Complete Python code¶

#!/usr/bin/env amspython
# coding: utf-8

# ## Initial imports

from scm.plams.recipes.adfcosmorsconformers import ADFCOSMORSConfJob, ADFCOSMORSConfFilter
from scm.plams import Molecule, from_smiles, Settings, init, config, JobRunner
from scm.conformers import ConformersJob

# this line is not required in AMS2025+
init()


config.default_jobrunner = JobRunner(parallel=True, maxjobs=8)  # Set the default jobrunner to be parallel
config.default_jobmanager.settings.hashing = None  # Disable rerun prevention
config.job.runscript.nproc = 1  # Number of cores for each job
config.log.stdout = 1  # Suppress plams output


# ## Set up conformer generator

# First, we input the acetic acid molecule with the `from_smiles` function

mol = from_smiles("CC(=O)O")


# Now, we'll specify a conformer generator (identical to the default) that generates only 50 initial structures:

conf_sett = Settings()
conf_sett.input.AMS.Generator.RDKit
conf_sett.input.AMS.Generator.RDKit.InitialNConformers = 50
conf_job = ConformersJob(name="conformers_uff", molecule=mol, settings=conf_sett)


# Let's also specify an additional step to add to the default workflow.  Here, we'll add a DFTB geometry optimization.

dftb_sett = Settings()
dftb_sett.input.DFTB
dftb_sett.input.AMS.Task = "Optimize"


# The final thing we need to specify are filters.  Let's make three filters, the first to take a maximum of 20 conformers with a maximum energy range of 22 kcal/mol, the second with 10 conformers and 12 kcal/mol and the third with 5 conformers and 7 kcal/mol.

# ADFCOSMORSConfFilter(max number of conformers, max energy range)
fil1 = ADFCOSMORSConfFilter(20, 22)  # applied to UFF
fil2 = ADFCOSMORSConfFilter(10, 12)  # applied to DFTB
fil3 = ADFCOSMORSConfFilter(5, 7)  # applied to ADF gas phase


# ## Run COSMO-RS conformers job

# Finally, we give this information to the `ADFCOSMORSConfJob` class.  We also specify the name of the coskf files as well as the directory in which we'll find them after the calculations complete.

job = ADFCOSMORSConfJob(
    mol,
    conf_gen=conf_job,
    first_filter=fil1,
    additional=[(dftb_sett, fil2)],
    final_filter=fil3,
    coskf_name="acetic_acid",
    coskf_dir="test_coskfs",
)
job.run()
job.results.wait()