About pymatnest

The pymatnest package is a software library written by Noam Bernstein in Fortran 95/python for the purpose of carrying out nested sampling calculations.

Long term support of the package is ensured by:

• Noam Bernstein (Naval Research Laboratory)

• Gabor Csanyi (University of Cambridge)

• Rob Baldock (EPFL)

• Livia Bartok-Partay (University of Warwick)

Copyright 2015-2016.

Most of the publicly available version is in the public domain. If you use this code please cite the following articles:

R.J.N. Baldock, N. Bernstein, K. M. Salerno, L.B. Partay, G. Csanyi, Constant-pressure nested sampling with atomistic dynamics, Phys. Rev. E (2017), 96, 043311, https://link.aps.org/doi/10.1103/PhysRevE.96.043311

L.B. Partay, G. Csanyi, N. Bernstein Nested sampling for materials Eur. Phys. J. B (2021) 94, 159, https://link.springer.com/article/10.1140/epjb/s10051-021-00172-1

Features

• both constant volume and constant pressure calculations (variable cell shapes)

• single and multicomponent systems

• Monte Carlo and Molecular Dynamics exploration

• 2D systems

• can be used with

  • the supplied fortran models

  • LAMMPS

  (- QUIP not currently compatible)

Contents

• Nested sampling method
  • Overview
  • Publications
  • Algorithm
  • pymatnest
    • MC and MD step algorithms
• Installation and quick start guide
  • System requirements
  • Compilation of the streamlined FORTRAN models and MC/MD walkers.
  • Using with LAMMPS
    • Mandatory compilation flags (for all LAMMPS versions)
    • Basic instructions for recent versions of LAMMPS and mpi4py version 2.0.0 or newer
    • Basic instructions for LAMMPS versions Nov 2020 or before:
    • Support for GMC within LAMMPS
    • Support for molecules
    • Mixed MPI-OpenMP
    • Other notes
    • For versions of mpi4py older than 2.0.0
    • For older versions of LAMMPS
  • Running
  • Running on ARCHER (UK National Supercomputing Service)
  • Analysis
  • Temperature averaged analysis workflow
  • About the documentation
• Getting started
  • List of input parameters
    • usage()
  • Example input files
    • LJ Cluster with the supplied fortran code, using MC
    • Periodic LJ with LAMMPS, using MD
    • Periodic binary LJ with the supplied fortran code or LAMMPS, using MD
    • Molecule with LAMMPS, using MD
  • Some tips on setting the input parameters
    • Setting the random walk parameters
    • Minimum lattice height: MC_cell_min_aspect_ratio
  • Restart a run
• Tutorials
  • Tutorial 1: 6 Lennard-Jones atoms at fixed volume
    • Create the input file ns_input_tutorial.inp
    • Starting the run
    • Output files and post-processing
    • Improving convergence
• pymatnest module
• ns_rng module
  • NsRng
    • NsRng.float_uniform()
    • NsRng.int_uniform()
    • NsRng.normal()
    • NsRng.seed_common()
    • NsRng.seed_init()
    • NsRng.seed_local()
    • NsRng.shuffle_in_place()
  • NsRngInternal
    • NsRngInternal.float_uniform()
    • NsRngInternal.int_uniform()
    • NsRngInternal.normal()
    • NsRngInternal.shuffle_in_place()
    • NsRngInternal.switch_to_common()
    • NsRngInternal.switch_to_local()
  • NsRngNumpy
    • NsRngNumpy.float_uniform()
    • NsRngNumpy.int_uniform()
    • NsRngNumpy.normal()
    • NsRngNumpy.shuffle_in_place()
    • NsRngNumpy.switch_to_common()
    • NsRngNumpy.switch_to_local()
  • NsRngStream
    • NsRngStream.float_uniform()
    • NsRngStream.int_uniform()
    • NsRngStream.normal()
    • NsRngStream.normal_variate()
    • NsRngStream.set_package_seed()
    • NsRngStream.shuffle_in_place()
    • NsRngStream.switch_to_common()
    • NsRngStream.switch_to_local()
  • os_random_uint32()
• rngstream module
  • RngStream
    • RngStream.create_stream()
    • RngStream.float_uniform_01()
    • RngStream.get_state()
    • RngStream.int_uniform()
    • RngStream.set_package_seed()
  • RngStream_InfoState
    • RngStream_InfoState.Anti
    • RngStream_InfoState.Bg
    • RngStream_InfoState.Cg
    • RngStream_InfoState.Ig
    • RngStream_InfoState.IncPrec
    • RngStream_InfoState.name
• lammpslib module
  • LAMMPSlib
    • LAMMPSlib.calculate()
    • LAMMPSlib.default_parameters
    • LAMMPSlib.implemented_properties
    • LAMMPSlib.initialise_lammps()
    • LAMMPSlib.initialized
    • LAMMPSlib.lammpsbc()
    • LAMMPSlib.parse_angles()
    • LAMMPSlib.parse_bonds()
    • LAMMPSlib.parse_dihedrals()
    • LAMMPSlib.parse_impropers()
    • LAMMPSlib.propagate()
    • LAMMPSlib.rebuild()
    • LAMMPSlib.redo_atom_types()
    • LAMMPSlib.restart_lammps()
    • LAMMPSlib.set_angles()
    • LAMMPSlib.set_bonds()
    • LAMMPSlib.set_cell()
    • LAMMPSlib.set_charges()
    • LAMMPSlib.set_dihedrals()
    • LAMMPSlib.set_impropers()
    • LAMMPSlib.set_lammps_pos()
    • LAMMPSlib.start_lammps()
    • LAMMPSlib.started
  • convert_cell()
  • is_upper_triangular()
  • unit_convert()
  • write_lammps_data()
• stacktrace module
  • debug()
  • listen()

Indices and tables

• Index

• Module Index

• Search Page