Merge pull request #82 from cesmix-mit/fix-paths

Fix paths.
cesmix-mit · Jul 13, 2024 · b49be2e · b49be2e
2 parents 66b1242 + bd9741e
commit b49be2e
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Showing 10 changed files with 33 additions and 33 deletions.
diff --git a/examples/ACE-aHfO2/fit-ace-ahfo2.jl b/examples/ACE-aHfO2/fit-ace-ahfo2.jl
@@ -8,12 +8,12 @@ using Unitful, UnitfulAtomic
 using LinearAlgebra, Random, DisplayAs
 
 # Define paths.
-path = joinpath(dirname(pathof(PotentialLearning)), "../examples/ACE-aHfO2")
-ds_path =  "$path/../data/a-HfO2/a-HfO2-300K-NVT-6000.extxyz"
-res_path = "$path/results/";
+base_path = match(r"^(.*/PotentialLearning/)", @__DIR__).match
+ds_path   = "$base_path/examples/data/a-HfO2/a-HfO2-300K-NVT-6000.extxyz"
+res_path  = "$base_path/examples/ACE-aHfO2/results/";
 
 # Load utility functions.
-include("$path/../utils/utils.jl")
+include("$base_path/examples/utils/utils.jl")
 
 # Create experiment folder.
 run(`mkdir -p $res_path`);

diff --git a/examples/DPP-ACE-Na/fit-dpp-ace-na.jl b/examples/DPP-ACE-Na/fit-dpp-ace-na.jl
@@ -8,8 +8,8 @@ using AtomsBase, InteratomicPotentials, PotentialLearning
 using LinearAlgebra, Plots
 
 # Define paths.
-path = joinpath(dirname(pathof(PotentialLearning)), "../examples/DPP-ACE-Na")
-ds_path = "$path/../data/Na/liquify_sodium.yaml";
+base_path = match(r"^(.*/PotentialLearning/)", @__DIR__).match
+ds_path   = "$base_path/examples/data/Na/liquify_sodium.yaml"
 
 # ## b. Load atomistic dataset and split it into training and test.
 

diff --git a/examples/DPP-ACE-Si/fit-dpp-ace-si.jl b/examples/DPP-ACE-Si/fit-dpp-ace-si.jl
@@ -13,12 +13,12 @@ using CSV, JLD, DataFrames
 elname, elspec = "Si", [:Si] 
 
 # Define paths.
-path = joinpath(dirname(pathof(PotentialLearning)), "../examples/DPP-ACE-Si")
-inpath = "$path/../data/Si-3Body-LAMMPS/"
-outpath = "$path/output/$elname/"
+base_path = match(r"^(.*/PotentialLearning/)", @__DIR__).match
+inpath   = "$base_path/examples/data/Si-3Body-LAMMPS/"
+outpath  = "$base_path/examples/DPP-ACE-Si/output/$elname/";
 
 # Load utility functions.
-include("$path/subsampling_utils.jl")
+include("$base_path/examples/DPP-ACE-Si/subsampling_utils.jl")
 
 # ## b. Load atomistic datasets.
 

diff --git a/examples/DPP-ACE-aHfO2-1/fit-dpp-ace-ahfo2.jl b/examples/DPP-ACE-aHfO2-1/fit-dpp-ace-ahfo2.jl
@@ -8,12 +8,12 @@ using Unitful, UnitfulAtomic
 using LinearAlgebra, Random, DisplayAs
 
 # Define paths.
-path = joinpath(dirname(pathof(PotentialLearning)), "../examples/DPP-ACE-aHfO2-1")
-ds_path =  "$path/../data/a-HfO2/a-HfO2-300K-NVT-6000.extxyz"
-res_path = "$path/results/";
+base_path = match(r"^(.*/PotentialLearning/)", @__DIR__).match
+ds_path   = "$base_path/examples/data/a-HfO2/a-HfO2-300K-NVT-6000.extxyz"
+res_path  = "$base_path/examples/DPP-ACE-aHfO2-1/results/";
 
 # Load utility functions.
-include("$path/../utils/utils.jl")
+include("$base_path/examples/utils/utils.jl")
 
 # Create experiment folder.
 run(`mkdir -p $res_path`);

diff --git a/examples/DPP-ACE-aHfO2-2/fit-dpp-ace-ahfo2.jl b/examples/DPP-ACE-aHfO2-2/fit-dpp-ace-ahfo2.jl
@@ -1,5 +1,3 @@
-push!(Base.LOAD_PATH, "../../")
-
 using LinearAlgebra, Random
 using Statistics, StatsBase, Distributions, Determinantal
 using Unitful, UnitfulAtomic
@@ -8,11 +6,13 @@ using JLD, CairoMakie
 
