Worked Example

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();

PLAMS working folder: /path/plams/examples/COSMORSConformers/plams_workdir

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()

[19.03|15:33:37] JOB plamsjob STARTED
[19.03|15:33:37] Waiting for job plamsjob to finish
[19.03|15:33:37] JOB plamsjob/conformers_uff STARTED
[19.03|15:33:37] JOB plamsjob/additional_1 STARTED
[19.03|15:33:37] JOB plamsjob/adf_conformers STARTED
[19.03|15:33:37] JOB plamsjob/adf_filter STARTED
[19.03|15:33:37] Waiting for job conformers_uff to finish
[19.03|15:33:37] Waiting for job adf_filter to finish
[19.03|15:33:37] Waiting for job additional_1 to finish
[19.03|15:33:37] Waiting for job adf_conformers to finish
[19.03|15:33:44] JOB plamsjob/conformers_uff SUCCESSFUL
[19.03|15:33:45] JOB plamsjob/additional_1 SUCCESSFUL
[19.03|15:43:18] JOB plamsjob/adf_conformers SUCCESSFUL
[19.03|15:43:19] JOB plamsjob/adf_filter SUCCESSFUL
[19.03|15:43:19] JOB plamsjob/replay STARTED
... (PLAMS log lines truncated) ...

!amsview test_coskfs/acetic_acid_0.coskf

!amsview test_coskfs/acetic_acid_1.coskf