Release 3.1.0

qcscine · Nov 20, 2023 · 53ae96e · 53ae96e
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,6 +1,22 @@
 Changelog
 =========
 
+Release 3.1.0
+-------------
+
+New features
+ - Add SteeringWheel infrastructure for actively steering explorations.
+ - Add ThermoAggregateHousekeeping gear which allows sorting of structures with a frequency check.
+ - AtomPairFunctionalGroupFilter for specifying pairs of functional groups that are allowed to react.
+ - CentralSiteFilter to focus explorations on certain elements, suited well for homogeneous catalysis.
+ - New ElementaryStepGear to focus explorations on certain structures.
+ - New ReactiveSiteFilter based on substructures provided in .xyz or .mol files. 
+ - The KineticModelingGear is now able to setup jobs for the puffin interface of the ReactionMechanismSimulator.
+
+Changes
+ - Queries and utility functions related only to the database are moved to the `scine_database` package. The functionality here is deprecated and the unittests are removed.
+ - Update address in license
+
 Release 3.0.0
 -------------
 

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,4 +1,4 @@
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group
 
 Redistribution and use in source and binary forms, with or without modification,
 are permitted provided that the following conditions are met:

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -11,5 +11,8 @@ recursive-include docs *.rst conf.py Makefile make.bat
 include versioneer.py
 include scine_chemoton/_version.py
 
+# Remove test files from install:
+prune tests
+
 # If including data files in the package, add them like:
-include scine_chemoton/tests/resources
+include scine_chemoton/resources/*xyz
diff --git a/conanfile.txt b/conanfile.txt
@@ -1,7 +1,7 @@
 [requires]
-scine_utilities/8.0.0@
-scine_molassembler/2.0.0@
-scine_database/1.2.0@
+scine_utilities/9.0.0@
+scine_molassembler/2.0.1@
+scine_database/1.3.0@
 
 [options]
 scine_utilities:python=True

diff --git a/dev b/dev
diff --git a/docs/source/api/api.rst b/docs/source/api/api.rst
@@ -7,4 +7,5 @@ Chemoton API
 
    engine
    gears
+   steering_wheel
    utilities
diff --git a/docs/source/api/gears.rst b/docs/source/api/gears.rst
@@ -23,6 +23,7 @@ Elementary Steps Exploration
 .. automodule:: scine_chemoton.gears.elementary_steps.brute_force
 .. automodule:: scine_chemoton.gears.elementary_steps.minimal
 .. automodule:: scine_chemoton.gears.elementary_steps.minimum_energy_conformer
+.. automodule:: scine_chemoton.gears.elementary_steps.selected_structures
 .. autoclass:: scine_chemoton.gears.elementary_steps.trial_generator.TrialGenerator
 .. automodule:: scine_chemoton.gears.elementary_steps.trial_generator.bond_based
 .. automodule:: scine_chemoton.gears.elementary_steps.trial_generator.fragment_based

diff --git a/docs/source/api/steering_wheel.rst b/docs/source/api/steering_wheel.rst
@@ -0,0 +1,30 @@
+Steering Wheel
+==============
+
+Interfaces
+----------
+.. autoclass:: scine_chemoton.steering_wheel.SteeringWheel
+.. autoclass:: scine_chemoton.steering_wheel.selections.Selection
+.. autoclass:: scine_chemoton.steering_wheel.selections.SelectionAndArray
+.. autoclass:: scine_chemoton.steering_wheel.selections.SelectionOrArray
+.. autoclass:: scine_chemoton.steering_wheel.network_expansions.NetworkExpansion
+
+Data Structures
+---------------
+.. automodule:: scine_chemoton.steering_wheel.datastructures
+
+Implementations
+---------------
+
+Selections
+~~~~~~~~~~
+.. automodule:: scine_chemoton.steering_wheel.selections.input_selections
+.. automodule:: scine_chemoton.steering_wheel.selections.basics
+.. automodule:: scine_chemoton.steering_wheel.selections.conformers
+.. automodule:: scine_chemoton.steering_wheel.selections.organometallic_complexes
+
+Network Expansions
+~~~~~~~~~~~~~~~~~~
+.. automodule:: scine_chemoton.steering_wheel.network_expansions.basics
+.. automodule:: scine_chemoton.steering_wheel.network_expansions.conformers
+.. automodule:: scine_chemoton.steering_wheel.network_expansions.reactions
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -48,7 +48,7 @@
 
