Usage

Package has two modes default registry and custom registries.

Using default registry

Default registry can be loaded with

using PotentialDB
d = defaultregistry()

Potential registry 8 potentials

You can list potentials stored in the default registry with listpotentials-command

listpotentials(d)


[key]  =>  Description

[3]  =>  cis-formic acid - argon potential. Max 5000 cm⁻¹
[4]  =>  trans-formic acid - argon potential. Max 5000 cm⁻¹
[1]  =>  cis-formic acid - argon potential. Max 20000 cm⁻¹
[5]  =>  benzene - argon potential. Max 5000 cm⁻¹
[2]  =>  trans-formic acid - argon potential. Max 20000 cm⁻¹
[6]  =>  benzene - neon potential. Max 5000 cm⁻¹
[7]  =>  glycolic acid - argon potential. Max 20000 cm⁻¹
[8]  =>  trans-formic acid - argon potential. Max 5000 cm⁻¹

To list more details of the selected potential, you can call it with its key

d["1"]

Dict{String, Any} with 8 entries:
  "CAS"         => ["64-18-6", "7440-37-1"]
  "method"      => "CCSD(T)-F12/RI"
  "hash"        => "5de11d919d19a921fa246219c32566bfdc99a1ddfb46b6cb6abaab944cb…
  "keywords"    => ["formic acid", "argon"]
  "file"        => "potential-1.jld2"
  "basis"       => "cc-pVDZ-F12 cc-pVDZ-F12-CABS cc-pVTZ/C"
  "authors"     => ["Teemu Järvinen"]
  "description" => "cis-formic acid - argon potential. Max 20000 cm⁻¹"

To load a wanted potential, call with loadpotential and key

p=loadpotential(d,"1")

Dict{String, Any} with 6 entries:
  "Method"   => "CCSD(T)-F12/RI"
  "cluster2" => Cluster{AtomOnlySymbol} of 1 atoms
  "Energy"   => [0.0699679 0.0829061 … 0.0811201 0.0828071; 0.0221226 0.0240231…
  "Points"   => Cluster{AtomOnlySymbol}[Cluster{AtomOnlySymbol} of 6 atoms Clus…
  "cluster1" => Cluster{AtomOnlySymbol} of 5 atoms
  "Basis"    => "cc-pVDZ-F12 cc-pVDZ-F12-CABS cc-pVTZ/C TIGHTSCF"

AtomsBase output

To load data in AtomsBase format use

data = load_data(d, "1")

Dict{String, Matrix{FlexibleSystem{3, Atom, Quantity{Float64, 𝐋, Unitful.FreeUnits{(a₀,), 𝐋, nothing}}}}} with 3 entries:
  "cluster2" => [FlexibleSystem(Ar, infinite) FlexibleSystem(Ar, infinite) … Fl…
  "Points"   => [FlexibleSystem(ArCH₂O₂, infinite) FlexibleSystem(ArCH₂O₂, infi…
  "cluster1" => [FlexibleSystem(CH₂O₂, infinite) FlexibleSystem(CH₂O₂, infinite…

Custom registries

Registries are defined by a TOML-file that holds information on where the file holding potential energy data is saved and some details on the potential itself. Example default registry has entry:

[1]
CAS = ["64-18-6", "7440-37-1"]
method = "CCSD(T)-F12/RI"
hash = "23284650a0739cbda33e82f4f16ca962e833fa6c320c492525033e492d1e2b87"
keywords = ["formic acid", "argon"]
file = "potential-1.jld"
basis = "cc-pVDZ-F12 cc-pVDZ-F12-CABS cc-pVTZ/C"
authors = ["Teemu Järvinen"]
description = "cis-formic acid - argon potential. Max 20000 cm⁻¹"

Some of keywords are mandatory, some are not. Also there can be as many keywords as you want to add.

List of mandatory keywords

authors - Identify persons who made the potential.
basis - Basis functions used in calculaton.
CAS - CAS numbers of molecules in the potential. Needed for identification.
description - Short desciption of potential.
file - location of potentialfile relative to location registry file.
keywords - Used to do search on potentials.
method - Method used to calculate potential.

