Output¶

Reactants, products, unstable¶

The results directory contains a file reactions_discovery.rkf. This file contains all the reaction network information. It can be read by the reactions_discovery workflow, which can use it to perform/redo the ranking process. Additionally, AMSmovie can be used to view the molecules in the reaction network.

All molecules in the reaction network are categorized either as “product”, “unstable”, or “reactant”.

• Reactants are the molecules that exist at the beginning of the MD runs.

• Products are the suggested stable side products in the reaction network.

• Unstable are the molecules that are not considered stable.

There are three reasons a molecule is considered unstable.

1. The number of bonds to the atoms deviates from the atom valence by more than a maximum amount. This maximum is hardcoded per element.

2. The assigned molecular charge deviates from the formal molecular charge of the molecule. This is a strong indication that the molecule is a radical.

3. By default all ions are considered unstable, but this can be changed in the input.

The suggested side products can be found in the file products.sdf in the results directory. This file contains all network intermediates that are considered stable.

The text output contains a list of ranked products, with an estimate of cost of formation (labeled ‘Barrier’) and reaction energy. This list of products is followed by a list containing for each stable product the shortest path from the initial reactants. The cost of formation is a soft maximum of all reaction energies in the shortest path to the product.

KF output files¶

General

Section content: General information about the amsbatch calculation.

General%account

Type:

string

Description:

Name of the account from the license

General%ElapsedTime

Type:

float

Description:

Elapsed time of the AMS workflow.

Unit:

second

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%ProcessTime

Type:

float

Description:

Time the AMS workflow spent in Python.

Unit:

second

General%program

Type:

string

Description:

The name of the program/engine that generated this kf file.

General%release

Type:

string

Description:

The version of the program that generated this kf file (including svn revision number and date).

General%termination status

Type:

string

Description:

The termination status. Possible values: ‘NORMAL TERMINATION’, ‘NORMAL TERMINATION with warnings’, ‘NORMAL TERMINATION with errors’, ‘ERROR’, ‘IN PROGRESS’.

General%title

Type:

string

Description:

Title of the calculation.

General%uid

Type:

string

Description:

SCM User ID

General%user input

Type:

string

Description:

The text input of the AMS workflow.

General%version

Type:

int

Description:

Version number?

MolecularDynamicsResults

Section content: Generic results.

MolecularDynamicsResults%NumSimulations

Type:

int

Description:

Number of molecular dynamics simulations that were performed.

ChemicalSystem(#)

Section content: Molecules

ChemicalSystem(#)%nAtoms

Type:

int

Description:

The number of atoms in the system

ChemicalSystem(#)%nAtomsTypes

Type:

int

Description:

The number different of atoms types

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(#)%EngineAtomicInfo

Type:

string_fixed_length

Description:

Atom-wise info possibly used by the engine.

ChemicalSystem(#)%Coords

Type:

float_array

Description:

Coordinates of the nuclei (x,y,z)

Unit:

bohr

Shape:

[3, 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(#)%toAtoms

Type:

int_array

Description:

Index of the second atom in a bond. See the bondOrders array

ChemicalSystem(#)%fromAtoms

Type:

int_array

Description:

Index of the first atom in a bond. See the bondOrders array

Categories

Section content: Different categories of molecules.

Categories%NumProducts

Type:

int

Description:

Number of products.

Categories%NumReactants

Type:

int

Description:

Number of reactants.

Categories%NumUnstable

Type:

int

Description:

Number of unstable systems.

Categories%Products

Type:

int_array

Description:

Indices of (RD)History entries that are products.

Shape:

[NumProducts]

Categories%Reactants

Type:

int_array

Description:

Indices of (RD)History entries that are reactants.

Shape:

[NumReactants]

Categories%Unstable

Type:

int_array

Description:

Indices of (RD)History entries that are unstable.

Shape:

[NumUnstable]

Reaction(#)

Section content: A reaction.

Reaction(#)%Composition

Type:

string

Description:

The description of the reaction (for example, A => B + C) where the molecules are described by their empirical formula.

Reaction(#)%Count

Type:

int

Description:

Total number of this this reaction was observed.

Reaction(#)%Hash

Type:

string

Description:

Unique identifier for this reaction.

