update test code of generate function

test_code/generate/README

@@ -0,0 +1,7 @@
+* Setting
+    - Set save_to_pickle (True/False) in [input.yaml] file
+    - Set save_directory (default: data/) in [input.yaml] file
+    - command "python run.py"
+* Output
+    If code runs correctly, show "COMPLET" message
+    If created data file has wrong value, show "ERROR" message

test_code/generate/input.yaml

@@ -0,0 +1,50 @@
+generate_features: true
+preprocess: false
+train_model: false
+atom_types:
+ - Si
+ - O
+
+symmetry_function:
+  params:
+    Si: params_Si
+    O: params_O
+  valid_rate: 0.1
+  remain_pickle: True
+  compress_outcar: False
+  save_to_pickle: False
+  save_directory: data
+
+neural_network:
+  pca: true
+  pca_whiten: true
+  weight_initializer:
+    type: he normal  
+  save_criteria: []
+  batch_size: 20
+  continue: false
+  double_precision: true
+  energy_coeff: 1.0
+  force_coeff:  0.1
+  full_batch: false
+  cache: false
+  learning_rate: 0.0001
+  loss_scale: 1.0
+  acti_func: tanh
+  method: Adam
+  nodes: 30-30
+  optimizer: {}
+  print_structure_rmse: true
+  regularization:
+    type: l2
+    params:
+      coeff: 1.0e-8
+  save_interval: 200
+  show_interval: 200
+  test: false
+  total_iteration: 50000
+  train: true
+  use_force: true
+  use_stress: true
+  intra_op_parallelism_threads: 20
+  inter_op_parallelism_threads: 2

test_code/generate/params_O

@@ -0,0 +1,70 @@
+2 1 0 6.0 0.003214 0.0 0.0
+2 1 0 6.0 0.035711 0.0 0.0
+2 1 0 6.0 0.071421 0.0 0.0
+2 1 0 6.0 0.124987 0.0 0.0
+2 1 0 6.0 0.214264 0.0 0.0
+2 1 0 6.0 0.357106 0.0 0.0
+2 1 0 6.0 0.714213 0.0 0.0
+2 1 0 6.0 1.428426 0.0 0.0
+2 2 0 6.0 0.003214 0.0 0.0
+2 2 0 6.0 0.035711 0.0 0.0
+2 2 0 6.0 0.071421 0.0 0.0
+2 2 0 6.0 0.124987 0.0 0.0
+2 2 0 6.0 0.214264 0.0 0.0
+2 2 0 6.0 0.357106 0.0 0.0
+2 2 0 6.0 0.714213 0.0 0.0
+2 2 0 6.0 1.428426 0.0 0.0
+4 1 1 6.0 0.000357 1.0 -1.0
+4 1 1 6.0 0.028569 1.0 -1.0
+4 1 1 6.0 0.089277 1.0 -1.0
+4 1 1 6.0 0.000357 2.0 -1.0
+4 1 1 6.0 0.028569 2.0 -1.0
+4 1 1 6.0 0.089277 2.0 -1.0
+4 1 1 6.0 0.000357 4.0 -1.0
+4 1 1 6.0 0.028569 4.0 -1.0
+4 1 1 6.0 0.089277 4.0 -1.0
+4 1 1 6.0 0.000357 1.0 1.0
+4 1 1 6.0 0.028569 1.0 1.0
+4 1 1 6.0 0.089277 1.0 1.0
+4 1 1 6.0 0.000357 2.0 1.0
+4 1 1 6.0 0.028569 2.0 1.0
+4 1 1 6.0 0.089277 2.0 1.0
+4 1 1 6.0 0.000357 4.0 1.0
+4 1 1 6.0 0.028569 4.0 1.0
+4 1 1 6.0 0.089277 4.0 1.0
+4 1 2 6.0 0.000357 1.0 -1.0
+4 1 2 6.0 0.028569 1.0 -1.0
+4 1 2 6.0 0.089277 1.0 -1.0
+4 1 2 6.0 0.000357 2.0 -1.0
+4 1 2 6.0 0.028569 2.0 -1.0
+4 1 2 6.0 0.089277 2.0 -1.0
+4 1 2 6.0 0.000357 4.0 -1.0
+4 1 2 6.0 0.028569 4.0 -1.0
+4 1 2 6.0 0.089277 4.0 -1.0
+4 1 2 6.0 0.000357 1.0 1.0
+4 1 2 6.0 0.028569 1.0 1.0
+4 1 2 6.0 0.089277 1.0 1.0
+4 1 2 6.0 0.000357 2.0 1.0
+4 1 2 6.0 0.028569 2.0 1.0
+4 1 2 6.0 0.089277 2.0 1.0
+4 1 2 6.0 0.000357 4.0 1.0
+4 1 2 6.0 0.028569 4.0 1.0
+4 1 2 6.0 0.089277 4.0 1.0
+4 2 2 6.0 0.000357 1.0 -1.0
+4 2 2 6.0 0.028569 1.0 -1.0
+4 2 2 6.0 0.089277 1.0 -1.0
+4 2 2 6.0 0.000357 2.0 -1.0
+4 2 2 6.0 0.028569 2.0 -1.0
+4 2 2 6.0 0.089277 2.0 -1.0
+4 2 2 6.0 0.000357 4.0 -1.0
+4 2 2 6.0 0.028569 4.0 -1.0
+4 2 2 6.0 0.089277 4.0 -1.0
+4 2 2 6.0 0.000357 1.0 1.0
+4 2 2 6.0 0.028569 1.0 1.0
+4 2 2 6.0 0.089277 1.0 1.0
+4 2 2 6.0 0.000357 2.0 1.0
+4 2 2 6.0 0.028569 2.0 1.0
+4 2 2 6.0 0.089277 2.0 1.0
+4 2 2 6.0 0.000357 4.0 1.0
+4 2 2 6.0 0.028569 4.0 1.0
+4 2 2 6.0 0.089277 4.0 1.0

