DL_POLY_4

1. DL_POLY_4 Ilian Todorov @ CCG CSED, STFC - Daresbury Laboratory, Daresbury Warrington WA4 1EP, Cheshire, England, UK

2. Where is Daresbury?

3. 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 13,000 licences taken out since 1994 (~1500 annually) • Over 1100 registered FORUM members since 2005 • Available free of charge (under licence) to University researchers (provided as code) and at cost to industry

4. DL_POLY_DD Development Statistics

5. DL_POLY_DD Licence Statistics

6. DL_POLY Licence Statistics

7. DL_POLY Licence Statistics

8. DL_POLY Licence Statistics

9. DL_POLY Licence Statistics

10. DL_POLY Project Current State • October 2010: DL_POLY_3 -> DL_POLY_4 still under STFC Licence, over 1600 licences taken out since November 2010 • Rigid Body dynamics (ITT) • Parallel I/O & netCDF I/O – NAG dCSE (IJB & ITT) • CUDA+OpenMP port (as source, ICHEC) & MS Windows ports (as MSI 32- and 64-bit self-installers) • SPME processor grid freed from 2^N decomposition – NAG dCSE (IJB) • January 2011: DL_POLY_2 -> DL_POLY_CLASSIC on a BSD type Licence (BS retired but supporting GUI and fixes) • Load Balancer development (finished 30/03/2011) • Continuous Development of the DL_FIELD field builder (pdb to DL_POLY input, Chin Yong), over 400 licences since November 2010 • October 2011: new DL_POLY GUI (Bill Smith)

11. DL_POLY Project Roadmap • August 2011 (PRACE-2IP funding): • further CUDA porting & support by ICHEC (2 PM) • CUDA to OpenCL port by SC@WUT (5 PM) • FMM library testing as substitute of SPME electrostatics • October 2011 (2 FTE years Software Development EPSRC funding with Kostya Trachenko) • Two temperature thermostat methodology (TTM) for high energy events in metals (Michael Seaton) • Fragmented I/O and on-the-fly thermodynamic properties calculations for very large systems (Michael Seaton) • November 2011 (1 FTE year dCSE funding with David Quigley): • OpenMP within the vanilla DD/MPI framework DL_POLY_4 (Ian Bush & Asimina Maniopoulou) • Beyond 2.1 billion particles limit – long integers (Ian Bush)

12. DL_POLY Project Roadmap II • December 2011 (MMM@HPC - FP7-eInfrastructure funding, 3 FTE years) • Gay-Berne particles (Laurence Ellison) • Implementing Gentle Stochastic Thermostat • Extension of NsT ensemble to handle liquid bio-chemical systems • nfold and bio-chemical verification • Modified Tersoff potential for band-gap materials • Porting the DL_POLY_Classic Hyper-dynamics

13. Current Versions • DL_POLY_4 (version 4.02) • Dynamic Decomposition parallelisation, based on domain decomposition but with dynamic load balancing • limits up to ≈2.1×109 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 1.8) • 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

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

15. 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.

16. 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 polarisationvia 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!!!

17. Force Field by Sums

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

19. Domain Decomposition B A C D

20. P2Local atomic indices P0Local atomic indices P1Local atomic indices Tricky! Global force field Processor Domains Bonded Forces within DD Molecular force field definition

21. DD Scheme for long-ranged part of SPME 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: 3M2 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)

22. Performance Weak Scaling on IBM p575 2005-2011

23. Rigid Bodies versus Constraints 450,000 particles with DL_POLY_4

24. 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).

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

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

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

28. Materials Force Filed Force fields for MgO, NaCl, simple ionic crystals - easy Two vdw descriptions: Mg2+ with O2- and O2- with O2-

