diff --git a/docs/source/_examples/01_Data_Loading_and_Selection.nblink b/docs/source/_examples/01_Data_Loading_and_Selection.nblink new file mode 100644 index 00000000..4949dc69 --- /dev/null +++ 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 new file mode 100644 index 00000000..43debfed --- /dev/null +++ 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 new file mode 100644 index 00000000..f73a3f83 --- /dev/null +++ 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 new file mode 100644 index 00000000..48f1d5a1 --- /dev/null +++ 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 new file mode 100644 index 00000000..56af6e18 --- /dev/null +++ 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 new file mode 100644 index 00000000..56b6c559 --- /dev/null +++ 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 new file mode 100644 index 00000000..62bafde7 --- /dev/null +++ b/docs/source/_examples/index.rst @@ -0,0 +1,30 @@ + + +.. _userdoc-examples: + +IPS is based on `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 new file mode 100644 index 00000000..a8116ab2 --- /dev/null +++ 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 new file mode 100644 index 00000000..b66183d5 --- /dev/null +++ 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 new file mode 100644 index 00000000..55e9653f --- /dev/null +++ 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 new file mode 100644 index 00000000..29166462 --- /dev/null +++ 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 new file mode 100644 index 00000000..ded615c5 --- /dev/null +++ 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 new file mode 100644 index 00000000..f09235c8 --- /dev/null +++ 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 new file mode 100644 index 00000000..35998d9b --- /dev/null +++ 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 new file mode 100644 index 00000000..88abaceb --- /dev/null +++ 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 new file mode 100644 index 00000000..9357f2ac --- /dev/null +++ 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 new file mode 100644 index 00000000..8ee20ffd --- /dev/null +++ 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 new file mode 100644 index 00000000..345e9ded --- /dev/null +++ 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 new file mode 100644 index 00000000..9f95b8b9 --- /dev/null +++ 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 new file mode 100644 index 00000000..0ed40d88 --- /dev/null +++ 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 diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst b/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst new file mode 100644 index 00000000..720cbb0f --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.base.protocol.rst @@ -0,0 +1,22 @@ +ipsuite.base.protocol +===================== + +.. automodule:: ipsuite.base.protocol + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + HasAtoms + HasSelectedConfigurations + ProcessAtoms diff --git a/docs/source/_get_started/_autosummary/ipsuite.base.rst b/docs/source/_get_started/_autosummary/ipsuite.base.rst new file mode 100644 index 00000000..d3507240 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.base.rst @@ -0,0 +1,31 @@ +ipsuite.base +============ + +.. automodule:: ipsuite.base + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.base.base + ipsuite.base.protocol diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst new file mode 100644 index 00000000..fb43e7d5 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.random_displacements.rst @@ -0,0 +1,23 @@ +ipsuite.bootstrap.random\_displacements +======================================= + +.. automodule:: ipsuite.bootstrap.random_displacements + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + Bootstrap + RattleAtoms + RotateMolecules + TranslateMolecules diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst new file mode 100644 index 00000000..a8850783 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.rst @@ -0,0 +1,31 @@ +ipsuite.bootstrap +================= + +.. automodule:: ipsuite.bootstrap + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.bootstrap.random_displacements + ipsuite.bootstrap.surface_mods diff --git a/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst new file mode 100644 index 00000000..87ed5dbc --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.bootstrap.surface_mods.rst @@ -0,0 +1,27 @@ +ipsuite.bootstrap.surface\_mods +=============================== + +.. automodule:: ipsuite.bootstrap.surface_mods + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + plot_ture_vs_pred + + + + + + .. rubric:: Classes + + .. autosummary:: + + SurfaceRasterMetrics + SurfaceRasterScan diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst new file mode 100644 index 00000000..7a9298b6 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.apax_jax_md.rst @@ -0,0 +1,20 @@ +ipsuite.calculators.apax\_jax\_md +================================= + +.. automodule:: ipsuite.calculators.apax_jax_md + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + ApaxJaxMD diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst new file mode 100644 index 00000000..4d87733f --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_geoopt.rst @@ -0,0 +1,21 @@ +ipsuite.calculators.ase\_geoopt +=============================== + +.. automodule:: ipsuite.calculators.ase_geoopt + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + ASEGeoOpt + BatchASEGeoOpt diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst new file mode 100644 index 00000000..b829a446 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_md.rst @@ -0,0 +1,36 @@ +ipsuite.calculators.ase\_md +=========================== + +.. automodule:: ipsuite.calculators.ase_md + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + get_desc + update_metrics_dict + + + + + + .. rubric:: Classes + + .. autosummary:: + + ASEMD + BoxOscillatingRampModifier + FixedLayerConstraint + FixedSphereConstraint + LangevinThermostat + NPTThermostat + PressureRampModifier + RescaleBoxModifier + TemperatureOscillatingRampModifier + TemperatureRampModifier diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst new file mode 100644 index 00000000..3effc4a2 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.ase_standard.rst @@ -0,0 +1,22 @@ +ipsuite.calculators.ase\_standard +================================= + +.. automodule:: ipsuite.calculators.ase_standard + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + EMTCalculator + EMTSinglePoint + LJSinglePoint diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst new file mode 100644 index 00000000..16663e1f --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.cp2k.rst @@ -0,0 +1,21 @@ +ipsuite.calculators.cp2k +======================== + +.. automodule:: ipsuite.calculators.cp2k + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + CP2KSinglePoint + CP2KYaml diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst new file mode 100644 index 00000000..9e71f215 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.lammps.rst @@ -0,0 +1,20 @@ +ipsuite.calculators.lammps +========================== + +.. automodule:: ipsuite.calculators.lammps + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + LammpsSimulator diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst new file mode 100644 index 00000000..9fc2a7de --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.mix.rst @@ -0,0 +1,21 @@ +ipsuite.calculators.mix +======================= + +.. automodule:: ipsuite.calculators.mix + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + CalculatorNode + MixCalculator diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst new file mode 100644 index 00000000..3135f426 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.orca.rst @@ -0,0 +1,20 @@ +ipsuite.calculators.orca +======================== + +.. automodule:: ipsuite.calculators.orca + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + OrcaSinglePoint diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.rst new file mode 100644 index 00000000..3e90e425 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.rst @@ -0,0 +1,39 @@ +ipsuite.calculators +=================== + +.. automodule:: ipsuite.calculators + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.calculators.apax_jax_md + ipsuite.calculators.ase_geoopt + ipsuite.calculators.ase_md + ipsuite.calculators.ase_standard + ipsuite.calculators.cp2k + ipsuite.calculators.lammps + ipsuite.calculators.mix + ipsuite.calculators.orca + ipsuite.calculators.torch_d3 + ipsuite.calculators.xtb diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst new file mode 100644 index 00000000..128bf78d --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.torch_d3.rst @@ -0,0 +1,21 @@ +ipsuite.calculators.torch\_d3 +============================= + +.. automodule:: ipsuite.calculators.torch_d3 + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + TorchD3 + TorchDFTD3CalculatorNL diff --git a/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst b/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst new file mode 100644 index 00000000..a40e989e --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.calculators.xtb.rst @@ -0,0 +1,20 @@ +ipsuite.calculators.xtb +======================= + +.. automodule:: ipsuite.calculators.xtb + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + xTBSinglePoint diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst new file mode 100644 index 00000000..7adeab24 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.MMKernel.rst @@ -0,0 +1,47 @@ +ipsuite.configuration\_comparison.MMKernel +========================================== + +.. currentmodule:: ipsuite.configuration_comparison + +.. autoclass:: MMKernel + + + .. automethod:: __init__ + + + .. rubric:: Methods + + .. autosummary:: + + ~MMKernel.