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kumaranukumaranu
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Got rid of try error blocks. Defined the newtonnet calculator model and config paths in the relative sense. Also got rid of the tags.
1 parent 52a8f53 commit 420fb7e

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8 files changed

+194
-410
lines changed

8 files changed

+194
-410
lines changed

‎pyproject.toml‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@ requires = ["setuptools"]
33
build-backend = "setuptools.build_meta"
44

55
[project]
6-
name = "ts-workflow examples"
6+
name = "ts-workflow-examples"
77
description="A Python package description goes here."
88
version = "0.0.1"
99
readme = "README.md"
@@ -25,7 +25,7 @@ classifiers = [
2525
"Operating System :: MacOS",
2626
]
2727
requires-python = ">=3.9"
28-
dependencies = ["numpy"]
28+
dependencies = []
2929

3030
[project.optional-dependencies]
3131
dev = ["pytest>=7.4.0", "pytest-cov>=3.0.0", "ruff>=0.0.285"]
@@ -39,15 +39,15 @@ docs = [
3939
]
4040

4141
[project.urls]
42-
repository = "https://github.com/Quantum-Accelerators/ts-workflow examples"
43-
documentation = "https://quantum-accelerators.github.io/ts-workflow examples/"
44-
changelog = "https://github.com/Quantum-Accelerators/ts-workflow examples/blob/main/CHANGELOG.md"
42+
repository = "https://github.com/Quantum-Accelerators/ts-workflow-examples"
43+
documentation = "https://quantum-accelerators.github.io/ts-workflow-examples/"
44+
changelog = "https://github.com/Quantum-Accelerators/ts-workflow-examples/blob/main/CHANGELOG.md"
4545

46-
[tool.setuptools.package-data]
47-
ts-workflow examples = ["py.typed"]
46+
# [tool.setuptools.package-data]
47+
# ts-workflow-examples = ["py.typed"]
4848

4949
[tool.pyright]
50-
include = ["ts-workflow examples"]
50+
include = ["ts-workflow-examples"]
5151
exclude = ["**/__pycache__"]
5252

5353
[tool.pytest.ini_options]
@@ -137,7 +137,7 @@ lint.unfixable = [
137137
"F841", # Removes unused variables
138138
]
139139
lint.pydocstyle.convention = "numpy"
140-
lint.isort.known-first-party = ["ts-workflow examples"]
140+
lint.isort.known-first-party = ["ts-workflow-examples"]
141141
lint.isort.required-imports = ["from __future__ import annotations"]
142142
extend-include = ["*.ipynb"]
143143

‎src/ts-workflow-examples/geodesic_ts_with_hessian/using_mace.py‎

Lines changed: 25 additions & 57 deletions
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,6 @@
1010
# Constants from TOML file
1111
REACTANT_XYZ_FILE = config['paths']['reactant']
1212
PRODUCT_XYZ_FILE = config['paths']['product']
13-
TAG = config['run']['tag']
1413

1514
# Setup logging
1615
logging.basicConfig(level=logging.INFO)
@@ -21,69 +20,38 @@
2120
}
2221

2322
def main():
24-
try:
25-
# Read reactant and product structures
26-
reactant = read(REACTANT_XYZ_FILE)
27-
product = read(PRODUCT_XYZ_FILE)
28-
logger.info("Successfully read reactant and product structures.")
29-
except Exception as e:
30-
logger.error(f"Error reading reactant and product structures: {e}")
31-
return
23+
# Read reactant and product structures
24+
reactant = read(REACTANT_XYZ_FILE)
25+
product = read(PRODUCT_XYZ_FILE)
26+
logger.info("Successfully read reactant and product structures.")
3227

33-
try:
34-
# Create NEB job
35-
job1 = geodesic_job(reactant, product, calc_kwargs=calc_kwargs)
36-
job1.update_metadata({"tag": f'geodesic_{TAG}'})
37-
logger.info("Created Geodesic job.")
38-
except Exception as e:
39-
logger.error(f"Error creating Geodesic job: {e}")
40-
return
28+
# Create NEB job
29+
job1 = geodesic_job(reactant, product, calc_kwargs=calc_kwargs)
30+
logger.info("Created Geodesic job.")
4131

