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Scripts/opt/dft_sella_quacc.py

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+
+"""
+Original Author: Samuel Blau
+Modifier: Anup Kumar
+
+Module for adding calculations to a FireWorks LaunchPad.
+
+Includes functions to add transition state and IRC (Intrinsic Reaction Coordinate)
+calculations to a LaunchPad for QChem using the FireWorks workflow management tool.
+
+"""
+
+import toml
+import glob
+import jobflow as jf
+from ase import Atoms
+from ase.io import read
+from fireworks import LaunchPad
+from quacc.recipes.qchem.ts import ts_job
+from quacc.recipes.qchem.ts import irc_job
+from quacc.recipes.qchem.core import freq_job
+from jobflow.managers.fireworks import flow_to_workflow
+
+
+def add_to_launchpad(
+        index: str,
+        atoms: Atoms,
+        tag: str,
+        lpad: LaunchPad,
+        run_job_locally: bool = False,
+        RUN: bool = False,
+) -> None:
+    """
+    Add QChem calculations to a LaunchPad.
+
+    Parameters:
+        index (str): Identifier for the calculation.
+        atoms (Atoms): ASE Atoms object representing the molecular structure.
+        tag (str): Tag to classify the calculation.
+        lpad (LaunchPad): FireWorks LaunchPad object.
+        run_job_locally (bool, optional): Whether to run the job locally. Defaults to False.
+        RUN (bool, optional): Whether to add the workflow to the LaunchPad. Defaults to False.
+
+    Returns:
+        None
+    """
+    job1 = ts_job(
+                  atoms,
+                  0,
+                  1,
+                  method="wb97x",
+                  basis="6-31G*",
+                 )
+    job1.name = f"ind{index}_{tag}_ts"
+
+    job1f = freq_job(
+                     job1.output,
+                     0,
+                     1,
+                     method="wb97x",
+                     basis="6-31G*",
+                    )
+    job1f.name = f"ind{index}_{tag}_freq"
+
+    job2 = irc_job(
+                   job1.output,
+                   0,
+                   1,
+                   direction="forward",
+                   method="wb97x",
+                   basis="6-31G*",
+                  )
+    job2.name = f"ind{index}_{tag}_firc"
+
+    job2f = freq_job(
+                     job2.output,
+                     0,
+                     1,
+                     method="wb97x",
+                     basis="6-31G*",
+                    )
+    job2f.name = f"ind{index}_{tag}_firc_freq"
+
+    job3 = irc_job(
+                   job1.output,
+                   0,
+                   1,
+                   direction="reverse",
+                   method="wb97x",
+                   basis="6-31G*",
+                  )
+    job3.name = f"ind{index}_{tag}_rirc"
+
+    job3f = freq_job(
+                     job3.output,
+                     0,
+                     1,
+                     method="wb97x",
+                     basis="6-31G*"
+                    )
+    job3f.name = f"ind{index}_{tag}_rirc_freq"
+
+    job_list = [job1, job1f, job2, job2f, job3, job3f]
+
+    for job in job_list:
+        job.update_metadata(
+            {
+                "class": f"{tag}"
+            }
+        )
+
+    flow = jf.Flow(job_list)
+
+    if run_job_locally:
+        responses = jf.run_locally(flow)
+        result = responses[job2.uuid][1].output
+        print(result)
+    else:
+        wf = flow_to_workflow(flow)
+
+        if RUN:
+            lpad.add_wf(wf)
+
+
+def main() -> None:
+    """
+    Main function to add QChem calculations to the LaunchPad.
+
+    Returns:
+        None
+    """
+    config = toml.load('inputs/config44.toml')
+
+    index_files = [index_file for index_file in glob.glob(config['indices']['xyz_files_dir'] + '/*')]
+    tag = config['general']['tag']
+    run = config['general']['run']
+    LAUNCHPAD_FILE = config['general']['launchpad_file']
+    lpad = LaunchPad.from_file(LAUNCHPAD_FILE)
+
+    for index_file in index_files:
+        atoms = read(index_file)
+        index = index_file.split('/')[-1].split('.')[0]
+        add_to_launchpad(
+            index,
+            atoms,
+            tag,
+            lpad,
+            RUN=run,
+        )
+
+
+if __name__ == '__main__':
+    main()