__init__ + ~MMKernel.compare + ~MMKernel.convert_notebook + ~MMKernel.from_rev + ~MMKernel.load + ~MMKernel.run + ~MMKernel.save + ~MMKernel.save_representation + ~MMKernel.unlink_database + + + + + + .. rubric:: Attributes + + .. autosummary:: + + ~MMKernel.analyte + ~MMKernel.init_descriptors + ~MMKernel.init_subclass_basecls + ~MMKernel.memory + ~MMKernel.name + ~MMKernel.nwd + ~MMKernel.reference + ~MMKernel.result + ~MMKernel.similarities + ~MMKernel.soap + ~MMKernel.state + ~MMKernel.use_jit + ~MMKernel.use_repr + ~MMKernel.uuid diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst new file mode 100644 index 00000000..bbe8ea70 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.REMatch.rst @@ -0,0 +1,50 @@ +ipsuite.configuration\_comparison.REMatch +========================================= + +.. currentmodule:: ipsuite.configuration_comparison + +.. autoclass:: REMatch + + + .. automethod:: __init__ + + + .. rubric:: Methods + + .. autosummary:: + + ~REMatch.__init__ + ~REMatch.compare + ~REMatch.convert_notebook + ~REMatch.from_rev + ~REMatch.load + ~REMatch.run + ~REMatch.save + ~REMatch.save_representation + ~REMatch.unlink_database + + + + + + .. rubric:: Attributes + + .. autosummary:: + + ~REMatch.alpha + ~REMatch.analyte + ~REMatch.init_descriptors + ~REMatch.init_subclass_basecls + ~REMatch.memory + ~REMatch.metric + ~REMatch.name + ~REMatch.nwd + ~REMatch.reference + ~REMatch.result + ~REMatch.similarities + ~REMatch.soap + ~REMatch.state + ~REMatch.threshold + ~REMatch.use_jit + ~REMatch.use_repr + ~REMatch.uuid diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst new file mode 100644 index 00000000..573796d3 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.base.rst @@ -0,0 +1,30 @@ +ipsuite.configuration\_comparison.base +====================================== + +.. automodule:: ipsuite.configuration_comparison.base + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + convert_to_df + create_dataset + write_dataset + + + + + + .. rubric:: Classes + + .. autosummary:: + + ConfigurationComparison + SOAPParameter + SOAPParameterConverter diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst new file mode 100644 index 00000000..e3defe7d --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_comparison.rst @@ -0,0 +1,32 @@ +ipsuite.configuration\_comparison +================================= + +.. automodule:: ipsuite.configuration_comparison + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.configuration_comparison.MMKernel + ipsuite.configuration_comparison.REMatch + ipsuite.configuration_comparison.base diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst new file mode 100644 index 00000000..1c66af6b --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.packmol.rst @@ -0,0 +1,21 @@ +ipsuite.configuration\_generation.packmol +========================================= + +.. automodule:: ipsuite.configuration_generation.packmol + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + MultiPackmol + Packmol diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst new file mode 100644 index 00000000..7f6b21b7 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.rst @@ -0,0 +1,31 @@ +ipsuite.configuration\_generation +================================= + +.. automodule:: ipsuite.configuration_generation + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.configuration_generation.packmol + ipsuite.configuration_generation.smiles_to_atoms diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst new file mode 100644 index 00000000..fb6227d0 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_generation.smiles_to_atoms.rst @@ -0,0 +1,21 @@ +ipsuite.configuration\_generation.smiles\_to\_atoms +=================================================== + +.. automodule:: ipsuite.configuration_generation.smiles_to_atoms + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + SmilesToAtoms + SmilesToConformers diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst new file mode 100644 index 00000000..2db8513e --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.base.rst @@ -0,0 +1,21 @@ +ipsuite.configuration\_selection.base +===================================== + +.. automodule:: ipsuite.configuration_selection.base + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + BatchConfigurationSelection + ConfigurationSelection diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst new file mode 100644 index 00000000..44fd9a9a --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.filter.rst @@ -0,0 +1,20 @@ +ipsuite.configuration\_selection.filter +======================================= + +.. automodule:: ipsuite.configuration_selection.filter + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + FilterOutlier diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst new file mode 100644 index 00000000..9a4e32d0 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.index.rst @@ -0,0 +1,20 @@ +ipsuite.configuration\_selection.index +====================================== + +.. automodule:: ipsuite.configuration_selection.index + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + IndexSelection diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst new file mode 100644 index 00000000..ecb538af --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.kernel.rst @@ -0,0 +1,20 @@ +ipsuite.configuration\_selection.kernel +======================================= + +.. automodule:: ipsuite.configuration_selection.kernel + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + KernelSelection diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst new file mode 100644 index 00000000..794a63fb --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.random.rst @@ -0,0 +1,20 @@ +ipsuite.configuration\_selection.random +======================================= + +.. automodule:: ipsuite.configuration_selection.random + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + RandomSelection diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst new file mode 100644 index 00000000..fc04d6e8 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.rst @@ -0,0 +1,39 @@ +ipsuite.configuration\_selection +================================ + +.. automodule:: ipsuite.configuration_selection + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.configuration_selection.base + ipsuite.configuration_selection.filter + ipsuite.configuration_selection.index + ipsuite.configuration_selection.kernel + ipsuite.configuration_selection.random + ipsuite.configuration_selection.split + ipsuite.configuration_selection.threshold + ipsuite.configuration_selection.uniform_arange + ipsuite.configuration_selection.uniform_energetic + ipsuite.configuration_selection.uniform_temporal diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst new file mode 100644 index 00000000..23aa1dba --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.split.rst @@ -0,0 +1,20 @@ +ipsuite.configuration\_selection.split +====================================== + +.. automodule:: ipsuite.configuration_selection.split + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + SplitSelection diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst new file mode 100644 index 00000000..ac297e54 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.threshold.rst @@ -0,0 +1,28 @@ +ipsuite.configuration\_selection.threshold +========================================== + +.. automodule:: ipsuite.configuration_selection.threshold + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + check_dimension + max_reduction + mean_reduction + + + + + + .. rubric:: Classes + + .. autosummary:: + + ThresholdSelection diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst new file mode 100644 index 00000000..ad5494bf --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_arange.rst @@ -0,0 +1,20 @@ +ipsuite.configuration\_selection.uniform\_arange +================================================ + +.. automodule:: ipsuite.configuration_selection.uniform_arange + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + UniformArangeSelection diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst new file mode 100644 index 00000000..a58532cf --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_energetic.rst @@ -0,0 +1,20 @@ +ipsuite.configuration\_selection.uniform\_energetic +=================================================== + +.. automodule:: ipsuite.configuration_selection.uniform_energetic + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + UniformEnergeticSelection diff --git a/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst new file mode 100644 index 00000000..fc0f04f5 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.configuration_selection.uniform_temporal.rst @@ -0,0 +1,20 @@ +ipsuite.configuration\_selection.uniform\_temporal +================================================== + +.. automodule:: ipsuite.configuration_selection.uniform_temporal + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + UniformTemporalSelection diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst new file mode 100644 index 00000000..2a5b6212 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_ase.rst @@ -0,0 +1,27 @@ +ipsuite.data\_loading.add\_data\_ase +==================================== + +.. automodule:: ipsuite.data_loading.add_data_ase + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + load_data + + + + + + .. rubric:: Classes + + .. autosummary:: + + AddData + ReadData diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst new file mode 100644 index 00000000..4586617f --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.add_data_h5md.rst @@ -0,0 +1,20 @@ +ipsuite.data\_loading.add\_data\_h5md +===================================== + +.. automodule:: ipsuite.data_loading.add_data_h5md + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + AddDataH5MD diff --git a/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst b/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst new file mode 100644 index 00000000..7a92b629 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.data_loading.rst @@ -0,0 +1,31 @@ +ipsuite.data\_loading +===================== + +.. automodule:: ipsuite.data_loading + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.data_loading.add_data_ase + ipsuite.data_loading.add_data_h5md diff --git a/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst b/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst new file mode 100644 index 00000000..6f650f93 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.fields.atoms.rst @@ -0,0 +1,20 @@ +ipsuite.fields.atoms +==================== + +.. automodule:: ipsuite.fields.atoms + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + Atoms diff --git a/docs/source/_get_started/_autosummary/ipsuite.fields.rst b/docs/source/_get_started/_autosummary/ipsuite.fields.rst new file mode 100644 index 00000000..ef4da94f --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.fields.rst @@ -0,0 +1,30 @@ +ipsuite.fields +============== + +.. automodule:: ipsuite.fields + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.fields.atoms diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst new file mode 100644 index 00000000..790d0303 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.barycenter_coarse_grain.rst @@ -0,0 +1,17 @@ +ipsuite.geometry.barycenter\_coarse\_grain +========================================== + +.. automodule:: ipsuite.geometry.barycenter_coarse_grain + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + barycenter_backmapping + coarse_grain_to_barycenter diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst new file mode 100644 index 00000000..e4e1cb6e --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.graphs.rst @@ -0,0 +1,19 @@ +ipsuite.geometry.graphs +======================= + +.. automodule:: ipsuite.geometry.graphs + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + atoms_to_graph + edges_from_atoms + identify_molecules + split_molecule diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst new file mode 100644 index 00000000..fe850898 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.mapping.rst @@ -0,0 +1,20 @@ +ipsuite.geometry.mapping +======================== + +.. automodule:: ipsuite.geometry.mapping + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + BarycenterMapping diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.rst new file mode 100644 index 00000000..6dd258b8 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.rst @@ -0,0 +1,33 @@ +ipsuite.geometry +================ + +.. automodule:: ipsuite.geometry + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.geometry.barycenter_coarse_grain + ipsuite.geometry.graphs + ipsuite.geometry.mapping + ipsuite.geometry.unwrap diff --git a/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst b/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst new file mode 100644 index 00000000..87728056 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.geometry.unwrap.rst @@ -0,0 +1,20 @@ +ipsuite.geometry.unwrap +======================= + +.. automodule:: ipsuite.geometry.unwrap + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + closest_atom_to_center + displace_neighbors + sort_atomic_edges + unwrap + unwrap_system diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst b/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst new file mode 100644 index 00000000..cab116c5 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.models.apax.rst @@ -0,0 +1,22 @@ +ipsuite.models.apax +=================== + +.. automodule:: ipsuite.models.apax + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + Apax + ApaxEnsemble + BatchKernelSelection diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.base.rst b/docs/source/_get_started/_autosummary/ipsuite.models.base.rst new file mode 100644 index 00000000..674be800 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.models.base.rst @@ -0,0 +1,20 @@ +ipsuite.models.base +=================== + +.. automodule:: ipsuite.models.base + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + MLModel diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst b/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst new file mode 100644 index 00000000..f42c02fe --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.models.ensemble.rst @@ -0,0 +1,21 @@ +ipsuite.models.ensemble +======================= + +.. automodule:: ipsuite.models.ensemble + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + EnsembleCalculator + EnsembleModel diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst b/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst new file mode 100644 index 00000000..3d3b7a85 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.models.gap.rst @@ -0,0 +1,26 @@ +ipsuite.models.gap +================== + +.. automodule:: ipsuite.models.gap + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + DistanceNb + DistanceNbConverter + GAP + GapParameter + GapParameterConverter + SOAP + SOAPConverter diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst b/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst new file mode 100644 index 00000000..b77873f0 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.models.mace_model.rst @@ -0,0 +1,26 @@ +ipsuite.models.mace\_model +========================== + +.. automodule:: ipsuite.models.mace_model + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + execute + + + + + + .. rubric:: Classes + + .. autosummary:: + + MACE diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst b/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst new file mode 100644 index 00000000..508ee5f4 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.models.nequip.rst @@ -0,0 +1,20 @@ +ipsuite.models.nequip +===================== + +.. automodule:: ipsuite.models.nequip + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + Nequip diff --git a/docs/source/_get_started/_autosummary/ipsuite.models.rst b/docs/source/_get_started/_autosummary/ipsuite.models.rst new file mode 100644 index 00000000..4bd01e37 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.models.rst @@ -0,0 +1,35 @@ +ipsuite.models +============== + +.. automodule:: ipsuite.models + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.models.apax + ipsuite.models.base + ipsuite.models.ensemble + ipsuite.models.gap + ipsuite.models.mace_model + ipsuite.models.nequip diff --git a/docs/source/_get_started/_autosummary/ipsuite.nodes.rst b/docs/source/_get_started/_autosummary/ipsuite.nodes.rst new file mode 100644 index 00000000..79e2bca2 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.nodes.rst @@ -0,0 +1,4 @@ +ipsuite.nodes +============= + +.. automodule:: ipsuite.nodes diff --git a/docs/source/_get_started/_autosummary/ipsuite.project.rst b/docs/source/_get_started/_autosummary/ipsuite.project.rst new file mode 100644 index 00000000..39eac890 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.project.rst @@ -0,0 +1,20 @@ +ipsuite.project +=============== + +.. automodule:: ipsuite.project + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + + Project diff --git a/docs/source/_get_started/_autosummary/ipsuite.rst b/docs/source/_get_started/_autosummary/ipsuite.rst new file mode 100644 index 00000000..5f8561aa --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.rst @@ -0,0 +1,44 @@ +ipsuite +======= + +.. automodule:: ipsuite + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.analysis + ipsuite.base + ipsuite.bootstrap + ipsuite.calculators + ipsuite.configuration_comparison + ipsuite.configuration_generation + ipsuite.configuration_selection + ipsuite.data_loading + ipsuite.fields + ipsuite.geometry + ipsuite.models + ipsuite.nodes + ipsuite.project + ipsuite.static_data + ipsuite.utils diff --git a/docs/source/_get_started/_autosummary/ipsuite.static_data.rst b/docs/source/_get_started/_autosummary/ipsuite.static_data.rst new file mode 100644 index 00000000..cb98b831 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.static_data.rst @@ -0,0 +1,4 @@ +ipsuite.static\_data +==================== + +.. automodule:: ipsuite.static_data diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst new file mode 100644 index 00000000..d860b798 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.ase_sim.rst @@ -0,0 +1,20 @@ +ipsuite.utils.ase\_sim +====================== + +.. automodule:: ipsuite.utils.ase_sim + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + freeze_copy_atoms + get_box_from_density + get_density_from_atoms + get_desc + get_energy diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst new file mode 100644 index 00000000..8659aecd --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.combine.rst @@ -0,0 +1,27 @@ +ipsuite.utils.combine +===================== + +.. automodule:: ipsuite.utils.combine + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + get_flat_data_from_dict + get_ids_per_key + + + + + + .. rubric:: Classes + + .. autosummary:: + + ExcludeIds diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst new file mode 100644 index 00000000..6c4606cd --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.docs.rst @@ -0,0 +1,16 @@ +ipsuite.utils.docs +================== + +.. automodule:: ipsuite.utils.docs + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + create_dvc_git_env_for_doctest diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst new file mode 100644 index 00000000..8446b16e --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.helpers.rst @@ -0,0 +1,18 @@ +ipsuite.utils.helpers +===================== + +.. automodule:: ipsuite.utils.helpers + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + check_duplicate_keys + get_deps_if_node + setup_ase diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst new file mode 100644 index 00000000..17b6c896 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.logs.rst @@ -0,0 +1,16 @@ +ipsuite.utils.logs +================== + +.. automodule:: ipsuite.utils.logs + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + setup_logging diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst new file mode 100644 index 00000000..16ab6dba --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.md.rst @@ -0,0 +1,16 @@ +ipsuite.utils.md +================ + +.. automodule:: ipsuite.utils.md + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + get_energy_terms diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst new file mode 100644 index 00000000..5a6420b4 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.metrics.rst @@ -0,0 +1,24 @@ +ipsuite.utils.metrics +===================== + +.. automodule:: ipsuite.utils.metrics + + + + + + + + .. rubric:: Functions + + .. autosummary:: + + calculate_l_p_norm + get_angles + get_full_metrics + get_u_vecs + maximum_error + mean_absolute_error + mean_squared_error + relative_rmse + root_mean_squared_error diff --git a/docs/source/_get_started/_autosummary/ipsuite.utils.rst b/docs/source/_get_started/_autosummary/ipsuite.utils.rst new file mode 100644 index 00000000..ff838736 --- /dev/null +++ b/docs/source/_get_started/_autosummary/ipsuite.utils.rst @@ -0,0 +1,36 @@ +ipsuite.utils +============= + +.. automodule:: ipsuite.utils + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + ipsuite.utils.ase_sim + ipsuite.utils.combine + ipsuite.utils.docs + ipsuite.utils.helpers + ipsuite.utils.logs + ipsuite.utils.md + ipsuite.utils.metrics diff --git a/docs/source/_get_started/index.rst b/docs/source/_get_started/index.rst new file mode 100644 index 00000000..1d51c41d --- /dev/null +++ b/docs/source/_get_started/index.rst @@ -0,0 +1,15 @@ + +.. _userdoc-get-started: + + +Getting Started +=============== + +TODO link to zntrack docs + + + +.. toctree:: + :maxdepth: 0 + + installation diff --git a/docs/source/_get_started/installation.rst b/docs/source/_get_started/installation.rst new file mode 100644 index 00000000..622c5858 --- /dev/null +++ b/docs/source/_get_started/installation.rst @@ -0,0 +1,35 @@ +Installation +============ + +IPS is available on PyPI and can be installed using + +.. code-block:: bash + + pip install ipsuite + + +Note that a default installation does not come with any of the models. +These are available as extras and can be installed by specifying the models you would like to install. +For example, the following code snippets install the GAP model (via `quippy `_ ) and all available models respectively + +.. code-block:: bash + + pip install ipsuite[gap] + +.. code-block:: bash + + pip install ipsuite[all] + + + +Developer Installation +---------------------- + +IPS is devloped using `Poetry `_. +To install a developer verions of IPS, clone the repository and install it with poetry: + +.. code-block:: bash + + git clone https://github.com/zincware/IPSuite.git + cd IPSuite + poetry install diff --git a/docs/source/_get_started/nodes_list.rst b/docs/source/_get_started/nodes_list.rst new file mode 100644 index 00000000..5f245ee0 --- /dev/null +++ b/docs/source/_get_started/nodes_list.rst @@ -0,0 +1,23 @@ +List of IPSuite Nodes +===================== + + + +.. autosummary:: + :toctree: _autosummary + :recursive: + + ipsuite.analysis + ipsuite.base + ipsuite.bootstrap + ipsuite.calculators + ipsuite.configuration_generation + ipsuite.configuration_selection + ipsuite.configuration_comparison + ipsuite.data_loading + ipsuite.fields + ipsuite.geometry + ipsuite.models + ipsuite.project + ipsuite.static_data + ipsuite.utils diff --git a/docs/source/_nodes/analysis.rst b/docs/source/_nodes/analysis.rst new file mode 100644 index 00000000..0e5fd368 --- /dev/null +++ b/docs/source/_nodes/analysis.rst @@ -0,0 +1,5 @@ +Analysis +======== +.. automodule:: ipsuite.analysis + :members: + :show-inheritance: diff --git a/docs/source/_nodes/bootstrap.rst b/docs/source/_nodes/bootstrap.rst new file mode 100644 index 00000000..08859e17 --- /dev/null +++ b/docs/source/_nodes/bootstrap.rst @@ -0,0 +1,5 @@ +Bootstrap +========= +.. automodule:: ipsuite.bootstrap + :members: + :show-inheritance: diff --git a/docs/source/_nodes/calculators.rst b/docs/source/_nodes/calculators.rst new file mode 100644 index 00000000..b6841898 --- /dev/null +++ b/docs/source/_nodes/calculators.rst @@ -0,0 +1,5 @@ +Calculators +=========== +.. automodule:: ipsuite.calculators + :members: + :show-inheritance: diff --git a/docs/source/_nodes/configuration_comparison.rst b/docs/source/_nodes/configuration_comparison.rst new file mode 100644 index 00000000..fc71452d --- /dev/null +++ b/docs/source/_nodes/configuration_comparison.rst @@ -0,0 +1,5 @@ +Configuration Comparison +======================== +.. automodule:: ipsuite.configuration_comparison + :members: + :show-inheritance: diff --git a/docs/source/_nodes/configuration_generation.rst b/docs/source/_nodes/configuration_generation.rst new file mode 100644 index 00000000..d4213157 --- /dev/null +++ b/docs/source/_nodes/configuration_generation.rst @@ -0,0 +1,5 @@ +Configuration Generation +======================== +.. automodule:: ipsuite.configuration_generation + :members: + :show-inheritance: diff --git a/docs/source/_nodes/configuration_selection.rst b/docs/source/_nodes/configuration_selection.rst new file mode 100644 index 00000000..36dda743 --- /dev/null +++ b/docs/source/_nodes/configuration_selection.rst @@ -0,0 +1,5 @@ +Configuration Selection +======================= +.. automodule:: ipsuite.configuration_selection + :members: + :show-inheritance: diff --git a/docs/source/_nodes/data_loading.rst b/docs/source/_nodes/data_loading.rst new file mode 100644 index 00000000..824ebf0d --- /dev/null +++ b/docs/source/_nodes/data_loading.rst @@ -0,0 +1,5 @@ +Data Loading +============ +.. automodule:: ipsuite.data_loading + :members: + :show-inheritance: diff --git a/docs/source/_nodes/geometry.rst b/docs/source/_nodes/geometry.rst new file mode 100644 index 00000000..8bdbc2c4 --- /dev/null +++ b/docs/source/_nodes/geometry.rst @@ -0,0 +1,5 @@ +Geometry +======== +.. automodule:: ipsuite.geometry + :members: + :show-inheritance: diff --git a/docs/source/_nodes/index.rst b/docs/source/_nodes/index.rst new file mode 100644 index 00000000..5b8cdf07 --- /dev/null +++ b/docs/source/_nodes/index.rst @@ -0,0 +1,19 @@ + + +.. _userdoc-modules: + +Nodes +===== + +.. toctree:: + :maxdepth: 2 + + data_loading + bootstrap + calculators + configuration_selection + models + analysis + configuration_comparison + configuration_generation + geometry diff --git a/docs/source/_nodes/models.rst b/docs/source/_nodes/models.rst new file mode 100644 index 00000000..6f66ee98 --- /dev/null +++ b/docs/source/_nodes/models.rst @@ -0,0 +1,5 @@ +Models +====== +.. automodule:: ipsuite.models + :members: + :show-inheritance: diff --git a/docs/source/conf.py b/docs/source/conf.py index 53f30f9d..3b158f3f 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -25,8 +25,10 @@ "sphinx.ext.doctest", "sphinx_copybutton", "sphinx.ext.viewcode", + "sphinx.ext.autosummary", ] +autosummary_generate = True templates_path = ["_templates"] exclude_patterns = [] diff --git a/docs/source/images/water_packmol.png b/docs/source/images/water_packmol.png index e0604e56..fecc8ed9 100644 Binary files a/docs/source/images/water_packmol.png and b/docs/source/images/water_packmol.png differ diff --git a/docs/source/index.rst b/docs/source/index.rst index 76bb3bf8..35df39c8 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -1,3 +1,44 @@ +.. IPSuite documentation master file, created by + sphinx-quickstart on Mon May 22 19:58:40 2023. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +IPS - The Inter Atomic Potential Suite +====================================== + +The Inter Atomic Potential Suite (IPS) allows for the fast construction and extension of atomistic machine learning workflows. +It is based on `ZnTrack `_ and thus allows for fully version controlled and reproducible workflows. +Within IPS, we provide numerous Nodes for creating atomistic data, training models, analyzing predictions and performing molecular dynamics. + + + +Example +======= + +Routine workflows are easy to set up and can be easily extended for more complex tasks. +Training any of the interfaced models only requires a few lines of code: + +.. code-block:: python + + import ipsuite as ips + + with ips.Project() as project: + data = ips.AddData(file="dataset.extxyz") + random_selection = ips.configuration_selection.RandomSelection( + data=data, n_configurations=100 + ) + + model = ips.models.GAP(data=random_selection) + + + +.. toctree:: + :hidden: + + _get_started/index + _examples/index + _nodes/index + .. IPSuite documentation master file, created by sphinx-quickstart on Fri Feb 2 12:58:52 2024. You can adapt this file completely to your liking, but it should at least @@ -16,8 +57,8 @@ Welcome to IPSuite's documentation! What is IPS? <_get_started/ips> Getting Started <_get_started/quickstart> - IPSuite <_nodes/ipsuite> - Modules <_nodes/modlules> + Nodes List <_get_started/nodes_list> + Modules <_nodes/modules> Indices and tables diff --git a/examples/01_Data_Loading_and_Selection.ipynb b/examples/01_Data_Loading_and_Selection.ipynb new file mode 100644 index 00000000..723f56f0 --- /dev/null +++ b/examples/01_Data_Loading_and_Selection.ipynb @@ -0,0 +1,567 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Data Loading and Selection" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Welcome to the first IPS example notebook!\n", + "Here we will demonstrate how to load existing datasets and perform some simple and more involved data splitting workflows.\n", + "\n", + "All examples are self-contained, and the data is created within the notebooks themselves." + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-31 23:10:07,791 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + } + ], + "source": [ + "import ipsuite as ips\n", + "from zntrack.utils import cwd_temp_dir\n", + "\n", + "temp_dir = cwd_temp_dir()\n", + "\n", + "import ipsuite as ips\n", + "\n", + "import os\n", + "from ase import units\n", + "from ase.calculators.emt import EMT\n", + "from ase.io.trajectory import TrajectoryWriter\n", + "from ase.lattice.cubic import FaceCenteredCubic\n", + "from ase.md.velocitydistribution import MaxwellBoltzmannDistribution\n", + "from ase.md.langevin import Langevin\n", + "from ase.visualize import view\n" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "hint: Using 'master' as the name for the initial branch. This default branch name\n", + "hint: is subject to change. To configure the initial branch name to use in all\n", + "hint: of your new repositories, which will suppress this warning, call:\n", + "hint: \n", + "hint: \tgit config --global init.defaultBranch \n", + "hint: \n", + "hint: Names commonly chosen instead of 'master' are 'main', 'trunk' and\n", + "hint: 'development'. The just-created branch can be renamed via this command:\n", + "hint: \n", + "hint: \tgit branch -m \n", + "Initialized empty Git repository in /tmp/tmpok_da3k5/.git/\n", + "Initialized DVC repository.