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dormrod merged 4 commits into from
Mar 11, 2026
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ams plumed example minor tweaks #372

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8b32897
Added missing plt.show() in ams_plumed example. SO--
Mar 11, 2026
5f960d7
Fixed missing plt.show() call and added rng seed for reproducibility …
Mar 11, 2026
26e19f2
Re-run and regenerate plumed notebook SO--
dormrod Mar 11, 2026
a0e2d32
Update cosmo-rs conformers example SO--
dormrod Mar 11, 2026
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46 changes: 26 additions & 20 deletions doc/source/examples/AMSPlumedMD/ams_plumed.ipynb.rst
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Expand Up @@ -100,6 +100,9 @@ Calculation settings
# s.input.MLPotential.Model = 'M3GNet-UP-2022' # if you have ML potential license and M3Gnet installed
# s.input.dftb # if you have a DFTB license

# setting the random seed to ensure reproducibility. You should generally not include this
s.input.ams.RNGSeed = 12345

# MD settings
s.input.ams.Task = "MolecularDynamics"
s.input.ams.MolecularDynamics.NSteps = nsteps
Expand Down Expand Up @@ -158,6 +161,8 @@ Calculation settings
End
End

RNGSeed 12345

Restraints
Distance 1 2 1.2661886450379047 1.0
End
Expand Down Expand Up @@ -188,10 +193,10 @@ Run the job

::

[12.01|16:08:19] JOB dissociating-carbonic-acid STARTED
[12.01|16:08:19] JOB dissociating-carbonic-acid RUNNING
[12.01|16:08:20] JOB dissociating-carbonic-acid FINISHED
[12.01|16:08:21] JOB dissociating-carbonic-acid SUCCESSFUL
[11.03|13:47:36] JOB dissociating-carbonic-acid STARTED
[11.03|13:47:36] JOB dissociating-carbonic-acid RUNNING
[11.03|13:47:37] JOB dissociating-carbonic-acid FINISHED
[11.03|13:47:37] JOB dissociating-carbonic-acid SUCCESSFUL

Analyze the trajectory
~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -222,6 +227,7 @@ Extract the O3H6 distances at each stored frame, and plot some of the molecules
view(mol, ax=axes[i_ax]) # mol is a PLAMS Molecule
axes[i_ax].set_title(f"frame {i}")
i_ax += 1
plt.show()

.. figure:: ams_plumed_files/ams_plumed_11_0.png

Expand Down Expand Up @@ -277,10 +283,10 @@ PLAMS makes it easy to extract any frame from an MD trajectory. As an example, l

::

[12.01|16:08:27] JOB ts-search STARTED
[12.01|16:08:27] JOB ts-search RUNNING
[12.01|16:09:07] JOB ts-search FINISHED
[12.01|16:09:07] JOB ts-search SUCCESSFUL
[11.03|13:47:44] JOB ts-search STARTED
[11.03|13:47:44] JOB ts-search RUNNING
[11.03|13:48:11] JOB ts-search FINISHED
[11.03|13:48:11] JOB ts-search SUCCESSFUL

.. code:: ipython3

Expand All @@ -303,15 +309,15 @@ PLAMS makes it easy to extract any frame from an MD trajectory. As an example, l
::