29. Biological Force Field Simple covalent molecules - bearable For example: dimethyl sulphoxide atoms 10 HD 1.00797 0.09000 1 HD 1.00797 0.09000 1 HD 1.00797 0.09000 1 CD 12.01115 -0.14800 1 HD 1.00797 0.09000 1 HD 1.00797 0.09000 1 HD 1.00797 0.09000 1 CD 12.01115 -0.14800 1 SD 32.06400 0.31200 1 OD 15.99940 -0.55600 1 angles 15 harm 1 4 2 71.00000 108.40000 harm 1 4 3 71.00000 108.40000 harm 1 4 9 92.20000 111.30000 harm 2 4 3 71.00000 108.40000 harm 2 4 9 92.20000 111.30000 harm 3 4 9 92.20000 111.30000 harm 5 8 6 71.00000 108.40000 harm 5 8 7 71.00000 108.40000 harm 5 8 9 92.20000 111.30000 harm 6 8 7 71.00000 108.40000 harm 6 8 9 92.20000 111.30000 harm 7 8 9 92.20000 111.30000 harm 4 9 8 68.00000 95.00000 harm 4 9 10 158.00000 106.75000 harm 8 9 10 158.00000 106.75000 bonds 21 harm 4 1 644 1.11000 harm 4 2 644 1.11000 harm 4 3 644 1.11000 harm 8 5 644 1.11000 harm 8 6 644 1.11000 harm 8 7 644 1.11000 harm 4 9 480 1.80000 harm 8 9 480 1.80000 harm 9 10 1080 1.53000 -126 1 8 96195 129.03 -126 1 10 33433 84.716 Also 12 dihedrals, and 10 vdw

30. Biological Force Field How about this? Protein molecules consist of hundreds of amino acids. 4382 atoms 19400 two-body 7993 three-body 13000 four body 730 vdw Clearly, manual entry is not practical!

31. Two Temperature Model • Superheating? Lattice temperature above the melting temperature with no track formation1. Continuum models cannot give accurate track radii; require MD-coupling! • Continuum neglects lattice straining and emission of shock waves (carry away some energy). CL in continuum is neither identical with Cv or Cp. • Volume change by a phase transition is not included, i.e. Silicon shrinks upon melting TTM+MD 50x50x10 unit Si cells 50keV/nm ~1ps 1. D.M. Duffy, N. Itoh, A.M. Rutherford and A.M. Stoneham, J. Phys: Condens. Matt.20 (2008), p. 082201

32. MD additions: Coarse-grained T-cells Choice of boundary conditions… Periodic for the atomistic lattice Electronic system: z-dir von-Neumann, xy-dir infinite sink Inhomogeneous Langevin thermostat Mechanism for electronic energy transfer to the lattice Depends on the local electronic temperature Towards Molecular Dynamics Molecular dynamics Continuum or

33. DL_POLY_4 Calling Tree Always Advise with the MANUAL Start up Parse INPUT data Set Limits & Array Bounds Allocate Arrays Read INPUT data, VERIFY & Make SENSE (semi-iterative) Initialise/Read Restart data Set Halo Decomposition Bookkeeping, VERIFY & Report Set Temperature/Motion (CS+CB+RB+CGM) Main MD Loop (Time & Steps Conditioned) Finalise & Report Statistics Shut Down

34. DL_POLY_4 Calling Tree Main MD Loop (Time & Steps Conditioned) LFV Evaluate Inter-molecular Forces & Collect Spatial Statistics (VNL) Make Adjustments & Evaluate Intra-molecular Forces Leap Frog Verlet RELOCATION & BOOKKEEPING & Set Halo Collect Statistics Print OUTPUT data Check on Loop Condition

35. DL_POLY_4 Calling Tree Main MD Loop (Time & Steps Conditioned) VV Velocity Verlet stage I Evaluate Inter-molecular Forces & Collect Spatial Statistics (VNL) Make Adjustments & Evaluate Intra-molecular Forces RELOCATION & BOOKKEEPING & Set Halo Velocity Verlet stage II Collect Statistics Print OUTPUT data Check on Loop Condition

36. DL_POLY on the Web WWW: http://www.ccp5.ac.uk/DL_POLY/ FTP: ftp://ftp.dl.ac.uk/ccp5/DL_POLY/ DEV: http://ccpforge.cse.rl.ac.uk/gf/project/dl-poly/ FORUM: http://www.cse.scitech.ac.uk/disco/forums.shtml

37. Acknowledgements • Thanks to • Bill Smith (retired) • Chin Yong (STFC – DL) • Michael Seaton (STFC – DL) • Szymon Draszewicz (UCL) • Ian Bush (NAG Ltd.)