\n", + "\n", + "You can now commit the changes to git.\n", + "\n", + "+---------------------------------------------------------------------+\n", + "| |\n", + "| DVC has enabled anonymous aggregate usage analytics. |\n", + "| Read the analytics documentation (and how to opt-out) here: |\n", + "| |\n", + "| |\n", + "+---------------------------------------------------------------------+\n", + "\n", + "What's next?\n", + "------------\n", + "- Check out the documentation: \n", + "- Get help and share ideas: \n", + "- Star us on GitHub: \n" + ] + } + ], + "source": [ + "!git init\n", + "!dvc init" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Data Creation\n", + "\n", + "First, we will create some sample data using ASE to perform a short molecular dynamics simulation.\n", + "\n", + "TODO make data and run MD\n", + "TODO combining multiple datasets" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "size = 3\n", + "\n", + "# Set up a crystal\n", + "atoms = FaceCenteredCubic(\n", + " directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],\n", + " symbol='Cu',\n", + " size=(size, size, size),\n", + " pbc=True\n", + ")\n" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "True" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "timestep = 5 * units.fs\n", + "steps = 100\n", + "temperature = 800\n", + "traj_path = os.path.join(temp_dir.name, \"trajectory.traj\")\n", + "\n", + "\n", + "atoms.calc = EMT()\n", + "MaxwellBoltzmannDistribution(atoms, temperature_K=temperature)\n", + "\n", + "dyn = Langevin(atoms, timestep, temperature_K=temperature, friction=0.002)\n", + "\n", + "writer = TrajectoryWriter(traj_path, \"w\", atoms=atoms)\n", + "dyn.attach(writer, interval=1)\n", + "\n", + "dyn.run(steps)" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Data Loading\n", + "\n", + "IPS uses ASE for many of its internals and datasets can be loaded from any ASE compatible format.\n", + "Here we are going to pretend that the above created sample data is some literature dataset that we have already downloaded." + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-31 23:10:17,739 (WARNING): Please run 'dvc add /tmp/tmpok_da3k5/trajectory.traj' to track the file with DVC. Otherwise, it might end up being git tracked.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Running DVC command: 'stage add --name trajectory --force ...'\n", + "Running DVC command: 'repro'\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-31 23:10:19,001 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Reading File: 101it [00:00, 3355.28it/s]\n" + ] + } + ], + "source": [ + "with ips.Project() as project:\n", + " trajectory = ips.AddData(file=traj_path, name=\"trajectory\")\n", + "project.run()" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The data is read from disk and is now available to both other Nodes in the project and for use in the notebook." + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "trajectory.load() # requires the project to have been run" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We obtain a list of ASE Atoms, with which we can work in our notebook and use other ASE functionality, e.g.:" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "view(trajectory)" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The H5MD standard offers substantial size and I/O speed advantages.\n", + "For this reason H5MD is used by Nodes which serialize atomistic data, including `AddData`." + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Data Selection\n", + "\n", + "A common way to split data into training, validation and test splits is to randomly partition them into fractions like 75:15:10.\n", + "We can add the respective selection Nodes to our existing project." + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Running DVC command: 'stage add --name trajectory --force ...'\n", + "Running DVC command: 'stage add --name random_test_selection --force ...'\n", + "Running DVC command: 'stage add --name random_val_selection --force ...'\n", + "Running DVC command: 'stage add --name random_train_selection --force ...'\n", + "Running DVC command: 'repro'\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-31 23:10:20,899 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-31 23:10:21,047 (DEBUG): Selecting from 101 configurations.\n", + "2023-05-31 23:10:22,301 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-31 23:10:22,491 (DEBUG): Selecting from 91 configurations.\n", + "2023-05-31 23:10:23,804 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-31 23:10:24,044 (DEBUG): Selecting from 76 configurations.\n" + ] + } + ], + "source": [ + "with project:\n", + " random_test_selection = ips.configuration_selection.RandomSelection(data=trajectory, n_configurations=10, name=\"random_test_selection\")\n", + " random_val_selection = ips.configuration_selection.RandomSelection(data=random_test_selection.excluded_atoms, n_configurations=15, name=\"random_val_selection\")\n", + " random_train_selection = ips.configuration_selection.RandomSelection(data=random_val_selection.excluded_atoms, n_configurations=75, name=\"random_train_selection\")\n", + "project.run()" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Selecting the testing data first means we can change our training and validation selection, e.g. by using a different selection method or a different number of configurations, without altering our test set.\n", + "Note that we had to give names to our selection nodes since we use multiple instances of that Node in our graph.\n", + "For convenience, it is also possible to assign numerical IDs by supplying `automatic_node_names=True` to the `Project`." + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We can visualize our workflow at any time using" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " +------------+ \n", + " | trajectory | \n", + " +------------+ \n", + " * \n", + " * \n", + " * \n", + "+-----------------------+ \n", + "| random_test_selection | \n", + "+-----------------------+ \n", + " * \n", + " * \n", + " * \n", + " +----------------------+ \n", + " | random_val_selection | \n", + " +----------------------+ \n", + " * \n", + " * \n", + " * \n", + "+------------------------+ \n", + "| random_train_selection | \n", + "+------------------------+ \n" + ] + } + ], + "source": [ + "!dvc dag" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "While straightforward, this is not necessarily advisable for molecular dynamics data.\n", + "Trajectories are created sequentially, and a random split will result in validation samples that are drawn from between training samples.\n", + "By instead separating the dataset into fixed fraction first, we can ensure that the splits do not temporally overlap.\n", + "\n", + "For demonstration purposes, we will delete the random splitting workflow we created above with `remove_existing_graph=True`." + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-31 23:11:14,183 (WARNING): Please run 'dvc add /tmp/tmpok_da3k5/trajectory.traj' to track the file with DVC. Otherwise, it might end up being git tracked.\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Running DVC command: 'stage add --name trajectory --force ...'\n", + "Running DVC command: 'stage add --name test_split --force ...'\n", + "Running DVC command: 'stage add --name val_split --force ...'\n", + "Running DVC command: 'stage add --name test_data --force ...'\n", + "Running DVC command: 'stage add --name val_data --force ...'\n", + "Running DVC command: 'stage add --name train_data --force ...'\n", + "Running DVC command: 'repro'\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-31 23:11:15,722 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-31 23:11:15,915 (DEBUG): Selecting from 101 configurations.\n", + "2023-05-31 23:11:17,228 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-31 23:11:17,459 (DEBUG): Selecting from 91 configurations.\n", + "2023-05-31 23:11:18,780 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-31 23:11:19,031 (DEBUG): Selecting from 76 configurations.\n", + "2023-05-31 23:11:19,031 (WARNING): Running search for 80 to max 76\n", + "2023-05-31 23:11:20,350 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-31 23:11:20,561 (DEBUG): Selecting from 10 configurations.\n", + "2023-05-31 23:11:21,836 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-31 23:11:22,081 (DEBUG): Selecting from 15 configurations.\n" + ] + } + ], + "source": [ + "with ips.Project(remove_existing_graph=True) as project:\n", + " trajectory = ips.AddData(file=traj_path, name=\"trajectory\")\n", + " test_split = ips.configuration_selection.SplitSelection(data=trajectory, split=0.1, name=\"test_split\")\n", + " val_split = ips.configuration_selection.SplitSelection(data=test_split.excluded_atoms, split=0.17, name=\"val_split\") # 0.15 / 0.9 * 1.0 \\approx 0.17\n", + " train_split = val_split.excluded_atoms # 0.8 of the total data\n", + "\n", + " test_data = ips.configuration_selection.UniformTemporalSelection(data=test_split, n_configurations=10, name=\"test_data\")\n", + " val_data = ips.configuration_selection.UniformTemporalSelection(data=val_split, n_configurations=15, name=\"val_data\")\n", + " train_data = ips.configuration_selection.UniformEnergeticSelection(data=train_split, n_configurations=80, name=\"train_data\")\n", + "\n", + "project.run()" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The selection methods here are purely for demonstration purposes.