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General Utility Lattice Program Version 4.5 Julian D General Utility Lattice Program Version 4.5 Julian D. Gale Curtin Institute for Computation, Department of Chemistry, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia email: [email protected] 1 Chapter 1 Introduction & background The General Utility Lattice Program (GULP) is designed to perform a variety of tasks based on force field methods. The original code was written to facilitate the fitting of interatomic potentials to both energy surfaces and empirical data. How- ever, it has expanded now to be a general purpose code for the modelling of con- densed phase problems. While version 1.0 focussed on solids, clusters and embed- ded defects, the latest version is also capable of handling surfaces, interfaces, and polymers. As with any large computer program (and GULP currently runs to about 460,000 lines) there is always the possibility of bugs. While every attempt is made to ensure that there aren’t any and to trap incorrect input there can be no guarantee that a user won’t find some way of breaking the program. So it is important to be vigilant and to think about your answers - remember GIGO! Immature optimising compilers can also be a common source of grief. As with most programs, the author accepts no liability for any errors but will attempt to correct any that are reported. As from GULP3.4, the program has migrated to Fortran 90 and should compile with any standard f90 compiler. From version 4.0 the code included several ma- jor additions, the most significant of which are the addition of the ReaxFF reactive force field and also the facility to use continuum dielectric solvation in multiple dimensions through the COSMIC algorithm, derived as the name would suggest from COSMO. A further major improvement is the addition of a stochastic thermo- stat/barostat with a new integrator in molecular dynamics. This is far more robust than the old schemes used and less sensitive to the choice of parameters. Finally, the ability to calculate PDF data has been added courtesy of Beth Cope and Mar- tin Dove (University of Cambridge at the time; now Queen Mary, University of London). In version 4.2 the calculation of thermal conductivity has been added based on the Allen-Feldman approach for diffusons. This was achieved through a collaboration with Jason Larkin (Carnegie Mellon, Pittsburgh). 2 1.1 References for GULP The following papers describe various aspects of GULP: Basic algorithms and symmetry adaption: • J.D. Gale, J.C.S. Faraday Transactions, 93, 629-637 (1997) Detailed background theory: • J.D. Gale and A.L. Rohl, Molecular Simulation, 29, 291-341 (2003) Free energy minimisation: • J.D. Gale, J. Phys. Chem. B, 102, 5423 (1998) Review of status and functionality: • J.D. Gale, Z. Krist., 220, 552-554 (2005) Solvent models in GULP: • J.D. Gale and A.L. Rohl, Molecular Simulation, 33, 1237-1246 (2007) ReaxFF in GULP: • J.D. Gale, P. Raiteri and A.C.T. van Duin, PCCP, 13, 16666-16679 (2011) Pair Distribution Functions in GULP: • E.R. Cope and M.T. Dove, J. Appl. Cryst., 40, 589-594 (2007) Thermal conductivity in GULP: • J.M. Larkin and A.J.H. McGaughey, Phys. Rev. B, 89, 144303 (2014) 1.2 Overview of program The following is intended to act as a brief summary of the capabilities of GULP to enable you to decide whether your required task can be performed without having to read the whole manual. Alternatively it may suggest some new possibilities for calculations! 3 System types • 0-D (clusters and embedded defects) • 1-D (polymers, screw dislocations) • 2-D (slabs, surfaces, grain boundaries, interfaces) • 3-D (bulk materials) Energy minimisation • constant pressure / constant volume / unit cell only / isotropic / orthorhombic • thermal/optical calculations • application of external isotropic or anisotropic pressure • user specification of degrees of freedom for relaxation • relaxation of spherical region about a given ion or point • symmetry constrained relaxation • unconstrained relaxation • constraints for fractional coordinates and cell strains • Newton/Raphson, conjugate gradients or Rational Function optimisers • BFGS or DFP updating of hessian • limited memory variant of BFGS for large systems • search for minima by genetic algorithms with simulated annealing • free energy minimisation with analytic first derivatives • choice of regular or domain decomposition algorithms for first derivatives • minimisation of gradient/force norm instead of energy • uniaxial stress Transition states • location of n-th order stationary points • mode following 4 Crystal properties • elastic constants • bulk modulus (Reuss/Voigt/Hill conventions) • shear modulus (Reuss/Voigt/Hill conventions) • Young’s modulus • Poisson ratios • compressibility • piezoelectric stress and strain constants • static dielectric