Auto stash before merge of "main" and "origin/main"

Did a lot of restructuring.

src/calcs.py

@@ -45,14 +45,3 @@ def calc():
         device=device
     )
     return mlcalculator
-
-'''
-h2 = Atoms(numbers=[1, 1], positions=[[0.0, 0.0, 0.0], [0.0, 0.0, 1.0]])
-mlcalculator.calculate(h2)
-
-print(mlcalculator.results['energy'])    # mean of calculated molecular energies, shape (1,)
-print(mlcalculator.results['forces'])    # mean of calculated atomic forces, shape (n_atom, 3)
-print(mlcalculator.results['hessian'])    # mean of calculated atomic Hessian, shape (n_atom, 3, n_atom, 3)
-print(mlcalculator.results['energy_disagreement'])    # disagreement among calculated molecular 
-'''
-

src/check_graph_iso.py

@@ -5,7 +5,7 @@
 from pymatgen.analysis.graphs import MoleculeGraph
 from pymatgen.analysis.local_env import OpenBabelNN
 from networkx.algorithms.graph_hashing import weisfeiler_lehman_graph_hash
-from plot2 import gen_energy_profile
+from src.mep_tests.tools.plot2 import gen_energy_profile
 
 
 def add_specie_suffix(graph):

src/check_neb_results.py

@@ -1,6 +1,6 @@
 import glob, os, sys
 from ase.io import read
-from calcs1 import calc
+from calcs import calc
 import numpy as np
 from ase import Atoms
 from multiprocessing import Pool
@@ -79,4 +79,3 @@ def process_file(i):
     for result in results:
         if result is not None:
             print(result)
-

src/initialize_path.py

@@ -126,4 +126,3 @@ def setup_analysis(
 
     print(f'Forward_barrier: {ts_e - r_e}')
     print(f'Reverse_barrier: {ts_e - p_e}')
-

src/check.py → src/mep_tests/tools/check_neb_convergence.py

@@ -12,7 +12,7 @@
             print(f'{i:03}: {INF[-1].split()[1]}')
         else:
             print(f'{i:03}: No NEB file.')
-        os.chdir('../')
+        os.chdir('../../../')
     else:
         print(f'{i:03} does not exist.')
 

src/plot2.py → src/mep_tests/tools/plot2.py

@@ -80,26 +80,33 @@ def gen_energy_profile(
     # if len(sys.argv) != 3:
     #     print("Usage: python script.py <xyz_file1> <xyz_file2>")
     #     sys.exit(1)
-    ref_dir = '/home/kumaranu/Downloads/neb_nn_inputs'
-    index = '001'
-    geodesic_xyz = os.path.join(
-        ref_dir,
-        index,
-        'geodesic_path.xyz',
-    )
-    neb_path_xyz = os.path.join(
-        ref_dir,
-        index,
-        'optimized_path_aseneb_NEBOptimizer_None.xyz'
-    )
-    ts_xyz = os.path.join(
-        ref_dir,
-        index,
-        'TS.xyz',
-    )
+    #ref_dir = '/home/kumaranu/Downloads/neb_nn_inputs'
+    #index = '001'
+    ref_dir = '/home/kumaranu/Downloads/neb_rgd1_inputs'
+    for i in range(999):
+        index = f'{i:03}'
+        # index = '679'
+        try:
+            geodesic_xyz = os.path.join(
+                ref_dir,
+                index,
+                'geodesic_path.xyz',
+            )
+            neb_path_xyz = os.path.join(
+                ref_dir,
+                index,
+                'optimized_path_aseneb_NEBOptimizer_None.xyz'
+            )
+            ts_xyz = os.path.join(
+                ref_dir,
+                index,
+                'TS.xyz',
+            )
 
-    barrier_err = gen_energy_profile(
-        geodesic_xyz,
-        neb_path_xyz,
-        ts_xyz,
-    )
+            barrier_err = gen_energy_profile(
+                geodesic_xyz,
+                neb_path_xyz,
+                ts_xyz,
+            )
+        except:
+            continue

src/setup_images.py

@@ -1,5 +1,4 @@
 import os
-import copy
 from calcs import calc
 from ase.io import read, write
 from typing import Any, Dict, Iterator, List, Sequence, Tuple, TypeVar, Union
@@ -40,4 +39,3 @@ def setup_images(
     write('geodesic_path.xyz', images)
 
     return images
-

src/test1.py

@@ -24,12 +24,12 @@ def main(config_file: str) -> None:
         run_neb_method(
             method=input_set['method'],
             optimizer=ase_optimizer,
+            opt_method=None,
             precon=None,
-            optmethod=None,
             logdir=inputs['input_paths']['logdir'],
             xyz_r_p=inputs['input_paths']['xyz_r_p'],
             xyz_ts=inputs['input_paths']['xyz_ts'],
-            N_intermediate=inputs['geodesic_inputs']['N_intermediate'],
+            n_intermediate=inputs['geodesic_inputs']['N_intermediate'],
         )