DL_POLY: Software and Applications I.T. Todorov & W. Smith ARC Group & CC Group CSED, STFC Daresbury Laboratory, Daresbury Warrington WA4 1EP, Cheshire, England, UK

Where is Daresbury?

Molecular Dynamics: Definitions Theoretical tool for modelling the detailed microscopic behaviour of many different types of systems, including gases, liquids, solids, surfaces and clusters. In an MD simulation, the classical equations of motion governing the microscopic time evolution of a many body system are solved numerically, subject to the boundary conditions appropriate for the geometry or symmetry of the system. Can be used to monitor the microscopic mechanisms of energy and mass transfer in chemical processes, and dynamical properties such as absorption spectra, rate constants and transport properties can be calculated. Can be employed as a means of sampling from a statistical mechanical ensemble and determining equilibrium properties. These properties include average thermodynamic quantities (pressure, volume, temperature, etc.), structure, and free energies along reaction paths.

DL_POLY Project Background General purpose parallel (classical) MD simulation software It was conceived to meet the needs of CCP5 - The Computer Simulation of Condensed Phases (academic collaboration community) Written in modularised Fortran90 (NagWare & FORCHECK compliant) with MPI2 (MPI1+MPI-I/O) fully self-contained 1994 – 2011: DL_POLY_2 (RD) by W. Smith & T.R. Forester (funded for 6 years by EPSRC at DL) -> DL_POLY_CLASSIC 2003 – 2011: DL_POLY_3 (DD) by I.T. Todorov & W. Smith (funded for 4 years by NERC at Cambridge) -> DL_POLY_4 Over 11,000 licences taken out since 1994 Over 1000 registered FORUM members since 2005 Available free of charge (under licence) to University researchers (provided as code) and at cost to industry

DL_POLY_DD Development Statistics

DL_POLY_DD Licence Statistics

DL_POLY Licence Statistics

DL_POLY Project Current State January 2011: DL_POLY_2 -> DL_POLY_CLASSIC on a BSD type Licence (BS retired but supporting GUI and fixes) October 2010: DL_POLY_3 -> DL_POLY_4 still under STFC Licence, over 1300 licences taken out since November 2010 Rigid Body dynamics Parallel I/O & netCDF I/O – NAG dCSE (IJB & ITT) CUDA+OpenMP port (source, ICHEC) & MS Windows port (installers) SPME processor grid freed from 2^N decomposition – NAG dCSE (IJB) Load Balancer development (LJE, finished 30/03/2011) Continuous Development of DL_FIELD (pdb to DLP I/O, CY)

DL_POLY_4 (version 1.2) –Dynamic Decomposition parallelisation, based on domain decomposition but with dynamic load balancing –limits up to ≈2.1×10 9 atoms with inherent parallelisation. –Full force field and molecular description with rigid body description –Free format (flexible) reading with some fail-safe features and basic reporting (but fully fool-proofed) DL_POLY Classic (version 1.6) –Replicated Data parallelisation, limits up to ≈30,000 atoms with good parallelisation up to 64 (system dependent) processors (running on any processor count) –Full force field and molecular description –Hyper-dynamics: Temperature Accelerated Dynamics & Biased Potential Dynamics, Solvation Dynamics – Spectral Shifts, Metadynamics, Path Integral MD –Free format reading but somewhat strict Current Versions

Supported Molecular Entities Point ions and atoms Polarisable ions (core+ shell) Flexible molecules Rigid bonds Rigid molecules Flexibly linked rigid molecules Rigid bond linked rigid molecules

Force Field Definitions – I particle: rigid ion or atom (charged or not), a core or a shell of a polarisable ion(with or without associated degrees of freedom), a massless charged site. A particle is a countable object and has a global ID index. site: a particle prototype that serves to defines the chemical & physical nature (topology/connectivity/stoichiometry) of a particle (mass, charge, frozen-ness). Sites are not atoms they are prototypes! Intra-molecular interactions: chemical bonds, bond angles, dihedral angles, improper dihedral angles, inversions. Usually, the members in a unit do not interact via an inter-molecular term. However, this can be overridden for some interactions. These are defined by site. Inter-molecular interactions: van der Waals, metal (EAM, Gupta, Finnis-Sinclair, Sutton-Chen), Tersoff, three-body, four-body. Defined by species.

