Release 2.0.0

.gitignore

@@ -13,6 +13,7 @@ venv/
 .coverage
 .coverage.*
 .cache
+.hypothesis
 coverage.xml
 
 # Sphinx documentation

CHANGELOG.rst

@@ -1,6 +1,32 @@
 Changelog
 =========
 
+Release 2.0.0
+-------------
+
+New Jobs:
+    - Automatic QM region selection for QM/MM.
+    - Job that tries to find a new reaction starting from a transition state guess only.
+    - Job that carries out a fast dissociation reaction trial protocol after optimizing the input structure.
+    - Remove `scine_step_refinement` job.
+
+New Settings:
+    - Add the option `allow_exhaustive_product_decomposition` to jobs that carry out reaction trials, which allows products to decompose and re-optimize them until no further decomposition is observed.
+    - Add the option `always_add_barrierless_step_for_reactive_complex` to jobs that carry out reaction trials, which enables that a barrierless elementary step is added for the reactive complex formation of a bimolecular reaction irrespective of the complexation energy.
+    - Add option `store_structures_with_frequency` and `store_structures_with_fraction` that allow storing a portion of structures per sub-task.
+    - Add option `spin_propensity_ts_check` to `scine_react_ts_guess` job to specify a spin multiplicity range to be checked for the transition state different to the spin multiplicity range to be checked for the reactants and products (`spin_propensity_check`)
+
+Technical changes:
+    - Ensure that the calculated spin states are considered in the calculation of the dissociation energy in the `DissociationCut` jobs and in structure optimizing jobs (`GeometryOptimization` and `ReactTsGuess`)
+    - Write normalized modes in database.
+    - Improve dependency handling and add more typehints.
+    - Optimize only unique structures of the endpoints of an IRC calculation.
+    - Deduplicate code for analyzing both sides of the IRC part in the `scine_react_job`.
+    - Stricter conditions to distribute charges if `expect_charge_separation` is set to `True` by prohibiting changing
+      already changed charge.
+    - Comply docstrings with numpy styling.
+    - Introduce Enums for ReaDuct calls.
+
 Release 1.3.0
 -------------
 

README.rst

@@ -242,7 +242,14 @@ release as archived on `Zenodo <https://doi.org/10.5281/zenodo.6695461>`_ (DOI
 In addition, we kindly request you to cite the following article when using Puffin:
 J. P. Unsleber, S. A. Grimmel, M. Reiher,
 "Chemoton 2.0: Autonomous Exploration of Chemical Reaction Networks",
-arXiv:2202.13011 [physics.chem-ph].
+*J. Chem. Theory Comput.*, **2022**, *18*, 5393.
+
+Furthermore, when publishing results obtained with any SCINE module, please cite the following paper:
+
+T. Weymuth, J. P. Unsleber, P. L. Türtscher, M. Steiner, J.-G. Sobez, C. H. Müller, M. Mörchen,
+V. Klasovita, S. A. Grimmel, M. Eckhoff, K.-S. Csizi, F. Bosia, M. Bensberg, M. Reiher,
+"SCINE—Software for chemical interaction networks", *J. Chem. Phys.*, **2024**, *160*, 222501
+(DOI `10.1063/5.0206974 <https://doi.org/10.1063/5.0206974>`_).
 
 
 Support and Contact

conanfile.txt

@@ -1,16 +1,18 @@
 [requires]
-scine_utilities/9.0.0@
-scine_molassembler/2.0.1@
-scine_database/1.3.0@
-scine_xtb_wrapper/3.0.0@
-scine_sparrow/5.0.0@
-scine_readuct/5.1.0@
+scine_utilities/10.0.0@
+scine_molassembler/3.0.0@
+scine_database/1.4.0@
+scine_xtb_wrapper/3.0.1@
+scine_sparrow/5.1.0@
+scine_swoose/2.1.0@
+scine_readuct/6.0.0@
 
