Merge pull request #34 from Kinetica-jl/ase_extension

Move KineticaASE.jl into main package

.gitignore

@@ -2,4 +2,7 @@ deps/build.log
 Manifest.toml
 .vscode
 .CondaPkg
-docs/build
+docs/build
+
+.envrc
+shell.nix

CondaPkg.toml

@@ -3,10 +3,13 @@ obcanonicalradicals = "0.1.1"
 rdkit = ""
 xtb = ""
 matplotlib = ""
-ase = ">=3.22.1"
+ase = "<3.23"
 graphviz = ""
 python = ">=3.7,<3.11"
-scipy = ""
+scipy = "<=1.5.4"
+numpy = "<2"
+autode = ""
+rmsd = ""
 
 [pip.deps]
 extxyz = "~=0.1.3"

Project.toml

@@ -1,7 +1,7 @@
 name = "Kinetica"
 uuid = "3847ce11-53ec-444b-aa85-3b6606472139"
 authors = ["joegilkes <[email protected]>"]
-version = "0.5.12"
+version = "0.6.0"
 
 [deps]
 BSON = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0"
@@ -13,6 +13,7 @@ Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 ExtXYZ = "352459e4-ddd7-4360-8937-99dcb397b478"
+Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 LoggingExtras = "e6f89c97-d47a-5376-807f-9c37f3926c36"
@@ -54,6 +55,7 @@ julia = "1.10"
 [extras]
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [targets]
-test = ["Test", "SafeTestsets"]
+test = ["Test", "SafeTestsets", "Random"]

docs/make.jl

@@ -26,6 +26,7 @@ makedocs(
             "CRN Representation" => "development/crn-representation.md",
             "Condition Profiles" => "development/condition-profiles.md",
             "Calculator Interface" => "development/calculator-interface.md",
+            "ASE Calculator Builders" => "development/ase-calculator-builders.md",
             "Implementation Details" => "development/implementation-details.md"
         ],
         "API" => [
@@ -36,7 +37,14 @@ makedocs(
                 "Analysis" => "api/kinetica/analysis.md",
                 "Open Babel" => "api/kinetica/openbabel.md",
                 "RDKit" => "api/kinetica/rdkit.md",
-                "Utilities" => "api/kinetica/utilities.md"
+                "Utilities" => "api/kinetica/utilities.md",
+                "ASE Interface" => [
+                    "Kinetic Calculator" => "api/kinetica/ase_calculator/calculator.md",
+                    "Optimisation" => "api/kinetica/ase_calculator/optimisation.md",
+                    "Builders" => "api/kinetica/ase_calculator/builders.md",
+                    "Utilities" => "api/kinetica/ase_calculator/utilities.md"
+                ],
+                "autodE Interface" => "api/kinetica/autode.md"
             ],
             "KineticaKPM.jl" => "api/kineticakpm.md"
         ]

docs/src/api/kinetica/ase_calculator/builders.md

@@ -0,0 +1,9 @@
+# Kinetica.jl API - ASE Interface
+
+## ASE Calculator Builders
+
+```@docs
+EMTBuilder
+NWChemDFTBuilder
+FHIAimsBuilder
+```

docs/src/api/kinetica/ase_calculator/calculator.md

@@ -0,0 +1,15 @@
+# [Kinetica.jl API - ASE Interface](@id api_ase_calculator)
+
+## Kinetic Calculator
+
+```@docs
+ASENEBCalculator
+```
+
+### Rate Constant Calculation
+
+```@docs
+Kinetica.get_entropy
+Kinetica.get_enthalpy
+calculate_entropy_enthalpy
+```

docs/src/api/kinetica/ase_calculator/optimisation.md

@@ -0,0 +1,42 @@
+# Kinetica.jl API - ASE Interface
+
+## Optimisation and Property Calculation
+
+### Basic Species Properties
+
+```@docs
+Kinetica.get_mult
+Kinetica.get_mult!
+Kinetica.get_charge
+Kinetica.get_charge!
+Kinetica.get_formal_charges
+Kinetica.get_formal_charges!
+Kinetica.get_initial_magmoms
+Kinetica.get_initial_magmoms!
+Kinetica.correct_magmoms_for_mult!
+Kinetica.get_hydrogen_idxs
+```
+
+### Geometry Optimisation
+
+```@docs
+Kinetica.geomopt!
+Kinetica.kabsch_fit!
+Kinetica.permute_hydrogens!
+```
+
+### NEB
+
+```@docs
+Kinetica.get_initial_sys_mult
+Kinetica.get_rxn_mult
+Kinetica.neb
+Kinetica.highest_energy_frame
+```
+
+### Vibrational Analysis
+
+```@docs
+Kinetica.calc_species_vibrations!
+Kinetica.calc_ts_vibrations!
+```

docs/src/api/kinetica/ase_calculator/utilities.md

@@ -0,0 +1,28 @@
+# Kinetica.jl API - ASE Interface
+
+## Utilities
+
+### Conversion
+
+```@docs
+frame_to_atoms
+atoms_to_frame
+Kinetica.imaginary_ve_tol
+```
+
+### I/O
+
+```@docs
+Kinetica.save_asecalc
+Kinetica.load_asecalc
+Kinetica.verify_sd
+Kinetica.verify_rd
+Kinetica.save_optgeom
+Kinetica.load_optgeom
+Kinetica.save_endpoints
+Kinetica.load_endpoints
+Kinetica.save_tsdata
+Kinetica.load_tsdata
+Kinetica.save_vibdata
+Kinetica.load_vibdata
+```

docs/src/api/kinetica/autode.md

@@ -0,0 +1,25 @@
+# Kinetica.jl API
+
+## autodE Interface
+
+### Conformer Searching
+
+```@docs
+Kinetica.autode_conformer_search!
+Kinetica.autode_NCI_conformer_search
+```
+
+### Species Conversion
+
+```@docs
+Kinetica.autode_to_frame
+Kinetica.frame_to_autode
+```
+
+### Utilities
+
+```@docs
+Kinetica.autode_get_graph
+Kinetica.autode_is_isomorphic
+Kinetica.autode_frame_symmetry
+```

docs/src/api/kinetica/exploration.md

@@ -18,6 +18,7 @@ push_unique!
 RxData
 Base.push!(::RxData{iType, fType}, ::SpeciesData, ::Vector{Vector{String}}, ::Vector{Vector{String}}, ::Vector{Dict{String, Any}}, ::Vector{Dict{String, Any}}, ::Vector{fType}, ::Int) where {iType, fType <: AbstractFloat}
 Base.splice!(::RxData, ::Vector{Int})
+get_reverse_rhash
 ```
 
 ### CRN Initialisation

docs/src/api/kinetica/solving.md

@@ -17,6 +17,8 @@ Base.splice!(rd::RxData, calculator::cType, rids::Vector{Int}) where {cType <: K
 PrecalculatedArrheniusCalculator
 ```
 
+The [`ASENEBCalculator`](@ref) ASE-driven NEB-based calculator also implemented in Kinetica.jl is significantly more complex, and has its own API page [here](@ref api_ase_calculator).
+
 ## Solvers
 
 ```@docs