CECAM Tutorial Stuttgart, Oct. 2012

Transcription

1 CECAM Tutorial Stuttgart, Oct ESPResSo++ CECAM Tutorial 1 / 40

2 ESPResSo++ ESPResSo++ is an open-source simulation package designed to perform molecular dynamics and monte carlo simulations of condensed matter systems using traditional and state-of-the-art techniques. The software is extensible due to its modular object-oriented C++ core. It is highly flexible due to its Python scripting interface. The package can be used as a research platform as well as a production tool ESPResSo++ CECAM Tutorial 2 / 40

3 ESPResSo++ Key Features and Advantages Flexibility due to Python/C++ integration Extensibility due to object oriented design Easy script-guided creation of complex topologies Quick incorporation of new interactions and algorithms Use of standard short- and long range interactions: e.g. Lennard-Jones, Morse, FENE, OPLS, Dihedrals, Ewald Coulomb, etc. Efficient implementation of advanced algorithms: e.g. AdResS, Parallel Tempering, dynamic bonds, etc. On-the-fly analysis and visualization Applicable to large systems and large numbers of CPUs Analysis NumPy SciPy PyMol Python scripting language Advanced C++ Kernel Parallelization Time-critical algorithms Data storage Extensible design Visualization VMD ESPResSo++ CECAM Tutorial 3 / 40

4 Multiple parallel systems, controlled by one Python script: 1 2 N Controlling Python script e.g. for Parallel Tempering, Replica Exchange, ESPResSo++ CECAM Tutorial 4 / 40

5 Current developers: ESPResSo++ Team: Torsten Stuehn (MPIP) Vitalii Starchenko (MPIP) Stas Bevc (NIC, Slovenia) Konstantin Koschke (MPIP) Livia Moreira (MPIP) Raffaello Potestio (MPIP) Karsten Kreis (MPIP) Former developers: Thomas Brandes (SCAI) Dirk Reith (SCAI) Axel Arnold (ICP) Olaf Lenz (ICP) Jonathan Halverson (BNL, USA) Victor Ruehle (Cambridge, UK) Christoph Junghans (LANL, USA) ESPResSo++ CECAM Tutorial 5 / 40

6 Outline of the tutorial Inside ESPReSo++ an overview of the C++ class structure Integrator, Interactions, Setting up a simulation with, Integrator and Interactions How to equilibrate a polymer melt Python script Installation of ESPResSo++ Basic Setup Simple Lennard Jones Advanced Lennard Jones with graphical output Polymer Melt C++ Core ESPResSo++ CECAM Tutorial 6 / 40

7 Inside ESPResSo++ Extension LangevinThermostat Integrator Interaction VerletListInteraction < LennardJones > Domain ESPResSo++ CECAM Tutorial 7 / 40

8 Extension LangevinThermostat Integrator Interaction VerletListInteraction < LennardJones > Domain ESPResSo++ CECAM Tutorial 8 / 40

9 Extension LangevinThermostat Integrator Init f i & t &= F i t Interaction VerletListInteraction < LennardJones > MD Loop v i & t + t 2& &= v i t &+& t 2 & &f i t r i & t + t & &= r i t &+& t & &v i t + t 2 f i & t &= F i t Domain v i & t + t & &= v i t + t 2 &+& t 2 & &f i t &&& ESPResSo++ CECAM Tutorial 9 / 40

10 Extension LangevinThermostat Integrator Init Interaction VerletListInteraction < LennardJones > MD Loop f i & t &= F i t v i & t + t 2& &= v i t &+& t 2 & &f i t r i & t + t & &= r i t &+& t & &v i t + t 2 f i & t &= F i t Domain v i & t + t & &= v i t + t 2 &+& t 2 & &f i t &&& ESPResSo++ CECAM Tutorial 10 / 40

11 Extension LangevinThermostat Integrator Init Interaction f i & t &= F i t +&L T, γ, v i t, θ v i & t + t 2& &= v i t &+& t 2 & &f i t VerletListInteraction < LennardJones > MD Loop r i & t + t & &= r i t &+& t & &v i t + t 2 f i & t v i & t + t &= F i t +&L T, γ, v i t + t 2, θ & &= v i t + t 2 &+& t 2 & &f i t &&& Domain ESPResSo++ CECAM Tutorial 11 / 40

12 Extension Integrator FixPositions Init Interaction VerletListInteraction < LennardJones > MD Loop f i & t &= F i t save positions v i & t + t 2& &= v i t &+& t 2 & &f i t r i & t + t & &= r i t &+& t & &v i t + t 2 restore positions f i & t &= F i t Domain v i & t + t & &= v i t + t 2 &+& t 2 & &f i t &&& ESPResSo++ CECAM Tutorial 12 / 40

