CLI: Add cli to project

Comonicon.toml

@@ -0,0 +1,12 @@
+name = "vibrationalanalysis"
+
+[install]
+completion = true
+quiet = false
+compile = "min"
+optimize = 2
+
+[command]
+static=true
+width=100
+dash=false

Project.toml

@@ -4,9 +4,11 @@ authors = ["Josef M. Gallmetzer"]
 version = "0.1.8"
 
 [deps]
+Comonicon = "863f3e99-da2a-4334-8734-de3dacbe5542"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]

README.md

@@ -11,10 +11,19 @@
 This package provides tools to perform [vibrational analysis](https://gaussian.com/vib/) of molecules. It is based on the output of QMCFC and [PQ](https://github.com/MolarVerse/PQ) molecular dynamics codes developed at the [University of Innsbruck](https://www.uibk.ac.at/).
 
 ## Installation
+To install the package, run the following command in the Julia REPL:
+```julia-repl
+julia> ]
+pkg> add VibrationalAnalysis
 ```
-using Pkg
-Pkg.add("VibrationalAnalysis")
+
+## Intallation of the CLI
+If you want to use the command line interface, you can install it by running the following command:
+```julia-repl
+julia> using VibrationalAnalysis
+julia> VibrationalAnalysis.comonicon_install()
 ```
+Make sure you have `~/.julia/bin` in your PATH.
 
