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dormrod merged 3 commits into from
Mar 13, 2026
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Update cosmo-rs examples #377

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2fd6f77
Update cosmors compound example
dormrod Mar 13, 2026
c53141e
Update property prediction example
dormrod Mar 13, 2026
cb65013
Update comment in conformers multiple molecules example
dormrod Mar 13, 2026
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105 changes: 60 additions & 45 deletions doc/source/examples/COSMORSCompound/cosmors_compound.ipynb.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -28,22 +28,31 @@ Enable the parallel calculation through ``JobRunner``. Here, we’ll assign one
config.job.runscript.nproc = 1 # Number of cores for each job
config.log.stdout = 1 # Suppress plams output

Optional compound metadata keyed by molecule name. This metadata is passed to ADFCOSMORSCompoundJob via ``mol_info``, written to the “Compound Data” section of the generated COSKF file, and used by AMSCrs GUI and ``pyCRS.Database`` to search compounds.

.. code:: ipython3

mol_info_by_name = {
"CO": {"CAS": "630-08-0", "IUPAC": "Carbon monoxide", "Other Name": ""},
"H2O": {"CAS": "7732-18-5", "IUPAC": "Water", "Other Name": ""},
}

.. code:: ipython3

molecules = read_molecules("./compounds_xyz")

results = []
for name, mol in molecules.items():
job = ADFCOSMORSCompoundJob(molecule=mol, coskf_name=name, coskf_dir="test_coskfs_xyz")
mol_info = mol_info_by_name.get(name)
job = ADFCOSMORSCompoundJob(molecule=mol, coskf_name=name, coskf_dir="test_coskfs_xyz", mol_info=mol_info)
results.append(job.run())

::

[19.03|15:14:40] JOB plamsjob STARTED
[19.03|15:14:40] JOB plamsjob STARTED
[19.03|15:14:40] JOB plamsjob/gas STARTED
[19.03|15:14:40] JOB plamsjob/solv STARTED
[19.03|15:14:40] JOB plamsjob/sigma STARTED
[13.03|09:03:55] JOB plamsjob STARTED
[13.03|09:03:55] JOB plamsjob STARTED
[13.03|09:03:55] JOB plamsjob/gas STARTED
[13.03|09:03:55] JOB plamsjob/solv STARTED

.. code:: ipython3

Expand All @@ -52,21 +61,23 @@ Enable the parallel calculation through ``JobRunner``. Here, we’ll assign one

::

[19.03|15:14:40] Waiting for job plamsjob to finish
[19.03|15:14:40] JOB plamsjob.002/gas STARTED
[19.03|15:14:40] JOB plamsjob.002/solv STARTED
[19.03|15:14:40] Waiting for job gas to finish
[19.03|15:14:40] JOB plamsjob.002/sigma STARTED
[19.03|15:14:40] Waiting for job solv to finish
[19.03|15:14:40] Waiting for job gas to finish
[19.03|15:14:40] Waiting for job solv to finish
[19.03|15:14:45] JOB plamsjob.002/gas SUCCESSFUL
[19.03|15:14:49] JOB plamsjob.002/solv SUCCESSFUL
[19.03|15:14:49] JOB plamsjob.002/sigma SUCCESSFUL
[19.03|15:14:50] JOB plamsjob.002 SUCCESSFUL
[19.03|15:14:57] JOB plamsjob/gas SUCCESSFUL
[19.03|15:15:10] JOB plamsjob/solv SUCCESSFUL
[19.03|15:15:10] JOB plamsjob/sigma SUCCESSFUL
[13.03|09:03:55] JOB plamsjob/sigma STARTED
[13.03|09:03:55] JOB plamsjob.002/gas STARTED
[13.03|09:03:55] Waiting for job plamsjob to finish
[13.03|09:03:55] JOB plamsjob.002/solv STARTED
[13.03|09:03:55] JOB plamsjob.002/sigma STARTED
[13.03|09:03:55] Waiting for job gas to finish
[13.03|09:03:55] Waiting for job solv to finish
[13.03|09:03:55] Waiting for job solv to finish
[13.03|09:03:55] Waiting for job gas to finish
[13.03|09:03:59] JOB plamsjob.002/gas SUCCESSFUL
[13.03|09:04:03] JOB plamsjob.002/solv SUCCESSFUL
[13.03|09:04:03] WARNING: Main KF file sigma.crskf not present in /path/plams/examples/COSMORSCompound/plams_workdir/plamsjob.002/sigma
[13.03|09:04:03] JOB plamsjob.002/sigma CRASHED
[13.03|09:04:05] JOB plamsjob.002 FAILED
[13.03|09:04:10] JOB plamsjob/gas SUCCESSFUL
[13.03|09:04:22] JOB plamsjob/solv SUCCESSFUL
[13.03|09:04:22] WARNING: Main KF file sigma.crskf not present in /path/plams/examples/COSMORSCompound/plams_workdir/plamsjob/sigma
... (PLAMS log lines truncated) ...

