New naming convention (#7)

* Change names suggestion * Bump version * fix * Update documentation
JuliaMolSim · Nov 29, 2024 · 7e60079 · 7e60079
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Showing 7 changed files with 50 additions and 130 deletions.
diff --git a/Artifacts.toml b/Artifacts.toml
@@ -1,36 +1,3 @@
-["pd_nc_sr_pbesol_standard_0.4.1_psp8"]
-extension = "psp8"
-functional = "pbesol"
-version = "0.4.1"
-git-tree-sha1 = "d5d914c4b8ae3119fae60f3a3e66225db41de579"
-lazy = true
-
-    [["pd_nc_sr_pbesol_standard_0.4.1_psp8".download]]
-    sha256 = "6870faeceb4f68196901160a6ac455016dc1b9b1ea4ec629607d8e1757d9055f"
-    url = "https://github.com/JuliaMolSim/PseudoLibrary/raw/main/artifacts/pd_nc_sr_pbesol_standard_0.4.1_psp8.tar.gz"
-
-["pd_nc_sr_pbe_standard_0.4.1_psp8"]
-extension = "psp8"
-functional = "pbe"
-version = "0.4.1"
-git-tree-sha1 = "054625d663e05d8c86bd3b8c1b7f371b85eb906f"
-lazy = true
-
-    [["pd_nc_sr_pbe_standard_0.4.1_psp8".download]]
-    sha256 = "cffaf5a4bf41cca1f45d9f6f1ae8a6d5b83083ef62e69052459c26913bcf555a"
-    url = "https://github.com/JuliaMolSim/PseudoLibrary/raw/main/artifacts/pd_nc_sr_pbe_standard_0.4.1_psp8.tar.gz"
-
-["pd_nc_sr_lda_standard_0.4.1_psp8"]
-extension = "psp8"
-functional = "lda"
-version = "0.4.1"
-git-tree-sha1 = "13a9394a722182e06cd28f7d8c0c6ed491b55c5d"
-lazy = true
-
-    [["pd_nc_sr_lda_standard_0.4.1_psp8".download]]
-    sha256 = "840a5f654e841ef8b42a5867c27d181996998535a118b7ccbfe355101352a5b7"
-    url = "https://github.com/JuliaMolSim/PseudoLibrary/raw/main/artifacts/pd_nc_sr_lda_standard_0.4.1_psp8.tar.gz"
-
 ["pd_nc_sr_lda_stringent_0.4.1_upf"]
 extension = "upf"
 functional = "lda"
@@ -42,17 +9,6 @@ lazy = true
     sha256 = "ba0c16c557f24e39b0b71d64a1ba3582421e016ce7a9cc799c4de195b7c4ec21"
     url = "https://github.com/JuliaMolSim/PseudoLibrary/raw/main/artifacts/pd_nc_sr_lda_stringent_0.4.1_upf.tar.gz"
 
-["pd_nc_fr_pbe_standard_0.4_psp8"]
-extension = "psp8"
-functional = "pbe"
-version = "0.4"
-git-tree-sha1 = "82ac4c373d1a564f97638f28bc39bcdf076c665a"
-lazy = true
-
-    [["pd_nc_fr_pbe_standard_0.4_psp8".download]]
-    sha256 = "7b56901e5a68adf9de79a00cd192904585bb8985f10fc70c3ee9c0c27dbf9467"
-    url = "https://github.com/JuliaMolSim/PseudoLibrary/raw/main/artifacts/pd_nc_fr_pbe_standard_0.4_psp8.tar.gz"
-
 ["pd_paw_pbe_standard_1.1_xml"]
 extension = "xml"
 functional = "pbe"
@@ -64,17 +20,6 @@ lazy = true
     sha256 = "83c288b1356d4322c51ebef61975e1434bbf5eb303a82d41c0f4b076958b9beb"
     url = "https://github.com/JuliaMolSim/PseudoLibrary/raw/main/artifacts/pd_paw_pbe_standard_1.1_xml.tar.gz"
 
-["pd_nc_sr_pbe_stringent_0.4.1_psp8"]
-extension = "psp8"
-functional = "pbe"
-version = "0.4.1"
-git-tree-sha1 = "a87b12bba53fc184bf2eef49ab89f76837615cec"
-lazy = true
-
-    [["pd_nc_sr_pbe_stringent_0.4.1_psp8".download]]
-    sha256 = "eb7e7845711fe280cc0a5ebfb18c7cbb3c014bdc1ceab1897fd10c41c916775c"
-    url = "https://github.com/JuliaMolSim/PseudoLibrary/raw/main/artifacts/pd_nc_sr_pbe_stringent_0.4.1_psp8.tar.gz"
-
 ["pd_nc_sr_lda_standard_0.4.1_upf"]
 extension = "upf"
 functional = "lda"
@@ -86,17 +31,6 @@ lazy = true
     sha256 = "7606cfa6d1cfab22ff584c548d13fc37872ec648c5c4f6636ee7b1221277128a"
     url = "https://github.com/JuliaMolSim/PseudoLibrary/raw/main/artifacts/pd_nc_sr_lda_standard_0.4.1_upf.tar.gz"
 