 ## Usage
 ```julia-repl

codecov.yml

@@ -0,0 +1,2 @@
+ignore:
+  - "src/main.jl"

deps/build.jl

@@ -0,0 +1 @@
+using VibrationalAnalysis; VibrationalAnalysis.comonicon_install()

docs/make.jl

@@ -9,6 +9,7 @@ makedocs(
 	pages = [
 		"Home" => "index.md",
 		"Installation" => "installation.md",
+		"CLI" => "cli.md",
 		"Examples" => "examples.md",
 		"License" => "license.md",
 		"API" => "api.md",

docs/src/cli.md

@@ -0,0 +1,30 @@
+# Intallation of the CLI
+
+If you want to use the command line interface, you can install it by running the following command:
+
+```julia-repl
+julia> using VibrationalAnalysis
+julia> VibrationalAnalysis.comonicon_install()
+```
+Make sure you have `~/.julia/bin` in your PATH.
+
+or by running the following command:
+
+```bash
+julia -e 'using Pkg; Pkg.add("VibrationalAnalysis"); using VibrationalAnalysis; VibrationalAnalysis.comonicon_install()'
+```
+
+or by build the package from in your default environment:
+
+```julia-repl
+julia> using Pkg
+julia> Pkg.build("VibrationalAnalysis")
+```
+
+## Usage
+
+Run the following command to see the available options:
+
+```bash
+vibrationalanalysis -h
+```

src/VibrationalAnalysis.jl

@@ -25,7 +25,9 @@ julia> write_wavenumber_intensity(wavenumbers, intensities, filename="wavenumber
 """
 module VibrationalAnalysis
 
+using Printf
 using LinearAlgebra
+using Comonicon
 
 include("massesdict.jl")
 include("read_files.jl")
@@ -35,5 +37,7 @@ include("transformation.jl")
 include("observables.jl")
 include("write.jl")
 include("calculate.jl")
+include("check.jl")
+include("main.jl")
 
 end # module VibrationalAnalysis

src/calculate.jl

@@ -1,79 +1,4 @@
-export calculate, read_calculate
-
-"""
-	read_calculate(rst_file, hessian_file; wavenumber=wavenumber_kcal)
-
-Reads the restart file, the hessian and the atom charges and calculates the wavenumbers, force constants and reduced masses.
-
-# Arguments
-- `rst_file::String`: The restart file.
-- `hessian_file::String`: The hessian file.
-
-# Keyword Arguments
-- `wavenumber::Function`: The wavenumber function to use. Either `wavenumber_kcal`, `wavenumber_eV` or `wavenumber_hartree`. Default is `wavenumber_kcal`.
-
-# Returns
-- `wavenumbers::Vector{Float64}`: The wavenumbers.
-- `force_constants::Vector{Float64}`: The force constants.
-- `reduced_masses::Vector{Float64}`: The reduced masses.
-
-# Example
-```julia-repl
-julia> read_calculate("restart.rst", "hessian.dat")
-```
-"""
-function read_calculate(rst_file::String, hessian_file::String; wavenumber = wavenumber_kcal)
-
-	# Read restart restart file 
-	atom_names, atom_masses, atom_coords, atom_types = read_rst(rst_file)
-
-	# Read the hessian
-	hessian = read_hessian(hessian_file)
-
-	wavenumbers, force_constants, reduced_masses = calculate(atom_masses, atom_coords, hessian, wavenumber=wavenumber)
-
-	return wavenumbers, force_constants, reduced_masses
-end
-
-"""
-	read_calculate(rst_file, hessian_file, moldescriptor_file; wavenumber=wavenumber_kcal)
-
-Reads the restart file, the hessian and the atom charges and calculates the wavenumbers, intensities, force constants and reduced masses.
-
-# Arguments
-- `rst_file::String`: The restart file.
-- `hessian_file::String`: The hessian file.
-- `moldescriptor_file::String`: The moldescriptor file.
-
-# Keyword Arguments
-- `wavenumber::Function`: The wavenumber function to use. Either `wavenumber_kcal`, `wavenumber_eV` or `wavenumber_hartree`. Default is `wavenumber_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.
-
-# Example
-```julia-repl
-julia> read_calculate("restart.rst", "hessian.dat", "moldescriptor.dat")
-```
-"""
-function read_calculate(rst_file::String, hessian_file::String, moldescriptor_file::String; wavenumber = wavenumber_kcal)
-
-	# Read restart restart file 
-	atom_names, atom_masses, atom_coords, atom_types = read_rst(rst_file)
-
-	# Read the hessian
-	hessian = read_hessian(hessian_file)
-
-	# Read the atom charges
-	atom_charges = read_moldescriptor(moldescriptor_file, atom_names, atom_types)
-
-	wavenumbers, intensities, force_constants, reduced_masses = calculate(atom_masses, atom_coords, atom_charges, hessian, wavenumber=wavenumber)
-
-	return wavenumbers, intensities, force_constants, reduced_masses
-end
+export calculate
 
 """
 	calculate(atom_masses, atom_coords, atom_charges, hessian)
@@ -92,6 +17,7 @@ Calculates the wavenumbers, force constants and reduced masses from the atom mas
 - `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-repl
@@ -113,7 +39,7 @@ function calculate(atom_masses::Vector{Float64}, atom_coords::Matrix{Float64}, h
 	reduced_masses = reduced_mass(normalization)
 	force_constants = force_constant(omega, reduced_masses)
 
-	return wavenumbers, force_constants, reduced_masses
+	return wavenumbers, force_constants, reduced_masses, eigenvectors_internal_normalized
 end
 
 """
@@ -135,6 +61,7 @@ Calculates the wavenumbers, intensities, force constants and reduced masses from
 - `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-repl
@@ -157,5 +84,5 @@ function calculate(atom_masses::Vector{Float64}, atom_coords::Matrix{Float64}, a
 	intensities = infrared_intensity(eigenvectors_internal_normalized, atom_charges, reduced_masses)
 	force_constants = force_constant(omega, reduced_masses)
 
-	return wavenumbers, intensities, force_constants, reduced_masses
+	return wavenumbers, intensities, force_constants, reduced_masses, eigenvectors_internal_normalized
 end

src/check.jl

@@ -0,0 +1,27 @@
+"""
+	check_unit(unit::String)
+
+Check if the unit is valid.
+
+# Arguments
+- `unit::String`: The unit to check.
+
+# Returns
+- `function`: The wavenumber function to use.
+"""
+function check_unit(unit::String)
+
+	# Check if the unit is valid - lowercase
+	unit = lowercase(unit)
+
+	# Check if the unit is valid
+	if unit == "kcal"
+		return wavenumber_kcal
+	elseif unit == "hartree"
+		return wavenumber_hartree
+	elseif unit == "ev"
+		return wavenumber_eV
+	else
+		throw(ArgumentError("Invalid unit. Options are kcal, hartree and eV."))
+	end
+end

src/main.jl

@@ -0,0 +1,68 @@
+import VibrationalAnalysis: check_unit
+
+"""
+CLI to calculate VibrationalAnalysis on a QMCFC or a PQ input.
+
+# Info
+
+Calculate the wavenumbers, intensities, force constants, reduced masses and eigenvectors of a QMCFC or a PQ input.
+
+# Args
+
+- `restart`: The restart file.
+- `hessian`: The hessian file.
+
+# Options
+
+- `--modesmatrix`: Write the modes in matrix notation to a file. If not specified, the modes in matrix notation will not be written.
+- `--moldescriptor`: The moldescriptor file. If not specified, the intensities will not be calculated.
+- `-o, --output`: The name of the output file. Default is stdout.
+- `-u, --unit`: The energy unit in the Hessian file. Options are kcal, Hartree and eV. Default is kcal.
+
+# Flags
+
+- `--modes`: Write the modes in xyz format. If not specified, the modes will not be written.
+
+"""
+@main function vibrationalanalalysis(restart::String, hessian::String; unit = "kcal", moldescriptor = nothing, output = nothing, modes_matrix = nothing, modes::Bool = false)
+
+	# Check if the unit is valid
+	wavenumber = check_unit(unit)
+
+	# Read restart restart file 
+	atom_names, atom_masses, atom_coords, atom_types = read_rst(restart)
+
+	# Read the hessian
+	hessian = read_hessian(hessian)
+
+	# if moldescriptor_file is not nothing
+	if moldescriptor == nothing
+
+		# calculate the wavenumbers, force constants, reduced masses and eigenvectors
+		wavenumbers, force_constants, reduced_masses, eigenvectors_internal_normalized = calculate(atom_masses, atom_coords, hessian, wavenumber = wavenumber)
+
+		# write wavenumbers, force constants, reduced masses
+		write_calculate_output(wavenumbers, force_constants, reduced_masses, filename = output)
+	else
+
+		# Read the atom charges
+		atom_charges = read_moldescriptor(moldescriptor, atom_names, atom_types)
+
+		# calculate the wavenumbers, intensities, force constants, reduced masses and eigenvectors
+		wavenumbers, intensities, force_constants, reduced_masses, eigenvectors_internal_normalized = calculate(atom_masses, atom_coords, atom_charges, hessian, wavenumber = wavenumber)
+
+		write_calculate_output(wavenumbers, intensities, force_constants, reduced_masses, filename = output)
+	end
+
+	# write the modes to a file
+	if modes_matrix != nothing
+		write_modes(eigenvectors_internal_normalized, filename = modes_matrix)
+	end
+
+	# write modes in xyz format
+	if modes
+		write_modes(eigenvectors_internal_normalized, atom_coords, atom_names, filename = "modes")
+	end
+
+	return
+end

src/observables.jl

@@ -91,7 +91,7 @@ end
 """
 	force_constant(wavenumbers::Vector{Float64}, reduced_mass::Vector{Float64}) -> force_const::Vector{Float64}
 
-Calculate the force constant from the wavenumbers and the reduced mass.
+Calculate the force constant from the wavenumbers and the reduced mass in mdyn Å^-1.
 
 # Arguments
 - `wavenumbers::Vector{Float64}`: The wavenumbers.