.. code:: ipython3
Expand Down Expand Up @@ -96,22 +107,24 @@ Lastly, we give this information to the ``ADFCOSMORSCompoundJob`` class, includi

results = []
for name, mol in molecules.items():
mol_info = mol_info_by_name.get(name)
job = ADFCOSMORSCompoundJob(
molecule=mol, # The initial structure
coskf_name=name, # a name to be used for coskf file
coskf_dir="test_coskfs_smiles", # a directory to put the .coskf files generated
preoptimization="GFN1-xTB", # perform preoptimize or not
singlepoint=False, # run a singlepoint in gasphase and solvation calculation without geometry optimization. Cannot be combined with `preoptimization`
name=name,
) # an optional name for the calculation directory
name=name, # an optional name for the calculation directory
mol_info=mol_info, # compound information to be stored in the Compound Data section of the COSKF file
)
results.append(job.run())

::

[19.03|15:15:16] JOB H2O STARTED
[19.03|15:15:16] JOB CO STARTED
[19.03|15:15:16] JOB H2O/preoptimization STARTED
[19.03|15:15:16] JOB CO/preoptimization STARTED
[13.03|09:04:25] JOB H2O STARTED
[13.03|09:04:25] JOB CO STARTED
[13.03|09:04:25] JOB H2O/preoptimization STARTED
[13.03|09:04:25] JOB H2O/gas STARTED

.. code:: ipython3

Expand All @@ -120,25 +133,27 @@ Lastly, we give this information to the ``ADFCOSMORSCompoundJob`` class, includi

::

[19.03|15:15:16] Waiting for job H2O to finish
[19.03|15:15:16] JOB CO/gas STARTED
[19.03|15:15:16] JOB H2O/gas STARTED
[19.03|15:15:16] JOB H2O/solv STARTED
[19.03|15:15:16] JOB CO/solv STARTED
[19.03|15:15:16] JOB H2O/sigma STARTED
[19.03|15:15:16] JOB CO/sigma STARTED
[19.03|15:15:16] Waiting for job gas to finish
[19.03|15:15:16] Waiting for job preoptimization to finish
[19.03|15:15:16] Waiting for job preoptimization to finish
[19.03|15:15:16] Waiting for job gas to finish
[19.03|15:15:16] Waiting for job solv to finish
[19.03|15:15:16] Waiting for job solv to finish
[19.03|15:15:16] JOB H2O/preoptimization SUCCESSFUL
[19.03|15:15:16] JOB CO/preoptimization SUCCESSFUL
[19.03|15:15:23] JOB H2O/gas SUCCESSFUL
[19.03|15:15:27] JOB H2O/solv SUCCESSFUL
[13.03|09:04:25] JOB H2O/solv STARTED
[13.03|09:04:25] Waiting for job H2O to finish
[13.03|09:04:25] JOB H2O/sigma STARTED
[13.03|09:04:25] JOB CO/preoptimization STARTED
[13.03|09:04:25] JOB CO/gas STARTED
[13.03|09:04:25] JOB CO/solv STARTED
[13.03|09:04:25] JOB CO/sigma STARTED
[13.03|09:04:25] Waiting for job gas to finish
[13.03|09:04:25] Waiting for job preoptimization to finish
[13.03|09:04:25] Waiting for job solv to finish
[13.03|09:04:25] Waiting for job preoptimization to finish
[13.03|09:04:25] Waiting for job gas to finish
[13.03|09:04:25] Waiting for job solv to finish
[13.03|09:04:26] JOB H2O/preoptimization SUCCESSFUL
[13.03|09:04:26] JOB CO/preoptimization SUCCESSFUL
[13.03|09:04:32] JOB H2O/gas SUCCESSFUL
[13.03|09:04:37] JOB H2O/solv SUCCESSFUL
[13.03|09:04:37] WARNING: Main KF file sigma.crskf not present in /path/plams/examples/COSMORSCompound/plams_workdir/H2O/sigma
... (PLAMS log lines truncated) ...
[19.03|15:15:31] Waiting for job CO to finish
[13.03|09:04:40] Waiting for job CO to finish
[13.03|09:05:06] WARNING: Main KF file sigma.crskf not present in /path/plams/examples/COSMORSCompound/plams_workdir/CO/sigma

