SCM-NV · mhellstr · Feb 13, 2026 · Feb 13, 2026 · Feb 13, 2026 · Feb 20, 2026
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -59,7 +59,8 @@ uv pip install $AMSHOME/scripting/scm/amspipe
 ```
 or:
 ```bash
-uv pip install $AMSHOME/scripting/wheels/amspipe-0.1-py3-none-any.whl
+uv pip install --index-url "https://<scm-username>:<pwd>@downloads.scm.com/Downloads/packages/uv/channels/2026.1/simple/" \
+  scm-amspipe scm-external-engines plams
 ```
 To run tests use:
 ```bash

diff --git a/doc/source/components/functions.rst b/doc/source/components/functions.rst
@@ -9,6 +9,7 @@ This chapter gathers information about public functions that can be used in PLAM
 
 .. autofunction:: init
 .. autofunction:: finish
+.. autofunction:: jobs_in_directory
 .. autofunction:: load
 .. autofunction:: load_all
 .. autofunction:: read_molecules

diff --git a/doc/source/components/settings.rst b/doc/source/components/settings.rst
@@ -15,7 +15,7 @@ Any derived settings class is interchangeable with the base |Settings| class of
 Tree-like structure
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 
-The |Settings| class is based on the regular Python dictionary (built-in class :class:`dict`, tutorial can be found :ref:`here<tut-dictionaries>`) and in many aspects works just like it::
+The |Settings| class is based on the regular Python dictionary (built-in class :class:`dict`, tutorial can be found `here <https://docs.python.org/3/tutorial/datastructures.html#tut-dictionaries>`__) and in many aspects works just like it::
 
     >>> s = Settings()
     >>> s['abc'] = 283
@@ -190,7 +190,16 @@ For example:
     config.job.pickle = False
     config.default_jobrunner = JobRunner(parallel=True, maxjobs=8)
 
-The structure for the defined options on the nested settings objects is defined below.
+A context manager ``config_context`` is provided to override the global ``config`` within a specific scope:
+
+.. autofunction:: scm.plams.core.functions.config_context
+
+This can be useful for temporarily disabling or changing global settings.
+If you use this context manager, obtain ``config`` with the ``get_config`` function:
+
+.. autofunction:: scm.plams.core.functions.get_config
+
+The structure for all the defined options on the nested settings objects is defined below.
 
 .. autoclass:: ConfigSettings
 

diff --git a/doc/source/components/utils.rst b/doc/source/components/utils.rst
@@ -57,6 +57,8 @@ the :ref:`BalanceReactionEquationsExample` example.
 
 .. autofunction:: scm.plams.tools.reaction.balance
 
+.. autoclass:: scm.plams.tools.reaction.ReactionEquation
+
 
 Older functions:
 

diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -191,7 +191,6 @@ def setup(app):
 
 extensions += [
     "sphinx.ext.autodoc",
-    "sphinx.ext.intersphinx",
     "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",
     "sphinx_copybutton",
@@ -206,9 +205,6 @@ def setup(app):
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = "sphinx"
 
-# configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {"python3": ("http://docs.python.org/3.8", None)}
-
 autodoc_default_options = {"members": True, "private-members": True, "special-members": True}
 autodoc_member_order = "bysource"
 autodoc_typehints = "description"

diff --git a/doc/source/examples/ADFFrag/ADFFrag.rst b/doc/source/examples/ADFFrag/ADFFrag.rst
@@ -21,6 +21,7 @@ It simply redirects the usual |AMSResults| methods to the results of the full sy
 
 
 .. literalinclude:: ../../../../src/scm/plams/recipes/adffragment.py
+   :language: python
 
 .. include:: ADFFrag.common_header.rst
 .. include:: adffrag.ipynb.rst

diff --git a/doc/source/examples/ADFNBO/ADFNBO.rst b/doc/source/examples/ADFNBO/ADFNBO.rst
@@ -18,7 +18,8 @@ No specialized |Results| subclass is defined for ``ADFNBOJob``.
 The source code of the whole module:
 
 .. literalinclude:: ../../../../src/scm/plams/recipes/adfnbo.py
+   :language: python
 
 .. include:: ADFNBO.common_header.rst
 .. include:: ADFNBO.ipynb.rst
-.. include:: ADFNBO.common_footer.rst
+.. include:: ADFNBO.common_footer.rst
diff --git a/doc/source/examples/AMSPlumedMD/ams_plumed.ipynb.rst b/doc/source/examples/AMSPlumedMD/ams_plumed.ipynb.rst
@@ -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
@@ -158,6 +161,8 @@ Calculation settings
      End
    End
 