 [options]
 scine_utilities:python=True
 scine_molassembler:python=True
 scine_database:python=True
 scine_sparrow:python=True
+scine_swoose:python=True
 scine_xtb_wrapper:python=True
 scine_readuct:python=True
 

container/apptainer/README.rst

@@ -52,3 +52,4 @@ A more complete run could thus look like this:
    apptainer run --bind /scratch/puffin:/socket \
                    --bind /scratch/puffin/jobs:/jobs \
                    puffin.sif
+

docs/source/api.rst

@@ -26,13 +26,6 @@ Module: jobloop
 .. automodule:: scine_puffin.jobloop
    :members:
 
-Module: jobs.templates.job
---------------------------
-
-.. automodule:: scine_puffin.jobs.templates.job
-   :members:
-
-
 Module: programs.program
 ------------------------
 

docs/source/conf.py

@@ -4,6 +4,8 @@
 import sphinx_rtd_theme
 import scine_puffin
 import recommonmark
+import sys
+import pathlib
 from recommonmark.transform import AutoStructify
 
 # -- General configuration ------------------------------------------------
@@ -25,7 +27,6 @@
     'sphinx.ext.githubpages',
     'sphinx.ext.intersphinx',
     'sphinx.ext.mathjax',
-    'sphinx_autodoc_typehints',
     'sphinx.ext.viewcode',
     'matplotlib.sphinxext.plot_directive',
     'numpydoc',
@@ -177,10 +178,21 @@
      'Miscellaneous'),
 ]
 
+autodoc_default_options = {
+    "autosummary": True,
+    "members": True,
+    "undoc-members": True,
+    "inherited-members": True,
+    "class-doc-from": "both",
+}
+
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
     'python': ('https://docs.python.org/3/', None),
     'numpy': ('https://numpy.org/doc/stable', None),
     'scipy': ('https://docs.scipy.org/doc/scipy-1.7.1/', None),
     'matplotlib': ('https://matplotlib.org/stable', None),
 }
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here.
+sys.path.insert(0, pathlib.Path(__file__).parents[2].resolve().as_posix())

docs/source/index.rst

@@ -15,4 +15,5 @@ Puffin
    programs
    jobs
    api
+   utilities
    changelog

docs/source/jobs.rst

@@ -12,77 +12,8 @@ the custom ``module``/``Calculator``.
 For more information  about this interface please see the documentation of
 SCINE: Core and possibly also SCINE: Utils.
 
-Conformer Generation
-````````````````````
-.. autoclass:: scine_puffin.jobs.conformers.Conformers
+.. autosummary::
+   :toctree: generated
+   :recursive:
 
-SCINE: AFIR
-```````````
-.. autoclass:: scine_puffin.jobs.scine_afir.ScineAfir
-
-SCINE: Bond Orders
-``````````````````
-.. autoclass:: scine_puffin.jobs.scine_bond_orders.ScineBondOrders
-
-SCINE: Geometry Optimization
-````````````````````````````
-.. autoclass:: scine_puffin.jobs.scine_geometry_optimization.ScineGeometryOptimization
-
-SCINE: Hessian
-``````````````````
-.. autoclass:: scine_puffin.jobs.scine_hessian.ScineHessian
-
-SCINE: IRC Scan
-``````````````````
-.. autoclass:: scine_puffin.jobs.scine_irc_scan.ScineIrcScan
-
-SCINE: Artificial Force Induced Reaction Probe
-``````````````````````````````````````````````
-.. autoclass:: scine_puffin.jobs.scine_react_complex_afir.ScineReactComplexAfir
-
-SCINE: Newton Trajectory Reaction Probe
-```````````````````````````````````````
-.. autoclass:: scine_puffin.jobs.scine_react_complex_nt.ScineReactComplexNt
-
-SCINE: Newton Trajectory 2 Reaction Probe
-`````````````````````````````````````````
-.. autoclass:: scine_puffin.jobs.scine_react_complex_nt2.ScineReactComplexNt2
-
-SCINE: Single Point
-```````````````````
-.. autoclass:: scine_puffin.jobs.scine_single_point.ScineSinglePoint
-
-SCINE: Transition State Optimization
-````````````````````````````````````
-.. autoclass:: scine_puffin.jobs.scine_ts_optimization.ScineTsOptimization
-
-Specialized Jobs
-----------------
-
-Gaussian: Partial Charges - Charge Model 5
-``````````````````````````````````````````
-.. autoclass:: scine_puffin.jobs.gaussian_charge_model_5.GaussianChargeModel5
-
-Orca: Geometry Optimization
-```````````````````````````
-.. autoclass:: scine_puffin.jobs.orca_geometry_optimization.OrcaGeometryOptimization
-
-Turbomole: Geometry Optimization
-`````````````````````````````````
-.. autoclass:: scine_puffin.jobs.turbomole_geometry_optimization.TurbomoleGeometryOptimization
-
-Turbomole: Single Point
-````````````````````````
-.. autoclass:: scine_puffin.jobs.turbomole_single_point.TurbomoleSinglePoint
-
-Turbomole: Hessian
-```````````````````
-.. autoclass:: scine_puffin.jobs.turbomole_hessian.TurbomoleHessian
-
-Turbomole: Bond Orders
-```````````````````````
-.. autoclass:: scine_puffin.jobs.turbomole_bond_orders.TurbomoleBondOrders
-
-Debugging: Sleep
-````````````````
-.. autoclass:: scine_puffin.jobs.sleep.Sleep
+   scine_puffin.jobs