Frequencies (at a TS there should be 1 imaginary [given as negative])
-1427.002 cm^-1
307.787 cm^-1
364.254 cm^-1
545.556 cm^-1
703.642 cm^-1
744.026 cm^-1
876.638 cm^-1
1080.218 cm^-1
1117.900 cm^-1
1760.451 cm^-1
2064.254 cm^-1
3475.147 cm^-1
-1431.372 cm^-1
321.023 cm^-1
367.843 cm^-1
544.548 cm^-1
703.407 cm^-1
742.540 cm^-1
877.320 cm^-1
1080.540 cm^-1
1124.406 cm^-1
1758.547 cm^-1
2063.143 cm^-1
3472.487 cm^-1
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38 changes: 22 additions & 16 deletions doc/source/examples/COSMORSConformers/cosmors_conformers.ipynb.rst
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Expand Up @@ -27,11 +27,16 @@ Initial imports
Set up conformer generator
~~~~~~~~~~~~~~~~~~~~~~~~~~

First, we input the acetic acid molecule with the ``from_smiles`` function
First, we input the acetic acid molecule with the ``from_smiles`` function and provide the optional compound information that can be written to the COSKF file.

.. code:: ipython3

mol = from_smiles("CC(=O)O")
mol_info = {
"CAS": "64-19-7",
"IUPAC": "Acetic acid",
"Other Name": "Ethanoic acid; Ethylic acid",
}

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

Expand Down Expand Up @@ -74,27 +79,28 @@ Finally, we give this information to the ``ADFCOSMORSConfJob`` class. We also sp
final_filter=fil3,
coskf_name="acetic_acid",
coskf_dir="test_coskfs",
mol_info=mol_info,
)
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
[11.03|14:09:35] JOB plamsjob STARTED
[11.03|14:09:35] Waiting for job plamsjob to finish
[11.03|14:09:35] JOB plamsjob/conformers_uff STARTED
[11.03|14:09:35] JOB plamsjob/additional_1 STARTED
[11.03|14:09:35] JOB plamsjob/adf_conformers STARTED
[11.03|14:09:35] JOB plamsjob/adf_filter STARTED
[11.03|14:09:35] Waiting for job adf_filter to finish
[11.03|14:09:35] Waiting for job conformers_uff to finish
[11.03|14:09:35] Waiting for job additional_1 to finish
[11.03|14:09:35] Waiting for job adf_conformers to finish
[11.03|14:09:42] JOB plamsjob/conformers_uff SUCCESSFUL
[11.03|14:09:44] JOB plamsjob/additional_1 SUCCESSFUL
[11.03|14:20:21] JOB plamsjob/adf_conformers SUCCESSFUL
[11.03|14:20:22] JOB plamsjob/adf_filter SUCCESSFUL
[11.03|14:20:22] JOB plamsjob/replay STARTED
... (PLAMS log lines truncated) ...

.. code:: ipython3
Expand Down
58 changes: 32 additions & 26 deletions examples/AMSPlumedMD/ams_plumed.ipynb
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4 changes: 4 additions & 0 deletions examples/AMSPlumedMD/ams_plumed.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,6 +81,9 @@ def get_molecule():
# s.input.MLPotential.Model = 'M3GNet-UP-2022' # if you have ML potential license and M3Gnet installed
# s.input.dftb # if you have a DFTB license

# setting the random seed to ensure reproducibility. You should generally not include this
s.input.ams.RNGSeed = 12345

# MD settings
s.input.ams.Task = "MolecularDynamics"
s.input.ams.MolecularDynamics.NSteps = nsteps
Expand Down Expand Up @@ -140,6 +143,7 @@ def get_molecule():
view(mol, ax=axes[i_ax]) # mol is a PLAMS Molecule
axes[i_ax].set_title(f"frame {i}")
i_ax += 1
plt.show()


# The above pictures show how the H(6) approaches the O(3). At the end, the carbonic acid molecule has dissociated into CO2 and H2O.
Expand Down
56 changes: 35 additions & 21 deletions examples/COSMORSConformers/cosmors_conformers.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@
"id": "47bc1ee7-def3-43f2-8cf9-9a89f99988d6",
"metadata": {},
"source": [
"First, we input the acetic acid molecule with the `from_smiles` function"
"First, we input the acetic acid molecule with the `from_smiles` function and provide the optional compound information that can be written to the COSKF file."
]
},
{
Expand All @@ -67,7 +67,12 @@
"metadata": {},
"outputs": [],
"source": [
