|
6 | 6 | from ase.calculators.socketio import SocketIOCalculator |
7 | 7 | from ase.vibrations import Vibrations |
8 | 8 | from ase.calculators.mixing import SumCalculator |
9 | | -from molecule.molecule import Molecule |
| 9 | +from molecule.molecule import Molecule, Group, ATOMTYPES |
10 | 10 | from sella import Sella, Constraints, IRC |
11 | 11 | from fireworks import * |
12 | 12 | from fireworks.core.rocket_launcher import rapidfire |
|
16 | 16 | from fireworks.core.fworker import FWorker |
17 | 17 | import fireworks.fw_config |
18 | 18 | from pysidt.sidt import * |
| 19 | +import pynta.models |
19 | 20 | from pynta.transitionstate import get_unique_optimized_adsorbates,determine_TS_construction,get_unique_TS_structs,generate_constraints_harmonic_parameters,get_unique_TS_templates_site_pairings |
20 | 21 | from pynta.utils import * |
21 | 22 | from pynta.calculator import run_harmonically_forced, map_harmonically_forced, add_sella_constraint |
|
36 | 37 | from contextlib import contextmanager |
37 | 38 | from copy import deepcopy |
38 | 39 | from joblib import Parallel, delayed |
| 40 | +import os |
39 | 41 |
|
40 | 42 | class OptimizationTask(FiretaskBase): |
41 | 43 | def run_task(self, fw_spec): |
@@ -1231,10 +1233,7 @@ def run_task(self, fw_spec): |
1231 | 1233 | nslab = len(slab) |
1232 | 1234 | allowed_structure_site_structures = generate_allowed_structure_site_structures(os.path.join(pynta_dir,"Adsorbates"),sites,site_adjacency,nslab,max_dist=np.inf) |
1233 | 1235 |
|
1234 | | - from pysidt.sidt import read_nodes, MultiEvalSubgraphIsomorphicDecisionTreeRegressor |
1235 | | - from molecule.molecule import Group, ATOMTYPES |
1236 | | - import pynta.models |
1237 | | - import os |
| 1236 | + |
1238 | 1237 | nodes_file = os.path.join(os.path.split(pynta.models.__file__)[0],"finetuned_to_dft_delta_model.json") |
1239 | 1238 | nodes = read_nodes(nodes_file) |
1240 | 1239 | def bond_decomposition_adsorbate(mol): |
|
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