42-
try:
43-
# Create TS job with custom Hessian
44-
job2 = ts_job(job1.output['highest_e_atoms'], use_custom_hessian=True, **calc_kwargs)
45-
job2.update_metadata({"tag": f'ts_hess_{TAG}'})
46-
logger.info("Created TS job with custom Hessian.")
47-
except Exception as e:
48-
logger.error(f"Error creating TS job: {e}")
49-
return
32+
# Create TS job with custom Hessian
33+
job2 = ts_job(job1.output['highest_e_atoms'], use_custom_hessian=True, **calc_kwargs)
34+
logger.info("Created TS job with custom Hessian.")
5035

51-
try:
52-
# Create IRC job in forward direction
53-
job3 = irc_job(job2.output['atoms'], direction='forward', **calc_kwargs)
54-
job3.update_metadata({"tag": f'ircf_hess_{TAG}'})
55-
logger.info("Created IRC job in forward direction.")
56-
except Exception as e:
57-
logger.error(f"Error creating IRC job in forward direction: {e}")
58-
return
36+
# Create IRC job in forward direction
37+
job3 = irc_job(job2.output['atoms'], direction='forward', **calc_kwargs)
38+
logger.info("Created IRC job in forward direction.")
5939

60-
try:
61-
# Create IRC job in reverse direction
62-
job4 = irc_job(job2.output['atoms'], direction='reverse', **calc_kwargs)
63-
job4.update_metadata({"tag": f'ircr_hess_{TAG}'})
64-
logger.info("Created IRC job in reverse direction.")
65-
except Exception as e:
66-
logger.error(f"Error creating IRC job in reverse direction: {e}")
67-
return
40+
# Create IRC job in reverse direction
41+
job4 = irc_job(job2.output['atoms'], direction='reverse', **calc_kwargs)
42+
logger.info("Created IRC job in reverse direction.")
6843

69-
try:
70-
# Combine jobs into a flow
71-
jobs = [job1, job2, job3, job4]
72-
flow = jf.Flow(jobs)
73-
logger.info("Jobs combined into a flow.")
74-
except Exception as e:
75-
logger.error(f"Error combining jobs into a flow: {e}")
76-
return
44+
# Combine jobs into a flow
45+
jobs = [job1, job2, job3, job4]
46+
flow = jf.Flow(jobs)
47+
logger.info("Jobs combined into a flow.")
7748

78-
try:
79-
# Execute the workflow locally
80-
responses = jf.managers.local.run_locally(flow)
81-
logger.info("Workflow executed successfully.")
82-
logger.info(f"Responses: {responses}")
83-
except Exception as e:
84-
logger.error(f"Error executing workflow: {e}")
85-
return
49+
# Execute the workflow locally
50+
responses = jf.managers.local.run_locally(flow)
51+
logger.info("Workflow executed successfully.")
52+
logger.info(f"Responses: {responses}")
8653

8754

8855
if __name__ == "__main__":
8956
main()
57+

‎src/ts-workflow-examples/geodesic_ts_with_hessian/using_newtonnet.py‎

Lines changed: 39 additions & 69 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,11 @@
11
import os
2-
import logging
32
import toml
3+
import logging
4+
import jobflow as jf
45
from ase.io import read
6+
from quacc import get_settings
57
from quacc.recipes.newtonnet.ts import ts_job, irc_job, geodesic_job
6-
import jobflow as jf
8+
79

810
# Load configuration from TOML file
911
config = toml.load('inputs_using_newtonnet.toml')
@@ -13,87 +15,55 @@
1315
PRODUCT_XYZ_FILE = config['paths']['product']
1416
MODEL_PATH = config['paths']['model_path']
1517
SETTINGS_PATH = config['paths']['settings_path']
16-
TAG = config['run']['tag']
1718

1819
# Setup logging
1920
logging.basicConfig(level=logging.INFO)
2021
logger = logging.getLogger(__name__)
2122

23+
settings = get_settings()
24+
settings.NEWTONNET_MODEL_PATH = os.getcwd() + MODEL_PATH
25+
settings.NEWTONNET_CONFIG_PATH = os.getcwd() + SETTINGS_PATH
26+
2227
# Calculation and optimization keyword arguments
2328
calc_kwargs1 = {
24-
'model_path': MODEL_PATH,
25-
'settings_path': SETTINGS_PATH,
2629
'hess_method': None,
2730
}
2831
calc_kwargs2 = {
29-
'model_path': MODEL_PATH,
30-
'settings_path': SETTINGS_PATH,
3132
'hess_method': 'autograd',
3233
}
3334

