cclib · rngil · Aug 21, 2023 · Aug 20, 2023 · Aug 20, 2023 · Aug 21, 2023
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "Cclib"
 uuid = "6bf0c929-756b-4df7-ab0b-d621f7ebeba1"
 authors = ["cclib development team"]
-version = "0.3.0"
+version = "0.4.0"
 
 [deps]
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"

diff --git a/docs/src/calculation.md b/docs/src/calculation.md
@@ -2,7 +2,7 @@
 
 Cclib also allows to further analyse calculation ouputs.
 
-# C squared population analysis (CSPA)
+## C squared population analysis (CSPA)
 **CSPA** can be used to determine and interpret the electron density of a molecule. The contribution of the a-th atomic orbital to the i-th molecular orbital can be written in terms of the molecular orbital coefficients:
 
 $$\Phi_{ai} = \frac{c^2_{ai}}{\sum_k c^2_{ki}}$$
@@ -17,7 +17,7 @@ julia> aoresults, fragresults, fragcharges = cspa("./Trp_polar.fchk")
 * ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1, 24, 5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital)
 * ``fragcharges``: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[3]`` gives the number of electrons in the 3rd fragment.
 
-# Mulliken population analysis (MPA)
+## Mulliken population analysis (MPA)
 MPA can be used to determine and interpret the electron density of a molecule. The contribution of the a-th atomic orbital to the i-th molecular orbital in this method is written in terms of the molecular orbital coefficients, c, and the overlap matrix, S:
 
 $$\Phi_{ai} = \sum_b c_{ai} c_{bi} S_{ab}$$
@@ -31,7 +31,7 @@ julia> aoresults, fragresults, fragcharges = mpa("./Trp_polar.fchk")
 * ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1, 24, 5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital)
 * ``fragcharges``: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[3]`` gives the number of electrons in the 3rd fragment.
 
-# Löwdin Population Analysis
+## Löwdin Population Analysis
 ```Julia
 julia> using Cclib
 julia> aoresults, fragresults, fragcharges = lpa("./Trp_polar.fchk")
@@ -41,7 +41,7 @@ julia> aoresults, fragresults, fragcharges = lpa("./Trp_polar.fchk")
 * ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1, 24, 5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital)
 * ``fragcharges``: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[3]`` gives the number of electrons in the 3rd fragment.
 
-# Bickelhaupt Population Analysis
+## Bickelhaupt Population Analysis
 The Bickelhaupt class available from cclib.method performs Bickelhaupt population analysis that has been proposed in *Organometallics* 1996, 15, 13, 2923–2931. [doi:10.1021/om950966x](https://pubs.acs.org/doi/abs/10.1021/om950966x)
 
 The contribution of the a-th atomic orbital to the i-th molecular orbital in this method is written in terms of the molecular orbital coefficients, c, and the overlap matrix, S:
@@ -63,21 +63,21 @@ julia> aoresults, fragresults, fragcharges = bpa("./Trp_polar.fchk")
 * ``fragresults``: a three dimensional array with spin, molecular orbital, and atoms as the axes, so that ``fragresults[1, 24, 5]`` gives the contribution of the 5th fragment orbitals to the 24th beta molecular orbital)
 * ``fragcharges``: a vector with the number of (partial) electrons in each fragment, so that ``fragcharges[3]`` gives the number of electrons in the 3rd fragment.
 
-# Density Matrix calculation
+## Density Matrix calculation
 Calculates the electron density matrix
 ```Julia
 julia> using Cclib
 julia> result = density("./Trp_polar.fchk")
 ```
 Returns an array with three axes. The first axis is for the spin contributions, the second and the third axes for the density matrix, which follows standard definition.
-# Mayer’s Bond Orders (MBO)
+## Mayer’s Bond Orders (MBO)
 Calculates Mayer's bond orders
 ```Julia
 julia> using Cclib
 julia> result = mbo("./Trp_polar.fchk")
 ```
 Returns an array with three axes. The first axis is for contributions of each spin to the MBO, while the second and the third correspond to the indices of the atoms.
-# Charge Decomposition Analysis
+## Charge Decomposition Analysis
 The Charge Decomposition Analysis (CDA) as developed by Gernot Frenking et al. is used to study the donor-acceptor interactions of a molecule in terms of two user-specified fragments.
 ```Julia
 julia> using Cclib

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -2,7 +2,7 @@
 
 [Cclib.jl](https://github.com/cclib/Cclib.jl) is a Julia wrapper around [Cclib](https://cclib.github.io/index.html) - an open source library written in Python for parsing and interpreting the results of computational chemistry packages.
 