-["pd_nc_fr_pbesol_stringent_0.4_psp8"]
-extension = "psp8"
-functional = "pbesol"
-version = "0.4"
-git-tree-sha1 = "9b3ace1374e6876109c9f38de8eaa3adc9ee0cfc"
-lazy = true
-
-    [["pd_nc_fr_pbesol_stringent_0.4_psp8".download]]
-    sha256 = "d32eae3c40ef4a64520b882378941864166673c94c3d69f067a1be2b3d1fbd12"
-    url = "https://github.com/JuliaMolSim/PseudoLibrary/raw/main/artifacts/pd_nc_fr_pbesol_stringent_0.4_psp8.tar.gz"
-
 ["pd_nc_fr_pbesol_stringent_0.4_upf"]
 extension = "upf"
 functional = "pbesol"
@@ -119,17 +53,6 @@ lazy = true
     sha256 = "63b71d31f22b06965c9dd484d406d3deb63ea21b58d7b658727f09d210850d72"
     url = "https://github.com/JuliaMolSim/PseudoLibrary/raw/main/artifacts/pd_nc_sr_pbe_stringent_0.4.1_upf.tar.gz"
 
-["pd_nc_sr_pbesol_stringent_0.4.1_psp8"]
-extension = "psp8"
-functional = "pbesol"
-version = "0.4.1"
-git-tree-sha1 = "d43d8c44e419608c67397263e63ff7c7d7993bd1"
-lazy = true
-
-    [["pd_nc_sr_pbesol_stringent_0.4.1_psp8".download]]
-    sha256 = "b2d64feabd3b338f62f66a3e5d50ee285c665d8e76db9ff5a446c993de348707"
-    url = "https://github.com/JuliaMolSim/PseudoLibrary/raw/main/artifacts/pd_nc_sr_pbesol_stringent_0.4.1_psp8.tar.gz"
-
 ["pd_nc_fr_pbesol_standard_0.4_upf"]
 extension = "upf"
 functional = "pbesol"
@@ -152,28 +75,6 @@ lazy = true
     sha256 = "56a9b15cac540357a67cf33b3219af59962bbaa7d4a1bac5b7dab72ed2462e88"
     url = "https://github.com/JuliaMolSim/PseudoLibrary/raw/main/artifacts/pd_nc_sr_pbesol_standard_0.4.1_upf.tar.gz"
 
-["pd_nc_fr_pbe_stringent_0.4_psp8"]
-extension = "psp8"
-functional = "pbe"
-version = "0.4"
-git-tree-sha1 = "05bf66898e0e961a583bd46d53eb18fda5fa239c"
-lazy = true
-
-    [["pd_nc_fr_pbe_stringent_0.4_psp8".download]]
-    sha256 = "020a3bfbe6a90adf8298272f1f98d617787cc0a622725e32c1f30393b438dc92"
-    url = "https://github.com/JuliaMolSim/PseudoLibrary/raw/main/artifacts/pd_nc_fr_pbe_stringent_0.4_psp8.tar.gz"
-
-["pd_nc_fr_pbesol_standard_0.4_psp8"]
-extension = "psp8"
-functional = "pbesol"
-version = "0.4"
-git-tree-sha1 = "793a9fccb2865d26c160595db36c785a4fbb9b4a"
-lazy = true
-
-    [["pd_nc_fr_pbesol_standard_0.4_psp8".download]]
-    sha256 = "b893fe721c51080fe5f3d19724042d6c9e2af2f245169e264b07bc58c7675273"
-    url = "https://github.com/JuliaMolSim/PseudoLibrary/raw/main/artifacts/pd_nc_fr_pbesol_standard_0.4_psp8.tar.gz"
-
 ["pd_nc_sr_pbe_standard_0.4.1_upf"]
 extension = "upf"
 functional = "pbe"
@@ -196,17 +97,6 @@ lazy = true
     sha256 = "1edd99303e7965091741be4286d9b6e3e1673fa3e8936a24a7ecd33dccc74985"
     url = "https://github.com/JuliaMolSim/PseudoLibrary/raw/main/artifacts/pd_nc_fr_pbe_standard_0.4_upf.tar.gz"
 
