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(#)%ReactantHashes

Type

lchar_string_array

Description

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

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%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%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

string

Description

The hash 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