35+
3436
def main():
35-
try:
36-
# Read reactant and product structures
37-
reactant = read(REACTANT_XYZ_FILE)
38-
product = read(PRODUCT_XYZ_FILE)
39-
logger.info("Successfully read reactant and product structures.")
40-
except Exception as e:
41-
logger.error(f"Error reading reactant and product structures: {e}")
42-
return
43-
44-
try:
45-
# Create NEB job
46-
job1 = geodesic_job(reactant, product, calc_kwargs=calc_kwargs1)
47-
job1.update_metadata({"tag": f'geodesic_{TAG}'})
48-
logger.info("Created Geodesic job.")
49-
except Exception as e:
50-
logger.error(f"Error creating Geodesic job: {e}")
51-
return
52-
53-
try:
54-
# Create TS job with custom Hessian
55-
job2 = ts_job(job1.output['highest_e_atoms'], use_custom_hessian=True, **calc_kwargs2)
56-
job2.update_metadata({"tag": f'ts_hess_{TAG}'})
57-
logger.info("Created TS job with custom Hessian.")
58-
except Exception as e:
59-
logger.error(f"Error creating TS job: {e}")
60-
return
61-
62-
try:
63-
# Create IRC job in forward direction
64-
job3 = irc_job(job2.output['atoms'], direction='forward', **calc_kwargs1)
65-
job3.update_metadata({"tag": f'ircf_hess_{TAG}'})
66-
logger.info("Created IRC job in forward direction.")
67-
except Exception as e:
68-
logger.error(f"Error creating IRC job in forward direction: {e}")
69-
return
70-
71-
try:
72-
# Create IRC job in reverse direction
73-
job4 = irc_job(job2.output['atoms'], direction='reverse', **calc_kwargs1)
74-
job4.update_metadata({"tag": f'ircr_hess_{TAG}'})
75-
logger.info("Created IRC job in reverse direction.")
76-
except Exception as e:
77-
logger.error(f"Error creating IRC job in reverse direction: {e}")
78-
return
79-
80-
try:
81-
# Combine jobs into a flow
82-
jobs = [job1, job2, job3, job4]
83-
flow = jf.Flow(jobs)
84-
logger.info("Jobs combined into a flow.")
85-
except Exception as e:
86-
logger.error(f"Error combining jobs into a flow: {e}")
87-
return
88-
89-
try:
90-
# Execute the workflow locally
91-
responses = jf.managers.local.run_locally(flow)
92-
logger.info("Workflow executed successfully.")
93-
logger.info(f"Responses: {responses}")
94-
except Exception as e:
95-
logger.error(f"Error executing workflow: {e}")
96-
return
37+
# Read reactant and product structures
38+
reactant = read(REACTANT_XYZ_FILE)
39+
product = read(PRODUCT_XYZ_FILE)
40+
logger.info("Successfully read reactant and product structures.")
41+
42+
# Create NEB job
43+
job1 = geodesic_job(reactant, product, calc_kwargs=calc_kwargs1)
44+
logger.info("Created Geodesic job.")
45+
46+
# Create TS job with custom Hessian
47+
job2 = ts_job(job1.output['highest_e_atoms'], use_custom_hessian=True, **calc_kwargs2)
48+
logger.info("Created TS job with custom Hessian.")
49+
50+
# Create IRC job in forward direction
51+
job3 = irc_job(job2.output['atoms'], direction='forward', **calc_kwargs1)
52+
logger.info("Created IRC job in forward direction.")
53+
54+
# Create IRC job in reverse direction
55+
job4 = irc_job(job2.output['atoms'], direction='reverse', **calc_kwargs1)
56+
logger.info("Created IRC job in reverse direction.")
57+
58+
# Combine jobs into a flow
59+
jobs = [job1, job2, job3, job4]
60+
flow = jf.Flow(jobs)
61+
logger.info("Jobs combined into a flow.")
62+
63+
# Execute the workflow locally
64+
responses = jf.managers.local.run_locally(flow)
65+
logger.info("Workflow executed successfully.")
66+
logger.info(f"Responses: {responses}")
9767

9868

9969
if __name__ == "__main__":

‎src/ts-workflow-examples/geodesic_ts_without_hessian/using_mace.py‎

Lines changed: 25 additions & 57 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,6 @@
1111
# Constants from TOML file
1212
REACTANT_XYZ_FILE = config['paths']['reactant']
1313
PRODUCT_XYZ_FILE = config['paths']['product']
14-
TAG = config['run']['tag']
1514