\n", + "Usually it makes sense to use all available test data and not perform a sub-selection since the test set should only be evaluated once which does not pose a performance bottleneck." + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " +------------+ \n", + " | trajectory | \n", + " +------------+ \n", + " * \n", + " * \n", + " * \n", + " +------------+ \n", + " | test_split | \n", + " +------------+ \n", + " *** *** \n", + " * * \n", + " ** ** \n", + "+-----------+ +-----------+ \n", + "| test_data | | val_split | \n", + "+-----------+ +-----------+ \n", + " *** *** \n", + " * * \n", + " ** ** \n", + " +----------+ +------------+ \n", + " | val_data | | train_data | \n", + " +----------+ +------------+ \n" + ] + } + ], + "source": [ + "!dvc dag" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Below is a list of all currently implemented selection methods.\n", + "Check out the API docs for more information about the methods not covered here." + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['ConfigurationSelection',\n", + " 'RandomSelection',\n", + " 'UniformEnergeticSelection',\n", + " 'UniformTemporalSelection',\n", + " 'UniformArangeSelection',\n", + " 'KernelSelection',\n", + " 'IndexSelection',\n", + " 'ThresholdSelection',\n", + " 'SplitSelection']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ips.configuration_selection.__all__" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Kernel Based Selection Methods" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# TODO" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "temp_dir.cleanup()" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "ips2", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.11" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/02_Training_Models.ipynb b/examples/02_Training_Models.ipynb new file mode 100644 index 00000000..cf1418ac --- /dev/null +++ b/examples/02_Training_Models.ipynb @@ -0,0 +1,113 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Training Models" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-26 15:16:04,580 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + } + ], + "source": [ + "import ipsuite as ips" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "IPS is interfaced with a series of models. A complete list of available models is found below." + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['Apax', 'EnsembleModel', 'GAP', 'MACE', 'MLModel', 'Nequip']" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ips.models.__all__" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Using the Trained Model\n", + "\n", + "Here we will briefly evaluate our model\"s predictions with a correlation plot of predicted and actual labels.\n", + "A more detailed presentation of the analysis capabilities contained in IPS can be found in the next notebook." + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Transfer Learning\n", + "\n", + "TODO" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "ips", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.11" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/03_Analysing_Datasets_and_Model_Predictions.ipynb b/examples/03_Analysing_Datasets_and_Model_Predictions.ipynb new file mode 100644 index 00000000..47afa1ec --- /dev/null +++ b/examples/03_Analysing_Datasets_and_Model_Predictions.ipynb @@ -0,0 +1,204 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Analysing Datasets and Model Predictions" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "In the last example we already saw how to obtain a simple prediction-label correlation plot.\n", + "However, for most real-life applications, this alone would be insufficient to ascertain the reliability of the model across configuration space.\n", + "This notebook goes into more detail about how to use the various analysis tools implemented in IPS." + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Data Generation and Training\n", + "\n", + "We will once again create a simple dataset." + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-06-06 22:00:51,620 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + } + ], + "source": [ + "import ipsuite as ips\n", + "from zntrack.utils import cwd_temp_dir\n", + "\n", + "temp_dir = cwd_temp_dir()\n", + "\n", + "import ipsuite as ips\n", + "\n", + "import os\n", + "from ase import units\n", + "from ase.calculators.emt import EMT\n", + "from ase.io.trajectory import TrajectoryWriter\n", + "from ase.lattice.cubic import FaceCenteredCubic\n", + "from ase.md.velocitydistribution import MaxwellBoltzmannDistribution\n", + "from ase.md.langevin import Langevin\n", + "from ase.visualize import view\n" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "hint: Using 'master' as the name for the initial branch. This default branch name\n", + "hint: is subject to change. To configure the initial branch name to use in all\n", + "hint: of your new repositories, which will suppress this warning, call:\n", + "hint: \n", + "hint: \tgit config --global init.defaultBranch \n", + "hint: \n", + "hint: Names commonly chosen instead of 'master' are 'main', 'trunk' and\n", + "hint: 'development'. The just-created branch can be renamed via this command:\n", + "hint: \n", + "hint: \tgit branch -m \n", + "Initialized empty Git repository in /tmp/tmpjx247w5h/.git/\n", + "Initialized DVC repository.\n", + "\n", + "You can now commit the changes to git.\n", + "\n", + "+---------------------------------------------------------------------+\n", + "| |\n", + "| DVC has enabled anonymous aggregate usage analytics. |\n", + "| Read the analytics documentation (and how to opt-out) here: |\n", + "| |\n", + "| |\n", + "+---------------------------------------------------------------------+\n", + "\n", + "What's next?\n", + "------------\n", + "- Check out the documentation: \n", + "- Get help and share ideas: \n", + "- Star us on GitHub: \n" + ] + } + ], + "source": [ + "!git init\n", + "!dvc init" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "size = 3\n", + "\n", + "# Set up a crystal\n", + "atoms = FaceCenteredCubic(\n", + " directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],\n", + " symbol='Cu',\n", + " size=(size, size, size),\n", + " pbc=True\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "True" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "timestep = 5 * units.fs\n", + "steps = 100\n", + "temperature = 800\n", + "traj_path = os.path.join(temp_dir.name, \"trajectory.traj\")\n", + "\n", + "atoms.calc = EMT()\n", + "MaxwellBoltzmannDistribution(atoms, temperature_K=temperature)\n", + "\n", + "dyn = Langevin(atoms, timestep, temperature_K=temperature, friction=0.002)\n", + "\n", + "writer = TrajectoryWriter(traj_path, \"w\", atoms=atoms)\n", + "dyn.attach(writer, interval=1)\n", + "\n", + "dyn.run(steps)" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Dataset Analysis" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "This time around, we will explore the dataset a bit before training models on it.\n", + "It is often useful to visualize the distribution of labels " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "ips2", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.10" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb b/examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb new file mode 100644 index 00000000..5fceda42 --- /dev/null +++ b/examples/04_Molecular_Dynamics_Structure_Generation_and_Simulation.ipynb @@ -0,0 +1,29 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Molecular Dynamics Structure Generation and Simulation" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import ipsuite as ips" + ] + } + ], + "metadata": { + "language_info": { + "name": "python" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/05_Labeling_with_Calculators.ipynb b/examples/05_Labeling_with_Calculators.ipynb new file mode 100644 index 00000000..707d18ca --- /dev/null +++ b/examples/05_Labeling_with_Calculators.ipynb @@ -0,0 +1,29 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Labeling with Calculators" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import ipsuite as ips" + ] + } + ], + "metadata": { + "language_info": { + "name": "python" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/examples/06_Bootstrapping_Datasets.ipynb b/examples/06_Bootstrapping_Datasets.ipynb new file mode 100644 index 00000000..fd679462 --- /dev/null +++ b/examples/06_Bootstrapping_Datasets.ipynb @@ -0,0 +1,548 @@ +{ + "cells": [ + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Bootstrapping Datasets" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "In previous examples we assumed that there was a pre-existing dataset available for us to use.\n", + "This is typically the case when working with literature datasets or if we perform the dataset aquisition with an external (molecular dyamics) program.\n", + "\n", + "However, in active learning scenarios one typically starts with a single (unlabeled) configuration. In these cases it is often convenient to bootstrap an initial training set in order to quickly obtain a stable force field with which to drive the sampling.\n", + "\n", + "A full active learning example can be found in a later notebook in this series." + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "This notebook requires packmol for setting up the initial configuration and the xtb. \n", + "`xtb-python` and `packmol` are available from conda and can be installed via\n", + "\n", + "```bash\n", + "conda install -c conda-forge xtb-python\n", + "conda install -c conda-forge packmol\n", + "```" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-30 16:18:18,325 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + } + ], + "source": [ + "import ipsuite as ips\n", + "import znflow\n", + "import matplotlib.pyplot as plt\n", + "\n", + "from zntrack.utils import cwd_temp_dir\n", + "\n", + "temp_dir = cwd_temp_dir()" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "hint: Using 'master' as the name for the initial branch. This default branch name\n", + "hint: is subject to change. To configure the initial branch name to use in all\n", + "hint: of your new repositories, which will suppress this warning, call:\n", + "hint: \n", + "hint: \tgit config --global init.defaultBranch \n", + "hint: \n", + "hint: Names commonly chosen instead of 'master' are 'main', 'trunk' and\n", + "hint: 'development'. The just-created branch can be renamed via this command:\n", + "hint: \n", + "hint: \tgit branch -m \n", + "Initialized empty Git repository in /tmp/tmp8k077isy/.git/\n", + "Initialized DVC repository.