MatrixLabTools · tjjarvinen · Jul 5, 2023 · Jul 4, 2023 · Jul 4, 2023 · Jul 4, 2023
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "PotentialCalculation"
 uuid = "76415700-ec45-11e8-0f65-f1df3c899b21"
 authors = ["Teemu Järvinen <teemu.j.jarvinen@student.jyu.fi>"]
-version = "0.5.1-DEV"
+version = "0.6.0-DEV"
 
 [deps]
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
@@ -11,7 +11,6 @@ FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Rotations = "6038ab10-8711-5258-84ad-4b1120ba62dc"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
@@ -25,7 +24,6 @@ Distances = "0.10"
 FileIO = "1"
 JLD2 = "0.4"
 ProgressMeter = "1.2"
-PyCall = "1.90"
 Reexport = "1.0"
 Rotations = "1.0"
 Unitful = "1"

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -13,7 +13,7 @@ experiments.
 
 - Calculate potentials with [ORCA](https://orcaforum.kofo.mpg.de) or [Psi4](http://www.psicode.org/)
 - Automatic sampling of calculation points
-- Supports parallelisation of calculation across compute nodes
+- Supports parallelization of calculation across compute nodes
 
 ### [PotentialFitting](https://github.com/MatrixLabTools/PotentialFitting.jl)
 

diff --git a/docs/src/install.md b/docs/src/install.md
@@ -9,7 +9,7 @@ pkg> add PotentialCalculation
 
 Currently there are two backends, [ORCA](https://orcaforum.kofo.mpg.de)
 and [Psi4](http://www.psicode.org/). To do any calculation, you need to have
-at least one of these installed.
+at least one of these installed. With Psi4 you need to also load [Psi4Calculator](https://github.com/MatrixLabTools/Psi4Calculator.jl)
 
 ## Testing installation
 

diff --git a/docs/src/use.md b/docs/src/use.md
@@ -89,7 +89,7 @@ data3 = continue_calculation(
 ## Calculators
 
 PotentilaCalculation can use either [Orca](@ref)
-or [Psi4](@ref) as a backend for calculations.
+or [Psi4](https://github.com/MatrixLabTools/Psi4Calculator.jl) as a backend for calculations.
 
 To create ORCA calculator you can use
 
@@ -108,18 +108,19 @@ PATH is searched for orca-binary. `tmp_dir` is by default created in `$TMP`.
 For Psi4 use
 
 ```julia
-using PotentialCalculation.psi4
+using PotentialCalculation
+using Psi4Calculator
 
 Psi4(
    memory="1GiB",
    nthreads=1,
 )
 ```
 
-You need to import Psi4 explicitly with `using PotentialCalculation.psi4`. All
-Psi4 global environmental variables are present. To access them you need to use
-`PotentialCalculation.psi4.gPsi4`-handel after using
-`PotentialCalculation.psi4.initpsi()`-function to initialize Psi4 environment.
+You need to install Psi4Calculator separately, as it has now been moved to its own package.
+All Psi4 global environmental variables are present. To access them you need to use
+`Psi4Calculator.gPsi4`-handel after using
+`Psi4Calculator.initpsi()`-function to initialize Psi4 environment.
 
 ### Adding Calculation Method and Basis Set
 
@@ -205,3 +206,5 @@ using ClusterManagers
 addprocs_slurm(number_of_processes) # ntasks option in Slurm job file
 @everywhere using PotentialCalculation
 ```
+
+Consider also using [SlurmClusterManager](https://github.com/kleinhenz/SlurmClusterManager.jl) to make things easy.
diff --git a/src/PotentialCalculation.jl b/src/PotentialCalculation.jl
@@ -33,6 +33,5 @@ include("SubModules/sample.jl")
 include("SubModules/restarttools.jl")
 @reexport using .Restarttools
 
-include("SubModules/psi4.jl")
 
 end # module
diff --git a/src/SubModules/clusters.jl b/src/SubModules/clusters.jl
@@ -233,23 +233,24 @@ end
 
 
 """
-    print_xyz(io::IO, c::AbstractClusterWithSymbols, note=""; printheader=true)
+    print_xyz(io::IO, c, note=""; printheader=true)
 
 Prints cluster in xyz file format
 
 # Arguments
 - `io::IO` : stream where writing is done
-- `c::AbstractClusterWithSymbols` : cluster that is writen
+- `c`      : `AtomsBase` compatable structure
 - `note=""` : message writen on note line
 - `printheader=true` : wheather or not header is writen (number of atoms and note)
 """
-function print_xyz(io::IO, c::AbstractClusterWithSymbols, note=""; printheader=true)
+function print_xyz(io::IO, c, note=""; printheader=true)
     if printheader
         println(io, "    ",length(c))
         println(io, note)
     end
     for i in 1:length(c)
-        println(io, c.atoms[i].id, "   ", c.xyz[1,i], "  ", c.xyz[2,i], "  ", c.xyz[3,i])
+        r = ustrip.(u"Å", position(c,i))
+        println(io, atomic_symbol(c, i), "   ", r[1], "  ", r[2], "  ", r[3])
     end
 end
 

diff --git a/src/SubModules/psi4.jl b/src/SubModules/psi4.jl
diff --git a/test/Project.toml b/test/Project.toml
@@ -1,5 +1,4 @@
 [deps]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
diff --git a/test/test_restarttools.jl b/test/test_restarttools.jl
@@ -1,11 +1,9 @@
 using Test
-using PyCall
 
 using Distributed
 
 addprocs(2)
 @everywhere using PotentialCalculation
-@everywhere using PotentialCalculation.psi4
 
 fname = tempname() * ".jld2"
 rname = tempname() * ".jld2"
@@ -31,7 +29,7 @@ pbar=true
 
 testrestarts = false
 
-if Sys.which("orca") != nothing && Sys.which("orca_scf") != nothing
+if Sys.which("orca") !== nothing && Sys.which("orca_scf") !== nothing
     @info "Orca binary found. Testing ORCA."
     @testset "Orca" begin
         ca = Calculator("blyp d3bj TIGHTSCF", "def2-svp", Orca())
@@ -55,37 +53,6 @@ end
 
 
 
-testpsi4 = true
-
-try
-    pyimport("psi4")
-catch
-    global testpsi4 = false
-    @warn "Psi4 was not detected. Skipping testing. Psi4 backend is not working!"
-end
-if  testpsi4
-    @info "Psi4 found. Testing Psi4."
-    @testset "Psi4" begin
-        ca = Calculator("blyp-d3bj", "def2-svp",Psi4(memory="1000MiB", nthreads=2))
-
-        input1=create_inputs(xyzname, Ar, ca)
-        inputs=create_inputs(xyzname, N2, ca; npoints=5)
-        inputss=create_inputs(xyzname, xyzname, ca)
-
-        data1=calculate_potential(inputs, save_file=fname, pbar=pbar)
-        data2=calculate_potential(fname,ca,save_file=sname, restart_file=rname, pbar=pbar)
-        data3=continue_calculation(rname,ca, save_file=sname, restart_file=rname, pbar=pbar)
-
-        calculate_energy(ca, N2)
-        calculate_energy(ca, [N2,N2])
-        @test all(isapprox.(data1["Energy"], data2["Energy"], atol=2E-6))
-        @test all(isapprox.(data1["Energy"], data3["Energy"], atol=2E-6))
-        @test all(isapprox.(data2["Energy"], data3["Energy"], atol=2E-6))
-    end
-    testrestarts = true
-end
-
-
 if testrestarts
     @testset "restarttools" begin
         savedata = load_data_file(sname)