Merge pull request #477 from atomistic-machine-learning/mg/update_docs

Updated docs and fixed problems

docs/api/md.rst

@@ -0,0 +1,262 @@
+schnetpack.md
+=============
+.. currentmodule:: md
+
+This module contains all functionality for performing various molecular dynamics simulations using SchNetPack.
+
+System
+------
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    System
+
+
+Initial Conditions
+------------------
+
+.. currentmodule:: md.initial_conditions
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    Initializer
+    MaxwellBoltzmannInit
+    UniformInit
+
+
+Integrators
+-----------
+
+.. currentmodule:: md.integrators
+
+Integrators for NVE and NVT simulations:
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    Integrator
+    VelocityVerlet
+    RingPolymer
+
+Integrators for NPT simulations:
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    NPTVelocityVerlet
+    NPTRingPolymer
+
+
+Calculators
+-----------
+
+.. currentmodule:: md.calculators
+
+Basic calculators:
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    MDCalculator
+    QMCalculator
+    EnsembleCalculator
+    LJCalculator
+
+Neural network potentials and ORCA calculators:
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    SchNetPackCalculator
+    SchNetPackEnsembleCalculator
+    OrcaCalculator
+
+
+Neighbor List
+-------------
+
+.. currentmodule:: md.neighborlist_md
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    NeighborListMD
+
+
+Simulator
+---------
+
+.. currentmodule:: md
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    Simulator
+
+
+Simulation hooks
+----------------
+
+.. currentmodule:: md.simulation_hooks
+
+Basic hooks:
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    SimulationHook
+    RemoveCOMMotion
+
+Thermostats:
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    ThermostatHook
+    BerendsenThermostat
+    LangevinThermostat
+    NHCThermostat
+    GLEThermostat
+
+Thermostats for ring-polymer MD:
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    PILELocalThermostat
+    PILEGlobalThermostat
+    TRPMDThermostat
+    RPMDGLEThermostat
+    PIGLETThermostat
+    NHCRingPolymerThermostat
+
+Barostats:
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    BarostatHook
+    NHCBarostatIsotropic
+    NHCBarostatAnisotropic
+
+Barostats for ring-polymer MD:
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    PILEBarostat
+
+Logging and callback
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    Checkpoint
+    DataStream
+    MoleculeStream
+    PropertyStream
+    FileLogger
+    BasicTensorboardLogger
+    TensorBoardLogger
+
+
+Simulation data and postprocessing
+----------------------------------
+
+.. currentmodule:: md.data
+
+Data loading:
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    HDF5Loader
+
+Vibrational spectra:
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    VibrationalSpectrum
+    PowerSpectrum
+    IRSpectrum
+    RamanSpectrum
+
+
+ORCA output parsing
+-------------------
+
+.. currentmodule:: md.parsers
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    OrcaParser
+    OrcaOutputParser
+    OrcaFormatter
+    OrcaPropertyParser
+    OrcaMainFileParser
+    OrcaHessianFileParser
+
+
+MD utilities
+------------
+
+.. currentmodule:: md.utils
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    NormalModeTransformer
+
+Utilities for thermostats
+
+.. currentmodule:: md.utils.thermostat_utils
+
+.. autosummary::
+    :toctree: generated
+    :nosignatures:
+    :template: classtemplate.rst
+
+    YSWeights
+    GLEMatrixParser
+    load_gle_matrices
+    StableSinhDiv

docs/index.rst

@@ -62,3 +62,4 @@ Contents
    api/nn
    api/train
    api/transform
+   api/md