VibrationalAnalysis API
VibrationalAnalysis — ModuleVibrationalAnalysis.jl
This module contains functions to perform vibrational analysis on a QMCFC output.
Usage
Can read directly from rst-file, moldescriptor-file and hessian-file and perform vibrational analysis on the system.
julia> read_calculate("restart.rst", "hessian.dat", "moldescriptor.dat")Or directly perform a vibrational analysis with atom masses, atom coordinates, atom charges and hessian of the system.
julia> wavenumbers, intensities, _, _ = calculate(atom_masses, atom_coords, atom_charges, hessian)
+julia> write_wavenumber_intensity(wavenumbers, intensities, filename="wavenumbers.dat")Module Index
VibrationalAnalysis.VibrationalAnalysisVibrationalAnalysis.calculateVibrationalAnalysis.calculateVibrationalAnalysis.read_hessianVibrationalAnalysis.read_moldescriptorVibrationalAnalysis.read_rstVibrationalAnalysis.wavenumber_eVVibrationalAnalysis.wavenumber_hartreeVibrationalAnalysis.wavenumber_kcalVibrationalAnalysis.write_calculate_outputVibrationalAnalysis.write_calculate_outputVibrationalAnalysis.write_calculate_outputVibrationalAnalysis.write_modesVibrationalAnalysis.write_modes
Detailed API
VibrationalAnalysis.VibrationalAnalysis — ModuleVibrationalAnalysis.jl
This module contains functions to perform vibrational analysis on a QMCFC output.
Usage
Can read directly from rst-file, moldescriptor-file and hessian-file and perform vibrational analysis on the system.
julia> read_calculate("restart.rst", "hessian.dat", "moldescriptor.dat")Or directly perform a vibrational analysis with atom masses, atom coordinates, atom charges and hessian of the system.
julia> wavenumbers, intensities, _, _ = calculate(atom_masses, atom_coords, atom_charges, hessian)
+julia> write_wavenumber_intensity(wavenumbers, intensities, filename="wavenumbers.dat")VibrationalAnalysis.calculate — Methodcalculate(atom_masses, atom_coords, atom_charges, hessian)Calculates the wavenumbers, force constants and reduced masses from the atom masses, atom coordinates, and the hessian.
Arguments
atom_masses::Vector{Float64}: Vector of atom_masses (n)atom_coords::Matrix{Float64}: Matrix of atom coordinates (3xn)hessian::Matrix{Float64}: Matrix of the hessian (3nx3n)
Keyword Arguments
wavenumber::Function: The wavenumber function to use. Eitherwavenumber_kcal,wavenumber_eVorwavenumber_hartree. Default iswavenumber_kcal.
Returns
wavenumbers::Vector{Float64}: The wavenumbers.force_constants::Vector{Float64}: The force constants.reduced_masses::Vector{Float64}: The reduced masses.eigenvectors_internal_normalized::Matrix{Float64}: The eigenvectors in internal coordinates.
Example
julia> calculate(atom_masses, atom_coords, hessian)
+julia> calculate(atom_masses, atom_coords, hessian, wavenumber=wavenumber_hartree)
+julia> calculate(atom_masses, atom_coords, hessian, wavenumber=wavenumber_eV)VibrationalAnalysis.calculate — Methodcalculate(atom_masses, atom_coords, atom_charges, hessian)Calculates the wavenumbers, intensities, force constants and reduced masses from the atom masses, atom coordinates, atom charges and the hessian.
Arguments
atom_masses::Vector{Float64}: Vector of atom_masses (n)atom_coords::Matrix{Float64}: Matrix of atom coordinates (3xn)atom_charges::Vector{Float64}: Vector of atom charges (n)hessian::Matrix{Float64}: Matrix of the hessian (3nx3n)
Keyword Arguments
wavenumber::Function: The wavenumber function to use. Eitherwavenumber_kcal,wavenumber_eVorwavenumber_hartree. Default iswavenumber_kcal.
Returns
wavenumbers::Vector{Float64}: The wavenumbers.intensities::Vector{Float64}: The intensities.force_constants::Vector{Float64}: The force constants.reduced_masses::Vector{Float64}: The reduced masses.eigenvectors_internal_normalized::Matrix{Float64}: The eigenvectors in internal coordinates.
Example
julia> calculate(atom_masses, atom_coords, atom_charges, hessian)
+julia> calculate(atom_masses, atom_coords, atom_charges, hessian, wavenumber=wavenumber_hartree)
+julia> calculate(atom_masses, atom_coords, atom_charges, hessian, wavenumber=wavenumber_eV)VibrationalAnalysis.read_hessian — Methodread_hessian(hessian_file::String) -> hessian::Matrix{Float64}Reads a hessian file and returns a nxn Matrix of the hessian.
Arguments
hessian_file::String: The hessian file.
VibrationalAnalysis.read_moldescriptor — Methodread_moldescriptor(moldescriptor_file::String) -> atom_charges::Vector{Float64}Reads a moldescriptor file and returns atom_charges.
