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:
?