- Type
string
- Description
?
MDHistory%KineticEnergy(#)- Type
float_array
- Description
The kinetic energy of the system. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
hartree
MDHistory%Length(#)- Type
float_array
- Description
The length of the cell (only for 1D PBC). This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
bohr
MDHistory%MaxBiasEnergy(#)- Type
float_array
- Description
? This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
hartree
MDHistory%MaxBoostFactor(#)- Type
float_array
- Description
The maximum boost factor for hyper-dynamics. Expand? This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
MDHistory%MeanCosineShearVelocity(#)- Type
float_array
- Description
?
MDHistory%MeanEng*FrcRgn*(#)- Type
float_array
- Description
?
MDHistory%MeanEngine*ForceRegion*(#)- Type
float_array
- Description
?
MDHistory%MovingRestr*Energy(#)- Type
float_array
- Description
Moving restraints energy, part of the potential energy
- Unit
hartree
MDHistory%nBlocks- Type
int
- Description
Explain the block-system… ?
MDHistory%nEntries- Type
int
- Description
Number of MD history entries.
MDHistory%NHCTstat#Energy(#)- Type
float_array
- Description
?
- Unit
hartree
MDHistory%NHCTstat#Temperature(#)- Type
float_array
- Description
Local temperature of the thermostat region
- Unit
kelvin
MDHistory%NHTBstat#Energy(#)- Type
float_array
- Description
?
- Unit
hartree
MDHistory%NHTBstat#Temperature(#)- Type
float_array
- Description
Local temperature of the thermostat region
- Unit
kelvin
MDHistory%Number of molecules(#)- Type
int_array
- Description
Number of molecules. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
MDHistory%PotentialEnergy(#)- Type
float_array
- Description
The potential energy, i.e. the energy as computed by the engine. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
hartree
MDHistory%Pressure(#)- Type
float_array
- Description
The pressure of the system (only for 3D PBC). This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
hartree/bohr^3
MDHistory%PressureTensor(#)- Type
float_array
- Description
Pressure tensor in Voigt notation.
- Unit
hartree/bohr^3
MDHistory%ReactionBoostEnergy(#)- Type
float_array
- Description
ReactionBoost energy, part of the potential energy
- Unit
hartree
MDHistory%ReactorEnergy(#)- Type
float_array
- Description
Reactor energy, part of the potential energy
- Unit
hartree
MDHistory%StdevCosineShearVelocity(#)- Type
float_array
- Description
?
MDHistory%StdevEng*FrcRgn*(#)- Type
float_array
- Description
?
MDHistory%StdevEngine*ForceRegion*(#)- Type
float_array
- Description
?
MDHistory%Step(#)- Type
int_array
- Description
The step number of the MD calculation. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
MDHistory%Temperature(#)- Type
float_array
- Description
The temperature of the system, computed from the kinetic energy?. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
kelvin
MDHistory%TempProfile_a(#)- Type
float_array
- Description
The temperature profile…? Some MD person, please fix.
- Unit
kelvin
MDHistory%TempProfile_b(#)- Type
float_array
- Description
The temperature profile…? Some MD person, please fix.
- Unit
kelvin
MDHistory%TempProfile_c(#)- Type
float_array
- Description
The temperature profile…? Some MD person, please fix.
- Unit
kelvin
MDHistory%Time(#)- Type
float_array
- Description
The MD simulation time. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
femtosecond
MDHistory%TotalEnergy(#)- Type
float_array
- Description
The total energy of the system: potential energy (as computed by the engine) + kinetic energy. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
hartree
MDHistory%Velocities(#)- Type
float_array
- Description
The velocity of the atoms.
- Unit
bohr/femtosecond
- Shape
[3, :]
MDHistory%Volume(#)- Type
float_array
- Description
The volume of the cell (only for 3D PBC). This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
- Unit
bohr^3
- MDHookState
Section content: Data related to MD hooks
- MDResults
Section content: Results of an MD calculation.
MDResults%EndStep- Type
int
- Description
Step number of the last step.
MDResults%EndTime[fs]- Type
float
- Description
The time at the end of the MD simulation.
- Unit
femtosecond
MDResults%EndVelocities- Type
float_array
- Description
The atomic velocities at the last step of the MD simulation.
- Unit
a.u.