 #################### Importing Data ###################
 
-path = joinpath(dirname(pathof(PotentialLearning)), "../examples/DPP-ACE-aHfO2")
+base_path = match(r"^(.*/PotentialLearning/)", @__DIR__).match
+ds_path   = "$base_path/examples/data/a-HfO2/aHfO2_diverse_descriptors_3600.jld"
+res_path  = "$base_path/examples/DPP-ACE-aHfO2-2/results/";
 
 # Import Raw Data
 energies, descriptors = JLD.load(
-    "$path/../data/aHfO2/aHfO2_diverse_descriptors_3600.jld",
+    ds_path,
     "energies",
     "descriptors",
 )
@@ -84,4 +84,4 @@ ax4 = Axis(
 )
 scatter!(ax4, [length(c.B) - 32 for c in configs], ips, markersize = 4.0)
 
-save("examples/aHfO2/figures/aHfO2_dpp_inclusion_probabilities.pdf", fig)
+save("$res_path/figures/aHfO2_dpp_inclusion_probabilities.pdf", fig)
diff --git a/examples/LJ-Ar/lennard-jones-ar.jl b/examples/LJ-Ar/lennard-jones-ar.jl
@@ -8,8 +8,8 @@ using AtomsBase, InteratomicPotentials, PotentialLearning
 using LinearAlgebra, Plots, DisplayAs
 
 # Define paths.
-path = joinpath(dirname(pathof(PotentialLearning)), "../examples/LJ-Ar")
-ds_path = "$path/../data/LJ-AR/lj-ar.yaml";
+base_path = match(r"^(.*/PotentialLearning/)", @__DIR__).match
+ds_path   = "$base_path/examples/data/LJ-AR/lj-ar.yaml"
 
 # ## b. Load atomistic dataset.
 ds, thermo = load_data(ds_path, YAML(:Ar, u"eV", u"Å"))

diff --git a/examples/Opt-ACE-aHfO2/fit-opt-ace-ahfo2.jl b/examples/Opt-ACE-aHfO2/fit-opt-ace-ahfo2.jl
@@ -9,12 +9,12 @@ using LinearAlgebra, Random, DisplayAs
 using DataFrames, Hyperopt
 
 # Define paths.
-path = joinpath(dirname(pathof(PotentialLearning)), "../examples/Opt-ACE-aHfO2")
-ds_path =  "$path/../data/a-HfO2/a-HfO2-300K-NVT-6000.extxyz"
-res_path = "$path/results/";
+base_path = match(r"^(.*/PotentialLearning/)", @__DIR__).match
+ds_path   = "$base_path/examples/data/a-HfO2/a-HfO2-300K-NVT-6000.extxyz"
+res_path  = "$base_path/examples/Opt-ACE-aHfO2/results/";
 
 # Load utility functions.
-include("$path/../utils/utils.jl")
+include("$base_path/examples/utils/utils.jl")
 
 # Create experiment folder.
 run(`mkdir -p $res_path`);

diff --git a/examples/PCA-ACE-aHfO2/fit-pca-ace-ahfo2.jl b/examples/PCA-ACE-aHfO2/fit-pca-ace-ahfo2.jl
@@ -8,12 +8,12 @@ using Unitful, UnitfulAtomic
 using LinearAlgebra, Random, DisplayAs
 
 # Define paths.
-path = joinpath(dirname(pathof(PotentialLearning)), "../examples/PCA-ACE-aHfO2")
-ds_path =  "$path/../data/a-HfO2/a-HfO2-300K-NVT-6000.extxyz"
-res_path = "$path/results/";
+base_path = match(r"^(.*/PotentialLearning/)", @__DIR__).match
+ds_path   = "$base_path/examples/data/a-HfO2/a-HfO2-300K-NVT-6000.extxyz"
+res_path  = "$base_path/examples/PCA-ACE-aHfO2/results/";
 
 # Load utility functions.
-include("$path/../utils/utils.jl")
+include("$base_path/examples/utils/utils.jl")
 
 # Create experiment folder.
 run(`mkdir -p $res_path`);

diff --git a/examples/utils/input.jl b/examples/utils/input.jl
@@ -1,5 +1,5 @@
 # New function to read XYZ files ###############################################
-include("$path/../utils/xyz.jl")
+include("$base_path/examples/utils/xyz.jl")
 
 # New functions to get input parameters from OrderedDict #######################
 

diff --git a/examples/utils/utils.jl b/examples/utils/utils.jl
@@ -6,9 +6,9 @@ using ProgressBars
 using Plots
 using CSV
 
-include("$path/../utils/input.jl")
-include("$path/../utils/macros.jl")
-include("$path/../utils/plots.jl")
+include("$base_path/examples/utils/input.jl")
+include("$base_path/examples/utils/macros.jl")
+include("$base_path/examples/utils/plots.jl")
 
 # Missing function
 Base.size(fd::ForceDescriptors) = (length(fd), )