-# Features
+## Features
 
 - Parsing outputs from 15 different programs: ADF, DALTON, Firefly, GAMESS (US), GAMESS-UK, Gaussian, Jaguar, Molpro, MOLCAS, MOPAC, NWChem, ORCA, Psi4, NBO, QChem and Turbomole.
 
@@ -12,7 +12,7 @@
     - By extension, provides interoperability with libraries that use AtomsBase.jl, such as [DFTK.jl](https://github.com/JuliaMolSim/DFTK.jl), [Molly.jl](https://github.com/JuliaMolSim/Molly.jl), and [InteratomicPotentials.jl](https://github.com/cesmix-mit/InteratomicPotentials.jl).
 - Integration with [Fermi.jl](https://github.com/FermiQC/Fermi.jl) - quantum chemistry framework written in Julia.
 
-# How to install
+## How to install
 To install [Cclib.jl](https://github.com/cclib/Cclib.jl), start up and type the following into the REPL.
 ```julia
 Pkg.add("Cclib")

diff --git a/docs/src/interop.md b/docs/src/interop.md
@@ -1,14 +1,14 @@
 # Interoperability With Other Tools
 
-# AtomsBase.jl
+## AtomsBase.jl
 
 Cclib.jl provides interoperability with [AtomsBase.jl](https://github.com/JuliaMolSim/AtomsBase.jl) by allowing to create AtomsBase systems.
 
 The documentaiton below provides some essential functionality, such as creating and editing AtomsBase.jl systems.
 
 For a detailed overview, or if you want to know how AtomsBase.jl operates behind the scenes, refer to its official documentation.
 
-## Creating AtomsBase Systems
+### Creating AtomsBase Systems
 We can load information contained in a Cclib.jl-supported file into a system by using the following functions:
 - `make_flexible_system` - for creating an AtomsBase `FlexibleSystem`
 
@@ -64,7 +64,7 @@ julia> atoms[1]
 Atom(O, atomic_number = 8, atomic_mass = 15.999 u):
     position          : [0,0,-0.066678532]u"Å"
 ```
-## Accessing System Properties
+### Accessing System Properties
 In case we need to look at what our system contains, we can use regular `keys` to see available system-level properties and `atomkeys` to see available atom-level properties
 
 ```Julia
@@ -90,7 +90,7 @@ julia> bounding_box(system)
  :H
 ```
 
-## Updating and/or adding system properties
+### Updating and/or adding system properties
 We can also update and/or add system properties by using `update_system` function that accepts keywords arguments. Below is an example of adding data that was parsed using `ccread` to a system.
 ```Julia
 julia> using Cclib
@@ -101,7 +101,7 @@ julia> system[:nbasis]
 7
 ```
 
-# AtomsBase.jl-supported libraries
+### AtomsBase.jl-supported libraries
 
 We can use data loaded with Cclib.jl to perform calculations using other libraries that use AtomsBase.jl, such as [InteratomicPotentials.jl](https://github.com/cesmix-mit/InteratomicPotentials.jl) or [DFTK.jl](https://github.com/JuliaMolSim/DFTK.jl).
 
@@ -155,7 +155,7 @@ n     Energy            log10(ΔE)   log10(Δρ)   Diag   Δtime
 For a full list of tools that support AtomsBase.jl, refer to its [official
 documentation](https://github.com/JuliaMolSim/AtomsBase.jl).
 
-# Fermi.jl
+## Fermi.jl
 
 We can use information loaded using Cclib and use it for [Fermi.jl](https://github.com/FermiQC/Fermi.jl) calculations, which accept atom numbers and XYZ coordinates as input. The latter is accessible using Cclib's `getXYZ` function.
 

diff --git a/docs/src/io.md b/docs/src/io.md
@@ -1,9 +1,9 @@
 # Reading and writing files
 
-# Supported formats
+## Supported formats
 Properties that can be parsed and supported file formats can be found [here](https://cclib.github.io/data.html#details-of-current-implementation").
 
-# How to read files
+## How to read files
 ```Julia
 # Input files can be found in the in the repo under "test" folder
 julia> using Cclib
@@ -22,5 +22,4 @@ Accessing the data is identical to how one would access data in a dictionary:
 ```Julia
 julia> mol["natom"]
 12
-```
-Note that files may contain more than one geometry, in which case the index of the geometry can be specified by passing `geomIdx` argument. Be default, `writeXYZ` will use the last read geometry.
+```