Reaction(#)%ProductHashes

Type:

lchar_string_array

Description:

Hashes (i.e. the unique identifiers) of the product molecules.

Reaction(#)%ProductIndices

Type:

int_array

Description:

Indices of the product molecules in the RDHistory section.

Reaction(#)%ReactantHashes

Type:

lchar_string_array

Description:

Hashes (i.e. the unique identifiers) of the reactant molecules.

Reaction(#)%ReactantIndices

Type:

int_array

Description:

Indices of the reactant molecules in the RDHistory section.

Reaction(#)%ReactionEnergy

Type:

float

Description:

The reaction energy for this reaction.

Unit:

hartree

Reaction(#)%SMILESDescription

Type:

string

Description:

The description of the reaction (for example, A => B + C) where the molecules are described by their SMILES strings.

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%Bonds

Type:

subsection

Description:

?

History%Coords(#)

Type:

float_array

Description:

Coordinates of the systems of a given entry.

Shape:

[3, :]

History%Energy(#)

Type:

float

Description:

Energy of the system of a given entry.

Unit:

hartree

History%LatticeVectors(#)

Type:

float_array

Description:

The lattice vectors of a given entry.

Unit:

bohr

Shape:

[3, :]

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%Step(#)

Type:

int

Description:

The step number in a Molecular Dynamics calculation.

History%SystemVersion(#)

Type:

int

Description:

Index of the versioned-chemical system of a given frame.

RDHistory

Section content: History of a Molecular dynamics simulation.

RDHistory%Balance(#)

Type:

string

Description:

The overall balanced reaction for this product

RDHistory%BalancedReaction(#)

Type:

int_array

Description:

Index of the estimated most efficient balanced reaction resulting in this molecule (estimated from the pool of all reactants and all stable products).

RDHistory%blockSize

Type:

int

Description:

Explain the block-system… ?

RDHistory%Cost(#)

Type:

float_array

Description:

The sum of the exponentials (exp(E/RT)+1) of the reaction energy of each reaction involved in formation of this product. Taking the logarithm of this effectively results in the highest ‘barrier’ along the path.

RDHistory%CreatedBy(#)

Type:

string

Description:

This command was used to obtain the coordinates for stability analysis for this molecule

RDHistory%currentEntryOpen

Type:

bool

Description:

?

RDHistory%Depth(#)

Type:

int_array

Description:

The depth of the molecule in the network (number of elementary reactions separating it from the reactants)

RDHistory%FinalCount(#)

Type:

int_array

Description:

Number of molecules of this kind at the end of the simulation.

RDHistory%GuessedCharge(#)

Type:

float_array

Description:

The formal charge of the molecule as estimated by PLAMS

RDHistory%Hash(#)

Type:

string

Description:

Unique identifier of the molecule.

RDHistory%Id(#)

Type:

string

Description:

The indexed formula of this molecule.

RDHistory%InitialCount(#)

Type:

int_array

Description:

Number of molecules of this kind at the beginning of the simulation.

RDHistory%ItemName(#)

Type:

string

Description:

?

RDHistory%MolecularFormula(#)

Type:

string

Description:

Molecular formula.

RDHistory%Name(#)

Type:

string

Description:

SMILES string

RDHistory%nBlocks

Type:

int

Description:

Explain the block-system… ?

RDHistory%nEntries

Type:

int

Description:

Number of MD history entries.

RDHistory%ParentReaction(#)

Type:

int_array

Description:

The index of the parent reaction in the shortest path from reactants to this compound

RDHistory%PathEnergy(#)

Type:

float_array

Description:

The overall energy balance of the full path to this product

RDHistory%PathTree(#)

Type:

string

Description:

The full path through the network to this product, as a string.

RDHistory%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

RDHistory%Radical(#)

Type:

bool_array

Description:

Is this molecule a radical or not.

RDHistory%ReactionsAsProduct(#)

Type:

int_array

Description:

Indices of the reactions in which this molecule was part of the products.

RDHistory%ReactionsAsReactant(#)

Type:

int_array

Description:

Indices of the reactions in which this molecule was part of the reactants.

RDHistory%Representative(#)

Type:

bool_array

Description:

Signifies if the coordinates are representative of the molecule (as defined by the connectivity)

RDHistory%SMILES(#)

Type:

string

Description:

SMILES string