Documentation build

docs/_build/html/.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 9e747c02196262440d033b6da27cdc10
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_downloads/1a62c028c9da69253548783ae8a76070/water_dimer.xyz

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+6
+
+O      -1.61075942       0.14972207       0.00000000
+O       1.27324620      -0.14984188       0.00000000
+H      -2.05173067      -0.71502154       0.00000000
+H      -0.65160034      -0.06225163       0.00000000
+H       1.52042212       0.38869649      -0.77034720
+H       1.52042212       0.38869649       0.77034720

docs/_build/html/_downloads/2a505c3581f7da7bf9082296ef7cb96f/frag_NH3BH3.py

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+from tcutility.job import ADFFragmentJob
+from tcutility import molecule
+
+# load a molecule
+mol = molecule.load('NH3BH3.xyz')
+
+# define a new job using the Job context-manager
+with ADFFragmentJob() as job:
+	# add the molecule
+	job.molecule(mol)
+	# add the fragments. The fragment atoms are defined in the input xyz file
+	for fragment_name, fragment in molecule.guess_fragments(mol).items():
+		job.add_fragment(fragment, fragment_name)

docs/_build/html/_downloads/4d6b7e579d62ed9e5d25258a67fecb73/NH3BH3.xyz

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+8
+
+N       0.00000000       0.00000000      -0.81474153 frag=Donor
+B      -0.00000000      -0.00000000       0.83567034 frag=Acceptor
+H       0.47608351      -0.82460084      -1.14410295 frag=Donor
+H       0.47608351       0.82460084      -1.14410295 frag=Donor
+H      -0.95216703       0.00000000      -1.14410295 frag=Donor
+H      -0.58149793       1.00718395       1.13712667 frag=Acceptor
+H      -0.58149793      -1.00718395       1.13712667 frag=Acceptor
+H       1.16299585      -0.00000000       1.13712667 frag=Acceptor

docs/_build/html/_downloads/d1984d07233b61c9fa5986aed5cd64fb/GO_water_dimer.py

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+import pathlib as pl
+
+from scm.plams import AMSJob, Molecule, Settings, config, finish, init
+from tcutility.job import ADFJob
+
+current_file_path = pl.Path(__file__).parent
+mol_path = current_file_path / "water_dimer.xyz"
+
+
+def try_plams_job(mol: Molecule) -> None:
+    # Test case with plams for checking if plams works solely on Windows
+    run_set = Settings()
+    run_set.input.ams.Task = "GeometryOptimization"
+    run_set.input.adf.Basis.Type = "DZP"
+    run_set.input.adf.XC.GGA = "BP86"
+
+    config.log.file = 7
+    config.log.stdout = 7
+
+    init(path=str(current_file_path), folder="GO_water_dimer", config_settings=config)
+    AMSJob(molecule=mol, name="water_dimer", settings=run_set).run()
+    finish()
+
+
+def try_tcutility_job(mol: Molecule) -> None:
+    # Test case with tcutility for checking if tcutility works solely on Windows
+    with ADFJob(use_slurm=False) as job:
+        job.molecule(mol)
+        job.rundir = str(current_file_path / "calculations")
+        job.name = "GO_water_dimer"
+        job.functional("BP86-D3(BJ)")
+        job.basis_set("TZ2P")
+        job.quality("Good")
+        job.optimization()
+
+
+def main():
+    current_file_path = pl.Path(__file__).parent
+    mol_path = current_file_path / "water_dimer.xyz"
+
+    mol = Molecule(str(mol_path))
+
+    # Use these functions to test if a plams and tcutility job can be run on Windows, Mac, and Linux. Both do not use slurm.
+    try_plams_job(mol)
+    try_tcutility_job(mol)
+
+
+if __name__ == "__main__":
+    main()