-["pd_nc_sr_lda_stringent_0.4.1_psp8"]
-extension = "psp8"
-functional = "lda"
-version = "0.4.1"
-git-tree-sha1 = "e85a22581ece0447fe495371807db281d59052f8"
-lazy = true
-
-    [["pd_nc_sr_lda_stringent_0.4.1_psp8".download]]
-    sha256 = "2ec784ac815d80c6c20d7f51ae7bb9c2ebec491d6225c85f0833cabcc5e12a63"
-    url = "https://github.com/JuliaMolSim/PseudoLibrary/raw/main/artifacts/pd_nc_sr_lda_stringent_0.4.1_psp8.tar.gz"
-
 ["pd_nc_fr_pbe_stringent_0.4_upf"]
 extension = "upf"
 functional = "pbe"

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "PseudoPotentialData"
 uuid = "5751a51d-ac76-4487-a056-413ecf6fbe19"
 authors = ["Michael F. Herbst <[email protected]> and contributors"]
-version = "0.1.2"
+version = "0.2.0"
 
 [deps]
 Artifacts = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"

diff --git a/README.md b/README.md
@@ -35,7 +35,3 @@ More details on the meaning of these keys is given
 in the README of the
 [PseudoLibrary](https://github.com/JuliaMolSim/PseudoLibrary/blob/7c4b71a3b9d70a229d757aa6d546ef22b83a85a9/README.md)
 repository.
-
-**Warning:**
-The current identifiers for the pseudopotential families is planned to be overhauled.
-This will be a breaking change, where the minor version of the package will be bumped.
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -16,12 +16,12 @@ care to automatically download it as needed.
 
 For example, the following code automatically downloads the pseudopotential
 file of the [stringent pseudodojo](http://www.pseudo-dojo.org/) pseudopotential
-for LDA pseudopotentials (referred to by the identifier `pd_nc_sr_lda_stringent_0.4.1_upf`)
+for LDA pseudopotentials (referred to by the identifier `dojo.nc.sr.lda.v0_4_1.oncvpsp3.standard.upf`)
 and places the full path to the downloaded pseudopotential file into the `filename` variable:
 
 ```@example index-example
 using PseudoPotentialData
-identifier = "pd_nc_sr_lda_stringent_0.4.1_upf"
+identifier = "dojo.nc.sr.lda.v0_4_1.oncvpsp3.standard.upf"
 family = PseudoFamily(identifier)
 filename = pseudofile(family, :Si)
 ```
@@ -53,18 +53,32 @@ for (k, v) in family
 end
 ```
 
-For a list of available identifiers see
+## Available keys and naming convention
+A list of available pseudopotential identifiers is available as
 ```@example index-example
 PseudoPotentialData.family_identifiers()
 ```
-More details on the meaning of these keys is given in the README of the
+
+The naming convention is as that each pseudo family name consists
+of a list of fields, which are concatenated using a `.` (dot).
+These are:
+1. An identifier for the pseudo family (like `dojo` for the [PseudoDojo](http://www.pseudo-dojo.org/) family of potentials.
+2. The type of pseudopotential (`nc`: norm-conserving, `us`: ultrasoft, `paw`: projected  augmented wave)
+3. Details on the level of relativistic effects employed when generating the pseudo (`fr`: Full relativistic, `sr`: Scalar relativistic, `nr`: No relativistic)
+4. The functional for which the pseudopotential was prepared
+5. The version of the pseudopotential construction (with version points replaced by underscores)
+6. The program used to generate the pseudopotential
+7. Some additional comments specifying the pseudopotential.
+   E.g. for PseudoDojo potentials there is usually a `stringent` version
+   (requiring slightly larger cutoffs) and a `standard` version being a bit softer.
+8. The format of the pseudopotential files in this library.
+
+More details on the meaning of these keys
+will be provided at a later stage.
+Some information is also available in the README of the
 [PseudoLibrary](https://github.com/JuliaMolSim/PseudoLibrary/blob/7c4b71a3b9d70a229d757aa6d546ef22b83a85a9/README.md)
 repository.
 
-!!! warning "Rename of pseudopotential identifier reserved"
-    The current identifiers for the pseudopotential families is planned to be overhauled.
-    This will be a breaking change, where the minor version of the package will be bumped.
-
 ## Interface
 
 ```@autodocs

diff --git a/src/PseudoPotentialData.jl b/src/PseudoPotentialData.jl
@@ -16,7 +16,12 @@ include("pseudofamily.jl")
 function family_identifiers()
     artifact_file = find_artifacts_toml(@__FILE__)
     @assert !isnothing(artifact_file)
-    collect(keys(TOML.parsefile(artifact_file)))
+
+    # TODO For compatibility already use new keys
+    artifactmap_inv = Dict(v => k for (k, v) in artifactmap)
+    map(collect(keys(TOML.parsefile(artifact_file)))) do key
+        artifactmap_inv[key]
+    end
 end
 
