OpenMD version 2.6 is now available for download at openmd.org. This is a major update with many new features, analysis scripts, force fields, and samples. In particular, there is a new and incredibly useful elasticConstants utility that is now part of OpenMD. In addition to hundreds of bug fixes and performance improvements, here are some of the new features that have been added since the 2.5 release:

New potential energy forms:

  • Magnetic fields have been added to perturbations. Invoke them with magneticField = (a, b, c);
  • The Density-Readjusting Embedded Atom Method (DR-EAM) is now part of OpenMD
  • Added InversePowerSeries non-bonded interactions
  • Added ZhouRose EAM type for Rose functionals
  • Added a new fluctuating charge type, EAMPoly, which allows polynomial self-potentials.

New force fields:

  • New entries in the Water.frc force field for OPC, NE6, TIP4P-Ice, and other water models.
  • graphene.frc file for simulating sheets of graphene
  • Added an “Air” force field file and some samples
  • DR-EAM force field and samples added

Changes in the OpenMD engine:

  • NPAT, NPTsz and NPTf can all use privilegedAxis keyword for defining the “special axis” for volume modifications
  • new AlphaHull selection: “select alphaHull(2.9)“
  • Added automatic file sync for StatWriter and DumpWriter (useful on afs systems)
  • Added a privilegedAxis to RNEMD engine
  • Changes for RNEMD to allow electrical currents (Current, KE+Current, KE+Pvector+Current)
  • Added option for “useSurfaceTerm” to do dipolar surface term outside of the Ewald sum
  • Added a “useSlabGeometry” flag so that 2-D surface term can be done in slab configurations
  • Added some new statFileFormat options to pull out embedding energy in metallic potentials
  • Lots of internal changes to support fluctuating charge (fluc-q) water and fluctuating density embedded atom methods (notably DR-EAM).
  • Added “doInitialOptimization” keyword to flucq section

Changes to StaticProps:

OpenMD 2.6 adds privilegedAxis functionality to spatially-dependent StaticProps modules. You can now specify which axis along which you wish to compute properties, but the default is the z-axis.

New static analysis modules:

  • RhoYZ (–pipe_density) for calculating density along two axes, e.g. ρ(y, z)
  • current density (-J, –current_density) for measuring non-equilibrium response to an applied electric field.
  • EAM density profile (-D, –eam_density) for calculating distributions of valence electron densities
  • Net charge (-q, –net_charge) for interrogating charge distributions for fluctuating charge models
  • Momentum distribution (-M, –momentum_distribution) for querying momentum distributions and looking at adherence to Maxwell-Boltzmann statistics

Changes to existing modules:

  • Added integration to g(r) (–gofr) calculation (useful for coordination calculations)

Changes to DynamicProps:

OpenMD 2.6 adds privilegedAxis functionality to spatially-dependent DynamicProps modules. You can now specify which axis along which you wish to compute correlations, but the default is the z-axis.

New correlation functions:

  • Displacement (–disp) and DisplacementZ (–dispZ) for looking at separations along specific axes in flowing systems
  • Hydrogen bond persistence correlation function: HBondPersistence (–persistence)
  • Hydrogen bond jump time correlation functions HBondJump (–jumptime) and HBondJumpZ (–jumptimeZ)
  • Legendre correlation functions (-l, –lcorr, –lcorrZ) have been converted to multipass (much faster)
  • Charge velocity autocorrelation function (-w, –wcorr) added for fluctuating charge models.

New Analysis and Utility Scripts:

In OpenMD 2.6, we have converted all of the utility scripts to python3, and made python3 a requirement. NumPy and SciPy are also now required.

  • Added powerful new elasticConstants utility that calculates the elastic properties of materials.
  • protonSampler generates proton disordered ice-Ih lattices given an (.xyz) coordinate file for the Oxygen lattice
  • Dump2XYZ now has globalID (-g) flag for printing the globalID of each Atom or StuntDouble to the xyz file (useful for debugging)
  • thermalizer can now scale the kinetic energy to match a pre-set total energy value (using the -e flag). It can also resample charge velocities to match a specific electronic temperature (with the -c flag).
  • lcorrzFit – a utility script to analyze of Legendre correlation functions (binned by Z)
  • omdLast – Makes a .omd file from the last good frame of OpenMD dump file.

New Samples:

  • Lots of new ice structures: Hayward and Reimers unit cells, Hirsch and Ojamae unit cells
  • Cleanup of the RNEMD samples
  • New DR-EAM samples for studying image charge effects, ordered alloys, and screening by metal surfaces.
  • Added Oxide Library for binary Metal Oxides.

Go grab it at the Download page!