OpenMD version 2.5 is now available for download at openmd.org.  This is a major update with many new features, system builders, analysis scripts, force fields, and samples. In addition to hundreds of bug fixes and performance improvements, here are some of the new features that have been added since the 2.4 release:

New builders:

  • New slabBuilder to create starting omd files for arbitrary surface cuts specified by Miller indices (hkl) of FCC, BCC and SC materials (can also optionally include charged capacitor plates)
  • icosahedralBuilder can now build Cuboctahedral and TruncatedCube nanoparticles, atoms now sorted by distance from center of nanoparticle
  • New atom2omd program for converting other file formats into OpenMD (.omd) format – defaults to openbabel’s atom typing in most cases

New potential energy forms:

  • Buckingham (Traditional and Modified) non-bonded interactions
  • SDK Bends and Mie Bonds to support the Shinoda, DeVane, Klein (SDK) CG force field
  • Bonded interactions (Bonds, Bends, Torsions, Inversions) may now span the periodic box – useful for polymers, graphene sheets, etc.

New force fields:

  • BKS model for Silicas and Aluminophosphates from van Beest, Kramer, and van Santen, Phys. Rev. Lett. 64(16), pp. 1955-1958 (1990)
  • BKS modified variant from Saika-Voivod, Sciortino, Grande, and Poole, Phys. Rev. E 70, 061507 (2004)
  • EAM Zhou2001 variant for alloys from Zhou et al., Acta Materialia 49(19), pp. 4005-4015 (2001)
  • EAM Zhou2004 implements parameterization in Zhou et al. Phys. Rev. B, 69, 144113 (2004)
  • EAM Zhou2005 implements EAM portion of Zhou and Wadley, J. Phys. Cond. Matter. 17 (2005) 3619-3635
  • Shinoda, DeVane, Klein (SDK) coarse grained model for lipids, surfactants, benzene, fullerenes, and ionic liquids
  • Water force field (Water.frc) has added support for most of the common non-polarizable water models (SPC*, TIP*, SSD*, OPC)

Changes in the OpenMD engine:

  • New stats file queries for net_charge, charge_momentum, electronic_kinetic
  • New stat file keyword: statFilePrecision
  • New NVE propagator for fluctuating charges. Set it with the propagator keyword in a flucq{} block.
  • Minimizer now reports to stats and dump files at each minimization step
  • Added a stats report file (.report) after run is completed (also written to stdout at end of run
  • When outputElectricField is turned on, the local field calculation is now done even when a site is not electrostatic
  • Added outputSelection keyword for rnemd{} blocks so that data can be collected for specific StuntDoubles that aren’t the exchange objects
  • Added dividingSurface keyword for rnemd{} blocks for instances when the dividing surface area should not be calculated using a convex hull
  • Added an outputDensity keyword which will adds EAM-style densities to site lines in dump files

Changes to StaticProps:

New static analysis modules:

  • Coordination Number (--cn) – number of atoms within a cutoff distance
  • Secondary Coordination Number (--scn) – mean coordination number of neighboring atoms
  • Generalized Coordination Number (--gcn) – coordination numbers described in F. Calle-Vallejo et al., Science 350(6257) pp. 185-189 (2015)
  • Tetrahedrality order parameter (--tet_param) computes distributions of P(Q) described in Errington and Debenedetti, Nature 409, pp. 318-321 (2001), but allowing for arbitrary numbers of neighbors
  • New --densityfield and --velocityfield analyzers for volume and stream line rendering
  • New 3-dimensional pair distribution  (--r_theta_omega) module for computing g(r, cos(θ), cos(ω))

Changes to existing modules:

  • Hxy (height of a surface) has been completely rewritten with new interpolation and gridding scheme, and new 2-d FFTs of the surface
  • HullVolume module now uses convex hulls and not alpha shapes
  • Many one-dimensional distribution functions now can compute using a --privilegedAxis (GofRZ, GofZ, RNEMDZStats)

Changes to DynamicProps:

New correlation functions:

  • Momentum / Angular momentum cross correlation functions (--pjcorr)
  • ForceTorque and TorqueForce cross correlation function (--ftcorr and --tfcorr)
  • Force and Torque autocorrelation functions (--facorr and --tacorr)

New Analysis and Utility Scripts:

  • New slipLength calculator for shearing simulations of solid / liquid simulations in slip boundary conditions
  • New solLiqFricCalc script for calculating solid liquid friction coefficients from results in .rnemd files
  • New stat2tension calculator for computing surface tensions from pressure tensors in stat files
  • New hbtetAnalyzer for doing analysis on Hydrogen Bond Tetrahedrality matrices
  • New funcflExtractor utility pulls density, embedding functional, and Z(r) information from DYNAMO86-style funcfl files
  • omd2omd can now rotate as well as replicating and translating the simulation box

New Samples:

  • New Graphene sheet sample demonstrating structures that span the box
  • New tip4p-ice sample

Go grab it at the Download page!