docs/source/utilities.rst

@@ -0,0 +1,10 @@
+Utilities
+=========
+
+A module that gathers various modules with helper functions for multiple jobs.
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   scine_puffin.utilities

scine_puffin/_version.py

@@ -3,4 +3,4 @@
 See LICENSE.txt for details.
 """
 
-__version__ = "1.3.0"
+__version__ = "2.0.0"

scine_puffin/bootstrap.py

@@ -18,7 +18,7 @@ def bootstrap(config: Configuration):
 
     Parameters
     ----------.
-    config :: scine_puffin.config.Configuration
+    config : scine_puffin.config.Configuration
        The current configuration of the Puffin.
     """
     # Prepare directories
@@ -71,25 +71,9 @@ def bootstrap(config: Configuration):
     utils = Utils(config.programs()["utils"])
     utils.install(utils_build_dir, install_dir, config["resources"]["cores"])
 
-    # Install all other programs
-    for program_name, settings in config.programs().items():
-        if program_name in ['core', 'utils'] or not settings["available"]:
-            continue
-        print("")
-        print("Preparing " + program_name.capitalize() + "...")
-        print("")
-        module = importlib.import_module("scine_puffin.programs." + program_name)
-        class_ = getattr(module, program_name.capitalize())
-        program = class_(settings)
-        program_build_dir = os.path.join(build_dir, program_name)
-        program.install(program_build_dir, install_dir, config["resources"]["cores"])
-
-    # Setup environment
-    #  General setup
+    # setup Python path already now for crosslinking for Python type stubs
     env = {}
-    executables = {}
     python_version = sys.version_info
-    executables["OMP_NUM_THREADS"] = str(config["resources"]["cores"])
     env["PYTHONPATH"] = (
         os.path.join(
             install_dir,
@@ -121,6 +105,25 @@ def bootstrap(config: Configuration):
             "dist-packages",
         )
     )
+    os.environ["PYTHONPATH"] = env["PYTHONPATH"]
+
+    # Install all other programs
+    for program_name, settings in config.programs().items():
+        if program_name in ['core', 'utils'] or not settings["available"]:
+            continue
+        print("")
+        print("Preparing " + program_name.capitalize() + "...")
+        print("")
+        module = importlib.import_module("scine_puffin.programs." + program_name)
+        class_ = getattr(module, program_name.capitalize())
+        program = class_(settings)
+        program_build_dir = os.path.join(build_dir, program_name)
+        program.install(program_build_dir, install_dir, config["resources"]["cores"])
+
+    # Setup environment
+    #  General setup
+    executables = {}
+    executables["OMP_NUM_THREADS"] = str(config["resources"]["cores"])
     env["PATH"] = os.path.join(install_dir, "bin")
     env["LD_LIBRARY_PATH"] = os.path.join(install_dir, "lib") + ":" + os.path.join(install_dir, "lib64")
     env["SCINE_MODULE_PATH"] = os.path.join(install_dir, "lib") + ":" + os.path.join(install_dir, "lib64")