Merge pull request #231 from iamveronika/ve/updt

WIP: New JSON Interface

Project.toml

@@ -4,6 +4,7 @@ version = "0.8.0-dev"
 
 [deps]
 ACEfit = "ad31a8ef-59f5-4a01-b543-a85c2f73e95c"
+ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 AtomsBase = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a"
 AtomsBuilder = "f5cc8831-eeb7-4288-8d9f-d6c1ddb77004"
 AtomsCalculators = "a3e0e189-c65a-42c1-833c-339540406eb1"
@@ -17,13 +18,15 @@ ExtXYZ = "352459e4-ddd7-4360-8937-99dcb397b478"
 Folds = "41a02a25-b8f0-4f67-bc48-60067656b558"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 LazyArtifacts = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Lux = "b2108857-7c20-44ae-9111-449ecde12c47"
 LuxCore = "bb33d45b-7691-41d6-9220-0943567d0623"
 NamedTupleTools = "d9ec5142-1e00-5aa0-9d6a-321866360f50"
 NeighbourLists = "2fcf5ba9-9ed4-57cf-b73f-ff513e316b9c"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
+Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 Optimisers = "3bd65402-5787-11e9-1adc-39752487f4e2"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"

scripts/example_params.json

@@ -0,0 +1,69 @@
+{
+  "model": {
+    "model_name": "ACE1",
+    "pair_basis": "legendre",
+    "elements": [
+      "Si"
+    ],
+    "pair_rin": 0.0,
+    "pure": false,
+    "pair_transform": [
+      "agnesi",
+      1,
+      3
+    ],
+    "totaldegree": 10,
+    "delete2b": false,
+    "wL": 1.5,
+    "pair_degree": 10,
+    "rbasis": "legendre",
+    "pure2b": false,
+    "pair_rcut": 6.7,
+    "rcut": 6.7,
+    "variable_cutoffs": false,
+    "rin": 0.0,
+    "order": 3,
+    "r0": 2.5,
+    "transform": [
+      "agnesi",
+      2,
+      4
+    ]
+  },
+  "solve": {
+    "weights": {
+      "FLD_TiAl": {
+        "V": 1.0,
+        "E": 30.0,
+        "F": 1.0
+      },
+      "TiAl_T5000": {
+        "V": 1.0,
+        "E": 5.0,
+        "F": 1.0
+      }
+    },
+    "prior": {
+      "name": "algebraic",
+      "param": 4
+    },
+    "solver": {
+      "name": "BLR",
+      "param": {
+        "factorization": "svd",
+        "committee_size": 20
+      }
+    }
+  },
+  "data": {
+    "train_file": "Si_tiny.xyz",
+    "force_key": "dft_force",
+    "test_file": "Si_tiny.xyz",
+    "energy_key": "dft_energy",
+    "virial_key": "dft_virial"
+  },
+  "output": {
+    "model": "results.json"
+  }
+}
+

scripts/runfit.jl

@@ -0,0 +1,64 @@
+#
+# julia --project=. runfit.jl -p example_params.json
+#
+
+using ACEpotentials
+using ACEpotentials: JSON, ExtXYZ
+using ACEpotentials.ArgParse: ArgParseSettings, @add_arg_table, parse_args
+
+parser = ArgParseSettings(description="Fit an ACE potential from parameters file")
+
+@add_arg_table parser begin
+    "--params", "-p"
+        help = "A JSON or YAML filename with parameters for the fit"
+    "--dry-run"
+        help = "Only quickly compute various sizes, etc"
+        action = :store_true
+    "--num-blas-threads"
+        help = "Number of processes for BLAS to use when solving the LsqDB"
+        arg_type = Int
+        default = 1
+end
+
+# parse the command 
+args = parse_args(parser)
+
+@info("Load parameter file") 
+args_dict = JSON.parsefile(args["params"])
+
+@info("Construct ACEmodel of type $(args_dict["model"]["model_name"])")
+model = ACEpotentials.make_model(args_dict["model"])
+
+@info("Load datasets")  
+train = ExtXYZ.load(args_dict["data"]["train_file"])
+
+data_keys = (
+    force_key = args_dict["data"]["force_key"],
+    energy_key = args_dict["data"]["energy_key"],
+    virial_key = args_dict["data"]["virial_key"])
+
+weights = args_dict["solve"]["weights"]
+
+solver = ACEpotentials.make_solver(args_dict["solve"]["solver"])
+
+# TODO: make prior
+
+acefit!(train, model;
+       data_keys..., weights = weights, solver = solver)
+
+# training errors
+err_train = ACEpotentials.linear_errors(train, model; data_keys..., weights=weights)
+err = Dict("train" => err_train)
+
+# test errors (if a test dataset exists)
+if haskey(args_dict["data"], "test_file")
+    test = ExtXYZ.load(args_dict["data"]["test_file"])
+    err_test = ACEpotentials.linear_errors(test, model; data_keys..., weights=weights)
+    err["test"] = err_test
+end
+
+# saving results
+result_file = args_dict["output"]["model"]
+ACEpotentials.save_model(model, joinpath(@__DIR__(), args_dict["output"]["model"]); 
+                         make_model_args = args_dict, 
+                         errors = err, )

src/ACEpotentials.jl

@@ -41,6 +41,7 @@ import ACEpotentials.Models: algebraic_smoothness_prior,
                              exp_smoothness_prior, 
                              gaussian_smoothness_prior, 
                              set_parameters!
+import JSON 
 
 export ace1_model,
        length_basis, 
@@ -49,4 +50,9 @@ export ace1_model,
        gaussian_smoothness_prior, 
          set_parameters!
 
+
+include("json_interface.jl")
+
+
+
 end

src/ace1_compat.jl

@@ -388,4 +388,3 @@ end
 
 end 
 
-