.. code:: ipython3

Expand Down
4 changes: 3 additions & 1 deletion doc/source/examples/ConformersMultipleMolecules/conformers.ipynb.rst
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Expand Up @@ -180,10 +180,12 @@ Here we plot the three lowest-energy conformers.

.. figure:: conformers_files/conformers_23_0.png

You can also open the conformers in AMSmovie to browse all conformers 1000+ conformers:
You can also open the conformers in AMSmovie to browse all 1000+ conformers:

.. code:: ipython3

# Open AMSmovie in a Jupyter Notebook, equivalent to the shell command:
# amsmovie /path/plams/examples/ConformersMultipleMolecules/plams_workdir/conformers/conformers.rkf
!amsmovie {rkf}

Finally in AMS2025+, you can also inspect the conformer data using the JobAnalysis tool.
Expand Down
28 changes: 19 additions & 9 deletions doc/source/examples/PropertyPrediction/property_prediction.ipynb.rst
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Expand Up @@ -8,23 +8,30 @@ Initial imports

import pyCRS
import matplotlib.pyplot as plt
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
import math

IPythonConsole.ipython_useSVG = True
IPythonConsole.molSize = 150, 150
import scm.plams as plams

try:
from scm.plams import view # view molecule using AMSview in a Jupyter Notebook in AMS2026+
except ImportError:
from scm.plams import plot_molecule # plot molecule in a Jupyter Notebook in AMS2023+

def view(molecule, **kwargs):
plot_molecule(molecule)

Property prediction from SMILES (ethyl acetate)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code:: ipython3

from scm.plams import from_smiles

# smiles = 'CCO' # ethanol
smiles = "O=C(OCC)C" # ethyl acetate
rdkit_mol = Chem.MolFromSmiles(smiles)
rdkit_mol # show the molecule in a Jupyter notebook
view(plams.from_smiles(smiles), width=300, height=300)

.. figure:: property_prediction_files/property_prediction_3_0.svg
.. figure:: property_prediction_files/property_prediction_3_0.png

Temperature-independent properties
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand All @@ -49,7 +56,7 @@ Temperature-independent properties
criticalpressure : 38.243 bar
criticaltemp : 544.189 K
criticalvol : 0.271 L/mol
density : 0.894 kg/L (298.15 K)
density : 0.894 kg/L
dielectricconstant : 6.834
entropygas : 382.780 J/(mol K)
flashpoint : 265.005 K
Expand Down Expand Up @@ -165,7 +172,10 @@ Continuing from the previous example, you can also create e.g. a bar chart with

prop = "boilingpoint"
values = [mol.properties.get(prop, None) for mol in mols]
plt.barh(smiles_list, values)
filtered = [(s, v) for s, v in zip(smiles_list, values) if not math.isnan(v)]
smiles_plot, values_plot = zip(*filtered)

plt.barh(smiles_plot, values_plot)
plt.title("Boiling point [K]");

.. figure:: property_prediction_files/property_prediction_13_0.png
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