 # General information about the project.
 project = "Chemoton"
-copyright = "2019, ETH Zurich, Laboratory for Physical Chemistry, Reiher Group"
+copyright = "ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group"
 author = "Reiher Group"
 
 # The version info for the project you're documenting, acts as replacement for

diff --git a/pytest.ini b/pytest.ini
@@ -0,0 +1,7 @@
+[pytest]
+filterwarnings =
+    error
+    ignore::ResourceWarning
+markers =
+    slow: marks tests as slow (deselect with '-m "not slow"')
+    serial
diff --git a/scine_chemoton/__init__.py b/scine_chemoton/__init__.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 __copyright__ = """ This code is licensed under the 3-clause BSD license.
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 See LICENSE.txt for details.
 """
 

diff --git a/scine_chemoton/__main__.py b/scine_chemoton/__main__.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 __copyright__ = """ This code is licensed under the 3-clause BSD license.
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 See LICENSE.txt for details.
 """
 
@@ -16,11 +16,10 @@
 
 # Third party imports
 import scine_database as db
-import scine_utilities as utils
 
 # Local application imports
 from scine_chemoton.utilities.insert_initial_structure import insert_initial_structure
-from scine_chemoton.default_settings import default_nt_settings
+from scine_chemoton.default_settings import default_nt_settings, default_cutting_settings, default_opt_settings
 from scine_chemoton.engine import Engine
 from scine_chemoton.gears.scheduler import Scheduler
 from scine_chemoton.gears.thermo import BasicThermoDataCompletion
@@ -74,34 +73,24 @@
     manager.init()
     time.sleep(1.0)
     # Load initial data
-    methanol = pkg_resources.resource_filename("scine_chemoton", "tests/resources/methanol.xyz")
-    formaldehyde = pkg_resources.resource_filename("scine_chemoton", "tests/resources/formaldehyde.xyz")
+    methanol = pkg_resources.resource_filename("scine_chemoton", os.path.join("resources", "methanol.xyz"))
+    formaldehyde = pkg_resources.resource_filename("scine_chemoton", os.path.join("resources", "formaldehyde.xyz"))
 
     structure, calculation = insert_initial_structure(
         manager,
         methanol,
         0,
         1,
         model,
-        settings=utils.ValueCollection(
-            {
-                "convergence_max_iterations": 1000,
-                "bfgs_use_trust_radius": True,
-            }
-        ),
+        settings=default_opt_settings()
     )
     structure, calculation = insert_initial_structure(
         manager,
         formaldehyde,
         0,
         1,
         model,
-        settings=utils.ValueCollection(
-            {
-                "convergence_max_iterations": 1000,
-                "bfgs_use_trust_radius": True,
-            }
-        ),
+        settings=default_opt_settings()
     )
 