- Shape
[3, :]
MDResults%MaxConservedEnergy- Type
float
- Description
Maximum value of the conserved energy during the MD simulation.
- Unit
hartree
MDResults%MaxKineticEnergy- Type
float
- Description
Maximum value of the kinetic energy during the MD simulation.
- Unit
hartree
MDResults%MaxPotentialEnergy- Type
float
- Description
Maximum value of the potential energy during the MD simulation.
- Unit
hartree
MDResults%MaxTemperature- Type
float
- Description
Maximum value of the temperature during the MD simulation.
- Unit
kelvin
MDResults%MaxTotalEnergy- Type
float
- Description
Maximum value of the total energy during the MD simulation.
- Unit
hartree
MDResults%MeanConservedEnergy- Type
float
- Description
Mean conserved energy during the MD simulation.
- Unit
hartree
MDResults%MeanKineticEnergy- Type
float
- Description
Mean kinetic energy during the MD simulation.
- Unit
hartree
MDResults%MeanPotentialEnergy- Type
float
- Description
Mean potential energy during the MD simulation. The potential energy is the energy computed by the engine.
- Unit
hartree
MDResults%MeanTemperature- Type
float
- Description
Mean temperature during the MD simulation.
- Unit
kelvin
MDResults%MeanTotalEnergy- Type
float
- Description
Mean total energy during the MD simulation (total energy = potential energy from engine + kinetic energy).
- Unit
hartree
MDResults%MinConservedEnergy- Type
float
- Description
Minimum value of the conserved energy during the MD simulation.
- Unit
hartree
MDResults%MinKineticEnergy- Type
float
- Description
Minimum value of the kinetic energy during the MD simulation.
- Unit
hartree
MDResults%MinPotentialEnergy- Type
float
- Description
Minimum value of the potential energy during the MD simulation.
- Unit
hartree
MDResults%MinTemperature- Type
float
- Description
Minimum value of the temperature during the MD simulation.
- Unit
kelvin
MDResults%MinTotalEnergy- Type
float
- Description
Minimum value of the total energy during the MD simulation.
- Unit
hartree
MDResults%StartStep- Type
int
- Description
Step number of the first step.
MDResults%StartTime[fs]- Type
float
- Description
The time at the beginning of the MD simulation.
- Unit
femtosecond
MDResults%StdDevConservedEnergy- Type
float
- Description
Standard deviation of the conserved energy during the MD simulation.
- Unit
hartree
MDResults%StdDevKineticEnergy- Type
float
- Description
Standard deviation of the kinetic energy during the MD simulation.
- Unit
hartree
MDResults%StdDevPotentialEnergy- Type
float
- Description
Standard deviation of the potential energy during the MD simulation.
- Unit
hartree
MDResults%StdDevTemperature- Type
float
- Description
Standard deviation of the temperature during the MD simulation.
- Unit
kelvin
MDResults%StdDevTotalEnergy- Type
float
- Description
Standard deviation of the total energy during the MD simulation.
- Unit
hartree
- Molecule
Section content: The final molecule in the calculation. What is stored here depends on the task of the AMS calculation. For example, for a GeometryOptimization this will contain the optimized molecule, while for a TransitionStateSearch this will contain the molecule at the TS geometry.
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
- Molecules
Section content: Results of the molecules detection algorithms. Note: molecules with the same formula are considered to be the same molecule.
Molecules%Molecule name #- Type
string
- Description
The name of the molecules, i.e. their molecular formula.
Molecules%Num molecules- Type
int
- Description
Number distinct (i.e. with different molecular formula) molecules found.
- NEB
Section content: Data related to the Nudge Elastic Band procedure.
NEB%climbing- Type
bool
- Description
Climb the highest image to the TS
NEB%climbingThresh- Type
float
- Description
Threshold on the max perpendicular force component for the climbing image
NEB%doubleNudge- Type
string
- Description
Henkelman: smoothly turns off the double nudging as the NEB converges; Trygubenko: JCP 120, 2082 (2005)
NEB%energy- Type
float_array
- Description
energy per image, including ends
- Unit
hartree
NEB%fixed- Type
bool_array
- Description
Flag fixed atoms
NEB%forces- Type
float_array
- Description
forces per image, including stress forces (1st nVectors ‘atoms’ of each image)
- Unit
hartree/bohr
NEB%highestIndex- Type
int
- Description
Index of the highest (or climbing) image
NEB%historyIndex- Type
int_array
- Description
(i,j) element contains history index of image i on iteration j
NEB%im#- Type
subsection
- Description
The molecule info of image #
NEB%im#%addedAtoms- Type
archived_int_array
- Description
Atom species indices
NEB%im#%AtomicInfo- Type
archived_string_array
- Description
NEB%im#%BondOrders- Type
archived_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
NEB%im#%Charge- Type
float
- Description
Net charge of the system
- Unit
e
NEB%im#%eeAttachTo- Type
archived_int_array
- Description
A multipole may be attached to an atom. This influences the energy gradient.
