University of Edinburgh January 2011 DL_POLY

University of Edinburgh January 2011 DL_POLY_4 Ilian Todorov @ CCG CSED, STFC - Daresbury Laboratory, Daresbury Warrington WA 4 1 EP, Cheshire, England, UK

Where is Daresbury? University of Edinburgh January 2011

DL_POLY Project Background University of Edinburgh January 2011 • General purpose parallel (classical) simulation software MD • It was conceived to meet the needs of CCP 5 - The Computer Simulation of Condensed Phases (academic collaboration community) • Written in modularised Fortran 90 (Nag. Ware & FORCHECK compliant) with MPI 2 (MPI 1+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 researcher (provided as code) and at cost to industry

DL_POLY_DD Development Statistics University of Edinburgh January 2011

DL_POLY_DD Licence Statistics University of Edinburgh January 2011 Licences 1600 Downloads 1200 800 400 0 1992 1996 2000 2004 Year 2008 2012

DL_POLY Licence Statistics University of Edinburgh January 2011

DL_POLY Project Current State University of Edinburgh January 2011 • 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 & net. CDF I/O – NAG d. CSE (IJB & ITT) • CUDA+Open. MP port (as source, ICHEC) & MS Windows ports (as MSI 32 - and 64 -bit self-installers) • SPME processor grid freed from 2^N decomposition – NAG d. CSE (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)

DL_POLY Project Roadmap University of Edinburgh January 2011 • August 2011 (PRACE-2 IP funding): • further CUDA porting & support by ICHEC (2 PM) • CUDA to Open. CL 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 d. CSE funding with David Quigley): • Open. MP within the vanilla DD/MPI framework DL_POLY_4 (Ian Bush & Asimina Maniopoulou) • Beyond 2. 1 billion particles limit – long integers (Ian Bush)

DL_POLY Project Roadmap II University of Edinburgh January 2011 • December 2011 (MMM@HPC - FP 7 -e. Infrastructure funding, 3 FTE years) • Gay-Berne particles (Laurence Ellison) • Implementing Gentle Stochastic Thermostat • Extension of Ns. T 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

Current Versions University of Edinburgh January 2011 • 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 Dataparallelisation, 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

Supported Molecular Entities University of Edinburgh January 2011 Rigid molecules Point ions and atoms Flexibly linked rigid molecules Polarisable ions (core+ shell) Flexible molecules Rigid bond linked rigid molecules

Force Field Definitions – I University of Edinburgh January 2011 • 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: der Waals, metal (EAM, Gupta, van Finnis-Sinclair, Sutton-Chen), Tersoff, three-body, four-body. Defined by species.

Force Field Definitions – II University of Edinburgh January 2011 • Electrostatics: Standard Ewald*, Hautman-Klein (2 D) Ewald*, SPM Ewald (3 D 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!!!

Force Field by Sums University of Edinburgh January 2011

Ensembles and Algorithms University of Edinburgh January 2011 Integration: Available as velocity Verlet (VV) or leapfrog Verlet (LFV) generating flavours of the following ensembles • NVE • NVT (E ) Evans kin • NVT Andersen^, Langevin^, Berendsen, Nosé-Hoover • NPT Langevin^, Berendsen, Nosé-Hoover, Martyna. Tuckerman-Klein^ • N T/NPn. A T/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 *

Domain Decomposition University of Edinburgh January 2011 A C 19 B D

Bonded Forces within DD P 0 Local atomic indices Tricky! P 1 Local atomic indices P 2 Local atomic indices Processor Domains Molecular force field definition Global force field University of Edinburgh January 2011

DD Scheme for long-ranged part of SPME University of Edinburgh January 2011 U. Essmann, L. Perera, M. L. Berkowtz, T. Darden, H. Lee, L. G. Pedersen, J. Chem. Phys. , 103, 8577 (1995) 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. Calculate self interaction correction Initialise FFT routine (FFT – IJB’s Da. FT: 3 M 2 1 D FFT) Calculate B-spline coefficients Convert atomic coordinates to scaled fractional units Construct B-splines Construct partial charge array Q Calculate FFT of Q array Construct partial array G Calculate FFT of G array Calculate net Coulombic energy Calculate atomic forces I. J. Bush, I. T. Todorov, W. Smith, Comp. Phys. Commun. , 175, 323 (2006)