\n", + "\n", + "You can now commit the changes to git.\n", + "\n", + "+---------------------------------------------------------------------+\n", + "| |\n", + "| DVC has enabled anonymous aggregate usage analytics. |\n", + "| Read the analytics documentation (and how to opt-out) here: |\n", + "| |\n", + "| |\n", + "+---------------------------------------------------------------------+\n", + "\n", + "What's next?\n", + "------------\n", + "- Check out the documentation: \n", + "- Get help and share ideas: \n", + "- Star us on GitHub: \n" + ] + } + ], + "source": [ + "!git init\n", + "!dvc init" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "We can use packmol to create an initial configuration.\n", + "Based on this, it is possible to bootstrap datasets using a combination of various methods.\n", + "Each of them is designed to probe a different seet of degrees of freedom.\n", + "Random atomic displacements will probe vibrations, while random translations and rotations of molecules, as well as box size scans probe slower degrees of freedom that depend on intermolecular interactions." + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Running DVC command: 'stage add --name SmilesToAtoms --force ...'\n", + "Running DVC command: 'stage add --name Packmol --force ...'\n", + "Running DVC command: 'stage add --name opt_calc --force ...'\n", + "Running DVC command: 'stage add --name ASEGeoOpt --force ...'\n", + "Running DVC command: 'stage add --name RattleAtoms --force ...'\n", + "Running DVC command: 'stage add --name RotateMolecules --force ...'\n", + "Running DVC command: 'stage add --name TranslateMolecules --force ...'\n", + "Running DVC command: 'stage add --name label_calc --force ...'\n", + "Running DVC command: 'stage add --name BoxScale --force ...'\n", + "Running DVC command: 'stage add --name BoxScale_mapping --force ...'\n", + "Could not create .gitignore entry in /tmp/tmp8k077isy/nodes/BoxScale_mapping/.gitignore. DVC will attempt to create .gitignore entry again when the stage is run.\n", + "Running DVC command: 'stage add --name EnergyHistogram --force ...'\n", + "Running DVC command: 'stage add --name ForcesHistogram --force ...'\n", + "Running DVC command: 'repro'\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-30 16:18:20,899 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-30 16:18:22,115 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-30 16:18:22,296 (INFO): estimated box size: [6.6946734740471925, 6.6946734740471925, 6.6946734740471925]\n", + "\n", + "################################################################################\n", + "\n", + " PACKMOL - Packing optimization for the automated generation of\n", + " starting configurations for molecular dynamics simulations.\n", + " \n", + " Version 20.010 \n", + "\n", + "################################################################################\n", + "\n", + " Packmol must be run with: packmol < inputfile.inp \n", + "\n", + " Userguide at: http://m3g.iqm.unicamp.br/packmol \n", + "\n", + " Reading input file... (Control-C aborts)\n", + " Seed for random number generator: 1234567\n", + " Output file: mixture.xyz\n", + " Reading coordinate file: 0.xyz\n", + " Number of independent structures: 1\n", + " The structures are: \n", + " Structure 1 :Properties=species:S:1:pos:R:3 pbc=\"F F F\"( 3 atoms)\n", + " Maximum number of GENCAN loops for all molecule packing: 200\n", + " Total number of restrictions: 1\n", + " Distance tolerance: 2.0000000000000000 \n", + " Number of molecules of type 1 : 10\n", + " Total number of atoms: 30\n", + " Total number of molecules: 10\n", + " Number of fixed molecules: 0\n", + " Number of free molecules: 10\n", + " Number of variables: 60\n", + " Total number of fixed atoms: 0\n", + " Maximum internal distance of type 1 : 1.5660731739637310 \n", + " All atoms must be within these coordinates: \n", + " x: [ -998.39999999999998 , 1001.6000000000000 ] \n", + " y: [ -999.17727845236561 , 1000.8227215476344 ] \n", + " z: [ -1000.0000000000000 , 1000.0000000000000 ] \n", + " If the system is larger than this, increase the sidemax parameter. \n", + "\n", + "################################################################################\n", + "\n", + " Building initial approximation ... \n", + "\n", + "################################################################################\n", + "\n", + " Adjusting initial point to fit the constraints \n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + " Molecules of type: 1\n", + "\n", + " Packing:|0 100%|\n", + " |*********************\n", + "\n", + " Restraint-only function value: 4.7908344210240500E-005\n", + " Maximum violation of the restraints: 3.3276214373314433E-005\n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + " Rescaling maximum and minimum coordinates... \n", + " Computing size of patches... \n", + " Add fixed molecules to permanent arrays... \n", + " Reseting center of mass... \n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + " Setting initial trial coordinates ... \n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + " Molecules of type: 1\n", + " Adjusting random positions to fit the constraints. \n", + " Restraint-only function value: 0.0000000000000000 \n", + " Maximum violation of the restraints: 0.0000000000000000 \n", + "\n", + "################################################################################\n", + "\n", + " Objective function at initial point: 305.75852348958790 \n", + "\n", + "################################################################################\n", + "\n", + " Packing molecules of type: 1\n", + "\n", + "################################################################################\n", + "\n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + " Starting GENCAN loop: 0\n", + " Scaling radii by: 1.1000000000000001 \n", + "\n", + " Packing:|0 100%|\n", + " |***********************************\n", + "\n", + " Function value from last GENCAN loop: f = .15568E-04\n", + " Best function value before: f = .30576E+03\n", + " Improvement from best function value: 99.99 %\n", + " Improvement from last loop: 99.99 %\n", + " Maximum violation of target distance: 0.000000\n", + " Maximum violation of the constraints: .15568E-04\n", + " Current structure written to file: mixture.xyz\n", + "--------------------------------------------------------------------------------\n", + " Packing solved for molecules of type 1\n", + " Objective function value: 1.5567789525860229E-005\n", + " Maximum violation of target distance: 0.0000000000000000 \n", + " Max. constraint violation: 1.5567789525860229E-005\n", + "--------------------------------------------------------------------------------\n", + "\n", + "################################################################################\n", + "\n", + " Packing all molecules together \n", + "\n", + "################################################################################\n", + "\n", + "\n", + " Initial approximation is a solution. Nothing to do. \n", + "\n", + " Solution written to file: mixture.xyz\n", + "\n", + "################################################################################\n", + "\n", + " Success! \n", + " Final objective function value: .31847E-01\n", + " Maximum violation of target distance: 0.000000\n", + " Maximum violation of the constraints: .15568E-04\n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + " Please cite this work if Packmol was useful: \n", + "\n", + " L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez, \n", + " PACKMOL: A package for building initial configurations for\n", + " molecular dynamics simulations. \n", + " Journal of Computational Chemistry, 30:2157-2164,2009.\n", + "\n", + "################################################################################\n", + "\n", + " Running time: 5.92000026E-04 seconds. \n", + "\n", + "--------------------------------------------------------------------------------\n", + "\n", + "\n", + "2023-05-30 16:18:23,396 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "100%|██████████| 1/1 [00:00<00:00, 10.92it/s]\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-30 16:18:24,687 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + " Step Time Energy fmax\n", + "BFGS: 0 16:18:24 -1452.227673 560.1183\n", + "BFGS: 1 16:18:25 -1525.179018 73.0175\n", + "BFGS: 2 16:18:25 -1541.432084 26.5437\n", + "BFGS: 3 16:18:25 -1548.847866 20.9261\n", + "BFGS: 4 16:18:25 -1553.041573 21.0507\n", + "BFGS: 5 16:18:25 -1557.985665 14.9412\n", + "BFGS: 6 16:18:25 -1560.632213 8.3526\n", + "BFGS: 7 16:18:25 -1562.409822 5.2405\n", + "BFGS: 8 16:18:25 -1563.889836 4.6672\n", + "BFGS: 9 16:18:26 -1565.320047 13.2885\n", + "BFGS: 10 16:18:26 -1566.448285 3.4639\n", + "BFGS: 11 16:18:26 -1567.953756 4.4025\n", + "BFGS: 12 16:18:26 -1568.948496 7.1006\n", + "BFGS: 13 16:18:26 -1569.550374 4.1206\n", + "BFGS: 14 16:18:26 -1570.227879 2.1917\n", + "BFGS: 15 16:18:26 -1570.532967 7.2313\n", + "BFGS: 16 16:18:26 -1570.847957 2.6559\n", + "BFGS: 17 16:18:27 -1571.138681 1.4818\n", + "BFGS: 18 16:18:27 -1571.662669 2.2882\n", + "BFGS: 19 16:18:27 -1571.800839 1.6854\n", + "BFGS: 20 16:18:27 -1571.956670 0.8907\n", + "2023-05-30 16:18:28,493 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-30 16:18:29,693 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-30 16:18:30,954 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-30 16:18:31,096 (WARNING): Setting maximum to 2 Pi.