Additionally hash-keyword is optional. It contains SHA256 sum of potential file and, if present, is used to check integrity of potential upon loading.

To load custom potential registry, use PotentialRegistry("Registry.toml"). If file "Registry.toml" exists, this call loads it and checks, if it has correct form, if not it will throw an error. If file does not exist, it creates a new registry.

r = PotentialRegistry("example.toml")

Potential registry 0 potentials

You can use addpotential!-function to add potentials to this file. As and example, lets add a potential from default registry.

Lets first load potential from default registry

d = defaultregistry()

p = loadpotential(d, "2")

Dict{String, Any} with 6 entries:
  "Method"   => "CCSD(T)-F12/RI"
  "cluster2" => Cluster{AtomOnlySymbol} of 1 atoms
  "Energy"   => [0.0828836 0.0901049 … 0.0792415 0.0679845; 0.0260046 0.0263087…
  "Points"   => Cluster{AtomOnlySymbol}[Cluster{AtomOnlySymbol} of 6 atoms Clus…
  "cluster1" => Cluster{AtomOnlySymbol} of 5 atoms
  "Basis"    => "cc-pVDZ-F12 cc-pVDZ-F12-CABS cc-pVTZ/C TIGHTSCF"

To add potential, you must create a Dict-that holds mandatory keywords needed for a registry entry. In the case of this example, we can load this data from the default registry.

k = d["2"]

Dict{String, Any} with 8 entries:
  "CAS"         => ["64-18-6", "7440-37-1"]
  "method"      => "CCSD(T)-F12/RI"
  "hash"        => "cf44a3c66a2aad0dd2022569267cf47f44fdeafd5c23f51ca6b2f03eb20…
  "keywords"    => ["formic acid", "argon"]
  "file"        => "potential-2.jld2"
  "basis"       => "cc-pVDZ-F12 cc-pVDZ-F12-CABS cc-pVTZ/C"
  "authors"     => ["Teemu Järvinen"]
  "description" => "trans-formic acid - argon potential. Max 20000 cm⁻¹"

We can now add potential to our example registry

addpotential!(r, p, k)

Potential registry 1 potentials

New potential was added and registry file was saved. To confirm, that we added a new potential correctly, we can do:

julia> rc = PotentialRegistry("example.toml")Potential registry 1 potentials
julia> listpotentials(rc)
[key]  =>  Description

[1]  =>  trans-formic acid - argon potential. Max 20000 cm⁻¹
julia> rc["1"]Dict{String, Any} with 9 entries:
  "CAS"              => ["64-18-6", "7440-37-1"]
  "method"           => "CCSD(T)-F12/RI"
  "number of points" => 640
  "hash"             => "2237efbf038102f5698acbc8c7bff33d5b1cb9f2800f2dfb9e7c7b…
  "keywords"         => ["formic acid", "argon"]
  "file"             => "potential-2.jld2"
  "basis"            => "cc-pVDZ-F12 cc-pVDZ-F12-CABS cc-pVTZ/C"
  "authors"          => ["Teemu Järvinen"]
  "description"      => "trans-formic acid - argon potential. Max 20000 cm⁻¹"
julia> loadpotential(rc, "1")Dict{String, Any} with 6 entries:
  "Method"   => "CCSD(T)-F12/RI"
  "cluster2" => Cluster{AtomOnlySymbol} of 1 atoms
  "Energy"   => [0.0828836 0.0901049 … 0.0792415 0.0679845; 0.0260046 0.0263087…
  "Points"   => Cluster{AtomOnlySymbol}[Cluster{AtomOnlySymbol} of 6 atoms Clus…
  "cluster1" => Cluster{AtomOnlySymbol} of 5 atoms
  "Basis"    => "cc-pVDZ-F12 cc-pVDZ-F12-CABS cc-pVTZ/C TIGHTSCF"

Add potentials to default registry

Default registry is just standard registy file located in data-directory of the package. While you can add entries there by had, it is recommended to use addpotential!-function. You can then submit a pull request to PotentialDB.jl, to have your potential to added for everyone's use.