test_code/generate/params_Si

@@ -0,0 +1,70 @@
+2 1 0 6.0 0.003214 0.0 0.0
+2 1 0 6.0 0.035711 0.0 0.0
+2 1 0 6.0 0.071421 0.0 0.0
+2 1 0 6.0 0.124987 0.0 0.0
+2 1 0 6.0 0.214264 0.0 0.0
+2 1 0 6.0 0.357106 0.0 0.0
+2 1 0 6.0 0.714213 0.0 0.0
+2 1 0 6.0 1.428426 0.0 0.0
+2 2 0 6.0 0.003214 0.0 0.0
+2 2 0 6.0 0.035711 0.0 0.0
+2 2 0 6.0 0.071421 0.0 0.0
+2 2 0 6.0 0.124987 0.0 0.0
+2 2 0 6.0 0.214264 0.0 0.0
+2 2 0 6.0 0.357106 0.0 0.0
+2 2 0 6.0 0.714213 0.0 0.0
+2 2 0 6.0 1.428426 0.0 0.0
+4 1 1 6.0 0.000357 1.0 -1.0
+4 1 1 6.0 0.028569 1.0 -1.0
+4 1 1 6.0 0.089277 1.0 -1.0
+4 1 1 6.0 0.000357 2.0 -1.0
+4 1 1 6.0 0.028569 2.0 -1.0
+4 1 1 6.0 0.089277 2.0 -1.0
+4 1 1 6.0 0.000357 4.0 -1.0
+4 1 1 6.0 0.028569 4.0 -1.0
+4 1 1 6.0 0.089277 4.0 -1.0
+4 1 1 6.0 0.000357 1.0 1.0
+4 1 1 6.0 0.028569 1.0 1.0
+4 1 1 6.0 0.089277 1.0 1.0
+4 1 1 6.0 0.000357 2.0 1.0
+4 1 1 6.0 0.028569 2.0 1.0
+4 1 1 6.0 0.089277 2.0 1.0
+4 1 1 6.0 0.000357 4.0 1.0
+4 1 1 6.0 0.028569 4.0 1.0
+4 1 1 6.0 0.089277 4.0 1.0
+4 1 2 6.0 0.000357 1.0 -1.0
+4 1 2 6.0 0.028569 1.0 -1.0
+4 1 2 6.0 0.089277 1.0 -1.0
+4 1 2 6.0 0.000357 2.0 -1.0
+4 1 2 6.0 0.028569 2.0 -1.0
+4 1 2 6.0 0.089277 2.0 -1.0
+4 1 2 6.0 0.000357 4.0 -1.0
+4 1 2 6.0 0.028569 4.0 -1.0
+4 1 2 6.0 0.089277 4.0 -1.0
+4 1 2 6.0 0.000357 1.0 1.0
+4 1 2 6.0 0.028569 1.0 1.0
+4 1 2 6.0 0.089277 1.0 1.0
+4 1 2 6.0 0.000357 2.0 1.0
+4 1 2 6.0 0.028569 2.0 1.0
+4 1 2 6.0 0.089277 2.0 1.0
+4 1 2 6.0 0.000357 4.0 1.0
+4 1 2 6.0 0.028569 4.0 1.0
+4 1 2 6.0 0.089277 4.0 1.0
+4 2 2 6.0 0.000357 1.0 -1.0
+4 2 2 6.0 0.028569 1.0 -1.0
+4 2 2 6.0 0.089277 1.0 -1.0
+4 2 2 6.0 0.000357 2.0 -1.0
+4 2 2 6.0 0.028569 2.0 -1.0
+4 2 2 6.0 0.089277 2.0 -1.0
+4 2 2 6.0 0.000357 4.0 -1.0
+4 2 2 6.0 0.028569 4.0 -1.0
+4 2 2 6.0 0.089277 4.0 -1.0
+4 2 2 6.0 0.000357 1.0 1.0
+4 2 2 6.0 0.028569 1.0 1.0
+4 2 2 6.0 0.089277 1.0 1.0
+4 2 2 6.0 0.000357 2.0 1.0
+4 2 2 6.0 0.028569 2.0 1.0
+4 2 2 6.0 0.089277 2.0 1.0
+4 2 2 6.0 0.000357 4.0 1.0
+4 2 2 6.0 0.028569 4.0 1.0
+4 2 2 6.0 0.089277 4.0 1.0

