AtomsBase output (#22)

Project.toml

@@ -1,9 +1,10 @@
 name = "PotentialDB"
 uuid = "e899a7e1-cf22-409b-b35c-84b9d10c2c8e"
-authors = ["Teemu Järvinen <[email protected]>"]
-version = "0.2.3"
+authors = ["Teemu Järvinen"]
+version = "0.2.4-DEV"
 
 [deps]
+AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 PotentialCalculation = "76415700-ec45-11e8-0f65-f1df3c899b21"
@@ -12,7 +13,8 @@ SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 
 [compat]
+AtomsBase = "0.3"
 JLD2 = "0.4"
-PotentialCalculation = "0.4.2, 0.5, 0.6"
+PotentialCalculation = "0.6"
 Reexport = "0.2, 1.0"
 julia = "1.6"

docs/src/usage.md

@@ -30,6 +30,14 @@ To load a wanted potential, call with `loadpotential` and key
 p=loadpotential(d,"1")
 ```
 
+### AtomsBase output
+
+To load data in [AtomsBase]() format use
+
+```@example 1
+data = load_data(d, "1")
+```
+
 ## Custom registries
 
 Registries are defined by a TOML-file that holds information on where the file

src/PotentialDB.jl

@@ -2,6 +2,7 @@ module PotentialDB
 
 using Reexport
 
+using AtomsBase
 using JLD2
 @reexport using PotentialCalculation
 using TOML
@@ -14,6 +15,7 @@ export addpotential!
 export defaultregistry
 export listpotentials
 export loadpotential
+export load_data
 export saveregistry
 
 

src/potentialregistry.jl

@@ -228,3 +228,37 @@ function listpotentials(r::PotentialRegistry)
     end
 end
 
+
+"""
+    load_data(reg, i; kwargs...)
+
+Load data from registry as AtomsBase FlexibleSystem.
+
+# kwargs
+
+- `energy_unit=u"hartree"`  : energy unit for output
+- `strip_unit=false`        ; whether or not strip energy unit or not
+"""
+function load_data(reg, i; energy_unit=u"hartree", strip_unit=false)
+    tmp = loadpotential(reg, i)
+    points = map(  zip( tmp["Points"], tmp["Energy"] )  ) do (xyz, e)
+        tmp_e = e *u"hartree"
+        e_out = strip_unit ? ustrip(energy_unit, tmp_e) : uconvert(energy_unit, tmp_e)
+        FlexibleSystem(xyz; energy = e_out )
+    end
+    lc1 = length(tmp["cluster1"])
+    lc2 = length(tmp["cluster2"])
+    r1 = 1:lc1
+    r2 = (1:lc2) .+ lc1
+    cluster1 = map( tmp["Points"] ) do xyz
+        tmp_e = 0.0 *u"hartree"
+        e_out = strip_unit ? ustrip(energy_unit, tmp_e) : uconvert(energy_unit, tmp_e)
+        FlexibleSystem(xyz(r1); energy = e_out )
+    end
+    cluster2 = map( tmp["Points"] ) do xyz
+        tmp_e = 0.0 *u"hartree"
+        e_out = strip_unit ? ustrip(energy_unit, tmp_e) : uconvert(energy_unit, tmp_e)
+        FlexibleSystem(xyz(r2); energy = e_out )
+    end
+    return Dict("Points" => points, "cluster1" => cluster1, "cluster2"=>cluster2)
+end

test/runtests.jl

@@ -38,3 +38,17 @@ end
     @test r.keywords == r2.keywords
     listpotentials(r)
 end
+
+
+@testset "AtomsBase" begin
+    reg = defaultregistry()
+    data_hartree = load_data(reg, 1)
+    data_ev = load_data(reg, 1; energy_unit=u"eV")
+    data_strip = load_data(reg, 1; strip_unit=true)
+    c_data = loadpotential(reg, 1)
+
+    @test data_hartree["Points"][1][:energy] |> unit == u"hartree"
+    @test data_hartree["Points"][1][:energy] ≈ data_ev["Points"][1][:energy]
+    @test data_hartree["Points"][1][:energy] |> ustrip ≈ data_strip["Points"][1][:energy]
+    @test c_data["Energy"][1] == data_strip["Points"][1][:energy]
+end