Scripts/opt/nn_sella_quacc.py

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+
+"""
+Author: Anup Kumar
+"""
+
+import toml
+import glob
+import jobflow as jf
+from ase import Atoms
+from ase.io import read
+from fireworks import LaunchPad
+from jobflow.managers.fireworks import flow_to_workflow
+from quacc.recipes.newtonnet.ts import ts_job
+from quacc.recipes.newtonnet.ts import irc_job
+from atomate.common.powerups import add_tags
+
+
+def add_to_launchpad(
+        index: str,
+        atoms: Atoms,
+        config: dict,
+        lpad: LaunchPad,
+        ts_type: int = 0,
+        run_job_locally: bool = True,
+) -> None:
+    """
+    Add transition state and IRC jobs to the FireWorks LaunchPad.
+
+    Args:
+        index (str): The index string.
+        atoms (Atoms): The ASE Atoms object.
+        config (dict): The configuration dictionary.
+        lpad (LaunchPad): The FireWorks LaunchPad.
+        ts_type (int, optional): The type of transition state. Defaults to 0.
+        run_job_locally (bool, optional): Whether to run the job locally or add to LaunchPad. Defaults to True.
+    """
+    tag = config['general']['tag'].format(ts_type)
+
+    if ts_type == 0:
+        job1 = ts_job(
+            atoms,
+            use_custom_hessian=True,
+        )
+        job1.update_metadata(
+            {
+                "tag": f'TS{ts_type}-{index}'
+            }
+        )
+    else:
+        job1 = ts_job(atoms, use_custom_hessian=False)
+        job1.update_metadata(
+            {
+                "tag": f'TS{ts_type}-{index}'
+            }
+        )
+
+    opt_swaps = {
+        "run_kwargs": {
+            "direction": "forward",
+        },
+    }
+
+    calc_swaps = {
+        "use_custom_hessian": False
+    }
+
+    job2 = irc_job(
+        job1.output["atoms"],
+        opt_swaps=opt_swaps,
+        calc_swaps=calc_swaps,
+    )
+    job2.update_metadata(
+        {
+            "tag": f'irc-forward{ts_type}-{index}',
+        }
+    )
+
+    opt_swaps = {
+        "run_kwargs": {
+            "direction": "reverse",
+        },
+    }
+
+    job3 = irc_job(
+        job1.output["atoms"],
+        opt_swaps=opt_swaps,
+        calc_swaps=calc_swaps,
+    )
+    job3.update_metadata(
+        {
+            "tag": f'irc-reverse{ts_type}-{index}',
+        }
+    )
+
+    flow = jf.Flow([job1, job2, job3])
+
+    if run_job_locally:
+        responses = jf.run_locally(flow)
+        result = responses[job2.uuid][1].output
+        print(result)
+    else:
+        wf = flow_to_workflow(flow)
+        wf = add_tags(wf, {"class": tag})
+        if config['general']['run']:
+            lpad.add_wf(wf)
+
+
+def main():
+    """
+    Main function to add transition state and IRC jobs to the LaunchPad.
+    """
+    config = toml.load('inputs/config43.toml')
+    index_files = [index_file for index_file in glob.glob(config['indices']['xyz_files_dir'] + '/*')]
+
+    LAUNCHPAD_FILE = config['general']['launchpad_file']
+    lpad = LaunchPad.from_file(LAUNCHPAD_FILE)
+
+    for index_file in index_files:
+        atoms = read(index_file)
+        index = index_file.split('/')[-1].split('.')[0]
+        add_to_launchpad(
+            index,
+            atoms,
+            config,
+            lpad,
+            ts_type=0,
+            run_job_locally=False,
+        )
+        add_to_launchpad(
+            index,
+            atoms,
+            config,
+            lpad,
+            ts_type=1,
+            run_job_locally=False,
+        )
+
+
+if __name__ == '__main__':
+    main()