 """The list of all known pseudopotential families."""

diff --git a/src/pseudofamily.jl b/src/pseudofamily.jl
@@ -21,7 +21,7 @@ an element symbol to the full path of the pseudopotential file.
 function PseudoFamily(identifier::AbstractString)
     artifact_file = find_artifacts_toml(@__FILE__)
     @assert !isnothing(artifact_file)
-    meta = artifact_meta(identifier, artifact_file)
+    meta = artifact_meta(artifactmap[identifier], artifact_file)
     isnothing(meta) && throw(ArgumentError("Invalid pseudo identifier: $identifier"))
     PseudoFamily(identifier,
                  meta["extension"],
@@ -39,11 +39,27 @@ Base.show(io::IO, ::MIME"text/plain", family::PseudoFamily) = show(io, family)
 # Helper functions (not exported)
 #
 
+# TODO For compatibility, map new to old ... will disappear at some point
+const artifactmap = Dict(
+    "dojo.nc.fr.pbesol.v0_4.oncvpsp3.standard.upf"   => "pd_nc_fr_pbesol_standard_0.4_upf",
+    "dojo.nc.fr.pbesol.v0_4.oncvpsp3.stringent.upf"  => "pd_nc_fr_pbesol_stringent_0.4_upf",
+    "dojo.nc.fr.pbe.v0_4.oncvpsp3.standard.upf"      => "pd_nc_fr_pbe_standard_0.4_upf",
+    "dojo.nc.fr.pbe.v0_4.oncvpsp3.stringent.upf"     => "pd_nc_fr_pbe_stringent_0.4_upf",
+    "dojo.nc.sr.lda.v0_4_1.oncvpsp3.standard.upf"    => "pd_nc_sr_lda_standard_0.4.1_upf",
+    "dojo.nc.sr.lda.v0_4_1.oncvpsp3.stringent.upf"   => "pd_nc_sr_lda_stringent_0.4.1_upf",
+    "dojo.nc.sr.pbesol.v0_4_1.oncvpsp3.standard.upf" => "pd_nc_sr_pbesol_standard_0.4.1_upf",
+    "dojo.nc.sr.pbe.v0_4_1.oncvpsp3.standard.upf"    => "pd_nc_sr_pbe_standard_0.4.1_upf",
+    "dojo.nc.sr.pbe.v0_4_1.oncvpsp3.stringent.upf"   => "pd_nc_sr_pbe_stringent_0.4.1_upf",
+    "dojo.paw.pbe.v1_1.jth.standard.xml"             => "pd_paw_pbe_standard_1.1_xml",
+)
+
 """
 Return the directory containing the pseudo files.
 This downloads the artifact if necessary.
 """
-artifact_directory(family::PseudoFamily) = (@artifact_str "$(family.identifier)")
+function artifact_directory(family::PseudoFamily)
+    @artifact_str "$(artifactmap[family.identifier])"
+end
 
 """Return the list of all pseudopotential files in the artifact"""
 function available_elements(family::PseudoFamily)

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -3,7 +3,7 @@ using Test
 
 @testset "PseudoPotentialData.jl" begin
     @testset "Test one family can be loaded" begin
-        identifier = "pd_nc_sr_lda_stringent_0.4.1_upf"
+        identifier = "dojo.nc.sr.lda.v0_4_1.oncvpsp3.stringent.upf"
         family = PseudoFamily(identifier)
         @test family.identifier == identifier
         @test family.extension  == "upf"
@@ -36,8 +36,7 @@ using Test
     end
 
     @testset "Dict interface of PseudoFamily" begin
-        identifier = "pd_nc_sr_pbe_stringent_0.4.1_upf"
-        family = PseudoFamily(identifier)
+        family = PseudoFamily("dojo.nc.sr.pbe.v0_4_1.oncvpsp3.stringent.upf")
         @test length(family) == 72
         @test   :Si  in keys(family)
         @test !(:Uub in keys(family))
@@ -51,7 +50,7 @@ using Test
 
     @testset "Printing of family objects" begin
         io = IOBuffer()
-        show(io, PseudoFamily("pd_nc_sr_pbe_stringent_0.4.1_upf"))
+        show(io, PseudoFamily("dojo.nc.sr.pbe.v0_4_1.oncvpsp3.stringent.upf"))
         @test occursin("PseudoFamily", String(take!(io)))
     end
 end