Small changes. File renaming.

Author: emmanuellujan

examples/atomistic/sme-iso17.jl

@@ -1,6 +1,6 @@
 using StreamingSampling
 
-include("utils/AtomsSampling.jl")
+include("utils/utils.jl")
 
 # Datase files
 file_paths = ["data/iso17/my_iso17_train.extxyz"]

examples/atomistic/srs-vs-sme-aspirin-rmd17.jl

@@ -1,6 +1,6 @@
 using StreamingSampling
 
-include("utils/AtomsSampling.jl")
+include("utils/utils.jl")
 
 # Define paths and create experiment folder
 train_path = ["data/md17/aspirin-train.xyz"]
@@ -115,7 +115,7 @@ for j in 1:n_experiments
         #Load atomistic configurations
         train_confs = get_confs(train_path, train_inds)
         #Adjust reference energies (permanent change)
-        adjust_energies(train_confs,vref_dict)
+        adjust_energies(train_confs, vref_dict)
         # Compute dataset with energy and force descriptors
         train_ds = calc_descr(train_confs, basis_fitting)
         # Create result folder
@@ -139,6 +139,8 @@ for j in 1:n_experiments
 
         #Load atomistic configurations
         train_confs = get_confs(train_path, train_inds)
+        #Adjust reference energies (permanent change)
+        adjust_energies(train_confs, vref_dict)
         # Compute dataset with energy and force descriptors
         train_ds = calc_descr(train_confs, basis_fitting)
         # Create result folder

examples/atomistic/srs-vs-sme-hfo2.jl

@@ -1,6 +1,6 @@
 using StreamingSampling
 
-include("utils/AtomsSampling.jl")
+include("utils/utils.jl")
 
 # Define paths and create experiment folder
 ds_paths = ["Hf_mp1009460_EOS_form_sorted.extxyz",
@@ -107,6 +107,7 @@ n_test = length(ds_test_rnd)
 # Compute reference energies
 s = 0.0
 m = 10_000
+read_element(io) = read_element_extxyz(io)
 ch, _ = chunk_iterator(ds_paths;
                        read_element=read_element,
                        chunksize=m,

examples/atomistic/srs-vs-sme-iso17.jl

@@ -1,6 +1,6 @@
 using StreamingSampling
 
-include("utils/AtomsSampling.jl")
+include("utils/utils.jl")
 
 # Define paths and create experiment folder
 train_path = ["data/iso17/my_iso17_train.extxyz"]
@@ -115,7 +115,7 @@ for j in 1:n_experiments
         #Load atomistic configurations
         train_confs = get_confs(train_path, train_inds)
         #Adjust reference energies (permanent change)
-        adjust_energies(train_confs,vref_dict)
+        adjust_energies(train_confs, vref_dict)
         # Compute dataset with energy and force descriptors
         train_ds = calc_descr(train_confs, basis_fitting)
         # Create result folder
@@ -139,6 +139,8 @@ for j in 1:n_experiments
 
         #Load atomistic configurations
         train_confs = get_confs(train_path, train_inds)
+        #Adjust reference energies (permanent change)
+        adjust_energies(train_confs, vref_dict)
         # Compute dataset with energy and force descriptors
         train_ds = calc_descr(train_confs, basis_fitting)
         # Create result folder

…/atomistic/utils/aux_sample_functions.jl examples/atomistic/utils/fitting-utils.jlexamples/atomistic/utils/aux_sample_functions.jl renamed to examples/atomistic/utils/fitting-utils.jl examples/atomistic/utils/aux_sample_functions.jl renamed to examples/atomistic/utils/fitting-utils.jl

@@ -21,10 +21,10 @@ using Unitful
 import PotentialLearning.BasisPotential
 
 include("read-element.jl")
-include("xyz.jl")
+include("read-dataset.jl")
 include("macros.jl")
+include("fitting-utils.jl")
 include("subtract_peratom_e.jl")
-include("aux_sample_functions.jl")
 #include("samplers.jl")
 include("plots.jl")
 include("plotmetrics.jl")