Performance Weak Scaling on IBM p 575 2005 -2011 University of Edinburgh January 2011

Rigid Bodies versus Constraints 450, 000 particles with DL_POLY_4 University of Edinburgh January 2011

I/O Solutions in DL_POLY_4 University of Edinburgh January 2011 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 Net. CDF read and write using Net. CDF libraries for machine-independent data formats of array-based, scientific data (widely used by various scientific communities).

MPI-I/O Write Performance for 216, 000 Ions of Na. Cl on XT 5 University of Edinburgh January 2011

MPI-I/O Read Performance for 216, 000 Ions of Na. Cl on XT 5 University of Edinburgh January 2011

DL_FILED University of Edinburgh January 2011 • AMBER & CHARM to DL_POLY • OPLSAA & Drieding to DL_POLY xyz, PDB Protonated DL_FIELD ‘black box’ FIELD CONFIG

Materials Force Filed University of Edinburgh January 2011 Force fields for Mg. O, Na. Cl, simple ionic crystals - easy Two vdw descriptions: Mg 2+ with O 2 - and O 2 - with O 2 -

Biological Force Field University of Edinburgh January 2011 Simple covalent molecules - bearable For example: dimethyl sulphoxide atoms 10 HD 1. 00797 0. 09000 1 CD 12. 01115 -0. 14800 1 SD 32. 06400 0. 31200 1 OD 15. 99940 -0. 55600 1 bonds 21 harm 4 2 harm 4 3 harm 8 5 harm 8 6 harm 8 7 harm 4 9 harm 8 9 harm 9 10 -126 1 8 -126 1 10 Also 12 dihedrals, and 10 vdw 644 644 644 480 1080 96195 33433 1. 11000 1. 80000 1. 53000 129. 03 84. 716 angles 15 harm 1 harm 2 harm 3 harm 5 harm 6 harm 7 harm 4 harm 8 4 2 71. 00000 108. 40000 4 3 71. 00000 108. 40000 4 9 92. 20000 111. 30000 8 6 71. 00000 108. 40000 8 7 71. 00000 108. 40000 8 9 92. 20000 111. 30000 9 8 68. 00000 95. 00000 9 10 158. 00000 106. 75000

Biological Force Field University of Edinburgh January 2011 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!

Two Temperature Model University of Edinburgh January 2011 • Superheating? Lattice temperature above the melting temperature with no track formation 1. 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 50 x 10 unit Si cells 50 ke. V/nm ~1 ps 1. D. M. Duffy, N. Itoh, A. M. Rutherford and A. M. Stoneham, J. Phys: Condens. Matt. 20 (2008), p. 082201

Towards Molecular Dynamics University of Edinburgh January 2011 • 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 Continuum or Molecular dynamics

DL_POLY_4 Calling Tree University of Edinburgh January 2011 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

DL_POLY_4 Calling Tree University of Edinburgh January 2011 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

DL_POLY_4 Calling Tree University of Edinburgh January 2011 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

DL_POLY on the Web University of Edinburgh January 2011 WWW: http: //www. ccp 5. ac. uk/DL_POLY/ FTP: ftp: //ftp. dl. ac. uk/ccp 5/DL_POLY/ DEV: http: //ccpforge. cse. rl. ac. uk/gf/project/dl-poly/ FORUM: http: //www. cse. scitech. ac. uk/disco/forums. shtml

Acknowledgements University of Edinburgh January 2011 Thanks to • • • Bill Smith (retired) Chin Yong (STFC – DL) Michael Seaton (STFC – DL) Szymon Draszewicz (UCL) Ian Bush (NAG Ltd. )