NEB%im#%eeChargeWidth- Type
float
- Description
If charge broadening was used for external charges, this represents the width of the charge distribution
NEB%im#%eeEField- Type
float_array
- Description
The external homogeneous electric field
- Unit
hartree/(e*bohr)
- Shape
[3]
NEB%im#%eeLatticeVectors- Type
archived_float_array
- Description
The lattice vectors used for the external point- or multipole- charges
- Unit
bohr
NEB%im#%eeMultipoles- Type
archived_float_array
- Description
The multiple charges.
- Unit
bohr
NEB%im#%eenMulti- Type
int
- Description
The number of multipoles.
NEB%im#%eeUseChargeBroadening- Type
bool
- Description
Whether or not the external charges are point-like or broadened
NEB%im#%eeXYZ- Type
archived_float_array
- Description
The position of the external point- or multipole- charges
- Unit
bohr
NEB%im#%FromAtoms- Type
archived_int_array
- Description
Index of the first atom in a bond. See the bondOrders array
NEB%im#%hasLatticeDisplacements- Type
bool
- Description
The integer lattice translations for the bonds defined in the variables bondOrders, fromAtoms and toAtoms.
NEB%im#%kVectors- Type
float_array
- Description
Reciprocal lattice vectors (corresponding to the strained lattice vectors)
- Unit
1/bohr
- Shape
[3, 3]
NEB%im#%LatticeDisplacements- Type
archived_int_array
- Description
The integer lattice translations for the bonds defined in the variables bondOrders, fromAtoms and toAtoms.
NEB%im#%nAtoms- Type
int
- Description
The number of atoms in the system
NEB%im#%nSpecies- Type
int
- Description
The number different of atoms types
NEB%im#%nVectors- Type
int
- Description
Number of lattice vectors (0:molecule, 1:chain, 2:slab, 3:bulk).
NEB%im#%removedAtoms- Type
archived_int_array
- Description
Atom species indices
NEB%im#%sp#inputSymbol- Type
string
- Description
Symbol as specified in the input
NEB%im#%sp#mass- Type
float
- Description
mass
NEB%im#%sp#regions- Type
archived_string_array
- Description
regions
NEB%im#%sp#symbol- Type
string
- Description
Element symbol
NEB%im#%sp#Z- Type
int
- Description
Atomic number
NEB%im#%SpIndices- Type
archived_int_array
- Description
Atom species indices
NEB%im#%SPlen- Type
int
- Description
Number of species
NEB%im#%strain- Type
float_array
- Description
The strain matrix.
- Shape
[3, 3]
NEB%im#%strainedVectors- Type
float_array
- Description
Strained real space lattice vectors
- Unit
bohr
- Shape
[3, 3]
NEB%im#%ToAtoms- Type
archived_int_array
- Description
Index of the second atom in a bond. See the bondOrders array
NEB%im#%unstrainedVectors- Type
float_array
- Description
Real space lattice vectors (unstrained).
