ULaMDyn

Getting Started:

  • Installation
    • Development version
    • Optional dependencies
  • Wrapper program
    • Step 1: create geom.xyz file
    • Step 2: run ULaMDyn Wrapper
      • method 1: command-line parser
      • method 2: configuration file

Tutorial:

  • Data curation
    • GetProperties:
      • 1. energies():
      • 2. oscillator_strength():
      • 3. populations():
      • 4. nac_norm()
  • Walking through
    • Installation of required packages
    • The NAMD dataset: fulvene
    • ULaMDyn via command-line interface
    • Unsupervised analysis pipeline
      • Read and inspect data
      • Build dataset with chemical properties
      • Geometry-based descriptors
      • Dimensionality reduction
      • Isomap
      • Gradient-based descriptors
      • Clustering analysis
    • Smooth Overlap of Atomic Positions (SOAP)

Source documentation:

  • ulamdyn package
    • Subpackages
      • ulamdyn.nma package
      • ulamdyn.wrappers package
      • ulamdyn.unsup_models package
    • Submodules
    • ulamdyn.data_loader module
      • GetCoords
      • GetCouplings
      • GetGradients
      • GetProperties
    • ulamdyn.data_writer module
      • Geometries
    • ulamdyn.descriptors module
      • R2
      • RingParams
      • SOAPDescriptor
      • ZMatrix
    • ulamdyn.kinetics module
      • GetVelocities
      • KineticEnergy
      • VibrationalSpectra
    • ulamdyn.nx_utils module
      • check_nx_trajs()
      • get_labels_masses()
      • get_num_atoms()
      • get_nx_version()
      • get_traj_dirs()
      • read_h5_nx()
      • read_nx_control()
    • ulamdyn.statistics module
      • aggregate_data()
      • bootstrap()
      • calc_avg_occupations()
      • create_bootstrap_stats()
      • create_stats()
      • stats_hopping()
    • Module contents
      • ClusterGeoms
      • ClusterTrajs
      • DimensionReduction
      • GeomSampling
      • Geometries
      • GetCoords
      • GetCouplings
      • GetGradients
      • GetProperties
      • GetVelocities
      • KineticEnergy
      • NormalModeAnalysis
      • R2
      • RingParams
      • SOAPDescriptor
      • VibrationalSpectra
      • ZMatrix
ULaMDyn
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© Copyright 2021, Max Pinheiro Jr.

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