Kinetica.jl API - ASE Interface
Utilities
Conversion
Kinetica.frame_to_atoms
— Functionframe_to_atoms(frame[, charges=nothing, magmoms=nothing])
Converts an ExtXYZ frame to an ASE Atoms object.
If the optional argument charges
is provided with an integer array of formal charges on the atoms in frame
, these will be applied to the resulting Atoms object through Atoms.set_initial_charges()
.
If the optional argument magmoms
is provided with an array of initial magnetic moments for the atoms in frame
, these will be applied to the resulting Atoms object through Atoms.set_initial_magnetic_moments()
.
Kinetica.atoms_to_frame
— Functionatoms_to_frame(atoms[, ase_energy=nothing, inertias=nothing])
Converts an ASE Atoms object to an ExtXYZ frame.
Optionally accepts values ase_energy and
inertiasthat can fill the "energy_ASE" and "inertias" keys of the resulting frame's "info" Dict.
ase_energyshould be a Julia float in eV and
inertiasshould be a
Vector{Float64}` for proper compatibility.
Kinetica.imaginary_ve_tol
— Functionimaginary_ve_tol(imaginary_freq_tol)
Converts a tolerance value for imaginary frequencies into a tolerance value for imaginary vibrational energies.
I/O
Kinetica.save_asecalc
— Functionsave_asecalc(calc::ASENEBCalculator, saveto::String)
Saves the state of an ASENEBCalculator
to a BSON file.
Deconstructs calc
into a dictionary tree suitable for saving as BSON, such that it can be reconstructed with load_asecalc()
.
Saves everything except for the calculator builder calc.calc_builder
, as this has an undefined structure that can contain Python bindings.
Kinetica.load_asecalc
— Functionload_asecalc(calcfile::String[, calc_builder=nothing])
Loads the state of an ASENEBCalculator
from a BSON file.
Reconstructs an ASENEBCalculator
with the exception of its calc_builder
field, which can optionally be provided to this function or otherwise set afterwards.
Kinetica.verify_sd
— Functionverify_sd(calc_sd::SpeciesData, real_sd::SpeciesData)
Checks that calc_sd
contains a subset of the data in real_sd
.
Provided less or as many species are present in calc_sd
as are in real_sd
, ensures that each species numerically indexed in the former SpeciesData
has a string representation which matches its numerical counterpart in real_sd
.
If either assumption is invalid, throws an error since calc_sd
cannot be extended to become real_sd
.
Kinetica.verify_rd
— Functionverify_rd(calc_rd::RxData, real_rd::RxData)
Checks that calc_rd
contains a subset of the data in real_rd
.
Provided less or as many species are present in calc_rd
as are in real_rd
, ensures that each reaction numerically indexed in the former RxData
has a reaction hash which matches its numerical counterpart in real_rd
.
If either assumption is invalid, throws an error since calc_rd
cannot be extended to become real_rd
.
Kinetica.save_optgeom
— Functionsave_optgeom(frame::Dict{String, Any}, sym, geom, saveto::String)
Saves an optimised frame
geometry to a BSON file.
Also includes symmetry number sym
and geometry identifier geom
.
Kinetica.load_optgeom
— Functionload_optgeom(savefile::String)
Loads an optimised geometry from a BSON file.
Kinetica.save_endpoints
— Functionsave_endpoints(reacsys::Dict{String, Any}, prodsys::Dict{String, Any}, saveto::String)
Saves reaction endpoint systems reacsys
and prodsys
to a BSON file.
Kinetica.load_endpoints
— Functionload_endpoints(savefile::String)
Loads reaction endpoint systems from a BSON file.
Kinetica.save_tsdata
— Functionsave_tsdata(ts::Dict{String, Any}, conv, mult, sym, geom, chg, saveto::String)
Saves transition state data to a BSON file.
Aside from the ExtXYZ frame ts
, saves the convergence status conv
, spin multiplicity mult
, charge chg
, symmetry number sym
and geometry identifier geom
.
Kinetica.load_tsdata
— Functionload_tsdata(savefile::String)
Loads transition state data from a BSON file.
Kinetica.save_vibdata
— Functionsave_vibdata(sd::SpeciesData, sids, ts_cache::Dict{Symbol, Any}, rid, saveto::String)
Saves vibrational analysis data to a BSON file.
Given species in sd
indexed by sids
and a transition state in ts_cache
indexed by rid
, saves calculated vibrational energies.
Kinetica.load_vibdata
— Functionload_vibdata(savefile::String)
Loads vibrational analysis data from a BSON file.