13 Extension Integrator ForceCapping Init Interaction VerletListInteraction < LennardJones > MD Loop f i & t &= F i t v i & t + t 2& &= v i t &+& t 2 & &f i t r i & t + t & &= r i t &+& t & &v i t + t 2 f i & t &= F i t cap forces v i & t + t & &= v i t + t 2 &+& t 2 & &f i t &&& Domain ESPResSo++ CECAM Tutorial 13 / 40

14 Extension Integrator LangevinThermo/Barostat BerendsenThermo/Barostat (T)DPDThermostat StochasticVelocityRescaling Isokinetic Interaction FixPositions VerletListInteraction < LennardJones > ExtForce / TDForce Domain ForceCapping AdResS ESPResSo++ CECAM Tutorial 14 / 40

15 Extension LangevinThermostat Integrator Interaction VerletListInteraction < LennardJones > Domain ESPResSo++ CECAM Tutorial 15 / 40

16 Extension LangevinThermostat Integrator Interaction Different types of interaction: 2-body (pair) 3-body (angular) 4-body (dihedral) N-body (coulomb k-space) non bonded (Verlet lists) bonded (bond lists) VerletListInteraction < LennardJones > Domain ESPResSo++ CECAM Tutorial 16 / 40

17 Integrator Extension 2-body 3-body 4-body N-body LangevinThermostat VerletList VerletListAdress Interaction VerletListInteraction < LennardJones > VerletListTriple CellListAllPairs CellListAllParticles Domain FixedPairList FixedTripleList FixedQuadrupleList ESPResSo++ CECAM Tutorial 17 / 40

18 2-body Integrator Extension 3-body 4-body N-body LangevinThermostat non bonded interaction templates VerletList VerletListAdress Interaction Interaction types have to be combined with potentials VerletListTriple CellListAllPairs CellListAllParticles Domain VerletListInteraction < LennardJones > FixedPairList FixedTripleList FixedQuadrupleList bonded interaction templates ESPResSo++ CECAM Tutorial 18 / 40

19 Integrator Angular Cosine Reaction FieldGen Tabulated Angular 2-body Tabulated Dihedral Extension FENE Harmonic 3-body Ewald KSpace Soft Cosine Angular Harmonic Ewald RSpace 4-body Cosine Squared Lennard Jones OPLS Tabulated Stillinger Weber Morse N-body Lennard JonesCap LangevinThermostat non bonded interaction templates VerletList VerletListAdress VerletListTriple CellListAllPairs CellListAllParticles Domain FixedPairList FixedTripleList FixedQuadrupleList bonded interaction templates ESPResSo++ CECAM Tutorial 19 / 40

20 Integrator Angular Cosine Reaction FieldGen Tabulated Angular 2-body Tabulated Dihedral Extension FENE Harmonic 3-body Ewald KSpace Soft Cosine Angular Harmonic Ewald RSpace 4-body Cosine Squared Lennard Jones OPLS Tabulated Stillinger Weber Morse N-body Lennard JonesCap LangevinThermostat non bonded interaction templates VerletList VerletListAdress VerletListTriple CellListAllPairs CellListAllParticles Domain FixedPairList C++ code: typedef class VerletListInteractionTemplate < LennardJones > VerletListLennardJones FixedTripleList FixedQuadrupleList bonded interaction templates ESPResSo++ CECAM Tutorial 20 / 40

21 Integrator Angular Cosine Reaction FieldGen Tabulated Angular 2-body Tabulated Dihedral Extension FENE Harmonic 3-body Ewald KSpace Soft Cosine Angular Harmonic Ewald RSpace 4-body Cosine Squared Lennard Jones OPLS Tabulated Stillinger Weber Morse N-body Lennard JonesCap LangevinThermostat non bonded interaction templates VerletList VerletListAdress VerletListTriple CellListAllPairs CellListAllParticles Domain FixedPairList C++ code: typedef class FixedPairListInteractionTemplate < LennardJones > FixedPairListLennardJones FixedTripleList FixedQuadrupleList bonded interaction templates ESPResSo++ CECAM Tutorial 21 / 40

22 Integrator Angular Cosine Reaction FieldGen Tabulated Angular 2-body Tabulated Dihedral Extension FENE Harmonic 3-body Ewald KSpace Soft Cosine Angular Harmonic Ewald RSpace 4-body Cosine Squared Lennard Jones OPLS Tabulated Stillinger Weber Morse N-body Lennard JonesCap LangevinThermostat non bonded interaction templates VerletList VerletListAdress VerletListTriple CellListAllPairs CellListAllParticles Domain FixedPairList C++ code: typedef class VerletListTripleInteractionTemplate < StillingerWeberTripleTerm > VerletListStillingerWeberTripleTerm FixedTripleList FixedQuadrupleList bonded interaction templates ESPResSo++ CECAM Tutorial 22 / 40