 
@@ -131,13 +120,7 @@
 conformer_gear.options.model = model
 conformer_gear.options.conformer_job = db.Job("conformers")
 conformer_gear.options.minimization_job = db.Job("scine_geometry_optimization")
-conformer_gear.options.minimization_settings = utils.ValueCollection(
-    {
-        "convergence_max_iterations": 1000,
-        "bfgs_use_trust_radius": True,
-        "geoopt_coordinate_system": "cartesianWithoutRotTrans",
-    }
-)
+conformer_gear.options.minimization_settings = default_opt_settings()
 conformer_engine = Engine(credentials)
 conformer_engine.set_gear(conformer_gear)
 conformer_engine.run()
@@ -177,7 +160,7 @@
 dissociations_gear.trial_generator.further_exploration_filter = FurtherExplorationFilter()
 dissociations_gear.trial_generator.options.model = model
 dissociations_gear.trial_generator.options.job = db.Job("scine_dissociation_cut")
-dissociations_gear.trial_generator.options.cutting_job_settings = utils.ValueCollection({})
+dissociations_gear.trial_generator.options.cutting_job_settings = default_cutting_settings()
 dissociations_gear.trial_generator.options.min_bond_dissociations = 1
 dissociations_gear.trial_generator.options.max_bond_dissociations = 1
 dissociations_gear.trial_generator.options.enable_further_explorations = False

diff --git a/scine_chemoton/_version.py b/scine_chemoton/_version.py
@@ -1,6 +1,6 @@
 __copyright__ = """ This code is licensed under the 3-clause BSD license.
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 See LICENSE.txt for details.
 """
 
-__version__ = "3.0.0"
+__version__ = "3.1.0"
diff --git a/scine_chemoton/default_settings.py b/scine_chemoton/default_settings.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 __copyright__ = """ This code is licensed under the 3-clause BSD license.
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 See LICENSE.txt for details.
 """
 
@@ -65,3 +65,37 @@ def default_nt_settings() -> utils.ValueCollection:
         # # # Settings for the optimisation of the reactive complex
         "rcopt_convergence_max_iterations": 1000,
     })
+
+
+def default_cutting_settings() -> utils.ValueCollection:
+    return utils.ValueCollection({
+        "opt_convergence_delta_value": 1.0e-06,
+        "opt_convergence_gradient_max_coefficient": 0.0002,
+        "opt_convergence_gradient_rms": 0.0001,
+        "opt_convergence_max_iterations": 1000,
+        "opt_convergence_requirement": 3,
+        "opt_convergence_step_max_coefficient": 0.002,
+        "opt_convergence_step_rms": 0.001,
+        "rcopt_convergence_delta_value": 1.0e-06,
+        "rcopt_convergence_gradient_max_coefficient": 0.0002,
+        "rcopt_convergence_gradient_rms": 0.0001,
+        "rcopt_convergence_max_iterations": 1000,
+        "rcopt_convergence_requirement": 3,
+        "rcopt_convergence_step_max_coefficient": 0.002,
+        "rcopt_convergence_step_rms": 0.001,
+    })
+
+
+def default_opt_settings() -> utils.ValueCollection:
+    return utils.ValueCollection({
+        "convergence_max_iterations": 1000,
+        "convergence_step_max_coefficient": 2.0e-3,
+        "convergence_step_rms": 1.0e-3,
+        "convergence_gradient_max_coefficient": 2.0e-4,
+        "convergence_gradient_rms": 1.0e-4,
+        "convergence_requirement": 3,
+        "convergence_delta_value": 1e-6,
+        "geoopt_coordinate_system": "cartesianWithoutRotTrans",
+        "bfgs_use_trust_radius": True,
+        "bfgs_trust_radius": 0.4,
+    })
diff --git a/scine_chemoton/engine.py b/scine_chemoton/engine.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 __copyright__ = """ This code is licensed under the 3-clause BSD license.
-Copyright ETH Zurich, Laboratory of Physical Chemistry, Reiher Group.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
 See LICENSE.txt for details.
 """
+7 −0		CHANGELOG.rst
+1 −1		CONTRIBUTING.rst
+1 −1		LICENSE.txt
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+3 −3		conan/base.py
+1 −1		conan/glue/gtest.cmake
+1 −1		conan/hook.cmake
+2 −2		conan/utils.py
-Original file line number
+Diff line change
@@ Expand Up / @@ -7,4 +7,5 @@ Chemoton API @@
        engine
        gears
+       steering_wheel
        utilities