all_geom about aarontools.py HOT 4 CLOSED

from AaronTools.geometry import Geometry
from AaronTools.theory import Theory, OptimizationJob, FrequencyJob
from AaronTools.job_control import SubmitProcess

# different levels of theory to use
theory1 = Theory(
    method="M06-2X",
    basis="6-31+G**",
    job_type=[OptimizationJob(), FrequencyJob()],
    processors=4,
    memory=4,
)

theory2 = Theory(
    method="M06-2X",
    basis="6-311+G**",
    job_type="energy", # optional, as ORCA calculates energy by default
    processors=4,
    memory=4,
)

theory3 = Theory(
    method="B3LYP",
    basis="def2-TZVP",
    job_type="energy",
    processors=4,
    memory=4,
)

mol = Geometry.from_string("water", form="iupac")

# run optimization job and wait for it to finish
mol.write(outfile="opt-freq.inp", theory=theory1)
proc1 = SubmitProcess("opt-freq.inp", 2, 4, 4)
print("submitting opt+freq")
proc1.submit(wait=30)
print("opt+freq done")

# read the output structure and run single points
optimized_mol = Geometry("opt-freq.out")

print("submitting SPs")
optimized_mol.write(outfile="M06-2X_SP.inp", theory=theory2)
proc2 = SubmitProcess("M06-2X_SP.inp", 2, 4, 4)
proc2.submit()

optimized_mol.write(outfile="B3LYP_SP.inp", theory=theory3)
proc3 = SubmitProcess("B3LYP_SP.inp", 2, 4, 4)
proc3.submit()

for item in fr.all_geom:
    print(item["data"]["energy"])
    geom = Geometry(item["atoms"])