+   RNGSeed 12345
+
    Restraints
      Distance 1 2 1.2661886450379047 1.0
    End
@@ -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
 ~~~~~~~~~~~~~~~~~~~~~~
@@ -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
 
@@ -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
 
@@ -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
diff --git a/doc/source/examples/AMSPlumedMD/ams_plumed_files/ams_plumed_11_0.png b/doc/source/examples/AMSPlumedMD/ams_plumed_files/ams_plumed_11_0.png
diff --git a/doc/source/examples/AMSPlumedMD/ams_plumed_files/ams_plumed_13_0.png b/doc/source/examples/AMSPlumedMD/ams_plumed_files/ams_plumed_13_0.png
diff --git a/doc/source/examples/AMSPlumedMD/ams_plumed_files/ams_plumed_14_0.png b/doc/source/examples/AMSPlumedMD/ams_plumed_files/ams_plumed_14_0.png
diff --git a/doc/source/examples/AMSPlumedMD/ams_plumed_files/ams_plumed_16_1.png b/doc/source/examples/AMSPlumedMD/ams_plumed_files/ams_plumed_16_1.png
diff --git a/doc/source/examples/AMSPlumedMD/ams_plumed_files/ams_plumed_18_1.png b/doc/source/examples/AMSPlumedMD/ams_plumed_files/ams_plumed_18_1.png
diff --git a/doc/source/examples/BAND_NiO_HubbardU.rst b/doc/source/examples/BAND_NiO_HubbardU.rst
@@ -5,16 +5,22 @@ BAND: NiO with DFT+U
 
 The hubbard method is a way to calculate band gaps for metal oxides for which a normal GGA fails to predict a band gap.
 
-**Example usage:** (:download:`Download BAND_NiO_HubbardU.py <../../../examples/BAND_NiO_HubbardU.py>`)
+**Example usage:**
+
+* Download :download:`BAND_NiO_HubbardU.py <../../../examples/BAND_NiO_HubbardU.py>` (run as ``$AMSBIN/amspython BAND_NiO_HubbardU.py``).
 
 .. literalinclude:: ../../../examples/BAND_NiO_HubbardU.py
 	:language: python
 
 Results
 -------
 
+The following results appear upon execution.
+
 .. parsed-literal::
 
    Top of valence band:       -6.67 eV
    Bottom of conduction band: -5.41 eV
    Band gap:                  1.25 eV
+
+A folder called ``NiO`` is also created containing other files.
diff --git a/doc/source/examples/BalanceReactionEquations/BalanceReactionEquations.ipynb.rst b/doc/source/examples/BalanceReactionEquations/BalanceReactionEquations.ipynb.rst
@@ -137,23 +137,6 @@ Reaction that cannot be balanced
    reaction.coeffs=None
    reaction.message='Empty nullspace'
 
-Sympy method
-~~~~~~~~~~~~
-
-By default, a native method is used to compute the nullspace. Optionally, this can be done with sympy. The result should be the same.
-
-.. code:: ipython3
-
-   reactants = ["C9H8O4", "H2O"]
-   products = ["C2H4O2", "C7H6O3"]
-
-   reaction = balance(reactants, products, method="sympy")
-   print(reaction)
-
-::
-
-   1 C9H8O4 + 1 H2O => 1 C2H4O2 + 1 C7H6O3
-
 Balance reactions with charged species
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

diff --git a/doc/source/examples/BandFrag/BandFrag.rst b/doc/source/examples/BandFrag/BandFrag.rst
@@ -20,6 +20,7 @@ It simply redirects the usual |AMSResults| methods to the results of the full sy
 A derived subclass |NOCVBandFragmentJob| is also provided. It can be usefull for generating NOCV plots after the PEDA-NOCV calculation.
 
 .. literalinclude:: ../../../../src/scm/plams/recipes/bandfragment.py
+   :language: python
 
 .. include:: BandFrag.common_header.rst
 .. include:: bandfrag.ipynb.rst

diff --git a/doc/source/examples/COSMORSCompound/COSMORSCompound.rst b/doc/source/examples/COSMORSCompound/COSMORSCompound.rst
@@ -15,10 +15,11 @@ Source code for ``ADFCOSMORSCompound``
 .. dropdown::
 
     .. literalinclude:: ../../../../src/scm/plams/recipes/adfcosmorscompound.py
+       :language: python
 
 Brief API Documentation
 -----------------------
 
 .. automodule:: scm.plams.recipes.adfcosmorscompound
     :no-special-members:
-    :exclude-members: _result_type, __init__, new_children, postrun, _get_radii, adf_settings
+    :exclude-members: _result_type, __init__, new_children, postrun, _get_radii, adf_settings
diff --git a/doc/source/examples/COSMORSCompound/cosmors_compound.ipynb.rst b/doc/source/examples/COSMORSCompound/cosmors_compound.ipynb.rst
@@ -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
 
@@ -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
@@ -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
 
@@ -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
Original file line number	Diff line number	Diff line change
Expand Up		@@ -57,6 +57,8 @@ the :ref:`BalanceReactionEquationsExample` example.

		.. autofunction:: scm.plams.tools.reaction.balance

		.. autoclass:: scm.plams.tools.reaction.ReactionEquation


		Older functions:

Expand Down