1615
# Setup logging
1716
logging.basicConfig(level=logging.INFO)
@@ -22,69 +21,38 @@
2221
}
2322

2423
def main():
25-
try:
26-
# Read reactant and product structures
27-
reactant = read(REACTANT_XYZ_FILE)
28-
product = read(PRODUCT_XYZ_FILE)
29-
logger.info("Successfully read reactant and product structures.")
30-
except Exception as e:
31-
logger.error(f"Error reading reactant and product structures: {e}")
32-
return
24+
# Read reactant and product structures
25+
reactant = read(REACTANT_XYZ_FILE)
26+
product = read(PRODUCT_XYZ_FILE)
27+
logger.info("Successfully read reactant and product structures.")
3328

34-
try:
35-
# Create NEB job
36-
job1 = geodesic_job(reactant, product, calc_kwargs=calc_kwargs)
37-
job1.update_metadata({"tag": f'geodesic_{TAG}'})
38-
logger.info("Created Geodesic job.")
39-
except Exception as e:
40-
logger.error(f"Error creating Geodesic job: {e}")
41-
return
29+
# Create NEB job
30+
job1 = geodesic_job(reactant, product, calc_kwargs=calc_kwargs)
31+
logger.info("Created Geodesic job.")
4232

43-
try:
44-
# Create TS job with custom Hessian
45-
job2 = ts_job(job1.output['highest_e_atoms'], use_custom_hessian=False, **calc_kwargs)
46-
job2.update_metadata({"tag": f'ts_no_hess_{TAG}'})
47-
logger.info("Created TS job without custom Hessian.")
48-
except Exception as e:
49-
logger.error(f"Error creating TS job: {e}")
50-
return
33+
# Create TS job with custom Hessian
34+
job2 = ts_job(job1.output['highest_e_atoms'], use_custom_hessian=False, **calc_kwargs)
35+
logger.info("Created TS job without custom Hessian.")
5136

52-
try:
53-
# Create IRC job in forward direction
54-
job3 = irc_job(job2.output['atoms'], direction='forward', **calc_kwargs)
55-
job3.update_metadata({"tag": f'ircf_no_hess_{TAG}'})
56-
logger.info("Created IRC job in forward direction.")
57-
except Exception as e:
58-
logger.error(f"Error creating IRC job in forward direction: {e}")
59-
return
37+
# Create IRC job in forward direction
38+
job3 = irc_job(job2.output['atoms'], direction='forward', **calc_kwargs)
39+
logger.info("Created IRC job in forward direction.")
6040

61-
try:
62-
# Create IRC job in reverse direction
63-
job4 = irc_job(job2.output['atoms'], direction='reverse', **calc_kwargs)
64-
job4.update_metadata({"tag": f'ircr_no_hess_{TAG}'})
65-
logger.info("Created IRC job in reverse direction.")
66-
except Exception as e:
67-
logger.error(f"Error creating IRC job in reverse direction: {e}")
68-
return
41+
# Create IRC job in reverse direction
42+
job4 = irc_job(job2.output['atoms'], direction='reverse', **calc_kwargs)
43+
logger.info("Created IRC job in reverse direction.")
6944

70-
try:
71-
# Combine jobs into a flow
72-
jobs = [job1, job2, job3, job4]
73-
flow = jf.Flow(jobs)
74-
logger.info("Jobs combined into a flow.")
75-
except Exception as e:
76-
logger.error(f"Error combining jobs into a flow: {e}")
77-
return
45+
# Combine jobs into a flow
46+
jobs = [job1, job2, job3, job4]
47+
flow = jf.Flow(jobs)
48+
logger.info("Jobs combined into a flow.")
7849

79-
try:
80-
# Execute the workflow locally
81-
responses = jf.managers.local.run_locally(flow)
82-
logger.info("Workflow executed successfully.")
83-
logger.info(f"Responses: {responses}")
84-
except Exception as e:
85-
logger.error(f"Error executing workflow: {e}")
86-
return
50+
# Execute the workflow locally
51+
responses = jf.managers.local.run_locally(flow)
52+
logger.info("Workflow executed successfully.")
53+
logger.info(f"Responses: {responses}")
8754

8855

8956
if __name__ == "__main__":
9057
main()
58+

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