23 Extension LangevinThermostat Integrator Interaction VerletListInteraction < LennardJones > Domain ESPResSo++ CECAM Tutorial 23 / 40

24 Extension VerletList Integrator VerletListAdress VerletListTriple Particle lists for different interactions are updated on from Domain LangevinThermostat Domain Interaction VerletListInteraction FixedPairList < LennardJones > FixedTripleList onparticleschanged beforesendparticles afterrecvparticles FixedQuadrupleList ESPResSo++ CECAM Tutorial 24 / 40

25 RNG BC Necessary modules to simulate a standard polymer melt with Langevin dynamics Particles Inter actions Integrator LJ FENE Cos 2 Extension Langevin ESPResSo++ CECAM Tutorial 25 / 40

26 Corresponding Python script : Inter actions RNG BC Particles LJ FENE Cos 2 s1 = () s1.rng = esutil.rng() s1.bc = bc.(<args>) s1.storage = storage.domain(<args>).. <create particlelist>. s1.storage.addparticles(*property_list, particle_list).. <define interactions with parameters>. s1.addinteraction(lj) s1.addinteraction(fene) s1.addinteraction(cossq) Integrator Extensions Langevin i1 = integrator.(s1).. <create thermostat with parameters>. i1.addextension(langevin_thermostat) i1.run(10000) ESPResSo++ CECAM Tutorial 26 / 40

27 Creating an equilibrated configuration of a dense polymer melt Input of system parameters N c, l c, ρ Create random polymer chains Warmup the system Equilibrate the system Output equilibrated configuration Snapshot of an equilibrated dense ring polymer melt, number of chains N c =200, chain length l c =200 particles, density ρ=0.85 [N/V 3 ] ESPResSo++ CECAM Tutorial 27 / 40

28 Creating an equilibrated configuration of a dense polymer melt Input of system parameters N c, l c, ρ Create random polymer chains Specify parameters of the simulation: Number of chains N c Number of monomers per chain (chainlength) l c Number density of the system ρ Warmup the system Equilibrate the system Average end-to-end distance of polymers: & R ee N 1 2 Equilibrated dense polymer melts have a random walk (RW) statistic. Output equilibrated configuration Starting configurations should be random walks ESPResSo++ CECAM Tutorial 28 / 40

29 Creating an equilibrated configuration of a dense polymer melt Input of system parameters N c, l c, ρ Create random polymer chains Warmup the system Equilibrate the system Output equilibrated configuration For each chain we have to define a random start position in the simulation box and then create a random walk with a fixed step length and a number of steps l c ESPResSo++ CECAM Tutorial 29 / 40

30 Creating an equilibrated configuration of a dense polymer melt Input of system parameters N c, l c, ρ Create random polymer chains Warmup the system Equilibrate the system Output equilibrated configuration Chains and therefore particles in a dense random walk system are very likely to have a strong overlap. This results in extremely strong repulsive forces between these overlapping particles ESPResSo++ CECAM Tutorial 30 / 40

31 Creating an equilibrated configuration of a dense polymer melt Input of system parameters N c, l c, ρ Create random polymer chains Warmup the system Equilibrate the system Output equilibrated configuration Solving the equations of motion by simply applying a Velocity-Verlet scheme to RW polymers will lead to a so called explosion of the system due to numerical errors caused by extremely large numbers for the forces between overlapping particles. Measures to be taken to avoid explosion : Decrease basic time step dt of the integrator Apply force capping to some or all of the interactions Gradually decrease the force capping radius Gradually increase epsilon or sigma of the WCA interaction Depending on the density of the system and the polymer model (e.g. totally flexible or bending stiffness included) not all of the above mentioned steps may be necessary ESPResSo++ CECAM Tutorial 31 / 40

32 Creating an equilibrated configuration of a dense polymer melt Input of system parameters N c, l c, ρ Create random polymer chains Warmup the system Equilibrate the system Output equilibrated configuration After the warmup evolve the system by running the Velocity-Verlet integrator with full potentials at the specified temperature for several thousands or millions of steps, depending on the chainlength and the interactions. During the equilibration the following observables of the system should be measured in regular time intervals: Temperature of the system Total energy of the system These will already give some hints about how long equilibration will take. Additionally the mean squared displacement (msd) of the center of mass of the polymer chains could be measured. As soon as this property has reached a value of the order of the size of the radius of gyration equilibration should be finished ESPResSo++ CECAM Tutorial 32 / 40

33 Thank you for your attention! Project website: / 40