Force Field Definitions – II Electrostatics: Standard Ewald*, Hautman-Klein (2D) Ewald*, SPM Ewald (3D FFTs), Force-Shifted Coulomb, Reaction Field, Fennell damped FSC+RF, Distance dependent dielectric constant, Fuchs correction for non charge neutral MD cells. Ion polarisation via Dynamic (Adiabatic) or Relaxed shell model. External fields: Electric, Magnetic, Gravitational,Oscillating & Continuous Shear, Containing Sphere, Repulsive Wall. Intra-molecular like interactions: tethers, core shells units, constraint and PMF units, rigid body units. These are also defined by site. Potentials: parameterised analytical forms defining the interactions. These are always spherically symmetric! THE CHEMICAL NATURE OF PARTICLES DOES NOT CHANGE IN SPACE AND TIME!!!

Force Field by Sums

Ensembles and Algorithms Integration: Available as velocity Verlet (VV) or leapfrog Verlet (LFV) generating flavours of the following ensembles NVE NVT (E kin ) Evans NVT Andersen^, Langevin^, Berendsen, Nosé-Hoover NPT Langevin^, Berendsen, Nosé-Hoover, Martyna- Tuckerman-Klein^ N  T/NPnAT/NPn  T Langevin^, Berendsen, Nosé- Hoover, Martyna-Tuckerman-Klein^ Constraints & Rigid Body Solvers: VV dependent – RATTLE, No_Squish, QSHAKE* LFV dependent – SHAKE, Euler-Quaternion, QSHAKE*

DL_POLY is designed for homogenious distributed parallel machines M1M1 P1P1 M2M2 P2P2 M3M3 P3P3 M0M0 P0P0 M4M4 P4P4 M5M5 P5P5 M6M6 P6P6 M7M7 P7P7 Assumed Parallel Architecture

Initialize Forces Motion Statistics Summary Initialize Forces Motion Statistics Summary Initialize Forces Motion Statistics Summary Initialize Forces Motion Statistics Summary A B CD Replicated Data

Molecular force field definition Global Force Field P 0 Local forceterms P 1 Local forceterms P 2 Local forceterms Processors Bonded Forces within RD

U. Essmann, L. Perera, M.L. Berkowtz, T. Darden, H. Lee, L.G. Pedersen, J. Chem. Phys., (1995), 103, Calculate self interaction correction 2.Initialise FFT routine (FFT – 3D FFT) 3.Calculate B-spline coefficients 4.Convert atomic coordinates to scaled fractional units 5.Construct B-splines 6.Construct charge array Q 7.Calculate FFT of Q array 8.Construct array G 9.Calculate FFT of G array 10.Calculate net Coulombic energy 11.Calculate atomic forces RD Scheme for long-ranged part of SPME

21 A B C D Domain Decomposition

Global force field P 0 Local atomicindices P 1 Local atomicindices P 2 Local atomicindices Processor Domains Tricky! Molecular force field definition Bonded Forces within DD

U. Essmann, L. Perera, M.L. Berkowtz, T. Darden, H. Lee, L.G. Pedersen, J. Chem. Phys., 103, 8577 (1995) 1.Calculate self interaction correction 2.Initialise FFT routine (FFT – IJB’s DaFT: 3M 2 1D FFT) 3.Calculate B-spline coefficients 4.Convert atomic coordinates to scaled fractional units 5.Construct B-splines 6.Construct partial charge array Q 7.Calculate FFT of Q array 8.Construct partial array G 9.Calculate FFT of G array 10.Calculate net Coulombic energy 11.Calculate atomic forces I.J. Bush, I.T. Todorov, W. Smith, Comp. Phys. Commun., 175, 323 (2006) DD Scheme for long-ranged part of SPME

