Update documentation for changes in NQCBase#11 (#351)

* Update documentation for changes in NQCBase#11

* Version bump. Compat bump for NQCModels.jl

* Replaced PyCall with PythonCall in CI test

* Forgot to switch Project.toml to PythonCall

Author: Alexsp32

Project.toml

@@ -1,7 +1,7 @@
 name = "NQCDynamics"
 uuid = "36248dfb-79eb-4f4d-ab9c-e29ea5f33e14"
 authors = ["James <[email protected]>"]
-version = "0.13.7"
+version = "0.14.0"
 
 [deps]
 AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
@@ -62,7 +62,7 @@ MKL_jll = "2023"
 MuladdMacro = "0.2"
 NQCBase = "0.2"
 NQCDistributions = "0.1"
-NQCModels = "0.8"
+NQCModels = "0.9"
 Optim = "1"
 OrdinaryDiffEq = "5, 6"
 Parameters = "0.12"
@@ -99,11 +99,27 @@ JuLIP = "945c410c-986d-556a-acb1-167a618e0462"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
+PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "SafeTestsets", "CSV", "DataFrames", "DiffEqNoiseProcess", "FiniteDiff", "DiffEqDevTools", "Logging", "MKL", "PyCall", "JuLIP", "Symbolics", "Statistics", "Plots", "JLD2"]
+test = [
+    "Test",
+    "SafeTestsets",
+    "CSV",
+    "DataFrames",
+    "DiffEqNoiseProcess",
+    "FiniteDiff",
+    "DiffEqDevTools",
+    "Logging",
+    "MKL",
+    "PythonCall",
+    "JuLIP",
+    "Symbolics",
+    "Statistics",
+    "Plots",
+    "JLD2",
+]

docs/src/atoms.md

@@ -4,10 +4,11 @@ start_time = time()
 ```
 # [Handling Atoms](@id atoms)
 
-This package makes the choice to separate the atomic parameters from their positions and
-velocities for ease of use with the differential equations solvers.
-This contrasts somewhat with most other software packages where these would be usually
-by joined together into a single object.
+!!! tip "Tip: NQCDynamics.jl handles atoms differently to `ase`"
+	This package makes the choice to separate the atomic parameters from their positions and
+	velocities for ease of use with the differential equations solvers.
+	This contrasts somewhat with most other software packages where these would be usually
+	be joined together into a single object.
 
 The atomic parameters here are contained within the
 [`Atoms`](@ref) type introduced earlier
@@ -40,32 +41,39 @@ When working with NQCDynamics, the most useful packages are [AtomsIO](https://gi
 for reading and writing structures and trajectories, and [ASEconvert](https://github.com/mfherbst/ASEconvert.jl)
 for working with [ASE](https://wiki.fysik.dtu.dk/ase/index.html) from within Julia.
 
-## Using ASE with ASEconvert.jl
+## Using Python's `ase` package from Julia
 
-This example shows how ASEconvert can be used to build a structure, then convert
-from the ASE format into an AtomsBase compatible system:
+Julia provides multiple options to run Python-based code from Julia scripts. The NQCD packages
+provide compatibility with [**PythonCall.jl**](https://github.com/JuliaPy/PythonCall.jl), and some deprecated interfaces for [**PyCall.jl**](https://github.com/JuliaPy/PyCall.jl) exist as well. 
+While both of these packages function similarly, PythonCall forces you as a user to think more about when data is copied in memory between Python and Julia, enabling more efficient code. 
+
+This example shows how `ase.build` can be used to build a structure from within Julia, then convert
+from the ASE format into the required objects for atoms, positions and unit cell for an NQCD simulation:
 
 ```julia
-using ASEconvert
+using PythonCall
+using NQCBase
 
-# Make a silicon supercell using ASE
-atoms_ase = ase.build.bulk("Si") * pytuple((4, 1, 1))
+ase_build = pyimport("ase.build")
 
-# Convert to an AtomsBase-compatible structure
-atoms_ab = pyconvert(AbstractSystem, atoms_ase)
+# Make a silicon supercell using ASE
+atoms_ase = ase_build.bulk("Si") * pytuple((4, 1, 1))
 ```
 
 It is currently not possible to use an AtomsBase system directly with NQCDynamics, but can
 be quickly converted to the correct format:
 
 ```julia
 using NQCDynamics
-atoms_nqcd = Atoms(atoms_ab)
-r = Position(atoms_ab)
-v = Velocity(atoms_ab)
-c = Cell(atoms_ab)
+
+atoms_nqcd, positions_nqcd, cell_nqcd = convert_from_ase_atoms(atoms_ase)
+
+println(atoms_nqcd)
+println(positions_nqcd)
+println(cell_nqcd)
 ```
 
+
 ## Saving and loading with AtomsIO.jl
 
 After running a simulation it often desirable to save the trajectory in a standard format for visualization.

test/Analysis/diatomic.jl

@@ -1,7 +1,7 @@
 using Test
 using NQCDynamics
 using Unitful, UnitfulAtomic
-using PyCall
+using PythonCall
 using NQCModels
 using JLD2