constants • high frequency dielectric constants • frequency dependent dielectric constants • static refractive indices • high frequency refractive indices • NMR chemical shifts • stress tensor • phonon frequencies • phonon densities of states (total and projected) • phonon dispersion curves • group velocities • S/P-wave velocities • Born effective charges • zero point vibrational energies • heat capacity (constant volume) • entropy (constant volume) • Helmholtz free energy 5 • pair distribution function (PDF) calculation • thermal conductivity (Allen-Feldman model) • Raman susceptibility tensors Molecular properties • centre of mass • moment of inertia tensor • rotational partition function • translational partition function • rotational/translational free energy Defect calculations • vacancies, interstitials and impurities can be treated • explicit relaxation of region 1 • implicit relaxation energy for region 2 • energy minimisation and transition state calculations are possible • defect frequencies can be calculated (assuming no coupling with 2a) Surface calculations • calculation of surface and attachment energies • multiple regions allowed with control over rigid or unconstrained movement • can be used to simulate grain boundaries and interfaces • calculation of phonons allowed for region 1 • continuum solvation of surfaces 6 Fitting • empirical fitting to structures, energies and most crystal properties • fit to multiple structures simultaneously • simultaneous relaxation of shell coordinates during fitting • fit to structures by either minimising gradients or displacements • variation of potential parameters, charges and core/shell charge splits • constraints available for fitted parameters • simplex or BFGS minimisation algorithms for fitting • generate initial parameter sets by the genetic algorithm for subsequent refine- ment • fit to quantum mechanically derived energy hypersurfaces • bond lengths, bond angles, volume and reaction energies now available as observables Structure analysis • calculate bond lengths/distances • calculate bond angles • calculate torsion angles • calculate improper torsion angles • calculate out of plane distances • calculation of the density and cell volume • electrostatic site potentials • electric field gradients Structure manipulation • convert centred cell to primitive form • creation of supercells 7 Electronegativity equalisation method • use EEM to calculate charges for systems containing H, C, N, O, F, Al, Si, P • use QEq to calculate charges for any element • new modified scheme for hydrogen within QEq that has correct forces • Gasteiger charge calculation based on bond increments • calculation of charges from ReaxFF Generation of files for other programs • GDIS (.gin/.res) • THBREL/THBPHON/CASCADE (.thb) • MARVIN (.mvn) • Insight (.xtl file) • Insight (.arc/.car files) • G-Vis (.xr) • Cerius2 (.arc/.xtl/.cssr) • Materials Studio • COSMO solvent accessible surface for Materials Studio • SIESTA (.fdf) • Molden (.xyz) • QMPOT (.frc) • General (.cif/.xml) • DLV (.str) • lammps_pot (Table of potentials for use in LAMMPS) 8 Output files for post-processing • Pressure tensor (.pre) • Oscillator strengths • Pair distribution function (.pdf) • Charges and bond orders (.qbo) • MD trajectory file (.trg) Interatomic potentials available • Buckingham • Four-range Buckingham • Buckingham in MM3 format • Lennard-Jones (with input as A and B) • Lennard-Jones (with input in e and s format) • Lennard-Jones (with ESFF combination rules) • Morse potential (with or without Coulomb subtract) • Harmonic (with or without Coulomb subtract) • MM3 bond stretching potential (with or without Coulomb subtract) • General potential (Del Re) with energy and gradient shifts • Spline • Spring (core-shell) • Spring with cosh functional form • Coulomb subtract • Coulomb with erfc • Coulomb with short range taper • Inverse Gaussian • Damped dispersion (Tang-Toennies) 9 • Rydberg potential • Covalent exponential form • Breathing shell harmonic • Breathing shell exponential • Coulomb with complementary error function • Coulomb with short range taper • Covalent-exponential • Fermi-Dirac form • Three body potentials - harmonic with or without exponential decay • Exponential three-body potential • Urey-Bradley three-body potential • Stillinger-Weber two- and three-body potentials • Stillinger-Weber with charge softening • Axilrod-Teller potential • Four-body torsional potential • Ryckaert-Bellemans cosine expansion for torsional potential • Out of plane distance potential • Tsuneyuki Coulomb correction potential • Squared harmonic • Mei-Davenport twobody • Glue potential • Short range potentials based on (complementary) error functions • Embedded atom method for metals (Sutton-Chen potentials and others) • Modified Embedded Atom Method
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