- Unit
bohr
- Shape
[3, 3]
NEB%im#%version- Type
int
- Description
NEB%im#%xyzAtoms- Type
archived_float_array
- Description
Coordinates of the nuclei (x,y,z)
- Unit
bohr
NEB%interIntCoords- Type
bool
- Description
Interpolate in the internal coords instead of Cartesian
NEB%interpolateOption- Type
int
- Description
1=only dist, 2=1+linear angles, 3=1+val. angles, 4=1+dihedrals, 99=all coordinates
NEB%interShortest- Type
bool
- Description
Interpolate across cell boundary if necessary
NEB%jacobian- Type
float
- Description
Scaling factor used to convert the lattice strain to a NEB coordinate value
NEB%LeftBarrier- Type
float
- Description
Left barrier energy
- Unit
hartree
NEB%mapToOriginalCell- Type
bool
- Description
Map atoms to the [-0.5,0.5] cell
NEB%nebImages- Type
int
- Description
number of intermediate NEB images, without ends. With them, there will be nebImages+2 images
NEB%nebIterations- Type
int
- Description
Max number of iterations
NEB%nParallel- Type
int
- Description
Number of images to do in parallel
NEB%oldTangent- Type
bool
- Description
use old tangent
NEB%optimizeEnds- Type
bool
- Description
Start NEB with optimization of the products/reactants
NEB%optimizeLattice- Type
bool
- Description
Optimize lattice vectors
NEB%ReactionEnergy- Type
float
- Description
Reaction energy
- Unit
hartree
NEB%RightBarrier- Type
float
- Description
Left barrier energy
- Unit
hartree
NEB%spring- Type
float
- Description
spring force constant
- Unit
a.u.
NEB%stressTensors- Type
float_array
- Description
stress tensor per image
NEB%success- Type
int_array
- Description
Single-point success flag (0 or 1)
- PESScan
Section content: Data related to the Potential Energy Surface (PES) Scan procedure.
PESScan%GOConverged- Type
bool_array
- Description
Whether the (constrained) optimization at the various PES scan points converged.
- Shape
[nPoints]
PESScan%HistoryIndices- Type
int_array
- Description
The indices of the frames in the History section corresponding to the PES point values.
- Shape
[nPoints]
PESScan%HistoryPESPoints- Type
int_array
- Description
?
PESScan%nPoints- Type
int
- Description
The total number of scanned PES points. This is the product of all nPoints(#) values.
PESScan%nPoints(#)- Type
int
- Description
Number of points along the corresponding scan coordinate.
PESScan%nScanCoord- Type
int
- Description
Number of (independent) coordinates along which the PES scan is performed.
PESScan%PES- Type
float_array
- Description
The total energy at each particular PES point.
- Unit
hartree
- Shape
[nPoints]
PESScan%PESCoords- Type
float_array
- Description
The values of all coordinates for each particular PES point.
- Shape
[:, nPoints]
PESScan%RangeEnd(#)- Type
float_array
- Description
The final value(s) for the corresponding scan coordinate.
PESScan%RangeStart(#)- Type
float_array
- Description
The starting value(s) for the corresponding scan coordinate.
PESScan%ScanCoord(#)- Type
string_fixed_length
- Description
A human readable description of the scan coordinate.
- Replay
Section content: Output of the Replay task of the AMS driver.
Replay%File- Type
string
- Description
The path to the file from which the trajectory was replayed.
Replay%Frames- Type
int_array
- Description
The indices of the frames in the history section that were replayed.
Replay%Type- Type
string
- Description
The type if job that was replayed, e.g. PESScan, NEB, IRC or Generic.
- ReplicaExchangeHistory
Section content: ?
ReplicaExchangeHistory%AvgSwapProbability #-#(#)- Type
float_array
- Description
?
ReplicaExchangeHistory%blockSize- Type
int
- Description
Explain the block-system… ?
ReplicaExchangeHistory%currentEntryOpen- Type
bool
- Description
?
ReplicaExchangeHistory%EnsembleOfSystem #(#)- Type
int_array
- Description
?
ReplicaExchangeHistory%ItemName(#)- Type
string
- Description
?
ReplicaExchangeHistory%MaxPotentialEnergy #(#)- Type
float_array
- Description
?
ReplicaExchangeHistory%MDHistoryFrame(#)- Type
int_array
- Description
?
ReplicaExchangeHistory%MeanPotentialEnergy #(#)- Type
float_array
- Description
?
ReplicaExchangeHistory%MinPotentialEnergy #(#)- Type
float_array
- Description
?
ReplicaExchangeHistory%nBlocks- Type
int
- Description
Explain the block-system… ?
ReplicaExchangeHistory%nEntries- Type
int
- Description
Number of MD history entries.
ReplicaExchangeHistory%StdDevPotentialEnergy #(#)- Type
float_array
- Description
?
ReplicaExchangeHistory%Step(#)- Type
int_array
- Description
The step number of the MD calculation. This is a ‘blocked’ property. See the ‘blockSize’ and ‘nBlocks’ variables for more details.