Arguments
moldescriptor_file::String: The moldescriptor file.
VibrationalAnalysis.read_rst — Methodread_rst(rst_file::String) -> atom_names::Vector{String}, atom_masses::Vector{Float64}, atom_coords::Matrix{Float64}, atom_types::Vector{Int64}Reads a restart file and returns a tuple of atom names, masses, and coordinates.
Arguments
rst_file::String: The restart file.
VibrationalAnalysis.wavenumber_eV — Methodwavenumber_eV(eigenvalues::Vector{Float64}) -> wavenumbers::Vector{Float64}, omega::Vector{Float64}Convert eigenvalues from eV Å^-2 g^-1 to wavenumbers in cm^-1. Made for ASE hessian files. Output include omega in s^-2.
$ω = √v$
$ν̃ = 1/(2π * c) * ω$
Arguments
eigenvalues::Vector{Float64}: The eigenvalues.
VibrationalAnalysis.wavenumber_hartree — Methodwavenumber_hartree(eigenvalues::Vector{Float64}) -> wavenumbers::Vector{Float64}, omega::Vector{Float64}Convert eigenvalues from hartree bor^-2 g^-1 to wavenumbers in cm^-1. Made for DFTB hessian files. Output include omega in s^-2.
$ω = √v$
$ν̃ = 1/(2π * c) * ω$
Arguments
eigenvalues::Vector{Float64}: The eigenvalues.
VibrationalAnalysis.wavenumber_kcal — Methodwavenumber_kcal(eigenvalues::Vector{Float64}) -> wavenumbers::Vector{Float64}, omega::Vector{Float64}Convert eigenvalues from kcal Å^-2 g^-1 to wavenumbers in cm^-1. Made for QMCFC hessian files. Output include omega in s^-2.
$ω = √v$
$ν̃ = 1/(2π * c) * ω$
Arguments
eigenvalues::Vector{Float64}: The eigenvalues.
VibrationalAnalysis.write_calculate_output — Methodwrite_calculate_output(wavenumbers, intensities, force_constants, reduced_masses; filename = stdout)Write the wavenumbers, intensities, force constants and reduced masses to a file.
Arguments
wavenumbers::Vector{Float64}: The wavenumbers.intensities::Vector{Float64}: The intensities.force_constants::Vector{Float64}: The force constants.reduced_masses::Vector{Float64}: The reduced masses.
Keyword Arguments
filename::String: The name of the file. Default is stdout
Example
julia> using VibrationalAnalysis
+julia> write_calculate_output(wavenumbers, intensities, force_constants, reduced_masses)VibrationalAnalysis.write_calculate_output — Methodwrite_calculate_output(wavenumbers, force_constants, reduced_masses, eigenvectors_internal_normalized; filename = stdout)Write the wavenumbers, force constants and reduced masses to a file.
Arguments
wavenumbers::Vector{Float64}: The wavenumbers.force_constants::Vector{Float64}: The force constants.reduced_masses::Vector{Float64}: The reduced masses.
Keyword Arguments
filename::String: The name of the file. Default is stdout.
Example
julia> using VibrationalAnalysis
+julia> write_calculate_output(wavenumbers, force_constants, reduced_masses)VibrationalAnalysis.write_calculate_output — Methodwrite_calculate_output(wavenumbers, intensities; filename = stdout)Write the wavenumbers and intensities to a file.
Arguments
wavenumbers::Vector{Float64}: The wavenumbers.intensities::Vector{Float64}: The intensities.
Keyword Arguments
filename::String: The name of the file. Default is stdout
Example
julia> using VibrationalAnalysis
+julia> write_calculate_output(wavenumbers, intensities)VibrationalAnalysis.write_modes — Methodwrite_modes(eigenvectors_internal_normalized, coord, atom_names; filename, amplitude, step)Write the modes to a file in xyz format.
Arguments
eigenvectors_internal_normalized::Matrix{Float64}: The eigenvectors in internal coordinates.coord::Matrix{Float64}: The coordinates of the atoms.atom_names::Vector{String}: The names of the atoms.
Keyword Arguments
filename::String: The name of the file. Default is "modes".amplitude::Float64: The amplitude of the mode. Default is 0.25.step::Float64: The step size of the mode. Default is 0.01.
Example
julia> using VibrationalAnalysis
+julia> write_modes(eigenvectors_internal_normalized, atom_coords, atom_names)
+shell> cat modes-1.xyzVibrationalAnalysis.write_modes — Methodwrite_modes(eigenvectors_internal_normalized)Write the modes to a file in matrix format.
Arguments
eigenvector_internal::Matrix{Float64}: The eigenvectors in internal coordinates.
Keyword Arguments
filename::String: The name of the file. Default is stdout.
Example
julia> using VibrationalAnalysis
+julia> write_modes(eigenvectors_internal_normalized)
+shell> cat modes.dat
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+}
diff --git a/v0.3.0/siteinfo.js b/v0.3.0/siteinfo.js
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diff --git a/versions.js b/versions.js
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