Use AtomsSystems instead of FlexibleSystem for more features

Project.toml

@@ -5,21 +5,27 @@ version = "0.2.2"
 [deps]
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
 AtomsIO = "1692102d-eeb4-4df9-807b-c9517f998d44"
+AtomsSystems = "bd665c09-60e6-46be-bbfe-8f6ec2b68ee8"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 PubChemCrawler = "30e472fa-2b12-4c0b-9705-07d174b7a4e1"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [compat]
 AtomsBase = "0.5"
 AtomsIO = "0.3"
+AtomsSystems = "0.1.2"
 JSON = "0.21.4"
 LinearAlgebra = "1.9"
 PubChemCrawler = "1.2"
 Random = "1.9"
+Reexport = "1"
 StaticArrays = "1.9"
+StatsBase = "0.34"
 Unitful = "1.19"
 julia = "1.10"
 

README.md

@@ -7,16 +7,22 @@
 This package provides utilities to build atomic structures. At the moment the functionality is limited - see examples below. The intention is that over time this package becomes the de facto standard for generating structures in the JuliaMolSim ecosystem. Contributions are very welcome.
 
 
-## Preliminary Documentation 
+## Functionality List
 
-Currently there are just two exported functions to build materials: 
-* `bulk`
-* `rattle!`
-In addition we overload 
-* `repeat` (with alias `*`)
+The following functions are used to build and manipulate systems
+
+* `bulk` - generate bulk solids
+* `rattle_positions` and `rattle_positions!` - reexports from [AtomsSystems](https://github.com/JuliaMolSim/AtomsSystems.jl)
+* `repeat` - repeating system - reexport from [AtomsSystems](https://github.com/JuliaMolSim/AtomsSystems.jl)
+* `random_species!` - randomize species
+* `load_from_pubchem` - download structures from [PubChem](https://pubchem.ncbi.nlm.nih.gov/)
+
+
+## Example
 
 ```julia
-using AtomsBuilder 
+using AtomsBuilder
+using Unitful
 
 # generate a diamond cubic bulk Si unit cell 
 at1 = bulk(:Si)
@@ -27,18 +33,20 @@ at2 = bulk(:Si, cubic=true)
 @show length(at2)
 
 # repeat the cell 3 times in each coordinate direction
-at3 = at2 * 3
+at3 = repeat(at2, 3)
 @show length(at3)
 
 # repeat the unit cell in only one direction
-at4 = at2 * (3, 1, 1)
+at4 = repeat(at2, (3, 1, 1) )
 @show length(at3)
 
 # create a bulk supercell and then rattle the atoms 
-at5 = rattle!( bulk(:Si, cubic=true) * 3 )
+at5 = rattle_positions( repeat(bulk(:Si, cubic=true), 3), 0.3u"Å" )
+
+random_species!(at5, [:Si, :P], Weights([0.9, 0.1]))
 ```
 
-See `?bulk` and `?rattle!` for more information. 
+For more information look for docstrings.
 
 ## PubChem Interface
 
@@ -51,6 +59,9 @@ using AtomsBuilder
 # using trivial name
 load_from_pubchem( "water" )
 
+# same with additional metadata
+load_from_pubchem( "water"; metadata=true )
+
 # using CID
 load_from_pubchem( 887 )
 

src/AtomsBuilder.jl

@@ -1,7 +1,21 @@
 module AtomsBuilder
 
-import AtomsBase
+using AtomsBase 
+using AtomsSystems
+using LinearAlgebra: norm, I 
+using Reexport
 using StaticArrays: SMatrix, SVector
+using StatsBase: sample
+import StatsBase
+using Unitful
+
+@reexport using AtomsSystems: rattle_positions!, rattle_positions
+@reexport using StatsBase: FrequencyWeights, ProbabilityWeights, Weights
+
+export bulk
+export rattle! 
+export randz!
+export random_species!
 
 const Mat3{T} = SMatrix{3, 3, T}
 const Vec3{T} = SVector{3, T}

src/bulk.jl

@@ -72,13 +72,16 @@ function bulk(sym::Symbol; cubic=false, pbc=(true, true, true),
         cubic && throw(ArgumentError("cubic=true cannot be selected for $symm lattices"))
         X, C = _bulk_hcp(sym; a, c, T)
     else
-        throw(ArgumentError("Currently bulk not immplemented for symmetry $symm"))
+        throw(ArgumentError("Currently bulk not implemented for symmetry $symm"))
     end
-    Z = Chemistry.atomic_number(sym)
+    #Z = Chemistry.atomic_number(sym)
     nat = length(X)
-    at = _flexible_system( X, fill(Z, nat), C, _convert_pbc(pbc))
+    # at = _flexible_system( X, fill(Z, nat), C, _convert_pbc(pbc))
+    spc = AtomsBase.ChemicalSpecies(sym)
+    at = generic_system( fill(spc, nat), X; cell_vectors=collect(eachrow(C)), periodicity=pbc)
     # I don't remember what this does so I'm commenting it out until I understand 
     # it again ...                         
     # (x !== nothing || y !== nothing || z !== nothing) && rotate!(at, x=x, y=y, z=z)
+    #return at
     return at
 end

src/pubchem.jl

@@ -1,19 +1,22 @@
-using AtomsBase: FastSystem
+using AtomsSystems: generic_system
 using AtomsIO: load_system
-using PubChemCrawler: get_cid, get_for_cids 
+using PubChemCrawler: get_cid, get_for_cids
+using Unitful
 
 export load_from_pubchem
 
 """
-    load_from_pubchem(cid::Int)
-    load_from_pubchem(name::AbstractString)
-    load_from_pubchem(;smiles::AbstractString)
+    load_from_pubchem(cid::Int; metadata=false)
+    load_from_pubchem(name::AbstractString; metadata=false)
+    load_from_pubchem(;smiles::AbstractString; metadata=false)
 
 Load a molecule from [PubChem](https://pubchem.ncbi.nlm.nih.gov/).
 
 You can use [PubChemCrawler](https://github.com/JuliaHealth/PubChemCrawler.jl)
 to search for `cid`.
 
+If `metadata` is `true` then the returned system will include PubChem metadata.
+
 # Example
 ```julia
 using AtomsBuilder
@@ -31,23 +34,26 @@ load_from_pubchem( smiles="CC(=O)C" )
 load_from_pubchem( "64-17-5" )
 ```
 """
-function load_from_pubchem(cid::Int)
+function load_from_pubchem(cid::Int; metadata=false)
     tmp_name = tempname() * ".sdf"
     open(tmp_name, "w") do io
         write(io, get_for_cids(cid, output="SDF", record_type="3d"))
     end
-    # parsing system does not work properly so we drop global features
-    sys = FastSystem( load_system(tmp_name) )
+    if metadata
+        sys = generic_system( load_system(tmp_name) )
+    else
+        sys = CellSystem( generic_system( load_system(tmp_name) ) )
+    end
     rm(tmp_name)
     return sys
 end
 
-function load_from_pubchem(name::AbstractString)
+function load_from_pubchem(name::AbstractString; metadata=false)
     cid = get_cid(name=name)
-    return load_from_pubchem(cid)
+    return load_from_pubchem(cid; metadata=metadata)
 end
 
-function load_from_pubchem(;smiles::AbstractString)
+function load_from_pubchem(;smiles::AbstractString, metadata=false)
     cid = get_cid(smiles=smiles)
-    return load_from_pubchem(cid)
+    return load_from_pubchem(cid; metadata=metadata)
 end