Performance Weak Scaling on IBM p

Rigid Bodies versus Constraints 450,000 particles with DL_POLY_4

I/O Weak Scaling on IBM p

Benchmarking BG/L Jülich 2007

Benchmarking XT4/5 UK 2010

Benchmarking on Various Platforms

Importance of I/O - I Types of MD studies most dependent on I/O Large length-scales (10 9 particles), short time-scale such as screw deformations Medium big length-scales (10 6 –10 8 particles), medium time-scale (ps-ns) such as radiation damage cascades Medium length-scale (10 5 –10 6 particles), long time-scale (ns-  s) such as membrane and protein processes Types of I/O: portable human readable loss of precision size ASCII++–– Binary–– ++ XDR Binary+–++

Importance of I/O - II Example: 15 million system simulated with 2048 MPI tasks MD time per timestep ~0.7 (2.7) seconds on Cray XT4 (BG/L) Configuration read ~100 sec. (once during the simulation) Configuration write ~600 sec. for 1.1 GB with the fastest I/O method – MPI-I/O for Cray XT4 (parallel direct access for BG/L). BG/L 16,000 MPI tasks – MD time per timestep 0.5 sec. with a configuration write a frame ~18,000 sec. I/O in native binary is only 3-5 times faster and 3-7 times smaller Some unpopular solutions Saving only the important fragments of the configuration Saving only fragments that have moved more than a given distance between two consecutive dumps Distributed dump – separated configuration in separate files for each MPI task (CFD)

I/O Solutions in DL_POLY_4 1. Serial read and write (sorted/unsorted) – where only a single MPI task, the master, handles it all and all the rest communicate in turn to or get broadcasted to while the master completes writing a configuration of the time evolution. 2. Parallel write via direct access or MPI-I/O (sorted/unsorted) – where ALL / SOME MPI tasks print in the same file in some orderly manner so (no overlapping occurs using Fortran direct access printing. However, it should be noted that the behaviour of this method is not defined by the Fortran standard, and in particular we have experienced problems when disk cache is not coherent with the memory). 3. Parallel read via MPI-I/O or Fortran 4. Serial NetCDF read and write using NetCDF libraries for machine-independent data formats of array-based, scientific data (widely used by various scientific communities).

Performance for 216,000 Ions of NaCl on XT5

MPI-I/O Write Performance for 216,000 Ions of NaCl on XT5

MPI-I/O Read Performance for 216,000 Ions of NaCl on XT5

DL_POLY Project Background Rigid body dynamics and decomposition freed SPME no topology and calcite potentials Fully parallel I/O: reading and writing in ASCII, optionally including netCDF binary in AMBER format CUDA (ICHEC) and Windows ports New GUI (Bill Smith) Over 1,300 licences taken out since November 2010 DL_FILED field builder (Chin Yong) – 300 licencesc

xyz, PDB DL_FIELD ‘black box’ FIELD CONFIG DL_FILED AMBER & CHARM to DL_POLY OPLSAA & Drieding to DL_POLY Protonated

DL_POLY Roadmap August 2011 – March 2012: PRACE-1IP-WP7 funds effort by ICHEC towards CUDA+OpenMP port, towards OpenCL+OpenMP port, and FZ Julich for FMP library testing October 2011 – October 2012: EPSRC’s dCSE funds effort by NAG Ltd. OpenMP within MPI vanilla Beyond 2.1 billion particles October 2011 – September 2012: 2 Temperature Thermostat Models, Fragmented I/O, On-the-Fly properties November 2011 – September 2013: Gentle thermostat, Hyperdynamics

Acknowledgements Thanks to Bill Smith (retired) Ian Bush (NAG Ltd.) Christos Kartsaklis (ORNL), Ruairi Nestor (ICHEC)