"mol = from_smiles(\"CC(=O)O\")"
"mol = from_smiles(\"CC(=O)O\")\n",
"mol_info = {\n",
" \"CAS\": \"64-19-7\",\n",
" \"IUPAC\": \"Acetic acid\",\n",
" \"Other Name\": \"Ethanoic acid; Ethylic acid\",\n",
"}"
]
},
{
Expand Down Expand Up @@ -158,23 +163,23 @@
"name": "stdout",
"output_type": "stream",
"text": [
"[19.03|15:33:37] JOB plamsjob STARTED\n",
"[19.03|15:33:37] Waiting for job plamsjob to finish\n",
"[19.03|15:33:37] JOB plamsjob/conformers_uff STARTED\n",
"[19.03|15:33:37] JOB plamsjob/additional_1 STARTED\n",
"[19.03|15:33:37] JOB plamsjob/adf_conformers STARTED\n",
"[19.03|15:33:37] JOB plamsjob/adf_filter STARTED\n",
"[19.03|15:33:37] Waiting for job conformers_uff to finish\n",
"[19.03|15:33:37] Waiting for job adf_filter to finish\n",
"[19.03|15:33:37] Waiting for job additional_1 to finish\n",
"[19.03|15:33:37] Waiting for job adf_conformers to finish\n",
"[19.03|15:33:44] JOB plamsjob/conformers_uff SUCCESSFUL\n",
"[19.03|15:33:45] JOB plamsjob/additional_1 SUCCESSFUL\n",
"[19.03|15:43:18] JOB plamsjob/adf_conformers SUCCESSFUL\n",
"[19.03|15:43:19] JOB plamsjob/adf_filter SUCCESSFUL\n",
"[19.03|15:43:19] JOB plamsjob/replay STARTED\n",
"[19.03|15:44:08] JOB plamsjob/replay SUCCESSFUL\n",
"[19.03|15:44:10] JOB plamsjob SUCCESSFUL\n"
"[11.03|14:09:35] JOB plamsjob STARTED\n",
"[11.03|14:09:35] Waiting for job plamsjob to finish\n",
"[11.03|14:09:35] JOB plamsjob/conformers_uff STARTED\n",
"[11.03|14:09:35] JOB plamsjob/additional_1 STARTED\n",
"[11.03|14:09:35] JOB plamsjob/adf_conformers STARTED\n",
"[11.03|14:09:35] JOB plamsjob/adf_filter STARTED\n",
"[11.03|14:09:35] Waiting for job adf_filter to finish\n",
"[11.03|14:09:35] Waiting for job conformers_uff to finish\n",
"[11.03|14:09:35] Waiting for job additional_1 to finish\n",
"[11.03|14:09:35] Waiting for job adf_conformers to finish\n",
"[11.03|14:09:42] JOB plamsjob/conformers_uff SUCCESSFUL\n",
"[11.03|14:09:44] JOB plamsjob/additional_1 SUCCESSFUL\n",
"[11.03|14:20:21] JOB plamsjob/adf_conformers SUCCESSFUL\n",
"[11.03|14:20:22] JOB plamsjob/adf_filter SUCCESSFUL\n",
"[11.03|14:20:22] JOB plamsjob/replay STARTED\n",
"[11.03|14:21:07] JOB plamsjob/replay SUCCESSFUL\n",
"[11.03|14:21:07] JOB plamsjob SUCCESSFUL\n"
]
}
],
Expand All @@ -187,14 +192,15 @@
" final_filter=fil3,\n",
" coskf_name=\"acetic_acid\",\n",
" coskf_dir=\"test_coskfs\",\n",
" mol_info=mol_info,\n",
")\n",
"job.run()\n",
"job.results.wait()"
]
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 8,
"id": "fa86e6a5-4098-4d31-96a4-5a338d62ccfc",
"metadata": {},
"outputs": [],
Expand All @@ -204,13 +210,21 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 9,
"id": "96fae9f9-5465-494c-accf-23bcb3783843",
"metadata": {},
"outputs": [],
"source": [
"!amsview test_coskfs/acetic_acid_1.coskf"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "7de25312-2f75-4209-a1e3-63ad4c388fd3",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand Down
8 changes: 7 additions & 1 deletion examples/COSMORSConformers/cosmors_conformers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,9 +19,14 @@

# ## Set up conformer generator

# First, we input the acetic acid molecule with the `from_smiles` function
# First, we input the acetic acid molecule with the `from_smiles` function and provide the optional compound information that can be written to the COSKF file.

mol = from_smiles("CC(=O)O")
mol_info = {
"CAS": "64-19-7",
"IUPAC": "Acetic acid",
"Other Name": "Ethanoic acid; Ethylic acid",
}


# Now, we'll specify a conformer generator (identical to the default) that generates only 50 initial structures:
Expand Down Expand Up @@ -59,6 +64,7 @@
final_filter=fil3,
coskf_name="acetic_acid",
coskf_dir="test_coskfs",
mol_info=mol_info,
)
job.run()
job.results.wait()
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