Core modules ============ These are the building blocks which are used to construct the CVs. NN -- This module implements the architectures with learnable weights that can be used to build CV models. Descriptors-based ^^^^^^^^^^^^^^^^ .. currentmodule:: mlcolvar.core.nn .. autosummary:: :toctree: autosummary :template: custom-class-template.rst FeedForward Graphs-based ^^^^^^^^^^^^ .. currentmodule:: mlcolvar.core.nn.graph Base class """""""""" .. autosummary:: :toctree: autosummary :template: custom-class-template.rst BaseGNN Architectures """"""""""""" .. autosummary:: :toctree: autosummary :template: custom-class-template.rst SchNetModel GVPModel Loss ---- This module implements the loss functions that can be used to optimize CV models. .. currentmodule:: mlcolvar.core.loss .. autosummary:: :toctree: autosummary :template: custom-class-template.rst MSELoss ELBOGaussiansLoss FisherDiscriminantLoss AutocorrelationLoss ReduceEigenvaluesLoss TDALoss CommittorLoss GeneratorLoss SmartDerivatives Stats ----- This module implements statistical methods with learnable weights that can be used in CV models. Base class ^^^^^^^^^^ .. currentmodule:: mlcolvar.core.stats .. autosummary:: :toctree: autosummary :template: custom-class-template.rst Stats Linear methods ^^^^^^^^^^^^^^ .. currentmodule:: mlcolvar.core.stats .. autosummary:: :toctree: autosummary :template: custom-class-template.rst PCA LDA TICA Transform --------- This module implements **non-learnable** pre/postprocessing tools Base class ^^^^^^^^^^ .. currentmodule:: mlcolvar.core.transform .. autosummary:: :toctree: autosummary :template: custom-class-template.rst Transform Descriptors ^^^^^^^^^^^ This submodule implements several descriptors that can be computed starting from atomic positions. .. currentmodule:: mlcolvar.core.transform.descriptors .. autosummary:: :toctree: autosummary :template: custom-class-template.rst PairwiseDistances TorsionalAngles CoordinationNumbers EigsAdjMat MultipleDescriptors Tools ^^^^^ This submodule implements pre/postporcessing tools. .. currentmodule:: mlcolvar.core.transform.tools .. autosummary:: :toctree: autosummary :template: custom-class-template.rst Normalization ContinuousHistogram SwitchingFunctions