ReplicaExchangeHistory%SystemInEnsemble #(#)- Type
int_array
- Description
?
ReplicaExchangeHistory%TemperatureOfSystem #(#)- Type
float_array
- Description
?
- SystemVersionHistory
Section content: ?
SystemVersionHistory%AddedAtoms(#)- Type
int_array
- Description
?
SystemVersionHistory%currentEntryOpen- Type
bool
- Description
?
SystemVersionHistory%ItemName(#)- Type
string
- Description
?
SystemVersionHistory%nEntries- Type
int
- Description
?
SystemVersionHistory%RemovedAtoms(#)- Type
int_array
- Description
?
SystemVersionHistory%SectionNum(#)- Type
int
- Description
?
- Vibrations
Section content: Data concerting the vibrational modes/spectra of the system.
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%FreqBeforeScan[cm-1]- Type
float_array
- Description
?
- 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%IRBeforeScan[km/mol]- Type
float_array
- Description
?
- Shape
[nNormalModes]
Vibrations%IrReps- Type
lchar_string_array
- Description
Symmetry symbol of the normal mode.
- Shape
[nNormalModes]
Vibrations%IrRepsBeforeScan- Type
lchar_string_array
- Description
?
- 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%RamanDepolRatioLinBeforeScan- Type
float_array
- Description
?
- Shape
[nNormalModes]
Vibrations%RamanDepolRatioNat- Type
float_array
- Description
Raman depol ratio (nat).
- Shape
[nNormalModes]
Vibrations%RamanDepolRatioNatBeforeScan- Type
float_array
- Description
?
- 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%RamanIntensBeforeScan[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%ScannedModes- Type
int_array
- Description
?
- 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%VROACIDBackwardBeforeScan- Type
float_array
- Description
?
- Shape
[nNormalModes]
Vibrations%VROACIDDePolarized- Type
float_array
- Description
VROA Circular Intensity Differential: Depolarized scattering.
- Unit
10⁻3
- Shape
[nNormalModes]
Vibrations%VROACIDDePolarizedBeforeScan- Type
float_array
- Description
?
- Shape
[nNormalModes]
Vibrations%VROACIDForward- Type
float_array
- Description
VROA Circular Intensity Differential: Forward scattering.
- Unit
10⁻3
- Shape
[nNormalModes]
Vibrations%VROACIDForwardBeforeScan- Type
float_array
- Description
?
- Shape
[nNormalModes]
Vibrations%VROACIDPolarized- Type
float_array
- Description
VROA Circular Intensity Differential: Polarized scattering.
- Unit
10⁻3
- Shape
[nNormalModes]
Vibrations%VROACIDPolarizedBeforeScan- Type
float_array
- Description
?
- Shape
[nNormalModes]
Vibrations%VROADeltaBackward- Type
float_array
- Description
VROA Intensity: Backward scattering.
- Unit
10⁻3 A^4/amu
- Shape
[nNormalModes]
Vibrations%VROADeltaBackwardBeforeScan- Type
float_array
- Description
?
- Shape
[nNormalModes]
Vibrations%VROADeltaDePolarized- Type
float_array
- Description
VROA Intensity: Depolarized scattering.
- Unit
10⁻3 A^4/amu
- Shape
[nNormalModes]
Vibrations%VROADeltaDePolarizedBeforeScan- Type
float_array
- Description
?
- Shape
[nNormalModes]
Vibrations%VROADeltaForward- Type
float_array
- Description
VROA Intensity: Forward scattering.
- Unit
10⁻3 A^4/amu
- Shape
[nNormalModes]
Vibrations%VROADeltaForwardBeforeScan- Type
float_array
- Description
?
- Shape
[nNormalModes]
Vibrations%VROADeltaPolarized- Type
float_array
- Description
VROA Intensity: Polarized scattering.
- Unit
10⁻3 A^4/amu
- Shape
[nNormalModes]
Vibrations%VROADeltaPolarizedBeforeScan- Type
float_array
- Description
?
- Shape
[nNormalModes]
Vibrations%ZeroPointEnergy- Type
float
- Description
Vibrational zero-point energy.
- Unit
hartree
- VibronicStructure
Section content: Data related to the Vibronic Structure Tracking procedure.
VibronicStructure%nspectrum- Type
int
- Description
?
VibronicStructure%spectrum- Type
float_array
- Description
?