zincware · MrJulEnergy · May 22, 2023 · May 22, 2023 · May 22, 2023 · May 22, 2023
diff --git a/docs/source/_examples/01_Data_Loading_and_Selection.nblink b/docs/source/_examples/01_Data_Loading_and_Selection.nblink
@@ -0,0 +1,3 @@
+{
+    "path": "../../../examples/01_Data_Loading_and_Selection.ipynb"
+}
diff --git a/docs/source/_examples/02_Training_Models.nblink b/docs/source/_examples/02_Training_Models.nblink
@@ -0,0 +1,3 @@
+{
+    "path": "../../../examples/02_Training_Models.ipynb"
+}
diff --git a/docs/source/_examples/03_Analysing_Datasets_and_Model_Predictions.nblink b/docs/source/_examples/03_Analysing_Datasets_and_Model_Predictions.nblink
@@ -0,0 +1,3 @@
+{
+    "path": "../../../examples/03_Analysing_Datasets_and_Model_Predictions.ipynb"
+}
diff --git a/docs/source/_examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink b/docs/source/_examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.nblink
@@ -0,0 +1,3 @@
+{
+    "path": "../../../examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb"
+}
diff --git a/docs/source/_examples/05_Labeling_with_Calculators.nblink b/docs/source/_examples/05_Labeling_with_Calculators.nblink
@@ -0,0 +1,3 @@
+{
+    "path": "../../../examples/05_Labeling_with_Calculators.ipynb"
+}
diff --git a/docs/source/_examples/06_Bootstrapping_Datasets.nblink b/docs/source/_examples/06_Bootstrapping_Datasets.nblink
@@ -0,0 +1,3 @@
+{
+    "path": "../../../examples/06_Bootstrapping_Datasets.ipynb"
+}
diff --git a/docs/source/_examples/index.rst b/docs/source/_examples/index.rst
@@ -0,0 +1,30 @@
+
+
+.. _userdoc-examples:
+
+IPS is based on `ZnTrack <https://github.com/zincware/ZnTrack/>`_, and we suggest working through the examples on the ZnTrack docs to understand how to construct version controlled workflows.
+The notebooks contained in this section cover the functionality of IPS and assume familiarity with the basics of running workflows and experiments.
+
+The utility of IPS is best demonstrated by some worked examples.
+This section starts out with some introductory notebooks demonstrating the capabilities of the Nodes from each submodule.
+Later notebooks feature some more complex workflows which are closer to real world use case.
+All notebooks can be found in `/examples/docs`.
+
+
+.. image:: https://mybinder.org/badge_logo.svg
+   :alt: Binder
+   :target: https://mybinder.org/v2/gh/zincware/IPSuite/HEAD
+
+
+Examples
+========
+
+.. toctree::
+    :maxdepth: 0
+
+    01_Data_Loading_and_Selection
+    02_Training_Models
+    03_Analysing_Datasets_and_Model_Predictions
+    04_Molecular_Dynamics_Structure_Generation_and_Simulation
+    05_Labeling_with_Calculators
+    06_Bootstrapping_Datasets
diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.bin_property.rst
@@ -0,0 +1,26 @@
+ipsuite.analysis.bin\_property
+==============================
+
+.. automodule:: ipsuite.analysis.bin_property
+
+
+
+
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      DipoleHistogram
+      EnergyHistogram
+      EnergyUncertaintyHistogram
+      ForcesHistogram
+      ForcesUncertaintyHistogram
+      LabelHistogram
+      StressHistogram
diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.bond_stretch.rst
@@ -0,0 +1,20 @@
+ipsuite.analysis.bond\_stretch
+==============================
+
+.. automodule:: ipsuite.analysis.bond_stretch
+
+
+
+
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      BondStretchAnalyses
diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.ensemble.rst
@@ -0,0 +1,26 @@
+ipsuite.analysis.ensemble
+=========================
+
+.. automodule:: ipsuite.analysis.ensemble
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      plot_with_uncertainty
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      ModelEnsembleAnalysis
diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.md.rst
@@ -0,0 +1,20 @@
+ipsuite.analysis.md
+===================
+
+.. automodule:: ipsuite.analysis.md
+
+
+
+
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      AnalyseDensity
diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics.rst
@@ -0,0 +1,29 @@
+ipsuite.analysis.model.dynamics
+===============================
+
+.. automodule:: ipsuite.analysis.model.dynamics
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      run_stability_nve
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      BoxHeatUp
+      BoxScale
+      MDStability
+      RattleAnalysis
diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.dynamics_checks.rst
@@ -0,0 +1,24 @@
+ipsuite.analysis.model.dynamics\_checks
+=======================================
+
+.. automodule:: ipsuite.analysis.model.dynamics_checks
+
+
+
+
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      ConnectivityCheck
+      EnergySpikeCheck
+      NaNCheck
+      TemperatureCheck
+      ThresholdCheck
diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.math.rst
@@ -0,0 +1,20 @@
+ipsuite.analysis.model.math
+===========================
+
+.. automodule:: ipsuite.analysis.model.math
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      compute_intertia_tensor
+      compute_rot_forces
+      compute_trans_forces
+      decompose_stress_tensor
+      force_decomposition
diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.plots.rst
@@ -0,0 +1,19 @@
+ipsuite.analysis.model.plots
+============================
+
+.. automodule:: ipsuite.analysis.model.plots
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      density_scatter
+      get_figure
+      get_hist
+      get_histogram_figure
diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.predict.rst
@@ -0,0 +1,23 @@
+ipsuite.analysis.model.predict
+==============================
+
+.. automodule:: ipsuite.analysis.model.predict
+
+
+
+
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      ForceAngles
+      ForceDecomposition
+      Prediction
+      PredictionMetrics
diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.model.rst
@@ -0,0 +1,34 @@
+ipsuite.analysis.model
+======================
+
+.. automodule:: ipsuite.analysis.model
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :recursive:
+
+   ipsuite.analysis.model.dynamics
+   ipsuite.analysis.model.dynamics_checks
+   ipsuite.analysis.model.math
+   ipsuite.analysis.model.plots
+   ipsuite.analysis.model.predict
diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.rst
@@ -0,0 +1,35 @@
+ipsuite.analysis
+================
+
+.. automodule:: ipsuite.analysis
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :recursive:
+
+   ipsuite.analysis.bin_property
+   ipsuite.analysis.bond_stretch
+   ipsuite.analysis.ensemble
+   ipsuite.analysis.md
+   ipsuite.analysis.model
+   ipsuite.analysis.sensitivity
diff --git a/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst b/docs/source/_get_started/_autosummary/ipsuite.analysis.sensitivity.rst
@@ -0,0 +1,29 @@
+ipsuite.analysis.sensitivity
+============================
+
+.. automodule:: ipsuite.analysis.sensitivity
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      nonuniform_imshow
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      AnalyseGlobalForceSensitivity
+      AnalyseSingleForceSensitivity
+      IsConstraintMD
+      MoveSingleParticle
diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.base.rst b/docs/source/_get_started/_autosummary/ipsuite.base.base.rst
@@ -0,0 +1,26 @@
+ipsuite.base.base
+=================
+
+.. automodule:: ipsuite.base.base
+
+
+
+
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      AnalyseAtoms
+      AnalyseProcessAtoms
+      CheckBase
+      IPSNode
+      Mapping
+      ProcessAtoms
+      ProcessSingleAtom