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Overview

pymatnext is a Python package for doing nested sampling (NS) which was developed as a complete rewrite of pymatnest. While it is coded with some generalizability in mind, it is designed for atomistic materials science applications, and currently supports single atomic configurations with the ASE atoms object.

Features

Nested Sampling

  • Sample on potential energy $E$, with or without enthalpy term $+ P V$ for fixed pressure and chemical potential term $- \sum_i \mu_i N_i$ for variable composition (but constant total number of atoms, i.e. semi-grand-canonical ensemble).

  • Output arbitrary sampled quantities, including NS quantity ($E + \delta_V P V - \delta_N \sum_i \mu_i N_i$), as well as configuration-type-specific quantities such as cell volume and composition.

  • Output sampled configurations, for postprocessed computation at any temperature of any quantity that can be computed from the configurations.

  • Save snapshots of population and random number generator states for restarts

  • One sample culled per NS iteration

Parallelization

  • Optionally parallelized with MPI by distributing configurations among $N_p$ MPI tasks and walking one configuration per task for a shorter trajectory length $L' = L / N_p$.

Configurations

  • Periodic or nonperiodic cells containing atoms of any chemical species. Use an extended version of the ase.atoms.Atoms class, which stores all important data in two np.ndarray objects, so that MPI parallelized runs can communicate them without having to pack/unpack the data each time.

Energy calculators

  • ASE ase.calculators.Calculator, with random walks carried out by Python code within pymatnext.

  • LAMMPS potentials with random walks carried out inside LAMMPS with a custom set of fixes.

Random walks

Walks consist of blocks of a several steps of a single type (position or cell or species).

Positions

  • Positions sampled with Galilean Monte Carlo, i.e. walking in a straight line in $3 N$ dimensional positions space until energy exceeds NS maximum, then reflecting specularly, and accepting or rejecting entire trajectory depending on on final energy.

Cell

  • Cell shape and size sampled with Monte Carlo moves. Volume may be sampled from a $V^{N}$ prior, which is the correct one for ensemble averages, or with a flat prior, which requires reweighting of the sampled configurations during analysis.

Species

  • Atom species sampled with Monte Carlso swap or semi-grand-canonical (total atom number conserving at an applied chemical potential) moves.

Usage

see here

complete parameters list

Analysis

see here

Using LAMMPS

LAMMPS compiled with cmake

To use lammps, set the env var LAMMPS_DIR to the top of the LAMMPS source directory, above src/ and cmake/, and do

cd $LAMMPS_DIR
patch_file=$( python3 -c 'import pymatnext; from pathlib import Path; print(str(Path(pymatnext.__file__).parent) + "/extras/lammps.patch")' )
patch -p1 < $patch_file

The NS package must then be added to enable the fix ns/* commands, and LAMMPS must be recompiled without MPI support. The LAMMPS python interface must then be installed.

If using cmake, this can be done by adding NS to the section set(STANDARD_PACKAGES... (the patch file in pymatnext/extras/lammps.patch should do this), and adding -D PKG_NS=ON to the cmake command (in addition to

-D BUILD_MPI=OFF
-D BUILD_SHARED_LIBS=ON
-D LAMMPS_EXCEPTIONS=ON

and whatever other options are needed). Installing the python package is most easily done with make install-python after the regular make.

TODO

(in order of priority?)

  • refactor <prefix>.NS_samples and <prefix>.traj.<suffix> truncation code (minor)
  • create ABC for NSConfig (med)
  • sample positions with TE-HMC (major)

Done

  • restart from snapshots
  • refactor NSConfig.n_quantities to be a class rather than instance attribute (minor)