\n", + "2023-05-30 16:18:32,202 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-30 16:18:33,349 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "100%|██████████| 16/16 [00:01<00:00, 8.80it/s]\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-30 16:18:36,564 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Could not load field atoms for node BoxScale_mapping.\n", + "100%|███████████████████████████████████| 5/5 [00:00<00:00, 8.29it/s]\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "2023-05-30 16:18:38,818 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n", + "2023-05-30 16:18:40,299 (DEBUG): Welcome to IPS - the Interatomic Potential Suite!\n" + ] + } + ], + "source": [ + "mapping = ips.geometry.BarycenterMapping(data=None)\n", + "\n", + "with ips.Project(automatic_node_names=True) as project:\n", + " water = ips.configuration_generation.SmilesToAtoms(smiles=\"O\")\n", + " packmol = ips.configuration_generation.Packmol(\n", + " data=[water.atoms], count=[10], density=997\n", + " )\n", + "\n", + " opt_calc = ips.calculators.xTBSinglePoint(data=packmol, method=\"gfn1-xtb\", name=\"opt_calc\")\n", + "\n", + " geopt = ips.calculators.ASEGeoOpt(\n", + " model=opt_calc,\n", + " data=packmol.atoms,\n", + " optimizer=\"BFGS\",\n", + " run_kwargs={\"fmax\": 1.0},\n", + " )\n", + "\n", + " n_configs = 5\n", + " rattle = ips.bootstrap.RattleAtoms(\n", + " data=geopt.atoms,\n", + " data_id=-1,\n", + " n_configurations=n_configs,\n", + " maximum=0.08, # Ang max atomic displacement\n", + " include_original=True\n", + " )\n", + " rotate = ips.bootstrap.RotateMolecules(\n", + " data=geopt.atoms,\n", + " data_id=-1,\n", + " n_configurations=n_configs,\n", + " maximum=15, # deg max rotation\n", + " include_original=False\n", + " )\n", + " translate = ips.bootstrap.TranslateMolecules(\n", + " data=geopt.atoms,\n", + " data_id=-1,\n", + " n_configurations=n_configs,\n", + " maximum=0.3, # Ang max molecular displacement\n", + " include_original=False\n", + " )\n", + "\n", + " bootstrap_configurations = rattle.atoms + rotate.atoms + translate.atoms\n", + "\n", + " labeling_calc = ips.calculators.xTBSinglePoint(data=bootstrap_configurations, method=\"gfn1-xtb\", name=\"label_calc\")\n", + " volume_scan = ips.analysis.BoxScale(\n", + " data=rattle.atoms,\n", + " data_id=0,\n", + " model=labeling_calc,\n", + " mapping=mapping,\n", + " start=0.8,\n", + " stop=1.5,\n", + " num=5,\n", + " )\n", + " bootstrap_dataset = znflow.combine([labeling_calc, volume_scan], attribute=\"atoms\")\n", + "\n", + " energy_hist = ips.analysis.EnergyHistogram(data=bootstrap_dataset, bins=10)\n", + " forces_hist = ips.analysis.ForcesHistogram(data=bootstrap_dataset, bins=10)\n", + "\n", + "project.run()" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Lets inspect the label distribution of our new dataset.\n", + "While they produce a plot in the respective `nodes` subdirectory, we will recreate them here to view them from within the notebook.\n", + "\n", + "In order to do that, we first have to load the histogram nodes.\n", + "Then we can create simple histogram with matplotlib.\n" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "energy_hist.load()\n", + "forces_hist.load()" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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", + "text/plain": [ + "
" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "counts, bin_edges = energy_hist.get_hist()\n", + "\n", + "plt.stairs(counts, bin_edges, fill=True)\n", + "plt.xlabel(energy_hist.xlabel)\n", + "plt.ylabel(energy_hist.ylabel)\n", + "plt.yscale(\"log\")\n", + "plt.show()\n" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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", + "text/plain": [ + "
" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "counts, bin_edges = forces_hist.get_hist()\n", + "\n", + "plt.stairs(counts, bin_edges, fill=True)\n", + "plt.xlabel(forces_hist.xlabel)\n", + "plt.ylabel(forces_hist.ylabel)\n", + "plt.yscale(\"log\")\n", + "plt.show()" + ] + }, + { + "attachments": {}, + "cell_type": "markdown", + "metadata": {}, + "source": [ + "In both histograms we can see some outliers with fairly high energies / large forces.\n", + "While a few configurations like this are usually not detrimental to model performance, one should tune the displacement parameters such as to not obtain completely unphysical configurations.\n", + "\n", + "The data created here could now be supplied to a model Node and used for training." + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [], + "source": [ + "temp_dir.cleanup()" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "ips", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.11" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/index.rst b/index.rst new file mode 100644 index 00000000..d6428eab --- /dev/null +++ b/index.rst @@ -0,0 +1,20 @@ +.. IPSuite documentation master file, created by + sphinx-quickstart on Mon May 22 19:56:43 2023. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to IPSuite's documentation! +=================================== + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/ipsuite/calculators/__init__.py b/ipsuite/calculators/__init__.py index 3327a4b4..4607f15b 100644 --- a/ipsuite/calculators/__init__.py +++ b/ipsuite/calculators/__init__.py @@ -1,5 +1,5 @@ -"""Calculators can be used for labeling a given set of data and -running molecular dynamics. For all cases, ASE calculators are used. +"""Calculators can be used for labeling a given set of data and running molecular dynamics. +For all cases, ASE calculators are used. """ import lazy_loader as lazy diff --git a/ipsuite/calculators/lammps.py b/ipsuite/calculators/lammps.py index 6e3227dd..c51e5904 100644 --- a/ipsuite/calculators/lammps.py +++ b/ipsuite/calculators/lammps.py @@ -1,3 +1,5 @@ +"""LAMMPS interface for MD Simulations using LAMMPS""" + import importlib.resources as pkg_resources import pathlib import subprocess @@ -12,7 +14,7 @@ class LammpsSimulator(base.ProcessSingleAtom): - """Can perform LAMMPS Simulations. + """Perform LAMMPS Simulations. Parameters ---------- diff --git a/ipsuite/configuration_comparison/__init__.py b/ipsuite/configuration_comparison/__init__.py index 546acd9c..6ffc1cc8 100644 --- a/ipsuite/configuration_comparison/__init__.py +++ b/ipsuite/configuration_comparison/__init__.py @@ -1,4 +1,4 @@ -"""Configuration Comparison Module.""" +"""Provides kernel based similarity measures for comparing configruations.""" import lazy_loader as lazy diff --git a/ipsuite/configuration_generation/__init__.py b/ipsuite/configuration_generation/__init__.py index 6d2952d5..f421ba23 100644 --- a/ipsuite/configuration_generation/__init__.py +++ b/ipsuite/configuration_generation/__init__.py @@ -1,4 +1,6 @@ -"""Module for generating new configurations based on smiles.""" +"""This module provides Nodes for creating molecular dynamics starting structures. +Workflows can be quickly created from just knowing the SMILES strings of the molecules within the simulation box. +The PACKMOL interface can then be used to create the actual starting configuration.""" import lazy_loader as lazy diff --git a/ipsuite/configuration_generation/packmol.py b/ipsuite/configuration_generation/packmol.py index 21b4eca2..d59ea802 100644 --- a/ipsuite/configuration_generation/packmol.py +++ b/ipsuite/configuration_generation/packmol.py @@ -18,6 +18,7 @@ class Packmol(base.IPSNode): """ + Pack molecules in defined regions of space Attributes ---------- diff --git a/ipsuite/configuration_generation/smiles_to_atoms.py b/ipsuite/configuration_generation/smiles_to_atoms.py index 5a29ddd4..1e9d73c9 100644 --- a/ipsuite/configuration_generation/smiles_to_atoms.py +++ b/ipsuite/configuration_generation/smiles_to_atoms.py @@ -1,3 +1,5 @@ +"""Use RDKit to convert Smiles strings to atoms""" + import pathlib import ase @@ -10,6 +12,8 @@ class SmilesToAtoms(base.IPSNode): + """Generate ase.atom object from smiles string""" + atoms = fields.Atoms() smiles: str = zntrack.params() @@ -45,6 +49,8 @@ def view(self) -> view: class SmilesToConformers(base.IPSNode): + """Generate random conformers of molecule from smiles string""" + atoms = fields.Atoms() smiles: str = zntrack.params() diff --git a/ipsuite/configuration_selection/__init__.py b/ipsuite/configuration_selection/__init__.py index 0c9664e6..2ce5de35 100644 --- a/ipsuite/configuration_selection/__init__.py +++ b/ipsuite/configuration_selection/__init__.py @@ -1,4 +1,5 @@ -"""Configuration Selection Nodes.""" +"""The configuration selection submodule contains Nodes for splitting datasets. +A simple 80:20 random split can be achieved with a single Node, but multiple Nodes can be chained to create complex splittings..""" from ipsuite.configuration_selection.base import ConfigurationSelection from ipsuite.configuration_selection.filter import FilterOutlier diff --git a/ipsuite/data_loading/__init__.py b/ipsuite/data_loading/__init__.py index 5ddcdccb..513b38f5 100644 --- a/ipsuite/data_loading/__init__.py +++ b/ipsuite/data_loading/__init__.py @@ -1,4 +1,5 @@ -"""ipsuite data loading module.""" +"""IPS can load datasets from ASE readable formats and HDF5 files. +Internally, atomistic data is represented by ASE's `Atoms` objects which are serialized to HDF5.""" from ipsuite.data_loading.add_data_ase import AddData, ReadData from ipsuite.data_loading.add_data_h5md import AddDataH5MD diff --git a/poetry.lock b/poetry.lock index cd1bb554..b5ee59e7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,25 +13,25 @@ files = [ [[package]] name = "aiobotocore" -version = "2.13.1" +version = "2.14.0" description = "Async client for aws services using botocore and aiohttp" optional = false python-versions = ">=3.8" files = [ - {file = "aiobotocore-2.13.1-py3-none-any.whl", hash = "sha256:1bef121b99841ee3cc788e4ed97c332ba32353b1f00e886d1beb3aae95520858"}, - {file = "aiobotocore-2.13.1.tar.gz", hash = "sha256:134f9606c2f91abde38cbc61c3241113e26ff244633e0c31abb7e09da3581c9b"}, + {file = "aiobotocore-2.14.0-py3-none-any.whl", hash = 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