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aimmd 0.10.1 documentation

  • GitHub
  • PyPI

The Basics

  • Installation

User guide

  • aimmd.distributed
    • Transition Path Sampling
      • Two way shooting pathmovers
      • Abstract base classes for pathmovers
      • Shooting point selectors
      • Abstract base classes for shooting point selectors
    • Committor Simulations

Community

  • Get support
  • Contributing to aimmd

Example notebooks

  • Overview
    • aimmd.distributed
      • TPS 1: Setup and run simulation
      • TPS 2: Continue simulation
      • TPS 3: Analyze simulation
      • TPS 4: Rerun with changed parameters or recover crashed simulations
      • TPS with EQ SPs 1: Generate SPs from UmbrellaSampling
      • TPS with EQ SPs 2: Setup and run simulation
      • TPS with EQ SPs 3: Continue and analyze simulation
      • TPS with EQ SPs 4: Rerun with changed parameters or recover crashed simulations
      • Committor simulation
      • Advanced topics: Customizing your TPS simulations using BrainTasks
    • classic
      • Toy system(s)
        • 1 toy pytorch simple: setup
        • 1 toy pytorch simple: setup XY diagpotential (Hummer-Szabo potential)
        • 2 toy pytorch simple: continuing simulations
        • 3 toy symbolic regression
        • 4 toy: loading and saving rcmodels
        • 1.5 toy pytorch multidomain model: setup
      • Lithium chloride dissociation
        • 1 pytorch ResNet reduced symmetry functions
        • 2 emulate production and postprocessing training pytorch pyramid SNN, ResNet top
        • 2 emulate production and postprocessing training pytorch pyramidal ResNet
        • 2 committor cross correlation
      • Capped alanine dipeptide
        • 1 pytorch: setup and TPS
        • 2: analysis
        • ANN assisted TPS on capped alanine dipeptide 1
        • 1.5 keras: continue TPS with new storage
    • Apply aimmd on existing data
      • Methane clathrate nucleation at different temperatures

Module layout

  • aimmd
    • aimmd.analysis
      • aimmd.analysis.gradient_movie
      • aimmd.analysis.hipr
    • aimmd.base
      • aimmd.base.density_collection
      • aimmd.base.rcmodel
      • aimmd.base.rcmodel_train_decision
      • aimmd.base.storage
      • aimmd.base.trainset
      • aimmd.base.utils
    • aimmd.coords
      • aimmd.coords.internal
      • aimmd.coords.symmetry
      • aimmd.coords.utils
    • aimmd.distributed
      • aimmd.distributed.committors
      • aimmd.distributed.config
      • aimmd.distributed.dataclasses
      • aimmd.distributed.dataclasses_internal
      • aimmd.distributed.pathmovers
      • aimmd.distributed.pathsampling
      • aimmd.distributed.spselectors
      • aimmd.distributed.utils
    • aimmd.ops
      • aimmd.ops.hooks
      • aimmd.ops.selector
      • aimmd.ops.utils
    • aimmd.tools

Changelog and Indices

  • Changelog
  • Module Index
  • Index
  • Repository
  • Show source
  • Suggest edit
  • .rst

aimmd

This file is part of AIMMD.

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By Hendrik Jung

© Copyright 2018-now, Hendrik Jung.