test_code/generate/run.py

@@ -0,0 +1,61 @@
+import sys
+sys.path.append('../../')
+
+from simple_nn_v2 import Simple_nn
+from simple_nn_v2.features.symmetry_function import Symmetry_function
+
+# 1. Make data files
+model = Simple_nn('input.yaml', descriptor=Symmetry_function())
+descriptor = Symmetry_function()
+descriptor.parent = model
+descriptor.set_inputs()
+
+print("Making data files...")
+descriptor.generate()
+print("Done!")
+
+# 2. Check if values are same as SIMPLE-NN ver.1
+import pickle
+import torch
+
+f=open('../test_data/SiO2/data1.pickle', 'rb')
+d1=pickle.load(f)
+f.close()
+
+DIR = descriptor.inputs['save_directory']
+if descriptor.inputs['save_to_pickle'] == True:
+    f=open(DIR+'/data1.pickle', 'rb')
+    d2=pickle.load(f)
+    f.close()
+else:
+    d2=torch.load(DIR+'/data1.pt')
+
+err_key = 0
+
+def comp(d1, d2):
+    if type(d1) == dict:
+        for key in d1.keys():
+            comp(d1[key], d2[key])
+    elif type(d1) == int or type(d1) == float or type(d1) == str:
+        if d1 != d2:
+            err_key = 1
+    else:
+        comp_list(d1, d2)
+
+def comp_list(l1, l2):
+    try:  # if l1 is list, numpy array type
+        len(l1)
+        for i in range(len(l1)):
+            comp_list(l1[i], l2[i])
+    except:  # if l1 is single value
+        if l1 != l2:
+            err_key = 1
+
+print("\nChecking data file values...")
+
+comp(d1, d2)
+
+if err_key == 0:
+    print("COMPLET: generate data Ok!")
+else:
+    print("ERROR: Wrong value in data file")

test_code/generate/str_list

@@ -0,0 +1 @@
+../test_data/SiO2/OUTCAR_comp :30:10

test_code/generate/test_function/README

@@ -0,0 +1,53 @@
+1. parsing_symf_params.py : test _parsing_symf_params()
+*Setting
+    input.yaml : match [symmetry_function][params] files to [atom_types]
+    params_XX : prepare for all atom_types
+*Output
+    - Check if all atom_types in symf_params_set keys
+    - Check if ['i', 'total', 'num', 'd'] keys are in all atom types
+    - Check if ['num'] value is matched with symmetry function numbers in params_XX
+    - If value in ['i'], ['d'] or ['total'] is not mathed with params_XX value, show mismatch index in screen
+        Else, "ok" sign in screen
+
+2. get_structure_info.py : test _get_structure_info()
+*Setting
+    set OUTCAR file path in "FILE" variable in [_get_structure_info.py] in line 22
+*Ouput
+    - Check if "atom_num" is total atom number
+    - Check "type_num" has correct element types and atom number for each elements
+    - Check if atom_type_idx has correct values
+    - Check "type_atom_idx" has correct atom index 
+    - Check lattice parameter
+    - Check Cartesian coordination in "cart" (first 5, last 5 coordination)
+    - Check Fractional coordination in "scale" (first 5, last 5 coordination)
+
+3. init_result.py : test _init_result()
+*Setting
+    set OUTCAR file path in "FILE" variable in [_init_result.py] in line 23
+    set example "structure_tags", "structure_weights", "idx" in line 31~33
+*Output
+   - Chcek if 'x', 'dx', 'da', 'params' is empty dictionary
+   - Check if 'N' has correct element types and atom number for each elements
+   - Check if 'tot_num' has total atom number
+   - Check if 'struct_type', 'struct_weight' has correct tag, weight with correspond to idx
+   - Check if 'atom_idx' set correctly
+
+4. init_sf_variables.py : test _init_sf_variables()
+*Setting
+    set OUTCAR file path in "FILE" variable in [_init_sf_variables.py] in line 25
+*Output
+    - Check if "jtem" atom number is correct
+    - Check if "jtem" atom idx is correct
+    - Check if 'x', 'dx', 'da' is initialze to 0
+
+5. set_result.py : test _set_result()
+*Setting
+    set OUTCAR file path in "FILE" variable in [_init_sf_variables.py] in line 33
+*Output
+    - Check if 'N', 'tot_num', 'struct_type', 'struct_weight' is identical to test3 results
+    - Check if 'x', 'dx', 'da' has available values (didn't check if has identical values)
+    - Check if 'E', 'F', 'S' value extract correctly
+
+6. datagenerator.py : test datagenerator() in util/
+*Output
+